*>>>>>>>Topology file for FAD, benzylamine and a patch for creating<<<
*>>>>>>>>>>>>>>>>the 8alpha-thioether linkage<<<<<<<<<<<<<<<<<<<<<<<<<


MASS     1 H      1.00800 H ! polar H
MASS     2 HC     1.00800 H ! N-ter H
MASS     3 HA     1.00800 H ! nonpolar H
MASS     4 HT     1.00800 H ! TIPS3P WATER HYDROGEN
MASS     5 HP     1.00800 H ! aromatic H
MASS     6 HB     1.00800 H ! backbone H
MASS     7 HR1    1.00800 H ! his he1, (+) his HG,HD2
MASS     8 HR2    1.00800 H ! (+) his HE1
MASS     9 HR3    1.00800 H ! neutral his HG, HD2
MASS    10 HS     1.00800 H ! thiol hydrogen
MASS    11 HE1    1.00800 H ! for alkene; RHC=CR
MASS    12 HE2    1.00800 H ! for alkene; H2C=CR
MASS    13 HA1    1.00800 H ! alkane, CH, new LJ params (see toppar_all22_prot_aliphatic_c27.str)
MASS    14 HA2    1.00800 H ! alkane, CH2, new LJ params (see toppar_all22_prot_aliphatic_c27.str)
MASS    15 HA3    1.00800 H ! alkane, CH3, new LJ params (see toppar_all22_prot_aliphatic_c27.str)
MASS    16 HF1    1.00800 H ! Aliphatic H on fluorinated C (see toppar_all22_prot_fluoro_alkanes.str)
MASS    17 HF2    1.00800 H ! Aliphatic H on fluorinated C (see toppar_all22_prot_fluoro_alkanes.str)
MASS    20 C     12.01100 C ! carbonyl C, peptide backbone
MASS    21 CA    12.01100 C ! aromatic C
MASS    22 CT1   12.01100 C ! aliphatic sp3 C for CH
MASS    23 CT2   12.01100 C ! aliphatic sp3 C for CH2
MASS    24 CT3   12.01100 C ! aliphatic sp3 C for CH3
MASS    25 CPH1  12.01100 C ! his CG and CD2 carbons
MASS    26 CPH2  12.01100 C ! his CE1 carbon
MASS    27 CPT   12.01100 C ! trp C between rings
MASS    28 CY    12.01100 C ! TRP C in pyrrole ring
MASS    29 CP1   12.01100 C ! tetrahedral C (proline CA)
MASS    30 CP2   12.01100 C ! tetrahedral C (proline CB/CG)
MASS    31 CP3   12.01100 C ! tetrahedral C (proline CD)
MASS    32 CC    12.01100 C ! carbonyl C, asn,asp,gln,glu,cter,ct2
MASS    33 CD    12.01100 C ! carbonyl C, pres aspp,glup,ct1
MASS    34 CPA   12.01100 C ! heme alpha-C
MASS    35 CPB   12.01100 C ! heme beta-C
MASS    36 CPM   12.01100 C ! heme meso-C
MASS    37 CM    12.01100 C ! heme CO carbon
MASS    38 CS    12.01100 C ! thiolate carbon
MASS    39 CE1   12.01100 C ! for alkene; RHC=CR
MASS    40 CE2   12.01100 C ! for alkene; H2C=CR
MASS    41 CST   12.01100 C ! CO2 carbon 
MASS    42 CT    12.01100 C ! aliphatic sp3 C, new LJ params, no hydrogens (see toppar_all22_prot_aliphatic_c27.str)
MASS    43 CT1x  12.01100 C ! aliphatic sp3 C for CH, new LJ params (see toppar_all22_prot_aliphatic_c27.str)
MASS    44 CT2x  12.01100 C ! aliphatic sp3 C for CH2, new LJ params (see toppar_all22_prot_aliphatic_c27.str)
MASS    45 CT3x  12.01100 C ! aliphatic sp3 C for CH3, new LJ params (see toppar_all22_prot_aliphatic_c27.str)
MASS    46 CN    12.01100 C ! C for cyano group (see toppar_all22_prot_pyridines.str)
MASS    47 CAP   12.01100 C ! aromatic C for pyrimidines (see toppar_all22_prot_pyridines.str)
MASS    48 COA   12.01100 C ! carbonyl C for pyrimidines (see toppar_all22_prot_pyridines.str)
MASS    49 C3    12.01100 C ! cyclopropyl carbon
MASS    50 N     14.00700 N ! proline N
MASS    51 NR1   14.00700 N ! neutral his protonated ring nitrogen
MASS    52 NR2   14.00700 N ! neutral his unprotonated ring nitrogen
MASS    53 NR3   14.00700 N ! charged his ring nitrogen
MASS    54 NH1   14.00700 N ! peptide nitrogen
MASS    55 NH2   14.00700 N ! amide nitrogen
MASS    56 NH3   14.00700 N ! ammonium nitrogen
MASS    57 NC2   14.00700 N ! guanidinium nitroogen
MASS    58 NY    14.00700 N ! TRP N in pyrrole ring
MASS    59 NP    14.00700 N ! Proline ring NH2+ (N-terminal)
MASS    60 NPH   14.00700 N ! heme pyrrole N
MASS    61 NC    14.00700 N ! N for cyano group (see toppar_all22_prot_pyridines.str)
MASS    62 CTL1 12.011000 C ! sp3 carbon with 1 H  (-CH1-)
MASS    63 OSL  15.999400 O ! Nucleic acid phosphate ester oxygen
MASS    65 OHL  15.999400 O ! Nucleic acid phosphate hydroxyl oxygen
MASS    66 HOL   1.008000 H ! Nucleic acid phosphate hydroxyl proton
MASS    67 HAL2  1.008000 H ! alphatic proton
MASS    68 CTL2 12.011000 C ! carbon of methylene group (-CH2-)
MASS    69 HAL1  1.008000 H ! alphatic proton
MASS    70 O     15.99900 O ! carbonyl oxygen
MASS    71 OB    15.99900 O ! carbonyl oxygen in acetic acid
MASS    72 OC    15.99900 O ! carboxylate oxygen
MASS    73 OH1   15.99900 O ! hydroxyl oxygen
MASS    74 OS    15.99940 O ! ester oxygen
MASS    75 OT    15.99940 O ! TIPS3P WATER OXYGEN
MASS    76 OM    15.99900 O ! heme CO/O2 oxygen
MASS    77 OST   15.99900 O ! CO2 oxygen
MASS    78 OCA   15.99900 O ! carbonyl O for pyrimidines (see toppar_all22_prot_pyridines.str)
MASS    81 S     32.06000 S ! sulphur
MASS    82 SM    32.06000 S ! sulfur C-S-S-C type
MASS    83 SS    32.06000 S ! thiolate sulfur
MASS    85 HE     4.00260 HE ! helium
MASS    86 NE    20.17970 NE ! neon
MASS    87 CF1   12.01100 C ! monofluoromethyl (see toppar_all22_prot_fluoro_alkanes.str)
MASS    88 CF2   12.01100 C ! difluoromethyl (see toppar_all22_prot_fluoro_alkanes.str)
MASS    89 CF3   12.01100 C ! trifluoromethyl (see toppar_all22_prot_fluoro_alkanes.str)
MASS    90 FE    55.84700 Fe ! heme iron 56
MASS    91 CLAL  35.45300 CL ! Chlorine Atom (see toppar_all22_prot_aldehydes.str)
MASS    92 FA    18.99800 F ! aromatic flourine (see toppar_all22_prot_pyridines.str)
MASS    93 F1    18.99800 F ! Fluorine, monofluoro (see toppar_all22_prot_fluoro_alkanes.str)
MASS    94 F2    18.99800 F ! Fluorine, difluoro (see toppar_all22_prot_fluoro_alkanes.str)
MASS    95 F3    18.99800 F ! Fluorine, trifluoro (see toppar_all22_prot_fluoro_alkanes.str)
MASS    99 DUM    0.00000 H ! dummy atom
!see NA section
!MASS   100 SOD  22.989770 NA ! Sodium Ion
!MASS   101 MG   24.305000 MG ! Magnesium Ion
!MASS   102 POT  39.102000 K  ! Potassium Ion! check masses
!MASS   103 CES 132.900000 CS ! Cesium Ion
!MASS   104 CAL  40.080000 CA ! Calcium Ion
!MASS   105 CLA  35.450000 CL ! Chloride Ion
!MASS   106 ZN   65.370000 ZN ! zinc (II) cation
!NA section
!MASS 101    HT    1.008000 H ! TIPS3P WATER HYDROGEN
MASS 102    HN1   1.008000 H ! Nucleic acid amine proton
MASS 103    HN2   1.008000 H ! Nucleic acid ring nitrogen proton
MASS 104    HN3   1.008000 H ! Nucleic acid aromatic carbon proton
MASS 105    HN3B  1.008000 H ! NAD+ aromatic hydrogen
MASS 106    HN3C  1.008000 H ! Standard aromatic hydrogen (as in benzene)
MASS 107    HNP   1.008000 H ! pure aromatic H
MASS 108    HN4   1.008000 H ! Nucleic acid phosphate hydroxyl proton
MASS 109    HN5   1.008000 H ! Nucleic acid ribose hydroxyl proton
MASS 110    HN6   1.008000 H ! Nucleic acid ribose aliphatic proton
MASS 111    HN7   1.008000 H ! Nucleic acid proton (equivalent to protein HA)
MASS 112    HN8   1.008000 H ! Bound to CN8 in nucleic acids/model compounds
MASS 113    HN9   1.008000 H ! Bound to CN9 in nucleic acids/model compounds
MASS 114    HNE1  1.008000 H ! for alkene; RHC=CR (modified thy patch Sasha)
MASS 115    HNE2  1.008000 H ! for alkene; H2C=CR (modified thy patch Sasha)
MASS 120    CN1  12.011000 C ! Nucleic acid carbonyl carbon
MASS 121    CN1A 12.011000 C ! NAD+/NADH amide carbonyl carbon
MASS 122    CN1T 12.011000 C ! Nucleic acid carbonyl carbon (T/U C2)
MASS 123    CN2  12.011000 C ! Nucleic acid aromatic carbon to amide
MASS 124    CN3  12.011000 C ! Nucleic acid aromatic carbon 
MASS 125    CN3A 12.011000 C ! NAD+ aromatic carbon
MASS 126    CN3B 12.011000 C ! NAD+ aromatic carbon
MASS 127    CN3C 12.011000 C ! NADH aromatic carbon
MASS 128    CN3D 12.011000 C ! Nucleic acid aromatic carbon for 5MC
MASS 129    CN3T 12.011000 C ! Nucleic acid aromatic carbon, Thy C5
MASS 130    CN4  12.011000 C ! Nucleic acid purine C8 and ADE C2  
MASS 131    CN5  12.011000 C ! Nucleic acid purine C4 and C5
MASS 132    CN5G 12.011000 C ! Nucleic acid guanine C5
MASS 133    CN7  12.011000 C ! Nucleic acid carbon (equivalent to protein CT1)
MASS 134    CN7B 12.011000 C ! Nucleic acid aliphatic carbon for C1'
MASS 135    CN7C 12.011000 C ! C2' in arabinose 
MASS 136    CN7D 12.011000 C ! C2' in nucleic acids fluorine derivatives 
MASS 137    CN8  12.011000 C ! Nucleic acid carbon (equivalent to protein CT2)
MASS 138    CN8B 12.011000 C ! Nucleic acid carbon (equivalent to protein CT2)
MASS 139    CN9  12.011000 C ! Nucleic acid carbon (equivalent to protein CT3)
MASS 140    CNE1 12.011000 C ! for alkene; RHC=CR (modified thy patch Sasha)
MASS 141    CNE2 12.011000 C ! for alkene; H2C=CR (modified thy patch Sasha)
MASS 142    CNA  12.011000 C ! pure aromatic carbon
MASS 143    CNA2 12.011000 C ! pure aromatic carbon bound to F
MASS 144    CN6  12.011000 C ! carbocyclic sugar (see toppar_all27_na_carbocyclic.str)
MASS 145    CN7E 12.011000 C ! carbocyclic sugar (see toppar_all27_na_carbocyclic.str)
MASS 150    NN1  14.007000 N ! Nucleic acid amide nitrogen
MASS 151    NN1C 14.007000 N ! Nucleic acid imino nitrogen (cyt taut Sasha)
MASS 152    NN2  14.007000 N ! Nucleic acid protonated ring nitrogen
MASS 153    NN2B 14.007000 N ! From NN2, for N9 in GUA different from ADE
MASS 154    NN2C 14.007000 N ! Nucleic acid protonated ring nitrogen (cyt taut Sasha)
MASS 155    NN2U 14.007000 N ! Nucleic acid protonated ring nitrogen, ura N3
MASS 156    NN2G 14.007000 N ! Nucleic acid protonated ring nitrogen, gua N1
MASS 157    NN3  14.007000 N ! Nucleic acid unprotonated ring nitrogen 
MASS 158    NN3A 14.007000 N ! Nucleic acid unprotonated ring nitrogen, ade N1 and N3
MASS 159    NN3I 14.007000 N ! Nucleic acid unprotonated ring nitrogen, inosine N3
MASS 160    NN3G 14.007000 N ! Nucleic acid unprotonated ring nitrogen, gua N3
MASS 161    NN4  14.007000 N ! Nucleic acid purine N7
MASS 162    NN5  14.007000 N ! Nucleic acid sp2 amine nitrogen
MASS 163    NN6  14.007000 N ! Nucleic acid sp3 amine nitrogen (equiv to protein nh3)
!MASS 170    OT   15.999400 O ! TIPS3P WATER OXYGEN
MASS 171    ON1  15.999400 O ! Nucleic acid carbonyl oxygen
MASS 172    ON1C 15.999400 O ! Nucleic acid carbonyl oxygen, cyt O2
MASS 173    ON2  15.999400 O ! Nucleic acid phosphate ester oxygen
MASS 174    ON3  15.999400 O ! Nucleic acid =O in phosphate 
MASS 175    ON4  15.999400 O ! Nucleic acid phosphate hydroxyl oxygen
MASS 176    ON5  15.999400 O ! Nucleic acid ribose hydroxyl oxygen
MASS 177    ON6  15.999400 O ! Nucleic acid deoxyribose ring oxygen
MASS 178    ON6B 15.999400 O ! Nucleic acid ribose ring oxygen
MASS 179    ON2B 15.999400 O ! Nucleic acid phosphate ester oxygen (pres tp1/tp2, toppar_tyr_ser_thr_phosphate.str)
MASS 180    FN1  18.998400 F ! Fluorine for sugar derivatives (NF) 
MASS 181    FNA  18.998400 F ! Aromatic fluorine
MASS 182    P    30.974000 P ! phosphorus
MASS 183    P2   30.974000 P ! pyrophosphate phosphorus (see toppar_all27_na_nad_ppi.str)
MASS 184    P3   30.974000 P ! protonated pyrophosphate phosphorus (see toppar_all27_na_nad_ppi.str)
MASS 190    SOD  22.989770 NA ! Sodium Ion
MASS 191    MG   24.305000 MG ! Magnesium Ion
MASS 192    POT  39.102000 K  ! Potassium Ion! check masses
MASS 193    CES 132.900000 CS ! Cesium Ion
MASS 194    CAL  40.080000 CA ! Calcium Ion
MASS 195    CLA  35.450000 CL ! Chloride Ion
MASS 196    ZN   65.370000 ZN ! zinc (II) cation
!MASS 199    DUM   0.001    H ! dummy atom
! Atoms not used but needed on DL_POLY
MASS 200    CTL3  12.011000 C 
MASS 201    CL    12.011000 C 
MASS 202    OBL   15.999400 O 
MASS 203    OCL   15.999400 O 
MASS 204    HAL3   1.008000 H
MASS 205    PL    30.974000 P 
MASS 206    O2L   15.999400 O 
MASS 207    NH3L  14.007000 N 
MASS 204    HCL    1.008000 H
MASS 207    NTL   14.007000 N 
MASS 200    CTL5  12.011000 C 
MASS 204    HL     1.008000 H
MASS 205    SL    32.060000 S 
MASS 200    CEL2  12.011000 C 
MASS 204    HEL2   1.008000 H
MASS 200    CEL1  12.011000 C 
MASS 204    HEL1   1.008000 H

DECL -CA  
DECL -C  
DECL -O  
DECL +N  
DECL +HN  
DECL +CA  
!nucleic acid section
DECL  +P
DECL  +O1P
DECL  +O2P
DECL  +O5'
DECL  -O3'

DEFA FIRS NTER LAST CTER   
AUTO ANGLES DIHE   


RESI FLA          0.00  !         H71   H6        O4
ATOM N1   NN3    -0.63  !          |    |         ||
ATOM C2   CN1     0.73  !     H72-C7A   C6   N5   C4    H3
ATOM O2   ON1    -0.47   !        /  \  / \\ / \\ /  \  /
ATOM N3   NN2    -0.54   !      H73   C7   C6A   C4A  N3
ATOM H3   HN2     0.45  !            ||    |    |    |
ATOM C4   CN1     0.59  !      H83   C8   C9A  C10A  C2
ATOM O4   ON1    -0.56  !         \ /  \ // \ / \\  / \\  
ATOM N5   NN3    -0.57  !      H82-C8A  C9   N10  N1   O2
ATOM C6A  CA      0.21  !           |   |     |     
ATOM C6   CA     -0.105 !          H81  H9    R      
ATOM H6   HP      0.125 !
ATOM C4A  CN3     0.21  !
ATOM C7   CA      0.01  !                              
ATOM C7A  CT3    -0.26
ATOM H71  HA3     0.10
ATOM H72  HA3     0.10
ATOM H73  HA3     0.10
ATOM C8   CA      0.01  !                              
ATOM C8A  CT3    -0.26  !                               
ATOM H81  HA3     0.10
ATOM H82  HA3     0.10
ATOM H83  HA3     0.10
ATOM C9   CA     -0.105 !                                
ATOM H9   HP      0.225
ATOM C9A  CA      0.24  ! 
ATOM N10  NN2B   -0.35  !                              
ATOM C10A CN3     0.45  ! 
BOND N1 C2  C2 N3  N3 H3  N3 C4  C4 C4A
BOND C4A N5  C4A C10A  N5 C6A  C6A C9A  C6A C6
BOND C6 H6  C6 C7  C7 C8  C7 C7A  C7A H71  C7A H72  C7A H73
BOND C8 C8A  C8 C9  C8A H81  C8A H82  C8A H83
BOND C9 C9A  C9 H9  C9A N10  N10 C10A  C10A N1
DOUBLE  C2   O2     C4   O4        
IMPR  C6A N5 N10 C4A


RESI RBL          0.00 ! Ribitol (bound to a phosporic acid)
! Edited from RESI GPE  (L-alpha-glycerylphosphorylethanolamine) from top_all27_na_lipid.rtf
!
!ATOM P    PL      1.50 !   (-) O13  O12
!ATOM O13  O2L    -0.78 !         \ /      alpha3
!ATOM O14  O2L    -0.78 !          P (+)
!ATOM O11  OSL    -0.57 !         / \      alpha2
!ATOM O12  OSL    -0.57 !   (-) O14  O11
ATOM C1   CTL2   -0.08 !            |     alpha1
ATOM HA   HAL2    0.09 !       HA---C1---HB
ATOM HB   HAL2    0.09 !            |     theta1
!GROUP                 !            | 
ATOM C2  CTL1     0.10 !            |
ATOM HS  HAL1     0.07 !         HS-C2-OH2-HO2
ATOM OH2  OHL    -0.66 !            |
ATOM HO2  HOL     0.43 !            |       
!GROUP                 !            |  
ATOM C3  CTL1     0.10 !            |
ATOM HX  HAL1     0.08 !         HX-C3-OH3-HO3
ATOM OH3  OHL    -0.66 !            |         
ATOM HO3  HOL     0.43 !            |
!GROUP                 !            |
ATOM C4   CTL1    0.10 !            |
ATOM HY   HAL1    0.07 !         HY-C4-OH4-HO4
ATOM OH4  OHL    -0.66 !            |         
ATOM HO4  HOL     0.43 !            |
!GROUP                 !            |
ATOM  C5   CN7B  -0.13    !     HZ1-C5-HZ2 
ATOM  HZ1  HN7    0.10    ! 
ATOM  HZ2  HN7    0.10    ! 





! Polar Head
!BOND  N    HN1       N    HN2       N    HN3       N    C12
!BOND  C12  H12A      C12  H12B      C12  C11
!BOND  C11  H11A      C11  H11B      C11  O12
!BOND  O12  P         P    O11       P    O13       P    O14
! Glycerol Backbone
BOND  C1   HA        C1    HB       C1   C2        
BOND  C2   HS        C2    C3       C2   OH2
BOND  C3   HX        C3    C4       C3   OH3
BOND  C4   HY        C4    C5       C4   OH4  
BOND  C5   HZ1       C5    HZ2      !C5   HZ3
BOND  OH2  HO2
BOND  OH3  HO3
BOND  OH4  HO4
!
! Polar head (angle names from Sundaralingam)
!IC       C2    C1    O11   P      0.0  0.0  180.0  0.0  0.0 !alpha1
!IC       C1    O11   P     O12    0.0  0.0  180.0  0.0  0.0 !alpha2
!IC       O11   O12  *P     O13    0.0  0.0  120.0  0.0  0.0
!IC       O11   O12  *P     O14    0.0  0.0  240.0  0.0  0.0
!IC       O11   P     O12   C11    0.0  0.0  180.0  0.0  0.0 !alpha3
!IC       O12   C12  *C11   H11A   0.0  0.0  120.0  0.0  0.0
!IC       O12   C12  *C11   H11B   0.0  0.0  240.0  0.0  0.0
!IC       P     O12   C11   C12    0.0  0.0  180.0  0.0  0.0 !alpha4
!IC       N     C11  *C12   H12A   0.0  0.0  120.0  0.0  0.0
!IC       N     C11  *C12   H12B   0.0  0.0  240.0  0.0  0.0
!IC       O12   C11   C12   N      0.0  0.0  180.0  0.0  0.0 !alpha5
!IC       C11   C12   N     HN1    0.0  0.0  180.0  0.0  0.0 !alpha6
!IC       C12   HN1  *N     HN2    0.0  0.0  120.0  0.0  0.0
!IC       C12   HN1  *N     HN3    0.0  0.0  240.0  0.0  0.0
! Glycerol
!IC       O11   C1    C2    C3     0.0  0.0  120.0  0.0  0.0 !theta1
!IC       C1    C2    C3    OH3    0.0  0.0  180.0  0.0  0.0 !theta3
!IC       C1    C3   *C2    OH2    0.0  0.0 -120.0  0.0  0.0
! for stereo-specific phopholipid at carbon C2 (labeled hydrogen S)
!IC       O11   C2   *C1    HA     0.0  0.0 +120.0  0.0  0.0
!IC       O11   C2   *C1    HB     0.0  0.0 -120.0  0.0  0.0
!IC       OH2   C1   *C2    HS     0.0  0.0 +120.0  0.0  0.0
!IC       OH3   C2   *C3    HX     0.0  0.0 +120.0  0.0  0.0
!IC       OH3   C2   *C3    HY     0.0  0.0 -120.0  0.0  0.0
!IC       C1    C2    OH2   HO2    0.0  0.0  180.0  0.0  0.0 !beta1
!IC       C2    C3    OH3   HO3    0.0  0.0 -120.0  0.0  0.0 !gamma1

RESI ADP         -2.00  ! adenosine diphosphate, jjp1/adm jr.
                        ! taken from RESI ADP in top_all36_cgenff.rtf but charges changed
GROUP
ATOM C4'  CN7     0.16  !                       H61  H62
ATOM H4'  HN7     0.09  !                         \  /
ATOM O4'  ON6B   -0.50  !                          N6
ATOM C1'  CN7B    0.16  !                          |
ATOM H1'  HN7     0.09  !                          C6
GROUP                   !                        //  \
ATOM C5   CN5     0.28  !                        N1   C5--N7\\
ATOM N7   NN4    -0.71  !                        |    ||     C8-H8
ATOM C8   CN4     0.34  !                        C2   C4--N9/
ATOM H8   HN3     0.12  !                       / \\ /     \
ATOM N9   NN2    -0.05  !                     H2   N3       \
                        !                                    \
ATOM N1   NN3A   -0.74  !                                     \
ATOM C2   CN4     0.50  !                                      \
ATOM H2   HN3     0.13  !           O3B    O1A    H5' H4'  O4'  \
ATOM N3   NN3A   -0.75  !           |       |      |    \ /   \  \
ATOM C4   CN5     0.43  !     -O1B-PB-O3A--PA-O5'-C5'---C4'    C1'
ATOM C6   CN2     0.46  !           |       |      |     \     / \
                        !           O2B    O2A    H5''   C3'--C2' H1'
ATOM N6   NN1    -0.77  !                               / \   / \
ATOM H61  HN1     0.38  !                            O3' H3' O2' H2''
ATOM H62  HN1     0.38  !                             |       |
GROUP                   !                            H3T     H2'
ATOM C2'  CN7B    0.14  !
ATOM H2'' HN7     0.09
ATOM O2'  ON5    -0.66
ATOM H2'  HN5     0.43
GROUP
ATOM C3'  CN7     0.14
ATOM H3'  HN7     0.09
ATOM O3'  ON5    -0.66
ATOM H3T  HN5     0.43
GROUP
ATOM C5'  CN8B   -0.08
ATOM H5'  HN8     0.09
ATOM H5'' HN8     0.09
ATOM O5'  ON2    -0.57
ATOM PA   P       1.50
ATOM O1A  ON3    -0.78
ATOM O2A  ON3    -0.78
ATOM O3A  ON2    -0.68
ATOM PB   P2      1.50
ATOM O1B  ON2    -0.65
ATOM O2B  ON3    -0.82
ATOM O3B  ON3    -0.82

BOND PB   O3A       PB   O1B       PB    O2B      PB   O3B       O3A  PA
BOND PA   O1A       PA   O2A       PA    O5'      O3'  H3T
BOND O5'  C5'       C5'  C4'       C4'  O4'       C4'  C3'       O4'  C1'
BOND C1'  N9        C1'  C2'       N9   C4        N9   C8        C4   N3
BOND C2   N1        C6   N6
BOND N6   H61       N6   H62       C6   C5        C5   N7
BOND C2'  C3'       C2'  O2'       O2'  H2'       C3'  O3'
BOND C1'  H1'       C2'  H2''      C3'  H3'       C4'  H4'       C5'  H5'
BOND C5'  H5''      C8   H8        C2   H2
DOUBLE N1   C6    N3   C2    C4   C5        N7   C8
IMPR N6   C6   H61  H62       C6   N1   C5   N6        
DONO H61  N6
DONO H62  N6
DONO H2'  O2'
ACCE N3
ACCE N7
ACCE N1
ACCE O1A  PA
ACCE O2A  PA
ACCE O2'
ACCE O3'
ACCE O4'
ACCE O5'
ACCE O3A
ACCE O3B
ACCE O2B
ACCE O1B
IC PA   O3A  PB   O1B    0.0000  000.00  180.0   000.00   0.0000
IC C5'  O5'  PA   O1A    0.0000  000.00   60.0   000.00   0.0000
IC C5'  O5'  PA   O2A    0.0000  000.00  -60.0   000.00   0.0000
IC PA   O3A  PB   O2B    0.0000  000.00   60.0   000.00   0.0000
IC PA   O3A  PB   O3B    0.0000  000.00  -60.0   000.00   0.0000
IC PA   O5'  C5'  C4'    1.5996  119.00 -151.39  110.04   1.5160
IC O5'  C5'  C4'  C3'    1.4401  108.83 -179.85  116.10   1.5284
IC C5'  C4'  C3'  O3'    1.5160  116.10   76.70  115.12   1.4212
IC H3T  O3'  C3'  C4'    0.9650  105.47   38.18  111.98   1.5386
IC O4'  C3'  *C4' C5'    1.4572  104.06 -120.04  116.10   1.5160
IC C2'  C4'  *C3' O3'    1.5284  100.16 -124.08  115.12   1.4212
IC C4'  C3'  C2'  C1'    1.5284  100.16   39.58  102.04   1.5251
IC C3'  C2'  C1'  N9     1.5284  101.97  144.39  113.71   1.4896
IC O4'  C1'  N9   C4     1.5251  113.71  -96.00  125.97   1.3703
IC C1'  C4   *N9  C8     1.4896  125.97 -179.94  106.0    1.367
IC C4   N9   C8   N7     1.376   106.0     0.0   113.6    1.312
IC C8   N9   C4   C5     1.367   106.0     0.0   105.6    1.382
IC C8   N7   C5   C6     0.0       0.0   180.0     0.0    0.0
IC N7   C5   C6   N1     0.0       0.0   180.0     0.0    0.0
IC C5   C6   N1   C2     0.0       0.0     0.0     0.0    0.0
IC N9   C5   *C4  N3     1.376   105.6  -180.0   126.9    1.342
IC C5   N1   *C6  N6     1.409   117.6  -180.0   121.2    1.337
IC N1   C6   N6   H61    1.337   121.2     0.0   119.0    1.01
IC H61  C6   *N6  H62    1.01    119.0   180.0   119.00   1.01
IC C5   N1   *C6  N6     1.409   117.6  -180.0   119.0    1.337
IC N1   C6   N6   H61    1.337   119.0     0.0   119.0    1.01
IC H61  C6   *N6  H62    1.01    119.0   180.0   121.00   1.01
IC N9   N7   *C8   H8    0.0       0.0   180.0     0.0    0.0
IC N1   N3   *C2   H2    0.0       0.0   180.0     0.0    0.0
IC C1'  C3'  *C2' O2'    1.5284  102.04 -114.67  110.81   1.4212
IC H2'  O2'  C2'  C3'    0.9600  114.97  148.63  111.92   1.5284
IC O4'  C2'  *C1' H1'    0.0       0.0  -115.0     0.0    0.0
IC C1'  C3'  *C2' H2''   0.0       0.0   115.0     0.0    0.0
IC C2'  C4'  *C3' H3'    0.0       0.0   115.0     0.0    0.0
IC C3'  O4'  *C4' H4'    0.0       0.0  -115.0     0.0    0.0
IC C4'  O5'  *C5' H5'    0.0       0.0  -115.0     0.0    0.0
IC C4'  O5'  *C5' H5''   0.0       0.0   115.0     0.0    0.0
PATC  FIRS NONE LAST NONE


RESI BZA          1.00
! Parameters taken from RESI PHE and RESI LYS
GROUP   
ATOM NZ   NH3    -0.30  !              HD1  HE1    
ATOM HZ1  HC      0.33  !               |    |   
ATOM HZ2  HC      0.33  ! HZ1     HB1  CD1--CE1
ATOM HZ3  HC      0.33  !    \    |    //     \\
!GROUP                  ! HZ2-NZ--CB--CG      CZ--HZ
ATOM CB   CT2     0.21  !    /    |    \  __  /
ATOM HB1  HA      0.05  ! HZ3     HB2  CD2--CE2
ATOM HB2  HA      0.05  !               |    |  
!GROUP                  !              HD2  HE2   
ATOM CG   CA      0.00
!GROUP   
ATOM CD1  CA     -0.115
ATOM HD1  HP      0.115
!GROUP   
ATOM CE1  CA     -0.115
ATOM HE1  HP      0.115
!GROUP
ATOM CZ   CA     -0.115
ATOM HZ   HP      0.115
!GROUP
ATOM CD2  CA     -0.115
ATOM HD2  HP      0.115
!GROUP
ATOM CE2  CA     -0.115
ATOM HE2  HP      0.115
BOND CB  NZ   CG CB   CD2 CG   CE1 CD1   
BOND CZ  CE2  NZ  HZ1   NZ  HZ2  NZ HZ3
BOND   CD1 CG  CZ CE1   CE2 CD2
BOND CE2 HE2  CZ HZ CE1 HE1 CD1 HD1 
BOND CD2 HD2  CB HB1 CB HB2



PRES FLRB       -0.26   ! Patch to bound the flavine ring with
ATOM 1N10 NN2B  -0.35   ! the ribitol sugar
ATOM 2C5   CN7B  -0.13
!DELETE HfromC5
BOND 1N10 2C5
ANGLE 1N10 2C5 2HZ1    1N10 2C5 2HZ2   1N10 2C5 2C4
ANGLE 1C10A 1N10 2C5   1C9A 1N10 2C5
DIHE  1C10A 1N10 2C5 2HZ1   1C10A 1N10 2C5 2HZ2    1C10A 1N10 2C5 2C4
DIHE  1C9A 1N10 2C5 2HZ1    1C9A 1N10 2C5 2HZ2     1C9A 1N10 2C5 2C4
DIHE  1N10 2C5 2C4 2HY      1N10 2C5 2C4 2OH4      1N10 2C5  2C4 2C3
DIHE  1C4A 1C10A 1N10 2C5   1N1 1C10A 1N10 2C5
DIHE  1C6A 1C9A 1N10 2C5    1C9 1C9A 1N10  2C5


PRES RADP        -0.73  ! Patch to bound the ribitol sugar
ATOM 1C1   CTL2  -0.08  ! with ADP
ATOM 2O1B  OSL   -0.65
BOND 1C1 2O1B
ANGLE 1HA 1C1 2O1B   1HB 1C1 2O1B   1C2 1C1 2O1B
ANGLE 1C1 2O1B 2PB
DIHE  1OH2 1C2 1C1 2O1B   1HS 1C2 1C1 2O1B
DIHE  1HA 1C1 2O1B 2PB    1HB 1C1 2O1B 2PB
DIHE  1C1 2O1B 2PB 2O3A   1C1 2O1B 2PB 2O3B     1C1 2O1B 2PB 2O2B


PRES FADS      -0.23    ! Patch to bound FAD to
ATOM 1C8A  CT2 -0.09    ! a cysteine S
ATOM 1H82  HA2  0.10 
ATOM 1H83  HA2  0.10
ATOM 2SG   S   -0.14
BOND 1C8A 2SG
DELETE ATOM 1H81
DELETE ATOM 2HG1
ANGLE  1C8A 2SG 2CB
ANGLE  1H82 1C8A 2SG   1H83 1C8A 2SG   1C8 1C8A 2SG
DIHE   1C7 1C8 1C8A 2SG   1C9 1C8 1C8A 2SG
DIHE   1C8A 2SG 2CB 2HB1  1C8A 2SG 2CB 2HB2   1C8A 2SG 2CB 2CA
DIHE   1H82 1C8A 2SG 2CB  1H83 1C8A 2SG 2CB   1C8 1C8A 2SG 2CB

PRES BZN          0.00 ! patch for neutral benzylamine based on PRES LSN
                       ! use in a patch statement
                       ! follow with AUTOgenerate ANGLes DIHEdrals command
!delete atom and reassign charges
DELETE ATOM HZ3
GROUP
ATOM CB   CT2     0.13
ATOM HB1  HA      0.075
ATOM HB2  HA      0.075
ATOM NZ   NH2    -0.96
ATOM HZ1  HC      0.34
ATOM HZ2  HC      0.34


