# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat May  2 22:36:58 2020
#   Inital geometry file: a 138 line input string
#   Ligand name: 2-{[(4-amino-2-methylpyrimidin-5-yl)methyl](formyl)amino}-1,2,4-trideoxy-3-S-(phenylcarbonyl)-5-O-phosphono-3-thio-D-erythro-pentitol
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[C@@H]([C@@H](CCO[P](O)(O)=O)SC(=O)c1ccccc1)N(Cc2cnc(C)nc2N)C=O
#
data_comp_list
loop_
_chem_comp.id
_chem_comp.three_letter_code
_chem_comp.name
_chem_comp.group
_chem_comp.number_atoms_all
_chem_comp.number_atoms_nh
_chem_comp.desc_level
_chem_comp.initial_date
_chem_comp.modified_date
_chem_comp.source
 BFT  BFT  2-{[(4-amino-2-methylpyrimidin-5-yl)methyl](formyl)amino}-1,2,4-trideoxy-3-S-(phenylcarbonyl)-5-O-phosphono-3-thio-D-erythro-pentitol  ligand  56  31  .  2021-08-07  2021-08-07  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_BFT
loop_
_chem_comp_atom.comp_id
_chem_comp_atom.atom_id
_chem_comp_atom.type_symbol
_chem_comp_atom.type_energy
_chem_comp_atom.charge
_chem_comp_atom.partial_charge
_chem_comp_atom.x
_chem_comp_atom.y
_chem_comp_atom.z
 BFT  CM2   C  CH3   0  -0.733  -4.7195   2.8035   1.4164
 BFT  N3    N  NT    0  -0.403  -1.8200  -2.3018  -0.7672
 BFT  C2    C  C1    0   0.260  -1.8477  -2.3150  -2.1108
 BFT  S1    S  S2    0   0.019   1.7966  -0.9011   0.5558
 BFT  C5    C  CH1   0  -0.411   0.2440  -0.9686  -0.4014
 BFT  C4    C  CH1   0  -0.083  -0.5393  -2.2543  -0.0520
 BFT  CM4   C  CH3   0  -0.648   0.2445  -3.5424  -0.2776
 BFT  C6    C  CH2   0  -0.463  -0.5471   0.2982  -0.0899
 BFT  C7    C  CH2   0  -0.145   0.0776   1.5514  -0.6637
 BFT  O7    O  O2    0  -0.583  -0.8141   2.6343  -0.3637
 BFT  N1A   N  N     0  -0.442  -4.7200   0.9313  -0.1102
 BFT  C2A   C  CR6   0   0.355  -4.3782   1.3844   1.0897
 BFT  N3A   N  N     0  -0.461  -3.7353   0.6915   2.0185
 BFT  C4A   C  CR6   0   0.459  -3.3451  -0.5508   1.7298
 BFT  N4A   N  NH2   0  -0.832  -2.6670  -1.2097   2.6926
 BFT  C5A   C  CR6   0  -0.040  -3.5965  -1.1085   0.4579
 BFT  C6A   C  CR16  0  -0.066  -4.3188  -0.3065  -0.3976
 BFT  C7A   C  CH2   0  -0.434  -3.0607  -2.4331  -0.0109
 BFT  P1    P  P     0   1.453  -0.2943   4.1385  -0.4433
 BFT  O1    O  O     0  -0.711   0.3837   4.5446  -1.6886
 BFT  O2    O  OH1   0  -0.727  -1.6819   4.8372  -0.0872
 BFT  O3    O  OH1   0  -0.742   0.6946   4.3542   0.7951
 BFT  O5    O  O     0  -0.482  -2.8519  -2.3672  -2.7995
 BFT  CB1   C  C     0   0.217   3.0108  -1.4336  -0.6289
 BFT  OB1   O  O     0  -0.373   2.7346  -1.6745  -1.7776
 BFT  CB2   C  CR6   0   0.019   4.3940  -1.5186  -0.0980
 BFT  CB3   C  CR16  0  -0.283   4.6787  -1.5229   1.2673
 BFT  CB4   C  CR16  0  -0.237   5.9909  -1.6109   1.7052
 BFT  CB5   C  CR16  0  -0.242   7.0280  -1.6931   0.7857
 BFT  CB6   C  CR16  0  -0.240   6.7500  -1.6927  -0.5759
 BFT  CB7   C  CR16  0  -0.257   5.4403  -1.6112  -1.0174
 BFT  HM21  H  HCH3  0   0.247  -5.5537   3.1554   0.8137
 BFT  HM22  H  HCH3  0   0.248  -4.9579   2.9213   2.4717
 BFT  HM23  H  HCH3  0   0.257  -3.8613   3.4446   1.2009
 BFT  H2    H  H     0   0.210  -0.8459  -2.2716  -2.5635
 BFT  H5    H  HCH1  0   0.301   0.5358  -0.9841  -1.4543
 BFT  H4    H  HCH1  0   0.267  -0.7924  -2.1946   1.0079
 BFT  HM41  H  HCH3  0   0.244   1.1053  -3.6036   0.3852
 BFT  HM42  H  HCH3  0   0.255  -0.3950  -4.3987  -0.0647
 BFT  HM43  H  HCH3  0   0.232   0.5982  -3.6303  -1.3048
 BFT  H61   H  HCH2  0   0.274  -1.5463   0.1939  -0.5138
 BFT  H62   H  HCH2  0   0.258  -0.6705   0.4077   0.9912
 BFT  H71   H  HCH2  0   0.238   1.0661   1.7311  -0.2331
 BFT  H72   H  HCH2  0   0.244   0.1914   1.4631  -1.7467
 BFT  H4A1  H  HNH2  0   0.398  -2.6663  -0.8043   3.6146
 BFT  H4A2  H  HNH2  0   0.402  -2.5942  -2.2119   2.6672
 BFT  H6A   H  HCR6  0   0.265  -4.5762  -0.6804  -1.3841
 BFT  H7A1  H  HCH2  0   0.293  -3.7963  -2.9162  -0.6518
 BFT  H7A2  H  HCH2  0   0.275  -2.8842  -3.1283   0.8116
 BFT  HO2   H  HOH1  0   0.504  -1.6816   5.7968  -0.2034
 BFT  HO3   H  HOH1  0   0.494   0.3275   4.1625   1.6684
 BFT  HB3   H  HCR6  0   0.271   3.8862  -1.4764   2.0033
 BFT  HB4   H  HCR6  0   0.271   6.2006  -1.6199   2.7663
 BFT  HB5   H  HCR6  0   0.271   8.0520  -1.7601   1.1292
 BFT  HB6   H  HCR6  0   0.269   7.5554  -1.7566  -1.2950
 BFT  HB7   H  HCR6  0   0.270   5.2325  -1.6098  -2.0789

loop_
_chem_comp_bond.comp_id
_chem_comp_bond.atom_id_1
_chem_comp_bond.atom_id_2
_chem_comp_bond.type
_chem_comp_bond.value_dist
_chem_comp_bond.value_dist_esd
_chem_comp_bond.value_dist_neutron
 BFT  CM2  C2A   single    1.496  0.020  1.496
 BFT  CM2  HM21  single    0.970  0.020  1.090
 BFT  CM2  HM22  single    0.970  0.020  1.090
 BFT  CM2  HM23  single    0.970  0.020  1.090
 BFT  N3   C2    single    1.344  0.020  1.344
 BFT  N3   C4    single    1.468  0.020  1.468
 BFT  N3   C7A   single    1.459  0.020  1.459
 BFT  C2   O5    double    1.219  0.020  1.219
 BFT  C2   H2    single    0.930  0.020  1.080
 BFT  S1   C5    single    1.825  0.020  1.825
 BFT  S1   CB1   single    1.778  0.020  1.778
 BFT  C5   C4    single    1.546  0.020  1.546
 BFT  C5   C6    single    1.526  0.020  1.526
 BFT  C5   H5    single    0.970  0.020  1.090
 BFT  C4   CM4   single    1.525  0.020  1.525
 BFT  C4   H4    single    0.970  0.020  1.090
 BFT  CM4  HM41  single    0.970  0.020  1.090
 BFT  CM4  HM42  single    0.970  0.020  1.090
 BFT  CM4  HM43  single    0.970  0.020  1.090
 BFT  C6   C7    single    1.513  0.020  1.513
 BFT  C6   H61   single    0.970  0.020  1.090
 BFT  C6   H62   single    0.970  0.020  1.090
 BFT  C7   O7    single    1.434  0.020  1.434
 BFT  C7   H71   single    0.970  0.020  1.090
 BFT  C7   H72   single    0.970  0.020  1.090
 BFT  O7   P1    single    1.593  0.020  1.593
 BFT  N1A  C2A   aromatic  1.327  0.020  1.327
 BFT  N1A  C6A   aromatic  1.333  0.020  1.333
 BFT  C2A  N3A   aromatic  1.325  0.020  1.325
 BFT  N3A  C4A   aromatic  1.334  0.020  1.334
 BFT  C4A  N4A   single    1.350  0.020  1.350
 BFT  C4A  C5A   aromatic  1.411  0.020  1.411
 BFT  N4A  H4A1  single    0.890  0.020  1.040
 BFT  N4A  H4A2  single    0.890  0.020  1.040
 BFT  C5A  C6A   aromatic  1.377  0.020  1.377
 BFT  C5A  C7A   single    1.504  0.020  1.504
 BFT  C6A  H6A   single    0.930  0.020  1.080
 BFT  C7A  H7A1  single    0.970  0.020  1.090
 BFT  C7A  H7A2  single    0.970  0.020  1.090
 BFT  P1   O1    double    1.475  0.020  1.475
 BFT  P1   O2    single    1.594  0.020  1.594
 BFT  P1   O3    single    1.599  0.020  1.599
 BFT  O2   HO2   single    0.850  0.020  0.980
 BFT  O3   HO3   single    0.850  0.020  0.980
 BFT  CB1  OB1   double    1.206  0.020  1.206
 BFT  CB1  CB2   single    1.484  0.020  1.484
 BFT  CB2  CB3   aromatic  1.395  0.020  1.395
 BFT  CB2  CB7   aromatic  1.396  0.020  1.396
 BFT  CB3  CB4   aromatic  1.386  0.020  1.386
 BFT  CB3  HB3   single    0.930  0.020  1.080
 BFT  CB4  CB5   aromatic  1.388  0.020  1.388
 BFT  CB4  HB4   single    0.930  0.020  1.080
 BFT  CB5  CB6   aromatic  1.390  0.020  1.390
 BFT  CB5  HB5   single    0.930  0.020  1.080
 BFT  CB6  CB7   aromatic  1.385  0.020  1.385
 BFT  CB6  HB6   single    0.930  0.020  1.080
 BFT  CB7  HB7   single    0.930  0.020  1.080

loop_
_chem_comp_angle.comp_id
_chem_comp_angle.atom_id_1
_chem_comp_angle.atom_id_2
_chem_comp_angle.atom_id_3
_chem_comp_angle.value_angle
_chem_comp_angle.value_angle_esd
 BFT  HM23  CM2  HM22  107.45  3.000
 BFT  HM23  CM2  HM21  107.65  3.000
 BFT  HM22  CM2  HM21  109.53  3.000
 BFT  HM23  CM2  C2A   109.54  3.000
 BFT  HM22  CM2  C2A   111.38  3.000
 BFT  HM21  CM2  C2A   111.15  3.000
 BFT  C7A   N3   C4    119.50  3.000
 BFT  C7A   N3   C2    119.99  3.000
 BFT  C4    N3   C2    120.36  3.000
 BFT  H2    C2   O5    121.29  3.000
 BFT  H2    C2   N3    113.09  3.000
 BFT  O5    C2   N3    125.62  3.000
 BFT  CB1   S1   C5    102.73  3.000
 BFT  H5    C5   C6    110.30  3.000
 BFT  H5    C5   C4    109.96  3.000
 BFT  C6    C5   C4    112.45  3.000
 BFT  H5    C5   S1    106.18  3.000
 BFT  C6    C5   S1    107.66  3.000
 BFT  C4    C5   S1    110.08  3.000
 BFT  H4    C4   CM4   108.01  3.000
 BFT  H4    C4   C5    106.95  3.000
 BFT  CM4   C4   C5    114.13  3.000
 BFT  H4    C4   N3    105.82  3.000
 BFT  CM4   C4   N3    110.44  3.000
 BFT  C5    C4   N3    111.04  3.000
 BFT  HM43  CM4  HM42  108.13  3.000
 BFT  HM43  CM4  HM41  108.23  3.000
 BFT  HM42  CM4  HM41  107.51  3.000
 BFT  HM43  CM4  C4    112.00  3.000
 BFT  HM42  CM4  C4    109.47  3.000
 BFT  HM41  CM4  C4    111.35  3.000
 BFT  H62   C6   H61   106.88  3.000
 BFT  H62   C6   C7    109.78  3.000
 BFT  H61   C6   C7    108.07  3.000
 BFT  H62   C6   C5    110.09  3.000
 BFT  H61   C6   C5    108.44  3.000
 BFT  C7    C6   C5    113.34  3.000
 BFT  H72   C7   H71   108.04  3.000
 BFT  H72   C7   O7    109.46  3.000
 BFT  H71   C7   O7    110.83  3.000
 BFT  H72   C7   C6    110.60  3.000
 BFT  H71   C7   C6    111.11  3.000
 BFT  O7    C7   C6    106.81  3.000
 BFT  P1    O7   C7    119.96  3.000
 BFT  C6A   N1A  C2A   115.76  3.000
 BFT  N3A   C2A  N1A   125.45  3.000
 BFT  N3A   C2A  CM2   116.98  3.000
 BFT  N1A   C2A  CM2   117.56  3.000
 BFT  C4A   N3A  C2A   118.50  3.000
 BFT  C5A   C4A  N4A   122.66  3.000
 BFT  C5A   C4A  N3A   120.73  3.000
 BFT  N4A   C4A  N3A   116.57  3.000
 BFT  H4A2  N4A  H4A1  115.12  3.000
 BFT  H4A2  N4A  C4A   120.34  3.000
 BFT  H4A1  N4A  C4A   117.19  3.000
 BFT  C7A   C5A  C6A   120.41  3.000
 BFT  C7A   C5A  C4A   124.44  3.000
 BFT  C6A   C5A  C4A   115.03  3.000
 BFT  H6A   C6A  C5A   119.22  3.000
 BFT  H6A   C6A  N1A   116.38  3.000
 BFT  C5A   C6A  N1A   124.39  3.000
 BFT  H7A2  C7A  H7A1  105.68  3.000
 BFT  H7A2  C7A  C5A   112.57  3.000
 BFT  H7A1  C7A  C5A   109.49  3.000
 BFT  H7A2  C7A  N3    108.09  3.000
 BFT  H7A1  C7A  N3    108.02  3.000
 BFT  C5A   C7A  N3    112.67  3.000
 BFT  O3    P1   O2    107.83  3.000
 BFT  O3    P1   O1    109.41  3.000
 BFT  O2    P1   O1    117.91  3.000
 BFT  O3    P1   O7    106.88  3.000
 BFT  O2    P1   O7     96.82  3.000
 BFT  O1    P1   O7    116.88  3.000
 BFT  HO2   O2   P1    114.08  3.000
 BFT  HO3   O3   P1    115.98  3.000
 BFT  CB2   CB1  OB1   122.88  3.000
 BFT  CB2   CB1  S1    114.54  3.000
 BFT  OB1   CB1  S1    122.56  3.000
 BFT  CB7   CB2  CB3   119.44  3.000
 BFT  CB7   CB2  CB1   117.83  3.000
 BFT  CB3   CB2  CB1   122.73  3.000
 BFT  HB3   CB3  CB4   118.75  3.000
 BFT  HB3   CB3  CB2   121.06  3.000
 BFT  CB4   CB3  CB2   120.18  3.000
 BFT  HB4   CB4  CB5   120.29  3.000
 BFT  HB4   CB4  CB3   119.60  3.000
 BFT  CB5   CB4  CB3   120.11  3.000
 BFT  HB5   CB5  CB6   120.02  3.000
 BFT  HB5   CB5  CB4   120.02  3.000
 BFT  CB6   CB5  CB4   119.96  3.000
 BFT  HB6   CB6  CB7   119.72  3.000
 BFT  HB6   CB6  CB5   120.17  3.000
 BFT  CB7   CB6  CB5   120.11  3.000
 BFT  HB7   CB7  CB6   119.65  3.000
 BFT  HB7   CB7  CB2   120.15  3.000
 BFT  CB6   CB7  CB2   120.20  3.000

loop_
_chem_comp_tor.comp_id
_chem_comp_tor.id
_chem_comp_tor.atom_id_1
_chem_comp_tor.atom_id_2
_chem_comp_tor.atom_id_3
_chem_comp_tor.atom_id_4
_chem_comp_tor.value_angle
_chem_comp_tor.value_angle_esd
_chem_comp_tor.period
 BFT  CONST_01  C4A   N3A  C2A  N1A     0.00   0.0  0
 BFT  CONST_02  C4A   C5A  C6A  N1A     0.00   0.0  0
 BFT  CONST_03  C5A   C6A  N1A  C2A     0.00   0.0  0
 BFT  CONST_04  C5A   C4A  N3A  C2A     0.00   0.0  0
 BFT  CONST_05  C6A   N1A  C2A  N3A     0.00   0.0  0
 BFT  CONST_06  C6A   C5A  C4A  N3A     0.00   0.0  0
 BFT  CONST_07  CB5   CB4  CB3  CB2     0.00   0.0  0
 BFT  CONST_08  CB5   CB6  CB7  CB2     0.00   0.0  0
 BFT  CONST_09  CB6   CB7  CB2  CB3     0.00   0.0  0
 BFT  CONST_10  CB6   CB5  CB4  CB3     0.00   0.0  0
 BFT  CONST_11  CB7   CB2  CB3  CB4     0.00   0.0  0
 BFT  CONST_12  CB7   CB6  CB5  CB4     0.00   0.0  0
 BFT  CONST_13  C6A   N1A  C2A  CM2   180.00   0.0  0
 BFT  CONST_14  C4A   N3A  C2A  CM2   180.00   0.0  0
 BFT  CONST_15  C7A   C5A  C6A  N1A   180.00   0.0  0
 BFT  CONST_16  N4A   C4A  N3A  C2A   180.00   0.0  0
 BFT  CONST_17  C7A   C5A  C4A  N3A   180.00   0.0  0
 BFT  CONST_18  C6A   C5A  C4A  N4A   180.00   0.0  0
 BFT  CONST_19  CB4   CB3  CB2  CB1   180.00   0.0  0
 BFT  CONST_20  CB6   CB7  CB2  CB1   180.00   0.0  0
 BFT  CONST_21  H6A   C6A  N1A  C2A   180.00   0.0  0
 BFT  CONST_22  HB4   CB4  CB3  CB2   180.00   0.0  0
 BFT  CONST_23  HB6   CB6  CB7  CB2   180.00   0.0  0
 BFT  CONST_24  HB7   CB7  CB2  CB3   180.00   0.0  0
 BFT  CONST_25  HB5   CB5  CB4  CB3   180.00   0.0  0
 BFT  CONST_26  HB3   CB3  CB4  CB5   180.00   0.0  0
 BFT  CONST_27  H4A1  N4A  C4A  N3A     0.00   0.0  0
 BFT  CONST_29  O5    C2   N3   C4    180.00   0.0  0
 BFT  CONST_30  O5    C2   N3   C7A     0.00   0.0  0
 BFT  Var_01    C4A   C5A  C7A  N3    -94.69  30.0  2
 BFT  Var_02    CB3   CB2  CB1  S1     15.77  30.0  2
 BFT  Var_03    HM21  CM2  C2A  N1A    24.07  30.0  2
 BFT  Var_04    C5A   C7A  N3   C2    -98.66  30.0  3
 BFT  Var_05    CB2   CB1  S1   C5   -178.08  30.0  3
 BFT  Var_06    O7    C7   C6   C5    176.44  30.0  3
 BFT  Var_07    O1    P1   O7   C7     51.58  30.0  3

loop_
_chem_comp_chir.comp_id
_chem_comp_chir.id
_chem_comp_chir.atom_id_centre
_chem_comp_chir.atom_id_1
_chem_comp_chir.atom_id_2
_chem_comp_chir.atom_id_3
_chem_comp_chir.volume_sign
 BFT  chir_01  C5  S1  C4  C6   negativ
 BFT  chir_02  C4  N3  C5  CM4  positiv

loop_
_chem_comp_plane_atom.comp_id
_chem_comp_plane_atom.plane_id
_chem_comp_plane_atom.atom_id
_chem_comp_plane_atom.dist_esd
 BFT  plan-1  CM2   0.020
 BFT  plan-1  N1A   0.020
 BFT  plan-1  C2A   0.020
 BFT  plan-1  N3A   0.020
 BFT  plan-1  C4A   0.020
 BFT  plan-1  N4A   0.020
 BFT  plan-1  C5A   0.020
 BFT  plan-1  C6A   0.020
 BFT  plan-1  C7A   0.020
 BFT  plan-1  H6A   0.020
 BFT  plan-2  CB1   0.020
 BFT  plan-2  CB2   0.020
 BFT  plan-2  CB3   0.020
 BFT  plan-2  CB4   0.020
 BFT  plan-2  CB5   0.020
 BFT  plan-2  CB6   0.020
 BFT  plan-2  CB7   0.020
 BFT  plan-2  HB3   0.020
 BFT  plan-2  HB4   0.020
 BFT  plan-2  HB5   0.020
 BFT  plan-2  HB6   0.020
 BFT  plan-2  HB7   0.020
 BFT  plan-3  N3    0.020
 BFT  plan-3  C2    0.020
 BFT  plan-3  C4    0.020
 BFT  plan-3  C7A   0.020
 BFT  plan-3  O5    0.020
 BFT  plan-3  H2    0.020
 BFT  plan-4  C4A   0.020
 BFT  plan-4  N4A   0.020
 BFT  plan-4  H4A1  0.020
 BFT  plan-4  H4A2  0.020
 BFT  plan-5  S1    0.020
 BFT  plan-5  CB1   0.020
 BFT  plan-5  OB1   0.020
 BFT  plan-5  CB2   0.020

