# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Mar  9 11:31:36 2022
#   Inital geometry file: a 112 line input string
#   Ligand name: N-(4-nitrophenyl)-5-[(3aS,4S,6aR)-2-oxohexahydro-1H-thieno[3,4-d]imidazol-4-yl]pentanamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: [O-][N+](=O)c1ccc(NC(=O)CCCC[C@@H]2SC[C@@H]3NC(=O)N[C@H]23)cc1
#
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
 BNI  BNI  N-(4-nitrophenyl)-5-[(3aS,4S,6aR)-2-oxohexahydro-1H-thieno[3,4-d]imidazol-4-yl]pentanamide  ligand  45  25  .  2022-03-15  2022-03-15
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_BNI
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
 BNI  C1    C  C      0   0.570  -1.8875  -0.1563  -0.4935
 BNI  C10   C  CH2    0  -0.601  -0.5627  -0.8651  -0.3332
 BNI  C9    C  CH2    0  -0.415   0.6457   0.0236  -0.5768
 BNI  C8    C  CH2    0  -0.418   1.9492  -0.7486  -0.4198
 BNI  C7    C  CH2    0  -0.421   3.1685   0.1258  -0.6814
 BNI  C2    C  CH1    0  -0.362   4.4864  -0.6202  -0.5911
 BNI  C6    C  CH2    0  -0.571   6.5402  -1.6002   0.5568
 BNI  C4    C  CR15   0  -0.064   5.7142   0.2144  -0.9753
 BNI  C5    C  CR15   0  -0.044   6.9795  -0.4451  -0.3505
 BNI  C3    C  CR5    0   0.643   6.8234   1.7808   0.3671
 BNI  O2    O  O      0  -0.450  -2.0127   0.9132  -1.0534
 BNI  O3    O  O      0  -0.529   7.0905   2.8316   0.9300
 BNI  N1    N  NR15   0  -0.661   7.5783   0.6538   0.3608
 BNI  N2    N  NR15   0  -0.656   5.7144   1.5265  -0.3803
 BNI  S1    S  S2     0  -0.024   4.8524  -1.2176   1.0928
 BNI  N17   N  NH1    0  -0.751  -2.9372  -0.8569   0.0394
 BNI  C18   C  CR6    0   0.411  -4.2898  -0.5701   0.0238
 BNI  C20   C  CR16   0  -0.313  -4.8494   0.5860  -0.5335
 BNI  C21   C  CR16   0  -0.256  -6.2174   0.7767  -0.4982
 BNI  C22   C  CR6    0   0.234  -7.0403  -0.1728   0.0895
 BNI  C23   C  CR16   0  -0.255  -6.5025  -1.3256   0.6503
 BNI  C24   C  CR16   0  -0.350  -5.1403  -1.5159   0.6141
 BNI  N25   N  N      1   0.326  -8.4689   0.0357   0.1202
 BNI  O26   O  O      0  -0.389  -9.1590  -0.8115   0.6417
 BNI  O27   O  O     -1  -0.389  -8.9121   1.0472  -0.3762
 BNI  H101  H  HCH2   0   0.269  -0.5101  -1.3142   0.6630
 BNI  H102  H  HCH2   0   0.284  -0.5589  -1.7061  -1.0364
 BNI  H91   H  HCH2   0   0.230   0.5962   0.4533  -1.5800
 BNI  H92   H  HCH2   0   0.230   0.6335   0.8640   0.1227
 BNI  H81   H  HCH2   0   0.223   2.0010  -1.1733   0.5879
 BNI  H82   H  HCH2   0   0.222   1.9567  -1.5990  -1.1097
 BNI  H71   H  HCH2   0   0.241   3.0923   0.5514  -1.6882
 BNI  H72   H  HCH2   0   0.233   3.1778   0.9698   0.0137
 BNI  H21A  H  HCH1   0   0.275   4.4589  -1.4911  -1.2551
 BNI  H61   H  HCH2   0   0.289   7.1953  -1.7196   1.4187
 BNI  H62   H  HCH2   0   0.275   6.5409  -2.5373  -0.0023
 BNI  HC4   H  HCR5   0   0.281   5.7825   0.2737  -2.0654
 BNI  HC5   H  HCR5   0   0.278   7.6552  -0.8289  -1.1177
 BNI  HN11  H  HNR5   0   0.399   8.3661   0.5407   0.9762
 BNI  HN21  H  HNR5   0   0.399   5.1772   2.2850  -0.7649
 BNI  H171  H  HNH1   0   0.425  -2.6948  -1.7304   0.4840
 BNI  H20   H  HCR6   0   0.297  -4.2327   1.3386  -0.9941
 BNI  H21   H  HCR6   0   0.298  -6.6283   1.6754  -0.9345
 BNI  H23   H  HCR6   0   0.299  -7.1296  -2.0739   1.1124
 BNI  H24   H  HCR6   0   0.290  -4.7235  -2.4150   1.0502

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
 BNI  C1   C10   single    1.511  0.020  1.511
 BNI  C1   O2    double    1.214  0.020  1.214
 BNI  C1   N17   single    1.370  0.020  1.370
 BNI  C10  C9    single    1.520  0.020  1.520
 BNI  C10  H101  single    0.970  0.020  1.090
 BNI  C10  H102  single    0.970  0.020  1.090
 BNI  C9   C8    single    1.523  0.020  1.523
 BNI  C9   H91   single    0.970  0.020  1.090
 BNI  C9   H92   single    0.970  0.020  1.090
 BNI  C8   C7    single    1.523  0.020  1.523
 BNI  C8   H81   single    0.970  0.020  1.090
 BNI  C8   H82   single    0.970  0.020  1.090
 BNI  C7   C2    single    1.517  0.020  1.517
 BNI  C7   H71   single    0.970  0.020  1.090
 BNI  C7   H72   single    0.970  0.020  1.090
 BNI  C2   C4    single    1.534  0.020  1.534
 BNI  C2   S1    single    1.824  0.020  1.824
 BNI  C2   H21A  single    0.970  0.020  1.090
 BNI  C6   C5    single    1.533  0.020  1.533
 BNI  C6   S1    single    1.812  0.020  1.812
 BNI  C6   H61   single    0.970  0.020  1.090
 BNI  C6   H62   single    0.970  0.020  1.090
 BNI  C4   C5    single    1.558  0.020  1.558
 BNI  C4   N2    single    1.441  0.020  1.441
 BNI  C4   HC4   single    0.970  0.020  1.090
 BNI  C5   N1    single    1.439  0.020  1.439
 BNI  C5   HC5   single    0.970  0.020  1.090
 BNI  C3   O3    double    1.222  0.020  1.222
 BNI  C3   N1    single    1.356  0.020  1.356
 BNI  C3   N2    single    1.361  0.020  1.361
 BNI  N1   HN11  single    0.860  0.020  1.020
 BNI  N2   HN21  single    0.890  0.020  1.040
 BNI  N17  C18   single    1.383  0.020  1.383
 BNI  N17  H171  single    0.860  0.020  1.020
 BNI  C18  C20   aromatic  1.400  0.020  1.400
 BNI  C18  C24   aromatic  1.402  0.020  1.402
 BNI  C20  C21   aromatic  1.382  0.020  1.382
 BNI  C20  H20   single    0.930  0.020  1.080
 BNI  C21  C22   aromatic  1.387  0.020  1.387
 BNI  C21  H21   single    0.930  0.020  1.080
 BNI  C22  C23   aromatic  1.390  0.020  1.390
 BNI  C22  N25   single    1.444  0.020  1.444
 BNI  C23  C24   aromatic  1.376  0.020  1.376
 BNI  C23  H23   single    0.930  0.020  1.080
 BNI  C24  H24   single    0.930  0.020  1.080
 BNI  N25  O26   double    1.211  0.020  1.211
 BNI  N25  O27   single    1.211  0.020  1.211

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
 BNI  N17   C1   O2    123.44  3.000
 BNI  N17   C1   C10   112.99  3.000
 BNI  O2    C1   C10   123.56  3.000
 BNI  H102  C10  H101  105.60  3.000
 BNI  H102  C10  C9    110.07  3.000
 BNI  H101  C10  C9    110.35  3.000
 BNI  H102  C10  C1    107.15  3.000
 BNI  H101  C10  C1    109.35  3.000
 BNI  C9    C10  C1    113.95  3.000
 BNI  H92   C9   H91   106.53  3.000
 BNI  H92   C9   C8    109.47  3.000
 BNI  H91   C9   C8    109.44  3.000
 BNI  H92   C9   C10   109.76  3.000
 BNI  H91   C9   C10   109.95  3.000
 BNI  C8    C9   C10   111.57  3.000
 BNI  H82   C8   H81   106.15  3.000
 BNI  H82   C8   C7    109.40  3.000
 BNI  H81   C8   C7    110.06  3.000
 BNI  H82   C8   C9    109.55  3.000
 BNI  H81   C8   C9    109.39  3.000
 BNI  C7    C8   C9    112.11  3.000
 BNI  H72   C7   H71   106.55  3.000
 BNI  H72   C7   C2    109.53  3.000
 BNI  H71   C7   C2    107.83  3.000
 BNI  H72   C7   C8    109.92  3.000
 BNI  H71   C7   C8    108.98  3.000
 BNI  C2    C7   C8    113.76  3.000
 BNI  H21A  C2   S1    107.71  3.000
 BNI  H21A  C2   C4    107.51  3.000
 BNI  S1    C2   C4    104.41  3.000
 BNI  H21A  C2   C7    109.45  3.000
 BNI  S1    C2   C7    112.98  3.000
 BNI  C4    C2   C7    114.39  3.000
 BNI  H62   C6   H61   108.11  3.000
 BNI  H62   C6   S1    109.48  3.000
 BNI  H61   C6   S1    110.45  3.000
 BNI  H62   C6   C5    110.10  3.000
 BNI  H61   C6   C5    112.24  3.000
 BNI  S1    C6   C5    106.44  3.000
 BNI  HC4   C4   N2    111.24  3.000
 BNI  HC4   C4   C5    111.83  3.000
 BNI  N2    C4   C5    102.70  3.000
 BNI  HC4   C4   C2    109.22  3.000
 BNI  N2    C4   C2    113.10  3.000
 BNI  C5    C4   C2    108.63  3.000
 BNI  HC5   C5   N1    110.98  3.000
 BNI  HC5   C5   C4    111.69  3.000
 BNI  N1    C5   C4    102.29  3.000
 BNI  HC5   C5   C6    109.17  3.000
 BNI  N1    C5   C6    113.70  3.000
 BNI  C4    C5   C6    108.88  3.000
 BNI  N2    C3   N1    107.19  3.000
 BNI  N2    C3   O3    126.28  3.000
 BNI  N1    C3   O3    126.52  3.000
 BNI  HN11  N1   C3    121.76  3.000
 BNI  HN11  N1   C5    122.83  3.000
 BNI  C3    N1   C5    113.89  3.000
 BNI  HN21  N2   C3    120.27  3.000
 BNI  HN21  N2   C4    121.92  3.000
 BNI  C3    N2   C4    113.39  3.000
 BNI  C6    S1   C2     89.02  3.000
 BNI  H171  N17  C18   114.79  3.000
 BNI  H171  N17  C1    115.46  3.000
 BNI  C18   N17  C1    129.72  3.000
 BNI  C24   C18  C20   118.82  3.000
 BNI  C24   C18  N17   116.66  3.000
 BNI  C20   C18  N17   124.52  3.000
 BNI  H20   C20  C21   118.79  3.000
 BNI  H20   C20  C18   121.24  3.000
 BNI  C21   C20  C18   119.97  3.000
 BNI  H21   C21  C22   120.99  3.000
 BNI  H21   C21  C20   118.76  3.000
 BNI  C22   C21  C20   120.25  3.000
 BNI  N25   C22  C23   119.60  3.000
 BNI  N25   C22  C21   119.80  3.000
 BNI  C23   C22  C21   120.60  3.000
 BNI  H23   C23  C24   119.36  3.000
 BNI  H23   C23  C22   121.49  3.000
 BNI  C24   C23  C22   119.15  3.000
 BNI  H24   C24  C23   119.04  3.000
 BNI  H24   C24  C18   119.75  3.000
 BNI  C23   C24  C18   121.22  3.000
 BNI  O27   N25  O26   123.54  3.000
 BNI  O27   N25  C22   118.30  3.000
 BNI  O26   N25  C22   118.16  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
 BNI  CONST_01  C22   C21  C20  C18     0.00   0.0  0
 BNI  CONST_02  C22   C23  C24  C18     0.00   0.0  0
 BNI  CONST_03  C23   C24  C18  C20     0.00   0.0  0
 BNI  CONST_04  C23   C22  C21  C20     0.00   0.0  0
 BNI  CONST_05  C24   C18  C20  C21     0.00   0.0  0
 BNI  CONST_06  C24   C23  C22  C21     0.00   0.0  0
 BNI  CONST_07  N1    C3   N2   C4      0.00   0.0  0
 BNI  CONST_08  N2    C3   N1   C5      0.00   0.0  0
 BNI  CONST_09  C21   C20  C18  N17   180.00   0.0  0
 BNI  CONST_10  C23   C24  C18  N17   180.00   0.0  0
 BNI  CONST_11  N25   C22  C21  C20   180.00   0.0  0
 BNI  CONST_12  N25   C22  C23  C24   180.00   0.0  0
 BNI  CONST_13  O3    C3   N2   C4    180.00   0.0  0
 BNI  CONST_14  O3    C3   N1   C5    180.00   0.0  0
 BNI  CONST_15  H21   C21  C20  C18   180.00   0.0  0
 BNI  CONST_16  H23   C23  C24  C18   180.00   0.0  0
 BNI  CONST_17  H24   C24  C18  C20   180.00   0.0  0
 BNI  CONST_18  H20   C20  C21  C22   180.00   0.0  0
 BNI  CONST_20  HN11  N1   C3   N2    180.00   0.0  0
 BNI  CONST_21  C20   C18  N17  C1      0.00   0.0  0
 BNI  CONST_22  C24   C18  N17  C1    180.00   0.0  0
 BNI  CONST_23  O26   N25  C22  C21   180.00   0.0  0
 BNI  CONST_24  O27   N25  C22  C21     0.00   0.0  0
 BNI  CONST_25  O26   N25  C22  C23     0.00   0.0  0
 BNI  CONST_26  O27   N25  C22  C23   180.00   0.0  0
 BNI  CONST_27  H171  N17  C18  C20   180.00   0.0  0
 BNI  CONST_28  C18   N17  C1   C10   180.00   0.0  0
 BNI  CONST_29  C18   N17  C1   O2      0.00   0.0  0
 BNI  Var_01    C5    C6   S1   C2     40.35  30.0  1
 BNI  Var_02    C2    C7   C8   C9   -177.62  30.0  3
 BNI  Var_03    C8    C9   C10  C1   -179.23  30.0  3
 BNI  Var_04    C7    C8   C9   C10   179.16  30.0  3
 BNI  Var_05    O2    C1   C10  C9     16.14  30.0  1

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
 BNI  chir_01  C2  C7  C4  S1  negativ
 BNI  chir_02  C4  N2  C5  C2  negativ
 BNI  chir_03  C5  N1  C4  C6  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
 BNI  plan-1  N17   0.020
 BNI  plan-1  C18   0.020
 BNI  plan-1  C20   0.020
 BNI  plan-1  C21   0.020
 BNI  plan-1  C22   0.020
 BNI  plan-1  C23   0.020
 BNI  plan-1  C24   0.020
 BNI  plan-1  N25   0.020
 BNI  plan-1  H20   0.020
 BNI  plan-1  H21   0.020
 BNI  plan-1  H23   0.020
 BNI  plan-1  H24   0.020
 BNI  plan-2  C1    0.020
 BNI  plan-2  C10   0.020
 BNI  plan-2  O2    0.020
 BNI  plan-2  N17   0.020
 BNI  plan-2  C18   0.020
 BNI  plan-2  H171  0.020
 BNI  plan-3  C22   0.020
 BNI  plan-3  N25   0.020
 BNI  plan-3  O26   0.020
 BNI  plan-3  O27   0.020
 BNI  plan-4  C4    0.020
 BNI  plan-4  C5    0.020
 BNI  plan-4  C3    0.020
 BNI  plan-4  O3    0.020
 BNI  plan-4  N1    0.020
 BNI  plan-4  N2    0.020
 BNI  plan-4  HN11  0.020
 BNI  plan-4  HN21  0.020

