# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Apr  3 14:45:47 2020
#   Inital geometry file: a 107 line input string
#   Ligand name: 3-(1H-benzimidazol-2-yl)-N-(1-benzothiophen-2-ylcarbonyl)-D-alanine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC(=O)[C@@H](Cc1[nH]c2ccccc2n1)NC(=O)c3sc4ccccc4c3
#
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
 4D9  4D9  3-(1H-benzimidazol-2-yl)-N-(1-benzothiophen-2-ylcarbonyl)-D-alanine  ligand  40  26  .  2021-08-04  2021-08-04  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_4D9
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
 4D9  C1    C  CR16   0  -0.311  -3.8865   2.4979  -1.1615
 4D9  C2    C  CR16   0  -0.280  -3.6667   3.7988  -0.7398
 4D9  C3    C  CR16   0  -0.274  -3.0244   4.0760   0.4761
 4D9  C4    C  CR16   0  -0.337  -2.5822   3.0604   1.3063
 4D9  N5    N  NR15   0  -0.694  -3.4747   0.1194  -0.4080
 4D9  C6    C  CR56   0   0.331  -3.4362   1.4856  -0.3228
 4D9  C7    C  CR56   0   0.142  -2.7920   1.7438   0.8992
 4D9  N8    N  N      0  -0.471  -2.4630   0.5591   1.5156
 4D9  C9    C  CR5    0   0.453  -2.8833  -0.3791   0.7102
 4D9  C10   C  CH2    0  -0.578  -2.6829  -1.8374   0.9170
 4D9  C11   C  CH1    0  -0.199  -1.6026  -2.3986  -0.0193
 4D9  C12   C  C      0   0.422  -1.3417  -3.8990   0.2858
 4D9  N13   N  NH1    0  -0.641  -0.4233  -1.5751   0.0771
 4D9  O14   O  O      0  -0.583  -0.1849  -4.2315   0.5832
 4D9  O15   O  OC    -1  -0.610  -2.3499  -4.6252   0.1970
 4D9  C16   C  C      0   0.555   0.4683  -1.4738  -0.9171
 4D9  C17   C  CR5    0  -0.324   1.6321  -0.5919  -0.6543
 4D9  O18   O  O      0  -0.485   0.3517  -2.0299  -2.0006
 4D9  C19   C  CR15   0  -0.218   2.8023  -0.6366  -1.3350
 4D9  S20   S  S2     0   0.233   1.6097   0.6589   0.5585
 4D9  C21   C  CR56   0  -0.217   3.2310   1.1207   0.1640
 4D9  C22   C  CR56   0   0.225   3.7485   0.3334  -0.8804
 4D9  C23   C  CR16   0  -0.316   5.0519   0.5762  -1.3331
 4D9  C24   C  CR16   0  -0.254   5.7937   1.5801  -0.7478
 4D9  C25   C  CR16   0  -0.265   5.2587   2.3564   0.2900
 4D9  C26   C  CR16   0  -0.276   3.9769   2.1377   0.7554
 4D9  H1    H  HCR6   0   0.263  -4.3837   2.2838  -2.0985
 4D9  H2    H  HCR6   0   0.253  -3.9970   4.6202  -1.3626
 4D9  H3    H  HCR6   0   0.250  -2.8733   5.1070   0.7684
 4D9  H4    H  HCR6   0   0.251  -2.0873   3.2798   2.2438
 4D9  H10   H  HCH2   0   0.269  -2.3988  -1.9932   1.9597
 4D9  H10A  H  HCH2   0   0.280  -3.6085  -2.3861   0.7443
 4D9  H11   H  HCH1   0   0.257  -1.9671  -2.3315  -1.0475
 4D9  HN13  H  HNH1   0   0.395  -0.1617  -1.2587   0.9989
 4D9  H19   H  HCR5   0   0.274   2.9966  -1.3422  -2.1306
 4D9  H23   H  HCR6   0   0.262   5.4669  -0.0219  -2.1345
 4D9  H24   H  HCR6   0   0.263   6.8015   1.7734  -1.0903
 4D9  H25   H  HCR6   0   0.265   5.8593   3.1383   0.7356
 4D9  H26   H  HCR6   0   0.272   3.5667   2.7377   1.5571
 4D9  HN5   H  HNR5   0   0.417  -3.8879  -0.4206  -1.1519

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
 4D9  C6   C1    aromatic  1.390  0.020  1.390
 4D9  C2   C1    aromatic  1.385  0.020  1.385
 4D9  C1   H1    single    0.930  0.020  1.080
 4D9  C3   C2    aromatic  1.403  0.020  1.403
 4D9  C2   H2    single    0.930  0.020  1.080
 4D9  C4   C3    aromatic  1.384  0.020  1.384
 4D9  C3   H3    single    0.930  0.020  1.080
 4D9  C4   C7    aromatic  1.394  0.020  1.394
 4D9  C4   H4    single    0.930  0.020  1.080
 4D9  C9   N5    aromatic  1.360  0.020  1.360
 4D9  N5   C6    aromatic  1.369  0.020  1.369
 4D9  C7   C6    aromatic  1.405  0.020  1.405
 4D9  N8   C7    aromatic  1.375  0.020  1.375
 4D9  N8   C9    aromatic  1.306  0.020  1.306
 4D9  C10  C9    single    1.486  0.020  1.486
 4D9  C11  C10   single    1.536  0.020  1.536
 4D9  C10  H10   single    0.970  0.020  1.090
 4D9  C10  H10A  single    0.970  0.020  1.090
 4D9  N13  C11   single    1.442  0.020  1.442
 4D9  C12  C11   single    1.553  0.020  1.553
 4D9  C11  H11   single    0.970  0.020  1.090
 4D9  O14  C12   deloc     1.240  0.020  1.240
 4D9  C12  O15   deloc     1.246  0.020  1.246
 4D9  C16  N13   single    1.339  0.020  1.339
 4D9  N13  HN13  single    0.860  0.020  1.020
 4D9  C17  C16   single    1.484  0.020  1.484
 4D9  C16  O18   double    1.223  0.020  1.223
 4D9  C19  C17   aromatic  1.355  0.020  1.355
 4D9  S20  C17   aromatic  1.742  0.020  1.742
 4D9  C22  C19   aromatic  1.429  0.020  1.429
 4D9  C19  H19   single    0.930  0.020  1.080
 4D9  C21  S20   aromatic  1.731  0.020  1.731
 4D9  C26  C21   aromatic  1.393  0.020  1.393
 4D9  C22  C21   aromatic  1.407  0.020  1.407
 4D9  C23  C22   aromatic  1.401  0.020  1.401
 4D9  C24  C23   aromatic  1.379  0.020  1.379
 4D9  C23  H23   single    0.930  0.020  1.080
 4D9  C24  C25   aromatic  1.402  0.020  1.402
 4D9  C24  H24   single    0.930  0.020  1.080
 4D9  C25  C26   aromatic  1.381  0.020  1.381
 4D9  C25  H25   single    0.930  0.020  1.080
 4D9  C26  H26   single    0.930  0.020  1.080
 4D9  N5   HN5   single    0.860  0.020  1.020

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
 4D9  H1    C1   C6   121.83  3.000
 4D9  H1    C1   C2   121.49  3.000
 4D9  C6    C1   C2   116.68  3.000
 4D9  H2    C2   C3   119.24  3.000
 4D9  H2    C2   C1   119.29  3.000
 4D9  C3    C2   C1   121.48  3.000
 4D9  H3    C3   C4   119.49  3.000
 4D9  H3    C3   C2   119.10  3.000
 4D9  C4    C3   C2   121.41  3.000
 4D9  H4    C4   C7   120.87  3.000
 4D9  H4    C4   C3   121.12  3.000
 4D9  C7    C4   C3   118.01  3.000
 4D9  HN5   N5   C9   126.08  3.000
 4D9  HN5   N5   C6   126.30  3.000
 4D9  C9    N5   C6   107.60  3.000
 4D9  C7    C6   N5   104.49  3.000
 4D9  C7    C6   C1   122.65  3.000
 4D9  N5    C6   C1   132.86  3.000
 4D9  N8    C7   C6   109.94  3.000
 4D9  N8    C7   C4   130.29  3.000
 4D9  C6    C7   C4   119.77  3.000
 4D9  C9    N8   C7   105.39  3.000
 4D9  C10   C9   N8   125.14  3.000
 4D9  C10   C9   N5   122.19  3.000
 4D9  N8    C9   N5   112.57  3.000
 4D9  H10A  C10  H10  107.49  3.000
 4D9  H10A  C10  C11  108.47  3.000
 4D9  H10   C10  C11  110.31  3.000
 4D9  H10A  C10  C9   110.94  3.000
 4D9  H10   C10  C9   107.94  3.000
 4D9  C11   C10  C9   111.62  3.000
 4D9  H11   C11  N13  107.50  3.000
 4D9  H11   C11  C12  107.46  3.000
 4D9  N13   C11  C12  113.66  3.000
 4D9  H11   C11  C10  108.45  3.000
 4D9  C12   C11  C10  110.57  3.000
 4D9  N13   C11  C10  109.02  3.000
 4D9  O15   C12  O14  128.01  3.000
 4D9  O15   C12  C11  114.41  3.000
 4D9  O14   C12  C11  117.57  3.000
 4D9  HN13  N13  C16  118.80  3.000
 4D9  HN13  N13  C11  116.89  3.000
 4D9  C16   N13  C11  122.56  3.000
 4D9  O18   C16  C17  120.12  3.000
 4D9  O18   C16  N13  124.02  3.000
 4D9  C17   C16  N13  115.83  3.000
 4D9  S20   C17  C19  112.62  3.000
 4D9  S20   C17  C16  122.68  3.000
 4D9  C19   C17  C16  124.68  3.000
 4D9  H19   C19  C22  123.92  3.000
 4D9  H19   C19  C17  123.14  3.000
 4D9  C22   C19  C17  112.93  3.000
 4D9  C21   S20  C17   91.19  3.000
 4D9  C26   C21  C22  121.79  3.000
 4D9  C22   C21  S20  111.38  3.000
 4D9  C26   C21  S20  126.83  3.000
 4D9  C23   C22  C21  119.03  3.000
 4D9  C23   C22  C19  129.10  3.000
 4D9  C21   C22  C19  111.87  3.000
 4D9  H23   C23  C24  120.68  3.000
 4D9  H23   C23  C22  120.00  3.000
 4D9  C24   C23  C22  119.32  3.000
 4D9  H24   C24  C25  119.40  3.000
 4D9  H24   C24  C23  119.80  3.000
 4D9  C25   C24  C23  120.80  3.000
 4D9  H25   C25  C26  119.40  3.000
 4D9  H25   C25  C24  119.55  3.000
 4D9  C26   C25  C24  121.05  3.000
 4D9  H26   C26  C25  120.91  3.000
 4D9  H26   C26  C21  121.09  3.000
 4D9  C25   C26  C21  118.00  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
 4D9  CONST_01  C9   N5   C6   C1   180.00   0.0  0
 4D9  CONST_02  C4   C7   C6   C1     0.00   0.0  0
 4D9  CONST_03  N8   C7   C6   C1   180.00   0.0  0
 4D9  CONST_04  C4   C3   C2   C1     0.00   0.0  0
 4D9  CONST_05  N5   C6   C1   C2   180.00   0.0  0
 4D9  CONST_06  C7   C6   C1   C2     0.00   0.0  0
 4D9  CONST_07  C7   C4   C3   C2     0.00   0.0  0
 4D9  CONST_08  C6   C1   C2   C3     0.00   0.0  0
 4D9  CONST_09  C6   C7   C4   C3     0.00   0.0  0
 4D9  CONST_10  N8   C7   C4   C3   180.00   0.0  0
 4D9  CONST_11  N5   C6   C7   C4   180.00   0.0  0
 4D9  CONST_12  C9   N8   C7   C4   180.00   0.0  0
 4D9  CONST_13  C7   N8   C9   N5     0.00   0.0  0
 4D9  CONST_14  N8   C7   C6   N5     0.00   0.0  0
 4D9  CONST_15  N8   C9   N5   C6     0.00   0.0  0
 4D9  CONST_16  C9   N8   C7   C6     0.00   0.0  0
 4D9  CONST_17  C9   N5   C6   C7     0.00   0.0  0
 4D9  CONST_18  C21  C22  C19  C17    0.00   0.0  0
 4D9  CONST_19  C23  C22  C19  C17  180.00   0.0  0
 4D9  CONST_20  C26  C21  S20  C17  180.00   0.0  0
 4D9  CONST_21  C22  C21  S20  C17    0.00   0.0  0
 4D9  CONST_22  C21  S20  C17  C19    0.00   0.0  0
 4D9  CONST_23  S20  C21  C22  C19    0.00   0.0  0
 4D9  CONST_24  C26  C21  C22  C19  180.00   0.0  0
 4D9  CONST_25  C24  C23  C22  C19  180.00   0.0  0
 4D9  CONST_26  C22  C19  C17  S20    0.00   0.0  0
 4D9  CONST_27  C25  C26  C21  S20  180.00   0.0  0
 4D9  CONST_28  C23  C22  C21  S20  180.00   0.0  0
 4D9  CONST_29  C24  C25  C26  C21    0.00   0.0  0
 4D9  CONST_30  C24  C23  C22  C21    0.00   0.0  0
 4D9  CONST_31  C25  C26  C21  C22    0.00   0.0  0
 4D9  CONST_32  C25  C24  C23  C22    0.00   0.0  0
 4D9  CONST_33  C26  C21  C22  C23    0.00   0.0  0
 4D9  CONST_34  C26  C25  C24  C23    0.00   0.0  0
 4D9  CONST_35  C10  C9   N5   C6   180.00   0.0  0
 4D9  CONST_36  C10  C9   N8   C7   180.00   0.0  0
 4D9  CONST_37  C22  C19  C17  C16  180.00   0.0  0
 4D9  CONST_38  C21  S20  C17  C16  180.00   0.0  0
 4D9  CONST_39  HN5  N5   C6   C1     0.00   0.0  0
 4D9  CONST_40  H3   C3   C2   C1   180.00   0.0  0
 4D9  CONST_41  H4   C4   C3   C2   180.00   0.0  0
 4D9  CONST_42  H1   C1   C2   C3   180.00   0.0  0
 4D9  CONST_43  H2   C2   C3   C4   180.00   0.0  0
 4D9  CONST_44  H23  C23  C22  C19    0.00   0.0  0
 4D9  CONST_45  H19  C19  C17  S20  180.00   0.0  0
 4D9  CONST_46  H26  C26  C21  S20    0.00   0.0  0
 4D9  CONST_47  H25  C25  C26  C21  180.00   0.0  0
 4D9  CONST_48  H24  C24  C23  C22  180.00   0.0  0
 4D9  CONST_49  C17  C16  N13  C11  180.00   0.0  0
 4D9  CONST_51  O18  C16  N13  C11    0.00   0.0  0
 4D9  Var_01    C11  C10  C9   N5    70.88  30.0  3
 4D9  Var_02    C19  C17  C16  N13  160.52  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
 4D9  chir_01  C11  C10  N13  C12  negativ

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
 4D9  plan-1  C1    0.020
 4D9  plan-1  C2    0.020
 4D9  plan-1  C3    0.020
 4D9  plan-1  C4    0.020
 4D9  plan-1  N5    0.020
 4D9  plan-1  C6    0.020
 4D9  plan-1  C7    0.020
 4D9  plan-1  N8    0.020
 4D9  plan-1  C9    0.020
 4D9  plan-1  C10   0.020
 4D9  plan-1  H1    0.020
 4D9  plan-1  H2    0.020
 4D9  plan-1  H3    0.020
 4D9  plan-1  H4    0.020
 4D9  plan-1  HN5   0.020
 4D9  plan-2  C16   0.020
 4D9  plan-2  C17   0.020
 4D9  plan-2  C19   0.020
 4D9  plan-2  S20   0.020
 4D9  plan-2  C21   0.020
 4D9  plan-2  C22   0.020
 4D9  plan-2  C23   0.020
 4D9  plan-2  C24   0.020
 4D9  plan-2  C25   0.020
 4D9  plan-2  C26   0.020
 4D9  plan-2  H19   0.020
 4D9  plan-2  H23   0.020
 4D9  plan-2  H24   0.020
 4D9  plan-2  H25   0.020
 4D9  plan-2  H26   0.020
 4D9  plan-3  C11   0.020
 4D9  plan-3  N13   0.020
 4D9  plan-3  C16   0.020
 4D9  plan-3  C17   0.020
 4D9  plan-3  O18   0.020
 4D9  plan-3  HN13  0.020
 4D9  plan-4  C11   0.020
 4D9  plan-4  C12   0.020
 4D9  plan-4  O14   0.020
 4D9  plan-4  O15   0.020

