# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Apr  3 17:54:59 2020
#   Inital geometry file: a 123 line input string
#   Ligand name: 3-(1H-benzimidazol-2-yl)-N-[(1-methyl-3-phenyl-1H-pyrazol-5-yl)carbonyl]-D-alanine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cn1nc(cc1C(=O)N[C@H](Cc2[nH]c3ccccc3n2)C(O)=O)c4ccccc4
#
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
 4DH  4DH  3-(1H-benzimidazol-2-yl)-N-[(1-methyl-3-phenyl-1H-pyrazol-5-yl)carbonyl]-D-alanine  ligand  47  29  .  2021-08-04  2021-08-04  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_4DH
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
 4DH  C1    C  CR16   0  -0.280   2.0709   4.2717   0.5641
 4DH  C2    C  CR16   0  -0.271   1.1380   4.2158  -0.4820
 4DH  C3    C  CR16   0  -0.339   1.0248   3.0954  -1.2872
 4DH  C4    C  CR16   0  -0.310   2.9159   3.2089   0.8388
 4DH  N5    N  NR15   0  -0.693   3.4306   0.8759   0.0077
 4DH  C6    C  CR56   0   0.336   2.7915   2.0872   0.0286
 4DH  C7    C  CR56   0   0.145   1.8668   2.0152  -1.0271
 4DH  N8    N  N      0  -0.481   1.9610   0.7927  -1.6501
 4DH  C9    C  CR5    0   0.448   2.8960   0.1452  -1.0055
 4DH  C10   C  CH2    0  -0.575   3.2804  -1.2700  -1.2530
 4DH  C11   C  CH1    0  -0.202   2.6251  -2.2097  -0.2258
 4DH  C12   C  C      0   0.420   2.9241  -3.6962  -0.5563
 4DH  O13   O  O      0  -0.580   1.9611  -4.4740  -0.6159
 4DH  O14   O  OC    -1  -0.609   4.1322  -3.9562  -0.7159
 4DH  N15   N  NH1    0  -0.622   1.2208  -1.8987  -0.1482
 4DH  C16   C  C      0   0.500   0.4986  -1.9766   0.9718
 4DH  C17   C  CR5    0   0.321  -0.8496  -1.3729   0.8500
 4DH  O18   O  O      0  -0.488   0.9082  -2.4263   2.0342
 4DH  N19   N  NR5    0  -0.317  -1.9207  -1.7496   1.5806
 4DH  N20   N  N      0  -0.293  -2.9705  -0.9807   1.3489
 4DH  C21   C  CR5    0   0.278  -2.5865  -0.0760   0.4568
 4DH  C22   C  CR15   0  -0.555  -1.2450  -0.2860   0.1006
 4DH  C23   C  CH3    0  -0.515  -2.0247  -2.8259   2.5433
 4DH  C24   C  C      0   0.063  -3.5024   0.9620  -0.0222
 4DH  C25   C  C1     0  -0.295  -4.8702   0.8953   0.2493
 4DH  C26   C  C1     0  -0.238  -5.7282   1.8855  -0.2034
 4DH  C27   C  C1     0  -0.267  -5.2374   2.9595  -0.9359
 4DH  C28   C  C1     0  -0.237  -3.8783   3.0351  -1.2097
 4DH  C29   C  C1     0  -0.324  -3.0187   2.0459  -0.7557
 4DH  H1    H  HCR6   0   0.254   2.1311   5.1654   1.1713
 4DH  H2    H  HCR6   0   0.251   0.4956   5.0683  -0.6609
 4DH  H3    H  HCR6   0   0.253   0.3068   3.0546  -2.0967
 4DH  H4    H  HCR6   0   0.265   3.6321   3.2524   1.6488
 4DH  H10   H  HCH2   0   0.270   2.9622  -1.5349  -2.2631
 4DH  H10A  H  HCH2   0   0.280   4.3614  -1.3965  -1.2062
 4DH  H11   H  HCH1   0   0.260   3.0612  -2.0018   0.7557
 4DH  HN15  H  HNH1   0   0.403   0.7520  -1.6340  -1.0007
 4DH  H22   H  HCR5   0   0.279  -0.6348   0.2761  -0.5880
 4DH  H23   H  HCH3   0   0.260  -1.5962  -2.5356   3.5001
 4DH  H23A  H  HCH3   0   0.266  -3.0780  -3.0526   2.6737
 4DH  H23B  H  HCH3   0   0.260  -1.5145  -3.7125   2.1791
 4DH  H25   H  H      0   0.251  -5.2654   0.0603   0.8130
 4DH  H26   H  H      0   0.258  -6.7861   1.8168   0.0152
 4DH  H27   H  H      0   0.257  -5.9086   3.7313  -1.2893
 4DH  H28   H  H      0   0.257  -3.4834   3.8698  -1.7741
 4DH  H29   H  H      0   0.240  -1.9600   2.1283  -0.9691
 4DH  HN5   H  HNR5   0   0.418   4.1662   0.5749   0.6274

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
 4DH  C4   C1    aromatic  1.385  0.020  1.385
 4DH  C1   C2    aromatic  1.403  0.020  1.403
 4DH  C1   H1    single    0.930  0.020  1.080
 4DH  C2   C3    aromatic  1.384  0.020  1.384
 4DH  C2   H2    single    0.930  0.020  1.080
 4DH  C7   C3    aromatic  1.394  0.020  1.394
 4DH  C3   H3    single    0.930  0.020  1.080
 4DH  C4   C6    aromatic  1.389  0.020  1.389
 4DH  C4   H4    single    0.930  0.020  1.080
 4DH  N5   C9    aromatic  1.359  0.020  1.359
 4DH  N5   C6    aromatic  1.370  0.020  1.370
 4DH  C6   C7    aromatic  1.405  0.020  1.405
 4DH  N8   C7    aromatic  1.375  0.020  1.375
 4DH  C9   N8    aromatic  1.307  0.020  1.307
 4DH  C10  C9    single    1.487  0.020  1.487
 4DH  C11  C10   single    1.539  0.020  1.539
 4DH  C10  H10   single    0.970  0.020  1.090
 4DH  C10  H10A  single    0.970  0.020  1.090
 4DH  N15  C11   single    1.440  0.020  1.440
 4DH  C12  C11   single    1.552  0.020  1.552
 4DH  C11  H11   single    0.970  0.020  1.090
 4DH  O13  C12   deloc     1.239  0.020  1.239
 4DH  C12  O14   deloc     1.246  0.020  1.246
 4DH  C16  N15   single    1.335  0.020  1.335
 4DH  N15  HN15  single    0.860  0.020  1.020
 4DH  C17  C16   single    1.482  0.020  1.482
 4DH  C16  O18   double    1.224  0.020  1.224
 4DH  C22  C17   aromatic  1.378  0.020  1.378
 4DH  N19  C17   aromatic  1.350  0.020  1.350
 4DH  N20  N19   aromatic  1.322  0.020  1.322
 4DH  N19  C23   single    1.448  0.020  1.448
 4DH  C21  N20   aromatic  1.327  0.020  1.327
 4DH  C24  C21   single    1.465  0.020  1.465
 4DH  C21  C22   aromatic  1.404  0.020  1.404
 4DH  C22  H22   single    0.930  0.020  1.080
 4DH  C23  H23   single    0.970  0.020  1.090
 4DH  C23  H23A  single    0.970  0.020  1.090
 4DH  C23  H23B  single    0.970  0.020  1.090
 4DH  C25  C24   aromatic  1.396  0.020  1.396
 4DH  C29  C24   aromatic  1.395  0.020  1.395
 4DH  C26  C25   aromatic  1.386  0.020  1.386
 4DH  C25  H25   single    0.930  0.020  1.080
 4DH  C27  C26   aromatic  1.390  0.020  1.390
 4DH  C26  H26   single    0.930  0.020  1.080
 4DH  C27  C28   aromatic  1.389  0.020  1.389
 4DH  C27  H27   single    0.930  0.020  1.080
 4DH  C28  C29   aromatic  1.387  0.020  1.387
 4DH  C28  H28   single    0.930  0.020  1.080
 4DH  C29  H29   single    0.930  0.020  1.080
 4DH  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
 4DH  H1    C1   C4    119.24  3.000
 4DH  H1    C1   C2    119.23  3.000
 4DH  C4    C1   C2    121.53  3.000
 4DH  H2    C2   C3    119.53  3.000
 4DH  H2    C2   C1    119.12  3.000
 4DH  C3    C2   C1    121.36  3.000
 4DH  H3    C3   C7    120.71  3.000
 4DH  H3    C3   C2    121.30  3.000
 4DH  C7    C3   C2    117.98  3.000
 4DH  H4    C4   C6    121.88  3.000
 4DH  H4    C4   C1    121.42  3.000
 4DH  C6    C4   C1    116.69  3.000
 4DH  HN5   N5   C9    125.81  3.000
 4DH  HN5   N5   C6    126.53  3.000
 4DH  C9    N5   C6    107.66  3.000
 4DH  C7    C6   N5    104.49  3.000
 4DH  C7    C6   C4    122.57  3.000
 4DH  N5    C6   C4    132.94  3.000
 4DH  N8    C7   C6    109.93  3.000
 4DH  N8    C7   C3    130.21  3.000
 4DH  C6    C7   C3    119.86  3.000
 4DH  C9    N8   C7    105.42  3.000
 4DH  C10   C9   N8    125.04  3.000
 4DH  C10   C9   N5    122.28  3.000
 4DH  N8    C9   N5    112.50  3.000
 4DH  H10A  C10  H10   107.51  3.000
 4DH  H10A  C10  C11   108.84  3.000
 4DH  H10   C10  C11   110.21  3.000
 4DH  H10A  C10  C9    111.09  3.000
 4DH  H10   C10  C9    108.03  3.000
 4DH  C11   C10  C9    111.09  3.000
 4DH  H11   C11  N15   107.41  3.000
 4DH  H11   C11  C12   107.24  3.000
 4DH  N15   C11  C12   113.96  3.000
 4DH  H11   C11  C10   108.25  3.000
 4DH  C12   C11  C10   111.14  3.000
 4DH  N15   C11  C10   108.62  3.000
 4DH  O14   C12  O13   128.04  3.000
 4DH  O14   C12  C11   114.45  3.000
 4DH  O13   C12  C11   117.50  3.000
 4DH  HN15  N15  C16   118.24  3.000
 4DH  HN15  N15  C11   117.68  3.000
 4DH  C16   N15  C11   124.05  3.000
 4DH  O18   C16  C17   121.69  3.000
 4DH  O18   C16  N15   124.65  3.000
 4DH  C17   C16  N15   113.54  3.000
 4DH  C22   C17  N19   106.66  3.000
 4DH  N19   C17  C16   124.30  3.000
 4DH  C22   C17  C16   128.82  3.000
 4DH  C23   N19  N20   119.47  3.000
 4DH  C23   N19  C17   128.62  3.000
 4DH  N20   N19  C17   111.90  3.000
 4DH  C21   N20  N19   106.53  3.000
 4DH  C24   C21  C22   128.36  3.000
 4DH  C22   C21  N20   110.18  3.000
 4DH  C24   C21  N20   121.46  3.000
 4DH  H22   C22  C21   128.67  3.000
 4DH  H22   C22  C17   126.59  3.000
 4DH  C21   C22  C17   104.73  3.000
 4DH  H23B  C23  H23A  109.01  3.000
 4DH  H23B  C23  H23   109.13  3.000
 4DH  H23A  C23  H23   109.41  3.000
 4DH  H23B  C23  N19   110.50  3.000
 4DH  H23A  C23  N19   107.76  3.000
 4DH  H23   C23  N19   110.99  3.000
 4DH  C29   C24  C25   118.61  3.000
 4DH  C29   C24  C21   120.38  3.000
 4DH  C25   C24  C21   121.01  3.000
 4DH  H25   C25  C26   119.69  3.000
 4DH  H25   C25  C24   119.73  3.000
 4DH  C26   C25  C24   120.58  3.000
 4DH  H26   C26  C27   120.05  3.000
 4DH  H26   C26  C25   119.58  3.000
 4DH  C27   C26  C25   120.38  3.000
 4DH  H27   C27  C28   120.26  3.000
 4DH  H27   C27  C26   120.29  3.000
 4DH  C28   C27  C26   119.45  3.000
 4DH  H28   C28  C29   119.65  3.000
 4DH  H28   C28  C27   120.13  3.000
 4DH  C29   C28  C27   120.22  3.000
 4DH  H29   C29  C28   119.15  3.000
 4DH  H29   C29  C24   120.10  3.000
 4DH  C28   C29  C24   120.76  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
 4DH  CONST_01  N5    C6   C4   C1   180.00   0.0  0
 4DH  CONST_02  C7    C6   C4   C1     0.00   0.0  0
 4DH  CONST_03  C7    C3   C2   C1     0.00   0.0  0
 4DH  CONST_04  C6    C4   C1   C2     0.00   0.0  0
 4DH  CONST_05  C6    C7   C3   C2     0.00   0.0  0
 4DH  CONST_06  N8    C7   C3   C2   180.00   0.0  0
 4DH  CONST_07  C4    C1   C2   C3     0.00   0.0  0
 4DH  CONST_08  C4    C6   C7   C3     0.00   0.0  0
 4DH  CONST_09  N5    C6   C7   C3   180.00   0.0  0
 4DH  CONST_10  C9    N8   C7   C3   180.00   0.0  0
 4DH  CONST_11  C9    N5   C6   C4   180.00   0.0  0
 4DH  CONST_12  N8    C7   C6   C4   180.00   0.0  0
 4DH  CONST_13  C7    N8   C9   N5     0.00   0.0  0
 4DH  CONST_14  N8    C7   C6   N5     0.00   0.0  0
 4DH  CONST_15  N8    C9   N5   C6     0.00   0.0  0
 4DH  CONST_16  C9    N8   C7   C6     0.00   0.0  0
 4DH  CONST_17  C9    N5   C6   C7     0.00   0.0  0
 4DH  CONST_18  N20   C21  C22  C17    0.00   0.0  0
 4DH  CONST_19  C24   C21  C22  C17  180.00   0.0  0
 4DH  CONST_20  C21   N20  N19  C17    0.00   0.0  0
 4DH  CONST_21  C21   C22  C17  N19    0.00   0.0  0
 4DH  CONST_22  C24   C21  N20  N19  180.00   0.0  0
 4DH  CONST_23  C22   C21  N20  N19    0.00   0.0  0
 4DH  CONST_24  C22   C17  N19  N20    0.00   0.0  0
 4DH  CONST_25  C25   C24  C21  N20    0.00   0.0  0
 4DH  CONST_26  C29   C24  C21  N20  180.00   0.0  0
 4DH  CONST_27  C26   C25  C24  C21  180.00   0.0  0
 4DH  CONST_28  C28   C29  C24  C21  180.00   0.0  0
 4DH  CONST_29  C25   C24  C21  C22  180.00   0.0  0
 4DH  CONST_30  C29   C24  C21  C22    0.00   0.0  0
 4DH  CONST_31  C27   C26  C25  C24    0.00   0.0  0
 4DH  CONST_32  C27   C28  C29  C24    0.00   0.0  0
 4DH  CONST_33  C28   C29  C24  C25    0.00   0.0  0
 4DH  CONST_34  C28   C27  C26  C25    0.00   0.0  0
 4DH  CONST_35  C29   C24  C25  C26    0.00   0.0  0
 4DH  CONST_36  C29   C28  C27  C26    0.00   0.0  0
 4DH  CONST_37  C10   C9   N5   C6   180.00   0.0  0
 4DH  CONST_38  C10   C9   N8   C7   180.00   0.0  0
 4DH  CONST_39  C21   C22  C17  C16  180.00   0.0  0
 4DH  CONST_40  N20   N19  C17  C16  180.00   0.0  0
 4DH  CONST_41  C23   N19  N20  C21  180.00   0.0  0
 4DH  CONST_42  C23   N19  C17  C22  180.00   0.0  0
 4DH  CONST_43  H3    C3   C2   C1   180.00   0.0  0
 4DH  CONST_44  H4    C4   C1   C2   180.00   0.0  0
 4DH  CONST_45  H1    C1   C2   C3   180.00   0.0  0
 4DH  CONST_46  H2    C2   C1   C4   180.00   0.0  0
 4DH  CONST_47  HN5   N5   C6   C4     0.00   0.0  0
 4DH  CONST_48  H22   C22  C17  N19  180.00   0.0  0
 4DH  CONST_49  H25   C25  C24  C21    0.00   0.0  0
 4DH  CONST_50  H29   C29  C24  C21    0.00   0.0  0
 4DH  CONST_51  H26   C26  C25  C24  180.00   0.0  0
 4DH  CONST_52  H28   C28  C29  C24  180.00   0.0  0
 4DH  CONST_53  H27   C27  C26  C25  180.00   0.0  0
 4DH  CONST_54  C17   C16  N15  C11  180.00   0.0  0
 4DH  CONST_55  HN15  N15  C16  C17    0.00   0.0  0
 4DH  CONST_56  O18   C16  N15  C11    0.00   0.0  0
 4DH  Var_01    C11   C10  C9   N5    75.75  30.0  2
 4DH  Var_02    C22   C17  C16  N15  -33.25  30.0  2
 4DH  Var_03    H23   C23  N19  C17   79.37  30.0  2

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
 4DH  chir_01  C11  C10  N15  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
 4DH  plan-1  C16   0.020
 4DH  plan-1  C17   0.020
 4DH  plan-1  N19   0.020
 4DH  plan-1  N20   0.020
 4DH  plan-1  C21   0.020
 4DH  plan-1  C22   0.020
 4DH  plan-1  C23   0.020
 4DH  plan-1  C24   0.020
 4DH  plan-1  H22   0.020
 4DH  plan-2  C21   0.020
 4DH  plan-2  C24   0.020
 4DH  plan-2  C25   0.020
 4DH  plan-2  C26   0.020
 4DH  plan-2  C27   0.020
 4DH  plan-2  C28   0.020
 4DH  plan-2  C29   0.020
 4DH  plan-2  H25   0.020
 4DH  plan-2  H26   0.020
 4DH  plan-2  H27   0.020
 4DH  plan-2  H28   0.020
 4DH  plan-2  H29   0.020
 4DH  plan-3  C1    0.020
 4DH  plan-3  C2    0.020
 4DH  plan-3  C3    0.020
 4DH  plan-3  C4    0.020
 4DH  plan-3  N5    0.020
 4DH  plan-3  C6    0.020
 4DH  plan-3  C7    0.020
 4DH  plan-3  N8    0.020
 4DH  plan-3  C9    0.020
 4DH  plan-3  C10   0.020
 4DH  plan-3  H1    0.020
 4DH  plan-3  H2    0.020
 4DH  plan-3  H3    0.020
 4DH  plan-3  H4    0.020
 4DH  plan-3  HN5   0.020
 4DH  plan-4  C11   0.020
 4DH  plan-4  N15   0.020
 4DH  plan-4  C16   0.020
 4DH  plan-4  C17   0.020
 4DH  plan-4  O18   0.020
 4DH  plan-4  HN15  0.020
 4DH  plan-5  C11   0.020
 4DH  plan-5  C12   0.020
 4DH  plan-5  O13   0.020
 4DH  plan-5  O14   0.020

