# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Apr  2 08:59:04 2020
#   Inital geometry file: a 115 line input string
#   Ligand name: 3-(6-fluoro-1H-benzimidazol-2-yl)-N-(naphthalen-2-ylcarbonyl)-D-alanine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC(=O)[C@@H](Cc1[nH]c2cc(F)ccc2n1)NC(=O)c3ccc4ccccc4c3
#
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
 39X  39X  3-(6-fluoro-1H-benzimidazol-2-yl)-N-(naphthalen-2-ylcarbonyl)-D-alanine  ligand  43  28  .  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_39X
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
 39X  O3   O  OC    -1  -0.607  -1.3331  -5.1958   0.0893
 39X  C21  C  C      0   0.423  -0.4264  -4.3420   0.1100
 39X  O2   O  O      0  -0.585   0.7949  -4.5311   0.2128
 39X  C20  C  CH1    0  -0.210  -0.9092  -2.8732  -0.0383
 39X  C12  C  CH2    0  -0.571  -2.0917  -2.5726   0.8966
 39X  C13  C  CR5    0   0.457  -2.5097  -1.1502   0.7955
 39X  N3   N  N      0  -0.476  -2.2178  -0.2107   1.6529
 39X  C15  C  CR56   0   0.140  -2.7297   0.9478   1.1152
 39X  C19  C  CR16   0  -0.320  -2.7063   2.2544   1.5961
 39X  C18  C  CR16   0  -0.427  -3.3049   3.2464   0.8388
 39X  C17  C  CR6    0   0.506  -3.9136   2.9230  -0.3739
 39X  F1   F  F      0  -0.324  -4.4843   3.9198  -1.0767
 39X  C16  C  CR16   0  -0.466  -3.9632   1.6469  -0.8912
 39X  C14  C  CR56   0   0.352  -3.3515   0.6703  -0.1142
 39X  N2   N  NR15   0  -0.694  -3.1914  -0.6751  -0.2844
 39X  N1   N  NH1    0  -0.624   0.1270  -1.9007   0.1926
 39X  C1   C  C      0   0.526   0.8850  -1.3646  -0.7710
 39X  O1   O  O      0  -0.497   0.8049  -1.6782  -1.9529
 39X  C2   C  CR6    0  -0.049   1.8458  -0.3126  -0.3138
 39X  C7   C  CR16   0  -0.294   1.5598   0.5287   0.7894
 39X  C6   C  CR16   0  -0.300   2.4433   1.4996   1.1687
 39X  C5   C  CR66   0   0.111   3.6642   1.6801   0.4780
 39X  C11  C  CR16   0  -0.308   4.6034   2.6682   0.8544
 39X  C10  C  CR16   0  -0.254   5.7738   2.8149   0.1608
 39X  C9   C  CR16   0  -0.257   6.0602   1.9830  -0.9431
 39X  C8   C  CR16   0  -0.308   5.1692   1.0208  -1.3313
 39X  C4   C  CR66   0   0.136   3.9511   0.8445  -0.6323
 39X  C3   C  CR16   0  -0.345   3.0121  -0.1379  -1.0136
 39X  H15  H  HCH1   0   0.260  -1.2432  -2.7498  -1.0723
 39X  H9   H  HCH2   0   0.277  -2.9181  -3.2376   0.6475
 39X  H10  H  HCH2   0   0.268  -1.8132  -2.7716   1.9333
 39X  H14  H  HCR6   0   0.265  -2.2322   2.4941   2.5387
 39X  H13  H  HCR6   0   0.274  -3.3063   4.2741   1.1770
 39X  H12  H  HCR6   0   0.286  -4.4440   1.4312  -1.8361
 39X  H11  H  HNR5   0   0.420  -3.5325  -1.2232  -1.0585
 39X  H1   H  HNH1   0   0.397   0.3643  -1.7061   1.1524
 39X  H4   H  HCR6   0   0.261   0.6199   0.4327   1.3204
 39X  H3   H  HCR6   0   0.260   2.2104   2.1489   2.0038
 39X  H8   H  HCR6   0   0.258   4.3859   3.3072   1.7015
 39X  H7   H  HCR6   0   0.262   6.4889   3.5706   0.4583
 39X  H6   H  HCR6   0   0.261   6.9906   2.1102  -1.4808
 39X  H5   H  HCR6   0   0.258   5.3852   0.3814  -2.1788
 39X  H2   H  HCR6   0   0.257   3.2307  -0.7656  -1.8692

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
 39X  C9   C8   aromatic  1.368  0.020  1.368
 39X  C9   C10  aromatic  1.412  0.020  1.412
 39X  C8   C4   aromatic  1.415  0.020  1.415
 39X  C10  C11  aromatic  1.368  0.020  1.368
 39X  O2   C21  deloc     1.240  0.020  1.240
 39X  C4   C3   aromatic  1.411  0.020  1.411
 39X  C4   C5   aromatic  1.419  0.020  1.419
 39X  C11  C5   aromatic  1.414  0.020  1.414
 39X  C3   C2   aromatic  1.371  0.020  1.371
 39X  C21  O3   deloc     1.246  0.020  1.246
 39X  C21  C20  single    1.553  0.020  1.553
 39X  C5   C6   aromatic  1.414  0.020  1.414
 39X  N3   C13  aromatic  1.305  0.020  1.305
 39X  N3   C15  aromatic  1.376  0.020  1.376
 39X  C12  C20  single    1.537  0.020  1.537
 39X  C12  C13  single    1.486  0.020  1.486
 39X  N1   C20  single    1.440  0.020  1.440
 39X  N1   C1   single    1.338  0.020  1.338
 39X  C2   C1   single    1.496  0.020  1.496
 39X  C2   C7   aromatic  1.417  0.020  1.417
 39X  C13  N2   aromatic  1.363  0.020  1.363
 39X  C19  C15  aromatic  1.393  0.020  1.393
 39X  C19  C18  aromatic  1.384  0.020  1.384
 39X  C15  C14  aromatic  1.405  0.020  1.405
 39X  C6   C7   aromatic  1.366  0.020  1.366
 39X  C1   O1   double    1.225  0.020  1.225
 39X  N2   C14  aromatic  1.366  0.020  1.366
 39X  C18  C17  aromatic  1.395  0.020  1.395
 39X  C14  C16  aromatic  1.390  0.020  1.390
 39X  C17  C16  aromatic  1.378  0.020  1.378
 39X  C17  F1   single    1.347  0.020  1.347
 39X  C20  H15  single    0.970  0.020  1.090
 39X  C12  H9   single    0.970  0.020  1.090
 39X  C12  H10  single    0.970  0.020  1.090
 39X  C19  H14  single    0.930  0.020  1.080
 39X  C18  H13  single    0.930  0.020  1.080
 39X  C16  H12  single    0.930  0.020  1.080
 39X  N2   H11  single    0.860  0.020  1.020
 39X  N1   H1   single    0.860  0.020  1.020
 39X  C7   H4   single    0.930  0.020  1.080
 39X  C6   H3   single    0.930  0.020  1.080
 39X  C11  H8   single    0.930  0.020  1.080
 39X  C10  H7   single    0.930  0.020  1.080
 39X  C9   H6   single    0.930  0.020  1.080
 39X  C8   H5   single    0.930  0.020  1.080
 39X  C3   H2   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
 39X  C20  C21  O2   117.27  3.000
 39X  C20  C21  O3   114.86  3.000
 39X  O2   C21  O3   127.87  3.000
 39X  H15  C20  N1   107.18  3.000
 39X  H15  C20  C12  108.54  3.000
 39X  N1   C20  C12  108.91  3.000
 39X  H15  C20  C21  106.97  3.000
 39X  N1   C20  C21  113.56  3.000
 39X  C12  C20  C21  111.47  3.000
 39X  H10  C12  H9   107.42  3.000
 39X  H10  C12  C13  108.11  3.000
 39X  H9   C12  C13  110.81  3.000
 39X  H10  C12  C20  110.22  3.000
 39X  H9   C12  C20  108.97  3.000
 39X  C13  C12  C20  111.24  3.000
 39X  N2   C13  N3   112.44  3.000
 39X  N2   C13  C12  121.90  3.000
 39X  N3   C13  C12  125.55  3.000
 39X  C15  N3   C13  105.44  3.000
 39X  C14  C15  C19  119.66  3.000
 39X  C14  C15  N3   109.89  3.000
 39X  C19  C15  N3   130.45  3.000
 39X  H14  C19  C18  120.49  3.000
 39X  H14  C19  C15  121.07  3.000
 39X  C18  C19  C15  118.44  3.000
 39X  H13  C18  C17  119.44  3.000
 39X  H13  C18  C19  120.68  3.000
 39X  C17  C18  C19  119.89  3.000
 39X  C16  C17  F1   118.32  3.000
 39X  F1   C17  C18  117.84  3.000
 39X  C16  C17  C18  123.84  3.000
 39X  H12  C16  C14  122.94  3.000
 39X  H12  C16  C17  121.91  3.000
 39X  C14  C16  C17  115.15  3.000
 39X  N2   C14  C16  132.40  3.000
 39X  C16  C14  C15  123.03  3.000
 39X  N2   C14  C15  104.58  3.000
 39X  H11  N2   C14  126.29  3.000
 39X  H11  N2   C13  126.04  3.000
 39X  C14  N2   C13  107.66  3.000
 39X  H1   N1   C1   118.37  3.000
 39X  H1   N1   C20  116.92  3.000
 39X  C1   N1   C20  124.25  3.000
 39X  C2   C1   O1   121.10  3.000
 39X  O1   C1   N1   123.71  3.000
 39X  C2   C1   N1   115.18  3.000
 39X  C3   C2   C7   119.57  3.000
 39X  C7   C2   C1   121.72  3.000
 39X  C3   C2   C1   118.67  3.000
 39X  H4   C7   C6   119.19  3.000
 39X  H4   C7   C2   120.27  3.000
 39X  C6   C7   C2   120.50  3.000
 39X  H3   C6   C5   119.06  3.000
 39X  H3   C6   C7   120.06  3.000
 39X  C5   C6   C7   120.89  3.000
 39X  C4   C5   C11  119.04  3.000
 39X  C11  C5   C6   122.17  3.000
 39X  C4   C5   C6   118.78  3.000
 39X  H8   C11  C10  120.32  3.000
 39X  H8   C11  C5   119.15  3.000
 39X  C10  C11  C5   120.53  3.000
 39X  H7   C10  C9   119.50  3.000
 39X  H7   C10  C11  120.05  3.000
 39X  C9   C10  C11  120.45  3.000
 39X  H6   C9   C8   120.12  3.000
 39X  H6   C9   C10  119.59  3.000
 39X  C8   C9   C10  120.29  3.000
 39X  H5   C8   C4   118.97  3.000
 39X  H5   C8   C9   120.48  3.000
 39X  C4   C8   C9   120.54  3.000
 39X  C3   C4   C8   121.72  3.000
 39X  C3   C4   C5   119.13  3.000
 39X  C8   C4   C5   119.15  3.000
 39X  H2   C3   C4   118.84  3.000
 39X  H2   C3   C2   120.05  3.000
 39X  C4   C3   C2   121.10  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
 39X  CONST_01  C19  C15  N3   C13   180.00   0.0  0
 39X  CONST_02  C14  C15  N3   C13     0.00   0.0  0
 39X  CONST_03  C15  C14  N2   C13     0.00   0.0  0
 39X  CONST_04  C16  C14  N2   C13   180.00   0.0  0
 39X  CONST_05  C14  N2   C13  N3      0.00   0.0  0
 39X  CONST_06  C18  C19  C15  N3    180.00   0.0  0
 39X  CONST_07  N2   C14  C15  N3      0.00   0.0  0
 39X  CONST_08  C16  C14  C15  N3    180.00   0.0  0
 39X  CONST_09  N2   C13  N3   C15     0.00   0.0  0
 39X  CONST_10  C17  C18  C19  C15     0.00   0.0  0
 39X  CONST_11  C17  C16  C14  C15     0.00   0.0  0
 39X  CONST_12  N2   C14  C15  C19   180.00   0.0  0
 39X  CONST_13  C16  C14  C15  C19     0.00   0.0  0
 39X  CONST_14  C16  C17  C18  C19     0.00   0.0  0
 39X  CONST_15  C14  C15  C19  C18     0.00   0.0  0
 39X  CONST_16  C14  C16  C17  C18     0.00   0.0  0
 39X  CONST_17  N2   C14  C16  C17   180.00   0.0  0
 39X  CONST_18  C8   C4   C3   C2    180.00   0.0  0
 39X  CONST_19  C5   C4   C3   C2      0.00   0.0  0
 39X  CONST_20  C5   C6   C7   C2      0.00   0.0  0
 39X  CONST_21  C4   C3   C2   C7      0.00   0.0  0
 39X  CONST_22  C4   C5   C6   C7      0.00   0.0  0
 39X  CONST_23  C11  C5   C6   C7    180.00   0.0  0
 39X  CONST_24  C8   C4   C5   C6    180.00   0.0  0
 39X  CONST_25  C3   C4   C5   C6      0.00   0.0  0
 39X  CONST_26  C10  C11  C5   C6    180.00   0.0  0
 39X  CONST_27  C3   C2   C7   C6      0.00   0.0  0
 39X  CONST_28  C9   C8   C4   C5      0.00   0.0  0
 39X  CONST_29  C9   C10  C11  C5      0.00   0.0  0
 39X  CONST_30  C8   C9   C10  C11     0.00   0.0  0
 39X  CONST_31  C8   C4   C5   C11     0.00   0.0  0
 39X  CONST_32  C3   C4   C5   C11   180.00   0.0  0
 39X  CONST_33  C4   C8   C9   C10     0.00   0.0  0
 39X  CONST_34  C4   C5   C11  C10     0.00   0.0  0
 39X  CONST_35  C3   C4   C8   C9    180.00   0.0  0
 39X  CONST_36  C15  N3   C13  C12   180.00   0.0  0
 39X  CONST_37  C14  N2   C13  C12   180.00   0.0  0
 39X  CONST_38  F1   C17  C18  C19   180.00   0.0  0
 39X  CONST_39  C14  C16  C17  F1    180.00   0.0  0
 39X  CONST_40  C4   C3   C2   C1    180.00   0.0  0
 39X  CONST_41  C6   C7   C2   C1    180.00   0.0  0
 39X  CONST_42  H11  N2   C13  N3    180.00   0.0  0
 39X  CONST_43  H14  C19  C15  N3      0.00   0.0  0
 39X  CONST_44  H13  C18  C19  C15   180.00   0.0  0
 39X  CONST_45  H12  C16  C14  C15   180.00   0.0  0
 39X  CONST_46  H3   C6   C7   C2    180.00   0.0  0
 39X  CONST_47  H2   C3   C2   C7    180.00   0.0  0
 39X  CONST_48  H8   C11  C5   C6      0.00   0.0  0
 39X  CONST_49  H5   C8   C4   C5    180.00   0.0  0
 39X  CONST_50  H7   C10  C11  C5    180.00   0.0  0
 39X  CONST_51  H4   C7   C6   C5    180.00   0.0  0
 39X  CONST_52  H6   C9   C10  C11   180.00   0.0  0
 39X  CONST_53  C2   C1   N1   C20   180.00   0.0  0
 39X  CONST_54  H1   N1   C1   C2      0.00   0.0  0
 39X  CONST_55  O1   C1   N1   C20     0.00   0.0  0
 39X  Var_01    N3   C13  C12  C20  -102.00  30.0  2
 39X  Var_02    C3   C2   C1   N1    151.26  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
 39X  chir_01  C20  C21  C12  N1  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
 39X  plan-1  C12  0.020
 39X  plan-1  C13  0.020
 39X  plan-1  N3   0.020
 39X  plan-1  C15  0.020
 39X  plan-1  C19  0.020
 39X  plan-1  C18  0.020
 39X  plan-1  C17  0.020
 39X  plan-1  F1   0.020
 39X  plan-1  C16  0.020
 39X  plan-1  C14  0.020
 39X  plan-1  N2   0.020
 39X  plan-1  H14  0.020
 39X  plan-1  H13  0.020
 39X  plan-1  H12  0.020
 39X  plan-1  H11  0.020
 39X  plan-2  C1   0.020
 39X  plan-2  C2   0.020
 39X  plan-2  C7   0.020
 39X  plan-2  C6   0.020
 39X  plan-2  C5   0.020
 39X  plan-2  C11  0.020
 39X  plan-2  C10  0.020
 39X  plan-2  C9   0.020
 39X  plan-2  C8   0.020
 39X  plan-2  C4   0.020
 39X  plan-2  C3   0.020
 39X  plan-2  H4   0.020
 39X  plan-2  H3   0.020
 39X  plan-2  H8   0.020
 39X  plan-2  H7   0.020
 39X  plan-2  H6   0.020
 39X  plan-2  H5   0.020
 39X  plan-2  H2   0.020
 39X  plan-3  C20  0.020
 39X  plan-3  N1   0.020
 39X  plan-3  C1   0.020
 39X  plan-3  O1   0.020
 39X  plan-3  C2   0.020
 39X  plan-3  H1   0.020
 39X  plan-4  O3   0.020
 39X  plan-4  C21  0.020
 39X  plan-4  O2   0.020
 39X  plan-4  C20  0.020

