# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Apr 11 03:59:24 2020
#   Inital geometry file: a 127 line input string
#   Ligand name: 5-{[6-chloro-5-(1-methyl-1H-indol-5-yl)-1H-benzimidazol-2-yl]oxy}-2-methylbenzoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cn1ccc2cc(ccc12)c3cc4nc([nH]c4cc3Cl)Oc5ccc(C)c(c5)C(O)=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
 992  992  '5-{[6-chloro-5-(1-methyl-1H-indol-5-yl)-1H-benzimidazol-2-yl]oxy}-2-methylbenzoic acid'  ligand  48  31  .  2021-08-06  2021-08-06  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_992
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
 992  C6    C   CR56   0   0.078   5.3299  -0.8105  -0.9096
 992  C21   C   CR16   0  -0.377   4.2085   0.0222  -0.9106
 992  C5    C   CR56   0   0.359   5.5735  -1.6398   0.2086
 992  N7    N   NR5    0  -0.515   6.7157  -2.3475  -0.0324
 992  C4    C   CR16   0  -0.302   4.7224  -1.6555   1.3118
 992  C3    C   CR16   0  -0.312   3.6214  -0.8226   1.2797
 992  C2    C   CR6    0   0.043   3.3555   0.0196   0.1814
 992  C1    C   CH3    0  -0.530   7.2972  -3.3190   0.8603
 992  C7    C   CR6    0   0.125   2.1317   0.8549   0.1959
 992  C10   C   CR6    0  -0.142   2.1693   2.2577   0.1270
 992  C11   C   CR16   0  -0.252   1.0300   3.0489   0.1413
 992  C12   C   CR56   0   0.340  -0.1785   2.3852   0.2331
 992  C13   C   CR56   0   0.176  -0.2675   0.9867   0.3165
 992  C14   C   CR16   0  -0.388   0.8917   0.2261   0.2956
 992  N21   N   NR15   0  -0.724  -1.4799   2.8223   0.2741
 992  N22   N   N      0  -0.507  -1.5866   0.5955   0.4040
 992  C23   C   CR5    0   0.660  -2.2480   1.7107   0.3764
 992  O25   O   O2     0  -0.505  -3.5612   1.8669   0.4363
 992  C26   C   CR6    0   0.343  -4.3322   0.7203   0.5853
 992  C27   C   CR16   0  -0.296  -4.6012   0.2412   1.8518
 992  C28   C   CR16   0  -0.308  -5.4117  -0.8767   1.9681
 992  C29   C   CR6    0   0.082  -5.9728  -1.5128   0.8595
 992  C30   C   CR6    0  -0.133  -5.6873  -1.0035  -0.4185
 992  C31   C   CR16   0  -0.335  -4.8485   0.1042  -0.5352
 992  C32   C   CH3    0  -0.705  -6.8287  -2.7243   1.1064
 992  CL1   CL  CL     0  -0.135   3.6988   3.0812   0.0677
 992  C8    C   CR15   0  -0.434   6.3843  -1.0604  -1.8406
 992  C9    C   CR15   0  -0.028   7.1945  -1.9957  -1.2650
 992  C18   C   C      0   0.384  -6.2534  -1.5845  -1.7143
 992  O19   O   OC    -1  -0.592  -5.5949  -1.3624  -2.7485
 992  O20   O   O      0  -0.583  -7.3275  -2.2074  -1.6365
 992  H21   H   HCR6   0   0.244   4.0005   0.6542  -1.7655
 992  H8    H   HCR5   0   0.247   6.5243  -0.6072  -2.8088
 992  H4    H   HCR6   0   0.263   4.9089  -2.2921   2.1675
 992  H11C  H   HCH3   0   0.252   6.6357  -4.1747   0.9964
 992  H12C  H   HCH3   0   0.264   8.2359  -3.6710   0.4416
 992  H13C  H   HCH3   0   0.253   7.5016  -2.8768   1.8350
 992  H9    H   HCR5   0   0.283   8.0963  -2.4508  -1.6442
 992  H3    H   HCR6   0   0.248   2.9451  -0.8103   2.1254
 992  H14   H   HCR6   0   0.259   0.8401  -0.8543   0.3440
 992  H11   H   HCR6   0   0.289   1.0927   4.1272   0.0934
 992  HA    H   HNR5   0   0.428  -1.8082   3.7755   0.2426
 992  H27   H   HCR6   0   0.269  -4.1912   0.7228   2.7304
 992  H31   H   HCR6   0   0.261  -4.6113   0.4900  -1.5182
 992  H28   H   HCR6   0   0.252  -5.6139  -1.2693   2.9573
 992  H321  H   HCH3   0   0.242  -7.8717  -2.5409   0.8563
 992  H322  H   HCH3   0   0.234  -6.5081  -3.5773   0.5100
 992  H323  H   HCH3   0   0.226  -6.7761  -3.0104   2.1567

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
 992  C6   C21   aromatic  1.397  0.020  1.397
 992  C6   C5    aromatic  1.413  0.020  1.413
 992  C6   C8    aromatic  1.429  0.020  1.429
 992  C21  C2    aromatic  1.386  0.020  1.386
 992  C5   N7    aromatic  1.365  0.020  1.365
 992  C5   C4    aromatic  1.393  0.020  1.393
 992  N7   C1    single    1.442  0.020  1.442
 992  N7   C9    aromatic  1.368  0.020  1.368
 992  C4   C3    aromatic  1.381  0.020  1.381
 992  C3   C2    aromatic  1.409  0.020  1.409
 992  C2   C7    single    1.482  0.020  1.482
 992  C7   C10   aromatic  1.405  0.020  1.405
 992  C7   C14   aromatic  1.394  0.020  1.394
 992  C10  C11   aromatic  1.387  0.020  1.387
 992  C10  CL1   single    1.738  0.020  1.738
 992  C11  C12   aromatic  1.382  0.020  1.382
 992  C12  C13   aromatic  1.404  0.020  1.404
 992  C12  N21   aromatic  1.373  0.020  1.373
 992  C13  C14   aromatic  1.387  0.020  1.387
 992  C13  N22   aromatic  1.379  0.020  1.379
 992  N21  C23   aromatic  1.355  0.020  1.355
 992  N22  C23   aromatic  1.297  0.020  1.297
 992  C23  O25   single    1.324  0.020  1.324
 992  O25  C26   single    1.390  0.020  1.390
 992  C26  C27   aromatic  1.381  0.020  1.381
 992  C26  C31   aromatic  1.379  0.020  1.379
 992  C27  C28   aromatic  1.386  0.020  1.386
 992  C28  C29   aromatic  1.396  0.020  1.396
 992  C29  C30   aromatic  1.405  0.020  1.405
 992  C29  C32   single    1.504  0.020  1.504
 992  C30  C31   aromatic  1.394  0.020  1.394
 992  C30  C18   single    1.529  0.020  1.529
 992  C8   C9    aromatic  1.365  0.020  1.365
 992  C18  O19   deloc     1.246  0.020  1.246
 992  C18  O20   deloc     1.244  0.020  1.244
 992  C21  H21   single    0.930  0.020  1.080
 992  C8   H8    single    0.930  0.020  1.080
 992  C4   H4    single    0.930  0.020  1.080
 992  C1   H11C  single    0.970  0.020  1.090
 992  C1   H12C  single    0.970  0.020  1.090
 992  C1   H13C  single    0.970  0.020  1.090
 992  C9   H9    single    0.930  0.020  1.080
 992  C3   H3    single    0.930  0.020  1.080
 992  C14  H14   single    0.930  0.020  1.080
 992  C11  H11   single    0.930  0.020  1.080
 992  N21  HA    single    0.860  0.020  1.020
 992  C27  H27   single    0.930  0.020  1.080
 992  C31  H31   single    0.930  0.020  1.080
 992  C28  H28   single    0.930  0.020  1.080
 992  C32  H321  single    0.970  0.020  1.090
 992  C32  H322  single    0.970  0.020  1.090
 992  C32  H323  single    0.970  0.020  1.090

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
 992  C8    C6   C5    106.61  3.000
 992  C8    C6   C21   134.13  3.000
 992  C5    C6   C21   119.26  3.000
 992  H21   C21  C2    120.32  3.000
 992  H21   C21  C6    120.17  3.000
 992  C2    C21  C6    119.51  3.000
 992  C4    C5   N7    130.16  3.000
 992  C4    C5   C6    121.86  3.000
 992  N7    C5   C6    107.98  3.000
 992  C9    N7   C1    126.14  3.000
 992  C9    N7   C5    108.58  3.000
 992  C1    N7   C5    125.27  3.000
 992  H4    C4   C3    120.68  3.000
 992  H4    C4   C5    121.82  3.000
 992  C3    C4   C5    117.50  3.000
 992  H3    C3   C2    118.95  3.000
 992  H3    C3   C4    119.12  3.000
 992  C2    C3   C4    121.93  3.000
 992  C7    C2   C3    119.01  3.000
 992  C7    C2   C21   121.01  3.000
 992  C3    C2   C21   119.94  3.000
 992  H13C  C1   H12C  108.31  3.000
 992  H13C  C1   H11C  108.71  3.000
 992  H12C  C1   H11C  108.55  3.000
 992  H13C  C1   N7    110.86  3.000
 992  H12C  C1   N7    109.16  3.000
 992  H11C  C1   N7    111.19  3.000
 992  C14   C7   C10   118.54  3.000
 992  C14   C7   C2    118.76  3.000
 992  C10   C7   C2    122.70  3.000
 992  CL1   C10  C11   116.93  3.000
 992  CL1   C10  C7    119.88  3.000
 992  C11   C10  C7    123.16  3.000
 992  H11   C11  C12   122.18  3.000
 992  H11   C11  C10   121.38  3.000
 992  C12   C11  C10   116.43  3.000
 992  N21   C12  C13   104.79  3.000
 992  N21   C12  C11   132.68  3.000
 992  C13   C12  C11   122.54  3.000
 992  N22   C13  C14   130.18  3.000
 992  N22   C13  C12   110.31  3.000
 992  C14   C13  C12   119.51  3.000
 992  H14   C14  C13   120.46  3.000
 992  H14   C14  C7    119.72  3.000
 992  C13   C14  C7    119.82  3.000
 992  HA    N21  C23   126.38  3.000
 992  HA    N21  C12   127.46  3.000
 992  C23   N21  C12   106.16  3.000
 992  C23   N22  C13   104.04  3.000
 992  O25   C23  N22   127.33  3.000
 992  O25   C23  N21   117.96  3.000
 992  N22   C23  N21   114.70  3.000
 992  C26   O25  C23   117.24  3.000
 992  C31   C26  C27   121.16  3.000
 992  C31   C26  O25   119.29  3.000
 992  C27   C26  O25   119.52  3.000
 992  H27   C27  C28   120.81  3.000
 992  H27   C27  C26   121.09  3.000
 992  C28   C27  C26   118.09  3.000
 992  H28   C28  C29   119.01  3.000
 992  H28   C28  C27   118.57  3.000
 992  C29   C28  C27   122.42  3.000
 992  C32   C29  C30   123.85  3.000
 992  C32   C29  C28   117.74  3.000
 992  C30   C29  C28   118.39  3.000
 992  C18   C30  C31   116.98  3.000
 992  C18   C30  C29   123.91  3.000
 992  C31   C30  C29   119.10  3.000
 992  H31   C31  C30   119.41  3.000
 992  H31   C31  C26   119.78  3.000
 992  C30   C31  C26   120.81  3.000
 992  H323  C32  H322  107.93  3.000
 992  H323  C32  H321  108.18  3.000
 992  H322  C32  H321  106.75  3.000
 992  H323  C32  C29   110.02  3.000
 992  H322  C32  C29   111.94  3.000
 992  H321  C32  C29   111.84  3.000
 992  H8    C8   C9    126.13  3.000
 992  H8    C8   C6    127.42  3.000
 992  C9    C8   C6    106.45  3.000
 992  H9    C9   C8    129.58  3.000
 992  H9    C9   N7    120.04  3.000
 992  C8    C9   N7    110.39  3.000
 992  O20   C18  O19   126.68  3.000
 992  O20   C18  C30   117.20  3.000
 992  O19   C18  C30   116.11  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
 992  CONST_01  C3    C2   C21  C6      0.00   0.0  0
 992  CONST_02  C7    C2   C21  C6    180.00   0.0  0
 992  CONST_03  C9    N7   C5   C6      0.00   0.0  0
 992  CONST_04  C3    C4   C5   C6      0.00   0.0  0
 992  CONST_05  N7    C9   C8   C6      0.00   0.0  0
 992  CONST_06  N7    C5   C6   C21   180.00   0.0  0
 992  CONST_07  C4    C5   C6   C21     0.00   0.0  0
 992  CONST_08  C9    C8   C6   C21   180.00   0.0  0
 992  CONST_09  C4    C3   C2   C21     0.00   0.0  0
 992  CONST_12  C2    C21  C6   C5      0.00   0.0  0
 992  CONST_13  C9    C8   C6   C5      0.00   0.0  0
 992  CONST_14  C8    C9   N7   C5      0.00   0.0  0
 992  CONST_15  C2    C3   C4   C5      0.00   0.0  0
 992  CONST_16  C8    C6   C5   N7      0.00   0.0  0
 992  CONST_17  C3    C4   C5   N7    180.00   0.0  0
 992  CONST_18  C8    C6   C5   C4    180.00   0.0  0
 992  CONST_19  C9    N7   C5   C4    180.00   0.0  0
 992  CONST_20  C7    C2   C3   C4    180.00   0.0  0
 992  CONST_23  C8    C6   C21  C2    180.00   0.0  0
 992  CONST_24  C11   C10  C7   C2    180.00   0.0  0
 992  CONST_25  C13   C14  C7   C2    180.00   0.0  0
 992  CONST_26  C12   C11  C10  C7      0.00   0.0  0
 992  CONST_27  C12   C13  C14  C7      0.00   0.0  0
 992  CONST_28  N22   C13  C14  C7    180.00   0.0  0
 992  CONST_29  C13   C14  C7   C10     0.00   0.0  0
 992  CONST_30  C13   C12  C11  C10     0.00   0.0  0
 992  CONST_31  N21   C12  C11  C10   180.00   0.0  0
 992  CONST_32  C14   C7   C10  C11     0.00   0.0  0
 992  CONST_33  C14   C13  C12  C11     0.00   0.0  0
 992  CONST_34  N22   C13  C12  C11   180.00   0.0  0
 992  CONST_35  C23   N21  C12  C11   180.00   0.0  0
 992  CONST_36  C23   N22  C13  C12     0.00   0.0  0
 992  CONST_37  N22   C23  N21  C12     0.00   0.0  0
 992  CONST_38  C23   N21  C12  C13     0.00   0.0  0
 992  CONST_39  N21   C23  N22  C13     0.00   0.0  0
 992  CONST_40  N21   C12  C13  C14   180.00   0.0  0
 992  CONST_41  C23   N22  C13  C14   180.00   0.0  0
 992  CONST_42  N22   C13  C12  N21     0.00   0.0  0
 992  CONST_43  C29   C28  C27  C26     0.00   0.0  0
 992  CONST_44  C29   C30  C31  C26     0.00   0.0  0
 992  CONST_45  C30   C31  C26  C27     0.00   0.0  0
 992  CONST_46  C30   C29  C28  C27     0.00   0.0  0
 992  CONST_47  C31   C26  C27  C28     0.00   0.0  0
 992  CONST_48  C31   C30  C29  C28     0.00   0.0  0
 992  CONST_49  C1    N7   C5   C6    180.00   0.0  0
 992  CONST_50  C1    N7   C5   C4      0.00   0.0  0
 992  CONST_51  CL1   C10  C7   C2      0.00   0.0  0
 992  CONST_52  C8    C9   N7   C1    180.00   0.0  0
 992  CONST_53  CL1   C10  C11  C12   180.00   0.0  0
 992  CONST_54  O25   C23  N21  C12   180.00   0.0  0
 992  CONST_55  O25   C23  N22  C13   180.00   0.0  0
 992  CONST_56  CL1   C10  C7   C14   180.00   0.0  0
 992  CONST_57  C28   C27  C26  O25   180.00   0.0  0
 992  CONST_58  C30   C31  C26  O25   180.00   0.0  0
 992  CONST_59  C18   C30  C31  C26   180.00   0.0  0
 992  CONST_60  C32   C29  C28  C27   180.00   0.0  0
 992  CONST_61  C18   C30  C29  C28   180.00   0.0  0
 992  CONST_62  C32   C29  C30  C31   180.00   0.0  0
 992  CONST_63  H4    C4   C5   C6    180.00   0.0  0
 992  CONST_64  H9    C9   C8   C6    180.00   0.0  0
 992  CONST_65  H8    C8   C6   C21     0.00   0.0  0
 992  CONST_66  H3    C3   C2   C21   180.00   0.0  0
 992  CONST_67  H21   C21  C6   C5    180.00   0.0  0
 992  CONST_68  H14   C14  C7   C2      0.00   0.0  0
 992  CONST_69  H11   C11  C10  C7    180.00   0.0  0
 992  CONST_70  HA    N21  C12  C11     0.00   0.0  0
 992  CONST_71  H28   C28  C27  C26   180.00   0.0  0
 992  CONST_72  H31   C31  C26  C27   180.00   0.0  0
 992  CONST_73  H27   C27  C28  C29   180.00   0.0  0
 992  Var_01    C27   C26  O25  C23    87.65  30.0  2
 992  Var_02    O19   C18  C30  C29  -156.12  30.0  2
 992  Var_03    H11C  C1   N7   C5     64.17  30.0  2
 992  Var_04    H321  C32  C29  C28   112.76  30.0  2

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
 992  plan-1  O25  0.020
 992  plan-1  C26  0.020
 992  plan-1  C27  0.020
 992  plan-1  C28  0.020
 992  plan-1  C29  0.020
 992  plan-1  C30  0.020
 992  plan-1  C31  0.020
 992  plan-1  C32  0.020
 992  plan-1  C18  0.020
 992  plan-1  H27  0.020
 992  plan-1  H31  0.020
 992  plan-1  H28  0.020
 992  plan-2  C6   0.020
 992  plan-2  C21  0.020
 992  plan-2  C5   0.020
 992  plan-2  N7   0.020
 992  plan-2  C4   0.020
 992  plan-2  C3   0.020
 992  plan-2  C2   0.020
 992  plan-2  C1   0.020
 992  plan-2  C7   0.020
 992  plan-2  C8   0.020
 992  plan-2  C9   0.020
 992  plan-2  H21  0.020
 992  plan-2  H8   0.020
 992  plan-2  H4   0.020
 992  plan-2  H9   0.020
 992  plan-2  H3   0.020
 992  plan-3  C2   0.020
 992  plan-3  C7   0.020
 992  plan-3  C10  0.020
 992  plan-3  C11  0.020
 992  plan-3  C12  0.020
 992  plan-3  C13  0.020
 992  plan-3  C14  0.020
 992  plan-3  N21  0.020
 992  plan-3  N22  0.020
 992  plan-3  C23  0.020
 992  plan-3  O25  0.020
 992  plan-3  CL1  0.020
 992  plan-3  H14  0.020
 992  plan-3  H11  0.020
 992  plan-3  HA   0.020
 992  plan-4  C30  0.020
 992  plan-4  C18  0.020
 992  plan-4  O19  0.020
 992  plan-4  O20  0.020

