# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed May  6 12:33:16 2020
#   Inital geometry file: a 137 line input string
#   Ligand name: methyl {5-[4-({[2-fluoro-5-(trifluoromethyl)phenyl]carbamoyl}amino)phenoxy]-1H-benzimidazol-2-yl}carbamate
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: COC(=O)Nc1[nH]c2ccc(Oc3ccc(NC(=O)Nc4cc(ccc4F)C(F)(F)F)cc3)cc2n1
#
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
 GIG  GIG  'methyl {5-[4-({[2-fluoro-5-(trifluoromethyl)phenyl]carbamoyl}amino)phenoxy]-1H-benzimidazol-2-yl}carbamate'  ligand  53  36  .  2021-08-10  2021-08-10  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_GIG
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
 GIG  C5    C  CR6   0  -0.180  13.0569  -2.2479   1.0253
 GIG  C6    C  CR16  0  -0.341  11.8223  -1.7174   0.6594
 GIG  C7    C  CR6   0   0.250  11.7097  -0.9096  -0.4686
 GIG  C8    C  CR6   0   0.482  12.8840  -0.6692  -1.1911
 GIG  C10   C  CR16  0  -0.297  14.2005  -1.9928   0.2885
 GIG  N12   N  NH1   0  -0.793  10.5438  -0.3207  -0.9338
 GIG  C13   C  C     0   0.739   9.2760  -0.4542  -0.4218
 GIG  C17   C  CR16  0  -0.306   6.0706   0.1407  -1.9104
 GIG  C20   C  CR16  0  -0.342   5.1044   0.4363   0.6685
 GIG  C21   C  CR16  0  -0.277   6.4728   0.4081   0.4356
 GIG  C24   C  CR16  0  -0.396   2.0032   1.6883   1.5151
 GIG  C36   C  CH3   0  -0.422  -1.4567   3.2712   8.8342
 GIG  O35   O  O2    0  -0.464  -0.8985   3.5921   7.5583
 GIG  C33   C  C     0   0.762  -0.4954   2.5834   6.8077
 GIG  O34   O  O     0  -0.492  -0.5607   1.4142   7.1122
 GIG  C27   C  CR5   0   0.680   0.5248   2.2770   4.6180
 GIG  N28   N  NR15  0  -0.716   0.5931   0.9264   4.6564
 GIG  C29   C  CR56  0   0.351   1.1686   0.5309   3.4722
 GIG  C30   C  CR16  0  -0.306   1.4848  -0.7137   2.9536
 GIG  C31   C  CR16  0  -0.327   2.0703  -0.7421   1.6975
 GIG  C23   C  CR6   0   0.294   2.3174   0.4438   0.9997
 GIG  C19   C  CR6   0   0.357   4.2162   0.3299  -0.3945
 GIG  C16   C  CR6   0   0.332   6.9707   0.2495  -0.8526
 GIG  N15   N  NH1   0  -0.786   8.3482   0.2491  -1.1323
 GIG  O14   O  O     0  -0.493   9.0106  -1.1178   0.5636
 GIG  C9    C  CR16  0  -0.393  14.1048  -1.1867  -0.8377
 GIG  F11   F  F     0  -0.310  12.7956   0.1093  -2.2815
 GIG  C2    C  CT    0   1.049  13.0991  -3.1239   2.2378
 GIG  F3    F  F     0  -0.301  14.3420  -3.4711   2.5802
 GIG  F4    F  F     0  -0.313  12.5511  -2.5245   3.3048
 GIG  F1    F  F     0  -0.315  12.4132  -4.2620   2.0507
 GIG  C18   C  CR16  0  -0.326   4.7063   0.1894  -1.6888
 GIG  C25   C  CR56  0   0.162   1.4144   1.7260   2.7763
 GIG  N26   N  N     0  -0.514   0.9992   2.8024   3.5211
 GIG  H6    H  HCR6  0   0.306  10.9436  -1.9277   1.2475
 GIG  H10   H  HCR6  0   0.280  15.1618  -2.4007   0.5643
 GIG  HN12  H  HNH1  0   0.418  10.6516   0.2695  -1.7439
 GIG  H17   H  HCR6  0   0.272   6.4394   0.0162  -2.9214
 GIG  H20   H  HCR6  0   0.280   4.7508   0.5605   1.6834
 GIG  H21   H  HCR6  0   0.271   7.1434   0.5253   1.2741
 GIG  H24   H  HCR6  0   0.269   2.2014   2.5946   0.9571
 GIG  H361  H  HCH3  0   0.245  -2.3475   2.6526   8.7333
 GIG  H362  H  HCH3  0   0.258  -1.7267   4.2219   9.2828
 GIG  H363  H  HCH3  0   0.245  -0.7299   2.7657   9.4685
 GIG  HN32  H  HNH1  0   0.431   0.0253   4.0450   5.4574
 GIG  HN28  H  HNR5  0   0.428   0.2777   0.3416   5.4147
 GIG  H30   H  HCR6  0   0.274   1.2873  -1.6283   3.4963
 GIG  H31   H  HCR6  0   0.271   2.3328  -1.6905   1.2469
 GIG  HN15  H  HNH1  0   0.412   8.6158   0.6334  -2.0260
 GIG  H9    H  HCR6  0   0.295  14.9763  -0.9641  -1.4386
 GIG  H18   H  HCR6  0   0.271   4.0183   0.1084  -2.5207
 GIG  O22   O  O2    0  -0.518   2.8616   0.3653  -0.2625
 GIG  N32   N  NH1   0  -0.755   0.0106   3.0490   5.6277

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
 GIG  C5   C6    aromatic  1.393  0.020  1.393
 GIG  C5   C10   aromatic  1.384  0.020  1.384
 GIG  C5   C2    single    1.496  0.020  1.496
 GIG  C6   C7    aromatic  1.392  0.020  1.392
 GIG  C6   H6    single    0.930  0.020  1.080
 GIG  C7   N12   single    1.387  0.020  1.387
 GIG  C7   C8    aromatic  1.400  0.020  1.400
 GIG  C8   F11   single    1.343  0.020  1.343
 GIG  C8   C9    aromatic  1.372  0.020  1.372
 GIG  C10  C9    aromatic  1.388  0.020  1.388
 GIG  C10  H10   single    0.930  0.020  1.080
 GIG  N12  C13   single    1.374  0.020  1.374
 GIG  N12  HN12  single    0.860  0.020  1.020
 GIG  C13  N15   single    1.364  0.020  1.364
 GIG  C13  O14   double    1.217  0.020  1.217
 GIG  C17  C18   aromatic  1.383  0.020  1.383
 GIG  C17  C16   aromatic  1.393  0.020  1.393
 GIG  C17  H17   single    0.930  0.020  1.080
 GIG  C20  C19   aromatic  1.389  0.020  1.389
 GIG  C20  C21   aromatic  1.388  0.020  1.388
 GIG  C20  H20   single    0.930  0.020  1.080
 GIG  C21  C16   aromatic  1.390  0.020  1.390
 GIG  C21  H21   single    0.930  0.020  1.080
 GIG  C24  C23   aromatic  1.383  0.020  1.383
 GIG  C24  C25   aromatic  1.392  0.020  1.392
 GIG  C24  H24   single    0.930  0.020  1.080
 GIG  C36  O35   single    1.429  0.020  1.429
 GIG  C36  H361  single    0.970  0.020  1.090
 GIG  C36  H362  single    0.970  0.020  1.090
 GIG  C36  H363  single    0.970  0.020  1.090
 GIG  O35  C33   single    1.320  0.020  1.320
 GIG  C33  N32   single    1.366  0.020  1.366
 GIG  C33  O34   double    1.210  0.020  1.210
 GIG  N32  C27   single    1.371  0.020  1.371
 GIG  N32  HN32  single    0.860  0.020  1.020
 GIG  C27  N28   aromatic  1.353  0.020  1.353
 GIG  C27  N26   aromatic  1.305  0.020  1.305
 GIG  N28  C29   aromatic  1.375  0.020  1.375
 GIG  N28  HN28  single    0.860  0.020  1.020
 GIG  C29  C30   aromatic  1.385  0.020  1.385
 GIG  C29  C25   aromatic  1.405  0.020  1.405
 GIG  C30  C31   aromatic  1.386  0.020  1.386
 GIG  C30  H30   single    0.930  0.020  1.080
 GIG  C31  C23   aromatic  1.398  0.020  1.398
 GIG  C31  H31   single    0.930  0.020  1.080
 GIG  C23  O22   single    1.377  0.020  1.377
 GIG  O22  C19   single    1.361  0.020  1.361
 GIG  C19  C18   aromatic  1.391  0.020  1.391
 GIG  C16  N15   single    1.406  0.020  1.406
 GIG  N15  HN15  single    0.860  0.020  1.020
 GIG  C9   H9    single    0.930  0.020  1.080
 GIG  C2   F1    single    1.342  0.020  1.342
 GIG  C2   F3    single    1.335  0.020  1.335
 GIG  C2   F4    single    1.341  0.020  1.341
 GIG  C18  H18   single    0.930  0.020  1.080
 GIG  C25  N26   aromatic  1.373  0.020  1.373

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
 GIG  C2    C5   C10   121.06  3.000
 GIG  C2    C5   C6    117.44  3.000
 GIG  C10   C5   C6    121.50  3.000
 GIG  H6    C6   C7    119.30  3.000
 GIG  H6    C6   C5    120.33  3.000
 GIG  C7    C6   C5    120.37  3.000
 GIG  N12   C7   C8    117.35  3.000
 GIG  C8    C7   C6    116.75  3.000
 GIG  N12   C7   C6    125.90  3.000
 GIG  F11   C8   C9    119.11  3.000
 GIG  C9    C8   C7    123.28  3.000
 GIG  F11   C8   C7    117.61  3.000
 GIG  H10   C10  C9    119.20  3.000
 GIG  H10   C10  C5    121.99  3.000
 GIG  C9    C10  C5    118.81  3.000
 GIG  HN12  N12  C13   117.07  3.000
 GIG  HN12  N12  C7    115.37  3.000
 GIG  C13   N12  C7    127.56  3.000
 GIG  O14   C13  N15   123.68  3.000
 GIG  O14   C13  N12   123.77  3.000
 GIG  N15   C13  N12   112.55  3.000
 GIG  H17   C17  C18   119.30  3.000
 GIG  H17   C17  C16   119.84  3.000
 GIG  C18   C17  C16   120.86  3.000
 GIG  H20   C20  C19   121.18  3.000
 GIG  H20   C20  C21   118.80  3.000
 GIG  C19   C20  C21   120.01  3.000
 GIG  H21   C21  C16   120.62  3.000
 GIG  H21   C21  C20   118.66  3.000
 GIG  C16   C21  C20   120.72  3.000
 GIG  H24   C24  C25   121.45  3.000
 GIG  H24   C24  C23   121.30  3.000
 GIG  C25   C24  C23   117.25  3.000
 GIG  H363  C36  H362  109.38  3.000
 GIG  H363  C36  H361  109.64  3.000
 GIG  H362  C36  H361  109.41  3.000
 GIG  H363  C36  O35   111.32  3.000
 GIG  H362  C36  O35   105.64  3.000
 GIG  H361  C36  O35   111.36  3.000
 GIG  C33   O35  C36   117.08  3.000
 GIG  N32   C33  O34   124.53  3.000
 GIG  O34   C33  O35   125.36  3.000
 GIG  N32   C33  O35   110.11  3.000
 GIG  N26   C27  N28   114.03  3.000
 GIG  N26   C27  N32   121.90  3.000
 GIG  N28   C27  N32   124.07  3.000
 GIG  HN28  N28  C29   127.73  3.000
 GIG  HN28  N28  C27   125.78  3.000
 GIG  C29   N28  C27   106.49  3.000
 GIG  C25   C29  C30   122.63  3.000
 GIG  C25   C29  N28   104.79  3.000
 GIG  C30   C29  N28   132.58  3.000
 GIG  H30   C30  C31   120.96  3.000
 GIG  H30   C30  C29   122.03  3.000
 GIG  C31   C30  C29   117.01  3.000
 GIG  H31   C31  C23   119.51  3.000
 GIG  H31   C31  C30   119.85  3.000
 GIG  C23   C31  C30   120.64  3.000
 GIG  O22   C23  C31   118.63  3.000
 GIG  O22   C23  C24   118.86  3.000
 GIG  C31   C23  C24   122.48  3.000
 GIG  C18   C19  O22   116.32  3.000
 GIG  C18   C19  C20   119.63  3.000
 GIG  O22   C19  C20   124.05  3.000
 GIG  N15   C16  C21   122.37  3.000
 GIG  N15   C16  C17   118.82  3.000
 GIG  C21   C16  C17   118.76  3.000
 GIG  HN15  N15  C16   115.85  3.000
 GIG  HN15  N15  C13   118.52  3.000
 GIG  C16   N15  C13   124.27  3.000
 GIG  H9    C9   C10   120.97  3.000
 GIG  H9    C9   C8    119.74  3.000
 GIG  C10   C9   C8    119.29  3.000
 GIG  F1    C2   F4    106.33  3.000
 GIG  F4    C2   F3    107.02  3.000
 GIG  F1    C2   F3    106.92  3.000
 GIG  F4    C2   C5    111.81  3.000
 GIG  F3    C2   C5    112.72  3.000
 GIG  F1    C2   C5    111.66  3.000
 GIG  H18   C18  C19   119.91  3.000
 GIG  H18   C18  C17   120.08  3.000
 GIG  C19   C18  C17   120.01  3.000
 GIG  N26   C25  C29   110.20  3.000
 GIG  N26   C25  C24   129.81  3.000
 GIG  C29   C25  C24   119.99  3.000
 GIG  C25   N26  C27   104.48  3.000
 GIG  C19   O22  C23   118.93  3.000
 GIG  HN32  N32  C27   115.17  3.000
 GIG  HN32  N32  C33   119.15  3.000
 GIG  C27   N32  C33   125.68  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
 GIG  CONST_01  C8    C7   C6   C5      0.00   0.0  0
 GIG  CONST_02  C8    C9   C10  C5      0.00   0.0  0
 GIG  CONST_03  C9    C10  C5   C6      0.00   0.0  0
 GIG  CONST_04  C9    C8   C7   C6      0.00   0.0  0
 GIG  CONST_05  C10   C5   C6   C7      0.00   0.0  0
 GIG  CONST_06  C10   C9   C8   C7      0.00   0.0  0
 GIG  CONST_07  C20   C19  C18  C17     0.00   0.0  0
 GIG  CONST_08  C20   C21  C16  C17     0.00   0.0  0
 GIG  CONST_09  C18   C19  C20  C21     0.00   0.0  0
 GIG  CONST_10  C18   C17  C16  C21     0.00   0.0  0
 GIG  CONST_11  C30   C31  C23  C24     0.00   0.0  0
 GIG  CONST_12  N28   C29  C25  C24   180.00   0.0  0
 GIG  CONST_13  C30   C29  C25  C24     0.00   0.0  0
 GIG  CONST_14  C27   N26  C25  C24   180.00   0.0  0
 GIG  CONST_15  C30   C29  N28  C27   180.00   0.0  0
 GIG  CONST_16  C25   C29  N28  C27     0.00   0.0  0
 GIG  CONST_17  C29   C25  N26  C27     0.00   0.0  0
 GIG  CONST_18  C25   N26  C27  N28     0.00   0.0  0
 GIG  CONST_19  C31   C30  C29  N28   180.00   0.0  0
 GIG  CONST_20  N26   C25  C29  N28     0.00   0.0  0
 GIG  CONST_21  N26   C27  N28  C29     0.00   0.0  0
 GIG  CONST_22  C23   C31  C30  C29     0.00   0.0  0
 GIG  CONST_23  C23   C24  C25  C29     0.00   0.0  0
 GIG  CONST_24  N26   C25  C29  C30   180.00   0.0  0
 GIG  CONST_25  C25   C29  C30  C31     0.00   0.0  0
 GIG  CONST_26  C25   C24  C23  C31     0.00   0.0  0
 GIG  CONST_27  N26   C25  C24  C23   180.00   0.0  0
 GIG  CONST_28  C16   C21  C20  C19     0.00   0.0  0
 GIG  CONST_29  C16   C17  C18  C19     0.00   0.0  0
 GIG  CONST_30  N12   C7   C6   C5    180.00   0.0  0
 GIG  CONST_31  F11   C8   C7   C6    180.00   0.0  0
 GIG  CONST_32  C2    C5   C6   C7    180.00   0.0  0
 GIG  CONST_33  F11   C8   C9   C10   180.00   0.0  0
 GIG  CONST_34  C9    C8   C7   N12   180.00   0.0  0
 GIG  CONST_35  O22   C19  C18  C17   180.00   0.0  0
 GIG  CONST_36  N15   C16  C21  C20   180.00   0.0  0
 GIG  CONST_37  O22   C19  C20  C21   180.00   0.0  0
 GIG  CONST_38  C29   N28  C27  N32   180.00   0.0  0
 GIG  CONST_39  C25   N26  C27  N32   180.00   0.0  0
 GIG  CONST_40  O22   C23  C31  C30   180.00   0.0  0
 GIG  CONST_41  C25   C24  C23  O22   180.00   0.0  0
 GIG  CONST_42  C18   C17  C16  N15   180.00   0.0  0
 GIG  CONST_43  C2    C5   C10  C9    180.00   0.0  0
 GIG  CONST_44  H9    C9   C10  C5    180.00   0.0  0
 GIG  CONST_45  H10   C10  C5   C6    180.00   0.0  0
 GIG  CONST_46  H6    C6   C7   C8    180.00   0.0  0
 GIG  CONST_47  H21   C21  C16  C17   180.00   0.0  0
 GIG  CONST_48  H18   C18  C19  C20   180.00   0.0  0
 GIG  CONST_49  H17   C17  C16  C21   180.00   0.0  0
 GIG  CONST_50  H31   C31  C23  C24   180.00   0.0  0
 GIG  CONST_51  H30   C30  C29  N28     0.00   0.0  0
 GIG  CONST_52  H24   C24  C25  C29   180.00   0.0  0
 GIG  CONST_53  HN28  N28  C29  C30     0.00   0.0  0
 GIG  CONST_54  H20   C20  C21  C16   180.00   0.0  0
 GIG  CONST_55  C13   N12  C7   C6      0.00   0.0  0
 GIG  CONST_56  C13   N12  C7   C8    180.00   0.0  0
 GIG  CONST_59  N28   C27  N32  C33     0.00   0.0  0
 GIG  CONST_60  N26   C27  N32  C33   180.00   0.0  0
 GIG  CONST_61  HN12  N12  C7   C6    180.00   0.0  0
 GIG  CONST_63  HN32  N32  C27  N28   180.00   0.0  0
 GIG  CONST_64  O14   C13  N12  C7      0.00   0.0  0
 GIG  CONST_65  O14   C13  N15  C16     0.00   0.0  0
 GIG  CONST_66  N15   C13  N12  C7    180.00   0.0  0
 GIG  CONST_67  C16   N15  C13  N12   180.00   0.0  0
 GIG  CONST_68  C27   N32  C33  O35   180.00   0.0  0
 GIG  CONST_69  C27   N32  C33  O34     0.00   0.0  0
 GIG  Var_01    C18   C19  O22  C23   177.18  30.0  2
 GIG  Var_02    F1    C2   C5   C6     65.90  30.0  2
 GIG  Var_03    N32   C33  O35  C36  -179.99  30.0  3
 GIG  Var_04    H361  C36  O35  C33   -60.95  30.0  3

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
 GIG  plan-1  C5    0.020
 GIG  plan-1  C6    0.020
 GIG  plan-1  C7    0.020
 GIG  plan-1  C8    0.020
 GIG  plan-1  C10   0.020
 GIG  plan-1  N12   0.020
 GIG  plan-1  C9    0.020
 GIG  plan-1  F11   0.020
 GIG  plan-1  C2    0.020
 GIG  plan-1  H6    0.020
 GIG  plan-1  H10   0.020
 GIG  plan-1  H9    0.020
 GIG  plan-2  O35   0.020
 GIG  plan-2  C33   0.020
 GIG  plan-2  O34   0.020
 GIG  plan-2  N32   0.020
 GIG  plan-3  C17   0.020
 GIG  plan-3  C20   0.020
 GIG  plan-3  C21   0.020
 GIG  plan-3  C19   0.020
 GIG  plan-3  C16   0.020
 GIG  plan-3  N15   0.020
 GIG  plan-3  C18   0.020
 GIG  plan-3  H17   0.020
 GIG  plan-3  H20   0.020
 GIG  plan-3  H21   0.020
 GIG  plan-3  H18   0.020
 GIG  plan-3  O22   0.020
 GIG  plan-4  C24   0.020
 GIG  plan-4  C27   0.020
 GIG  plan-4  N28   0.020
 GIG  plan-4  C29   0.020
 GIG  plan-4  C30   0.020
 GIG  plan-4  C31   0.020
 GIG  plan-4  C23   0.020
 GIG  plan-4  C25   0.020
 GIG  plan-4  N26   0.020
 GIG  plan-4  H24   0.020
 GIG  plan-4  HN28  0.020
 GIG  plan-4  H30   0.020
 GIG  plan-4  H31   0.020
 GIG  plan-4  O22   0.020
 GIG  plan-4  N32   0.020
 GIG  plan-5  C7    0.020
 GIG  plan-5  N12   0.020
 GIG  plan-5  C13   0.020
 GIG  plan-5  C16   0.020
 GIG  plan-5  N15   0.020
 GIG  plan-5  O14   0.020
 GIG  plan-5  HN12  0.020
 GIG  plan-5  HN15  0.020
 GIG  plan-6  C33   0.020
 GIG  plan-6  C27   0.020
 GIG  plan-6  HN32  0.020
 GIG  plan-6  N32   0.020

