# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat May  2 01:45:24 2020
#   Inital geometry file: a 144 line input string
#   Ligand name: 5-{[6-chloro-5-(2'-hydroxy[1,1'-biphenyl]-4-yl)-1H-benzimidazol-2-yl]oxy}-N-hydroxy-2-methylbenzamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cc1ccc(Oc2[nH]c3cc(Cl)c(cc3n2)c4ccc(cc4)c5ccccc5O)cc1C(=O)NO
#
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
 R93  R93  5-{[6-chloro-5-(2'-hydroxy[1,1'-biphenyl]-4-yl)-1H-benzimidazol-2-yl]oxy}-N-hydroxy-2-methylbenzamide  ligand  55  35  .  2021-08-23  2021-08-23  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_R93
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
 R93  O20  O   O     0  -0.453   7.9793   2.4058   0.8803
 R93  C18  C   C     0   0.467   6.7962   2.1281   0.8294
 R93  N8   N   NH1   0  -0.358   5.8659   2.6221   1.6697
 R93  O21  O   OH1   0  -0.540   6.2121   3.6025   2.5484
 R93  C30  C   CR6   0  -0.112   6.2293   1.1512  -0.1531
 R93  C29  C   CR6   0   0.102   6.4755   1.2959  -1.5241
 R93  C32  C   CH3   0  -0.730   7.2495   2.4537  -2.0844
 R93  C28  C   CR16  0  -0.303   5.9655   0.3248  -2.3807
 R93  C27  C   CR16  0  -0.281   5.2472  -0.7651  -1.9109
 R93  C31  C   CR16  0  -0.299   5.5014   0.0692   0.3304
 R93  C26  C   CR6   0   0.343   5.0278  -0.8816  -0.5534
 R93  O25  O   O2    0  -0.503   4.3729  -1.9943  -0.0550
 R93  C23  C   CR5   0   0.662   3.0511  -1.9340   0.0331
 R93  N21  N   NR15  0  -0.723   2.3988  -3.0121   0.5285
 R93  C12  C   CR56  0   0.343   1.0643  -2.6901   0.5118
 R93  C11  C   CR16  0  -0.249  -0.0686  -3.3808   0.8985
 R93  C10  C   CR6   0  -0.139  -1.2773  -2.7235   0.7304
 R93  CL1  CL  CL    0  -0.130  -2.7101  -3.5509   1.2595
 R93  N22  N   N     0  -0.504   2.2873  -0.9441  -0.3065
 R93  C13  C   CR56  0   0.177   1.0155  -1.3895  -0.0145
 R93  C14  C   CR16  0  -0.382  -0.2104  -0.7600  -0.1688
 R93  C7   C   CR6   0   0.125  -1.3769  -1.4269   0.1989
 R93  C2   C   CR6   0   0.048  -2.6756  -0.7367   0.0303
 R93  C21  C   CR16  0  -0.278  -2.9173   0.4668   0.6890
 R93  C3   C   CR16  0  -0.269  -3.6627  -1.2391  -0.8142
 R93  C4   C   CR16  0  -0.288  -4.8579  -0.5593  -0.9871
 R93  C5   C   CR6   0   0.087  -5.1075   0.6394  -0.3189
 R93  C6   C   CR16  0  -0.275  -4.1159   1.1428   0.5218
 R93  C34  C   CR6   0  -0.049  -6.3794   1.3608  -0.5420
 R93  C9   C   CR16  0  -0.284  -6.7957   1.6598  -1.8377
 R93  C35  C   CR16  0  -0.273  -7.9892   2.3215  -2.0874
 R93  C33  C   CR16  0  -0.251  -8.7931   2.6930  -1.0195
 R93  C8   C   CR16  0  -0.378  -8.4075   2.3994   0.2796
 R93  C1   C   CR6   0   0.324  -7.2085   1.7345   0.5244
 R93  O23  O   OH1   0  -0.623  -6.8183   1.4088   1.7722
 R93  H1   H   HNH1  0   0.421   4.8789   2.5709   1.4573
 R93  H2   H   HOH1  0   0.481   6.3146   3.1689   3.4056
 R93  H3   H   HCH3  0   0.257   8.3117   2.3704  -1.8568
 R93  H4   H   HCH3  0   0.250   7.1426   2.4942  -3.1669
 R93  H5   H   HCH3  0   0.248   6.9069   3.4068  -1.6814
 R93  H6   H   HCR6  0   0.266   6.1333   0.4203  -3.4461
 R93  H7   H   HCR6  0   0.281   4.8721  -1.5139  -2.5966
 R93  H8   H   HCR6  0   0.285   5.3261  -0.0493   1.3926
 R93  H9   H   HNR5  0   0.430   2.8188  -3.8697   0.8533
 R93  H10  H   HCR6  0   0.291  -0.0219  -4.3758   1.3190
 R93  H12  H   HCR6  0   0.262  -0.2687   0.2385  -0.5831
 R93  H13  H   HCR6  0   0.253  -2.1621   0.8800   1.3461
 R93  H14  H   HCR6  0   0.253  -3.4968  -2.1642  -1.3512
 R93  H15  H   HCR6  0   0.253  -5.6112  -0.9741  -1.6454
 R93  H16  H   HCR6  0   0.250  -4.2691   2.0796   1.0412
 R93  H17  H   HCR6  0   0.254  -6.1576   1.3772  -2.6666
 R93  H18  H   HCR6  0   0.254  -8.2847   2.5458  -3.1033
 R93  H19  H   HCR6  0   0.260  -9.7267   3.2126  -1.1925
 R93  H20  H   HCR6  0   0.270  -9.0466   2.6800   1.1101
 R93  H21  H   HOH1  0   0.476  -7.4767   1.7000   2.4127

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
 R93  C27  C28  aromatic  1.387  0.020  1.387
 R93  C27  C26  aromatic  1.380  0.020  1.380
 R93  C28  C29  aromatic  1.392  0.020  1.392
 R93  C21  C6   aromatic  1.386  0.020  1.386
 R93  C21  C2   aromatic  1.393  0.020  1.393
 R93  C9   C35  aromatic  1.387  0.020  1.387
 R93  C9   C34  aromatic  1.393  0.020  1.393
 R93  C6   C5   aromatic  1.394  0.020  1.394
 R93  C35  C33  aromatic  1.387  0.020  1.387
 R93  C26  O25  single    1.384  0.020  1.384
 R93  C26  C31  aromatic  1.382  0.020  1.382
 R93  C29  C32  single    1.501  0.020  1.501
 R93  C29  C30  aromatic  1.400  0.020  1.400
 R93  O25  C23  single    1.326  0.020  1.326
 R93  C23  N21  aromatic  1.354  0.020  1.354
 R93  C23  N22  aromatic  1.296  0.020  1.296
 R93  N21  C12  aromatic  1.373  0.020  1.373
 R93  N22  C13  aromatic  1.379  0.020  1.379
 R93  C12  C13  aromatic  1.404  0.020  1.404
 R93  C12  C11  aromatic  1.382  0.020  1.382
 R93  C13  C14  aromatic  1.387  0.020  1.387
 R93  C11  C10  aromatic  1.386  0.020  1.386
 R93  C14  C7   aromatic  1.393  0.020  1.393
 R93  C10  C7   aromatic  1.405  0.020  1.405
 R93  C10  CL1  single    1.737  0.020  1.737
 R93  C7   C2   single    1.480  0.020  1.480
 R93  C2   C3   aromatic  1.393  0.020  1.393
 R93  C5   C34  single    1.479  0.020  1.479
 R93  C5   C4   aromatic  1.395  0.020  1.395
 R93  C34  C1   aromatic  1.401  0.020  1.401
 R93  C33  C8   aromatic  1.387  0.020  1.387
 R93  C30  C31  aromatic  1.391  0.020  1.391
 R93  C30  C18  single    1.497  0.020  1.497
 R93  C3   C4   aromatic  1.386  0.020  1.386
 R93  C1   C8   aromatic  1.393  0.020  1.393
 R93  C1   O23  single    1.347  0.020  1.347
 R93  C18  N8   single    1.347  0.020  1.347
 R93  C18  O20  double    1.216  0.020  1.216
 R93  N8   O21  single    1.361  0.020  1.361
 R93  N8   H1   single    0.890  0.020  1.040
 R93  O21  H2   single    0.850  0.020  0.980
 R93  C32  H3   single    0.970  0.020  1.090
 R93  C32  H4   single    0.970  0.020  1.090
 R93  C32  H5   single    0.970  0.020  1.090
 R93  C28  H6   single    0.930  0.020  1.080
 R93  C27  H7   single    0.930  0.020  1.080
 R93  C31  H8   single    0.930  0.020  1.080
 R93  N21  H9   single    0.860  0.020  1.020
 R93  C11  H10  single    0.930  0.020  1.080
 R93  C14  H12  single    0.930  0.020  1.080
 R93  C21  H13  single    0.930  0.020  1.080
 R93  C3   H14  single    0.930  0.020  1.080
 R93  C4   H15  single    0.930  0.020  1.080
 R93  C6   H16  single    0.930  0.020  1.080
 R93  C9   H17  single    0.930  0.020  1.080
 R93  C35  H18  single    0.930  0.020  1.080
 R93  C33  H19  single    0.930  0.020  1.080
 R93  C8   H20  single    0.930  0.020  1.080
 R93  O23  H21  single    0.850  0.020  0.980

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
 R93  C30  C18  N8   112.77  3.000
 R93  N8   C18  O20  124.18  3.000
 R93  C30  C18  O20  123.01  3.000
 R93  H1   N8   O21  114.86  3.000
 R93  H1   N8   C18  121.63  3.000
 R93  O21  N8   C18  119.41  3.000
 R93  H2   O21  N8   106.05  3.000
 R93  C31  C30  C29  120.84  3.000
 R93  C31  C30  C18  118.54  3.000
 R93  C29  C30  C18  120.57  3.000
 R93  C28  C29  C32  119.83  3.000
 R93  C32  C29  C30  122.39  3.000
 R93  C28  C29  C30  117.78  3.000
 R93  H5   C32  H4   107.72  3.000
 R93  H5   C32  H3   107.22  3.000
 R93  H4   C32  H3   107.84  3.000
 R93  H5   C32  C29  111.98  3.000
 R93  H4   C32  C29  110.44  3.000
 R93  H3   C32  C29  111.45  3.000
 R93  H6   C28  C27  118.86  3.000
 R93  H6   C28  C29  119.16  3.000
 R93  C27  C28  C29  121.98  3.000
 R93  H7   C27  C26  120.64  3.000
 R93  H7   C27  C28  120.56  3.000
 R93  C26  C27  C28  118.80  3.000
 R93  H8   C31  C26  119.77  3.000
 R93  H8   C31  C30  120.72  3.000
 R93  C26  C31  C30  119.50  3.000
 R93  O25  C26  C31  119.02  3.000
 R93  C31  C26  C27  121.10  3.000
 R93  O25  C26  C27  119.82  3.000
 R93  C23  O25  C26  117.32  3.000
 R93  N22  C23  N21  114.85  3.000
 R93  N22  C23  O25  127.22  3.000
 R93  N21  C23  O25  117.92  3.000
 R93  H9   N21  C12  127.45  3.000
 R93  H9   N21  C23  126.46  3.000
 R93  C12  N21  C23  106.08  3.000
 R93  C13  C12  C11  122.64  3.000
 R93  C11  C12  N21  132.55  3.000
 R93  C13  C12  N21  104.81  3.000
 R93  H10  C11  C10  121.41  3.000
 R93  H10  C11  C12  122.23  3.000
 R93  C10  C11  C12  116.35  3.000
 R93  C7   C10  CL1  119.76  3.000
 R93  CL1  C10  C11  117.16  3.000
 R93  C7   C10  C11  123.05  3.000
 R93  C13  N22  C23  103.97  3.000
 R93  C14  C13  N22  130.19  3.000
 R93  C14  C13  C12  119.54  3.000
 R93  N22  C13  C12  110.28  3.000
 R93  H12  C14  C7   119.83  3.000
 R93  H12  C14  C13  120.59  3.000
 R93  C7   C14  C13  119.58  3.000
 R93  C2   C7   C14  118.78  3.000
 R93  C2   C7   C10  122.38  3.000
 R93  C14  C7   C10  118.84  3.000
 R93  C3   C2   C21  118.38  3.000
 R93  C3   C2   C7   121.51  3.000
 R93  C21  C2   C7   120.07  3.000
 R93  H13  C21  C6   119.35  3.000
 R93  H13  C21  C2   119.71  3.000
 R93  C6   C21  C2   120.95  3.000
 R93  H14  C3   C4   119.31  3.000
 R93  H14  C3   C2   120.03  3.000
 R93  C4   C3   C2   120.66  3.000
 R93  H15  C4   C5   119.73  3.000
 R93  H15  C4   C3   119.20  3.000
 R93  C5   C4   C3   121.07  3.000
 R93  C34  C5   C6   121.76  3.000
 R93  C34  C5   C4   120.05  3.000
 R93  C6   C5   C4   118.16  3.000
 R93  H16  C6   C5   120.10  3.000
 R93  H16  C6   C21  119.12  3.000
 R93  C5   C6   C21  120.77  3.000
 R93  C1   C34  C9   118.27  3.000
 R93  C1   C34  C5   121.60  3.000
 R93  C9   C34  C5   120.12  3.000
 R93  H17  C9   C35  119.56  3.000
 R93  H17  C9   C34  118.65  3.000
 R93  C35  C9   C34  121.78  3.000
 R93  H18  C35  C33  120.61  3.000
 R93  H18  C35  C9   120.20  3.000
 R93  C33  C35  C9   119.19  3.000
 R93  H19  C33  C8   119.43  3.000
 R93  H19  C33  C35  120.35  3.000
 R93  C8   C33  C35  120.22  3.000
 R93  H20  C8   C1   119.74  3.000
 R93  H20  C8   C33  119.91  3.000
 R93  C1   C8   C33  120.35  3.000
 R93  O23  C1   C8   121.84  3.000
 R93  O23  C1   C34  117.96  3.000
 R93  C8   C1   C34  120.19  3.000
 R93  H21  O23  C1   110.16  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
 R93  CONST_01  C27  C28  C29  C30     0.00   0.0  0
 R93  CONST_02  C27  C26  C31  C30     0.00   0.0  0
 R93  CONST_03  C26  C27  C28  C29     0.00   0.0  0
 R93  CONST_04  C26  C31  C30  C29     0.00   0.0  0
 R93  CONST_05  C31  C26  C27  C28     0.00   0.0  0
 R93  CONST_06  C31  C30  C29  C28     0.00   0.0  0
 R93  CONST_07  C13  C12  N21  C23     0.00   0.0  0
 R93  CONST_08  C11  C12  N21  C23   180.00   0.0  0
 R93  CONST_09  C12  C13  N22  C23     0.00   0.0  0
 R93  CONST_10  C14  C13  N22  C23   180.00   0.0  0
 R93  CONST_11  C13  N22  C23  N21     0.00   0.0  0
 R93  CONST_12  N22  C13  C12  N21     0.00   0.0  0
 R93  CONST_13  C14  C13  C12  N21   180.00   0.0  0
 R93  CONST_14  C10  C11  C12  N21   180.00   0.0  0
 R93  CONST_15  N22  C23  N21  C12     0.00   0.0  0
 R93  CONST_16  C7   C14  C13  C12     0.00   0.0  0
 R93  CONST_17  C7   C10  C11  C12     0.00   0.0  0
 R93  CONST_18  N22  C13  C12  C11   180.00   0.0  0
 R93  CONST_19  C14  C13  C12  C11     0.00   0.0  0
 R93  CONST_20  C14  C7   C10  C11     0.00   0.0  0
 R93  CONST_21  C2   C7   C10  C11   180.00   0.0  0
 R93  CONST_22  C13  C12  C11  C10     0.00   0.0  0
 R93  CONST_23  C13  C14  C7   C10     0.00   0.0  0
 R93  CONST_26  C7   C14  C13  N22   180.00   0.0  0
 R93  CONST_27  C2   C7   C14  C13   180.00   0.0  0
 R93  CONST_30  C6   C21  C2   C7    180.00   0.0  0
 R93  CONST_31  C4   C3   C2   C7    180.00   0.0  0
 R93  CONST_32  C5   C6   C21  C2      0.00   0.0  0
 R93  CONST_33  C5   C4   C3   C2      0.00   0.0  0
 R93  CONST_34  C34  C5   C6   C21   180.00   0.0  0
 R93  CONST_35  C4   C5   C6   C21     0.00   0.0  0
 R93  CONST_36  C4   C3   C2   C21     0.00   0.0  0
 R93  CONST_37  C6   C21  C2   C3      0.00   0.0  0
 R93  CONST_38  C6   C5   C4   C3      0.00   0.0  0
 R93  CONST_39  C34  C5   C4   C3    180.00   0.0  0
 R93  CONST_42  C35  C9   C34  C5    180.00   0.0  0
 R93  CONST_43  C8   C1   C34  C5    180.00   0.0  0
 R93  CONST_46  C33  C35  C9   C34     0.00   0.0  0
 R93  CONST_47  C33  C8   C1   C34     0.00   0.0  0
 R93  CONST_48  C8   C33  C35  C9      0.00   0.0  0
 R93  CONST_49  C8   C1   C34  C9      0.00   0.0  0
 R93  CONST_50  C1   C34  C9   C35     0.00   0.0  0
 R93  CONST_51  C1   C8   C33  C35     0.00   0.0  0
 R93  CONST_52  C28  C29  C30  C18   180.00   0.0  0
 R93  CONST_53  C26  C31  C30  C18   180.00   0.0  0
 R93  CONST_54  O25  C26  C31  C30   180.00   0.0  0
 R93  CONST_55  C27  C28  C29  C32   180.00   0.0  0
 R93  CONST_56  C31  C30  C29  C32   180.00   0.0  0
 R93  CONST_57  O25  C26  C27  C28   180.00   0.0  0
 R93  CONST_58  C12  N21  C23  O25   180.00   0.0  0
 R93  CONST_59  C13  N22  C23  O25   180.00   0.0  0
 R93  CONST_60  CL1  C10  C11  C12   180.00   0.0  0
 R93  CONST_61  C14  C7   C10  CL1   180.00   0.0  0
 R93  CONST_62  C2   C7   C10  CL1     0.00   0.0  0
 R93  CONST_63  O23  C1   C34  C5      0.00   0.0  0
 R93  CONST_64  O23  C1   C34  C9    180.00   0.0  0
 R93  CONST_65  O23  C1   C8   C33   180.00   0.0  0
 R93  CONST_66  H6   C28  C29  C30   180.00   0.0  0
 R93  CONST_67  H7   C27  C28  C29   180.00   0.0  0
 R93  CONST_68  H8   C31  C30  C29   180.00   0.0  0
 R93  CONST_69  H10  C11  C12  N21     0.00   0.0  0
 R93  CONST_70  H12  C14  C13  C12   180.00   0.0  0
 R93  CONST_71  H9   N21  C12  C11     0.00   0.0  0
 R93  CONST_72  H13  C21  C2   C7      0.00   0.0  0
 R93  CONST_73  H14  C3   C2   C7      0.00   0.0  0
 R93  CONST_74  H16  C6   C21  C2    180.00   0.0  0
 R93  CONST_75  H15  C4   C3   C2    180.00   0.0  0
 R93  CONST_76  H17  C9   C34  C5      0.00   0.0  0
 R93  CONST_77  H18  C35  C9   C34   180.00   0.0  0
 R93  CONST_78  H20  C8   C1   C34   180.00   0.0  0
 R93  CONST_79  H19  C33  C35  C9    180.00   0.0  0
 R93  CONST_80  C30  C18  N8   O21   180.00   0.0  0
 R93  CONST_82  O21  N8   C18  O20     0.00   0.0  0
 R93  Var_01    N21  C23  O25  C26  -179.51  30.0  2
 R93  Var_02    C29  C30  C18  O20   -53.38  30.0  2
 R93  Var_03    H3   C32  C29  C30    72.45  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
 R93  plan-1  C18  0.020
 R93  plan-1  C30  0.020
 R93  plan-1  C29  0.020
 R93  plan-1  C32  0.020
 R93  plan-1  C28  0.020
 R93  plan-1  C27  0.020
 R93  plan-1  C31  0.020
 R93  plan-1  C26  0.020
 R93  plan-1  O25  0.020
 R93  plan-1  H6   0.020
 R93  plan-1  H7   0.020
 R93  plan-1  H8   0.020
 R93  plan-2  C7   0.020
 R93  plan-2  C2   0.020
 R93  plan-2  C21  0.020
 R93  plan-2  C3   0.020
 R93  plan-2  C4   0.020
 R93  plan-2  C5   0.020
 R93  plan-2  C6   0.020
 R93  plan-2  C34  0.020
 R93  plan-2  H13  0.020
 R93  plan-2  H14  0.020
 R93  plan-2  H15  0.020
 R93  plan-2  H16  0.020
 R93  plan-3  C5   0.020
 R93  plan-3  C34  0.020
 R93  plan-3  C9   0.020
 R93  plan-3  C35  0.020
 R93  plan-3  C33  0.020
 R93  plan-3  C8   0.020
 R93  plan-3  C1   0.020
 R93  plan-3  O23  0.020
 R93  plan-3  H17  0.020
 R93  plan-3  H18  0.020
 R93  plan-3  H19  0.020
 R93  plan-3  H20  0.020
 R93  plan-4  O25  0.020
 R93  plan-4  C23  0.020
 R93  plan-4  N21  0.020
 R93  plan-4  C12  0.020
 R93  plan-4  C11  0.020
 R93  plan-4  C10  0.020
 R93  plan-4  CL1  0.020
 R93  plan-4  N22  0.020
 R93  plan-4  C13  0.020
 R93  plan-4  C14  0.020
 R93  plan-4  C7   0.020
 R93  plan-4  C2   0.020
 R93  plan-4  H9   0.020
 R93  plan-4  H10  0.020
 R93  plan-4  H12  0.020
 R93  plan-5  O20  0.020
 R93  plan-5  C18  0.020
 R93  plan-5  N8   0.020
 R93  plan-5  O21  0.020
 R93  plan-5  C30  0.020
 R93  plan-5  H1   0.020

