# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri May  1 14:21:02 2020
#   Inital geometry file: a 131 line input string
#   Ligand name: 5-{[6-chloro-5-(1-methyl-1H-indol-5-yl)-1H-benzimidazol-2-yl]oxy}-N-hydroxy-2-methylbenzamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cn1ccc2cc(ccc12)c3cc4nc([nH]c4cc3Cl)Oc5ccc(C)c(c5)C(=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
 R34  R34  5-{[6-chloro-5-(1-methyl-1H-indol-5-yl)-1H-benzimidazol-2-yl]oxy}-N-hydroxy-2-methylbenzamide  ligand  51  32  .  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_R34
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
 R34  C6   C   CR56  0   0.077  -5.3550   0.9096  -1.0498
 R34  C21  C   CR16  0  -0.378  -4.2677   0.0336  -1.0136
 R34  C5   C   CR56  0   0.360  -5.6359   1.7095   0.0810
 R34  N7   N   NR5   0  -0.516  -6.7382   2.4643  -0.1998
 R34  C4   C   CR16  0  -0.302  -4.8515   1.6573   1.2314
 R34  C3   C   CR16  0  -0.312  -3.7828   0.7827   1.2358
 R34  C2   C   CR6   0   0.043  -3.4837  -0.0343   0.1270
 R34  C1   C   CH3   0  -0.530  -7.3352   3.4306   0.6887
 R34  C7   C   CR6   0   0.125  -2.3002  -0.9237   0.1888
 R34  C10  C   CR6   0  -0.141  -2.3934  -2.3203   0.0594
 R34  C11  C   CR16  0  -0.251  -1.2938  -3.1631   0.1198
 R34  C12  C   CR56  0   0.341  -0.0672  -2.5597   0.3222
 R34  C13  C   CR56  0   0.176   0.0758  -1.1713   0.4695
 R34  C14  C   CR16  0  -0.387  -1.0446  -0.3571   0.4000
 R34  N21  N   NR15  0  -0.723   1.2080  -3.0582   0.4344
 R34  N22  N   N     0  -0.503   1.4015  -0.8456   0.6654
 R34  C23  C   CR5   0   0.662   2.0120  -1.9879   0.6357
 R34  O25  O   O2    0  -0.503   3.3127  -2.2050   0.7828
 R34  C26  C   CR6   0   0.341   4.1229  -1.0974   0.9594
 R34  C27  C   CR16  0  -0.283   4.5194  -0.7456   2.2330
 R34  C28  C   CR16  0  -0.302   5.3815   0.3307   2.3925
 R34  C29  C   CR6   0   0.100   5.8596   1.0583   1.3077
 R34  C30  C   CR6   0  -0.107   5.4334   0.6782   0.0285
 R34  C31  C   CR16  0  -0.301   4.5637  -0.3924  -0.1450
 R34  C32  C   CH3   0  -0.731   6.7868   2.2170   1.5334
 R34  CL1  CL  CL    0  -0.134  -3.9485  -3.0711  -0.1368
 R34  C8   C   CR15  0  -0.433  -6.3431   1.2285  -2.0310
 R34  C9   C   CR15  0  -0.027  -7.1542   2.1719  -1.4702
 R34  C18  C   C     0   0.464   5.9561   1.3768  -1.1879
 R34  N8   N   NH1   0  -0.355   4.9795   1.8541  -1.9773
 R34  O20  O   O     0  -0.458   7.1445   1.5005  -1.4220
 R34  O21  O   OH1   0  -0.539   5.2726   2.3419  -3.2118
 R34  H1   H   HCR6  0   0.244  -4.0331  -0.5778  -1.8766
 R34  H2   H   HCR6  0   0.264  -5.0644   2.2727   2.0964
 R34  H3   H   HCR6  0   0.247  -3.1595   0.7165   2.1188
 R34  H4   H   HCH3  0   0.252  -6.6717   4.2799   0.8533
 R34  H5   H   HCH3  0   0.264  -8.2607   3.7940   0.2507
 R34  H6   H   HCH3  0   0.253  -7.5684   2.9772   1.6516
 R34  H7   H   HCR6  0   0.290  -1.3994  -4.2348   0.0241
 R34  H8   H   HCR6  0   0.260  -0.9498   0.7170   0.4969
 R34  H9   H   HNR5  0   0.429   1.4960  -4.0236   0.3844
 R34  H11  H   HCR6  0   0.281   4.1692  -1.3024   3.0925
 R34  H12  H   HCR6  0   0.266   5.6857   0.6124   3.3926
 R34  H13  H   HCR6  0   0.287   4.2503  -0.6957  -1.1366
 R34  H14  H   HCH3  0   0.257   7.8013   1.9865   1.2099
 R34  H15  H   HCH3  0   0.248   6.4665   3.1050   0.9877
 R34  H16  H   HCH3  0   0.250   6.8238   2.4745   2.5905
 R34  H17  H   HCR5  0   0.247  -6.4420   0.8120  -3.0205
 R34  H18  H   HCR5  0   0.283  -8.0179   2.6688  -1.8840
 R34  H19  H   HNH1  0   0.423   3.9978   1.7103  -1.7864
 R34  H20  H   HOH1  0   0.480   5.3419   3.3012  -3.1160

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
 R34  C27  C28  aromatic  1.388  0.020  1.388
 R34  C27  C26  aromatic  1.379  0.020  1.379
 R34  C28  C29  aromatic  1.391  0.020  1.391
 R34  C8   C9   aromatic  1.365  0.020  1.365
 R34  C8   C6   aromatic  1.429  0.020  1.429
 R34  O25  C26  single    1.384  0.020  1.384
 R34  O25  C23  single    1.327  0.020  1.327
 R34  C21  C6   aromatic  1.397  0.020  1.397
 R34  C21  C2   aromatic  1.386  0.020  1.386
 R34  C9   N7   aromatic  1.368  0.020  1.368
 R34  C26  C31  aromatic  1.382  0.020  1.382
 R34  C6   C5   aromatic  1.413  0.020  1.413
 R34  C23  N22  aromatic  1.296  0.020  1.296
 R34  C23  N21  aromatic  1.354  0.020  1.354
 R34  C29  C32  single    1.501  0.020  1.501
 R34  C29  C30  aromatic  1.401  0.020  1.401
 R34  N22  C13  aromatic  1.379  0.020  1.379
 R34  N21  C12  aromatic  1.374  0.020  1.374
 R34  C13  C12  aromatic  1.403  0.020  1.403
 R34  C13  C14  aromatic  1.387  0.020  1.387
 R34  C12  C11  aromatic  1.382  0.020  1.382
 R34  C14  C7   aromatic  1.394  0.020  1.394
 R34  C11  C10  aromatic  1.387  0.020  1.387
 R34  C7   C10  aromatic  1.406  0.020  1.406
 R34  C7   C2   single    1.482  0.020  1.482
 R34  C10  CL1  single    1.738  0.020  1.738
 R34  C2   C3   aromatic  1.409  0.020  1.409
 R34  N7   C5   aromatic  1.365  0.020  1.365
 R34  N7   C1   single    1.442  0.020  1.442
 R34  C5   C4   aromatic  1.393  0.020  1.393
 R34  C31  C30  aromatic  1.390  0.020  1.390
 R34  C30  C18  single    1.497  0.020  1.497
 R34  C3   C4   aromatic  1.381  0.020  1.381
 R34  O21  N8   single    1.359  0.020  1.359
 R34  C18  O20  double    1.217  0.020  1.217
 R34  C18  N8   single    1.343  0.020  1.343
 R34  C21  H1   single    0.930  0.020  1.080
 R34  C4   H2   single    0.930  0.020  1.080
 R34  C3   H3   single    0.930  0.020  1.080
 R34  C1   H4   single    0.970  0.020  1.090
 R34  C1   H5   single    0.970  0.020  1.090
 R34  C1   H6   single    0.970  0.020  1.090
 R34  C11  H7   single    0.930  0.020  1.080
 R34  C14  H8   single    0.930  0.020  1.080
 R34  N21  H9   single    0.860  0.020  1.020
 R34  C27  H11  single    0.930  0.020  1.080
 R34  C28  H12  single    0.930  0.020  1.080
 R34  C31  H13  single    0.930  0.020  1.080
 R34  C32  H14  single    0.970  0.020  1.090
 R34  C32  H15  single    0.970  0.020  1.090
 R34  C32  H16  single    0.970  0.020  1.090
 R34  C8   H17  single    0.930  0.020  1.080
 R34  C9   H18  single    0.930  0.020  1.080
 R34  N8   H19  single    0.860  0.020  1.020
 R34  O21  H20  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
 R34  C8   C6   C5   106.60  3.000
 R34  C5   C6   C21  119.27  3.000
 R34  C8   C6   C21  134.13  3.000
 R34  H1   C21  C2   120.36  3.000
 R34  H1   C21  C6   120.12  3.000
 R34  C2   C21  C6   119.51  3.000
 R34  C4   C5   N7   130.18  3.000
 R34  C4   C5   C6   121.84  3.000
 R34  N7   C5   C6   107.99  3.000
 R34  C9   N7   C1   126.11  3.000
 R34  C1   N7   C5   125.31  3.000
 R34  C9   N7   C5   108.56  3.000
 R34  H2   C4   C3   120.64  3.000
 R34  H2   C4   C5   121.84  3.000
 R34  C3   C4   C5   117.52  3.000
 R34  H3   C3   C2   118.94  3.000
 R34  H3   C3   C4   119.12  3.000
 R34  C2   C3   C4   121.93  3.000
 R34  C7   C2   C3   118.99  3.000
 R34  C3   C2   C21  119.94  3.000
 R34  C7   C2   C21  121.04  3.000
 R34  H6   C1   H5   108.25  3.000
 R34  H6   C1   H4   108.72  3.000
 R34  H5   C1   H4   108.58  3.000
 R34  H6   C1   N7   110.75  3.000
 R34  H5   C1   N7   109.17  3.000
 R34  H4   C1   N7   111.29  3.000
 R34  C14  C7   C10  118.53  3.000
 R34  C10  C7   C2   122.65  3.000
 R34  C14  C7   C2   118.81  3.000
 R34  CL1  C10  C11  116.86  3.000
 R34  CL1  C10  C7   119.93  3.000
 R34  C11  C10  C7   123.18  3.000
 R34  H7   C11  C12  122.18  3.000
 R34  H7   C11  C10  121.41  3.000
 R34  C12  C11  C10  116.41  3.000
 R34  N21  C12  C13  104.82  3.000
 R34  C13  C12  C11  122.53  3.000
 R34  N21  C12  C11  132.64  3.000
 R34  N22  C13  C14  130.17  3.000
 R34  C14  C13  C12  119.55  3.000
 R34  N22  C13  C12  110.27  3.000
 R34  H8   C14  C13  120.49  3.000
 R34  H8   C14  C7   119.72  3.000
 R34  C13  C14  C7   119.79  3.000
 R34  H9   N21  C23  126.48  3.000
 R34  H9   N21  C12  127.46  3.000
 R34  C23  N21  C12  106.06  3.000
 R34  C23  N22  C13  103.97  3.000
 R34  O25  C23  N22  127.13  3.000
 R34  N22  C23  N21  114.87  3.000
 R34  O25  C23  N21  117.99  3.000
 R34  C26  O25  C23  117.20  3.000
 R34  C31  C26  C27  121.05  3.000
 R34  C31  C26  O25  119.54  3.000
 R34  C27  C26  O25  119.36  3.000
 R34  H11  C27  C28  120.57  3.000
 R34  H11  C27  C26  120.59  3.000
 R34  C28  C27  C26  118.84  3.000
 R34  H12  C28  C29  119.19  3.000
 R34  H12  C28  C27  118.84  3.000
 R34  C29  C28  C27  121.97  3.000
 R34  C32  C29  C30  122.32  3.000
 R34  C30  C29  C28  117.75  3.000
 R34  C32  C29  C28  119.92  3.000
 R34  C18  C30  C31  118.45  3.000
 R34  C18  C30  C29  120.61  3.000
 R34  C31  C30  C29  120.88  3.000
 R34  H13  C31  C30  120.72  3.000
 R34  H13  C31  C26  119.75  3.000
 R34  C30  C31  C26  119.51  3.000
 R34  H16  C32  H15  107.66  3.000
 R34  H16  C32  H14  107.86  3.000
 R34  H15  C32  H14  107.29  3.000
 R34  H16  C32  C29  110.46  3.000
 R34  H15  C32  C29  111.83  3.000
 R34  H14  C32  C29  111.55  3.000
 R34  H17  C8   C9   126.13  3.000
 R34  H17  C8   C6   127.42  3.000
 R34  C9   C8   C6   106.45  3.000
 R34  H18  C9   C8   129.53  3.000
 R34  H18  C9   N7   120.07  3.000
 R34  C8   C9   N7   110.40  3.000
 R34  O20  C18  N8   124.09  3.000
 R34  N8   C18  C30  112.92  3.000
 R34  O20  C18  C30  122.98  3.000
 R34  H19  N8   O21  115.61  3.000
 R34  H19  N8   C18  123.01  3.000
 R34  O21  N8   C18  120.29  3.000
 R34  H20  O21  N8   106.36  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
 R34  CONST_01  N7   C9   C8   C6     0.00   0.0  0
 R34  CONST_02  C7   C2   C21  C6   180.00   0.0  0
 R34  CONST_03  C3   C2   C21  C6     0.00   0.0  0
 R34  CONST_04  C9   N7   C5   C6     0.00   0.0  0
 R34  CONST_05  C3   C4   C5   C6     0.00   0.0  0
 R34  CONST_06  C9   C8   C6   C21  180.00   0.0  0
 R34  CONST_07  N7   C5   C6   C21  180.00   0.0  0
 R34  CONST_08  C4   C5   C6   C21    0.00   0.0  0
 R34  CONST_11  C4   C3   C2   C21    0.00   0.0  0
 R34  CONST_12  C9   C8   C6   C5     0.00   0.0  0
 R34  CONST_13  C2   C21  C6   C5     0.00   0.0  0
 R34  CONST_14  C8   C9   N7   C5     0.00   0.0  0
 R34  CONST_15  C2   C3   C4   C5     0.00   0.0  0
 R34  CONST_16  C8   C6   C5   N7     0.00   0.0  0
 R34  CONST_17  C3   C4   C5   N7   180.00   0.0  0
 R34  CONST_18  C8   C6   C5   C4   180.00   0.0  0
 R34  CONST_19  C9   N7   C5   C4   180.00   0.0  0
 R34  CONST_20  C7   C2   C3   C4   180.00   0.0  0
 R34  CONST_23  C8   C6   C21  C2   180.00   0.0  0
 R34  CONST_24  C13  C14  C7   C2   180.00   0.0  0
 R34  CONST_25  C11  C10  C7   C2   180.00   0.0  0
 R34  CONST_26  N22  C13  C14  C7   180.00   0.0  0
 R34  CONST_27  C12  C13  C14  C7     0.00   0.0  0
 R34  CONST_28  C12  C11  C10  C7     0.00   0.0  0
 R34  CONST_29  N21  C12  C11  C10  180.00   0.0  0
 R34  CONST_30  C13  C12  C11  C10    0.00   0.0  0
 R34  CONST_31  C13  C14  C7   C10    0.00   0.0  0
 R34  CONST_32  C23  N21  C12  C11  180.00   0.0  0
 R34  CONST_33  N22  C13  C12  C11  180.00   0.0  0
 R34  CONST_34  C14  C13  C12  C11    0.00   0.0  0
 R34  CONST_35  C14  C7   C10  C11    0.00   0.0  0
 R34  CONST_36  N22  C23  N21  C12    0.00   0.0  0
 R34  CONST_37  C23  N22  C13  C12    0.00   0.0  0
 R34  CONST_38  N21  C23  N22  C13    0.00   0.0  0
 R34  CONST_39  C23  N21  C12  C13    0.00   0.0  0
 R34  CONST_40  C23  N22  C13  C14  180.00   0.0  0
 R34  CONST_41  N21  C12  C13  C14  180.00   0.0  0
 R34  CONST_42  N22  C13  C12  N21    0.00   0.0  0
 R34  CONST_43  C29  C28  C27  C26    0.00   0.0  0
 R34  CONST_44  C29  C30  C31  C26    0.00   0.0  0
 R34  CONST_45  C30  C29  C28  C27    0.00   0.0  0
 R34  CONST_46  C30  C31  C26  C27    0.00   0.0  0
 R34  CONST_47  C31  C26  C27  C28    0.00   0.0  0
 R34  CONST_48  C31  C30  C29  C28    0.00   0.0  0
 R34  CONST_49  C1   N7   C5   C6   180.00   0.0  0
 R34  CONST_50  C1   N7   C5   C4     0.00   0.0  0
 R34  CONST_51  CL1  C10  C7   C2     0.00   0.0  0
 R34  CONST_52  C8   C9   N7   C1   180.00   0.0  0
 R34  CONST_53  O25  C23  N21  C12  180.00   0.0  0
 R34  CONST_54  CL1  C10  C11  C12  180.00   0.0  0
 R34  CONST_55  O25  C23  N22  C13  180.00   0.0  0
 R34  CONST_56  CL1  C10  C7   C14  180.00   0.0  0
 R34  CONST_57  C28  C27  C26  O25  180.00   0.0  0
 R34  CONST_58  C30  C31  C26  O25  180.00   0.0  0
 R34  CONST_59  C18  C30  C31  C26  180.00   0.0  0
 R34  CONST_60  C32  C29  C28  C27  180.00   0.0  0
 R34  CONST_61  C18  C30  C29  C28  180.00   0.0  0
 R34  CONST_62  C32  C29  C30  C31  180.00   0.0  0
 R34  CONST_63  H18  C9   C8   C6   180.00   0.0  0
 R34  CONST_64  H2   C4   C5   C6   180.00   0.0  0
 R34  CONST_65  H17  C8   C6   C21    0.00   0.0  0
 R34  CONST_66  H3   C3   C2   C21  180.00   0.0  0
 R34  CONST_67  H1   C21  C6   C5   180.00   0.0  0
 R34  CONST_68  H8   C14  C7   C2     0.00   0.0  0
 R34  CONST_69  H7   C11  C10  C7   180.00   0.0  0
 R34  CONST_70  H9   N21  C12  C11    0.00   0.0  0
 R34  CONST_71  H12  C28  C27  C26  180.00   0.0  0
 R34  CONST_72  H13  C31  C26  C27  180.00   0.0  0
 R34  CONST_73  H11  C27  C28  C29  180.00   0.0  0
 R34  CONST_74  O21  N8   C18  C30  180.00   0.0  0
 R34  CONST_75  H19  N8   C18  C30    0.00   0.0  0
 R34  CONST_76  O21  N8   C18  O20    0.00   0.0  0
 R34  Var_01    C27  C26  O25  C23   98.77  30.0  2
 R34  Var_02    O20  C18  C30  C29   53.83  30.0  2
 R34  Var_03    H4   C1   N7   C5    66.64  30.0  2
 R34  Var_04    H14  C32  C29  C28  108.64  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
 R34  plan-1  O25  0.020
 R34  plan-1  C26  0.020
 R34  plan-1  C27  0.020
 R34  plan-1  C28  0.020
 R34  plan-1  C29  0.020
 R34  plan-1  C30  0.020
 R34  plan-1  C31  0.020
 R34  plan-1  C32  0.020
 R34  plan-1  C18  0.020
 R34  plan-1  H11  0.020
 R34  plan-1  H12  0.020
 R34  plan-1  H13  0.020
 R34  plan-2  C2   0.020
 R34  plan-2  C7   0.020
 R34  plan-2  C10  0.020
 R34  plan-2  C11  0.020
 R34  plan-2  C12  0.020
 R34  plan-2  C13  0.020
 R34  plan-2  C14  0.020
 R34  plan-2  N21  0.020
 R34  plan-2  N22  0.020
 R34  plan-2  C23  0.020
 R34  plan-2  O25  0.020
 R34  plan-2  CL1  0.020
 R34  plan-2  H7   0.020
 R34  plan-2  H8   0.020
 R34  plan-2  H9   0.020
 R34  plan-3  C6   0.020
 R34  plan-3  C21  0.020
 R34  plan-3  C5   0.020
 R34  plan-3  N7   0.020
 R34  plan-3  C4   0.020
 R34  plan-3  C3   0.020
 R34  plan-3  C2   0.020
 R34  plan-3  C1   0.020
 R34  plan-3  C7   0.020
 R34  plan-3  C8   0.020
 R34  plan-3  C9   0.020
 R34  plan-3  H1   0.020
 R34  plan-3  H2   0.020
 R34  plan-3  H3   0.020
 R34  plan-3  H17  0.020
 R34  plan-3  H18  0.020
 R34  plan-4  C30  0.020
 R34  plan-4  C18  0.020
 R34  plan-4  N8   0.020
 R34  plan-4  O20  0.020
 R34  plan-4  O21  0.020
 R34  plan-4  H19  0.020

