# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Apr  6 04:39:37 2020
#   Inital geometry file: a 117 line input string
#   Ligand name: cis-4-{[2-(1H-benzimidazol-5-ylamino)quinazolin-8-yl]oxy}cyclohexanol
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: O[C@H]1CC[C@H](CC1)Oc2cccc3cnc(Nc4ccc5[nH]cnc5c4)nc23
#
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
 58C  58C  cis-4-{[2-(1H-benzimidazol-5-ylamino)quinazolin-8-yl]oxy}cyclohexanol  ligand  49  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 OK
;

data_comp_58C
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
 58C  C1   C  CR66  0  -0.003   0.3879  -2.7790   0.1502
 58C  C2   C  CR66  0   0.177   0.9513  -1.4866   0.1988
 58C  C3   C  CR16  0  -0.003  -1.0174  -2.8092   0.0547
 58C  C4   C  CR6   0   0.578  -1.1160  -0.5508   0.0824
 58C  C5   C  CR16  0  -0.261   2.5465  -3.7856   0.2961
 58C  C6   C  CR16  0  -0.385   3.1366  -2.5023   0.3458
 58C  C7   C  CR16  0  -0.323   1.1940  -3.9358   0.1960
 58C  C20  C  CR56  0   0.156  -5.5249   0.2419  -0.2842
 58C  C21  C  CR15  0   0.101  -7.6436   0.3103  -0.4130
 58C  N2   N  N     0  -0.451  -1.7591  -1.7386   0.0208
 58C  O1   O  O2    0  -0.476   2.8237  -0.1009   0.3502
 58C  N1   N  N     0  -0.485   0.1873  -0.3843   0.1615
 58C  C8   C  CR6   0   0.341   2.3724  -1.3605   0.2975
 58C  C9   C  CH2   0  -0.445   4.3939   1.5805   0.9182
 58C  C10  C  CH1   0   0.037   4.2255   0.1612   0.4022
 58C  C11  C  CH2   0  -0.494   5.8755   1.9395   0.9941
 58C  C12  C  CH1   0   0.042   6.5843   1.7700  -0.3470
 58C  C13  C  CH2   0  -0.462   6.3625   0.3642  -0.8867
 58C  C14  C  CH2   0  -0.472   4.8812  -0.0019  -0.9637
 58C  C15  C  CR16  0  -0.371  -3.6382   2.1222   0.3963
 58C  N3   N  NH1   0  -0.773  -1.8540   0.5918   0.0668
 58C  C16  C  CR6   0   0.357  -3.2336   0.8107   0.0507
 58C  C17  C  CR16  0  -0.289  -4.9613   2.5091   0.4048
 58C  C18  C  CR56  0   0.319  -5.9029   1.5458   0.0642
 58C  C19  C  CR16  0  -0.406  -4.1823  -0.1397  -0.3016
 58C  N4   N  NR15  0  -0.660  -7.2699   1.5519  -0.0305
 58C  N5   N  N     0  -0.470  -6.6407  -0.5074  -0.5788
 58C  O2   O  OH1   0  -0.676   6.0994   2.6807  -1.3171
 58C  H1   H  HCR6  0   0.278  -1.5310  -3.7653   0.0051
 58C  H2   H  HCR6  0   0.264   3.1944  -4.6507   0.3366
 58C  H3   H  HCR6  0   0.284   4.2136  -2.4480   0.4253
 58C  H4   H  HCR6  0   0.258   0.7353  -4.9155   0.1532
 58C  H6   H  HCH2  0   0.228   3.8716   2.2764   0.2556
 58C  H7   H  HCH2  0   0.244   3.9405   1.6745   1.9074
 58C  H8   H  HCH1  0   0.223   4.6979  -0.5208   1.1229
 58C  H9   H  HCH2  0   0.245   5.9954   2.9648   1.3560
 58C  H10  H  HCH2  0   0.229   6.3717   1.3006   1.7311
 58C  H11  H  HCH1  0   0.215   7.6620   1.9208  -0.1919
 58C  H12  H  HCH2  0   0.244   6.8239   0.2614  -1.8715
 58C  H13  H  HCH2  0   0.230   6.8806  -0.3400  -0.2291
 58C  H14  H  HCH2  0   0.247   4.7785  -1.0263  -1.3279
 58C  H15  H  HCH2  0   0.234   4.3672   0.6395  -1.6846
 58C  H16  H  HCR6  0   0.267  -2.8799   2.8491   0.6628
 58C  H17  H  HNH1  0   0.405  -1.2897   1.4212   0.1716
 58C  H18  H  HCR6  0   0.270  -5.2406   3.5190   0.6739
 58C  H19  H  HCR6  0   0.276  -3.9045  -1.1441  -0.5755
 58C  H20  H  HNR5  0   0.421  -7.8903   2.3218   0.1621
 58C  H22  H  HOH1  0   0.447   6.1504   3.5689  -0.9504
 58C  H5   H  HCR5  0   0.285  -8.6834   0.0573  -0.5568

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
 58C  N4   C18  aromatic  1.370  0.020  1.370
 58C  N4   C21  aromatic  1.352  0.020  1.352
 58C  C17  C18  aromatic  1.389  0.020  1.389
 58C  C17  C15  aromatic  1.379  0.020  1.379
 58C  C18  C20  aromatic  1.402  0.020  1.402
 58C  C15  C16  aromatic  1.415  0.020  1.415
 58C  C21  N5   aromatic  1.305  0.020  1.305
 58C  C20  N5   aromatic  1.376  0.020  1.376
 58C  C20  C19  aromatic  1.396  0.020  1.396
 58C  C16  C19  aromatic  1.388  0.020  1.388
 58C  C16  N3   single    1.397  0.020  1.397
 58C  N3   C4   single    1.360  0.020  1.360
 58C  O2   C12  single    1.416  0.020  1.416
 58C  C4   N2   aromatic  1.352  0.020  1.352
 58C  C4   N1   aromatic  1.316  0.020  1.316
 58C  N2   C3   aromatic  1.303  0.020  1.303
 58C  N1   C2   aromatic  1.342  0.020  1.342
 58C  C12  C13  single    1.522  0.020  1.522
 58C  C12  C11  single    1.526  0.020  1.526
 58C  C3   C1   aromatic  1.409  0.020  1.409
 58C  C13  C14  single    1.528  0.020  1.528
 58C  C2   C1   aromatic  1.411  0.020  1.411
 58C  C2   C8   aromatic  1.430  0.020  1.430
 58C  C11  C9   single    1.526  0.020  1.526
 58C  C1   C7   aromatic  1.411  0.020  1.411
 58C  O1   C8   single    1.339  0.020  1.339
 58C  O1   C10  single    1.427  0.020  1.427
 58C  C14  C10  single    1.524  0.020  1.524
 58C  C8   C6   aromatic  1.375  0.020  1.375
 58C  C10  C9   single    1.520  0.020  1.520
 58C  C7   C5   aromatic  1.365  0.020  1.365
 58C  C6   C5   aromatic  1.413  0.020  1.413
 58C  C3   H1   single    0.930  0.020  1.080
 58C  C5   H2   single    0.930  0.020  1.080
 58C  C6   H3   single    0.930  0.020  1.080
 58C  C7   H4   single    0.930  0.020  1.080
 58C  C21  H5   single    0.930  0.020  1.080
 58C  C9   H6   single    0.970  0.020  1.090
 58C  C9   H7   single    0.970  0.020  1.090
 58C  C10  H8   single    0.970  0.020  1.090
 58C  C11  H9   single    0.970  0.020  1.090
 58C  C11  H10  single    0.970  0.020  1.090
 58C  C12  H11  single    0.970  0.020  1.090
 58C  C13  H12  single    0.970  0.020  1.090
 58C  C13  H13  single    0.970  0.020  1.090
 58C  C14  H14  single    0.970  0.020  1.090
 58C  C14  H15  single    0.970  0.020  1.090
 58C  C15  H16  single    0.930  0.020  1.080
 58C  N3   H17  single    0.860  0.020  1.020
 58C  C17  H18  single    0.930  0.020  1.080
 58C  C19  H19  single    0.930  0.020  1.080
 58C  N4   H20  single    0.860  0.020  1.020
 58C  O2   H22  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
 58C  C7   C1   C3   123.68  3.000
 58C  C7   C1   C2   121.46  3.000
 58C  C3   C1   C2   114.86  3.000
 58C  C8   C2   N1   119.69  3.000
 58C  C8   C2   C1   118.69  3.000
 58C  N1   C2   C1   121.62  3.000
 58C  H1   C3   N2   116.92  3.000
 58C  H1   C3   C1   119.57  3.000
 58C  N2   C3   C1   123.50  3.000
 58C  N3   C4   N1   115.57  3.000
 58C  N1   C4   N2   125.79  3.000
 58C  N3   C4   N2   118.64  3.000
 58C  H2   C5   C7   120.56  3.000
 58C  H2   C5   C6   118.35  3.000
 58C  C7   C5   C6   121.09  3.000
 58C  H3   C6   C8   120.96  3.000
 58C  H3   C6   C5   117.65  3.000
 58C  C8   C6   C5   121.39  3.000
 58C  H4   C7   C5   121.50  3.000
 58C  H4   C7   C1   119.91  3.000
 58C  C5   C7   C1   118.59  3.000
 58C  N5   C20  C19  128.93  3.000
 58C  C19  C20  C18  121.12  3.000
 58C  N5   C20  C18  109.95  3.000
 58C  H5   C21  N5   125.20  3.000
 58C  H5   C21  N4   121.28  3.000
 58C  N5   C21  N4   113.52  3.000
 58C  C4   N2   C3   116.74  3.000
 58C  C10  O1   C8   120.35  3.000
 58C  C4   N1   C2   117.49  3.000
 58C  O1   C8   C6   126.34  3.000
 58C  C6   C8   C2   118.78  3.000
 58C  O1   C8   C2   114.87  3.000
 58C  H7   C9   H6   107.20  3.000
 58C  H7   C9   C11  109.73  3.000
 58C  H6   C9   C11  110.12  3.000
 58C  H7   C9   C10  110.00  3.000
 58C  H6   C9   C10  109.61  3.000
 58C  C11  C9   C10  110.13  3.000
 58C  H8   C10  C14  109.66  3.000
 58C  H8   C10  C9   108.01  3.000
 58C  C14  C10  C9   110.89  3.000
 58C  H8   C10  O1   109.40  3.000
 58C  C9   C10  O1   107.02  3.000
 58C  C14  C10  O1   111.74  3.000
 58C  H10  C11  H9   105.95  3.000
 58C  H10  C11  C12  108.44  3.000
 58C  H9   C11  C12  110.11  3.000
 58C  H10  C11  C9   109.65  3.000
 58C  H9   C11  C9   110.07  3.000
 58C  C12  C11  C9   112.39  3.000
 58C  H11  C12  O2   110.13  3.000
 58C  H11  C12  C13  108.64  3.000
 58C  O2   C12  C13  107.53  3.000
 58C  H11  C12  C11  108.43  3.000
 58C  C13  C12  C11  110.27  3.000
 58C  O2   C12  C11  111.81  3.000
 58C  H13  C13  H12  106.33  3.000
 58C  H13  C13  C14  109.59  3.000
 58C  H12  C13  C14  109.97  3.000
 58C  H13  C13  C12  108.20  3.000
 58C  H12  C13  C12  110.18  3.000
 58C  C14  C13  C12  112.36  3.000
 58C  H15  C14  H14  106.63  3.000
 58C  H15  C14  C13  110.40  3.000
 58C  H14  C14  C13  109.44  3.000
 58C  H15  C14  C10  109.02  3.000
 58C  H14  C14  C10  111.03  3.000
 58C  C13  C14  C10  110.26  3.000
 58C  H16  C15  C17  118.80  3.000
 58C  H16  C15  C16  118.79  3.000
 58C  C17  C15  C16  122.41  3.000
 58C  H17  N3   C16  115.14  3.000
 58C  H17  N3   C4   112.71  3.000
 58C  C16  N3   C4   131.87  3.000
 58C  C19  C16  N3   124.79  3.000
 58C  N3   C16  C15  115.13  3.000
 58C  C19  C16  C15  120.07  3.000
 58C  H18  C17  C18  122.23  3.000
 58C  H18  C17  C15  120.75  3.000
 58C  C18  C17  C15  117.02  3.000
 58C  N4   C18  C17  133.62  3.000
 58C  C17  C18  C20  121.55  3.000
 58C  N4   C18  C20  104.83  3.000
 58C  H19  C19  C16  121.76  3.000
 58C  H19  C19  C20  120.40  3.000
 58C  C16  C19  C20  117.83  3.000
 58C  H20  N4   C18  127.21  3.000
 58C  H20  N4   C21  125.85  3.000
 58C  C18  N4   C21  106.93  3.000
 58C  C21  N5   C20  104.76  3.000
 58C  H22  O2   C12  108.33  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
 58C  CONST_01  C4   N2   C3   C1     0.00   0.0  0
 58C  CONST_02  C4   N1   C2   C1     0.00   0.0  0
 58C  CONST_03  C6   C8   C2   C1     0.00   0.0  0
 58C  CONST_04  C6   C5   C7   C1     0.00   0.0  0
 58C  CONST_05  N2   C4   N1   C2     0.00   0.0  0
 58C  CONST_06  N2   C3   C1   C2     0.00   0.0  0
 58C  CONST_07  C5   C7   C1   C2     0.00   0.0  0
 58C  CONST_08  C5   C6   C8   C2     0.00   0.0  0
 58C  CONST_09  N1   C4   N2   C3     0.00   0.0  0
 58C  CONST_10  N1   C2   C1   C3     0.00   0.0  0
 58C  CONST_11  C8   C2   C1   C3   180.00   0.0  0
 58C  CONST_12  C5   C7   C1   C3   180.00   0.0  0
 58C  CONST_13  C8   C2   N1   C4   180.00   0.0  0
 58C  CONST_14  N1   C2   C8   C6   180.00   0.0  0
 58C  CONST_15  N2   C3   C1   C7   180.00   0.0  0
 58C  CONST_16  N1   C2   C1   C7   180.00   0.0  0
 58C  CONST_17  C8   C2   C1   C7     0.00   0.0  0
 58C  CONST_18  C8   C6   C5   C7     0.00   0.0  0
 58C  CONST_19  C21  N4   C18  C20    0.00   0.0  0
 58C  CONST_20  C15  C17  C18  C20    0.00   0.0  0
 58C  CONST_21  N4   C21  N5   C20    0.00   0.0  0
 58C  CONST_22  C15  C16  C19  C20    0.00   0.0  0
 58C  CONST_23  C17  C18  N4   C21  180.00   0.0  0
 58C  CONST_24  C18  C20  N5   C21    0.00   0.0  0
 58C  CONST_25  C19  C20  N5   C21  180.00   0.0  0
 58C  CONST_26  N4   C18  C17  C15  180.00   0.0  0
 58C  CONST_27  C18  C17  C15  C16    0.00   0.0  0
 58C  CONST_28  C18  C20  C19  C16    0.00   0.0  0
 58C  CONST_29  N5   C20  C19  C16  180.00   0.0  0
 58C  CONST_30  N5   C20  C18  C17  180.00   0.0  0
 58C  CONST_31  C19  C20  C18  C17    0.00   0.0  0
 58C  CONST_32  C19  C16  C15  C17    0.00   0.0  0
 58C  CONST_33  N5   C21  N4   C18    0.00   0.0  0
 58C  CONST_34  N4   C18  C20  C19  180.00   0.0  0
 58C  CONST_35  N5   C20  C18  N4     0.00   0.0  0
 58C  CONST_36  O1   C8   C2   C1   180.00   0.0  0
 58C  CONST_37  N3   C4   N1   C2   180.00   0.0  0
 58C  CONST_38  N3   C4   N2   C3   180.00   0.0  0
 58C  CONST_39  O1   C8   C6   C5   180.00   0.0  0
 58C  CONST_40  N3   C16  C19  C20  180.00   0.0  0
 58C  CONST_41  N1   C2   C8   O1     0.00   0.0  0
 58C  CONST_42  C17  C15  C16  N3   180.00   0.0  0
 58C  CONST_43  H2   C5   C7   C1   180.00   0.0  0
 58C  CONST_44  H1   C3   C1   C2   180.00   0.0  0
 58C  CONST_45  H4   C7   C1   C2   180.00   0.0  0
 58C  CONST_46  H3   C6   C8   C2   180.00   0.0  0
 58C  CONST_47  H20  N4   C18  C20  180.00   0.0  0
 58C  CONST_48  H18  C17  C18  C20  180.00   0.0  0
 58C  CONST_49  H5   C21  N5   C20  180.00   0.0  0
 58C  CONST_50  H19  C19  C16  C15  180.00   0.0  0
 58C  CONST_51  H16  C15  C17  C18  180.00   0.0  0
 58C  Var_01    C12  C13  C14  C10  -55.95  30.0  1
 58C  Var_02    C12  C11  C9   C10   56.30  30.0  1
 58C  Var_03    C15  C16  N3   C4   163.74  30.0  1
 58C  Var_04    C16  N3   C4   N2     3.04  30.0  1

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
 58C  chir_01  C10  O1  C14  C9   negativ
 58C  chir_02  C12  O2  C13  C11  positiv

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
 58C  plan-1  C20  0.020
 58C  plan-1  C21  0.020
 58C  plan-1  C15  0.020
 58C  plan-1  N3   0.020
 58C  plan-1  C16  0.020
 58C  plan-1  C17  0.020
 58C  plan-1  C18  0.020
 58C  plan-1  C19  0.020
 58C  plan-1  N4   0.020
 58C  plan-1  N5   0.020
 58C  plan-1  H16  0.020
 58C  plan-1  H18  0.020
 58C  plan-1  H19  0.020
 58C  plan-1  H20  0.020
 58C  plan-1  H5   0.020
 58C  plan-2  C1   0.020
 58C  plan-2  C2   0.020
 58C  plan-2  C3   0.020
 58C  plan-2  C4   0.020
 58C  plan-2  C5   0.020
 58C  plan-2  C6   0.020
 58C  plan-2  C7   0.020
 58C  plan-2  N2   0.020
 58C  plan-2  O1   0.020
 58C  plan-2  N1   0.020
 58C  plan-2  C8   0.020
 58C  plan-2  N3   0.020
 58C  plan-2  H1   0.020
 58C  plan-2  H2   0.020
 58C  plan-2  H3   0.020
 58C  plan-2  H4   0.020

