# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Apr 14 23:23:37 2020
#   Inital geometry file: a 147 line input string
#   Ligand name: N-[2-({2-[(2-hydroxyethyl)amino]ethyl}amino)quinolin-5-yl]-2-[(3s,5s,7s)-tricyclo[3.3.1.1~3,7~]decan-1-yl]acetamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OCCNCCNc1ccc2c(NC(=O)CC34CC5CC(CC(C5)C3)C4)cccc2n1
#
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
 7RY  7RY  N-[2-({2-[(2-hydroxyethyl)amino]ethyl}amino)quinolin-5-yl]-2-[(3s,5s,7s)-tricyclo[3.3.1.1~3,7~]decan-1-yl]acetamide  ligand  65  31  .  2021-08-05  2021-08-05  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_7RY
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
 7RY  C10  C  CH2   0  -0.278   5.4707   0.3073   0.0023
 7RY  N12  N  NH1   0  -0.602   7.6190   1.4491   0.1041
 7RY  C13  C  CH2   0  -0.290   9.0450   1.3760   0.3582
 7RY  C17  C  CR16  0  -0.310  -0.8627  -3.4614  -0.6866
 7RY  C21  C  CH2   0  -0.592  -3.4526   0.1531  -1.1666
 7RY  C22  C  CR6   0  -0.083  -4.6850   0.6740  -0.4260
 7RY  C24  C  CH1   0  -0.247  -5.5882   1.6978   1.6898
 7RY  C26  C  CR16  0  -0.246  -6.4245   2.5114  -0.5155
 7RY  C28  C  C     0  -0.417  -7.5415   1.4670  -0.4845
 7RY  C01  C  CR16  0  -0.262   0.0998  -4.4353  -0.3718
 7RY  C02  C  CR16  0  -0.320   1.4067  -4.0984  -0.1395
 7RY  C03  C  CR66  0   0.203   1.8104  -2.7461  -0.1974
 7RY  C04  C  CR66  0  -0.004   0.8371  -1.7536  -0.4781
 7RY  C05  C  CR16  0  -0.173   1.2855  -0.4094  -0.4642
 7RY  C06  C  CR16  0  -0.384   2.5922  -0.1204  -0.2289
 7RY  C07  C  CR6   0   0.480   3.5024  -1.1964   0.0049
 7RY  N08  N  N     0  -0.512   3.1079  -2.4517   0.0276
 7RY  N09  N  NH1   0  -0.665   4.8131  -0.9571   0.2396
 7RY  C11  C  CH2   0  -0.289   6.9437   0.1960   0.3598
 7RY  C14  C  CH2   0  -0.170   9.7288   2.6969   0.0878
 7RY  O15  O  OH1   0  -0.676   9.2474   3.6569   1.0060
 7RY  C16  C  CR6   0   0.319  -0.5039  -2.1353  -0.7428
 7RY  N18  N  NH1   0  -0.761  -1.4303  -1.1350  -1.0806
 7RY  C19  C  C     0   0.559  -2.6860  -1.0066  -0.5620
 7RY  O20  O  O     0  -0.460  -3.1196  -1.7721   0.2780
 7RY  C23  C  CH2   0  -0.406  -4.3499   1.1115   1.0081
 7RY  C25  C  CH2   0  -0.417  -6.0703   2.9247   0.9142
 7RY  C27  C  C     0  -0.401  -5.1892   1.9136  -1.1898
 7RY  C29  C  CR16  0  -0.249  -7.0607   0.2380   0.2882
 7RY  C30  C  CH2   0  -0.417  -6.6978   0.6441   1.7194
 7RY  C31  C  C     0  -0.405  -5.8264  -0.3544  -0.3941
 7RY  H1   H  HCH2  0   0.231   5.3773   0.6215  -1.0433
 7RY  H2   H  HCH2  0   0.235   5.0116   1.0879   0.6162
 7RY  H3   H  HNH1  0   0.342   7.2192   2.1662   0.6978
 7RY  H5   H  HCH2  0   0.197   9.2799   1.0431   1.3822
 7RY  H6   H  HCH2  0   0.227   9.4812   0.6306  -0.3128
 7RY  H7   H  HCR6  0   0.263  -1.8754  -3.7659  -0.9064
 7RY  H8   H  HCH2  0   0.281  -3.7498  -0.1602  -2.1754
 7RY  H9   H  HCH2  0   0.259  -2.7549   0.9850  -1.3150
 7RY  H10  H  HCH1  0   0.220  -5.3295   1.9886   2.7125
 7RY  H11  H  HCR6  0   0.220  -6.7540   3.3882  -1.0820
 7RY  H12  H  H     0   0.219  -8.4379   1.8832  -0.0134
 7RY  H13  H  H     0   0.219  -7.8228   1.1837  -1.5040
 7RY  H14  H  HCR6  0   0.260  -0.2022  -5.4740  -0.3309
 7RY  H15  H  HCR6  0   0.252   2.1489  -4.8535   0.0857
 7RY  H16  H  HCR6  0   0.257   0.5903   0.4042  -0.6255
 7RY  H17  H  HCR6  0   0.279   2.9268   0.9072  -0.2102
 7RY  H18  H  HNH1  0   0.382   5.3938  -1.7815   0.2618
 7RY  H19  H  HCH2  0   0.206   7.0402  -0.1446   1.4029
 7RY  H20  H  HCH2  0   0.229   7.4052  -0.5779  -0.2622
 7RY  H21  H  HCH2  0   0.200  10.8128   2.5565   0.1831
 7RY  H22  H  HCH2  0   0.197   9.5290   2.9964  -0.9484
 7RY  H23  H  HOH1  0   0.456   9.5939   4.5173   0.7546
 7RY  H24  H  HNH1  0   0.411  -1.1257  -0.4298  -1.7338
 7RY  H25  H  HCH2  0   0.231  -3.9809   0.2633   1.5886
 7RY  H26  H  HCH2  0   0.215  -3.5452   1.8563   0.9869
 7RY  H27  H  HCH2  0   0.219  -6.9420   3.3671   1.4076
 7RY  H28  H  HCH2  0   0.219  -5.2908   3.6937   0.9021
 7RY  H29  H  H     0   0.220  -4.3923   2.6652  -1.2400
 7RY  H30  H  H     0   0.220  -5.4225   1.6390  -2.2250
 7RY  H31  H  HCR6  0   0.220  -7.8535  -0.5160   0.3116
 7RY  H32  H  HCH2  0   0.219  -6.3662  -0.2332   2.2848
 7RY  H33  H  HCH2  0   0.219  -7.5798   1.0380   2.2360
 7RY  H34  H  H     0   0.212  -6.0737  -0.6577  -1.4182
 7RY  H35  H  H     0   0.237  -5.5122  -1.2542   0.1355

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
 7RY  O15  C14  single    1.413  0.020  1.413
 7RY  C14  C13  single    1.512  0.020  1.512
 7RY  C13  N12  single    1.450  0.020  1.450
 7RY  N12  C11  single    1.446  0.020  1.446
 7RY  C11  C10  single    1.520  0.020  1.520
 7RY  C10  N09  single    1.445  0.020  1.445
 7RY  N09  C07  single    1.353  0.020  1.353
 7RY  C07  C06  aromatic  1.429  0.020  1.429
 7RY  C07  N08  aromatic  1.316  0.020  1.316
 7RY  C06  C05  aromatic  1.359  0.020  1.359
 7RY  N08  C03  aromatic  1.349  0.020  1.349
 7RY  C05  C04  aromatic  1.417  0.020  1.417
 7RY  C03  C04  aromatic  1.418  0.020  1.418
 7RY  C03  C02  aromatic  1.413  0.020  1.413
 7RY  C04  C16  aromatic  1.419  0.020  1.419
 7RY  C02  C01  aromatic  1.370  0.020  1.370
 7RY  C16  N18  single    1.405  0.020  1.405
 7RY  C16  C17  aromatic  1.375  0.020  1.375
 7RY  N18  C19  single    1.365  0.020  1.365
 7RY  C01  C17  aromatic  1.405  0.020  1.405
 7RY  C19  C21  single    1.516  0.020  1.516
 7RY  C19  O20  double    1.216  0.020  1.216
 7RY  C21  C22  single    1.529  0.020  1.529
 7RY  C22  C27  single    1.541  0.020  1.541
 7RY  C22  C23  single    1.536  0.020  1.536
 7RY  C22  C31  single    1.537  0.020  1.537
 7RY  C27  C26  single    1.529  0.020  1.529
 7RY  C23  C24  single    1.530  0.020  1.530
 7RY  C26  C25  single    1.530  0.020  1.530
 7RY  C26  C28  single    1.530  0.020  1.530
 7RY  C31  C29  single    1.530  0.020  1.530
 7RY  C24  C25  single    1.530  0.020  1.530
 7RY  C24  C30  single    1.531  0.020  1.531
 7RY  C28  C29  single    1.529  0.020  1.529
 7RY  C29  C30  single    1.531  0.020  1.531
 7RY  C10  H1   single    0.970  0.020  1.090
 7RY  C10  H2   single    0.970  0.020  1.090
 7RY  N12  H3   single    0.890  0.020  1.040
 7RY  C13  H5   single    0.970  0.020  1.090
 7RY  C13  H6   single    0.970  0.020  1.090
 7RY  C17  H7   single    0.930  0.020  1.080
 7RY  C21  H8   single    0.970  0.020  1.090
 7RY  C21  H9   single    0.970  0.020  1.090
 7RY  C24  H10  single    0.970  0.020  1.090
 7RY  C26  H11  single    0.970  0.020  1.090
 7RY  C28  H12  single    0.970  0.020  1.090
 7RY  C28  H13  single    0.970  0.020  1.090
 7RY  C01  H14  single    0.930  0.020  1.080
 7RY  C02  H15  single    0.930  0.020  1.080
 7RY  C05  H16  single    0.930  0.020  1.080
 7RY  C06  H17  single    0.930  0.020  1.080
 7RY  N09  H18  single    0.890  0.020  1.040
 7RY  C11  H19  single    0.970  0.020  1.090
 7RY  C11  H20  single    0.970  0.020  1.090
 7RY  C14  H21  single    0.970  0.020  1.090
 7RY  C14  H22  single    0.970  0.020  1.090
 7RY  O15  H23  single    0.850  0.020  0.980
 7RY  N18  H24  single    0.860  0.020  1.020
 7RY  C23  H25  single    0.970  0.020  1.090
 7RY  C23  H26  single    0.970  0.020  1.090
 7RY  C25  H27  single    0.970  0.020  1.090
 7RY  C25  H28  single    0.970  0.020  1.090
 7RY  C27  H29  single    0.970  0.020  1.090
 7RY  C27  H30  single    0.970  0.020  1.090
 7RY  C29  H31  single    0.970  0.020  1.090
 7RY  C30  H32  single    0.970  0.020  1.090
 7RY  C30  H33  single    0.970  0.020  1.090
 7RY  C31  H34  single    0.970  0.020  1.090
 7RY  C31  H35  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
 7RY  H2   C10  H1   107.16  3.000
 7RY  H2   C10  C11  109.08  3.000
 7RY  H1   C10  C11  109.15  3.000
 7RY  H2   C10  N09  109.95  3.000
 7RY  H1   C10  N09  111.64  3.000
 7RY  C11  C10  N09  109.78  3.000
 7RY  H3   N12  C11  108.98  3.000
 7RY  H3   N12  C13  108.73  3.000
 7RY  C11  N12  C13  112.61  3.000
 7RY  H6   C13  H5   106.22  3.000
 7RY  H6   C13  C14  107.78  3.000
 7RY  H5   C13  C14  109.49  3.000
 7RY  H6   C13  N12  108.60  3.000
 7RY  H5   C13  N12  112.80  3.000
 7RY  C14  C13  N12  111.68  3.000
 7RY  H7   C17  C16  120.55  3.000
 7RY  H7   C17  C01  119.51  3.000
 7RY  C16  C17  C01  119.93  3.000
 7RY  H9   C21  H8   105.34  3.000
 7RY  H9   C21  C19  108.23  3.000
 7RY  H8   C21  C19  106.58  3.000
 7RY  H9   C21  C22  108.67  3.000
 7RY  H8   C21  C22  108.91  3.000
 7RY  C19  C21  C22  118.36  3.000
 7RY  C31  C22  C27  107.79  3.000
 7RY  C31  C22  C23  109.47  3.000
 7RY  C27  C22  C23  107.76  3.000
 7RY  C31  C22  C21  112.37  3.000
 7RY  C23  C22  C21  111.92  3.000
 7RY  C27  C22  C21  107.32  3.000
 7RY  H10  C24  C30  109.65  3.000
 7RY  H10  C24  C25  109.59  3.000
 7RY  C30  C24  C25  109.49  3.000
 7RY  H10  C24  C23  109.08  3.000
 7RY  C30  C24  C23  109.36  3.000
 7RY  C25  C24  C23  109.66  3.000
 7RY  H11  C26  C27  109.15  3.000
 7RY  H11  C26  C25  109.69  3.000
 7RY  C27  C26  C25  109.31  3.000
 7RY  H11  C26  C28  109.73  3.000
 7RY  C25  C26  C28  109.55  3.000
 7RY  C27  C26  C28  109.38  3.000
 7RY  H13  C28  H12  106.78  3.000
 7RY  H13  C28  C29  110.08  3.000
 7RY  H12  C28  C29  110.22  3.000
 7RY  H13  C28  C26  110.21  3.000
 7RY  H12  C28  C26  110.31  3.000
 7RY  C29  C28  C26  109.23  3.000
 7RY  H14  C01  C02  119.72  3.000
 7RY  H14  C01  C17  118.85  3.000
 7RY  C02  C01  C17  121.42  3.000
 7RY  H15  C02  C03  118.72  3.000
 7RY  H15  C02  C01  121.20  3.000
 7RY  C03  C02  C01  120.08  3.000
 7RY  N08  C03  C04  122.70  3.000
 7RY  C04  C03  C02  118.82  3.000
 7RY  N08  C03  C02  118.48  3.000
 7RY  C16  C04  C05  123.78  3.000
 7RY  C16  C04  C03  119.82  3.000
 7RY  C05  C04  C03  116.40  3.000
 7RY  H16  C05  C06  118.92  3.000
 7RY  H16  C05  C04  120.55  3.000
 7RY  C06  C05  C04  120.52  3.000
 7RY  H17  C06  C07  121.06  3.000
 7RY  H17  C06  C05  120.20  3.000
 7RY  C07  C06  C05  118.74  3.000
 7RY  N09  C07  N08  117.14  3.000
 7RY  N08  C07  C06  122.02  3.000
 7RY  N09  C07  C06  120.82  3.000
 7RY  C07  N08  C03  119.57  3.000
 7RY  H18  N09  C07  114.65  3.000
 7RY  H18  N09  C10  117.18  3.000
 7RY  C07  N09  C10  124.56  3.000
 7RY  H20  C11  H19  106.41  3.000
 7RY  H20  C11  N12  108.37  3.000
 7RY  H19  C11  N12  113.23  3.000
 7RY  H20  C11  C10  109.06  3.000
 7RY  H19  C11  C10  109.29  3.000
 7RY  N12  C11  C10  110.33  3.000
 7RY  H22  C14  H21  107.27  3.000
 7RY  H22  C14  O15  111.48  3.000
 7RY  H21  C14  O15  111.53  3.000
 7RY  H22  C14  C13  108.98  3.000
 7RY  H21  C14  C13  108.64  3.000
 7RY  O15  C14  C13  108.86  3.000
 7RY  H23  O15  C14  108.39  3.000
 7RY  N18  C16  C04  118.46  3.000
 7RY  N18  C16  C17  121.64  3.000
 7RY  C04  C16  C17  119.90  3.000
 7RY  H24  N18  C19  117.28  3.000
 7RY  H24  N18  C16  117.04  3.000
 7RY  C19  N18  C16  125.63  3.000
 7RY  O20  C19  N18  122.09  3.000
 7RY  O20  C19  C21  125.21  3.000
 7RY  N18  C19  C21  112.69  3.000
 7RY  H26  C23  H25  106.85  3.000
 7RY  H26  C23  C24  110.01  3.000
 7RY  H25  C23  C24  109.52  3.000
 7RY  H26  C23  C22  109.60  3.000
 7RY  H25  C23  C22  110.41  3.000
 7RY  C24  C23  C22  110.39  3.000
 7RY  H28  C25  H27  106.73  3.000
 7RY  H28  C25  C26  110.14  3.000
 7RY  H27  C25  C26  110.24  3.000
 7RY  H28  C25  C24  110.15  3.000
 7RY  H27  C25  C24  110.27  3.000
 7RY  C26  C25  C24  109.28  3.000
 7RY  H30  C27  H29  106.44  3.000
 7RY  H30  C27  C26  110.03  3.000
 7RY  H29  C27  C26  109.83  3.000
 7RY  H30  C27  C22  109.65  3.000
 7RY  H29  C27  C22  109.65  3.000
 7RY  C26  C27  C22  111.12  3.000
 7RY  H31  C29  C31  109.10  3.000
 7RY  H31  C29  C30  109.53  3.000
 7RY  C31  C29  C30  109.17  3.000
 7RY  H31  C29  C28  109.68  3.000
 7RY  C30  C29  C28  109.49  3.000
 7RY  C31  C29  C28  109.85  3.000
 7RY  H33  C30  H32  106.76  3.000
 7RY  H33  C30  C29  110.20  3.000
 7RY  H32  C30  C29  109.99  3.000
 7RY  H33  C30  C24  110.20  3.000
 7RY  H32  C30  C24  110.00  3.000
 7RY  C29  C30  C24  109.65  3.000
 7RY  H35  C31  H34  106.88  3.000
 7RY  H35  C31  C29  109.60  3.000
 7RY  H34  C31  C29  109.99  3.000
 7RY  H35  C31  C22  110.38  3.000
 7RY  H34  C31  C22  109.47  3.000
 7RY  C29  C31  C22  110.45  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
 7RY  CONST_01  C05  C04  C16  C17   180.00   0.0  0
 7RY  CONST_02  C03  C04  C16  C17     0.00   0.0  0
 7RY  CONST_03  C03  C02  C01  C17     0.00   0.0  0
 7RY  CONST_04  N08  C03  C02  C01   180.00   0.0  0
 7RY  CONST_05  C04  C03  C02  C01     0.00   0.0  0
 7RY  CONST_06  C04  C16  C17  C01     0.00   0.0  0
 7RY  CONST_07  C07  N08  C03  C02   180.00   0.0  0
 7RY  CONST_08  C05  C04  C03  C02   180.00   0.0  0
 7RY  CONST_09  C16  C04  C03  C02     0.00   0.0  0
 7RY  CONST_10  C16  C17  C01  C02     0.00   0.0  0
 7RY  CONST_11  C06  C07  N08  C03     0.00   0.0  0
 7RY  CONST_12  C06  C05  C04  C03     0.00   0.0  0
 7RY  CONST_13  C07  C06  C05  C04     0.00   0.0  0
 7RY  CONST_14  C07  N08  C03  C04     0.00   0.0  0
 7RY  CONST_15  N08  C07  C06  C05     0.00   0.0  0
 7RY  CONST_16  N08  C03  C04  C05     0.00   0.0  0
 7RY  CONST_17  C16  C04  C05  C06   180.00   0.0  0
 7RY  CONST_18  C16  C04  C03  N08   180.00   0.0  0
 7RY  CONST_19  N18  C16  C17  C01   180.00   0.0  0
 7RY  CONST_20  N09  C07  N08  C03   180.00   0.0  0
 7RY  CONST_21  N18  C16  C04  C03   180.00   0.0  0
 7RY  CONST_22  N09  C07  C06  C05   180.00   0.0  0
 7RY  CONST_23  N18  C16  C04  C05     0.00   0.0  0
 7RY  CONST_24  H15  C02  C01  C17   180.00   0.0  0
 7RY  CONST_25  H7   C17  C01  C02   180.00   0.0  0
 7RY  CONST_26  H16  C05  C04  C03   180.00   0.0  0
 7RY  CONST_27  H14  C01  C02  C03   180.00   0.0  0
 7RY  CONST_28  H17  C06  C05  C04   180.00   0.0  0
 7RY  CONST_29  C06  C07  N09  C10     0.00   0.0  0
 7RY  CONST_30  N08  C07  N09  C10   180.00   0.0  0
 7RY  CONST_34  H18  N09  C07  C06   180.00   0.0  0
 7RY  CONST_35  C16  N18  C19  C21   180.00   0.0  0
 7RY  CONST_36  O20  C19  N18  C16     0.00   0.0  0
 7RY  Var_01    N18  C19  C21  C22  -162.52  30.0  1
 7RY  Var_02    C11  C10  N09  C07  -179.09  30.0  1
 7RY  Var_03    C13  N12  C11  C10  -176.77  30.0  2
 7RY  Var_04    O15  C14  C13  N12    64.77  30.0  2
 7RY  Var_05    N09  C10  C11  N12   178.98  30.0  3
 7RY  Var_06    C14  C13  N12  C11  -179.86  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
 7RY  chir_01  C22  C27  C23  C31  negativ
 7RY  chir_02  C24  C23  C25  C30  negativ
 7RY  chir_03  C26  C27  C25  C28  positiv
 7RY  chir_04  C29  C31  C28  C30  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
 7RY  plan-1  C17  0.020
 7RY  plan-1  C01  0.020
 7RY  plan-1  C02  0.020
 7RY  plan-1  C03  0.020
 7RY  plan-1  C04  0.020
 7RY  plan-1  C05  0.020
 7RY  plan-1  C06  0.020
 7RY  plan-1  C07  0.020
 7RY  plan-1  N08  0.020
 7RY  plan-1  N09  0.020
 7RY  plan-1  C16  0.020
 7RY  plan-1  N18  0.020
 7RY  plan-1  H7   0.020
 7RY  plan-1  H14  0.020
 7RY  plan-1  H15  0.020
 7RY  plan-1  H16  0.020
 7RY  plan-1  H17  0.020
 7RY  plan-2  C21  0.020
 7RY  plan-2  C16  0.020
 7RY  plan-2  N18  0.020
 7RY  plan-2  C19  0.020
 7RY  plan-2  O20  0.020
 7RY  plan-2  H24  0.020
 7RY  plan-3  C10  0.020
 7RY  plan-3  C07  0.020
 7RY  plan-3  N09  0.020
 7RY  plan-3  H18  0.020

