# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Apr 24 09:37:35 2020
#   Inital geometry file: a 142 line input string
#   Ligand name: (3S,4R,4aS,5S,8aR)-4-amino-5-fluoro-3-[(2R,3aR,5R,7aR)-5-(4-methylpiperazin-1-yl)octahydro-1H-benzimidazol-2-yl]octahydroquinolin-2(1H)-one
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CN1CCN(CC1)[C@@H]2CC[C@H]3N[C@H](N[C@@H]3C2)[C@@H]4[C@@H](N)[C@@H]5[C@@H](F)CCC[C@H]5NC4=O
#
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
 DOV  DOV  (3S,4R,4aS,5S,8aR)-4-amino-5-fluoro-3-[(2R,3aR,5R,7aR)-5-(4-methylpiperazin-1-yl)octahydro-1H-benzimidazol-2-yl]octahydroquinolin-2(1H)-one  ligand  66  29  .  2022-07-24  2022-07-26
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_DOV
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
 DOV  F27   F  F     0  -0.378   5.5323  -2.3663  -0.9638
 DOV  C4    C  CH1   0   0.258   5.8591  -1.2310  -0.2179
 DOV  C5    C  CH2   0  -0.494   7.1249  -0.6650  -0.8403
 DOV  C6    C  CH2   0  -0.461   7.5485   0.6546  -0.2107
 DOV  C1    C  CH2   0  -0.450   6.4072   1.6584  -0.2655
 DOV  C2    C  CH1   0  -0.006   5.1843   1.0654   0.4164
 DOV  N7    N  NH1   0  -0.650   4.1046   2.0291   0.4554
 DOV  C8    C  C     0   0.566   2.7802   1.7849   0.4705
 DOV  O28   O  O     0  -0.488   1.9953   2.6722   0.7783
 DOV  C9    C  CH1   0  -0.428   2.3239   0.3787   0.0791
 DOV  C10   C  CH1   0  -0.051   3.4116  -0.6616   0.4681
 DOV  N29   N  NH2   0  -0.791   3.1017  -2.0498   0.2056
 DOV  C3    C  CH1   0  -0.353   4.7086  -0.2282  -0.2388
 DOV  C11   C  CH1   0   0.083   0.9103   0.1645   0.6433
 DOV  N15   N  NH1   0  -0.624   0.4058  -1.2047   0.5147
 DOV  C14   C  CH1   0  -0.066  -1.0361  -1.0086   0.5806
 DOV  C19   C  CH2   0  -0.448  -1.9572  -2.1416   0.1951
 DOV  C18   C  CH2   0  -0.459  -3.3951  -1.6165   0.3108
 DOV  C17   C  CH1   0  -0.046  -3.6366  -0.3302  -0.5053
 DOV  C16   C  CH2   0  -0.460  -2.6268   0.7736  -0.1505
 DOV  C13   C  CH1   0  -0.049  -1.2402   0.1927  -0.3236
 DOV  N12   N  NH1   0  -0.619  -0.0851   1.0349  -0.0382
 DOV  N20   N  NT    0  -0.432  -4.9998   0.1763  -0.4693
 DOV  C25   C  CH2   0  -0.318  -5.9498  -0.6302  -1.2127
 DOV  C24   C  CH2   0  -0.337  -7.2601   0.1345  -1.3661
 DOV  N23   N  NT    0  -0.410  -7.8373   0.5572  -0.1011
 DOV  C26   C  CH3   0  -0.562  -8.4865  -0.5167   0.6233
 DOV  C22   C  CH2   0  -0.335  -6.8398   1.2685   0.6807
 DOV  C21   C  CH2   0  -0.317  -5.5263   0.5083   0.8427
 DOV  H4    H  HCH1  0   0.196   6.0495  -1.5601   0.8094
 DOV  H51C  H  HCH2  0   0.250   7.9259  -1.4031  -0.7589
 DOV  H52C  H  HCH2  0   0.229   6.9401  -0.5084  -1.9082
 DOV  H3    H  HCH1  0   0.243   4.4808  -0.0171  -1.2935
 DOV  H61C  H  HCH2  0   0.227   7.8487   0.4958   0.8298
 DOV  H62C  H  HCH2  0   0.249   8.4257   1.0438  -0.7291
 DOV  H11C  H  HCH2  0   0.246   6.6911   2.5884   0.2340
 DOV  H12C  H  HCH2  0   0.231   6.1654   1.9086  -1.3029
 DOV  H2    H  HCH1  0   0.234   5.4740   0.8255   1.4505
 DOV  H7    H  HNH1  0   0.385   4.3616   2.9532   0.7754
 DOV  H9    H  HCH1  0   0.268   2.2339   0.3673  -1.0165
 DOV  H10   H  HCH1  0   0.225   3.5790  -0.5848   1.5507
 DOV  H11   H  HCH1  0   0.224   0.9294   0.3906   1.7163
 DOV  H291  H  HNH2  0   0.354   2.2279  -2.2804   0.6616
 DOV  H292  H  HNH2  0   0.332   2.9602  -2.2019  -0.7861
 DOV  H15   H  HNH1  0   0.337   0.6219  -1.5513  -0.4174
 DOV  H12   H  HNH1  0   0.343  -0.3333   1.8080   0.5632
 DOV  H14   H  HCH1  0   0.222  -1.2755  -0.7097   1.6119
 DOV  H191  H  HCH2  0   0.217  -1.7522  -2.4632  -0.8324
 DOV  H192  H  HCH2  0   0.235  -1.8209  -3.0118   0.8408
 DOV  H13   H  HCH1  0   0.196  -1.1634  -0.1663  -1.3625
 DOV  H181  H  HCH2  0   0.236  -4.0939  -2.3922  -0.0116
 DOV  H182  H  HCH2  0   0.220  -3.6105  -1.4237   1.3671
 DOV  H17   H  HCH1  0   0.216  -3.4501  -0.5847  -1.5568
 DOV  H161  H  HCH2  0   0.232  -2.7937   1.6351  -0.8018
 DOV  H162  H  HCH2  0   0.217  -2.7547   1.1124   0.8832
 DOV  H251  H  HCH2  0   0.240  -5.5398  -0.8407  -2.2044
 DOV  H252  H  HCH2  0   0.210  -6.1424  -1.6067  -0.7380
 DOV  H211  H  HCH2  0   0.213  -5.6848  -0.3797   1.4764
 DOV  H212  H  HCH2  0   0.238  -4.8197   1.1470   1.3766
 DOV  H241  H  HCH2  0   0.234  -7.0710   1.0255  -1.9744
 DOV  H242  H  HCH2  0   0.247  -7.9874  -0.4759  -1.9069
 DOV  H261  H  HCH3  0   0.218  -7.8342  -1.3459   0.9288
 DOV  H262  H  HCH3  0   0.236  -8.9519  -0.1185   1.5270
 DOV  H263  H  HCH3  0   0.243  -9.2808  -0.9412   0.0068
 DOV  H221  H  HCH2  0   0.237  -6.6255   2.2198   0.1821
 DOV  H222  H  HCH2  0   0.245  -7.2560   1.5046   1.6628

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
 DOV  F27  C4    single  1.397  0.020  1.397
 DOV  C4   C5    single  1.520  0.020  1.520
 DOV  C4   C3    single  1.526  0.020  1.526
 DOV  C5   C6    single  1.522  0.020  1.522
 DOV  C6   C1    single  1.521  0.020  1.521
 DOV  C1   C2    single  1.521  0.020  1.521
 DOV  C2   N7    single  1.448  0.020  1.448
 DOV  C2   C3    single  1.526  0.020  1.526
 DOV  N7   C8    single  1.347  0.020  1.347
 DOV  C8   O28   double  1.224  0.020  1.224
 DOV  C8   C9    single  1.529  0.020  1.529
 DOV  C9   C10   single  1.554  0.020  1.554
 DOV  C9   C11   single  1.537  0.020  1.537
 DOV  C10  N29   single  1.446  0.020  1.446
 DOV  C10  C3    single  1.539  0.020  1.539
 DOV  C11  N15   single  1.465  0.020  1.465
 DOV  C11  N12   single  1.488  0.020  1.488
 DOV  N15  C14   single  1.457  0.020  1.457
 DOV  C14  C19   single  1.510  0.020  1.510
 DOV  C14  C13   single  1.517  0.020  1.517
 DOV  C19  C18   single  1.535  0.020  1.535
 DOV  C18  C17   single  1.542  0.020  1.542
 DOV  C17  C16   single  1.538  0.020  1.538
 DOV  C17  N20   single  1.455  0.020  1.455
 DOV  C16  C13   single  1.513  0.020  1.513
 DOV  C13  N12   single  1.458  0.020  1.458
 DOV  N20  C25   single  1.451  0.020  1.451
 DOV  N20  C21   single  1.452  0.020  1.452
 DOV  C25  C24   single  1.525  0.020  1.525
 DOV  C24  N23   single  1.453  0.020  1.453
 DOV  N23  C26   single  1.449  0.020  1.449
 DOV  N23  C22   single  1.453  0.020  1.453
 DOV  C22  C21   single  1.526  0.020  1.526
 DOV  C4   H4    single  0.970  0.020  1.090
 DOV  C5   H51C  single  0.970  0.020  1.090
 DOV  C5   H52C  single  0.970  0.020  1.090
 DOV  C3   H3    single  0.970  0.020  1.090
 DOV  C6   H61C  single  0.970  0.020  1.090
 DOV  C6   H62C  single  0.970  0.020  1.090
 DOV  C1   H11C  single  0.970  0.020  1.090
 DOV  C1   H12C  single  0.970  0.020  1.090
 DOV  C2   H2    single  0.970  0.020  1.090
 DOV  N7   H7    single  0.890  0.020  1.040
 DOV  C9   H9    single  0.970  0.020  1.090
 DOV  C10  H10   single  0.970  0.020  1.090
 DOV  C11  H11   single  0.970  0.020  1.090
 DOV  N29  H291  single  0.890  0.020  1.040
 DOV  N29  H292  single  0.890  0.020  1.040
 DOV  N15  H15   single  0.890  0.020  1.040
 DOV  N12  H12   single  0.890  0.020  1.040
 DOV  C14  H14   single  0.970  0.020  1.090
 DOV  C19  H191  single  0.970  0.020  1.090
 DOV  C19  H192  single  0.970  0.020  1.090
 DOV  C13  H13   single  0.970  0.020  1.090
 DOV  C18  H181  single  0.970  0.020  1.090
 DOV  C18  H182  single  0.970  0.020  1.090
 DOV  C17  H17   single  0.970  0.020  1.090
 DOV  C16  H161  single  0.970  0.020  1.090
 DOV  C16  H162  single  0.970  0.020  1.090
 DOV  C25  H251  single  0.970  0.020  1.090
 DOV  C25  H252  single  0.970  0.020  1.090
 DOV  C21  H211  single  0.970  0.020  1.090
 DOV  C21  H212  single  0.970  0.020  1.090
 DOV  C24  H241  single  0.970  0.020  1.090
 DOV  C24  H242  single  0.970  0.020  1.090
 DOV  C26  H261  single  0.970  0.020  1.090
 DOV  C26  H262  single  0.970  0.020  1.090
 DOV  C26  H263  single  0.970  0.020  1.090
 DOV  C22  H221  single  0.970  0.020  1.090
 DOV  C22  H222  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
 DOV  H4    C4   C3    109.96  3.000
 DOV  H4    C4   C5    110.56  3.000
 DOV  C3    C4   C5    112.18  3.000
 DOV  H4    C4   F27   107.29  3.000
 DOV  C3    C4   F27   110.50  3.000
 DOV  C5    C4   F27   106.18  3.000
 DOV  H52C  C5   H51C  107.05  3.000
 DOV  H52C  C5   C6    109.05  3.000
 DOV  H51C  C5   C6    110.54  3.000
 DOV  H52C  C5   C4    108.18  3.000
 DOV  H51C  C5   C4    109.18  3.000
 DOV  C6    C5   C4    112.65  3.000
 DOV  H62C  C6   H61C  106.44  3.000
 DOV  H62C  C6   C1    110.54  3.000
 DOV  H61C  C6   C1    109.62  3.000
 DOV  H62C  C6   C5    109.67  3.000
 DOV  H61C  C6   C5    110.10  3.000
 DOV  C1    C6   C5    110.39  3.000
 DOV  H12C  C1   H11C  107.22  3.000
 DOV  H12C  C1   C2    109.67  3.000
 DOV  H11C  C1   C2    109.62  3.000
 DOV  H12C  C1   C6    110.54  3.000
 DOV  H11C  C1   C6    110.50  3.000
 DOV  C2    C1   C6    109.27  3.000
 DOV  H2    C2   C3    107.50  3.000
 DOV  H2    C2   N7    108.43  3.000
 DOV  C3    C2   N7    110.08  3.000
 DOV  H2    C2   C1    107.14  3.000
 DOV  C3    C2   C1    112.87  3.000
 DOV  N7    C2   C1    110.62  3.000
 DOV  H7    N7   C8    114.34  3.000
 DOV  H7    N7   C2    115.30  3.000
 DOV  C8    N7   C2    127.80  3.000
 DOV  C9    C8   O28   122.66  3.000
 DOV  C9    C8   N7    117.21  3.000
 DOV  O28   C8   N7    120.13  3.000
 DOV  H9    C9   C11   106.80  3.000
 DOV  H9    C9   C10   107.45  3.000
 DOV  C11   C9   C10   117.28  3.000
 DOV  H9    C9   C8    106.80  3.000
 DOV  C11   C9   C8    107.97  3.000
 DOV  C10   C9   C8    110.03  3.000
 DOV  H10   C10  C3    107.73  3.000
 DOV  H10   C10  N29   106.18  3.000
 DOV  C3    C10  N29   111.55  3.000
 DOV  H10   C10  C9    107.85  3.000
 DOV  C3    C10  C9    106.63  3.000
 DOV  N29   C10  C9    116.55  3.000
 DOV  H292  N29  H291  106.63  3.000
 DOV  H292  N29  C10   110.59  3.000
 DOV  H291  N29  C10   108.78  3.000
 DOV  H3    C3   C10   108.66  3.000
 DOV  H3    C3   C2    108.28  3.000
 DOV  C10   C3   C2    107.70  3.000
 DOV  H3    C3   C4    107.19  3.000
 DOV  C10   C3   C4    116.35  3.000
 DOV  C2    C3   C4    108.43  3.000
 DOV  H11   C11  N12   109.83  3.000
 DOV  H11   C11  N15   106.53  3.000
 DOV  N12   C11  N15   106.03  3.000
 DOV  H11   C11  C9    108.33  3.000
 DOV  N12   C11  C9    111.45  3.000
 DOV  N15   C11  C9    114.51  3.000
 DOV  H15   N15  C14   107.31  3.000
 DOV  H15   N15  C11   109.00  3.000
 DOV  C14   N15  C11   102.19  3.000
 DOV  H14   C14  C13   108.32  3.000
 DOV  H14   C14  C19   108.08  3.000
 DOV  C13   C14  C19   111.09  3.000
 DOV  H14   C14  N15   107.12  3.000
 DOV  C13   C14  N15   102.29  3.000
 DOV  C19   C14  N15   119.42  3.000
 DOV  H192  C19  H191  107.28  3.000
 DOV  H192  C19  C18   110.17  3.000
 DOV  H191  C19  C18   110.26  3.000
 DOV  H192  C19  C14   111.76  3.000
 DOV  H191  C19  C14   110.20  3.000
 DOV  C18   C19  C14   107.19  3.000
 DOV  H182  C18  H181  106.48  3.000
 DOV  H182  C18  C17   109.43  3.000
 DOV  H181  C18  C17   109.62  3.000
 DOV  H182  C18  C19   108.49  3.000
 DOV  H181  C18  C19   109.51  3.000
 DOV  C17   C18  C19   113.08  3.000
 DOV  H17   C17  N20   105.29  3.000
 DOV  H17   C17  C16   106.01  3.000
 DOV  N20   C17  C16   111.08  3.000
 DOV  H17   C17  C18   106.67  3.000
 DOV  N20   C17  C18   115.09  3.000
 DOV  C16   C17  C18   111.95  3.000
 DOV  H162  C16  H161  107.51  3.000
 DOV  H162  C16  C13   109.49  3.000
 DOV  H161  C16  C13   111.98  3.000
 DOV  H162  C16  C17   111.29  3.000
 DOV  H161  C16  C17   109.16  3.000
 DOV  C13   C16  C17   107.44  3.000
 DOV  H13   C13  N12   108.52  3.000
 DOV  H13   C13  C16   107.26  3.000
 DOV  N12   C13  C16   118.80  3.000
 DOV  H13   C13  C14   107.13  3.000
 DOV  N12   C13  C14   103.54  3.000
 DOV  C16   C13  C14   111.04  3.000
 DOV  H12   N12  C13   111.34  3.000
 DOV  H12   N12  C11   109.84  3.000
 DOV  C13   N12  C11   106.37  3.000
 DOV  C21   N20  C25   110.65  3.000
 DOV  C21   N20  C17   116.22  3.000
 DOV  C25   N20  C17   114.03  3.000
 DOV  H252  C25  H251  106.59  3.000
 DOV  H252  C25  C24   109.71  3.000
 DOV  H251  C25  C24   109.11  3.000
 DOV  H252  C25  N20   112.70  3.000
 DOV  H251  C25  N20   109.04  3.000
 DOV  C24   C25  N20   109.60  3.000
 DOV  H242  C24  H241  107.13  3.000
 DOV  H242  C24  N23   109.20  3.000
 DOV  H241  C24  N23   108.39  3.000
 DOV  H242  C24  C25   109.97  3.000
 DOV  H241  C24  C25   108.38  3.000
 DOV  N23   C24  C25   113.55  3.000
 DOV  C22   N23  C26   113.66  3.000
 DOV  C22   N23  C24   109.75  3.000
 DOV  C26   N23  C24   113.43  3.000
 DOV  H263  C26  H262  107.41  3.000
 DOV  H263  C26  H261  107.20  3.000
 DOV  H262  C26  H261  107.35  3.000
 DOV  H263  C26  N23   109.38  3.000
 DOV  H262  C26  N23   109.55  3.000
 DOV  H261  C26  N23   115.63  3.000
 DOV  H222  C22  H221  107.22  3.000
 DOV  H222  C22  C21   109.88  3.000
 DOV  H221  C22  C21   108.22  3.000
 DOV  H222  C22  N23   109.13  3.000
 DOV  H221  C22  N23   108.34  3.000
 DOV  C21   C22  N23   113.83  3.000
 DOV  H212  C21  H211  106.45  3.000
 DOV  H212  C21  C22   108.51  3.000
 DOV  H211  C21  C22   109.79  3.000
 DOV  H212  C21  N20   109.93  3.000
 DOV  H211  C21  N20   112.78  3.000
 DOV  C22   C21  N20   109.27  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
 DOV  CONST_03  H7    N7   C8   C9    180.00   0.0  0
 DOV  Var_01    C1    C6   C5   C4    -54.80  30.0  1
 DOV  Var_02    C2    C1   C6   C5     56.27  30.0  1
 DOV  Var_03    C17   C18  C19  C14    54.46  30.0  1
 DOV  Var_04    C24   C25  N20  C17  -167.74  30.0  1
 DOV  Var_05    C22   C21  N20  C17   169.06  30.0  1
 DOV  Var_06    N23   C24  C25  N20   -56.11  30.0  1
 DOV  Var_07    N23   C22  C21  N20    56.04  30.0  1
 DOV  Var_08    C22   N23  C24  C25    51.80  30.0  1
 DOV  Var_09    C21   C22  N23  C24   -51.94  30.0  1
 DOV  Var_10    H261  C26  N23  C24    62.24  30.0  3

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
 DOV  chir_01  C4   F27  C5   C3   negativ
 DOV  chir_02  C2   N7   C3   C1   negativ
 DOV  chir_03  C9   C8   C10  C11  negativ
 DOV  chir_04  C10  N29  C9   C3   positiv
 DOV  chir_05  C3   C4   C2   C10  positiv
 DOV  chir_06  C11  N12  N15  C9   negativ
 DOV  chir_07  C14  N15  C13  C19  negativ
 DOV  chir_08  C17  N20  C16  C18  negativ
 DOV  chir_09  C13  N12  C14  C16  negativ

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
 DOV  plan-1  C2   0.020
 DOV  plan-1  N7   0.020
 DOV  plan-1  C8   0.020
 DOV  plan-1  O28  0.020
 DOV  plan-1  C9   0.020
 DOV  plan-1  H7   0.020

