# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Apr 14 09:50:18 2020
#   Inital geometry file: a 111 line input string
#   Ligand name: 6-{[(1R,2S)-2-aminocyclohexyl]amino}-7-fluoro-4-(1-methyl-1H-pyrazol-4-yl)-1,2-dihydro-3H-pyrrolo[3,4-c]pyridin-3-one
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cn1cc(cn1)c2nc(N[C@@H]3CCCC[C@@H]3N)c(F)c4CNC(=O)c24
#
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
 7KG  7KG  6-{[(1R,2S)-2-aminocyclohexyl]amino}-7-fluoro-4-(1-methyl-1H-pyrazol-4-yl)-1,2-dihydro-3H-pyrrolo[3,4-c]pyridin-3-one  ligand  46  25  .  2022-07-23  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_7KG
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
 7KG  C4   C  CR5   0  -0.199   2.2547  -0.9900  -0.1621
 7KG  C5   C  CR15  0  -0.126   3.5881  -1.1698  -0.5889
 7KG  C7   C  CR6   0   0.217   1.4019   0.1861  -0.0127
 7KG  C13  C  C     0  -0.448  -2.4153  -1.7528  -0.7305
 7KG  C15  C  C     0  -0.436  -4.7920  -1.2581  -1.3575
 7KG  C17  C  CR16  0  -0.109  -4.0091  -0.9236   1.0229
 7KG  C20  C  CR6   0   0.365  -0.4755   2.1802   0.2739
 7KG  C22  C  CR56  0   0.014   0.8306   2.5146   0.1469
 7KG  N2   N  NR5   0  -0.268   2.8362  -3.1025  -0.1940
 7KG  C3   C  CR15  0   0.075   1.8162  -2.2843   0.0756
 7KG  N6   N  N     0  -0.280   3.9205  -2.4449  -0.6046
 7KG  N8   N  N     0  -0.511   0.1059  -0.1137   0.1310
 7KG  C9   C  CR6   0   0.389  -0.8305   0.8141   0.2694
 7KG  N10  N  NH1   0  -0.676  -2.1224   0.4457   0.3850
 7KG  C11  C  CR16  0  -0.069  -2.5467  -0.9331   0.5541
 7KG  C14  C  C     0  -0.429  -3.3431  -1.2560  -1.8307
 7KG  C16  C  C     0  -0.433  -4.9511  -0.4434  -0.0797
 7KG  F21  F  F     0  -0.303  -1.4325   3.1148   0.4111
 7KG  C23  C  CH2   0  -0.264   1.4646   3.8671   0.1423
 7KG  N24  N  NR15  0  -0.670   2.8557   3.5252  -0.0005
 7KG  C25  C  CR5   0   0.524   3.1213   2.1998  -0.0739
 7KG  O26  O  O     0  -0.480   4.2391   1.7175  -0.1721
 7KG  C27  C  CR56  0  -0.229   1.8079   1.5199  -0.0001
 7KG  H1   H  HCR5  0   0.267   4.2999  -0.4203  -0.8867
 7KG  H2   H  H     0   0.250  -1.3759  -1.7535  -1.0583
 7KG  H3   H  H     0   0.218  -2.6663  -2.7913  -0.4870
 7KG  H4   H  H     0   0.230  -5.4511  -0.8643  -2.1347
 7KG  H5   H  H     0   0.211  -5.1100  -2.2904  -1.1738
 7KG  H6   H  HCR6  0   0.220  -4.2591  -1.9736   1.2402
 7KG  H7   H  HCH3  0   0.262   3.1216  -4.9959  -1.0225
 7KG  H8   H  HCH3  0   0.262   3.5985  -4.8394   0.6789
 7KG  H9   H  HCH3  0   0.260   1.8849  -4.8881   0.2392
 7KG  H10  H  HCR5  0   0.293   0.8624  -2.6502   0.4173
 7KG  H11  H  HNH1  0   0.389  -2.7501   1.1204   0.8005
 7KG  H12  H  HCR6  0   0.242  -1.9340  -1.4087   1.3316
 7KG  H13  H  H     0   0.215  -3.0553  -0.2426  -2.1275
 7KG  H14  H  H     0   0.228  -3.2339  -1.8849  -2.7173
 7KG  H15  H  H     0   0.215  -4.7594   0.6142  -0.2908
 7KG  H16  H  H     0   0.233  -5.9819  -0.5032   0.2821
 7KG  H20  H  HCH2  0   0.278   1.1053   4.4817  -0.6870
 7KG  H19  H  HCH2  0   0.278   1.2696   4.4117   1.0695
 7KG  H21  H  HNR5  0   0.406   3.5849   4.2191  -0.0173
 7KG  C1   C  CH3   0  -0.508   2.8663  -4.5396  -0.0683
 7KG  N19  N  NH2   0  -0.802  -4.1434  -0.0597   2.1858
 7KG  H17  H  HNH2  0   0.351  -5.1128  -0.0251   2.4760
 7KG  H18  H  HNH2  0   0.348  -3.6293  -0.4466   2.9683

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
 7KG  C14  C13  single    1.523  0.020  1.523
 7KG  C14  C15  single    1.524  0.020  1.524
 7KG  C13  C11  single    1.529  0.020  1.529
 7KG  C15  C16  single    1.524  0.020  1.524
 7KG  C11  N10  single    1.453  0.020  1.453
 7KG  C11  C17  single    1.536  0.020  1.536
 7KG  N10  C9   single    1.348  0.020  1.348
 7KG  C16  C17  single    1.528  0.020  1.528
 7KG  C9   N8   aromatic  1.325  0.020  1.325
 7KG  C9   C20  aromatic  1.411  0.020  1.411
 7KG  C17  N19  single    1.455  0.020  1.455
 7KG  F21  C20  single    1.345  0.020  1.345
 7KG  N8   C7   aromatic  1.338  0.020  1.338
 7KG  C20  C22  aromatic  1.354  0.020  1.354
 7KG  C5   N6   aromatic  1.318  0.020  1.318
 7KG  C5   C4   aromatic  1.412  0.020  1.412
 7KG  C7   C4   single    1.460  0.020  1.460
 7KG  C7   C27  aromatic  1.394  0.020  1.394
 7KG  N6   N2   aromatic  1.333  0.020  1.333
 7KG  C22  C27  aromatic  1.402  0.020  1.402
 7KG  C22  C23  single    1.494  0.020  1.494
 7KG  C4   C3   aromatic  1.387  0.020  1.387
 7KG  C27  C25  single    1.481  0.020  1.481
 7KG  C23  N24  single    1.440  0.020  1.440
 7KG  N2   C3   aromatic  1.335  0.020  1.335
 7KG  N2   C1   single    1.443  0.020  1.443
 7KG  C25  N24  single    1.354  0.020  1.354
 7KG  C25  O26  double    1.221  0.020  1.221
 7KG  C5   H1   single    0.930  0.020  1.080
 7KG  C13  H2   single    0.970  0.020  1.090
 7KG  C13  H3   single    0.970  0.020  1.090
 7KG  C15  H4   single    0.970  0.020  1.090
 7KG  C15  H5   single    0.970  0.020  1.090
 7KG  C17  H6   single    0.970  0.020  1.090
 7KG  C1   H7   single    0.970  0.020  1.090
 7KG  C1   H8   single    0.970  0.020  1.090
 7KG  C1   H9   single    0.970  0.020  1.090
 7KG  C3   H10  single    0.930  0.020  1.080
 7KG  N10  H11  single    0.890  0.020  1.040
 7KG  C11  H12  single    0.970  0.020  1.090
 7KG  C14  H13  single    0.970  0.020  1.090
 7KG  C14  H14  single    0.970  0.020  1.090
 7KG  C16  H15  single    0.970  0.020  1.090
 7KG  C16  H16  single    0.970  0.020  1.090
 7KG  N19  H17  single    0.890  0.020  1.040
 7KG  N19  H18  single    0.890  0.020  1.040
 7KG  C23  H20  single    0.970  0.020  1.090
 7KG  C23  H19  single    0.970  0.020  1.090
 7KG  N24  H21  single    0.860  0.020  1.020

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
 7KG  C3   C4   C7   123.33  3.000
 7KG  C3   C4   C5   103.39  3.000
 7KG  C7   C4   C5   133.24  3.000
 7KG  H1   C5   N6   120.27  3.000
 7KG  H1   C5   C4   128.32  3.000
 7KG  N6   C5   C4   111.41  3.000
 7KG  C27  C7   N8   119.70  3.000
 7KG  C27  C7   C4   126.96  3.000
 7KG  N8   C7   C4   113.33  3.000
 7KG  H3   C13  H2   106.55  3.000
 7KG  H3   C13  C14  109.28  3.000
 7KG  H2   C13  C14  111.34  3.000
 7KG  H3   C13  C11  107.55  3.000
 7KG  H2   C13  C11  109.56  3.000
 7KG  C14  C13  C11  112.31  3.000
 7KG  H5   C15  H4   106.48  3.000
 7KG  H5   C15  C16  109.44  3.000
 7KG  H4   C15  C16  109.93  3.000
 7KG  H5   C15  C14  109.23  3.000
 7KG  H4   C15  C14  110.62  3.000
 7KG  C16  C15  C14  111.03  3.000
 7KG  H6   C17  N19  112.80  3.000
 7KG  H6   C17  C16  107.59  3.000
 7KG  N19  C17  C16  109.47  3.000
 7KG  H6   C17  C11  105.70  3.000
 7KG  N19  C17  C11  109.61  3.000
 7KG  C16  C17  C11  111.64  3.000
 7KG  F21  C20  C9   119.61  3.000
 7KG  F21  C20  C22  121.62  3.000
 7KG  C9   C20  C22  118.77  3.000
 7KG  C27  C22  C23  110.25  3.000
 7KG  C23  C22  C20  129.29  3.000
 7KG  C27  C22  C20  120.45  3.000
 7KG  N6   N2   C3   112.42  3.000
 7KG  C3   N2   C1   127.49  3.000
 7KG  N6   N2   C1   120.08  3.000
 7KG  H10  C3   N2   122.17  3.000
 7KG  H10  C3   C4   130.63  3.000
 7KG  N2   C3   C4   107.20  3.000
 7KG  N2   N6   C5   105.57  3.000
 7KG  C9   N8   C7   122.59  3.000
 7KG  N10  C9   N8   119.64  3.000
 7KG  N8   C9   C20  120.01  3.000
 7KG  N10  C9   C20  120.34  3.000
 7KG  H11  N10  C11  113.85  3.000
 7KG  H11  N10  C9   116.61  3.000
 7KG  C11  N10  C9   123.31  3.000
 7KG  H12  C11  N10  109.30  3.000
 7KG  H12  C11  C17  108.53  3.000
 7KG  N10  C11  C17  107.93  3.000
 7KG  H12  C11  C13  108.34  3.000
 7KG  C17  C11  C13  109.97  3.000
 7KG  N10  C11  C13  112.70  3.000
 7KG  H14  C14  H13  106.66  3.000
 7KG  H14  C14  C15  110.26  3.000
 7KG  H13  C14  C15  109.60  3.000
 7KG  H14  C14  C13  109.73  3.000
 7KG  H13  C14  C13  109.74  3.000
 7KG  C15  C14  C13  110.76  3.000
 7KG  H16  C16  H15  106.34  3.000
 7KG  H16  C16  C17  108.97  3.000
 7KG  H15  C16  C17  109.56  3.000
 7KG  H16  C16  C15  110.27  3.000
 7KG  H15  C16  C15  109.66  3.000
 7KG  C17  C16  C15  111.89  3.000
 7KG  H19  C23  H20  107.75  3.000
 7KG  H19  C23  N24  112.02  3.000
 7KG  H20  C23  N24  112.09  3.000
 7KG  H19  C23  C22  111.89  3.000
 7KG  H20  C23  C22  111.83  3.000
 7KG  N24  C23  C22  101.27  3.000
 7KG  H21  N24  C25  122.13  3.000
 7KG  H21  N24  C23  122.54  3.000
 7KG  C25  N24  C23  115.31  3.000
 7KG  C27  C25  O26  129.38  3.000
 7KG  O26  C25  N24  124.78  3.000
 7KG  C27  C25  N24  105.83  3.000
 7KG  C25  C27  C22  107.32  3.000
 7KG  C25  C27  C7   134.19  3.000
 7KG  C22  C27  C7   118.47  3.000
 7KG  H9   C1   H8   108.98  3.000
 7KG  H9   C1   H7   109.02  3.000
 7KG  H8   C1   H7   109.19  3.000
 7KG  H9   C1   N2   108.99  3.000
 7KG  H8   C1   N2   110.37  3.000
 7KG  H7   C1   N2   110.25  3.000
 7KG  H18  N19  H17  106.11  3.000
 7KG  H18  N19  C17  110.10  3.000
 7KG  H17  N19  C17  109.74  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
 7KG  CONST_01  N2   N6   C5   C4     0.00   0.0  0
 7KG  CONST_02  C9   N8   C7   C4   180.00   0.0  0
 7KG  CONST_03  C22  C27  C7   C4   180.00   0.0  0
 7KG  CONST_04  N6   N2   C3   C4     0.00   0.0  0
 7KG  CONST_05  C3   N2   N6   C5     0.00   0.0  0
 7KG  CONST_06  N8   C7   C4   C5   180.00   0.0  0
 7KG  CONST_07  C27  C7   C4   C5     0.00   0.0  0
 7KG  CONST_08  N2   C3   C4   C5     0.00   0.0  0
 7KG  CONST_09  C20  C9   N8   C7     0.00   0.0  0
 7KG  CONST_10  N6   C5   C4   C7   180.00   0.0  0
 7KG  CONST_11  N2   C3   C4   C7   180.00   0.0  0
 7KG  CONST_12  C20  C22  C27  C7     0.00   0.0  0
 7KG  CONST_13  N8   C9   C20  C22    0.00   0.0  0
 7KG  CONST_14  N8   C7   C27  C22    0.00   0.0  0
 7KG  CONST_15  N6   C5   C4   C3     0.00   0.0  0
 7KG  CONST_16  N8   C7   C4   C3     0.00   0.0  0
 7KG  CONST_17  C27  C7   C4   C3   180.00   0.0  0
 7KG  CONST_18  C27  C7   N8   C9     0.00   0.0  0
 7KG  CONST_19  C27  C22  C20  C9     0.00   0.0  0
 7KG  CONST_20  C25  C27  C7   C4     0.00   0.0  0
 7KG  CONST_21  C27  C25  N24  C23    0.00   0.0  0
 7KG  CONST_22  C1   N2   C3   C4   180.00   0.0  0
 7KG  CONST_23  C1   N2   N6   C5   180.00   0.0  0
 7KG  CONST_24  N10  C9   N8   C7   180.00   0.0  0
 7KG  CONST_25  N10  C9   C20  C22  180.00   0.0  0
 7KG  CONST_26  F21  C20  C9   N8   180.00   0.0  0
 7KG  CONST_27  C27  C22  C20  F21  180.00   0.0  0
 7KG  CONST_28  C23  C22  C20  F21    0.00   0.0  0
 7KG  CONST_29  C11  N10  C9   C20  180.00   0.0  0
 7KG  CONST_30  C11  N10  C9   N8     0.00   0.0  0
 7KG  CONST_31  O26  C25  N24  C23  180.00   0.0  0
 7KG  CONST_32  H10  C3   C4   C5   180.00   0.0  0
 7KG  CONST_33  H1   C5   C4   C7     0.00   0.0  0
 7KG  CONST_34  H21  N24  C25  C27  180.00   0.0  0
 7KG  Var_01    C16  C15  C14  C13   55.44  30.0  1
 7KG  Var_02    C11  C13  C14  C15  -56.60  30.0  1
 7KG  Var_03    C14  C15  C16  C17  -55.11  30.0  1
 7KG  Var_04    H20  C23  C22  C20  -61.52  30.0  1
 7KG  Var_05    H7   C1   N2   C3   122.75  30.0  2

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
 7KG  chir_01  C17  C11  C16  N19  positiv
 7KG  chir_02  C11  N10  C13  C17  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
 7KG  plan-1  C4   0.020
 7KG  plan-1  C5   0.020
 7KG  plan-1  C7   0.020
 7KG  plan-1  N2   0.020
 7KG  plan-1  C3   0.020
 7KG  plan-1  N6   0.020
 7KG  plan-1  H1   0.020
 7KG  plan-1  H10  0.020
 7KG  plan-1  C1   0.020
 7KG  plan-2  C9   0.020
 7KG  plan-2  N10  0.020
 7KG  plan-2  C11  0.020
 7KG  plan-2  H11  0.020
 7KG  plan-3  C4   0.020
 7KG  plan-3  C7   0.020
 7KG  plan-3  C20  0.020
 7KG  plan-3  C22  0.020
 7KG  plan-3  N8   0.020
 7KG  plan-3  C9   0.020
 7KG  plan-3  N10  0.020
 7KG  plan-3  F21  0.020
 7KG  plan-3  C23  0.020
 7KG  plan-3  N24  0.020
 7KG  plan-3  C25  0.020
 7KG  plan-3  O26  0.020
 7KG  plan-3  C27  0.020
 7KG  plan-3  H21  0.020

