# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Apr 14 09:24:27 2020
#   Inital geometry file: a 120 line input string
#   Ligand name: 2-{[(1R,2S)-2-aminocyclohexyl]amino}-4-[(3-methylphenyl)amino]-6,7-dihydro-5H-pyrrolo[3,4-d]pyrimidin-5-one
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cc1cccc(Nc2nc(N[C@@H]3CCCC[C@@H]3N)nc4CNC(=O)c24)c1
#
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
 7KF  7KF  2-{[(1R,2S)-2-aminocyclohexyl]amino}-4-[(3-methylphenyl)amino]-6,7-dihydro-5H-pyrrolo[3,4-d]pyrimidin-5-one  ligand  50  26  .  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_7KF
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
 7KF  C4   C  CR16  0  -0.235   0.1681   3.9609  -0.1662
 7KF  C5   C  CR16  0  -0.341   0.3808   2.5884  -0.1558
 7KF  C6   C  CR6   0   0.392   1.6578   2.1028   0.1244
 7KF  C8   C  CR6   0   0.586   1.2662  -0.3688   0.0599
 7KF  C10  C  CR6   0   0.606  -0.7283  -1.4703  -0.1826
 7KF  C15  C  CH2   0  -0.431  -3.8006  -0.0407   1.8049
 7KF  C17  C  CH2   0  -0.437  -5.0615  -1.2458   0.0021
 7KF  C22  C  CR56  0   0.230   1.0967  -2.7346   0.0077
 7KF  C28  C  CR16  0  -0.422   2.6888   3.0124   0.3850
 7KF  C2   C  CR6   0   0.115   2.4750   4.3826   0.3694
 7KF  C3   C  CR16  0  -0.318   1.1927   4.8562   0.0919
 7KF  N7   N  NH1   0  -0.782   2.0107   0.7534   0.1583
 7KF  N9   N  N     0  -0.531  -0.0485  -0.3192  -0.0944
 7KF  N11  N  NH1   0  -0.646  -2.0574  -1.4018  -0.3215
 7KF  C12  C  CH1   0  -0.078  -2.8186  -0.1854  -0.5313
 7KF  C14  C  CH2   0  -0.449  -2.9589   0.6527   0.7412
 7KF  C16  C  CH2   0  -0.436  -5.1793  -0.3977   1.2623
 7KF  C18  C  CH1   0  -0.104  -4.2080  -0.5627  -1.0652
 7KF  N20  N  NH2   0  -0.800  -4.0755  -1.4416  -2.2161
 7KF  N21  N  N     0  -0.509  -0.2074  -2.7169  -0.1459
 7KF  C23  C  CH2   0  -0.287   1.9583  -3.9592   0.0891
 7KF  N24  N  NR15  0  -0.669   3.2752  -3.3851   0.2521
 7KF  C25  C  CR5   0   0.540   3.2908  -2.0309   0.2828
 7KF  O26  O  O     0  -0.500   4.2761  -1.3129   0.4190
 7KF  C27  C  CR56  0  -0.309   1.9005  -1.6213   0.1218
 7KF  H1   H  HCR6  0   0.252  -0.8263   4.3310  -0.3817
 7KF  H2   H  HCR6  0   0.303  -0.4321   1.9107  -0.3554
 7KF  H4   H  HCH2  0   0.231  -3.8911   0.6058   2.6808
 7KF  H5   H  HCH2  0   0.215  -4.6336  -2.2225   0.2522
 7KF  H6   H  HCH2  0   0.235  -6.0527  -1.4477  -0.4149
 7KF  H7   H  HCR6  0   0.258   3.6818   2.6366   0.6108
 7KF  H11  H  HCR6  0   0.245   1.0009   5.9222   0.0793
 7KF  H12  H  HNH1  0   0.413   2.9976   0.5764   0.2948
 7KF  H13  H  HNH1  0   0.388  -2.5036  -2.2665  -0.5894
 7KF  H14  H  HCH1  0   0.250  -2.3127   0.4211  -1.2928
 7KF  H15  H  HCH2  0   0.221  -3.4304   1.6012   0.4637
 7KF  H16  H  HCH2  0   0.247  -1.9710   0.9026   1.1288
 7KF  H17  H  HCH2  0   0.231  -5.7634  -0.9295   2.0164
 7KF  H18  H  HCH2  0   0.212  -5.7288   0.5216   1.0333
 7KF  H19  H  HCH1  0   0.220  -4.6947   0.3931  -1.3135
 7KF  H20  H  HNH2  0   0.350  -4.9956  -1.6766  -2.5679
 7KF  H21  H  HNH2  0   0.346  -3.6041  -0.9572  -2.9708
 7KF  H23  H  HCH2  0   0.279   1.6759  -4.5901   0.9356
 7KF  H22  H  HCH2  0   0.279   1.8815  -4.5629  -0.8185
 7KF  H24  H  HNR5  0   0.406   4.1037  -3.9461   0.3628
 7KF  C1   C  CH3   0  -0.724   3.6071   5.3346   0.6249
 7KF  H3   H  HCH2  0   0.215  -3.2911  -0.9490   2.1416
 7KF  H8   H  HCH3  0   0.250   4.0097   5.7202  -0.3138
 7KF  H9   H  HCH3  0   0.245   3.2802   6.1935   1.2110
 7KF  H10  H  HCH3  0   0.244   4.4257   4.8531   1.1580

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
 7KF  C15  C14  single    1.523  0.020  1.523
 7KF  C15  C16  single    1.524  0.020  1.524
 7KF  C14  C12  single    1.530  0.020  1.530
 7KF  C16  C17  single    1.524  0.020  1.524
 7KF  C12  N11  single    1.450  0.020  1.450
 7KF  C12  C18  single    1.536  0.020  1.536
 7KF  N11  C10  single    1.338  0.020  1.338
 7KF  C17  C18  single    1.528  0.020  1.528
 7KF  C10  N9   aromatic  1.340  0.020  1.340
 7KF  C10  N21  aromatic  1.352  0.020  1.352
 7KF  C18  N20  single    1.454  0.020  1.454
 7KF  C4   C5   aromatic  1.389  0.020  1.389
 7KF  C4   C3   aromatic  1.385  0.020  1.385
 7KF  C5   C6   aromatic  1.395  0.020  1.395
 7KF  N9   C8   aromatic  1.325  0.020  1.325
 7KF  N21  C22  aromatic  1.313  0.020  1.313
 7KF  C3   C2   aromatic  1.395  0.020  1.395
 7KF  C8   N7   single    1.350  0.020  1.350
 7KF  C8   C27  aromatic  1.405  0.020  1.405
 7KF  C6   N7   single    1.395  0.020  1.395
 7KF  C6   C28  aromatic  1.399  0.020  1.399
 7KF  C22  C27  aromatic  1.378  0.020  1.378
 7KF  C22  C23  single    1.499  0.020  1.499
 7KF  C27  C25  single    1.458  0.020  1.458
 7KF  C2   C28  aromatic  1.387  0.020  1.387
 7KF  C2   C1   single    1.501  0.020  1.501
 7KF  C23  N24  single    1.446  0.020  1.446
 7KF  C25  N24  single    1.355  0.020  1.355
 7KF  C25  O26  double    1.227  0.020  1.227
 7KF  C4   H1   single    0.930  0.020  1.080
 7KF  C5   H2   single    0.930  0.020  1.080
 7KF  C15  H3   single    0.970  0.020  1.090
 7KF  C15  H4   single    0.970  0.020  1.090
 7KF  C17  H5   single    0.970  0.020  1.090
 7KF  C17  H6   single    0.970  0.020  1.090
 7KF  C28  H7   single    0.930  0.020  1.080
 7KF  C1   H8   single    0.970  0.020  1.090
 7KF  C1   H9   single    0.970  0.020  1.090
 7KF  C1   H10  single    0.970  0.020  1.090
 7KF  C3   H11  single    0.930  0.020  1.080
 7KF  N7   H12  single    0.860  0.020  1.020
 7KF  N11  H13  single    0.890  0.020  1.040
 7KF  C12  H14  single    0.970  0.020  1.090
 7KF  C14  H15  single    0.970  0.020  1.090
 7KF  C14  H16  single    0.970  0.020  1.090
 7KF  C16  H17  single    0.970  0.020  1.090
 7KF  C16  H18  single    0.970  0.020  1.090
 7KF  C18  H19  single    0.970  0.020  1.090
 7KF  N20  H20  single    0.890  0.020  1.040
 7KF  N20  H21  single    0.890  0.020  1.040
 7KF  C23  H23  single    0.970  0.020  1.090
 7KF  C23  H22  single    0.970  0.020  1.090
 7KF  N24  H24  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
 7KF  H1   C4   C3   119.71  3.000
 7KF  H1   C4   C5   118.68  3.000
 7KF  C3   C4   C5   121.61  3.000
 7KF  H2   C5   C6   120.61  3.000
 7KF  H2   C5   C4   120.32  3.000
 7KF  C6   C5   C4   119.07  3.000
 7KF  N7   C6   C28  115.96  3.000
 7KF  C28  C6   C5   119.06  3.000
 7KF  N7   C6   C5   124.98  3.000
 7KF  C27  C8   N9   119.11  3.000
 7KF  C27  C8   N7   119.25  3.000
 7KF  N9   C8   N7   121.64  3.000
 7KF  N21  C10  N11  115.65  3.000
 7KF  N21  C10  N9   126.52  3.000
 7KF  N11  C10  N9   117.83  3.000
 7KF  H4   C15  H3   106.45  3.000
 7KF  H4   C15  C16  110.44  3.000
 7KF  H3   C15  C16  109.65  3.000
 7KF  H4   C15  C14  109.64  3.000
 7KF  H3   C15  C14  109.59  3.000
 7KF  C16  C15  C14  110.96  3.000
 7KF  H6   C17  H5   106.05  3.000
 7KF  H6   C17  C18  108.80  3.000
 7KF  H5   C17  C18  109.87  3.000
 7KF  H6   C17  C16  110.36  3.000
 7KF  H5   C17  C16  109.74  3.000
 7KF  C18  C17  C16  111.84  3.000
 7KF  C27  C22  C23  108.67  3.000
 7KF  C23  C22  N21  126.02  3.000
 7KF  C27  C22  N21  125.31  3.000
 7KF  H7   C28  C2   119.04  3.000
 7KF  H7   C28  C6   119.19  3.000
 7KF  C2   C28  C6   121.77  3.000
 7KF  C3   C2   C1   120.79  3.000
 7KF  C1   C2   C28  120.56  3.000
 7KF  C3   C2   C28  118.64  3.000
 7KF  H11  C3   C2   119.94  3.000
 7KF  H11  C3   C4   120.20  3.000
 7KF  C2   C3   C4   119.85  3.000
 7KF  H12  N7   C8   113.72  3.000
 7KF  H12  N7   C6   114.78  3.000
 7KF  C8   N7   C6   131.49  3.000
 7KF  C10  N9   C8   118.63  3.000
 7KF  H13  N11  C12  116.63  3.000
 7KF  H13  N11  C10  115.02  3.000
 7KF  C12  N11  C10  125.40  3.000
 7KF  H14  C12  C18  108.16  3.000
 7KF  H14  C12  C14  108.46  3.000
 7KF  C18  C12  C14  109.92  3.000
 7KF  H14  C12  N11  108.79  3.000
 7KF  C18  C12  N11  108.61  3.000
 7KF  C14  C12  N11  112.79  3.000
 7KF  H16  C14  H15  106.36  3.000
 7KF  H16  C14  C12  109.76  3.000
 7KF  H15  C14  C12  107.65  3.000
 7KF  H16  C14  C15  110.90  3.000
 7KF  H15  C14  C15  109.47  3.000
 7KF  C12  C14  C15  112.46  3.000
 7KF  H18  C16  H17  106.54  3.000
 7KF  H18  C16  C17  109.46  3.000
 7KF  H17  C16  C17  109.96  3.000
 7KF  H18  C16  C15  109.38  3.000
 7KF  H17  C16  C15  110.61  3.000
 7KF  C17  C16  C15  110.79  3.000
 7KF  H19  C18  N20  112.74  3.000
 7KF  H19  C18  C12  105.37  3.000
 7KF  N20  C18  C12  109.96  3.000
 7KF  H19  C18  C17  107.38  3.000
 7KF  N20  C18  C17  109.48  3.000
 7KF  C12  C18  C17  111.87  3.000
 7KF  H21  N20  H20  105.95  3.000
 7KF  H21  N20  C18  110.06  3.000
 7KF  H20  N20  C18  109.42  3.000
 7KF  C22  N21  C10  113.48  3.000
 7KF  H22  C23  H23  107.83  3.000
 7KF  H22  C23  N24  112.15  3.000
 7KF  H23  C23  N24  112.16  3.000
 7KF  H22  C23  C22  111.45  3.000
 7KF  H23  C23  C22  111.41  3.000
 7KF  N24  C23  C22  101.85  3.000
 7KF  H24  N24  C25  123.03  3.000
 7KF  H24  N24  C23  122.74  3.000
 7KF  C25  N24  C23  114.20  3.000
 7KF  C27  C25  O26  127.85  3.000
 7KF  O26  C25  N24  126.65  3.000
 7KF  C27  C25  N24  105.51  3.000
 7KF  C25  C27  C22  109.78  3.000
 7KF  C25  C27  C8   133.28  3.000
 7KF  C22  C27  C8   116.94  3.000
 7KF  H10  C1   H9   108.09  3.000
 7KF  H10  C1   H8   107.45  3.000
 7KF  H9   C1   H8   107.14  3.000
 7KF  H10  C1   C2   111.70  3.000
 7KF  H9   C1   C2   111.41  3.000
 7KF  H8   C1   C2   110.84  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
 7KF  CONST_01  C28  C6   C5   C4     0.00   0.0  0
 7KF  CONST_02  C28  C2   C3   C4     0.00   0.0  0
 7KF  CONST_03  C2   C3   C4   C5     0.00   0.0  0
 7KF  CONST_04  C2   C28  C6   C5     0.00   0.0  0
 7KF  CONST_05  C3   C4   C5   C6     0.00   0.0  0
 7KF  CONST_06  C3   C2   C28  C6     0.00   0.0  0
 7KF  CONST_07  N21  C10  N9   C8     0.00   0.0  0
 7KF  CONST_08  N21  C22  C27  C8     0.00   0.0  0
 7KF  CONST_09  C27  C8   N9   C10    0.00   0.0  0
 7KF  CONST_10  C27  C22  N21  C10    0.00   0.0  0
 7KF  CONST_11  N9   C10  N21  C22    0.00   0.0  0
 7KF  CONST_12  N9   C8   C27  C22    0.00   0.0  0
 7KF  CONST_13  C27  C25  N24  C23    0.00   0.0  0
 7KF  CONST_14  N7   C6   C5   C4   180.00   0.0  0
 7KF  CONST_15  C1   C2   C3   C4   180.00   0.0  0
 7KF  CONST_16  C1   C2   C28  C6   180.00   0.0  0
 7KF  CONST_17  N11  C10  N9   C8   180.00   0.0  0
 7KF  CONST_18  N7   C8   N9   C10  180.00   0.0  0
 7KF  CONST_19  N11  C10  N21  C22  180.00   0.0  0
 7KF  CONST_20  N7   C8   C27  C22  180.00   0.0  0
 7KF  CONST_21  N7   C6   C28  C2   180.00   0.0  0
 7KF  CONST_22  C25  C27  C8   N7     0.00   0.0  0
 7KF  CONST_23  C12  N11  C10  N9     0.00   0.0  0
 7KF  CONST_24  N21  C10  N11  C12  180.00   0.0  0
 7KF  CONST_25  O26  C25  N24  C23  180.00   0.0  0
 7KF  CONST_26  H11  C3   C4   C5   180.00   0.0  0
 7KF  CONST_27  H7   C28  C6   C5   180.00   0.0  0
 7KF  CONST_28  H1   C4   C5   C6   180.00   0.0  0
 7KF  CONST_29  H2   C5   C6   C28  180.00   0.0  0
 7KF  CONST_30  H24  N24  C25  C27  180.00   0.0  0
 7KF  CONST_31  H13  N11  C10  N9   180.00   0.0  0
 7KF  Var_01    C18  C17  C16  C15  -55.35  30.0  1
 7KF  Var_02    C14  C15  C16  C17   55.55  30.0  1
 7KF  Var_03    C16  C15  C14  C12  -56.36  30.0  1
 7KF  Var_04    C8   N7   C6   C5    -6.37  30.0  2
 7KF  Var_05    N9   C8   N7   C6    -0.29  30.0  3
 7KF  Var_06    H23  C23  C22  N21  -60.33  30.0  1
 7KF  Var_07    H8   C1   C2   C28   98.64  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
 7KF  chir_01  C12  C14  N11  C18  negativ
 7KF  chir_02  C18  N20  C17  C12  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
 7KF  plan-1  C4   0.020
 7KF  plan-1  C5   0.020
 7KF  plan-1  C6   0.020
 7KF  plan-1  C28  0.020
 7KF  plan-1  C2   0.020
 7KF  plan-1  C3   0.020
 7KF  plan-1  N7   0.020
 7KF  plan-1  H1   0.020
 7KF  plan-1  H2   0.020
 7KF  plan-1  H7   0.020
 7KF  plan-1  H11  0.020
 7KF  plan-1  C1   0.020
 7KF  plan-2  C10  0.020
 7KF  plan-2  N11  0.020
 7KF  plan-2  C12  0.020
 7KF  plan-2  H13  0.020
 7KF  plan-3  C8   0.020
 7KF  plan-3  C10  0.020
 7KF  plan-3  C22  0.020
 7KF  plan-3  N7   0.020
 7KF  plan-3  N9   0.020
 7KF  plan-3  N11  0.020
 7KF  plan-3  N21  0.020
 7KF  plan-3  C23  0.020
 7KF  plan-3  N24  0.020
 7KF  plan-3  C25  0.020
 7KF  plan-3  O26  0.020
 7KF  plan-3  C27  0.020
 7KF  plan-3  H24  0.020

