# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr  1 01:42:44 2020
#   Inital geometry file: a 118 line input string
#   Ligand name: 2-amino-8-(trans-4-methoxycyclohexyl)-4-methyl-6-(1H-pyrazol-3-yl)pyrido[2,3-d]pyrimidin-7(8H)-one
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CO[C@@H]1CC[C@H](CC1)N2C(=O)C(=Cc3c(C)nc(N)nc23)c4cc[nH]n4
#
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
 3RE  3RE  2-amino-8-(trans-4-methoxycyclohexyl)-4-methyl-6-(1H-pyrazol-3-yl)pyrido[2,3-d]pyrimidin-7(8H)-one  ligand  48  26  .  2021-08-04  2022-09-16
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_3RE
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
 3RE  N1    N  N     0  -0.482  -2.0763   3.6611   0.0595
 3RE  C2    C  CR6   0   0.570  -0.7308   3.6025   0.0196
 3RE  N3    N  N     0  -0.513   0.0016   2.4942  -0.0262
 3RE  C4    C  CR66  0   0.576  -0.6467   1.3407  -0.0392
 3RE  C5    C  CR66  0  -0.111  -2.0502   1.2829  -0.0067
 3RE  C6    C  CR6   0   0.273  -2.7250   2.5188   0.0451
 3RE  N7    N  NR6   0  -0.630   0.0834   0.1763  -0.0831
 3RE  C8    C  CR6   0   0.563  -0.5177  -1.0830  -0.0989
 3RE  C9    C  CR6   0  -0.150  -1.9769  -1.1276  -0.0966
 3RE  C10   C  CR16  0  -0.230  -2.6896   0.0215  -0.0429
 3RE  N11   N  NH2   0  -0.813  -0.0833   4.7707   0.0240
 3RE  C12   C  CH3   0  -0.762  -4.2185   2.5743   0.0862
 3RE  O13   O  O     0  -0.463   0.1666  -2.0921  -0.1052
 3RE  C14   C  CH1   0  -0.087   1.5588   0.2673  -0.0948
 3RE  C15   C  CH2   0  -0.446   2.1931  -0.2797  -1.3704
 3RE  C16   C  CH2   0  -0.472   3.6867   0.0380  -1.3697
 3RE  C17   C  CH1   0   0.099   4.3674  -0.5191  -0.1280
 3RE  C18   C  CH2   0  -0.480   3.7084   0.0205   1.1398
 3RE  C19   C  CH2   0  -0.442   2.2146  -0.2994   1.1612
 3RE  O20   O  O2    0  -0.498   5.7392  -0.1944  -0.2075
 3RE  C21   C  CR5   0   0.252  -2.6601  -2.4232  -0.1044
 3RE  C22   C  CR15  0  -0.511  -3.8155  -2.7608   0.6338
 3RE  C23   C  CR15  0   0.015  -4.1003  -4.0513   0.2604
 3RE  N24   N  NR15  0  -0.420  -3.1567  -4.3984  -0.6297
 3RE  N25   N  N     0  -0.288  -2.2767  -3.4373  -0.8667
 3RE  C26   C  CH3   0  -0.407   6.5651  -0.9385   0.6519
 3RE  H10   H  HCR6  0   0.275  -3.7714  -0.0232  -0.0441
 3RE  HN11  H  HNH2  0   0.406  -0.5926   5.6343   0.0856
 3RE  HN1A  H  HNH2  0   0.405   0.9208   4.7990   0.0217
 3RE  H12   H  HCH3  0   0.265  -4.6512   2.1480  -0.8206
 3RE  H12A  H  HCH3  0   0.263  -4.6124   2.0049   0.9290
 3RE  H12B  H  HCH3  0   0.268  -4.5542   3.6042   0.1764
 3RE  H14   H  HCH1  0   0.275   1.7569   1.3372  -0.0879
 3RE  H15   H  HCH2  0   0.239   2.0506  -1.3571  -1.4509
 3RE  H15A  H  HCH2  0   0.243   1.7192   0.1753  -2.2432
 3RE  H16   H  HCH2  0   0.241   4.1504  -0.3840  -2.2644
 3RE  H16A  H  HCH2  0   0.223   3.8379   1.1222  -1.4127
 3RE  H17   H  HCH1  0   0.191   4.2488  -1.6164  -0.1348
 3RE  H18   H  HCH2  0   0.243   4.1756  -0.4069   2.0300
 3RE  H18A  H  HCH2  0   0.222   3.8610   1.1043   1.1902
 3RE  H19   H  HCH2  0   0.241   1.7561   0.1423   2.0489
 3RE  H19A  H  HCH2  0   0.239   2.0735  -1.3779   1.2285
 3RE  H22   H  HCR5  0   0.264  -4.3444  -2.1529   1.3485
 3RE  H23   H  HCR5  0   0.290  -4.8786  -4.7319   0.5635
 3RE  H26   H  HCH3  0   0.205   6.4015  -0.7111   1.7108
 3RE  H26A  H  HCH3  0   0.202   6.4275  -2.0181   0.5163
 3RE  H26B  H  HCH3  0   0.234   7.6000  -0.6942   0.4136
 3RE  HN24  H  HNR5  0   0.422  -3.0671  -5.2830  -1.1036

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
 3RE  N1   C6    aromatic  1.314  0.020  1.314
 3RE  N1   C2    aromatic  1.347  0.020  1.347
 3RE  N11  C2    single    1.336  0.020  1.336
 3RE  C2   N3    aromatic  1.329  0.020  1.329
 3RE  N3   C4    aromatic  1.323  0.020  1.323
 3RE  C5   C4    aromatic  1.405  0.020  1.405
 3RE  C4   N7    single    1.375  0.020  1.375
 3RE  C6   C5    aromatic  1.409  0.020  1.409
 3RE  C5   C10   single    1.415  0.020  1.415
 3RE  C12  C6    single    1.495  0.020  1.495
 3RE  N7   C8    single    1.396  0.020  1.396
 3RE  N7   C14   single    1.478  0.020  1.478
 3RE  C9   C8    single    1.460  0.020  1.460
 3RE  C8   O13   double    1.219  0.020  1.219
 3RE  C10  C9    double    1.353  0.020  1.353
 3RE  C9   C21   single    1.465  0.020  1.465
 3RE  C10  H10   single    0.930  0.020  1.080
 3RE  N11  HN11  single    0.860  0.020  1.020
 3RE  N11  HN1A  single    0.860  0.020  1.020
 3RE  C12  H12   single    0.970  0.020  1.090
 3RE  C12  H12A  single    0.970  0.020  1.090
 3RE  C12  H12B  single    0.970  0.020  1.090
 3RE  C19  C14   single    1.526  0.020  1.526
 3RE  C14  C15   single    1.526  0.020  1.526
 3RE  C14  H14   single    0.970  0.020  1.090
 3RE  C15  C16   single    1.527  0.020  1.527
 3RE  C15  H15   single    0.970  0.020  1.090
 3RE  C15  H15A  single    0.970  0.020  1.090
 3RE  C17  C16   single    1.522  0.020  1.522
 3RE  C16  H16   single    0.970  0.020  1.090
 3RE  C16  H16A  single    0.970  0.020  1.090
 3RE  C18  C17   single    1.527  0.020  1.527
 3RE  C17  O20   single    1.412  0.020  1.412
 3RE  C17  H17   single    0.970  0.020  1.090
 3RE  C19  C18   single    1.528  0.020  1.528
 3RE  C18  H18   single    0.970  0.020  1.090
 3RE  C18  H18A  single    0.970  0.020  1.090
 3RE  C19  H19   single    0.970  0.020  1.090
 3RE  C19  H19A  single    0.970  0.020  1.090
 3RE  O20  C26   single    1.405  0.020  1.405
 3RE  C22  C21   aromatic  1.412  0.020  1.412
 3RE  C21  N25   aromatic  1.325  0.020  1.325
 3RE  C22  C23   aromatic  1.373  0.020  1.373
 3RE  C22  H22   single    0.930  0.020  1.080
 3RE  C23  N24   aromatic  1.343  0.020  1.343
 3RE  C23  H23   single    0.930  0.020  1.080
 3RE  N25  N24   aromatic  1.324  0.020  1.324
 3RE  C26  H26   single    0.970  0.020  1.090
 3RE  C26  H26A  single    0.970  0.020  1.090
 3RE  C26  H26B  single    0.970  0.020  1.090
 3RE  N24  HN24  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
 3RE  C6    N1   C2    117.06  3.000
 3RE  N11   C2   N3    117.53  3.000
 3RE  N3    C2   N1    125.98  3.000
 3RE  N11   C2   N1    116.49  3.000
 3RE  C4    N3   C2    117.21  3.000
 3RE  N7    C4   C5    119.75  3.000
 3RE  N7    C4   N3    118.58  3.000
 3RE  C5    C4   N3    121.67  3.000
 3RE  C10   C5   C6    124.51  3.000
 3RE  C10   C5   C4    119.18  3.000
 3RE  C6    C5   C4    116.31  3.000
 3RE  C12   C6   C5    120.80  3.000
 3RE  C12   C6   N1    117.43  3.000
 3RE  C5    C6   N1    121.77  3.000
 3RE  C14   N7   C8    119.04  3.000
 3RE  C14   N7   C4    118.56  3.000
 3RE  C8    N7   C4    122.40  3.000
 3RE  O13   C8   C9    122.40  3.000
 3RE  O13   C8   N7    120.34  3.000
 3RE  C9    C8   N7    117.26  3.000
 3RE  C21   C9   C10   120.37  3.000
 3RE  C21   C9   C8    119.55  3.000
 3RE  C10   C9   C8    120.04  3.000
 3RE  H10   C10  C9    119.41  3.000
 3RE  H10   C10  C5    119.24  3.000
 3RE  C9    C10  C5    121.34  3.000
 3RE  HN1A  N11  HN11  118.86  3.000
 3RE  HN1A  N11  C2    120.61  3.000
 3RE  HN11  N11  C2    120.42  3.000
 3RE  H12B  C12  H12A  108.60  3.000
 3RE  H12B  C12  H12   108.46  3.000
 3RE  H12A  C12  H12   107.16  3.000
 3RE  H12B  C12  C6    110.24  3.000
 3RE  H12A  C12  C6    111.26  3.000
 3RE  H12   C12  C6    111.02  3.000
 3RE  H14   C14  C19   106.36  3.000
 3RE  H14   C14  C15   106.39  3.000
 3RE  C19   C14  C15   112.10  3.000
 3RE  H14   C14  N7    104.01  3.000
 3RE  C15   C14  N7    113.54  3.000
 3RE  C19   C14  N7    113.55  3.000
 3RE  H15A  C15  H15   107.22  3.000
 3RE  H15A  C15  C16   109.76  3.000
 3RE  H15   C15  C16   109.49  3.000
 3RE  H15A  C15  C14   109.76  3.000
 3RE  H15   C15  C14   111.21  3.000
 3RE  C16   C15  C14   109.36  3.000
 3RE  H16A  C16  H16   106.95  3.000
 3RE  H16A  C16  C17   109.42  3.000
 3RE  H16   C16  C17   109.70  3.000
 3RE  H16A  C16  C15   109.93  3.000
 3RE  H16   C16  C15   109.54  3.000
 3RE  C17   C16  C15   111.21  3.000
 3RE  H17   C17  O20   109.43  3.000
 3RE  H17   C17  C18   108.06  3.000
 3RE  O20   C17  C18   112.63  3.000
 3RE  H17   C17  C16   108.11  3.000
 3RE  O20   C17  C16   107.73  3.000
 3RE  C18   C17  C16   110.79  3.000
 3RE  H18A  C18  H18   106.85  3.000
 3RE  H18A  C18  C19   110.04  3.000
 3RE  H18   C18  C19   108.95  3.000
 3RE  H18A  C18  C17   109.12  3.000
 3RE  H18   C18  C17   110.71  3.000
 3RE  C19   C18  C17   111.07  3.000
 3RE  H19A  C19  H19   107.20  3.000
 3RE  H19A  C19  C18   109.55  3.000
 3RE  H19   C19  C18   109.70  3.000
 3RE  H19A  C19  C14   111.27  3.000
 3RE  H19   C19  C14   109.77  3.000
 3RE  C18   C19  C14   109.32  3.000
 3RE  C26   O20  C17   114.51  3.000
 3RE  N25   C21  C22   110.76  3.000
 3RE  N25   C21  C9    123.02  3.000
 3RE  C22   C21  C9    126.18  3.000
 3RE  H22   C22  C23   127.51  3.000
 3RE  H22   C22  C21   127.87  3.000
 3RE  C23   C22  C21   104.61  3.000
 3RE  H23   C23  N24   122.06  3.000
 3RE  H23   C23  C22   131.84  3.000
 3RE  N24   C23  C22   106.10  3.000
 3RE  HN24  N24  N25   119.59  3.000
 3RE  HN24  N24  C23   126.96  3.000
 3RE  N25   N24  C23   113.45  3.000
 3RE  N24   N25  C21   105.08  3.000
 3RE  H26B  C26  H26A  108.23  3.000
 3RE  H26B  C26  H26   107.86  3.000
 3RE  H26A  C26  H26   107.77  3.000
 3RE  H26B  C26  O20   107.80  3.000
 3RE  H26A  C26  O20   111.84  3.000
 3RE  H26   C26  O20   113.18  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
 3RE  CONST_01  C4    C5   C6   N1     0.00   0.0  0
 3RE  CONST_02  C4    N3   C2   N1     0.00   0.0  0
 3RE  CONST_03  C5    C6   N1   C2     0.00   0.0  0
 3RE  CONST_04  C5    C4   N3   C2     0.00   0.0  0
 3RE  CONST_05  C6    N1   C2   N3     0.00   0.0  0
 3RE  CONST_06  C6    C5   C4   N3     0.00   0.0  0
 3RE  CONST_07  N24   C23  C22  C21    0.00   0.0  0
 3RE  CONST_08  C23   N24  N25  C21    0.00   0.0  0
 3RE  CONST_09  N24   N25  C21  C22    0.00   0.0  0
 3RE  CONST_10  N25   N24  C23  C22    0.00   0.0  0
 3RE  CONST_11  N25   C21  C22  C23    0.00   0.0  0
 3RE  CONST_12  C23   C22  C21  C9   180.00   0.0  0
 3RE  CONST_13  N24   N25  C21  C9   180.00   0.0  0
 3RE  CONST_14  C9    C8   N7   C4     0.00   0.0  0
 3RE  CONST_15  C14   N7   C8   C9   180.00   0.0  0
 3RE  CONST_16  C12   C6   N1   C2   180.00   0.0  0
 3RE  CONST_17  N11   C2   N3   C4   180.00   0.0  0
 3RE  CONST_18  C12   C6   C5   C4   180.00   0.0  0
 3RE  CONST_19  N11   C2   N1   C6   180.00   0.0  0
 3RE  CONST_20  C12   C6   C5   C10    0.00   0.0  0
 3RE  CONST_21  O13   C8   N7   C4   180.00   0.0  0
 3RE  CONST_22  C14   N7   C8   O13    0.00   0.0  0
 3RE  CONST_23  H22   C22  C21  C9     0.00   0.0  0
 3RE  CONST_24  H23   C23  C22  C21  180.00   0.0  0
 3RE  CONST_25  HN24  N24  N25  C21  180.00   0.0  0
 3RE  CONST_26  HN11  N11  C2   N1     0.00   0.0  0
 3RE  CONST_27  HN1A  N11  C2   N1   180.00   0.0  0
 3RE  Var_01    C22   C21  C9   C8   139.61  30.0  2
 3RE  Var_02    C17   C18  C19  C14  -56.54  30.0  1
 3RE  Var_03    C17   C16  C15  C14   56.54  30.0  1
 3RE  Var_04    H12   C12  C6   N1   117.24  30.0  2
 3RE  Var_05    H26   C26  O20  C17  -67.88  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
 3RE  chir_01  C14  N7   C19  C15  negativ
 3RE  chir_02  C17  O20  C16  C18  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
 3RE  plan-1  C9    0.020
 3RE  plan-1  C21   0.020
 3RE  plan-1  C22   0.020
 3RE  plan-1  C23   0.020
 3RE  plan-1  N24   0.020
 3RE  plan-1  N25   0.020
 3RE  plan-1  H22   0.020
 3RE  plan-1  H23   0.020
 3RE  plan-1  HN24  0.020
 3RE  plan-2  N1    0.020
 3RE  plan-2  C2    0.020
 3RE  plan-2  N3    0.020
 3RE  plan-2  C4    0.020
 3RE  plan-2  C5    0.020
 3RE  plan-2  C6    0.020
 3RE  plan-2  N7    0.020
 3RE  plan-2  C8    0.020
 3RE  plan-2  C9    0.020
 3RE  plan-2  C10   0.020
 3RE  plan-2  N11   0.020
 3RE  plan-2  C12   0.020
 3RE  plan-2  O13   0.020
 3RE  plan-2  C14   0.020
 3RE  plan-2  C21   0.020
 3RE  plan-2  H10   0.020
 3RE  plan-3  C2    0.020
 3RE  plan-3  N11   0.020
 3RE  plan-3  HN11  0.020
 3RE  plan-3  HN1A  0.020

