# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Mar 18 06:46:15 2020
#   Inital geometry file: a 104 line input string
#   Ligand name: 2-amino-8-cyclopentyl-4-methyl-6-(1H-pyrazol-4-yl)pyrido[2,3-d]pyrimidin-7(8H)-one
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cc1nc(N)nc2N(C3CCCC3)C(=O)C(=Cc12)c4c[nH]nc4
#
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
 0TA  0TA  2-amino-8-cyclopentyl-4-methyl-6-(1H-pyrazol-4-yl)pyrido[2,3-d]pyrimidin-7(8H)-one  ligand  41  23  .  2021-08-03  2021-08-03  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_0TA
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
 0TA  N1   N  NH2   0  -0.814   4.8413  -0.2065   0.1327
 0TA  N3   N  NR6   0  -0.614   0.3686   0.8457  -0.0743
 0TA  C4   C  CH1   0  -0.094   0.7264   2.2726  -0.1305
 0TA  C5   C  CH2   0  -0.447   0.3860   3.0612   1.1461
 0TA  C6   C  CH2   0  -0.453   0.1350   4.4791   0.6351
 0TA  C7   C  CH2   0  -0.434  -0.6002   4.2574  -0.6865
 0TA  C8   C  CH2   0  -0.448   0.1306   3.0706  -1.3181
 0TA  C10  C  CR6   0  -0.133  -1.3195  -0.9166  -0.0377
 0TA  C13  C  CR5   0  -0.108  -2.7291  -1.2952  -0.0360
 0TA  C15  C  CR15  0  -0.002  -3.2710  -2.4296   0.5405
 0TA  C9   C  CR6   0   0.541  -0.9799   0.5031  -0.0616
 0TA  N5   N  NR15  0  -0.427  -4.5810  -2.4130   0.2639
 0TA  N4   N  N     0  -0.268  -4.9513  -1.3557  -0.4488
 0TA  C14  C  CR15  0  -0.097  -3.8436  -0.6654  -0.6363
 0TA  C11  C  CR16  0  -0.257  -0.3298  -1.8401   0.0085
 0TA  C12  C  CR66  0  -0.108   1.0332  -1.4580   0.0503
 0TA  C1   C  CR6   0   0.269   2.1139  -2.3584   0.1272
 0TA  C    C  CH3   0  -0.762   1.8779  -3.8337   0.1735
 0TA  C3   C  CR66  0   0.568   1.3676  -0.0941   0.0056
 0TA  N2   N  N     0  -0.510   2.6245   0.3195   0.0379
 0TA  C2   C  CR6   0   0.564   3.5670  -0.6139   0.1132
 0TA  N    N  N     0  -0.482   3.3606  -1.9438   0.1604
 0TA  H5   H  HNH2  0   0.403   5.0587   0.7730   0.1852
 0TA  H4   H  HNH2  0   0.404   5.5786  -0.8711   0.2863
 0TA  H6   H  HCH1  0   0.290   1.8047   2.2737  -0.2402
 0TA  H8   H  HCH2  0   0.239  -0.5128   2.6780   1.6283
 0TA  H7   H  HCH2  0   0.235   1.1969   3.0033   1.8735
 0TA  H9   H  HCH2  0   0.233  -0.4281   5.0867   1.3449
 0TA  H10  H  HCH2  0   0.219   1.0846   4.9903   0.4527
 0TA  H12  H  HCH2  0   0.226  -1.6406   3.9966  -0.4900
 0TA  H11  H  HCH2  0   0.225  -0.5959   5.1398  -1.3282
 0TA  H13  H  HCH2  0   0.233   0.9588   3.4301  -1.9324
 0TA  H14  H  HCH2  0   0.243  -0.5049   2.4768  -1.9725
 0TA  H17  H  HCR5  0   0.290  -2.8244  -3.2160   1.1273
 0TA  H    H  HNR5  0   0.422  -5.2682  -3.0912   0.5514
 0TA  H16  H  HCR5  0   0.254  -3.8681   0.2526  -1.2000
 0TA  H15  H  HCR6  0   0.270  -0.5807  -2.8941   0.0075
 0TA  H2   H  HCH3  0   0.264   1.3827  -4.1767  -0.7364
 0TA  H1   H  HCH3  0   0.268   2.8206  -4.3650   0.2744
 0TA  H3   H  HCH3  0   0.262   1.2344  -4.1058   1.0112
 0TA  O    O  O     0  -0.463  -1.8333   1.3765  -0.0739

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
 0TA  C    C1   single    1.495  0.020  1.495
 0TA  N    C1   aromatic  1.314  0.020  1.314
 0TA  N    C2   aromatic  1.347  0.020  1.347
 0TA  C1   C12  aromatic  1.409  0.020  1.409
 0TA  N1   C2   single    1.338  0.020  1.338
 0TA  C2   N2   aromatic  1.329  0.020  1.329
 0TA  C12  C11  single    1.416  0.020  1.416
 0TA  C12  C3   aromatic  1.405  0.020  1.405
 0TA  C11  C10  double    1.354  0.020  1.354
 0TA  N2   C3   aromatic  1.324  0.020  1.324
 0TA  C3   N3   single    1.374  0.020  1.374
 0TA  C14  N4   aromatic  1.319  0.020  1.319
 0TA  C14  C13  aromatic  1.414  0.020  1.414
 0TA  C10  C13  single    1.460  0.020  1.460
 0TA  C10  C9   single    1.460  0.020  1.460
 0TA  N4   N5   aromatic  1.328  0.020  1.328
 0TA  N3   C9   single    1.391  0.020  1.391
 0TA  N3   C4   single    1.472  0.020  1.472
 0TA  C13  C15  aromatic  1.383  0.020  1.383
 0TA  C9   O    double    1.221  0.020  1.221
 0TA  C8   C4   single    1.550  0.020  1.550
 0TA  C8   C7   single    1.530  0.020  1.530
 0TA  C4   C5   single    1.539  0.020  1.539
 0TA  N5   C15  aromatic  1.339  0.020  1.339
 0TA  C7   C6   single    1.529  0.020  1.529
 0TA  C5   C6   single    1.528  0.020  1.528
 0TA  N1   H5   single    0.860  0.020  1.020
 0TA  N1   H4   single    0.860  0.020  1.020
 0TA  C4   H6   single    0.970  0.020  1.090
 0TA  C5   H8   single    0.970  0.020  1.090
 0TA  C5   H7   single    0.970  0.020  1.090
 0TA  C6   H9   single    0.970  0.020  1.090
 0TA  C6   H10  single    0.970  0.020  1.090
 0TA  C7   H12  single    0.970  0.020  1.090
 0TA  C7   H11  single    0.970  0.020  1.090
 0TA  C8   H13  single    0.970  0.020  1.090
 0TA  C8   H14  single    0.970  0.020  1.090
 0TA  C15  H17  single    0.930  0.020  1.080
 0TA  N5   H    single    0.860  0.020  1.020
 0TA  C14  H16  single    0.930  0.020  1.080
 0TA  C11  H15  single    0.930  0.020  1.080
 0TA  C    H2   single    0.970  0.020  1.090
 0TA  C    H1   single    0.970  0.020  1.090
 0TA  C    H3   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
 0TA  H4   N1   H5   118.57  3.000
 0TA  H4   N1   C2   119.99  3.000
 0TA  H5   N1   C2   120.25  3.000
 0TA  C3   N3   C9   122.39  3.000
 0TA  C9   N3   C4   118.33  3.000
 0TA  C3   N3   C4   119.25  3.000
 0TA  H6   C4   C8   107.72  3.000
 0TA  H6   C4   C5   107.67  3.000
 0TA  C8   C4   C5   106.67  3.000
 0TA  H6   C4   N3   104.28  3.000
 0TA  C5   C4   N3   114.29  3.000
 0TA  C8   C4   N3   115.78  3.000
 0TA  H7   C5   H8   107.43  3.000
 0TA  H7   C5   C6   113.23  3.000
 0TA  H8   C5   C6   109.81  3.000
 0TA  H7   C5   C4   111.20  3.000
 0TA  H8   C5   C4   111.68  3.000
 0TA  C6   C5   C4   103.56  3.000
 0TA  H10  C6   H9   107.24  3.000
 0TA  H10  C6   C7   109.95  3.000
 0TA  H9   C6   C7   113.27  3.000
 0TA  H10  C6   C5   110.30  3.000
 0TA  H9   C6   C5   112.58  3.000
 0TA  C7   C6   C5   103.51  3.000
 0TA  H11  C7   H12  107.65  3.000
 0TA  H11  C7   C8   112.50  3.000
 0TA  H12  C7   C8   110.16  3.000
 0TA  H11  C7   C6   112.91  3.000
 0TA  H12  C7   C6   109.74  3.000
 0TA  C8   C7   C6   103.86  3.000
 0TA  H14  C8   H13  106.51  3.000
 0TA  H14  C8   C7   113.10  3.000
 0TA  H13  C8   C7   109.81  3.000
 0TA  H14  C8   C4   113.85  3.000
 0TA  H13  C8   C4   108.00  3.000
 0TA  C7   C8   C4   105.47  3.000
 0TA  C11  C10  C9   119.58  3.000
 0TA  C9   C10  C13  118.48  3.000
 0TA  C11  C10  C13  121.93  3.000
 0TA  C14  C13  C15  103.50  3.000
 0TA  C15  C13  C10  126.27  3.000
 0TA  C14  C13  C10  130.18  3.000
 0TA  H17  C15  N5   121.79  3.000
 0TA  H17  C15  C13  131.52  3.000
 0TA  N5   C15  C13  106.68  3.000
 0TA  O    C9   C10  122.22  3.000
 0TA  O    C9   N3   120.07  3.000
 0TA  C10  C9   N3   117.71  3.000
 0TA  H    N5   N4   119.94  3.000
 0TA  H    N5   C15  126.87  3.000
 0TA  N4   N5   C15  113.18  3.000
 0TA  C14  N4   N5   105.01  3.000
 0TA  H16  C14  N4   120.09  3.000
 0TA  H16  C14  C13  128.28  3.000
 0TA  N4   C14  C13  111.63  3.000
 0TA  H15  C11  C12  119.04  3.000
 0TA  H15  C11  C10  119.61  3.000
 0TA  C12  C11  C10  121.35  3.000
 0TA  C3   C12  C1   116.08  3.000
 0TA  C3   C12  C11  119.34  3.000
 0TA  C1   C12  C11  124.57  3.000
 0TA  N    C1   C    117.41  3.000
 0TA  N    C1   C12  121.83  3.000
 0TA  C    C1   C12  120.76  3.000
 0TA  H3   C    H1   108.57  3.000
 0TA  H3   C    H2   107.11  3.000
 0TA  H1   C    H2   108.50  3.000
 0TA  H3   C    C1   111.29  3.000
 0TA  H1   C    C1   110.38  3.000
 0TA  H2   C    C1   110.86  3.000
 0TA  N2   C3   C12  121.91  3.000
 0TA  N2   C3   N3   118.56  3.000
 0TA  C12  C3   N3   119.53  3.000
 0TA  C2   N2   C3   117.09  3.000
 0TA  N    C2   N2   125.95  3.000
 0TA  N2   C2   N1   117.55  3.000
 0TA  N    C2   N1   116.50  3.000
 0TA  C2   N    C1   117.13  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
 0TA  CONST_01  N5   N4   C14  C13    0.00   0.0  0
 0TA  CONST_02  N4   N5   C15  C13    0.00   0.0  0
 0TA  CONST_03  N4   C14  C13  C15    0.00   0.0  0
 0TA  CONST_04  C14  N4   N5   C15    0.00   0.0  0
 0TA  CONST_05  C14  C13  C15  N5     0.00   0.0  0
 0TA  CONST_06  C2   N    C1   C12    0.00   0.0  0
 0TA  CONST_07  C2   N2   C3   C12    0.00   0.0  0
 0TA  CONST_08  N2   C2   N    C1     0.00   0.0  0
 0TA  CONST_09  N2   C3   C12  C1     0.00   0.0  0
 0TA  CONST_10  N    C1   C12  C3     0.00   0.0  0
 0TA  CONST_11  N    C2   N2   C3     0.00   0.0  0
 0TA  CONST_12  N4   C14  C13  C10  180.00   0.0  0
 0TA  CONST_13  N5   C15  C13  C10  180.00   0.0  0
 0TA  CONST_14  C10  C9   N3   C4   180.00   0.0  0
 0TA  CONST_15  C3   N3   C9   C10    0.00   0.0  0
 0TA  CONST_16  C1   N    C2   N1   180.00   0.0  0
 0TA  CONST_17  C3   N2   C2   N1   180.00   0.0  0
 0TA  CONST_18  C    C1   C12  C11    0.00   0.0  0
 0TA  CONST_19  C2   N    C1   C    180.00   0.0  0
 0TA  CONST_20  C3   C12  C1   C    180.00   0.0  0
 0TA  CONST_21  O    C9   N3   C4     0.00   0.0  0
 0TA  CONST_22  C3   N3   C9   O    180.00   0.0  0
 0TA  CONST_23  H16  C14  C13  C10    0.00   0.0  0
 0TA  CONST_24  H17  C15  C13  C10    0.00   0.0  0
 0TA  CONST_25  H    N5   C15  C13  180.00   0.0  0
 0TA  CONST_26  H5   N1   C2   N2     0.00   0.0  0
 0TA  CONST_27  H4   N1   C2   N2   180.00   0.0  0
 0TA  Var_01    C6   C7   C8   C4    26.60  30.0  1
 0TA  Var_02    C7   C6   C5   C4    38.47  30.0  1
 0TA  Var_03    C8   C7   C6   C5   -40.66  30.0  1
 0TA  Var_04    C11  C10  C13  C15   28.73  30.0  1
 0TA  Var_05    H2   C    C1   C12   62.18  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
 0TA  chir_01  C4  N3  C8  C5  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
 0TA  plan-1  C10  0.020
 0TA  plan-1  C13  0.020
 0TA  plan-1  C15  0.020
 0TA  plan-1  N5   0.020
 0TA  plan-1  N4   0.020
 0TA  plan-1  C14  0.020
 0TA  plan-1  H17  0.020
 0TA  plan-1  H    0.020
 0TA  plan-1  H16  0.020
 0TA  plan-2  N1   0.020
 0TA  plan-2  N3   0.020
 0TA  plan-2  C4   0.020
 0TA  plan-2  C10  0.020
 0TA  plan-2  C13  0.020
 0TA  plan-2  C9   0.020
 0TA  plan-2  C11  0.020
 0TA  plan-2  C12  0.020
 0TA  plan-2  C1   0.020
 0TA  plan-2  C    0.020
 0TA  plan-2  C3   0.020
 0TA  plan-2  N2   0.020
 0TA  plan-2  C2   0.020
 0TA  plan-2  N    0.020
 0TA  plan-2  H15  0.020
 0TA  plan-2  O    0.020
 0TA  plan-3  N1   0.020
 0TA  plan-3  C2   0.020
 0TA  plan-3  H5   0.020
 0TA  plan-3  H4   0.020

