# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Mar 23 16:56:08 2020
#   Inital geometry file: a 105 line input string
#   Ligand name: (1R,2S)-2-{[8-oxo-2-(1H-pyrazol-4-yl)-5,8-dihydropyrido[3,4-d]pyrimidin-4-yl]amino}cyclopentanecarbonitrile
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: O=C1N=CCc2c(N[C@H]3CCC[C@H]3C#N)nc(nc12)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
 1Q3  1Q3  (1R,2S)-2-{[8-oxo-2-(1H-pyrazol-4-yl)-5,8-dihydropyrido[3,4-d]pyrimidin-4-yl]amino}cyclopentanecarbonitrile  ligand  39  24  .  2021-08-03  2021-08-03  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_1Q3
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
 1Q3  C1   C  C     0  -0.625   0.9101  -2.6271   0.4273
 1Q3  C2   C  CR16  0   0.018   0.2099  -3.9304   0.5119
 1Q3  N3   N  N     0  -0.409  -1.0417  -4.1440   0.4181
 1Q3  C5   C  CR6   0   0.440  -1.9143  -3.0692   0.2085
 1Q3  O6   O  O     0  -0.379  -3.0956  -3.2816   0.0952
 1Q3  C7   C  CR66  0   0.067  -1.3660  -1.6805   0.1276
 1Q3  C8   C  CR66  0   0.002  -0.0134  -1.4833   0.2344
 1Q3  C9   C  CR6   0   0.575   0.4222  -0.1345   0.1305
 1Q3  N10  N  N     0  -0.489  -0.4544   0.8402  -0.0509
 1Q3  C11  C  CR6   0   0.345  -1.7465   0.5208  -0.1373
 1Q3  N12  N  N     0  -0.464  -2.2513  -0.6974  -0.0558
 1Q3  C13  C  CR5   0  -0.187  -2.6718   1.6241  -0.3340
 1Q3  C14  C  CR15  0   0.033  -4.0479   1.5587  -0.4491
 1Q3  N15  N  NR15  0  -0.422  -4.4667   2.8157  -0.6144
 1Q3  N17  N  N     0  -0.262  -3.4780   3.7084  -0.6180
 1Q3  C18  C  CR15  0  -0.080  -2.3816   2.9997  -0.4487
 1Q3  N19  N  NH1   0  -0.689   1.7312   0.1646   0.1992
 1Q3  C20  C  CH1   0  -0.122   2.2685   1.5062   0.1427
 1Q3  C21  C  CH2   0  -0.442   2.8021   1.9829   1.4930
 1Q3  C22  C  CH2   0  -0.463   4.1518   1.2674   1.6532
 1Q3  C23  C  CH2   0  -0.460   4.6456   0.9557   0.2220
 1Q3  C24  C  CH1   0  -0.366   3.5531   1.5317  -0.7061
 1Q3  C25  C  CSP   0   0.136   3.4243   0.8317  -1.9714
 1Q3  N26  N  NS    0  -0.266   3.3260   0.2712  -2.9718
 1Q3  H1   H  H     0   0.315   1.5130  -2.5271   1.3396
 1Q3  H2   H  H     0   0.314   1.6437  -2.7045  -0.3861
 1Q3  H3   H  HCR6  0   0.292   0.8472  -4.7965   0.6736
 1Q3  H4   H  HCR5  0   0.294  -4.7283   0.7243  -0.4244
 1Q3  H5   H  HNR5  0   0.427  -5.4196   3.1237  -0.7289
 1Q3  H6   H  HCR5  0   0.262  -1.4151   3.4781  -0.4121
 1Q3  H7   H  HNH1  0   0.415   2.3638  -0.5751   0.4620
 1Q3  H8   H  HCH1  0   0.302   1.5004   2.1575  -0.2659
 1Q3  H9   H  HCH2  0   0.250   2.9449   3.0644   1.4479
 1Q3  H10  H  HCH2  0   0.261   2.1026   1.7793   2.3034
 1Q3  H11  H  HCH2  0   0.256   4.8644   1.8811   2.2018
 1Q3  H12  H  HCH2  0   0.247   4.0336   0.3431   2.2200
 1Q3  H13  H  HCH2  0   0.275   5.6109   1.4061  -0.0009
 1Q3  H14  H  HCH2  0   0.258   4.7580  -0.1186   0.0691
 1Q3  H15  H  HCH1  0   0.339   3.7810   2.5765  -0.9320

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
 1Q3  N15  C14  aromatic  1.335  0.020  1.335
 1Q3  N15  N17  aromatic  1.332  0.020  1.332
 1Q3  C14  C13  aromatic  1.382  0.020  1.382
 1Q3  N17  C18  aromatic  1.316  0.020  1.316
 1Q3  C13  C18  aromatic  1.411  0.020  1.411
 1Q3  C13  C11  single    1.453  0.020  1.453
 1Q3  N12  C11  aromatic  1.321  0.020  1.321
 1Q3  N12  C7   aromatic  1.336  0.020  1.336
 1Q3  C11  N10  aromatic  1.334  0.020  1.334
 1Q3  O6   C5   double    1.206  0.020  1.206
 1Q3  C5   C7   single    1.495  0.020  1.495
 1Q3  C5   N3   single    1.400  0.020  1.400
 1Q3  C7   C8   aromatic  1.371  0.020  1.371
 1Q3  N10  C9   aromatic  1.323  0.020  1.323
 1Q3  C9   C8   aromatic  1.421  0.020  1.421
 1Q3  C9   N19  single    1.345  0.020  1.345
 1Q3  N3   C2   double    1.273  0.020  1.273
 1Q3  C8   C1   single    1.483  0.020  1.483
 1Q3  N19  C20  single    1.446  0.020  1.446
 1Q3  C2   C1   single    1.482  0.020  1.482
 1Q3  C21  C20  single    1.528  0.020  1.528
 1Q3  C21  C22  single    1.536  0.020  1.536
 1Q3  C20  C24  single    1.540  0.020  1.540
 1Q3  C22  C23  single    1.546  0.020  1.546
 1Q3  C23  C24  single    1.545  0.020  1.545
 1Q3  C24  C25  single    1.452  0.020  1.452
 1Q3  C25  N26  triple    1.151  0.020  1.151
 1Q3  C1   H1   single    0.970  0.020  1.090
 1Q3  C1   H2   single    0.970  0.020  1.090
 1Q3  C2   H3   single    0.930  0.020  1.080
 1Q3  C14  H4   single    0.930  0.020  1.080
 1Q3  N15  H5   single    0.860  0.020  1.020
 1Q3  C18  H6   single    0.930  0.020  1.080
 1Q3  N19  H7   single    0.860  0.020  1.020
 1Q3  C20  H8   single    0.970  0.020  1.090
 1Q3  C21  H9   single    0.970  0.020  1.090
 1Q3  C21  H10  single    0.970  0.020  1.090
 1Q3  C22  H11  single    0.970  0.020  1.090
 1Q3  C22  H12  single    0.970  0.020  1.090
 1Q3  C23  H13  single    0.970  0.020  1.090
 1Q3  C23  H14  single    0.970  0.020  1.090
 1Q3  C24  H15  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
 1Q3  H2   C1   H1   104.77  3.000
 1Q3  H2   C1   C8   111.97  3.000
 1Q3  H1   C1   C8   112.33  3.000
 1Q3  H2   C1   C2   107.21  3.000
 1Q3  H1   C1   C2   106.98  3.000
 1Q3  C8   C1   C2   113.05  3.000
 1Q3  H3   C2   N3   116.97  3.000
 1Q3  H3   C2   C1   115.60  3.000
 1Q3  N3   C2   C1   127.44  3.000
 1Q3  C5   N3   C2   119.66  3.000
 1Q3  C7   C5   O6   121.19  3.000
 1Q3  C7   C5   N3   119.50  3.000
 1Q3  O6   C5   N3   119.30  3.000
 1Q3  N12  C7   C8   123.97  3.000
 1Q3  C8   C7   C5   119.42  3.000
 1Q3  N12  C7   C5   116.61  3.000
 1Q3  C9   C8   C7   115.67  3.000
 1Q3  C9   C8   C1   123.42  3.000
 1Q3  C7   C8   C1   120.91  3.000
 1Q3  N19  C9   N10  119.21  3.000
 1Q3  N19  C9   C8   120.38  3.000
 1Q3  N10  C9   C8   120.40  3.000
 1Q3  C11  N10  C9   118.30  3.000
 1Q3  C13  C11  N12  117.72  3.000
 1Q3  N12  C11  N10  125.94  3.000
 1Q3  C13  C11  N10  116.34  3.000
 1Q3  C11  N12  C7   115.72  3.000
 1Q3  C18  C13  C14  104.13  3.000
 1Q3  C18  C13  C11  128.35  3.000
 1Q3  C14  C13  C11  127.52  3.000
 1Q3  H4   C14  N15  122.28  3.000
 1Q3  H4   C14  C13  131.58  3.000
 1Q3  N15  C14  C13  106.14  3.000
 1Q3  H5   N15  N17  119.77  3.000
 1Q3  H5   N15  C14  126.75  3.000
 1Q3  N17  N15  C14  113.48  3.000
 1Q3  C18  N17  N15  104.89  3.000
 1Q3  H6   C18  N17  120.77  3.000
 1Q3  H6   C18  C13  127.87  3.000
 1Q3  N17  C18  C13  111.36  3.000
 1Q3  H7   N19  C20  117.24  3.000
 1Q3  H7   N19  C9   117.45  3.000
 1Q3  C20  N19  C9   124.48  3.000
 1Q3  H8   C20  C24  111.86  3.000
 1Q3  H8   C20  C21  113.09  3.000
 1Q3  C24  C20  C21  100.99  3.000
 1Q3  H8   C20  N19  107.94  3.000
 1Q3  C24  C20  N19  110.29  3.000
 1Q3  C21  C20  N19  112.62  3.000
 1Q3  H10  C21  H9   107.44  3.000
 1Q3  H10  C21  C22  113.54  3.000
 1Q3  H9   C21  C22  110.54  3.000
 1Q3  H10  C21  C20  112.01  3.000
 1Q3  H9   C21  C20  108.55  3.000
 1Q3  C22  C21  C20  104.70  3.000
 1Q3  H12  C22  H11  106.66  3.000
 1Q3  H12  C22  C23  110.17  3.000
 1Q3  H11  C22  C23  111.78  3.000
 1Q3  H12  C22  C21  110.72  3.000
 1Q3  H11  C22  C21  111.42  3.000
 1Q3  C23  C22  C21  106.15  3.000
 1Q3  H14  C23  H13  106.70  3.000
 1Q3  H14  C23  C24  110.84  3.000
 1Q3  H13  C23  C24  110.48  3.000
 1Q3  H14  C23  C22  111.18  3.000
 1Q3  H13  C23  C22  112.93  3.000
 1Q3  C24  C23  C22  104.78  3.000
 1Q3  H15  C24  C25  107.41  3.000
 1Q3  H15  C24  C23  109.46  3.000
 1Q3  C25  C24  C23  113.99  3.000
 1Q3  H15  C24  C20  107.68  3.000
 1Q3  C25  C24  C20  113.49  3.000
 1Q3  C23  C24  C20  104.63  3.000
 1Q3  N26  C25  C24  180.00  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
 1Q3  CONST_01  C13  C11  N12  C7    180.00   0.0  0
 1Q3  CONST_02  N10  C11  N12  C7      0.00   0.0  0
 1Q3  CONST_03  N10  C9   C8   C7      0.00   0.0  0
 1Q3  CONST_04  C11  N12  C7   C8      0.00   0.0  0
 1Q3  CONST_05  C11  N10  C9   C8      0.00   0.0  0
 1Q3  CONST_06  C13  C11  N10  C9    180.00   0.0  0
 1Q3  CONST_07  N12  C11  N10  C9      0.00   0.0  0
 1Q3  CONST_08  N12  C7   C8   C9      0.00   0.0  0
 1Q3  CONST_09  C14  C13  C11  N10   180.00   0.0  0
 1Q3  CONST_10  C18  C13  C11  N10     0.00   0.0  0
 1Q3  CONST_11  N15  C14  C13  C11   180.00   0.0  0
 1Q3  CONST_12  N17  C18  C13  C11   180.00   0.0  0
 1Q3  CONST_13  C14  C13  C11  N12     0.00   0.0  0
 1Q3  CONST_14  C18  C13  C11  N12   180.00   0.0  0
 1Q3  CONST_15  N17  N15  C14  C13     0.00   0.0  0
 1Q3  CONST_16  N15  N17  C18  C13     0.00   0.0  0
 1Q3  CONST_17  C18  N17  N15  C14     0.00   0.0  0
 1Q3  CONST_18  N17  C18  C13  C14     0.00   0.0  0
 1Q3  CONST_19  C18  C13  C14  N15     0.00   0.0  0
 1Q3  CONST_20  N19  C9   C8   C1      0.00   0.0  0
 1Q3  CONST_21  N19  C9   C8   C7    180.00   0.0  0
 1Q3  CONST_22  N19  C9   N10  C11   180.00   0.0  0
 1Q3  CONST_23  C20  N19  C9   C8    180.00   0.0  0
 1Q3  CONST_24  C20  N19  C9   N10     0.00   0.0  0
 1Q3  CONST_25  H4   C14  C13  C11     0.00   0.0  0
 1Q3  CONST_26  H6   C18  C13  C11     0.00   0.0  0
 1Q3  CONST_27  H5   N15  C14  C13   180.00   0.0  0
 1Q3  CONST_28  H7   N19  C9   C8      0.00   0.0  0
 1Q3  Var_01    C7   C5   N3   C2     -1.34  30.0  1
 1Q3  Var_02    C7   C8   C1   C2     -1.12  30.0  1
 1Q3  Var_03    N12  C7   C5   N3   -179.14  30.0  1
 1Q3  Var_04    C8   C1   C2   N3      1.12  30.0  1
 1Q3  Var_05    C23  C22  C21  C20    25.30  30.0  1
 1Q3  Var_06    C24  C23  C22  C21     0.80  30.0  1
 1Q3  Var_07    H3   C2   N3   C5   -179.94  30.0  1

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
 1Q3  chir_01  C20  N19  C21  C24  negativ
 1Q3  chir_02  C24  C20  C23  C25  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
 1Q3  plan-1  C11  0.020
 1Q3  plan-1  C13  0.020
 1Q3  plan-1  C14  0.020
 1Q3  plan-1  N15  0.020
 1Q3  plan-1  N17  0.020
 1Q3  plan-1  C18  0.020
 1Q3  plan-1  H4   0.020
 1Q3  plan-1  H5   0.020
 1Q3  plan-1  H6   0.020
 1Q3  plan-2  C9   0.020
 1Q3  plan-2  N19  0.020
 1Q3  plan-2  C20  0.020
 1Q3  plan-2  H7   0.020
 1Q3  plan-3  C1   0.020
 1Q3  plan-3  C5   0.020
 1Q3  plan-3  C7   0.020
 1Q3  plan-3  C8   0.020
 1Q3  plan-3  C9   0.020
 1Q3  plan-3  N10  0.020
 1Q3  plan-3  C11  0.020
 1Q3  plan-3  N12  0.020
 1Q3  plan-3  C13  0.020
 1Q3  plan-3  N19  0.020
 1Q3  plan-4  N3   0.020
 1Q3  plan-4  C5   0.020
 1Q3  plan-4  O6   0.020
 1Q3  plan-4  C7   0.020

