# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon May  4 12:29:54 2020
#   Inital geometry file: a 62 line input string
#   Ligand name: 2-azanyl-5,6,7,8-tetrahydro-3~{H}-pyrido[2,3-d]pyrimidin-4-one
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: NC1=NC2=C(CCCN2)C(=O)N1
#
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
 T0A  T0A  2-azanyl-5,6,7,8-tetrahydro-3~{H}-pyrido[2,3-d]pyrimidin-4-one  ligand  22  12  .  2021-08-23  2021-08-23  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_T0A
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
 T0A  NAH  N  NR16  0  -0.713   1.9013  -0.6897  -0.0366
 T0A  CAL  C  CR6   0   0.500   0.6929  -1.3949  -0.0889
 T0A  OAB  O  O     0  -0.520   0.7311  -2.6257  -0.1270
 T0A  CAK  C  CR6   0  -0.271  -0.4608  -0.5803  -0.0935
 T0A  CAE  C  CH2   0  -0.460  -1.8301  -1.1969  -0.1190
 T0A  CAC  C  CH2   0  -0.470  -2.8699  -0.2138   0.4090
 T0A  CAD  C  CH2   0  -0.272  -2.7042   1.1450  -0.2521
 T0A  NAG  N  NH1   0  -0.657  -1.3549   1.6246  -0.0592
 T0A  CAJ  C  CR6   0   0.516  -0.2928   0.7993  -0.0547
 T0A  NAF  N  N     0  -0.534   0.9120   1.4194   0.0044
 T0A  CAI  C  CR6   0   0.678   1.9728   0.6591   0.0081
 T0A  NAA  N  NH2   0  -0.829   3.1953   1.2164   0.0168
 T0A  H1   H  HNR6  0   0.413   2.7503  -1.2383  -0.0478
 T0A  H3   H  HCH2  0   0.228  -2.1053  -1.5054  -1.1338
 T0A  H4   H  HCH2  0   0.238  -1.8426  -2.1066   0.4855
 T0A  H5   H  HCH2  0   0.241  -3.8783  -0.5846   0.2210
 T0A  H6   H  HCH2  0   0.232  -2.7617  -0.1020   1.4909
 T0A  H7   H  HCH2  0   0.226  -2.9436   1.0687  -1.3195
 T0A  H8   H  HCH2  0   0.251  -3.3911   1.8726   0.1801
 T0A  H9   H  HNH2  0   0.410   4.0058   0.6684   0.2502
 T0A  H10  H  HNH2  0   0.406   3.2541   2.2022   0.2065
 T0A  H2   H  HNH1  0   0.387  -1.1709   2.6123  -0.1162

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
 T0A  OAB  CAL  double  1.232  0.020  1.232
 T0A  NAH  CAL  single  1.400  0.020  1.400
 T0A  NAH  CAI  single  1.351  0.020  1.351
 T0A  CAL  CAK  single  1.412  0.020  1.412
 T0A  NAA  CAI  single  1.344  0.020  1.344
 T0A  CAI  NAF  double  1.305  0.020  1.305
 T0A  CAK  CAE  single  1.502  0.020  1.502
 T0A  CAK  CAJ  double  1.390  0.020  1.390
 T0A  CAE  CAC  single  1.525  0.020  1.525
 T0A  NAF  CAJ  single  1.356  0.020  1.356
 T0A  CAJ  NAG  single  1.345  0.020  1.345
 T0A  CAC  CAD  single  1.520  0.020  1.520
 T0A  NAG  CAD  single  1.445  0.020  1.445
 T0A  NAH  H1   single  0.860  0.020  1.020
 T0A  CAE  H3   single  0.970  0.020  1.090
 T0A  CAE  H4   single  0.970  0.020  1.090
 T0A  CAC  H5   single  0.970  0.020  1.090
 T0A  CAC  H6   single  0.970  0.020  1.090
 T0A  CAD  H7   single  0.970  0.020  1.090
 T0A  CAD  H8   single  0.970  0.020  1.090
 T0A  NAA  H9   single  0.890  0.020  1.040
 T0A  NAA  H10  single  0.890  0.020  1.040
 T0A  NAG  H2   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
 T0A  H1   NAH  CAI  119.84  3.000
 T0A  H1   NAH  CAL  116.82  3.000
 T0A  CAI  NAH  CAL  123.34  3.000
 T0A  CAK  CAL  OAB  126.98  3.000
 T0A  CAK  CAL  NAH  114.50  3.000
 T0A  OAB  CAL  NAH  118.53  3.000
 T0A  CAJ  CAK  CAE  121.20  3.000
 T0A  CAJ  CAK  CAL  118.26  3.000
 T0A  CAE  CAK  CAL  120.53  3.000
 T0A  H4   CAE  H3   105.97  3.000
 T0A  H4   CAE  CAC  109.72  3.000
 T0A  H3   CAE  CAC  109.32  3.000
 T0A  H4   CAE  CAK  110.06  3.000
 T0A  H3   CAE  CAK  111.12  3.000
 T0A  CAC  CAE  CAK  110.55  3.000
 T0A  H6   CAC  H5   107.27  3.000
 T0A  H6   CAC  CAD  109.16  3.000
 T0A  H5   CAC  CAD  109.25  3.000
 T0A  H6   CAC  CAE  109.94  3.000
 T0A  H5   CAC  CAE  110.58  3.000
 T0A  CAD  CAC  CAE  110.57  3.000
 T0A  H8   CAD  H7   107.15  3.000
 T0A  H8   CAD  NAG  108.30  3.000
 T0A  H7   CAD  NAG  110.91  3.000
 T0A  H8   CAD  CAC  110.83  3.000
 T0A  H7   CAD  CAC  109.71  3.000
 T0A  NAG  CAD  CAC  109.90  3.000
 T0A  H2   NAG  CAJ  117.26  3.000
 T0A  H2   NAG  CAD  119.27  3.000
 T0A  CAJ  NAG  CAD  122.29  3.000
 T0A  NAF  CAJ  NAG  114.90  3.000
 T0A  NAG  CAJ  CAK  120.89  3.000
 T0A  NAF  CAJ  CAK  124.21  3.000
 T0A  CAI  NAF  CAJ  117.11  3.000
 T0A  NAA  CAI  NAF  119.86  3.000
 T0A  NAF  CAI  NAH  122.57  3.000
 T0A  NAA  CAI  NAH  117.54  3.000
 T0A  H10  NAA  H9   116.31  3.000
 T0A  H10  NAA  CAI  117.45  3.000
 T0A  H9   NAA  CAI  120.58  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
 T0A  CONST_01  CAJ  NAF  CAI  NAH    0.00   0.0  0
 T0A  CONST_02  NAF  CAI  NAH  CAL    0.00   0.0  0
 T0A  CONST_03  CAI  NAH  CAL  CAK    0.00   0.0  0
 T0A  CONST_04  CAI  NAF  CAJ  CAK    0.00   0.0  0
 T0A  CONST_05  CAD  NAG  CAJ  CAK    0.00   0.0  0
 T0A  CONST_06  NAF  CAJ  NAG  CAD  180.00   0.0  0
 T0A  CONST_07  CAI  NAF  CAJ  NAG  180.00   0.0  0
 T0A  CONST_08  NAA  CAI  NAH  CAL  180.00   0.0  0
 T0A  CONST_09  CAI  NAH  CAL  OAB  180.00   0.0  0
 T0A  CONST_10  NAA  CAI  NAF  CAJ  180.00   0.0  0
 T0A  CONST_11  H1   NAH  CAL  CAK  180.00   0.0  0
 T0A  CONST_12  H2   NAG  CAJ  CAK  180.00   0.0  0
 T0A  CONST_14  H10  NAA  CAI  NAH  180.00   0.0  0
 T0A  Var_01    CAC  CAE  CAK  CAL  158.26  30.0  1
 T0A  Var_02    CAD  CAC  CAE  CAK   48.38  30.0  1
 T0A  Var_03    NAG  CAD  CAC  CAE  -55.70  30.0  1
 T0A  Var_04    CAJ  NAG  CAD  CAC   35.68  30.0  1

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
 T0A  plan-1  NAH  0.020
 T0A  plan-1  CAL  0.020
 T0A  plan-1  OAB  0.020
 T0A  plan-1  CAK  0.020
 T0A  plan-1  CAE  0.020
 T0A  plan-1  CAD  0.020
 T0A  plan-1  NAG  0.020
 T0A  plan-1  CAJ  0.020
 T0A  plan-1  NAF  0.020
 T0A  plan-1  CAI  0.020
 T0A  plan-1  NAA  0.020
 T0A  plan-1  H1   0.020
 T0A  plan-1  H9   0.020
 T0A  plan-1  H10  0.020
 T0A  plan-1  H2   0.020

