# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr  8 15:20:29 2020
#   Inital geometry file: a 110 line input string
#   Ligand name: methyl 4-chloro-3-{[(2-methoxy-7-oxo-7,8-dihydropyrido[2,3-d]pyrimidin-6-yl)carbonyl]amino}benzoate
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: COC(=O)c1ccc(Cl)c(NC(=O)C2=Cc3cnc(OC)nc3NC2=O)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
 2C4  2C4  'methyl 4-chloro-3-{[(2-methoxy-7-oxo-7,8-dihydropyrido[2,3-d]pyrimidin-6-yl)carbonyl]amino}benzoate'  ligand  40  27  .  2022-07-22  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_2C4
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
 2C4  N3   N   N     0  -0.467   5.8449  -1.6304   0.3452
 2C4  C4   C   CR6   0   0.621   6.1706  -0.4134  -0.0967
 2C4  C6   C   CH3   0  -0.420   8.4284  -1.1027   0.0292
 2C4  C8   C   CR66  0   0.561   4.0584   0.3133  -0.2327
 2C4  C10  C   CR6   0   0.601   1.7915   1.1673  -0.3997
 2C4  C13  C   CR16  0  -0.154   2.1865  -1.1102   0.3750
 2C4  C17  C   CR6   0   0.477  -2.3944   0.5329   0.0455
 2C4  C20  C   CR16  0  -0.294  -5.1965   0.5767   0.2288
 2C4  C21  C   CR16  0  -0.192  -4.4733   1.7457   0.3792
 2C4  C22  C   CR6   0  -0.139  -3.0918   1.7212   0.2921
 2C4  O11  O   O     0  -0.470   1.0855   2.1258  -0.6899
 2C4  N9   N   NR16  0  -0.720   3.1576   1.2814  -0.5214
 2C4  N7   N   N     0  -0.458   5.3424   0.5738  -0.3962
 2C4  O5   O   O2    0  -0.432   7.4386  -0.1176  -0.2670
 2C4  C2   C   CR16  0   0.000   4.5626  -1.8732   0.5037
 2C4  C1   C   CR66  0  -0.106   3.5805  -0.9232   0.2286
 2C4  C12  C   CR6   0  -0.331   1.3008  -0.1237   0.0789
 2C4  C14  C   C     0   0.588  -0.1505  -0.4252   0.2687
 2C4  O15  O   O     0  -0.461  -0.5048  -1.5081   0.7021
 2C4  N16  N   NH1   0  -0.797  -1.0067   0.5698  -0.0672
 2C4  C18  C   CR16  0  -0.319  -3.1385  -0.6322  -0.1166
 2C4  CL2  CL  CL    0  -0.095  -2.2215   3.1996   0.4983
 2C4  C19  C   CR6   0  -0.067  -4.5249  -0.6164  -0.0212
 2C4  O25  O   O     0  -0.443  -4.6791  -2.9625  -0.3846
 2C4  O26  O   O2    0  -0.455  -6.5517  -1.7709  -0.1653
 2C4  C27  C   CH3   0  -0.423  -7.3451  -2.9454  -0.3413
 2C4  H1   H   HCH3  0   0.243   8.3818  -1.4146   1.0716
 2C4  H2   H   HCH3  0   0.243   8.3234  -1.9767  -0.6124
 2C4  H3   H   HCH3  0   0.257   9.3825  -0.6218  -0.1647
 2C4  H4   H   HCR6  0   0.296   1.8248  -2.0664   0.7326
 2C4  H5   H   HCR6  0   0.275  -6.2732   0.6138   0.3075
 2C4  H6   H   HCR6  0   0.292  -4.9826   2.6793   0.5734
 2C4  H7   H   HNR6  0   0.430   3.5139   2.1703  -0.8540
 2C4  H8   H   HCR6  0   0.297   4.2816  -2.8573   0.8639
 2C4  H9   H   HNH1  0   0.433  -0.5689   1.4435  -0.3557
 2C4  H10  H   HCR6  0   0.285  -2.6362  -1.5605  -0.3362
 2C4  H11  H   HCH3  0   0.243  -7.1522  -3.4135  -1.3059
 2C4  H12  H   HCH3  0   0.243  -7.1636  -3.6682   0.4535
 2C4  H13  H   HCH3  0   0.255  -8.3781  -2.6140  -0.2996
 2C4  C24  C   C     0   0.605  -5.2387  -1.9074  -0.2089

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
 2C4  N3   C2   aromatic  1.315  0.020  1.315
 2C4  N3   C4   aromatic  1.335  0.020  1.335
 2C4  C2   C1   aromatic  1.394  0.020  1.394
 2C4  C27  O26  single    1.428  0.020  1.428
 2C4  O5   C4   single    1.313  0.020  1.313
 2C4  O5   C6   single    1.428  0.020  1.428
 2C4  C4   N7   aromatic  1.323  0.020  1.323
 2C4  C1   C13  single    1.414  0.020  1.414
 2C4  C1   C8   aromatic  1.404  0.020  1.404
 2C4  O26  C24  single    1.321  0.020  1.321
 2C4  C13  C12  double    1.358  0.020  1.358
 2C4  N7   C8   aromatic  1.320  0.020  1.320
 2C4  O15  C14  double    1.219  0.020  1.219
 2C4  C8   N9   single    1.354  0.020  1.354
 2C4  C24  O25  double    1.207  0.020  1.207
 2C4  C24  C19  single    1.487  0.020  1.487
 2C4  C12  C14  single    1.494  0.020  1.494
 2C4  C12  C10  single    1.462  0.020  1.462
 2C4  C14  N16  single    1.355  0.020  1.355
 2C4  C18  C19  aromatic  1.390  0.020  1.390
 2C4  C18  C17  aromatic  1.392  0.020  1.392
 2C4  N9   C10  single    1.376  0.020  1.376
 2C4  C19  C20  aromatic  1.392  0.020  1.392
 2C4  C10  O11  double    1.225  0.020  1.225
 2C4  N16  C17  single    1.393  0.020  1.393
 2C4  C17  C22  aromatic  1.400  0.020  1.400
 2C4  C20  C21  aromatic  1.383  0.020  1.383
 2C4  C22  C21  aromatic  1.384  0.020  1.384
 2C4  C22  CL2  single    1.728  0.020  1.728
 2C4  C6   H1   single    0.970  0.020  1.090
 2C4  C6   H2   single    0.970  0.020  1.090
 2C4  C6   H3   single    0.970  0.020  1.090
 2C4  C13  H4   single    0.930  0.020  1.080
 2C4  C20  H5   single    0.930  0.020  1.080
 2C4  C21  H6   single    0.930  0.020  1.080
 2C4  N9   H7   single    0.860  0.020  1.020
 2C4  C2   H8   single    0.930  0.020  1.080
 2C4  N16  H9   single    0.860  0.020  1.020
 2C4  C18  H10  single    0.930  0.020  1.080
 2C4  C27  H11  single    0.970  0.020  1.090
 2C4  C27  H12  single    0.970  0.020  1.090
 2C4  C27  H13  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
 2C4  C2   N3   C4   116.50  3.000
 2C4  O5   C4   N7   114.02  3.000
 2C4  N7   C4   N3   127.05  3.000
 2C4  O5   C4   N3   118.94  3.000
 2C4  H3   C6   H2   109.56  3.000
 2C4  H3   C6   H1   109.59  3.000
 2C4  H2   C6   H1   109.26  3.000
 2C4  H3   C6   O5   105.46  3.000
 2C4  H2   C6   O5   111.39  3.000
 2C4  H1   C6   O5   111.50  3.000
 2C4  C1   C8   N7   123.07  3.000
 2C4  N7   C8   N9   118.67  3.000
 2C4  C1   C8   N9   118.27  3.000
 2C4  C12  C10  N9   115.81  3.000
 2C4  N9   C10  O11  119.09  3.000
 2C4  C12  C10  O11  125.10  3.000
 2C4  H4   C13  C12  119.69  3.000
 2C4  H4   C13  C1   118.70  3.000
 2C4  C12  C13  C1   121.61  3.000
 2C4  C18  C17  N16  123.05  3.000
 2C4  N16  C17  C22  119.22  3.000
 2C4  C18  C17  C22  117.69  3.000
 2C4  H5   C20  C19  121.57  3.000
 2C4  H5   C20  C21  118.97  3.000
 2C4  C19  C20  C21  119.46  3.000
 2C4  H6   C21  C22  119.78  3.000
 2C4  H6   C21  C20  120.21  3.000
 2C4  C22  C21  C20  120.01  3.000
 2C4  CL2  C22  C21  118.68  3.000
 2C4  CL2  C22  C17  119.76  3.000
 2C4  C21  C22  C17  121.55  3.000
 2C4  H7   N9   C10  116.78  3.000
 2C4  H7   N9   C8   117.59  3.000
 2C4  C10  N9   C8   125.63  3.000
 2C4  C8   N7   C4   115.69  3.000
 2C4  C6   O5   C4   119.15  3.000
 2C4  H8   C2   C1   120.09  3.000
 2C4  H8   C2   N3   117.40  3.000
 2C4  C1   C2   N3   122.52  3.000
 2C4  C2   C1   C13  125.74  3.000
 2C4  C13  C1   C8   119.09  3.000
 2C4  C2   C1   C8   115.18  3.000
 2C4  C14  C12  C13  117.33  3.000
 2C4  C14  C12  C10  123.08  3.000
 2C4  C13  C12  C10  119.59  3.000
 2C4  N16  C14  O15  123.84  3.000
 2C4  N16  C14  C12  115.72  3.000
 2C4  O15  C14  C12  120.44  3.000
 2C4  H9   N16  C14  115.36  3.000
 2C4  H9   N16  C17  118.28  3.000
 2C4  C14  N16  C17  126.16  3.000
 2C4  H10  C18  C19  119.24  3.000
 2C4  H10  C18  C17  119.69  3.000
 2C4  C19  C18  C17  121.05  3.000
 2C4  C18  C19  C24  117.41  3.000
 2C4  C18  C19  C20  120.23  3.000
 2C4  C24  C19  C20  122.36  3.000
 2C4  C27  O26  C24  117.59  3.000
 2C4  H13  C27  H12  109.45  3.000
 2C4  H13  C27  H11  109.49  3.000
 2C4  H12  C27  H11  109.35  3.000
 2C4  H13  C27  O26  105.83  3.000
 2C4  H12  C27  O26  111.29  3.000
 2C4  H11  C27  O26  111.35  3.000
 2C4  O26  C24  O25  123.77  3.000
 2C4  O25  C24  C19  123.69  3.000
 2C4  O26  C24  C19  112.54  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
 2C4  CONST_01  C8   C1   C2   N3      0.00   0.0  0
 2C4  CONST_02  C8   N7   C4   N3      0.00   0.0  0
 2C4  CONST_03  C1   C2   N3   C4      0.00   0.0  0
 2C4  CONST_04  C1   C8   N7   C4      0.00   0.0  0
 2C4  CONST_05  C20  C19  C18  C17     0.00   0.0  0
 2C4  CONST_06  C20  C21  C22  C17     0.00   0.0  0
 2C4  CONST_07  C18  C19  C20  C21     0.00   0.0  0
 2C4  CONST_08  C18  C17  C22  C21     0.00   0.0  0
 2C4  CONST_09  C19  C18  C17  C22     0.00   0.0  0
 2C4  CONST_10  C19  C20  C21  C22     0.00   0.0  0
 2C4  CONST_11  C2   N3   C4   N7      0.00   0.0  0
 2C4  CONST_12  C2   C1   C8   N7      0.00   0.0  0
 2C4  CONST_13  C12  C10  N9   C8      0.00   0.0  0
 2C4  CONST_14  O5   C4   N7   C8    180.00   0.0  0
 2C4  CONST_15  C24  C19  C18  C17   180.00   0.0  0
 2C4  CONST_16  CL2  C22  C21  C20   180.00   0.0  0
 2C4  CONST_17  C24  C19  C20  C21   180.00   0.0  0
 2C4  CONST_18  N16  C17  C22  C21   180.00   0.0  0
 2C4  CONST_19  C2   N3   C4   O5    180.00   0.0  0
 2C4  CONST_20  C19  C18  C17  N16   180.00   0.0  0
 2C4  CONST_21  CL2  C22  C17  C18   180.00   0.0  0
 2C4  CONST_22  O11  C10  N9   C8    180.00   0.0  0
 2C4  CONST_23  H8   C2   N3   C4    180.00   0.0  0
 2C4  CONST_24  H6   C21  C22  C17   180.00   0.0  0
 2C4  CONST_25  H10  C18  C19  C20   180.00   0.0  0
 2C4  CONST_26  H5   C20  C21  C22   180.00   0.0  0
 2C4  CONST_27  H7   N9   C10  C12   180.00   0.0  0
 2C4  CONST_28  C12  C14  N16  C17   180.00   0.0  0
 2C4  CONST_32  O15  C14  N16  C17     0.00   0.0  0
 2C4  Var_01    N7   C4   O5   C6    179.74  30.0  2
 2C4  Var_02    O15  C14  C12  C10  -178.18  30.0  2
 2C4  Var_03    O26  C24  C19  C20     2.59  30.0  2
 2C4  Var_04    H1   C6   O5   C4    -59.82  30.0  3
 2C4  Var_05    H11  C27  O26  C24   -59.55  30.0  3

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
 2C4  plan-1  C17  0.020
 2C4  plan-1  C20  0.020
 2C4  plan-1  C21  0.020
 2C4  plan-1  C22  0.020
 2C4  plan-1  N16  0.020
 2C4  plan-1  C18  0.020
 2C4  plan-1  CL2  0.020
 2C4  plan-1  C19  0.020
 2C4  plan-1  H5   0.020
 2C4  plan-1  H6   0.020
 2C4  plan-1  H10  0.020
 2C4  plan-1  C24  0.020
 2C4  plan-2  N3   0.020
 2C4  plan-2  C4   0.020
 2C4  plan-2  C8   0.020
 2C4  plan-2  C10  0.020
 2C4  plan-2  C13  0.020
 2C4  plan-2  O11  0.020
 2C4  plan-2  N9   0.020
 2C4  plan-2  N7   0.020
 2C4  plan-2  O5   0.020
 2C4  plan-2  C2   0.020
 2C4  plan-2  C1   0.020
 2C4  plan-2  C12  0.020
 2C4  plan-2  C14  0.020
 2C4  plan-2  H4   0.020
 2C4  plan-2  H7   0.020
 2C4  plan-2  H8   0.020
 2C4  plan-3  C17  0.020
 2C4  plan-3  C12  0.020
 2C4  plan-3  C14  0.020
 2C4  plan-3  O15  0.020
 2C4  plan-3  N16  0.020
 2C4  plan-3  H9   0.020
 2C4  plan-4  C19  0.020
 2C4  plan-4  O25  0.020
 2C4  plan-4  O26  0.020
 2C4  plan-4  C24  0.020

