# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Apr  9 11:50:42 2020
#   Inital geometry file: a 154 line input string
#   Ligand name: N-(5-{[(1R)-3-amino-1-(3-chlorophenyl)propyl]carbamoyl}-2-chlorophenyl)-2-methoxy-7-oxo-7,8-dihydropyrido[2,3-d]pyrimidine-6-carboxamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: COc1ncc2C=C(C(=O)Nc3cc(ccc3Cl)C(=O)N[C@H](CCN)c4cccc(Cl)c4)C(=O)Nc2n1
#
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
 2C3  2C3  N-(5-{[(1R)-3-amino-1-(3-chlorophenyl)propyl]carbamoyl}-2-chlorophenyl)-2-methoxy-7-oxo-7,8-dihydropyrido[2,3-d]pyrimidine-6-carboxamide  ligand  59  37  .  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_2C3
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
 2C3  N3   N   N     0  -0.467   7.9160  -2.6401   0.7238
 2C3  C4   C   CR6   0   0.621   8.4704  -1.5137   1.1779
 2C3  C6   C   CH3   0  -0.421  10.4403  -2.7703   1.5341
 2C3  C8   C   CR66  0   0.561   6.6419  -0.2615   0.8669
 2C3  C10  C   CR6   0   0.601   4.6932   1.1537   0.5557
 2C3  C13  C   CR16  0  -0.153   4.5944  -1.2095  -0.0336
 2C3  C17  C   CR6   0   0.471   0.6233   1.5545  -0.6318
 2C3  C20  C   CR16  0  -0.324  -2.0001   2.2518  -1.3188
 2C3  C21  C   CR16  0  -0.193  -0.9767   3.1690  -1.4791
 2C3  C22  C   CR6   0  -0.140   0.3208   2.8180  -1.1496
 2C3  C28  C   CH2   0  -0.462  -5.9673  -0.7321  -2.3322
 2C3  O11  O   O     0  -0.471   4.2308   2.2832   0.6635
 2C3  N9   N   NR16  0  -0.720   5.9971   0.9267   0.9335
 2C3  N7   N   N     0  -0.459   7.8979  -0.3245   1.2693
 2C3  O5   O   O2    0  -0.432   9.7172  -1.5407   1.5896
 2C3  C2   C   CR16  0  -0.000   6.6648  -2.5604   0.3281
 2C3  C1   C   CR66  0  -0.107   5.9394  -1.3713   0.3721
 2C3  C12  C   CR6   0  -0.331   3.9666  -0.0075   0.0453
 2C3  C14  C   C     0   0.585   2.5433   0.0559  -0.4061
 2C3  O15  O   O     0  -0.461   1.9946  -0.9316  -0.8637
 2C3  N16  N   NH1   0  -0.795   1.9368   1.2596  -0.2703
 2C3  C18  C   CR16  0  -0.325  -0.4237   0.6559  -0.4524
 2C3  CL2  CL  CL    0  -0.098   1.5836   3.9745  -1.3822
 2C3  C19  C   CR6   0  -0.018  -1.7246   0.9864  -0.8099
 2C3  O25  O   O     0  -0.473  -2.6291  -0.9304   0.2546
 2C3  N26  N   NH1   0  -0.676  -3.9006   0.0624  -1.3111
 2C3  C27  C   CH1   0  -0.136  -5.0110  -0.8529  -1.1460
 2C3  N30  N   NH2   0  -0.798  -6.3302  -1.0391  -4.7248
 2C3  C31  C   CR6   0   0.158  -5.7466  -0.6152   0.1551
 2C3  C32  C   CR16  0  -0.273  -6.2225  -1.7039   0.8751
 2C3  C33  C   CR6   0  -0.023  -6.9437  -1.4946   2.0398
 2C3  CL3  CL  CL    0  -0.132  -7.5279  -2.8656   2.9292
 2C3  C35  C   CR16  0  -0.231  -7.2009  -0.2182   2.5132
 2C3  C36  C   CR16  0  -0.246  -6.7212   0.8642   1.7886
 2C3  C37  C   CR16  0  -0.297  -6.0026   0.6710   0.6179
 2C3  H1   H   HCH3  0   0.243   9.9686  -3.5383   2.1455
 2C3  H2   H   HCH3  0   0.243  10.5324  -3.1323   0.5109
 2C3  H3   H   HCH3  0   0.257  11.4258  -2.5450   1.9304
 2C3  H4   H   HCR6  0   0.295   4.0596  -2.0712  -0.4138
 2C3  H5   H   HCR6  0   0.268  -3.0063   2.5596  -1.5700
 2C3  H6   H   HCR6  0   0.291  -1.1878   4.1575  -1.8625
 2C3  H7   H   HCH2  0   0.253  -6.8131  -1.3972  -2.1388
 2C3  H8   H   HCH2  0   0.239  -6.3742   0.2828  -2.3836
 2C3  H9   H   HNR6  0   0.430   6.5147   1.7238   1.2865
 2C3  H10  H   HCR6  0   0.297   6.2008  -3.4680  -0.0430
 2C3  H11  H   HNH1  0   0.430   2.5339   2.0195   0.0522
 2C3  H12  H   HCR6  0   0.279  -0.2278  -0.3126  -0.0192
 2C3  H13  H   HNH1  0   0.413  -3.9592   0.7549  -2.0393
 2C3  H14  H   HCH1  0   0.264  -4.6144  -1.8732  -1.1289
 2C3  H15  H   HCH2  0   0.220  -4.5350  -0.4052  -3.9146
 2C3  H16  H   HCH2  0   0.199  -4.8578  -2.0926  -3.5693
 2C3  H17  H   HNH2  0   0.350  -5.8865  -1.2067  -5.6184
 2C3  H18  H   HNH2  0   0.341  -6.9988  -1.7899  -4.6053
 2C3  H20  H   HCR6  0   0.272  -6.0255  -2.7115   0.5303
 2C3  H21  H   HCR6  0   0.278  -7.7593  -0.0685   3.4271
 2C3  H22  H   HCR6  0   0.267  -6.9120   1.8674   2.1460
 2C3  H23  H   HCR6  0   0.251  -5.6322   1.5290   0.0708
 2C3  C24  C   C     0   0.559  -2.7846  -0.0421  -0.5698
 2C3  C29  C   CH2   0  -0.277  -5.3352  -1.1067  -3.6669

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
 2C3  N30  C29  single    1.454  0.020  1.454
 2C3  C29  C28  single    1.524  0.020  1.524
 2C3  C28  C27  single    1.528  0.020  1.528
 2C3  C36  C37  aromatic  1.387  0.020  1.387
 2C3  C36  C35  aromatic  1.388  0.020  1.388
 2C3  C37  C31  aromatic  1.391  0.020  1.391
 2C3  C35  C33  aromatic  1.385  0.020  1.385
 2C3  N3   C2   aromatic  1.315  0.020  1.315
 2C3  N3   C4   aromatic  1.335  0.020  1.335
 2C3  C31  C27  single    1.513  0.020  1.513
 2C3  C31  C32  aromatic  1.389  0.020  1.389
 2C3  C2   C1   aromatic  1.393  0.020  1.393
 2C3  C27  N26  single    1.448  0.020  1.448
 2C3  C33  C32  aromatic  1.386  0.020  1.386
 2C3  C33  CL3  single    1.735  0.020  1.735
 2C3  O5   C4   single    1.313  0.020  1.313
 2C3  O5   C6   single    1.428  0.020  1.428
 2C3  C4   N7   aromatic  1.323  0.020  1.323
 2C3  N26  C24  single    1.344  0.020  1.344
 2C3  C1   C13  single    1.414  0.020  1.414
 2C3  C1   C8   aromatic  1.404  0.020  1.404
 2C3  C13  C12  double    1.358  0.020  1.358
 2C3  O15  C14  double    1.219  0.020  1.219
 2C3  N7   C8   aromatic  1.320  0.020  1.320
 2C3  C8   N9   single    1.353  0.020  1.353
 2C3  C24  O25  double    1.222  0.020  1.222
 2C3  C24  C19  single    1.496  0.020  1.496
 2C3  C12  C14  single    1.494  0.020  1.494
 2C3  C12  C10  single    1.462  0.020  1.462
 2C3  C14  N16  single    1.355  0.020  1.355
 2C3  C18  C19  aromatic  1.389  0.020  1.389
 2C3  C18  C17  aromatic  1.391  0.020  1.391
 2C3  C19  C20  aromatic  1.391  0.020  1.391
 2C3  N9   C10  single    1.376  0.020  1.376
 2C3  C10  O11  double    1.225  0.020  1.225
 2C3  N16  C17  single    1.394  0.020  1.394
 2C3  C17  C22  aromatic  1.399  0.020  1.399
 2C3  C20  C21  aromatic  1.384  0.020  1.384
 2C3  C22  C21  aromatic  1.384  0.020  1.384
 2C3  C22  CL2  single    1.728  0.020  1.728
 2C3  C6   H1   single    0.970  0.020  1.090
 2C3  C6   H2   single    0.970  0.020  1.090
 2C3  C6   H3   single    0.970  0.020  1.090
 2C3  C13  H4   single    0.930  0.020  1.080
 2C3  C20  H5   single    0.930  0.020  1.080
 2C3  C21  H6   single    0.930  0.020  1.080
 2C3  C28  H7   single    0.970  0.020  1.090
 2C3  C28  H8   single    0.970  0.020  1.090
 2C3  N9   H9   single    0.860  0.020  1.020
 2C3  C2   H10  single    0.930  0.020  1.080
 2C3  N16  H11  single    0.860  0.020  1.020
 2C3  C18  H12  single    0.930  0.020  1.080
 2C3  N26  H13  single    0.860  0.020  1.020
 2C3  C27  H14  single    0.970  0.020  1.090
 2C3  C29  H15  single    0.970  0.020  1.090
 2C3  C29  H16  single    0.970  0.020  1.090
 2C3  N30  H17  single    0.890  0.020  1.040
 2C3  N30  H18  single    0.890  0.020  1.040
 2C3  C32  H20  single    0.930  0.020  1.080
 2C3  C35  H21  single    0.930  0.020  1.080
 2C3  C36  H22  single    0.930  0.020  1.080
 2C3  C37  H23  single    0.930  0.020  1.080

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
 2C3  C2   N3   C4   116.52  3.000
 2C3  O5   C4   N7   114.06  3.000
 2C3  N7   C4   N3   127.02  3.000
 2C3  O5   C4   N3   118.92  3.000
 2C3  H3   C6   H2   109.58  3.000
 2C3  H3   C6   H1   109.54  3.000
 2C3  H2   C6   H1   109.25  3.000
 2C3  H3   C6   O5   105.47  3.000
 2C3  H2   C6   O5   111.45  3.000
 2C3  H1   C6   O5   111.48  3.000
 2C3  C1   C8   N7   123.08  3.000
 2C3  N7   C8   N9   118.69  3.000
 2C3  C1   C8   N9   118.23  3.000
 2C3  C12  C10  N9   115.83  3.000
 2C3  N9   C10  O11  119.04  3.000
 2C3  C12  C10  O11  125.13  3.000
 2C3  H4   C13  C12  119.75  3.000
 2C3  H4   C13  C1   118.64  3.000
 2C3  C12  C13  C1   121.62  3.000
 2C3  C18  C17  N16  122.61  3.000
 2C3  N16  C17  C22  119.41  3.000
 2C3  C18  C17  C22  117.94  3.000
 2C3  H5   C20  C19  121.86  3.000
 2C3  H5   C20  C21  118.20  3.000
 2C3  C19  C20  C21  119.92  3.000
 2C3  H6   C21  C22  119.96  3.000
 2C3  H6   C21  C20  120.18  3.000
 2C3  C22  C21  C20  119.85  3.000
 2C3  CL2  C22  C21  118.90  3.000
 2C3  CL2  C22  C17  119.76  3.000
 2C3  C21  C22  C17  121.34  3.000
 2C3  H8   C28  H7   106.55  3.000
 2C3  H8   C28  C29  109.94  3.000
 2C3  H7   C28  C29  109.05  3.000
 2C3  H8   C28  C27  110.02  3.000
 2C3  H7   C28  C27  107.38  3.000
 2C3  C29  C28  C27  113.63  3.000
 2C3  H9   N9   C10  116.71  3.000
 2C3  H9   N9   C8   117.65  3.000
 2C3  C10  N9   C8   125.63  3.000
 2C3  C8   N7   C4   115.69  3.000
 2C3  C6   O5   C4   119.11  3.000
 2C3  H10  C2   C1   120.13  3.000
 2C3  H10  C2   N3   117.34  3.000
 2C3  C1   C2   N3   122.52  3.000
 2C3  C2   C1   C13  125.71  3.000
 2C3  C13  C1   C8   119.12  3.000
 2C3  C2   C1   C8   115.17  3.000
 2C3  C14  C12  C13  117.40  3.000
 2C3  C14  C12  C10  123.03  3.000
 2C3  C13  C12  C10  119.57  3.000
 2C3  N16  C14  O15  123.78  3.000
 2C3  N16  C14  C12  115.71  3.000
 2C3  O15  C14  C12  120.52  3.000
 2C3  H11  N16  C14  115.60  3.000
 2C3  H11  N16  C17  118.46  3.000
 2C3  C14  N16  C17  125.73  3.000
 2C3  H12  C18  C19  119.14  3.000
 2C3  H12  C18  C17  119.67  3.000
 2C3  C19  C18  C17  121.19  3.000
 2C3  C18  C19  C24  117.30  3.000
 2C3  C18  C19  C20  119.73  3.000
 2C3  C24  C19  C20  122.93  3.000
 2C3  H13  N26  C27  118.20  3.000
 2C3  H13  N26  C24  120.06  3.000
 2C3  C27  N26  C24  121.65  3.000
 2C3  H14  C27  C31  108.00  3.000
 2C3  H14  C27  N26  108.24  3.000
 2C3  C31  C27  N26  111.80  3.000
 2C3  H14  C27  C28  108.21  3.000
 2C3  N26  C27  C28  109.96  3.000
 2C3  C31  C27  C28  110.52  3.000
 2C3  H18  N30  H17  105.72  3.000
 2C3  H18  N30  C29  109.36  3.000
 2C3  H17  N30  C29  109.56  3.000
 2C3  C37  C31  C32  119.29  3.000
 2C3  C32  C31  C27  119.27  3.000
 2C3  C37  C31  C27  121.39  3.000
 2C3  H20  C32  C33  120.19  3.000
 2C3  H20  C32  C31  120.11  3.000
 2C3  C33  C32  C31  119.70  3.000
 2C3  C35  C33  CL3  119.35  3.000
 2C3  CL3  C33  C32  119.11  3.000
 2C3  C35  C33  C32  121.53  3.000
 2C3  H21  C35  C36  120.78  3.000
 2C3  H21  C35  C33  120.81  3.000
 2C3  C36  C35  C33  118.42  3.000
 2C3  H22  C36  C37  119.95  3.000
 2C3  H22  C36  C35  119.32  3.000
 2C3  C37  C36  C35  120.73  3.000
 2C3  H23  C37  C36  119.55  3.000
 2C3  H23  C37  C31  120.11  3.000
 2C3  C36  C37  C31  120.33  3.000
 2C3  N26  C24  O25  122.30  3.000
 2C3  O25  C24  C19  121.19  3.000
 2C3  N26  C24  C19  116.51  3.000
 2C3  H16  C29  H15  106.13  3.000
 2C3  H16  C29  N30  113.79  3.000
 2C3  H15  C29  N30  107.84  3.000
 2C3  H16  C29  C28  108.83  3.000
 2C3  H15  C29  C28  110.16  3.000
 2C3  N30  C29  C28  110.00  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
 2C3  CONST_01  C8   C1   C2   N3      0.00   0.0  0
 2C3  CONST_02  C8   N7   C4   N3      0.00   0.0  0
 2C3  CONST_03  C1   C2   N3   C4      0.00   0.0  0
 2C3  CONST_04  C1   C8   N7   C4      0.00   0.0  0
 2C3  CONST_05  C20  C19  C18  C17     0.00   0.0  0
 2C3  CONST_06  C20  C21  C22  C17     0.00   0.0  0
 2C3  CONST_07  C18  C19  C20  C21     0.00   0.0  0
 2C3  CONST_08  C18  C17  C22  C21     0.00   0.0  0
 2C3  CONST_09  C19  C18  C17  C22     0.00   0.0  0
 2C3  CONST_10  C19  C20  C21  C22     0.00   0.0  0
 2C3  CONST_11  C2   N3   C4   N7      0.00   0.0  0
 2C3  CONST_12  C2   C1   C8   N7      0.00   0.0  0
 2C3  CONST_13  C35  C36  C37  C31     0.00   0.0  0
 2C3  CONST_14  C35  C33  C32  C31     0.00   0.0  0
 2C3  CONST_15  C36  C37  C31  C32     0.00   0.0  0
 2C3  CONST_16  C36  C35  C33  C32     0.00   0.0  0
 2C3  CONST_17  C37  C36  C35  C33     0.00   0.0  0
 2C3  CONST_18  C37  C31  C32  C33     0.00   0.0  0
 2C3  CONST_19  C12  C10  N9   C8      0.00   0.0  0
 2C3  CONST_20  O5   C4   N7   C8    180.00   0.0  0
 2C3  CONST_21  C24  C19  C18  C17   180.00   0.0  0
 2C3  CONST_22  CL2  C22  C21  C20   180.00   0.0  0
 2C3  CONST_23  C24  C19  C20  C21   180.00   0.0  0
 2C3  CONST_24  N16  C17  C22  C21   180.00   0.0  0
 2C3  CONST_25  C2   N3   C4   O5    180.00   0.0  0
 2C3  CONST_26  C19  C18  C17  N16   180.00   0.0  0
 2C3  CONST_27  CL2  C22  C17  C18   180.00   0.0  0
 2C3  CONST_28  C36  C37  C31  C27   180.00   0.0  0
 2C3  CONST_29  C33  C32  C31  C27   180.00   0.0  0
 2C3  CONST_30  CL3  C33  C32  C31   180.00   0.0  0
 2C3  CONST_31  C36  C35  C33  CL3   180.00   0.0  0
 2C3  CONST_32  O11  C10  N9   C8    180.00   0.0  0
 2C3  CONST_33  H10  C2   N3   C4    180.00   0.0  0
 2C3  CONST_34  H6   C21  C22  C17   180.00   0.0  0
 2C3  CONST_35  H12  C18  C19  C20   180.00   0.0  0
 2C3  CONST_36  H5   C20  C21  C22   180.00   0.0  0
 2C3  CONST_37  H22  C36  C37  C31   180.00   0.0  0
 2C3  CONST_38  H23  C37  C31  C32   180.00   0.0  0
 2C3  CONST_39  H21  C35  C33  C32   180.00   0.0  0
 2C3  CONST_40  H20  C32  C33  C35   180.00   0.0  0
 2C3  CONST_41  H9   N9   C10  C12   180.00   0.0  0
 2C3  CONST_42  C12  C14  N16  C17   180.00   0.0  0
 2C3  CONST_46  O15  C14  N16  C17     0.00   0.0  0
 2C3  CONST_47  C27  N26  C24  C19   180.00   0.0  0
 2C3  CONST_48  H13  N26  C24  C19     0.00   0.0  0
 2C3  CONST_49  C27  N26  C24  O25     0.00   0.0  0
 2C3  Var_01    N7   C4   O5   C6   -179.79  30.0  2
 2C3  Var_02    O15  C14  C12  C10   177.66  30.0  2
 2C3  Var_03    N26  C24  C19  C20    25.24  30.0  2
 2C3  Var_04    H1   C6   O5   C4    -60.63  30.0  3
 2C3  Var_05    N30  C29  C28  C27   176.71  30.0  1
 2C3  Var_06    H17  N30  C29  C28   174.91  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
 2C3  chir_01  C27  C28  C31  N26  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
 2C3  plan-1  C17  0.020
 2C3  plan-1  C20  0.020
 2C3  plan-1  C21  0.020
 2C3  plan-1  C22  0.020
 2C3  plan-1  N16  0.020
 2C3  plan-1  C18  0.020
 2C3  plan-1  CL2  0.020
 2C3  plan-1  C19  0.020
 2C3  plan-1  H5   0.020
 2C3  plan-1  H6   0.020
 2C3  plan-1  H12  0.020
 2C3  plan-1  C24  0.020
 2C3  plan-2  C27  0.020
 2C3  plan-2  C31  0.020
 2C3  plan-2  C32  0.020
 2C3  plan-2  C33  0.020
 2C3  plan-2  CL3  0.020
 2C3  plan-2  C35  0.020
 2C3  plan-2  C36  0.020
 2C3  plan-2  C37  0.020
 2C3  plan-2  H20  0.020
 2C3  plan-2  H21  0.020
 2C3  plan-2  H22  0.020
 2C3  plan-2  H23  0.020
 2C3  plan-3  N3   0.020
 2C3  plan-3  C4   0.020
 2C3  plan-3  C8   0.020
 2C3  plan-3  C10  0.020
 2C3  plan-3  C13  0.020
 2C3  plan-3  O11  0.020
 2C3  plan-3  N9   0.020
 2C3  plan-3  N7   0.020
 2C3  plan-3  O5   0.020
 2C3  plan-3  C2   0.020
 2C3  plan-3  C1   0.020
 2C3  plan-3  C12  0.020
 2C3  plan-3  C14  0.020
 2C3  plan-3  H4   0.020
 2C3  plan-3  H9   0.020
 2C3  plan-3  H10  0.020
 2C3  plan-4  C17  0.020
 2C3  plan-4  C12  0.020
 2C3  plan-4  C14  0.020
 2C3  plan-4  O15  0.020
 2C3  plan-4  N16  0.020
 2C3  plan-4  H11  0.020
 2C3  plan-5  C19  0.020
 2C3  plan-5  O25  0.020
 2C3  plan-5  N26  0.020
 2C3  plan-5  C27  0.020
 2C3  plan-5  H13  0.020
 2C3  plan-5  C24  0.020

