# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Mar 18 09:41:59 2022
#   Inital geometry file: a 113 line input string
#   Ligand name: 6-(2,6-dichlorophenyl)-2-[(4-fluoro-3-methylphenyl)amino]-8-methylpyrido[2,3-d]pyrimidin-7(8H)-one
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CN1C(=O)C(=Cc2cnc(Nc3ccc(F)c(C)c3)nc12)c4c(Cl)cccc4Cl
#
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
 JIN  JIN  6-(2,6-dichlorophenyl)-2-[(4-fluoro-3-methylphenyl)amino]-8-methylpyrido[2,3-d]pyrimidin-7(8H)-one  ligand  44  29  .  2022-09-15  2022-09-16
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_JIN
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
 JIN  C10   C   CR16  0  -0.141  -0.1441   -4.9657  -1.4282
 JIN  C12   C   CR6   0   0.571   1.9451   -5.3195  -0.2057
 JIN  C13   C   CH3   0  -0.548   3.0500   -3.4184   0.8951
 JIN  C15   C   CR16  0  -0.188   1.6009   -9.0784  -2.7364
 JIN  C16   C   CR16  0  -0.285   0.8162   -9.9579  -2.0068
 JIN  C19   C   CR6   0   0.280   0.8309   -7.2363  -1.3456
 JIN  C20   C   CR6   0  -0.123   1.5990   -7.7366  -2.3948
 JIN  C27   C   CR6   0   0.367   1.0050    1.0270   0.7573
 JIN  C30   C   CR6   0   0.498   2.6419    2.6640   2.2674
 JIN  C31   C   CR16  0  -0.394   1.5431    3.2102   1.6366
 JIN  F35   F   F     0  -0.315   3.4356    3.4653   3.0037
 JIN  C29   C   CR6   0  -0.074   2.9584    1.3194   2.1737
 JIN  C28   C   CR16  0  -0.352   2.1249    0.5081   1.4089
 JIN  C26   C   CR16  0  -0.350   0.7249    2.3900   0.8810
 JIN  N08   N   NH1   0  -0.765   0.1176    0.2813  -0.0179
 JIN  C04   C   CR6   0   0.620   0.0932   -1.0273  -0.3534
 JIN  N03   N   N     0  -0.468  -0.9697   -1.3761  -1.1067
 JIN  C02   C   CR16  0  -0.043  -1.0464   -2.6367  -1.4521
 JIN  N05   N   N     0  -0.513   1.0572   -1.8392   0.0531
 JIN  C06   C   CR66  0   0.608   0.9675   -3.1111  -0.3065
 JIN  N11   N   NR6   0  -0.587   1.9535   -3.9606   0.1017
 JIN  O14   O   OC    0  -0.451   2.8292   -6.0605   0.1879
 JIN  C09   C   CR6   0  -0.228   0.8318   -5.7989  -1.0143
 JIN  C01   C   CR66  0  -0.120  -0.0977   -3.5926  -1.0816
 JIN  C18   C   CR6   0  -0.133   0.0636   -8.1545  -0.6330
 JIN  C17   C   CR16  0  -0.186   0.0435   -9.5036  -0.9506
 JIN  CL4   CL  CL    0  -0.112  -0.8913   -7.6010   0.6989
 JIN  CL5   CL  CL    0  -0.111   2.5789   -6.6414  -3.3062
 JIN  H10   H   HCR6  0   0.284  -0.9701   -5.3323  -2.0263
 JIN  H131  H   HCH3  0   0.259   2.6778   -3.0255   1.8395
 JIN  H132  H   HCH3  0   0.260   3.5473   -2.6193   0.3497
 JIN  H133  H   HCH3  0   0.280   3.7627   -4.2085   1.0954
 JIN  H15   H   HCR6  0   0.287   2.2039   -9.4328  -3.5607
 JIN  H16   H   HCR6  0   0.281   0.8068  -11.0079  -2.2649
 JIN  H31   H   HCR6  0   0.280   1.3228    4.2652   1.7331
 JIN  H341  H   HCH3  0   0.254   5.0841    1.2017   2.5017
 JIN  H342  H   HCH3  0   0.253   4.1226    0.9302   3.9463
 JIN  H343  H   HCH3  0   0.244   4.2264   -0.3200   2.7126
 JIN  H28   H   HCR6  0   0.304   2.3576   -0.5408   1.3248
 JIN  H26   H   HCR6  0   0.280  -0.1395    2.8154   0.3859
 JIN  HN08  H   HNH1  0   0.416  -0.6630    0.7985  -0.3946
 JIN  H02   H   HCR6  0   0.287  -1.8991   -2.9328  -2.0554
 JIN  H17   H   HCR6  0   0.288  -0.5675  -10.1895  -0.3811
 JIN  C34   C   CH3   0  -0.716   4.1600    0.7550   2.8706

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
 JIN  C10  C01   aromatic  1.417  0.020  1.417
 JIN  C10  C09   aromatic  1.348  0.020  1.348
 JIN  C10  H10   single    0.930  0.020  1.080
 JIN  C12  C09   aromatic  1.457  0.020  1.457
 JIN  C12  N11   aromatic  1.393  0.020  1.393
 JIN  C12  O14   double    1.219  0.020  1.219
 JIN  C13  N11   single    1.458  0.020  1.458
 JIN  C13  H131  single    0.970  0.020  1.090
 JIN  C13  H132  single    0.970  0.020  1.090
 JIN  C13  H133  single    0.970  0.020  1.090
 JIN  C15  C16   aromatic  1.386  0.020  1.386
 JIN  C15  C20   aromatic  1.385  0.020  1.385
 JIN  C15  H15   single    0.930  0.020  1.080
 JIN  C16  C17   aromatic  1.385  0.020  1.385
 JIN  C16  H16   single    0.930  0.020  1.080
 JIN  C19  C18   aromatic  1.393  0.020  1.393
 JIN  C19  C09   single    1.475  0.020  1.475
 JIN  C19  C20   aromatic  1.393  0.020  1.393
 JIN  C20  CL5   single    1.729  0.020  1.729
 JIN  C27  C28   aromatic  1.396  0.020  1.396
 JIN  C27  N08   single    1.394  0.020  1.394
 JIN  C27  C26   aromatic  1.397  0.020  1.397
 JIN  C30  C29   aromatic  1.385  0.020  1.385
 JIN  C30  F35   single    1.347  0.020  1.347
 JIN  C30  C31   aromatic  1.380  0.020  1.380
 JIN  C31  C26   aromatic  1.383  0.020  1.383
 JIN  C31  H31   single    0.930  0.020  1.080
 JIN  C34  C29   single    1.499  0.020  1.499
 JIN  C34  H341  single    0.970  0.020  1.090
 JIN  C34  H342  single    0.970  0.020  1.090
 JIN  C34  H343  single    0.970  0.020  1.090
 JIN  C29  C28   aromatic  1.392  0.020  1.392
 JIN  C28  H28   single    0.930  0.020  1.080
 JIN  C26  H26   single    0.930  0.020  1.080
 JIN  N08  C04   single    1.351  0.020  1.351
 JIN  N08  HN08  single    0.860  0.020  1.020
 JIN  C04  N03   aromatic  1.349  0.020  1.349
 JIN  C04  N05   aromatic  1.324  0.020  1.324
 JIN  N03  C02   aromatic  1.309  0.020  1.309
 JIN  C02  C01   aromatic  1.397  0.020  1.397
 JIN  C02  H02   single    0.930  0.020  1.080
 JIN  N05  C06   aromatic  1.325  0.020  1.325
 JIN  C06  C01   aromatic  1.403  0.020  1.403
 JIN  C06  N11   aromatic  1.364  0.020  1.364
 JIN  C18  CL4   single    1.730  0.020  1.730
 JIN  C18  C17   aromatic  1.386  0.020  1.386
 JIN  C17  H17   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
 JIN  H10   C10  C01   119.19  3.000
 JIN  H10   C10  C09   120.80  3.000
 JIN  C01   C10  C09   120.01  3.000
 JIN  C09   C12  O14   122.24  3.000
 JIN  O14   C12  N11   121.15  3.000
 JIN  C09   C12  N11   116.61  3.000
 JIN  H133  C13  H132  109.14  3.000
 JIN  H133  C13  H131  109.15  3.000
 JIN  H132  C13  H131  109.04  3.000
 JIN  H133  C13  N11   108.92  3.000
 JIN  H132  C13  N11   110.13  3.000
 JIN  H131  C13  N11   110.44  3.000
 JIN  H15   C15  C20   120.44  3.000
 JIN  H15   C15  C16   120.61  3.000
 JIN  C20   C15  C16   118.95  3.000
 JIN  H16   C16  C17   119.71  3.000
 JIN  H16   C16  C15   119.69  3.000
 JIN  C17   C16  C15   120.60  3.000
 JIN  C18   C19  C09   121.86  3.000
 JIN  C09   C19  C20   121.24  3.000
 JIN  C18   C19  C20   116.89  3.000
 JIN  CL5   C20  C19   118.81  3.000
 JIN  CL5   C20  C15   118.88  3.000
 JIN  C19   C20  C15   122.31  3.000
 JIN  N08   C27  C26   116.32  3.000
 JIN  C26   C27  C28   118.84  3.000
 JIN  N08   C27  C28   124.84  3.000
 JIN  C29   C30  F35   118.69  3.000
 JIN  F35   C30  C31   118.93  3.000
 JIN  C29   C30  C31   122.38  3.000
 JIN  H31   C31  C26   120.43  3.000
 JIN  H31   C31  C30   120.48  3.000
 JIN  C26   C31  C30   119.09  3.000
 JIN  C28   C29  C34   121.05  3.000
 JIN  C28   C29  C30   117.79  3.000
 JIN  C34   C29  C30   121.15  3.000
 JIN  H28   C28  C29   118.74  3.000
 JIN  H28   C28  C27   119.91  3.000
 JIN  C29   C28  C27   121.35  3.000
 JIN  H26   C26  C31   119.27  3.000
 JIN  H26   C26  C27   120.18  3.000
 JIN  C31   C26  C27   120.55  3.000
 JIN  HN08  N08  C04   112.93  3.000
 JIN  HN08  N08  C27   115.19  3.000
 JIN  C04   N08  C27   131.87  3.000
 JIN  N05   C04  N03   125.92  3.000
 JIN  N05   C04  N08   120.30  3.000
 JIN  N03   C04  N08   113.79  3.000
 JIN  C02   N03  C04   116.27  3.000
 JIN  H02   C02  C01   119.62  3.000
 JIN  H02   C02  N03   117.08  3.000
 JIN  C01   C02  N03   123.31  3.000
 JIN  C06   N05  C04   117.13  3.000
 JIN  C01   C06  N11   120.04  3.000
 JIN  N11   C06  N05   117.89  3.000
 JIN  C01   C06  N05   122.07  3.000
 JIN  C06   N11  C13   118.35  3.000
 JIN  C06   N11  C12   122.49  3.000
 JIN  C13   N11  C12   119.16  3.000
 JIN  C19   C09  C12   116.47  3.000
 JIN  C19   C09  C10   122.20  3.000
 JIN  C12   C09  C10   121.33  3.000
 JIN  C06   C01  C02   115.31  3.000
 JIN  C06   C01  C10   119.52  3.000
 JIN  C02   C01  C10   125.17  3.000
 JIN  CL4   C18  C17   118.68  3.000
 JIN  C17   C18  C19   122.17  3.000
 JIN  CL4   C18  C19   119.15  3.000
 JIN  H17   C17  C18   120.34  3.000
 JIN  H17   C17  C16   120.60  3.000
 JIN  C18   C17  C16   119.06  3.000
 JIN  H343  C34  H342  107.70  3.000
 JIN  H343  C34  H341  107.68  3.000
 JIN  H342  C34  H341  107.27  3.000
 JIN  H343  C34  C29   110.68  3.000
 JIN  H342  C34  C29   111.75  3.000
 JIN  H341  C34  C29   111.57  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
 JIN  CONST_01  N03   C02  C01  C10   180.00   0.0  0
 JIN  CONST_02  N05   C06  C01  C10   180.00   0.0  0
 JIN  CONST_03  N11   C06  C01  C10     0.00   0.0  0
 JIN  CONST_04  N11   C12  C09  C10     0.00   0.0  0
 JIN  CONST_07  C01   C10  C09  C12     0.00   0.0  0
 JIN  CONST_10  N05   C06  N11  C12   180.00   0.0  0
 JIN  CONST_11  C01   C06  N11  C12     0.00   0.0  0
 JIN  CONST_12  C18   C17  C16  C15     0.00   0.0  0
 JIN  CONST_13  C18   C19  C20  C15     0.00   0.0  0
 JIN  CONST_14  C09   C19  C20  C15   180.00   0.0  0
 JIN  CONST_15  C19   C20  C15  C16     0.00   0.0  0
 JIN  CONST_16  C19   C18  C17  C16     0.00   0.0  0
 JIN  CONST_17  C01   C10  C09  C19   180.00   0.0  0
 JIN  CONST_18  N11   C12  C09  C19   180.00   0.0  0
 JIN  CONST_19  C17   C16  C15  C20     0.00   0.0  0
 JIN  CONST_20  C17   C18  C19  C20     0.00   0.0  0
 JIN  CONST_21  C30   C29  C28  C27     0.00   0.0  0
 JIN  CONST_22  C30   C31  C26  C27     0.00   0.0  0
 JIN  CONST_23  C28   C29  C30  C31     0.00   0.0  0
 JIN  CONST_24  C28   C27  C26  C31     0.00   0.0  0
 JIN  CONST_25  C26   C31  C30  C29     0.00   0.0  0
 JIN  CONST_26  C26   C27  C28  C29     0.00   0.0  0
 JIN  CONST_27  C01   C02  N03  C04     0.00   0.0  0
 JIN  CONST_28  C01   C06  N05  C04     0.00   0.0  0
 JIN  CONST_29  N11   C06  N05  C04   180.00   0.0  0
 JIN  CONST_30  C06   N05  C04  N03     0.00   0.0  0
 JIN  CONST_31  C06   C01  C02  N03     0.00   0.0  0
 JIN  CONST_32  N05   C04  N03  C02     0.00   0.0  0
 JIN  CONST_33  C09   C10  C01  C02   180.00   0.0  0
 JIN  CONST_34  N05   C06  C01  C02     0.00   0.0  0
 JIN  CONST_35  N11   C06  C01  C02   180.00   0.0  0
 JIN  CONST_36  C09   C10  C01  C06     0.00   0.0  0
 JIN  CONST_37  C09   C12  N11  C06     0.00   0.0  0
 JIN  CONST_38  C17   C18  C19  C09   180.00   0.0  0
 JIN  CONST_39  O14   C12  C09  C10   180.00   0.0  0
 JIN  CONST_40  C09   C12  N11  C13   180.00   0.0  0
 JIN  CONST_41  N05   C06  N11  C13     0.00   0.0  0
 JIN  CONST_42  C01   C06  N11  C13   180.00   0.0  0
 JIN  CONST_43  CL5   C20  C15  C16   180.00   0.0  0
 JIN  CONST_44  CL4   C18  C17  C16   180.00   0.0  0
 JIN  CONST_45  O14   C12  C09  C19     0.00   0.0  0
 JIN  CONST_46  CL4   C18  C19  C20   180.00   0.0  0
 JIN  CONST_47  C34   C29  C28  C27   180.00   0.0  0
 JIN  CONST_48  C34   C29  C30  C31   180.00   0.0  0
 JIN  CONST_49  N08   C27  C26  C31   180.00   0.0  0
 JIN  CONST_50  C28   C29  C30  F35   180.00   0.0  0
 JIN  CONST_51  C26   C31  C30  F35   180.00   0.0  0
 JIN  CONST_52  N08   C27  C28  C29   180.00   0.0  0
 JIN  CONST_53  C02   N03  C04  N08   180.00   0.0  0
 JIN  CONST_54  C06   N05  C04  N08   180.00   0.0  0
 JIN  CONST_55  O14   C12  N11  C06   180.00   0.0  0
 JIN  CONST_56  CL4   C18  C19  C09     0.00   0.0  0
 JIN  CONST_57  CL5   C20  C19  C09     0.00   0.0  0
 JIN  CONST_58  CL5   C20  C19  C18   180.00   0.0  0
 JIN  CONST_59  H02   C02  C01  C10     0.00   0.0  0
 JIN  CONST_60  H10   C10  C09  C12   180.00   0.0  0
 JIN  CONST_61  H17   C17  C16  C15   180.00   0.0  0
 JIN  CONST_62  H15   C15  C20  C19   180.00   0.0  0
 JIN  CONST_63  H16   C16  C15  C20   180.00   0.0  0
 JIN  CONST_64  H31   C31  C26  C27   180.00   0.0  0
 JIN  CONST_65  H28   C28  C29  C30   180.00   0.0  0
 JIN  CONST_66  H26   C26  C31  C30   180.00   0.0  0
 JIN  CONST_67  O14   C12  N11  C13     0.00   0.0  0
 JIN  Var_01    N03   C04  N08  C27   178.39  30.0  2
 JIN  Var_02    C04   N08  C27  C28    -1.19  30.0  2
 JIN  Var_03    H131  C13  N11  C12  -116.98  30.0  2
 JIN  Var_04    H341  C34  C29  C30   -62.19  30.0  2

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
 JIN  plan-1  C15  0.020
 JIN  plan-1  C16  0.020
 JIN  plan-1  C19  0.020
 JIN  plan-1  C20  0.020
 JIN  plan-1  C09  0.020
 JIN  plan-1  C18  0.020
 JIN  plan-1  C17  0.020
 JIN  plan-1  CL4  0.020
 JIN  plan-1  CL5  0.020
 JIN  plan-1  H15  0.020
 JIN  plan-1  H16  0.020
 JIN  plan-1  H17  0.020
 JIN  plan-2  C27  0.020
 JIN  plan-2  C30  0.020
 JIN  plan-2  C31  0.020
 JIN  plan-2  F35  0.020
 JIN  plan-2  C29  0.020
 JIN  plan-2  C28  0.020
 JIN  plan-2  C26  0.020
 JIN  plan-2  N08  0.020
 JIN  plan-2  H31  0.020
 JIN  plan-2  H28  0.020
 JIN  plan-2  H26  0.020
 JIN  plan-2  C34  0.020
 JIN  plan-3  C10  0.020
 JIN  plan-3  C12  0.020
 JIN  plan-3  C13  0.020
 JIN  plan-3  C19  0.020
 JIN  plan-3  N08  0.020
 JIN  plan-3  C04  0.020
 JIN  plan-3  N03  0.020
 JIN  plan-3  C02  0.020
 JIN  plan-3  N05  0.020
 JIN  plan-3  C06  0.020
 JIN  plan-3  N11  0.020
 JIN  plan-3  O14  0.020
 JIN  plan-3  C09  0.020
 JIN  plan-3  C01  0.020
 JIN  plan-3  H10  0.020
 JIN  plan-3  H02  0.020

