# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr 22 06:38:55 2020
#   Inital geometry file: a 114 line input string
#   Ligand name: 1-(3-nitrophenyl)-3-(pyridin-4-ylmethyl)pyrido[2,3-d]pyrimidine-2,4(1H,3H)-dione
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: [O-][N+](=O)c1cccc(c1)N2C(=O)N(Cc3ccncc3)C(=O)c4cccnc24
#
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
 D71  D71  1-(3-nitrophenyl)-3-(pyridin-4-ylmethyl)pyrido[2,3-d]pyrimidine-2,4(1H,3H)-dione  ligand  41  28  .  2022-07-24  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_D71
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
 D71  C1    C  CR16   0  -0.141   0.8668   3.8785   0.2246
 D71  C2    C  CR66   0  -0.185   0.8039   2.4951   0.3475
 D71  C3    C  CR66   0   0.541  -0.3263   1.8484  -0.1469
 D71  C5    C  CR16   0  -0.037  -1.2594   3.7944  -0.8286
 D71  C6    C  CR16   0  -0.336  -0.1831   4.5465  -0.3736
 D71  C14   C  CR6    0   0.778   0.5704  -0.2991   0.5348
 D71  O56   O  O      0  -0.372  -4.8869  -0.8303   1.6981
 D71  O58   O  O     -1  -0.371  -5.8761  -1.8203   0.0876
 D71  C40   C  CR6    0   0.255  -3.7509  -1.0586  -0.2740
 D71  C39   C  CR16   0  -0.276  -2.6585  -0.3860   0.2506
 D71  C41   C  CR16   0  -0.256  -3.7582  -1.5527  -1.5696
 D71  C42   C  CR16   0  -0.260  -2.6360  -1.3634  -2.3586
 D71  C43   C  CR16   0  -0.227  -1.5315  -0.6909  -1.8580
 D71  C22   C  CR6    0   0.316  -1.5522  -0.2108  -0.5583
 D71  N13   N  NR6    0  -0.716  -0.4118   0.4731  -0.0412
 D71  N4    N  N      0  -0.438  -1.3357   2.4759  -0.7220
 D71  O52   O  O      0  -0.448   0.4693  -1.5012   0.6095
 D71  N15   N  NR6    0  -0.610   1.6830   0.3653   1.0252
 D71  C16   C  CR6    0   0.602   1.8854   1.7356   0.9667
 D71  O50   O  O      0  -0.430   2.8943   2.2491   1.3998
 D71  C24   C  CH2    0  -0.392   2.7012  -0.4839   1.6354
 D71  C26   C  CR6    0   0.216   3.4601  -1.2977   0.6239
 D71  C32   C  CR16   0  -0.364   3.9315  -0.7428  -0.5600
 D71  C31   C  CR16   0  -0.058   4.6600  -1.5389  -1.4298
 D71  N30   N  N      0  -0.409   4.9465  -2.8148  -1.1962
 D71  C29   C  CR16   0  -0.059   4.4991  -3.3397  -0.0619
 D71  C28   C  CR16   0  -0.376   3.7558  -2.6312   0.8698
 D71  H1    H  HCR6   0   0.288   1.7302   4.4139   0.5958
 D71  H5    H  HCR6   0   0.286  -2.1025   4.2813  -1.3038
 D71  H6    H  HCR6   0   0.285  -0.1770   5.6202  -0.4897
 D71  H39   H  HCR6   0   0.308  -2.6577  -0.0055   1.2621
 D71  H41   H  HCR6   0   0.306  -4.6156  -2.0767  -1.9648
 D71  H42   H  HCR6   0   0.289  -2.6235  -1.7428  -3.3704
 D71  H43   H  HCR6   0   0.289  -0.6569  -0.5419  -2.4774
 D71  H24   H  HCH2   0   0.308   3.3911   0.1665   2.1691
 D71  H24A  H  HCH2   0   0.296   2.2314  -1.1308   2.3743
 D71  H32   H  HCR6   0   0.268   3.7458   0.2920  -0.8180
 D71  H31   H  HCR6   0   0.266   5.0312  -1.1204  -2.3585
 D71  H29   H  HCR6   0   0.266   4.7359  -4.3825   0.1177
 D71  H28   H  HCR6   0   0.269   3.4103  -3.1222   1.7705
 D71  N54   N  N      1   0.329  -4.9255  -1.2507   0.5666

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
 D71  C1   C2    aromatic  1.390  0.020  1.390
 D71  C1   H1    single    0.930  0.020  1.080
 D71  C2   C16   single    1.459  0.020  1.459
 D71  C3   C2    aromatic  1.393  0.020  1.393
 D71  C3   N13   single    1.382  0.020  1.382
 D71  C5   C6    aromatic  1.390  0.020  1.390
 D71  C5   N4    aromatic  1.325  0.020  1.325
 D71  C5   H5    single    0.930  0.020  1.080
 D71  C6   C1    aromatic  1.381  0.020  1.381
 D71  C6   H6    single    0.930  0.020  1.080
 D71  C14  N15   single    1.385  0.020  1.385
 D71  C14  O52   double    1.209  0.020  1.209
 D71  N54  O56   double    1.208  0.020  1.208
 D71  O58  N54   single    1.207  0.020  1.207
 D71  C40  N54   single    1.457  0.020  1.457
 D71  C40  C39   aromatic  1.386  0.020  1.386
 D71  C39  H39   single    0.930  0.020  1.080
 D71  C41  C40   aromatic  1.387  0.020  1.387
 D71  C41  H41   single    0.930  0.020  1.080
 D71  C42  C41   aromatic  1.385  0.020  1.385
 D71  C42  C43   aromatic  1.387  0.020  1.387
 D71  C42  H42   single    0.930  0.020  1.080
 D71  C43  C22   aromatic  1.386  0.020  1.386
 D71  C43  H43   single    0.930  0.020  1.080
 D71  C22  C39   aromatic  1.382  0.020  1.382
 D71  C22  N13   single    1.427  0.020  1.427
 D71  N13  C14   single    1.376  0.020  1.376
 D71  N4   C3    aromatic  1.320  0.020  1.320
 D71  N15  C24   single    1.460  0.020  1.460
 D71  C16  N15   single    1.386  0.020  1.386
 D71  C16  O50   double    1.212  0.020  1.212
 D71  C24  C26   single    1.504  0.020  1.504
 D71  C24  H24   single    0.970  0.020  1.090
 D71  C24  H24A  single    0.970  0.020  1.090
 D71  C26  C32   aromatic  1.390  0.020  1.390
 D71  C32  C31   aromatic  1.386  0.020  1.386
 D71  C32  H32   single    0.930  0.020  1.080
 D71  C31  H31   single    0.930  0.020  1.080
 D71  N30  C31   aromatic  1.328  0.020  1.328
 D71  C29  N30   aromatic  1.328  0.020  1.328
 D71  C29  H29   single    0.930  0.020  1.080
 D71  C28  C26   aromatic  1.388  0.020  1.388
 D71  C28  C29   aromatic  1.387  0.020  1.387
 D71  C28  H28   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
 D71  H1    C1   C6   121.08  3.000
 D71  C6    C1   C2   119.03  3.000
 D71  H1    C1   C2   119.89  3.000
 D71  C16   C2   C3   120.69  3.000
 D71  C3    C2   C1   117.86  3.000
 D71  C16   C2   C1   121.45  3.000
 D71  N4    C3   N13  117.32  3.000
 D71  N4    C3   C2   123.67  3.000
 D71  N13   C3   C2   119.02  3.000
 D71  H5    C5   N4   115.96  3.000
 D71  H5    C5   C6   120.21  3.000
 D71  N4    C5   C6   123.83  3.000
 D71  H6    C6   C5   120.47  3.000
 D71  H6    C6   C1   121.56  3.000
 D71  C5    C6   C1   117.97  3.000
 D71  N15   C14  O52  121.48  3.000
 D71  O52   C14  N13  121.63  3.000
 D71  N15   C14  N13  116.89  3.000
 D71  C41   C40  C39  122.05  3.000
 D71  C41   C40  N54  119.20  3.000
 D71  C39   C40  N54  118.75  3.000
 D71  H39   C39  C22  120.18  3.000
 D71  C22   C39  C40  118.10  3.000
 D71  H39   C39  C40  121.71  3.000
 D71  H41   C41  C42  120.09  3.000
 D71  C42   C41  C40  118.65  3.000
 D71  H41   C41  C40  121.26  3.000
 D71  H42   C42  C43  119.94  3.000
 D71  H42   C42  C41  119.66  3.000
 D71  C43   C42  C41  120.40  3.000
 D71  H43   C43  C22  120.08  3.000
 D71  H43   C43  C42  120.26  3.000
 D71  C22   C43  C42  119.66  3.000
 D71  N13   C22  C43  119.61  3.000
 D71  N13   C22  C39  119.25  3.000
 D71  C43   C22  C39  121.14  3.000
 D71  C22   N13  C14  116.96  3.000
 D71  C14   N13  C3   123.12  3.000
 D71  C22   N13  C3   119.92  3.000
 D71  C5    N4   C3   117.64  3.000
 D71  C24   N15  C16  119.40  3.000
 D71  C16   N15  C14  125.19  3.000
 D71  C24   N15  C14  115.42  3.000
 D71  O50   C16  N15  121.68  3.000
 D71  O50   C16  C2   123.23  3.000
 D71  N15   C16  C2   115.09  3.000
 D71  H24A  C24  H24  107.22  3.000
 D71  H24A  C24  C26  110.66  3.000
 D71  H24   C24  C26  109.48  3.000
 D71  H24A  C24  N15  109.17  3.000
 D71  H24   C24  N15  107.43  3.000
 D71  C26   C24  N15  112.69  3.000
 D71  C28   C26  C32  117.54  3.000
 D71  C28   C26  C24  120.55  3.000
 D71  C32   C26  C24  121.87  3.000
 D71  H32   C32  C31  119.32  3.000
 D71  H32   C32  C26  121.77  3.000
 D71  C31   C32  C26  118.91  3.000
 D71  H31   C31  N30  116.59  3.000
 D71  N30   C31  C32  123.69  3.000
 D71  H31   C31  C32  119.72  3.000
 D71  C29   N30  C31  117.22  3.000
 D71  H29   C29  C28  119.82  3.000
 D71  C28   C29  N30  123.56  3.000
 D71  H29   C29  N30  116.63  3.000
 D71  H28   C28  C29  119.90  3.000
 D71  H28   C28  C26  121.01  3.000
 D71  C29   C28  C26  119.09  3.000
 D71  C40   N54  O58  117.91  3.000
 D71  C40   N54  O56  117.96  3.000
 D71  O58   N54  O56  124.13  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
 D71  CONST_01  N4   C3   C2   C1     0.00   0.0  0
 D71  CONST_02  N4   C5   C6   C1     0.00   0.0  0
 D71  CONST_03  C5   C6   C1   C2     0.00   0.0  0
 D71  CONST_04  C5   N4   C3   C2     0.00   0.0  0
 D71  CONST_05  C6   C1   C2   C3     0.00   0.0  0
 D71  CONST_06  C6   C5   N4   C3     0.00   0.0  0
 D71  CONST_07  C43  C22  C39  C40    0.00   0.0  0
 D71  CONST_08  C43  C42  C41  C40    0.00   0.0  0
 D71  CONST_09  C42  C41  C40  C39    0.00   0.0  0
 D71  CONST_10  C42  C43  C22  C39    0.00   0.0  0
 D71  CONST_11  C22  C39  C40  C41    0.00   0.0  0
 D71  CONST_12  C22  C43  C42  C41    0.00   0.0  0
 D71  CONST_13  N30  C31  C32  C26    0.00   0.0  0
 D71  CONST_14  N30  C29  C28  C26    0.00   0.0  0
 D71  CONST_15  C29  C28  C26  C32    0.00   0.0  0
 D71  CONST_16  C29  N30  C31  C32    0.00   0.0  0
 D71  CONST_17  C28  C26  C32  C31    0.00   0.0  0
 D71  CONST_18  C28  C29  N30  C31    0.00   0.0  0
 D71  CONST_19  N13  C22  C39  C40  180.00   0.0  0
 D71  CONST_20  N13  C22  C43  C42  180.00   0.0  0
 D71  CONST_21  C14  N15  C16  C2     0.00   0.0  0
 D71  CONST_22  N15  C14  N13  C3     0.00   0.0  0
 D71  CONST_23  N15  C14  N13  C22  180.00   0.0  0
 D71  CONST_24  C16  N15  C14  N13    0.00   0.0  0
 D71  CONST_25  C22  C39  C40  N54  180.00   0.0  0
 D71  CONST_26  C42  C41  C40  N54  180.00   0.0  0
 D71  CONST_27  C31  C32  C26  C24  180.00   0.0  0
 D71  CONST_28  C29  C28  C26  C24  180.00   0.0  0
 D71  CONST_29  C24  N15  C16  C2   180.00   0.0  0
 D71  CONST_30  O52  C14  N13  C3   180.00   0.0  0
 D71  CONST_31  O50  C16  N15  C14  180.00   0.0  0
 D71  CONST_32  O52  C14  N13  C22    0.00   0.0  0
 D71  CONST_33  C24  N15  C14  N13  180.00   0.0  0
 D71  CONST_34  C16  N15  C14  O52  180.00   0.0  0
 D71  CONST_35  H5   C5   C6   C1   180.00   0.0  0
 D71  CONST_36  H6   C6   C1   C2   180.00   0.0  0
 D71  CONST_37  H1   C1   C2   C3   180.00   0.0  0
 D71  CONST_38  H42  C42  C41  C40  180.00   0.0  0
 D71  CONST_39  H41  C41  C40  C39  180.00   0.0  0
 D71  CONST_40  H43  C43  C22  C39  180.00   0.0  0
 D71  CONST_41  H39  C39  C40  C41  180.00   0.0  0
 D71  CONST_42  H31  C31  C32  C26  180.00   0.0  0
 D71  CONST_43  H29  C29  C28  C26  180.00   0.0  0
 D71  CONST_44  H28  C28  C26  C32  180.00   0.0  0
 D71  CONST_45  H32  C32  C31  N30  180.00   0.0  0
 D71  CONST_46  C39  C40  N54  O56    0.00   0.0  0
 D71  CONST_47  C41  C40  N54  O56  180.00   0.0  0
 D71  CONST_48  C39  C40  N54  O58  180.00   0.0  0
 D71  CONST_49  C41  C40  N54  O58    0.00   0.0  0
 D71  CONST_50  C24  N15  C14  O52    0.00   0.0  0
 D71  CONST_51  C24  N15  C16  O50    0.00   0.0  0
 D71  Var_01    C43  C22  N13  C3    91.96  30.0  2
 D71  Var_02    C26  C24  N15  C14   71.97  30.0  3
 D71  Var_03    C32  C26  C24  N15   44.85  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
 D71  plan-1  C40  0.020
 D71  plan-1  C39  0.020
 D71  plan-1  C41  0.020
 D71  plan-1  C42  0.020
 D71  plan-1  C43  0.020
 D71  plan-1  C22  0.020
 D71  plan-1  N13  0.020
 D71  plan-1  H39  0.020
 D71  plan-1  H41  0.020
 D71  plan-1  H42  0.020
 D71  plan-1  H43  0.020
 D71  plan-1  N54  0.020
 D71  plan-2  C24  0.020
 D71  plan-2  C26  0.020
 D71  plan-2  C32  0.020
 D71  plan-2  C31  0.020
 D71  plan-2  N30  0.020
 D71  plan-2  C29  0.020
 D71  plan-2  C28  0.020
 D71  plan-2  H32  0.020
 D71  plan-2  H31  0.020
 D71  plan-2  H29  0.020
 D71  plan-2  H28  0.020
 D71  plan-3  C1   0.020
 D71  plan-3  C2   0.020
 D71  plan-3  C3   0.020
 D71  plan-3  C5   0.020
 D71  plan-3  C6   0.020
 D71  plan-3  C14  0.020
 D71  plan-3  C22  0.020
 D71  plan-3  N13  0.020
 D71  plan-3  N4   0.020
 D71  plan-3  O52  0.020
 D71  plan-3  N15  0.020
 D71  plan-3  C16  0.020
 D71  plan-3  O50  0.020
 D71  plan-3  C24  0.020
 D71  plan-3  H1   0.020
 D71  plan-3  H5   0.020
 D71  plan-3  H6   0.020
 D71  plan-4  O56  0.020
 D71  plan-4  O58  0.020
 D71  plan-4  C40  0.020
 D71  plan-4  N54  0.020

