# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Apr 26 00:49:43 2020
#   Inital geometry file: a 124 line input string
#   Ligand name: 5-(5-methoxypyridin-3-yl)-3-methyl-8-(piperidin-4-ylamino)-1H-1,7-naphthyridin-2-one
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: COc1cncc(c1)c2cnc(NC3CCNCC3)c4NC(=O)C(=Cc24)C
#
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
 NP8  NP8  5-(5-methoxypyridin-3-yl)-3-methyl-8-(piperidin-4-ylamino)-1H-1,7-naphthyridin-2-one  ligand  50  27  .  2021-08-15  2021-08-15  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_NP8
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
 NP8  C01   C  CH3   0  -0.440   6.5670  -2.9391   0.7997
 NP8  O05   O  O2    0  -0.466   5.2032  -2.6389   1.0377
 NP8  C06   C  CR6   0   0.335   4.5806  -1.7932   0.2037
 NP8  C07   C  CR16  0  -0.195   5.1721  -1.1863  -0.9029
 NP8  N09   N  N     0  -0.378   4.5058  -0.3549  -1.6974
 NP8  C10   C  CR16  0  -0.123   3.2407  -0.0853  -1.4362
 NP8  C12   C  CR6   0  -0.048   2.5528  -0.6307  -0.3473
 NP8  C13   C  CR16  0  -0.298   3.2464  -1.5000   0.4795
 NP8  C15   C  CR6   0  -0.070   1.1289  -0.3319  -0.1166
 NP8  C16   C  CR16  0  -0.118   0.2157  -1.3550  -0.0116
 NP8  N18   N  N     0  -0.458  -1.1016  -1.1811   0.1230
 NP8  C19   C  CR6   0   0.502  -1.5987   0.0361   0.1843
 NP8  N20   N  NH1   0  -0.692  -2.9445   0.2052   0.3208
 NP8  C22   C  CH1   0  -0.077  -3.8732  -0.9108   0.3031
 NP8  C24   C  CH2   0  -0.432  -5.1870  -0.4754   0.9453
 NP8  C27   C  CH2   0  -0.298  -6.2061  -1.6045   0.8942
 NP8  N30   N  NH1   0  -0.594  -6.4179  -2.0221  -0.4796
 NP8  C32   C  CH2   0  -0.298  -5.1964  -2.5395  -1.0703
 NP8  C35   C  CH2   0  -0.429  -4.1342  -1.4497  -1.1039
 NP8  C38   C  CR66  0   0.223  -0.7367   1.1702   0.1713
 NP8  N39   N  NR16  0  -0.753  -1.2276   2.4394   0.3452
 NP8  C41   C  CR6   0   0.513  -0.4882   3.5903   0.3507
 NP8  O42   O  O     0  -0.476  -1.0186   4.6814   0.5142
 NP8  C43   C  CR6   0  -0.107   0.9507   3.4049   0.1730
 NP8  C44   C  CH3   0  -0.711   1.8010   4.6296   0.1977
 NP8  C48   C  CR16  0  -0.225   1.4551   2.1619   0.0229
 NP8  C50   C  CR66  0   0.138   0.6293   0.9888   0.0035
 NP8  H011  H  HCH3  0   0.263   6.8732  -3.6236   1.5863
 NP8  H012  H  HCH3  0   0.233   6.7125  -3.4264  -0.1675
 NP8  H013  H  HCH3  0   0.233   7.1929  -2.0445   0.8448
 NP8  H07   H  HCR6  0   0.279   6.2070  -1.3706  -1.1655
 NP8  H13   H  HCR6  0   0.275   2.7648  -1.9434   1.3431
 NP8  H10   H  HCR6  0   0.262   2.7309   0.5820  -2.1237
 NP8  H16   H  HCR6  0   0.259   0.5499  -2.3852  -0.0753
 NP8  H20   H  HNH1  0   0.383  -3.3329   1.0483  -0.0752
 NP8  H22   H  HCH1  0   0.239  -3.4379  -1.7092   0.9098
 NP8  H241  H  HCH2  0   0.240  -5.0172  -0.1729   1.9808
 NP8  H242  H  HCH2  0   0.220  -5.5839   0.3943   0.4102
 NP8  H351  H  HCH2  0   0.215  -4.4768  -0.6282  -1.7419
 NP8  H352  H  HCH2  0   0.239  -3.2109  -1.8400  -1.5351
 NP8  H271  H  HCH2  0   0.189  -5.8514  -2.4297   1.5345
 NP8  H272  H  HCH2  0   0.236  -7.1551  -1.2655   1.3140
 NP8  H30   H  HNH1  0   0.352  -7.1350  -2.7350  -0.5084
 NP8  H321  H  HCH2  0   0.189  -4.7987  -3.4069  -0.5171
 NP8  H322  H  HCH2  0   0.234  -5.4092  -2.8831  -2.0844
 NP8  H39   H  HNR6  0   0.409  -2.2094   2.5659   0.5479
 NP8  H441  H  HCH3  0   0.252   1.5294   5.3146  -0.6071
 NP8  H442  H  HCH3  0   0.252   1.6797   5.1779   1.1331
 NP8  H443  H  HCH3  0   0.249   2.8531   4.3752   0.0858
 NP8  H48   H  HCR6  0   0.275   2.5270   2.0422  -0.0729

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
 NP8  C01  O05   single    1.417  0.020  1.417
 NP8  O05  C06   single    1.341  0.020  1.341
 NP8  C06  C07   aromatic  1.394  0.020  1.394
 NP8  C06  C13   aromatic  1.394  0.020  1.394
 NP8  C07  N09   aromatic  1.329  0.020  1.329
 NP8  N09  C10   aromatic  1.320  0.020  1.320
 NP8  C10  C12   aromatic  1.399  0.020  1.399
 NP8  C12  C13   aromatic  1.386  0.020  1.386
 NP8  C12  C15   single    1.473  0.020  1.473
 NP8  C15  C16   aromatic  1.375  0.020  1.375
 NP8  C15  C50   aromatic  1.417  0.020  1.417
 NP8  C16  N18   aromatic  1.336  0.020  1.336
 NP8  N18  C19   aromatic  1.316  0.020  1.316
 NP8  C19  N20   single    1.363  0.020  1.363
 NP8  C19  C38   aromatic  1.425  0.020  1.425
 NP8  N20  C22   single    1.452  0.020  1.452
 NP8  C22  C24   single    1.526  0.020  1.526
 NP8  C22  C35   single    1.529  0.020  1.529
 NP8  C24  C27   single    1.522  0.020  1.522
 NP8  C27  N30   single    1.451  0.020  1.451
 NP8  N30  C32   single    1.452  0.020  1.452
 NP8  C32  C35   single    1.522  0.020  1.522
 NP8  C38  N39   single    1.372  0.020  1.372
 NP8  C38  C50   aromatic  1.388  0.020  1.388
 NP8  N39  C41   single    1.368  0.020  1.368
 NP8  C41  O42   double    1.224  0.020  1.224
 NP8  C41  C43   single    1.462  0.020  1.462
 NP8  C43  C44   single    1.491  0.020  1.491
 NP8  C43  C48   double    1.350  0.020  1.350
 NP8  C48  C50   single    1.435  0.020  1.435
 NP8  C01  H011  single    0.970  0.020  1.090
 NP8  C01  H012  single    0.970  0.020  1.090
 NP8  C01  H013  single    0.970  0.020  1.090
 NP8  C07  H07   single    0.930  0.020  1.080
 NP8  C13  H13   single    0.930  0.020  1.080
 NP8  C10  H10   single    0.930  0.020  1.080
 NP8  C16  H16   single    0.930  0.020  1.080
 NP8  N20  H20   single    0.890  0.020  1.040
 NP8  C22  H22   single    0.970  0.020  1.090
 NP8  C24  H241  single    0.970  0.020  1.090
 NP8  C24  H242  single    0.970  0.020  1.090
 NP8  C35  H351  single    0.970  0.020  1.090
 NP8  C35  H352  single    0.970  0.020  1.090
 NP8  C27  H271  single    0.970  0.020  1.090
 NP8  C27  H272  single    0.970  0.020  1.090
 NP8  N30  H30   single    0.890  0.020  1.040
 NP8  C32  H321  single    0.970  0.020  1.090
 NP8  C32  H322  single    0.970  0.020  1.090
 NP8  N39  H39   single    0.860  0.020  1.020
 NP8  C44  H441  single    0.970  0.020  1.090
 NP8  C44  H442  single    0.970  0.020  1.090
 NP8  C44  H443  single    0.970  0.020  1.090
 NP8  C48  H48   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
 NP8  H013  C01  H012  108.99  3.000
 NP8  H013  C01  H011  108.93  3.000
 NP8  H012  C01  H011  108.80  3.000
 NP8  H013  C01  O05   111.77  3.000
 NP8  H012  C01  O05   111.80  3.000
 NP8  H011  C01  O05   106.45  3.000
 NP8  C06   O05  C01   118.43  3.000
 NP8  C13   C06  C07   118.15  3.000
 NP8  C13   C06  O05   117.01  3.000
 NP8  C07   C06  O05   124.85  3.000
 NP8  H07   C07  N09   116.13  3.000
 NP8  H07   C07  C06   121.58  3.000
 NP8  N09   C07  C06   122.30  3.000
 NP8  C10   N09  C07   119.34  3.000
 NP8  H10   C10  C12   120.12  3.000
 NP8  H10   C10  N09   116.78  3.000
 NP8  C12   C10  N09   123.09  3.000
 NP8  C15   C12  C13   121.17  3.000
 NP8  C15   C12  C10   121.22  3.000
 NP8  C13   C12  C10   117.58  3.000
 NP8  H13   C13  C12   120.65  3.000
 NP8  H13   C13  C06   119.80  3.000
 NP8  C12   C13  C06   119.54  3.000
 NP8  C50   C15  C16   116.91  3.000
 NP8  C50   C15  C12   122.89  3.000
 NP8  C16   C15  C12   120.19  3.000
 NP8  H16   C16  N18   115.68  3.000
 NP8  H16   C16  C15   119.82  3.000
 NP8  N18   C16  C15   124.46  3.000
 NP8  C19   N18  C16   119.84  3.000
 NP8  C38   C19  N20   119.97  3.000
 NP8  C38   C19  N18   120.49  3.000
 NP8  N20   C19  N18   119.48  3.000
 NP8  H20   N20  C22   113.03  3.000
 NP8  H20   N20  C19   116.37  3.000
 NP8  C22   N20  C19   122.33  3.000
 NP8  H22   C22  C35   108.75  3.000
 NP8  H22   C22  C24   108.52  3.000
 NP8  C35   C22  C24   109.93  3.000
 NP8  H22   C22  N20   107.45  3.000
 NP8  C35   C22  N20   113.03  3.000
 NP8  C24   C22  N20   109.04  3.000
 NP8  H242  C24  H241  107.43  3.000
 NP8  H242  C24  C27   109.27  3.000
 NP8  H241  C24  C27   109.96  3.000
 NP8  H242  C24  C22   109.45  3.000
 NP8  H241  C24  C22   110.14  3.000
 NP8  C27   C24  C22   110.53  3.000
 NP8  H272  C27  H271  106.78  3.000
 NP8  H272  C27  N30   109.05  3.000
 NP8  H271  C27  N30   112.40  3.000
 NP8  H272  C27  C24   109.81  3.000
 NP8  H271  C27  C24   108.68  3.000
 NP8  N30   C27  C24   110.06  3.000
 NP8  H30   N30  C32   109.49  3.000
 NP8  H30   N30  C27   109.46  3.000
 NP8  C32   N30  C27   111.39  3.000
 NP8  H322  C32  H321  106.78  3.000
 NP8  H322  C32  C35   109.93  3.000
 NP8  H321  C32  C35   108.82  3.000
 NP8  H322  C32  N30   109.03  3.000
 NP8  H321  C32  N30   112.30  3.000
 NP8  C35   C32  N30   109.93  3.000
 NP8  H352  C35  H351  107.63  3.000
 NP8  H352  C35  C32   110.06  3.000
 NP8  H351  C35  C32   109.37  3.000
 NP8  H352  C35  C22   110.19  3.000
 NP8  H351  C35  C22   108.97  3.000
 NP8  C32   C35  C22   110.55  3.000
 NP8  C50   C38  N39   119.23  3.000
 NP8  C50   C38  C19   119.50  3.000
 NP8  N39   C38  C19   121.25  3.000
 NP8  H39   N39  C41   114.78  3.000
 NP8  H39   N39  C38   119.27  3.000
 NP8  C41   N39  C38   125.83  3.000
 NP8  C43   C41  O42   123.77  3.000
 NP8  C43   C41  N39   115.15  3.000
 NP8  O42   C41  N39   121.08  3.000
 NP8  C48   C43  C44   123.03  3.000
 NP8  C48   C43  C41   119.88  3.000
 NP8  C44   C43  C41   117.08  3.000
 NP8  H443  C44  H442  108.25  3.000
 NP8  H443  C44  H441  108.16  3.000
 NP8  H442  C44  H441  106.81  3.000
 NP8  H443  C44  C43   110.95  3.000
 NP8  H442  C44  C43   111.32  3.000
 NP8  H441  C44  C43   111.19  3.000
 NP8  H48   C48  C50   118.57  3.000
 NP8  H48   C48  C43   118.79  3.000
 NP8  C50   C48  C43   122.64  3.000
 NP8  C48   C50  C38   117.25  3.000
 NP8  C48   C50  C15   124.07  3.000
 NP8  C38   C50  C15   118.62  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
 NP8  CONST_01  C10   N09  C07  C06    0.00   0.0  0
 NP8  CONST_02  C10   C12  C13  C06    0.00   0.0  0
 NP8  CONST_03  C15   C12  C13  C06  180.00   0.0  0
 NP8  CONST_04  C12   C13  C06  C07    0.00   0.0  0
 NP8  CONST_05  C12   C10  N09  C07    0.00   0.0  0
 NP8  CONST_06  C13   C06  C07  N09    0.00   0.0  0
 NP8  CONST_07  C13   C12  C10  N09    0.00   0.0  0
 NP8  CONST_08  C15   C12  C10  N09  180.00   0.0  0
 NP8  CONST_11  N18   C16  C15  C12  180.00   0.0  0
 NP8  CONST_12  C38   C50  C15  C12  180.00   0.0  0
 NP8  CONST_15  C19   N18  C16  C15    0.00   0.0  0
 NP8  CONST_16  C19   C38  C50  C15    0.00   0.0  0
 NP8  CONST_17  C38   C50  C15  C16    0.00   0.0  0
 NP8  CONST_18  C38   C19  N18  C16    0.00   0.0  0
 NP8  CONST_19  C50   C15  C16  N18    0.00   0.0  0
 NP8  CONST_20  C50   C38  C19  N18    0.00   0.0  0
 NP8  CONST_21  C48   C50  C15  C12    0.00   0.0  0
 NP8  CONST_22  C43   C41  N39  C38    0.00   0.0  0
 NP8  CONST_23  N09   C07  C06  O05  180.00   0.0  0
 NP8  CONST_24  C12   C13  C06  O05  180.00   0.0  0
 NP8  CONST_25  N20   C19  N18  C16  180.00   0.0  0
 NP8  CONST_26  N39   C38  C19  N20    0.00   0.0  0
 NP8  CONST_27  C50   C38  C19  N20  180.00   0.0  0
 NP8  CONST_28  C22   N20  C19  N18    0.00   0.0  0
 NP8  CONST_29  C38   C19  N20  C22  180.00   0.0  0
 NP8  CONST_30  O42   C41  N39  C38  180.00   0.0  0
 NP8  CONST_31  H13   C13  C06  C07  180.00   0.0  0
 NP8  CONST_32  H10   C10  N09  C07  180.00   0.0  0
 NP8  CONST_33  H07   C07  N09  C10  180.00   0.0  0
 NP8  CONST_34  H16   C16  C15  C12    0.00   0.0  0
 NP8  CONST_35  H39   N39  C41  C43  180.00   0.0  0
 NP8  Var_01    N30   C27  C24  C22  -57.30  30.0  1
 NP8  Var_02    N30   C32  C35  C22   57.27  30.0  1
 NP8  Var_03    C32   N30  C27  C24   62.01  30.0  1
 NP8  Var_04    C35   C32  N30  C27  -61.98  30.0  1
 NP8  Var_05    C07   C06  O05  C01    0.66  30.0  2
 NP8  Var_06    H441  C44  C43  C41  -61.24  30.0  3
 NP8  Var_07    H011  C01  O05  C06  179.39  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
 NP8  chir_01  C22  N20  C24  C35  negativ

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
 NP8  plan-1  O05  0.020
 NP8  plan-1  C06  0.020
 NP8  plan-1  C07  0.020
 NP8  plan-1  N09  0.020
 NP8  plan-1  C10  0.020
 NP8  plan-1  C12  0.020
 NP8  plan-1  C13  0.020
 NP8  plan-1  C15  0.020
 NP8  plan-1  H07  0.020
 NP8  plan-1  H13  0.020
 NP8  plan-1  H10  0.020
 NP8  plan-2  C12  0.020
 NP8  plan-2  C15  0.020
 NP8  plan-2  C16  0.020
 NP8  plan-2  N18  0.020
 NP8  plan-2  C19  0.020
 NP8  plan-2  N20  0.020
 NP8  plan-2  C38  0.020
 NP8  plan-2  N39  0.020
 NP8  plan-2  C41  0.020
 NP8  plan-2  O42  0.020
 NP8  plan-2  C43  0.020
 NP8  plan-2  C44  0.020
 NP8  plan-2  C48  0.020
 NP8  plan-2  C50  0.020
 NP8  plan-2  H16  0.020
 NP8  plan-2  H39  0.020
 NP8  plan-2  H48  0.020
 NP8  plan-3  C19  0.020
 NP8  plan-3  N20  0.020
 NP8  plan-3  C22  0.020
 NP8  plan-3  H20  0.020

