# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr  1 19:03:11 2020
#   Inital geometry file: a 100 line input string
#   Ligand name: N~6~-methyl-N~6~-(naphthalen-1-yl)pyrido[2,3-d]pyrimidine-2,4,6-triamine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CN(c1cnc2nc(N)nc(N)c2c1)c3cccc4ccccc34
#
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
 33M  33M  N~6~-methyl-N~6~-(naphthalen-1-yl)pyrido[2,3-d]pyrimidine-2,4,6-triamine  ligand  40  24  .  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_33M
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
 33M  CAL  C  CR16  0  -0.309   1.3174  -1.2381   0.2202
 33M  C5   C  CR66  0  -0.110   2.4675  -0.4394   0.1921
 33M  C6   C  CR6   0   0.476   3.7266  -0.7831   0.8031
 33M  NAC  N  NH2   0  -0.828   3.8862  -1.9395   1.4563
 33M  N1   N  N     0  -0.506   4.7609   0.0231   0.7173
 33M  C2   C  CR6   0   0.523   4.6068   1.1828   0.0444
 33M  NAB  N  NH2   0  -0.821   5.6987   1.9846   0.0245
 33M  N3   N  N     0  -0.497   3.5133   1.6134  -0.5458
 33M  C4   C  CR66  0   0.330   2.4402   0.8001  -0.4703
 33M  NAM  N  N     0  -0.413   1.3129   1.2231  -1.0734
 33M  CAK  C  CR16  0  -0.119   0.2480   0.4662  -1.0464
 33M  CAR  C  CR6   0   0.286   0.1677  -0.7999  -0.4128
 33M  NAX  N  NT    0  -0.587  -0.9934  -1.5425  -0.4663
 33M  CAA  C  CH3   0  -0.554  -1.0320  -2.8500   0.1512
 33M  CAS  C  CR6   0   0.191  -2.2278  -0.9139  -0.7666
 33M  CAV  C  CR66  0   0.152  -2.8418  -0.0426   0.1781
 33M  CAJ  C  CR16  0  -0.323  -2.2694   0.2371   1.4414
 33M  CAE  C  CR16  0  -0.249  -2.8918   1.0838   2.3185
 33M  CAD  C  CR16  0  -0.258  -4.1159   1.6945   1.9780
 33M  CAH  C  CR16  0  -0.311  -4.6968   1.4367   0.7671
 33M  CAT  C  CR66  0   0.092  -4.0808   0.5638  -0.1603
 33M  CAI  C  CR16  0  -0.317  -4.6802   0.2744  -1.4087
 33M  CAF  C  CR16  0  -0.264  -4.0759  -0.5785  -2.2887
 33M  CAG  C  CR16  0  -0.289  -2.8380  -1.1692  -1.9659
 33M  H1   H  HCR6  0   0.272   1.3243  -2.1905   0.7333
 33M  H2   H  HNH2  0   0.416   3.1148  -2.5383   1.6887
 33M  H3   H  HNH2  0   0.403   4.7485  -2.1020   1.9485
 33M  H4   H  HNH2  0   0.388   6.5903   1.5700   0.2331
 33M  H5   H  HNH2  0   0.387   5.7078   2.7458  -0.6324
 33M  H6   H  HCR6  0   0.273  -0.6255   0.8575  -1.5586
 33M  H7   H  HCH3  0   0.233  -0.9179  -2.8089   1.2405
 33M  H8   H  HCH3  0   0.268  -1.9866  -3.3187  -0.0720
 33M  H9   H  HCH3  0   0.248  -0.2448  -3.4919  -0.2496
 33M  H10  H  HCR6  0   0.253  -1.3322  -0.2247   1.7212
 33M  H11  H  HCR6  0   0.261  -2.4434   1.2862   3.2823
 33M  H12  H  HCR6  0   0.261  -4.5951   2.3640   2.6800
 33M  H13  H  HCR6  0   0.258  -5.6417   1.8964   0.5033
 33M  H14  H  HCR6  0   0.259  -5.6287   0.7360  -1.6546
 33M  H15  H  HCR6  0   0.262  -4.5372  -0.7988  -3.2422
 33M  H16  H  HCR6  0   0.264  -2.3546  -1.8306  -2.6736

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
 33M  CAD  CAH  aromatic  1.368  0.020  1.368
 33M  CAD  CAE  aromatic  1.410  0.020  1.410
 33M  CAH  CAT  aromatic  1.415  0.020  1.415
 33M  CAE  CAJ  aromatic  1.369  0.020  1.369
 33M  CAT  CAI  aromatic  1.415  0.020  1.415
 33M  CAT  CAV  aromatic  1.420  0.020  1.420
 33M  CAI  CAF  aromatic  1.366  0.020  1.366
 33M  CAJ  CAV  aromatic  1.415  0.020  1.415
 33M  CAV  CAS  aromatic  1.424  0.020  1.424
 33M  NAM  CAK  aromatic  1.307  0.020  1.307
 33M  NAM  C4   aromatic  1.347  0.020  1.347
 33M  CAF  CAG  aromatic  1.409  0.020  1.409
 33M  CAK  CAR  aromatic  1.418  0.020  1.418
 33M  N3   C4   aromatic  1.349  0.020  1.349
 33M  N3   C2   aromatic  1.315  0.020  1.315
 33M  CAS  CAG  aromatic  1.370  0.020  1.370
 33M  CAS  NAX  single    1.417  0.020  1.417
 33M  C4   C5   aromatic  1.406  0.020  1.406
 33M  NAB  C2   single    1.355  0.020  1.355
 33M  CAR  NAX  single    1.379  0.020  1.379
 33M  CAR  CAL  aromatic  1.384  0.020  1.384
 33M  C2   N1   aromatic  1.350  0.020  1.350
 33M  NAX  CAA  single    1.447  0.020  1.447
 33M  C5   CAL  aromatic  1.401  0.020  1.401
 33M  C5   C6   aromatic  1.441  0.020  1.441
 33M  N1   C6   aromatic  1.314  0.020  1.314
 33M  C6   NAC  single    1.338  0.020  1.338
 33M  CAL  H1   single    0.930  0.020  1.080
 33M  NAC  H2   single    0.860  0.020  1.020
 33M  NAC  H3   single    0.860  0.020  1.020
 33M  NAB  H4   single    0.890  0.020  1.040
 33M  NAB  H5   single    0.890  0.020  1.040
 33M  CAK  H6   single    0.930  0.020  1.080
 33M  CAA  H7   single    0.970  0.020  1.090
 33M  CAA  H8   single    0.970  0.020  1.090
 33M  CAA  H9   single    0.970  0.020  1.090
 33M  CAJ  H10  single    0.930  0.020  1.080
 33M  CAE  H11  single    0.930  0.020  1.080
 33M  CAD  H12  single    0.930  0.020  1.080
 33M  CAH  H13  single    0.930  0.020  1.080
 33M  CAI  H14  single    0.930  0.020  1.080
 33M  CAF  H15  single    0.930  0.020  1.080
 33M  CAG  H16  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
 33M  H1   CAL  CAR  120.07  3.000
 33M  H1   CAL  C5   120.42  3.000
 33M  CAR  CAL  C5   119.51  3.000
 33M  C4   C5   C6   115.28  3.000
 33M  C6   C5   CAL  124.96  3.000
 33M  C4   C5   CAL  119.76  3.000
 33M  N1   C6   NAC  117.92  3.000
 33M  NAC  C6   C5   121.16  3.000
 33M  N1   C6   C5   120.91  3.000
 33M  H3   NAC  H2   116.68  3.000
 33M  H3   NAC  C6   118.74  3.000
 33M  H2   NAC  C6   122.48  3.000
 33M  C2   N1   C6   118.03  3.000
 33M  N3   C2   NAB  118.02  3.000
 33M  NAB  C2   N1   115.08  3.000
 33M  N3   C2   N1   126.87  3.000
 33M  H5   NAB  H4   116.09  3.000
 33M  H5   NAB  C2   117.71  3.000
 33M  H4   NAB  C2   117.89  3.000
 33M  C4   N3   C2   116.05  3.000
 33M  NAM  C4   N3   116.85  3.000
 33M  N3   C4   C5   122.87  3.000
 33M  NAM  C4   C5   120.28  3.000
 33M  CAK  NAM  C4   119.41  3.000
 33M  H6   CAK  CAR  119.15  3.000
 33M  H6   CAK  NAM  115.92  3.000
 33M  CAR  CAK  NAM  124.93  3.000
 33M  NAX  CAR  CAK  120.73  3.000
 33M  NAX  CAR  CAL  123.14  3.000
 33M  CAK  CAR  CAL  116.11  3.000
 33M  CAS  NAX  CAA  117.91  3.000
 33M  CAA  NAX  CAR  119.51  3.000
 33M  CAS  NAX  CAR  120.17  3.000
 33M  H9   CAA  H8   107.72  3.000
 33M  H9   CAA  H7   108.17  3.000
 33M  H8   CAA  H7   108.17  3.000
 33M  H9   CAA  NAX  110.81  3.000
 33M  H8   CAA  NAX  109.01  3.000
 33M  H7   CAA  NAX  112.81  3.000
 33M  CAG  CAS  CAV  120.18  3.000
 33M  CAG  CAS  NAX  119.39  3.000
 33M  CAV  CAS  NAX  120.41  3.000
 33M  CAT  CAV  CAJ  118.77  3.000
 33M  CAJ  CAV  CAS  122.60  3.000
 33M  CAT  CAV  CAS  118.63  3.000
 33M  H10  CAJ  CAE  119.49  3.000
 33M  H10  CAJ  CAV  119.81  3.000
 33M  CAE  CAJ  CAV  120.70  3.000
 33M  H11  CAE  CAD  119.60  3.000
 33M  H11  CAE  CAJ  119.87  3.000
 33M  CAD  CAE  CAJ  120.54  3.000
 33M  H12  CAD  CAH  120.20  3.000
 33M  H12  CAD  CAE  119.73  3.000
 33M  CAH  CAD  CAE  120.07  3.000
 33M  H13  CAH  CAT  118.81  3.000
 33M  H13  CAH  CAD  120.40  3.000
 33M  CAT  CAH  CAD  120.79  3.000
 33M  CAI  CAT  CAH  121.34  3.000
 33M  CAI  CAT  CAV  119.51  3.000
 33M  CAH  CAT  CAV  119.15  3.000
 33M  H14  CAI  CAF  120.48  3.000
 33M  H14  CAI  CAT  118.96  3.000
 33M  CAF  CAI  CAT  120.57  3.000
 33M  H15  CAF  CAG  119.42  3.000
 33M  H15  CAF  CAI  120.40  3.000
 33M  CAG  CAF  CAI  120.18  3.000
 33M  H16  CAG  CAF  119.91  3.000
 33M  H16  CAG  CAS  119.17  3.000
 33M  CAF  CAG  CAS  120.92  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
 33M  CONST_01  NAM  CAK  CAR  CAL    0.00   0.0  0
 33M  CONST_02  NAM  C4   C5   CAL    0.00   0.0  0
 33M  CONST_03  N3   C4   C5   CAL  180.00   0.0  0
 33M  CONST_04  N1   C6   C5   CAL  180.00   0.0  0
 33M  CONST_05  CAK  NAM  C4   C5     0.00   0.0  0
 33M  CONST_06  C2   N3   C4   C5     0.00   0.0  0
 33M  CONST_07  CAK  CAR  CAL  C5     0.00   0.0  0
 33M  CONST_08  C2   N1   C6   C5     0.00   0.0  0
 33M  CONST_09  NAM  C4   C5   C6   180.00   0.0  0
 33M  CONST_10  N3   C4   C5   C6     0.00   0.0  0
 33M  CONST_11  CAR  CAL  C5   C6   180.00   0.0  0
 33M  CONST_12  N3   C2   N1   C6     0.00   0.0  0
 33M  CONST_13  C4   N3   C2   N1     0.00   0.0  0
 33M  CONST_14  C4   C5   C6   N1     0.00   0.0  0
 33M  CONST_15  NAM  C4   N3   C2   180.00   0.0  0
 33M  CONST_16  CAK  NAM  C4   N3   180.00   0.0  0
 33M  CONST_17  CAR  CAK  NAM  C4     0.00   0.0  0
 33M  CONST_18  CAR  CAL  C5   C4     0.00   0.0  0
 33M  CONST_19  CAH  CAT  CAV  CAS  180.00   0.0  0
 33M  CONST_20  CAI  CAT  CAV  CAS    0.00   0.0  0
 33M  CONST_21  CAE  CAJ  CAV  CAS  180.00   0.0  0
 33M  CONST_22  CAI  CAF  CAG  CAS    0.00   0.0  0
 33M  CONST_23  CAD  CAH  CAT  CAV    0.00   0.0  0
 33M  CONST_24  CAF  CAI  CAT  CAV    0.00   0.0  0
 33M  CONST_25  CAD  CAE  CAJ  CAV    0.00   0.0  0
 33M  CONST_26  CAF  CAG  CAS  CAV    0.00   0.0  0
 33M  CONST_27  CAH  CAD  CAE  CAJ    0.00   0.0  0
 33M  CONST_28  CAH  CAT  CAV  CAJ    0.00   0.0  0
 33M  CONST_29  CAI  CAT  CAV  CAJ  180.00   0.0  0
 33M  CONST_30  CAG  CAS  CAV  CAJ  180.00   0.0  0
 33M  CONST_31  CAT  CAH  CAD  CAE    0.00   0.0  0
 33M  CONST_32  CAT  CAV  CAJ  CAE    0.00   0.0  0
 33M  CONST_33  CAI  CAT  CAH  CAD  180.00   0.0  0
 33M  CONST_34  CAF  CAI  CAT  CAH  180.00   0.0  0
 33M  CONST_35  CAG  CAF  CAI  CAT    0.00   0.0  0
 33M  CONST_36  CAG  CAS  CAV  CAT    0.00   0.0  0
 33M  CONST_37  NAC  C6   C5   CAL    0.00   0.0  0
 33M  CONST_38  NAX  CAR  CAL  C5   180.00   0.0  0
 33M  CONST_39  NAB  C2   N1   C6   180.00   0.0  0
 33M  CONST_40  C4   C5   C6   NAC  180.00   0.0  0
 33M  CONST_41  C2   N1   C6   NAC  180.00   0.0  0
 33M  CONST_42  C4   N3   C2   NAB  180.00   0.0  0
 33M  CONST_43  NAX  CAR  CAK  NAM  180.00   0.0  0
 33M  CONST_44  CAT  CAV  CAS  NAX  180.00   0.0  0
 33M  CONST_45  CAJ  CAV  CAS  NAX    0.00   0.0  0
 33M  CONST_46  CAF  CAG  CAS  NAX  180.00   0.0  0
 33M  CONST_47  H6   CAK  CAR  CAL  180.00   0.0  0
 33M  CONST_48  H1   CAL  C5   C6     0.00   0.0  0
 33M  CONST_49  H10  CAJ  CAV  CAS    0.00   0.0  0
 33M  CONST_50  H15  CAF  CAG  CAS  180.00   0.0  0
 33M  CONST_51  H13  CAH  CAT  CAV  180.00   0.0  0
 33M  CONST_52  H14  CAI  CAT  CAV  180.00   0.0  0
 33M  CONST_53  H11  CAE  CAJ  CAV  180.00   0.0  0
 33M  CONST_54  H16  CAG  CAS  CAV  180.00   0.0  0
 33M  CONST_55  H12  CAD  CAE  CAJ  180.00   0.0  0
 33M  CONST_56  H2   NAC  C6   C5     0.00   0.0  0
 33M  CONST_57  H3   NAC  C6   C5   180.00   0.0  0
 33M  CONST_59  H5   NAB  C2   N1   180.00   0.0  0
 33M  Var_01    CAS  NAX  CAR  CAL  161.44  30.0  2
 33M  Var_02    CAV  CAS  NAX  CAR  -70.69  30.0  2
 33M  Var_03    H7   CAA  NAX  CAR   65.13  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
 33M  plan-1  CAL  0.020
 33M  plan-1  C5   0.020
 33M  plan-1  C6   0.020
 33M  plan-1  NAC  0.020
 33M  plan-1  N1   0.020
 33M  plan-1  C2   0.020
 33M  plan-1  NAB  0.020
 33M  plan-1  N3   0.020
 33M  plan-1  C4   0.020
 33M  plan-1  NAM  0.020
 33M  plan-1  CAK  0.020
 33M  plan-1  CAR  0.020
 33M  plan-1  NAX  0.020
 33M  plan-1  H1   0.020
 33M  plan-1  H6   0.020
 33M  plan-2  NAX  0.020
 33M  plan-2  CAS  0.020
 33M  plan-2  CAV  0.020
 33M  plan-2  CAJ  0.020
 33M  plan-2  CAE  0.020
 33M  plan-2  CAD  0.020
 33M  plan-2  CAH  0.020
 33M  plan-2  CAT  0.020
 33M  plan-2  CAI  0.020
 33M  plan-2  CAF  0.020
 33M  plan-2  CAG  0.020
 33M  plan-2  H10  0.020
 33M  plan-2  H11  0.020
 33M  plan-2  H12  0.020
 33M  plan-2  H13  0.020
 33M  plan-2  H14  0.020
 33M  plan-2  H15  0.020
 33M  plan-2  H16  0.020
 33M  plan-3  C6   0.020
 33M  plan-3  NAC  0.020
 33M  plan-3  H2   0.020
 33M  plan-3  H3   0.020
 33M  plan-4  C2   0.020
 33M  plan-4  NAB  0.020
 33M  plan-4  H4   0.020
 33M  plan-4  H5   0.020

