# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr 22 09:09:35 2020
#   Inital geometry file: a 90 line input string
#   Ligand name: 6-(2,6-dimethoxyphenyl)pyrido[2,3-d]pyrimidine-2,7-diamine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: COc1cccc(OC)c1c2cc3cnc(N)nc3nc2N
#
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
 LZK  LZK  6-(2,6-dimethoxyphenyl)pyrido[2,3-d]pyrimidine-2,7-diamine  ligand  37  22  .  2021-08-12  2021-08-12  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_LZK
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
 LZK  N20   N  NH2   0  -0.817  1.9727  -27.6237  24.7183
 LZK  C19   C  CR6   0   0.539  2.3362  -26.3353  24.8417
 LZK  N17   N  N     0  -0.485  3.0844  -25.8072  23.8882
 LZK  N18   N  N     0  -0.462  1.8664  -25.6993  25.9457
 LZK  C16   C  CR16  0  -0.047  2.1932  -24.4388  26.0633
 LZK  C11   C  CR66  0  -0.115  2.9772  -23.7599  25.1249
 LZK  C15   C  CR66  0   0.372  3.4169  -24.5137  24.0110
 LZK  N12   N  N     0  -0.493  4.1750  -23.9752  23.0469
 LZK  C6    C  CR6   0   0.454  4.5234  -22.7032  23.1475
 LZK  N13   N  NH2   0  -0.821  5.2936  -22.1979  22.1757
 LZK  C5    C  CR16  0  -0.208  3.3577  -22.4034  25.2119
 LZK  C2    C  CR6   0  -0.005  4.1301  -21.8513  24.2411
 LZK  C1    C  CR6   0  -0.266  4.5674  -20.4397  24.2827
 LZK  C4    C  CR6   0   0.406  5.7558  -20.0880  24.9311
 LZK  O1    O  O2    0  -0.460  6.4330  -21.1061  25.4866
 LZK  C45   C  CH3   0  -0.437  7.6407  -20.8278  26.1690
 LZK  C3    C  CR6   0   0.404  3.8013  -19.4454  23.6652
 LZK  O7    O  O2    0  -0.459  2.6836  -19.8735  23.0559
 LZK  C43   C  CH3   0  -0.438  1.8828  -18.9309  22.3694
 LZK  C7    C  CR16  0  -0.412  4.2091  -18.1122  23.7024
 LZK  C14   C  CR16  0  -0.229  5.3887  -17.7935  24.3561
 LZK  C9    C  CR16  0  -0.412  6.1720  -18.7575  24.9712
 LZK  H201  H  HNH2  0   0.396  2.3971  -28.1924  24.0070
 LZK  H202  H  HNH2  0   0.397  1.5391  -28.0911  25.4948
 LZK  H16   H  HCR6  0   0.270  1.8274  -23.9129  26.9412
 LZK  H5    H  HCR6  0   0.262  3.0305  -21.8075  26.0565
 LZK  H131  H  HNH2  0   0.397  5.5372  -22.7681  21.3845
 LZK  H132  H  HNH2  0   0.410  5.5485  -21.2264  22.1554
 LZK  H9    H  HCR6  0   0.277  7.0870  -18.4621  25.4645
 LZK  H451  H  HCH3  0   0.229  8.3934  -20.3923  25.5071
 LZK  H452  H  HCH3  0   0.230  7.4840  -20.1569  27.0171
 LZK  H453  H  HCH3  0   0.260  8.0103  -21.7805  26.5395
 LZK  H7    H  HCR6  0   0.278  3.6304  -17.3279  23.2353
 LZK  H431  H  HCH3  0   0.230  1.4867  -18.1646  23.0404
 LZK  H432  H  HCH3  0   0.230  2.4323  -18.4433  21.5606
 LZK  H433  H  HCH3  0   0.260  1.0508  -19.4869  21.9447
 LZK  H14   H  HCR6  0   0.264  5.7092  -16.7603  24.3863

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
 LZK  N20  C19   single    1.344  0.020  1.344
 LZK  C19  N17   aromatic  1.322  0.020  1.322
 LZK  C19  N18   aromatic  1.358  0.020  1.358
 LZK  N17  C15   aromatic  1.341  0.020  1.341
 LZK  N18  C16   aromatic  1.307  0.020  1.307
 LZK  C16  C11   aromatic  1.399  0.020  1.399
 LZK  C11  C15   aromatic  1.415  0.020  1.415
 LZK  C11  C5    aromatic  1.412  0.020  1.412
 LZK  C15  N12   aromatic  1.339  0.020  1.339
 LZK  N12  C6    aromatic  1.323  0.020  1.323
 LZK  C6   N13   single    1.339  0.020  1.339
 LZK  C6   C2    aromatic  1.441  0.020  1.441
 LZK  C5   C2    aromatic  1.358  0.020  1.358
 LZK  C2   C1    single    1.478  0.020  1.478
 LZK  C1   C4    aromatic  1.399  0.020  1.399
 LZK  C1   C3    aromatic  1.399  0.020  1.399
 LZK  C4   O1    single    1.343  0.020  1.343
 LZK  C4   C9    aromatic  1.395  0.020  1.395
 LZK  O1   C45   single    1.415  0.020  1.415
 LZK  C3   O7    single    1.343  0.020  1.343
 LZK  C3   C7    aromatic  1.395  0.020  1.395
 LZK  O7   C43   single    1.415  0.020  1.415
 LZK  C7   C14   aromatic  1.386  0.020  1.386
 LZK  C14  C9    aromatic  1.386  0.020  1.386
 LZK  N20  H201  single    0.890  0.020  1.040
 LZK  N20  H202  single    0.890  0.020  1.040
 LZK  C16  H16   single    0.930  0.020  1.080
 LZK  C5   H5    single    0.930  0.020  1.080
 LZK  N13  H131  single    0.860  0.020  1.020
 LZK  N13  H132  single    0.860  0.020  1.020
 LZK  C9   H9    single    0.930  0.020  1.080
 LZK  C45  H451  single    0.970  0.020  1.090
 LZK  C45  H452  single    0.970  0.020  1.090
 LZK  C45  H453  single    0.970  0.020  1.090
 LZK  C7   H7    single    0.930  0.020  1.080
 LZK  C43  H431  single    0.970  0.020  1.090
 LZK  C43  H432  single    0.970  0.020  1.090
 LZK  C43  H433  single    0.970  0.020  1.090
 LZK  C14  H14   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
 LZK  H202  N20  H201  117.79  3.000
 LZK  H202  N20  C19   119.45  3.000
 LZK  H201  N20  C19   119.55  3.000
 LZK  N18   C19  N17   126.51  3.000
 LZK  N18   C19  N20   115.46  3.000
 LZK  N17   C19  N20   118.02  3.000
 LZK  C15   N17  C19   117.36  3.000
 LZK  C16   N18  C19   115.99  3.000
 LZK  H16   C16  C11   119.72  3.000
 LZK  H16   C16  N18   117.07  3.000
 LZK  C11   C16  N18   123.21  3.000
 LZK  C5    C11  C15   118.47  3.000
 LZK  C5    C11  C16   125.18  3.000
 LZK  C15   C11  C16   116.34  3.000
 LZK  N12   C15  C11   121.89  3.000
 LZK  N12   C15  N17   117.52  3.000
 LZK  C11   C15  N17   120.59  3.000
 LZK  C6    N12  C15   118.75  3.000
 LZK  C2    C6   N13   118.99  3.000
 LZK  C2    C6   N12   123.67  3.000
 LZK  N13   C6   N12   117.34  3.000
 LZK  H132  N13  H131  118.11  3.000
 LZK  H132  N13  C6    121.70  3.000
 LZK  H131  N13  C6    119.78  3.000
 LZK  H5    C5   C2    120.34  3.000
 LZK  H5    C5   C11   119.66  3.000
 LZK  C2    C5   C11   120.00  3.000
 LZK  C1    C2   C5    122.43  3.000
 LZK  C1    C2   C6    120.34  3.000
 LZK  C5    C2   C6    117.22  3.000
 LZK  C3    C1   C4    119.42  3.000
 LZK  C3    C1   C2    120.28  3.000
 LZK  C4    C1   C2    120.29  3.000
 LZK  C9    C4   O1    124.11  3.000
 LZK  C9    C4   C1    120.45  3.000
 LZK  O1    C4   C1    115.44  3.000
 LZK  C45   O1   C4    118.74  3.000
 LZK  H453  C45  H452  108.81  3.000
 LZK  H453  C45  H451  108.76  3.000
 LZK  H452  C45  H451  108.92  3.000
 LZK  H453  C45  O1    106.39  3.000
 LZK  H452  C45  O1    111.88  3.000
 LZK  H451  C45  O1    111.98  3.000
 LZK  C7    C3   O7    124.06  3.000
 LZK  C7    C3   C1    120.50  3.000
 LZK  O7    C3   C1    115.44  3.000
 LZK  C43   O7   C3    118.62  3.000
 LZK  H433  C43  H432  108.90  3.000
 LZK  H433  C43  H431  108.73  3.000
 LZK  H432  C43  H431  108.89  3.000
 LZK  H433  C43  O7    106.39  3.000
 LZK  H432  C43  O7    111.83  3.000
 LZK  H431  C43  O7    111.99  3.000
 LZK  H7    C7   C14   119.52  3.000
 LZK  H7    C7   C3    121.71  3.000
 LZK  C14   C7   C3    118.77  3.000
 LZK  H14   C14  C9    118.97  3.000
 LZK  H14   C14  C7    119.00  3.000
 LZK  C9    C14  C7    122.03  3.000
 LZK  H9    C9   C14   119.40  3.000
 LZK  H9    C9   C4    121.77  3.000
 LZK  C14   C9   C4    118.82  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
 LZK  CONST_01  C11   C15  N17  C19    0.00   0.0  0
 LZK  CONST_02  N12   C15  N17  C19  180.00   0.0  0
 LZK  CONST_03  C11   C16  N18  C19    0.00   0.0  0
 LZK  CONST_04  C16   N18  C19  N17    0.00   0.0  0
 LZK  CONST_05  C16   C11  C15  N17    0.00   0.0  0
 LZK  CONST_06  C5    C11  C15  N17  180.00   0.0  0
 LZK  CONST_07  C6    N12  C15  N17  180.00   0.0  0
 LZK  CONST_08  C15   N17  C19  N18    0.00   0.0  0
 LZK  CONST_09  C15   C11  C16  N18    0.00   0.0  0
 LZK  CONST_10  C5    C11  C16  N18  180.00   0.0  0
 LZK  CONST_11  N12   C15  C11  C16  180.00   0.0  0
 LZK  CONST_12  C2    C5   C11  C16  180.00   0.0  0
 LZK  CONST_13  C6    N12  C15  C11    0.00   0.0  0
 LZK  CONST_14  C6    C2   C5   C11    0.00   0.0  0
 LZK  CONST_15  C1    C2   C5   C11  180.00   0.0  0
 LZK  CONST_16  C2    C5   C11  C15    0.00   0.0  0
 LZK  CONST_17  C2    C6   N12  C15    0.00   0.0  0
 LZK  CONST_18  C5    C11  C15  N12    0.00   0.0  0
 LZK  CONST_19  C5    C2   C6   N12    0.00   0.0  0
 LZK  CONST_20  C1    C2   C6   N12  180.00   0.0  0
 LZK  CONST_25  C9    C4   C1   C2   180.00   0.0  0
 LZK  CONST_26  C7    C3   C1   C2   180.00   0.0  0
 LZK  CONST_27  C14   C9   C4   C1     0.00   0.0  0
 LZK  CONST_28  C14   C7   C3   C1     0.00   0.0  0
 LZK  CONST_29  C7    C3   C1   C4     0.00   0.0  0
 LZK  CONST_30  C7    C14  C9   C4     0.00   0.0  0
 LZK  CONST_31  C9    C4   C1   C3     0.00   0.0  0
 LZK  CONST_32  C9    C14  C7   C3     0.00   0.0  0
 LZK  CONST_33  C15   N17  C19  N20  180.00   0.0  0
 LZK  CONST_34  C16   N18  C19  N20  180.00   0.0  0
 LZK  CONST_35  N13   C6   N12  C15  180.00   0.0  0
 LZK  CONST_36  C5    C2   C6   N13  180.00   0.0  0
 LZK  CONST_37  C1    C2   C6   N13    0.00   0.0  0
 LZK  CONST_38  O1    C4   C1   C2     0.00   0.0  0
 LZK  CONST_39  O7    C3   C1   C2     0.00   0.0  0
 LZK  CONST_40  O7    C3   C1   C4   180.00   0.0  0
 LZK  CONST_41  C3    C1   C4   O1   180.00   0.0  0
 LZK  CONST_42  C14   C9   C4   O1   180.00   0.0  0
 LZK  CONST_43  C14   C7   C3   O7   180.00   0.0  0
 LZK  CONST_44  H16   C16  N18  C19  180.00   0.0  0
 LZK  CONST_45  H5    C5   C11  C16    0.00   0.0  0
 LZK  CONST_46  H9    C9   C4   C1   180.00   0.0  0
 LZK  CONST_47  H7    C7   C3   C1   180.00   0.0  0
 LZK  CONST_48  H14   C14  C9   C4   180.00   0.0  0
 LZK  CONST_49  H201  N20  C19  N17    0.00   0.0  0
 LZK  CONST_50  H202  N20  C19  N17  180.00   0.0  0
 LZK  CONST_51  H131  N13  C6   N12    0.00   0.0  0
 LZK  CONST_52  H132  N13  C6   N12  180.00   0.0  0
 LZK  Var_01    C9    C4   O1   C45    0.56  30.0  1
 LZK  Var_02    C7    C3   O7   C43    2.09  30.0  1
 LZK  Var_03    H451  C45  O1   C4   -61.72  30.0  3
 LZK  Var_04    H431  C43  O7   C3   -62.19  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
 LZK  plan-1  C2    0.020
 LZK  plan-1  C1    0.020
 LZK  plan-1  C4    0.020
 LZK  plan-1  O1    0.020
 LZK  plan-1  C3    0.020
 LZK  plan-1  O7    0.020
 LZK  plan-1  C7    0.020
 LZK  plan-1  C14   0.020
 LZK  plan-1  C9    0.020
 LZK  plan-1  H9    0.020
 LZK  plan-1  H7    0.020
 LZK  plan-1  H14   0.020
 LZK  plan-2  N20   0.020
 LZK  plan-2  C19   0.020
 LZK  plan-2  N17   0.020
 LZK  plan-2  N18   0.020
 LZK  plan-2  C16   0.020
 LZK  plan-2  C11   0.020
 LZK  plan-2  C15   0.020
 LZK  plan-2  N12   0.020
 LZK  plan-2  C6    0.020
 LZK  plan-2  N13   0.020
 LZK  plan-2  C5    0.020
 LZK  plan-2  C2    0.020
 LZK  plan-2  C1    0.020
 LZK  plan-2  H16   0.020
 LZK  plan-2  H5    0.020
 LZK  plan-3  N20   0.020
 LZK  plan-3  C19   0.020
 LZK  plan-3  H201  0.020
 LZK  plan-3  H202  0.020
 LZK  plan-4  C6    0.020
 LZK  plan-4  N13   0.020
 LZK  plan-4  H131  0.020
 LZK  plan-4  H132  0.020

