# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr 22 07:38:27 2020
#   Inital geometry file: a 137 line input string
#   Ligand name: 4-(4-amino-6-{[(1R)-1-naphthalen-2-ylethyl]amino}-1,3,5-triazin-2-yl)-L-phenylalanine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[C@@H](Nc1nc(N)nc(n1)c2ccc(C[C@H](N)C(O)=O)cc2)c3ccc4ccccc4c3
#
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
 LX0  LX0  4-(4-amino-6-{[(1R)-1-naphthalen-2-ylethyl]amino}-1,3,5-triazin-2-yl)-L-phenylalanine  ligand  55  32  .  2022-07-25  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_LX0
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
 LX0  O3    O  OC    -1  -0.622  -7.9719  -3.2970   0.1994
 LX0  C1    C  C      0   0.384  -8.2281  -2.0905   0.0038
 LX0  O2    O  O      0  -0.603  -9.3562  -1.5616   0.0001
 LX0  C4    C  CH1    0  -0.207  -7.0025  -1.1714  -0.2443
 LX0  N5    N  NH2    0  -0.776  -7.3058   0.1857  -0.6578
 LX0  C6    C  CH2    0  -0.525  -6.1277  -1.1547   1.0212
 LX0  C7    C  CR6    0   0.165  -4.8166  -0.4605   0.8134
 LX0  C12   C  CR16   0  -0.290  -4.6722   0.9073   1.0366
 LX0  C11   C  CR16   0  -0.269  -3.4631   1.5451   0.8149
 LX0  C10   C  CR6    0  -0.026  -2.3551   0.8298   0.3601
 LX0  C9    C  CR16   0  -0.265  -2.4926  -0.5398   0.1367
 LX0  C8    C  CR16   0  -0.301  -3.7057  -1.1697   0.3589
 LX0  C13   C  CR6    0   0.397  -1.0609   1.5056   0.1289
 LX0  N18   N  N      0  -0.508  -0.0354   0.7489  -0.2251
 LX0  C17   C  CR6    0   0.622   1.1185   1.4091  -0.4168
 LX0  N16   N  N      0  -0.516   1.2757   2.7229  -0.2904
 LX0  C15   C  CR6    0   0.566   0.1745   3.3818   0.0706
 LX0  N19   N  NH2    0  -0.818   0.2677   4.7046   0.2266
 LX0  N14   N  N      0  -0.504  -1.0212   2.8206   0.2953
 LX0  N20   N  NH1    0  -0.659   2.1794   0.6628  -0.7466
 LX0  C21   C  CH1    0  -0.162   3.5052   1.1882  -1.0259
 LX0  C22   C  CH3    0  -0.651   3.6213   1.7109  -2.4561
 LX0  C23   C  CR6    0   0.151   4.5280   0.1178  -0.7281
 LX0  C28   C  CR16   0  -0.304   4.5364  -1.0875  -1.4731
 LX0  C27   C  CR16   0  -0.297   5.4475  -2.0705  -1.2088
 LX0  C26   C  CR66   0   0.099   6.4159  -1.9063  -0.1901
 LX0  C32   C  CR16   0  -0.308   7.3724  -2.9044   0.1082
 LX0  C31   C  CR16   0  -0.259   8.2961  -2.7095   1.0991
 LX0  C30   C  CR16   0  -0.258   8.3061  -1.5066   1.8363
 LX0  C29   C  CR16   0  -0.313   7.3911  -0.5244   1.5697
 LX0  C25   C  CR66   0   0.143   6.4234  -0.6983   0.5526
 LX0  C24   C  CR16   0  -0.403   5.4583   0.2948   0.2606
 LX0  H4    H  HCH1   0   0.223  -6.4072  -1.6345  -1.0403
 LX0  HN5   H  HNH2   0   0.336  -7.7886   0.1529  -1.5478
 LX0  HN5A  H  HNH2   0   0.323  -7.9914   0.5669  -0.0151
 LX0  H6    H  HCH2   0   0.235  -6.6837  -0.6693   1.8302
 LX0  H6A   H  HCH2   0   0.245  -5.9530  -2.1858   1.3304
 LX0  H12   H  HCR6   0   0.240  -5.5181   1.4797   1.3958
 LX0  H11   H  HCR6   0   0.247  -3.3738   2.6077   0.9962
 LX0  H9    H  HCR6   0   0.248  -1.6428  -1.1122  -0.2100
 LX0  H8    H  HCR6   0   0.244  -3.7905  -2.2357   0.1805
 LX0  HN19  H  HNH2   0   0.401   1.1247   5.1837   0.0143
 LX0  HN1A  H  HNH2   0   0.402  -0.5485   5.2473   0.4464
 LX0  HN20  H  HNH1   0   0.399   2.0063  -0.3215  -0.8777
 LX0  H21   H  HCH1   0   0.265   3.6762   2.0199  -0.3409
 LX0  H22   H  HCH3   0   0.228   3.4487   0.9189  -3.1858
 LX0  H22A  H  HCH3   0   0.242   2.8898   2.4995  -2.6301
 LX0  H22B  H  HCH3   0   0.235   4.6151   2.1238  -2.6305
 LX0  H28   H  HCR6   0   0.261   3.8131  -1.2351  -2.2668
 LX0  H27   H  HCR6   0   0.256   5.4393  -2.9885  -1.7840
 LX0  H32   H  HCR6   0   0.256   7.3636  -3.8275  -0.4591
 LX0  H31   H  HCR6   0   0.259   9.0234  -3.4792   1.3220
 LX0  H30   H  HCR6   0   0.259   9.0425  -1.3653   2.6165
 LX0  H29   H  HCR6   0   0.255   7.3972   0.3985   2.1373
 LX0  H24   H  HCR6   0   0.252   5.4632   1.2113   0.8410

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
 LX0  C1   O3    deloc     1.249  0.020  1.249
 LX0  O2   C1    deloc     1.246  0.020  1.246
 LX0  C1   C4    single    1.552  0.020  1.552
 LX0  C6   C4    single    1.539  0.020  1.539
 LX0  C4   N5    single    1.451  0.020  1.451
 LX0  C4   H4    single    0.970  0.020  1.090
 LX0  N5   HN5   single    0.890  0.020  1.040
 LX0  N5   HN5A  single    0.890  0.020  1.040
 LX0  C6   C7    single    1.498  0.020  1.498
 LX0  C6   H6    single    0.970  0.020  1.090
 LX0  C6   H6A   single    0.970  0.020  1.090
 LX0  C8   C7    aromatic  1.394  0.020  1.394
 LX0  C7   C12   aromatic  1.393  0.020  1.393
 LX0  C12  C11   aromatic  1.385  0.020  1.385
 LX0  C12  H12   single    0.930  0.020  1.080
 LX0  C10  C11   aromatic  1.395  0.020  1.395
 LX0  C11  H11   single    0.930  0.020  1.080
 LX0  C9   C10   aromatic  1.395  0.020  1.395
 LX0  C10  C13   single    1.478  0.020  1.478
 LX0  C8   C9    aromatic  1.385  0.020  1.385
 LX0  C9   H9    single    0.930  0.020  1.080
 LX0  C8   H8    single    0.930  0.020  1.080
 LX0  N14  C13   aromatic  1.326  0.020  1.326
 LX0  C13  N18   aromatic  1.323  0.020  1.323
 LX0  N18  C17   aromatic  1.343  0.020  1.343
 LX0  N16  C17   aromatic  1.329  0.020  1.329
 LX0  C17  N20   single    1.338  0.020  1.338
 LX0  C15  N16   aromatic  1.333  0.020  1.333
 LX0  N19  C15   single    1.335  0.020  1.335
 LX0  N14  C15   aromatic  1.340  0.020  1.340
 LX0  N19  HN19  single    0.860  0.020  1.020
 LX0  N19  HN1A  single    0.860  0.020  1.020
 LX0  N20  C21   single    1.453  0.020  1.453
 LX0  N20  HN20  single    0.860  0.020  1.020
 LX0  C23  C21   single    1.510  0.020  1.510
 LX0  C21  C22   single    1.527  0.020  1.527
 LX0  C21  H21   single    0.970  0.020  1.090
 LX0  C22  H22   single    0.970  0.020  1.090
 LX0  C22  H22A  single    0.970  0.020  1.090
 LX0  C22  H22B  single    0.970  0.020  1.090
 LX0  C28  C23   aromatic  1.417  0.020  1.417
 LX0  C23  C24   aromatic  1.369  0.020  1.369
 LX0  C27  C28   aromatic  1.366  0.020  1.366
 LX0  C28  H28   single    0.930  0.020  1.080
 LX0  C27  C26   aromatic  1.415  0.020  1.415
 LX0  C27  H27   single    0.930  0.020  1.080
 LX0  C32  C26   aromatic  1.414  0.020  1.414
 LX0  C26  C25   aromatic  1.418  0.020  1.418
 LX0  C32  C31   aromatic  1.369  0.020  1.369
 LX0  C32  H32   single    0.930  0.020  1.080
 LX0  C31  C30   aromatic  1.411  0.020  1.411
 LX0  C31  H31   single    0.930  0.020  1.080
 LX0  C30  C29   aromatic  1.369  0.020  1.369
 LX0  C30  H30   single    0.930  0.020  1.080
 LX0  C25  C29   aromatic  1.415  0.020  1.415
 LX0  C29  H29   single    0.930  0.020  1.080
 LX0  C25  C24   aromatic  1.415  0.020  1.415
 LX0  C24  H24   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
 LX0  C4    C1   O2    117.59  3.000
 LX0  C4    C1   O3    115.80  3.000
 LX0  O2    C1   O3    126.61  3.000
 LX0  H4    C4   C6    107.04  3.000
 LX0  H4    C4   N5    107.56  3.000
 LX0  C6    C4   N5    110.07  3.000
 LX0  H4    C4   C1    107.13  3.000
 LX0  N5    C4   C1    115.76  3.000
 LX0  C6    C4   C1    108.90  3.000
 LX0  HN5A  N5   HN5   104.29  3.000
 LX0  HN5A  N5   C4    108.19  3.000
 LX0  HN5   N5   C4    108.65  3.000
 LX0  H6A   C6   H6    106.92  3.000
 LX0  H6A   C6   C7    109.71  3.000
 LX0  H6    C6   C7    109.96  3.000
 LX0  H6A   C6   C4    108.30  3.000
 LX0  H6    C6   C4    108.90  3.000
 LX0  C7    C6   C4    112.87  3.000
 LX0  C8    C7   C12   117.97  3.000
 LX0  C12   C7   C6    121.56  3.000
 LX0  C8    C7   C6    120.45  3.000
 LX0  H12   C12  C11   119.46  3.000
 LX0  H12   C12  C7    119.41  3.000
 LX0  C11   C12  C7    121.13  3.000
 LX0  H11   C11  C10   119.52  3.000
 LX0  H11   C11  C12   119.85  3.000
 LX0  C10   C11  C12   120.63  3.000
 LX0  C13   C10  C9    120.68  3.000
 LX0  C13   C10  C11   120.80  3.000
 LX0  C9    C10  C11   118.52  3.000
 LX0  H9    C9   C8    119.93  3.000
 LX0  H9    C9   C10   119.58  3.000
 LX0  C8    C9   C10   120.49  3.000
 LX0  H8    C8   C9    119.30  3.000
 LX0  H8    C8   C7    119.44  3.000
 LX0  C9    C8   C7    121.26  3.000
 LX0  N14   C13  N18   125.28  3.000
 LX0  N18   C13  C10   117.33  3.000
 LX0  N14   C13  C10   117.39  3.000
 LX0  C17   N18  C13   115.03  3.000
 LX0  N20   C17  N16   118.74  3.000
 LX0  N20   C17  N18   116.24  3.000
 LX0  N16   C17  N18   125.02  3.000
 LX0  C15   N16  C17   114.62  3.000
 LX0  N14   C15  N19   117.23  3.000
 LX0  N14   C15  N16   125.14  3.000
 LX0  N19   C15  N16   117.63  3.000
 LX0  HN1A  N19  HN19  118.80  3.000
 LX0  HN1A  N19  C15   120.28  3.000
 LX0  HN19  N19  C15   120.48  3.000
 LX0  C15   N14  C13   114.90  3.000
 LX0  HN20  N20  C21   119.00  3.000
 LX0  HN20  N20  C17   116.13  3.000
 LX0  C21   N20  C17   124.68  3.000
 LX0  H21   C21  C23   108.08  3.000
 LX0  H21   C21  C22   108.37  3.000
 LX0  C23   C21  C22   112.07  3.000
 LX0  H21   C21  N20   107.33  3.000
 LX0  C22   C21  N20   111.91  3.000
 LX0  C23   C21  N20   108.89  3.000
 LX0  H22B  C22  H22A  108.20  3.000
 LX0  H22B  C22  H22   108.19  3.000
 LX0  H22A  C22  H22   108.21  3.000
 LX0  H22B  C22  C21   110.41  3.000
 LX0  H22A  C22  C21   110.26  3.000
 LX0  H22   C22  C21   111.47  3.000
 LX0  C24   C23  C28   119.06  3.000
 LX0  C24   C23  C21   120.73  3.000
 LX0  C28   C23  C21   120.21  3.000
 LX0  H28   C28  C27   119.26  3.000
 LX0  H28   C28  C23   119.79  3.000
 LX0  C27   C28  C23   120.95  3.000
 LX0  H27   C27  C26   119.06  3.000
 LX0  H27   C27  C28   120.13  3.000
 LX0  C26   C27  C28   120.81  3.000
 LX0  C25   C26  C32   119.15  3.000
 LX0  C25   C26  C27   118.65  3.000
 LX0  C32   C26  C27   122.19  3.000
 LX0  H32   C32  C31   120.39  3.000
 LX0  H32   C32  C26   119.03  3.000
 LX0  C31   C32  C26   120.58  3.000
 LX0  H31   C31  C30   119.60  3.000
 LX0  H31   C31  C32   120.10  3.000
 LX0  C30   C31  C32   120.30  3.000
 LX0  H30   C30  C29   120.11  3.000
 LX0  H30   C30  C31   119.53  3.000
 LX0  C29   C30  C31   120.36  3.000
 LX0  H29   C29  C25   119.03  3.000
 LX0  H29   C29  C30   120.37  3.000
 LX0  C25   C29  C30   120.61  3.000
 LX0  C24   C25  C29   121.91  3.000
 LX0  C24   C25  C26   119.08  3.000
 LX0  C29   C25  C26   119.01  3.000
 LX0  H24   C24  C25   118.64  3.000
 LX0  H24   C24  C23   119.91  3.000
 LX0  C25   C24  C23   121.44  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
 LX0  CONST_01  C10   C9   C8   C7     0.00   0.0  0
 LX0  CONST_02  C10   C11  C12  C7     0.00   0.0  0
 LX0  CONST_03  C9    C8   C7   C12    0.00   0.0  0
 LX0  CONST_04  C9    C10  C11  C12    0.00   0.0  0
 LX0  CONST_05  C13   C10  C11  C12  180.00   0.0  0
 LX0  CONST_06  C8    C7   C12  C11    0.00   0.0  0
 LX0  CONST_07  C8    C9   C10  C11    0.00   0.0  0
 LX0  CONST_08  N14   C13  C10  C11    0.00   0.0  0
 LX0  CONST_09  N18   C13  C10  C11  180.00   0.0  0
 LX0  CONST_10  C15   N14  C13  C10  180.00   0.0  0
 LX0  CONST_11  C17   N18  C13  C10  180.00   0.0  0
 LX0  CONST_12  N14   C13  C10  C9   180.00   0.0  0
 LX0  CONST_13  N18   C13  C10  C9     0.00   0.0  0
 LX0  CONST_14  C13   C10  C9   C8   180.00   0.0  0
 LX0  CONST_15  N16   C15  N14  C13    0.00   0.0  0
 LX0  CONST_16  N16   C17  N18  C13    0.00   0.0  0
 LX0  CONST_17  C15   N14  C13  N18    0.00   0.0  0
 LX0  CONST_18  C15   N16  C17  N18    0.00   0.0  0
 LX0  CONST_19  N14   C13  N18  C17    0.00   0.0  0
 LX0  CONST_20  N14   C15  N16  C17    0.00   0.0  0
 LX0  CONST_21  C26   C27  C28  C23    0.00   0.0  0
 LX0  CONST_22  C26   C25  C24  C23    0.00   0.0  0
 LX0  CONST_23  C29   C25  C24  C23  180.00   0.0  0
 LX0  CONST_24  C25   C24  C23  C28    0.00   0.0  0
 LX0  CONST_25  C32   C26  C27  C28  180.00   0.0  0
 LX0  CONST_26  C25   C26  C27  C28    0.00   0.0  0
 LX0  CONST_27  C24   C23  C28  C27    0.00   0.0  0
 LX0  CONST_28  C31   C32  C26  C27  180.00   0.0  0
 LX0  CONST_29  C29   C25  C26  C27  180.00   0.0  0
 LX0  CONST_30  C24   C25  C26  C27    0.00   0.0  0
 LX0  CONST_31  C30   C31  C32  C26    0.00   0.0  0
 LX0  CONST_32  C30   C29  C25  C26    0.00   0.0  0
 LX0  CONST_33  C29   C25  C26  C32    0.00   0.0  0
 LX0  CONST_34  C24   C25  C26  C32  180.00   0.0  0
 LX0  CONST_35  C29   C30  C31  C32    0.00   0.0  0
 LX0  CONST_36  C25   C26  C32  C31    0.00   0.0  0
 LX0  CONST_37  C25   C29  C30  C31    0.00   0.0  0
 LX0  CONST_38  C24   C25  C29  C30  180.00   0.0  0
 LX0  CONST_39  C9    C8   C7   C6   180.00   0.0  0
 LX0  CONST_40  C11   C12  C7   C6   180.00   0.0  0
 LX0  CONST_41  N19   C15  N14  C13  180.00   0.0  0
 LX0  CONST_42  N20   C17  N18  C13  180.00   0.0  0
 LX0  CONST_43  N19   C15  N16  C17  180.00   0.0  0
 LX0  CONST_44  N20   C17  N16  C15  180.00   0.0  0
 LX0  CONST_45  C27   C28  C23  C21  180.00   0.0  0
 LX0  CONST_46  C25   C24  C23  C21  180.00   0.0  0
 LX0  CONST_47  H9    C9   C8   C7   180.00   0.0  0
 LX0  CONST_48  H11   C11  C12  C7   180.00   0.0  0
 LX0  CONST_49  H8    C8   C7   C12  180.00   0.0  0
 LX0  CONST_50  H12   C12  C11  C10  180.00   0.0  0
 LX0  CONST_51  H27   C27  C28  C23  180.00   0.0  0
 LX0  CONST_52  H24   C24  C23  C28  180.00   0.0  0
 LX0  CONST_53  H32   C32  C26  C27    0.00   0.0  0
 LX0  CONST_54  H28   C28  C27  C26  180.00   0.0  0
 LX0  CONST_55  H31   C31  C32  C26  180.00   0.0  0
 LX0  CONST_56  H29   C29  C25  C26  180.00   0.0  0
 LX0  CONST_57  H30   C30  C31  C32  180.00   0.0  0
 LX0  CONST_58  C21   N20  C17  N18  180.00   0.0  0
 LX0  CONST_59  C21   N20  C17  N16    0.00   0.0  0
 LX0  CONST_60  HN20  N20  C17  N18    0.00   0.0  0
 LX0  CONST_61  HN19  N19  C15  N16    0.00   0.0  0
 LX0  CONST_62  HN1A  N19  C15  N16  180.00   0.0  0
 LX0  Var_01    C8    C7   C6   C4   -88.73  30.0  2

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
 LX0  chir_01  C4   C1   C6   N5   positiv
 LX0  chir_02  C21  N20  C23  C22  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
 LX0  plan-1  C6    0.020
 LX0  plan-1  C7    0.020
 LX0  plan-1  C12   0.020
 LX0  plan-1  C11   0.020
 LX0  plan-1  C10   0.020
 LX0  plan-1  C9    0.020
 LX0  plan-1  C8    0.020
 LX0  plan-1  C13   0.020
 LX0  plan-1  H12   0.020
 LX0  plan-1  H11   0.020
 LX0  plan-1  H9    0.020
 LX0  plan-1  H8    0.020
 LX0  plan-2  O3    0.020
 LX0  plan-2  C1    0.020
 LX0  plan-2  O2    0.020
 LX0  plan-2  C4    0.020
 LX0  plan-3  C10   0.020
 LX0  plan-3  C13   0.020
 LX0  plan-3  N18   0.020
 LX0  plan-3  C17   0.020
 LX0  plan-3  N16   0.020
 LX0  plan-3  C15   0.020
 LX0  plan-3  N19   0.020
 LX0  plan-3  N14   0.020
 LX0  plan-3  N20   0.020
 LX0  plan-4  C21   0.020
 LX0  plan-4  C23   0.020
 LX0  plan-4  C28   0.020
 LX0  plan-4  C27   0.020
 LX0  plan-4  C26   0.020
 LX0  plan-4  C32   0.020
 LX0  plan-4  C31   0.020
 LX0  plan-4  C30   0.020
 LX0  plan-4  C29   0.020
 LX0  plan-4  C25   0.020
 LX0  plan-4  C24   0.020
 LX0  plan-4  H28   0.020
 LX0  plan-4  H27   0.020
 LX0  plan-4  H32   0.020
 LX0  plan-4  H31   0.020
 LX0  plan-4  H30   0.020
 LX0  plan-4  H29   0.020
 LX0  plan-4  H24   0.020
 LX0  plan-5  C15   0.020
 LX0  plan-5  N19   0.020
 LX0  plan-5  HN19  0.020
 LX0  plan-5  HN1A  0.020
 LX0  plan-6  C17   0.020
 LX0  plan-6  N20   0.020
 LX0  plan-6  C21   0.020
 LX0  plan-6  HN20  0.020

