# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed May  6 05:20:53 2020
#   Inital geometry file: a 99 line input string
#   Ligand name: 7-[[5-[(methylideneamino)methyl]pyridin-3-yl]oxymethyl]quinolin-2-amine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Nc1ccc2ccc(COc3cncc(CN=C)c3)cc2n1
#
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
 TUE  TUE  7-[[5-[(methylideneamino)methyl]pyridin-3-yl]oxymethyl]quinolin-2-amine  ligand  38  22  .  2021-08-23  2021-08-23  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_TUE
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
 TUE  N01   N  N     0  -0.507  -4.2916  -1.0289  -0.9657
 TUE  C02   C  CR6   0   0.441  -5.4681  -1.2562  -0.4282
 TUE  N02   N  NH2   0  -0.835  -6.3077  -2.1132  -1.0572
 TUE  C03   C  CR16  0  -0.375  -5.8784  -0.6657   0.8094
 TUE  C04   C  CR16  0  -0.179  -5.0174   0.1573   1.4578
 TUE  C05   C  CR66  0   0.048  -3.7360   0.4165   0.9071
 TUE  C06   C  CR16  0  -0.306  -2.7873   1.2578   1.5207
 TUE  C07   C  CR16  0  -0.296  -1.5667   1.4744   0.9389
 TUE  C08   C  CR6   0   0.094  -1.2467   0.8518  -0.2871
 TUE  C09   C  CR16  0  -0.367  -2.1591   0.0272  -0.8966
 TUE  C10   C  CR66  0   0.236  -3.4276  -0.2112  -0.3214
 TUE  C11   C  CH2   0  -0.269   0.0926   1.0970  -0.9117
 TUE  O12   O  O2    0  -0.465   1.0739   0.5241  -0.0557
 TUE  N21   N  N     0  -0.384   4.1340   1.4262  -1.7941
 TUE  C22   C  CR16  0  -0.191   2.8398   1.3126  -1.5238
 TUE  C23   C  CR6   0   0.335   2.3707   0.6699  -0.3775
 TUE  C24   C  CR16  0  -0.277   3.3043   0.1354   0.5049
 TUE  C25   C  CR6   0   0.039   4.6542   0.2589   0.2233
 TUE  C26   C  CR16  0  -0.126   5.0155   0.9140  -0.9504
 TUE  C27   C  CH2   0  -0.387   5.7006  -0.3018   1.1468
 TUE  N28   N  N     0  -0.294   5.5085  -1.7270   1.3115
 TUE  C29   C  C2    0  -0.288   6.4593  -2.4864   0.9881
 TUE  HN02  H  HNH2  0   0.388  -6.0983  -2.3608  -2.0098
 TUE  HN0A  H  HNH2  0   0.398  -7.2826  -2.1122  -0.8125
 TUE  H03   H  HCR6  0   0.275  -6.8606  -0.8794   1.2106
 TUE  H04   H  HCR6  0   0.270  -5.2996   0.6187   2.3962
 TUE  H06   H  HCR6  0   0.258  -3.0373   1.7349   2.4611
 TUE  H07   H  HCR6  0   0.253  -0.8490   2.1302   1.4154
 TUE  H09   H  HCR6  0   0.252  -1.9222  -0.4558  -1.8374
 TUE  H11   H  HCH2  0   0.251   0.1406   0.6487  -1.9093
 TUE  H11A  H  HCH2  0   0.247   0.2714   2.1729  -1.0190
 TUE  H24   H  HCR6  0   0.274   2.9674  -0.3683   1.4035
 TUE  H26   H  HCR6  0   0.256   6.0631   1.0243  -1.2112
 TUE  H27   H  HCH2  0   0.232   6.7001  -0.0461   0.7719
 TUE  H27A  H  HCH2  0   0.265   5.5958   0.1648   2.1305
 TUE  H29   H  H     0   0.215   7.4155  -2.1327   0.5931
 TUE  H29A  H  H     0   0.240   6.3432  -3.5610   1.0992
 TUE  H22   H  HCR6  0   0.279   2.1617   1.7478  -2.2486

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
 TUE  N01  C02   aromatic  1.313  0.020  1.313
 TUE  N01  C10   aromatic  1.353  0.020  1.353
 TUE  C02  N02   single    1.355  0.020  1.355
 TUE  C02  C03   aromatic  1.431  0.020  1.431
 TUE  C03  C04   aromatic  1.356  0.020  1.356
 TUE  C04  C05   aromatic  1.419  0.020  1.419
 TUE  C05  C06   aromatic  1.409  0.020  1.409
 TUE  C05  C10   aromatic  1.414  0.020  1.414
 TUE  C06  C07   aromatic  1.369  0.020  1.369
 TUE  C07  C08   aromatic  1.412  0.020  1.412
 TUE  C08  C09   aromatic  1.373  0.020  1.373
 TUE  C08  C11   single    1.498  0.020  1.498
 TUE  C09  C10   aromatic  1.413  0.020  1.413
 TUE  C11  O12   single    1.423  0.020  1.423
 TUE  O12  C23   single    1.344  0.020  1.344
 TUE  N21  C22   aromatic  1.327  0.020  1.327
 TUE  N21  C26   aromatic  1.323  0.020  1.323
 TUE  C22  C23   aromatic  1.395  0.020  1.395
 TUE  C23  C24   aromatic  1.391  0.020  1.391
 TUE  C24  C25   aromatic  1.384  0.020  1.384
 TUE  C25  C26   aromatic  1.392  0.020  1.392
 TUE  C25  C27   single    1.504  0.020  1.504
 TUE  C27  N28   single    1.447  0.020  1.447
 TUE  N28  C29   double    1.259  0.020  1.259
 TUE  N02  HN02  single    0.890  0.020  1.040
 TUE  N02  HN0A  single    0.890  0.020  1.040
 TUE  C03  H03   single    0.930  0.020  1.080
 TUE  C04  H04   single    0.930  0.020  1.080
 TUE  C06  H06   single    0.930  0.020  1.080
 TUE  C07  H07   single    0.930  0.020  1.080
 TUE  C09  H09   single    0.930  0.020  1.080
 TUE  C11  H11   single    0.970  0.020  1.090
 TUE  C11  H11A  single    0.970  0.020  1.090
 TUE  C22  H22   single    0.930  0.020  1.080
 TUE  C24  H24   single    0.930  0.020  1.080
 TUE  C26  H26   single    0.930  0.020  1.080
 TUE  C27  H27   single    0.970  0.020  1.090
 TUE  C27  H27A  single    0.970  0.020  1.090
 TUE  C29  H29   single    0.930  0.020  1.080
 TUE  C29  H29A  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
 TUE  C10   N01  C02   118.80  3.000
 TUE  C03   C02  N02   119.00  3.000
 TUE  C03   C02  N01   122.63  3.000
 TUE  N02   C02  N01   118.34  3.000
 TUE  HN0A  N02  HN02  115.62  3.000
 TUE  HN0A  N02  C02   119.17  3.000
 TUE  HN02  N02  C02   117.80  3.000
 TUE  H03   C03  C04   121.25  3.000
 TUE  H03   C03  C02   119.95  3.000
 TUE  C04   C03  C02   118.80  3.000
 TUE  H04   C04  C05   119.59  3.000
 TUE  H04   C04  C03   120.49  3.000
 TUE  C05   C04  C03   119.92  3.000
 TUE  C10   C05  C06   119.79  3.000
 TUE  C10   C05  C04   116.95  3.000
 TUE  C06   C05  C04   123.26  3.000
 TUE  H06   C06  C07   120.31  3.000
 TUE  H06   C06  C05   119.05  3.000
 TUE  C07   C06  C05   120.64  3.000
 TUE  H07   C07  C08   119.94  3.000
 TUE  H07   C07  C06   119.98  3.000
 TUE  C08   C07  C06   120.08  3.000
 TUE  C11   C08  C09   120.50  3.000
 TUE  C11   C08  C07   119.51  3.000
 TUE  C09   C08  C07   119.99  3.000
 TUE  H09   C09  C10   118.32  3.000
 TUE  H09   C09  C08   120.53  3.000
 TUE  C10   C09  C08   121.15  3.000
 TUE  C09   C10  C05   118.34  3.000
 TUE  C09   C10  N01   118.77  3.000
 TUE  C05   C10  N01   122.88  3.000
 TUE  H11A  C11  H11   107.80  3.000
 TUE  H11A  C11  O12   109.98  3.000
 TUE  H11   C11  O12   110.68  3.000
 TUE  H11A  C11  C08   110.33  3.000
 TUE  H11   C11  C08   110.61  3.000
 TUE  O12   C11  C08   107.45  3.000
 TUE  C23   O12  C11   118.54  3.000
 TUE  C26   N21  C22   119.12  3.000
 TUE  H22   C22  C23   121.60  3.000
 TUE  H22   C22  N21   116.08  3.000
 TUE  C23   C22  N21   122.32  3.000
 TUE  C24   C23  C22   118.19  3.000
 TUE  C24   C23  O12   116.99  3.000
 TUE  C22   C23  O12   124.82  3.000
 TUE  H24   C24  C25   120.88  3.000
 TUE  H24   C24  C23   119.72  3.000
 TUE  C25   C24  C23   119.40  3.000
 TUE  C27   C25  C26   120.84  3.000
 TUE  C27   C25  C24   121.34  3.000
 TUE  C26   C25  C24   117.82  3.000
 TUE  H26   C26  C25   120.07  3.000
 TUE  H26   C26  N21   116.78  3.000
 TUE  C25   C26  N21   123.15  3.000
 TUE  H27A  C27  H27   107.16  3.000
 TUE  H27A  C27  N28   107.76  3.000
 TUE  H27   C27  N28   112.89  3.000
 TUE  H27A  C27  C25   109.06  3.000
 TUE  H27   C27  C25   109.69  3.000
 TUE  N28   C27  C25   110.15  3.000
 TUE  C29   N28  C27   117.67  3.000
 TUE  H29A  C29  H29   116.76  3.000
 TUE  H29A  C29  N28   119.31  3.000
 TUE  H29   C29  N28   123.93  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
 TUE  CONST_01  C04   C03  C02  N01    0.00   0.0  0
 TUE  CONST_02  C04   C05  C10  N01    0.00   0.0  0
 TUE  CONST_03  C06   C05  C10  N01  180.00   0.0  0
 TUE  CONST_04  C08   C09  C10  N01  180.00   0.0  0
 TUE  CONST_05  C05   C10  N01  C02    0.00   0.0  0
 TUE  CONST_06  C09   C10  N01  C02  180.00   0.0  0
 TUE  CONST_07  C05   C04  C03  C02    0.00   0.0  0
 TUE  CONST_08  C10   N01  C02  C03    0.00   0.0  0
 TUE  CONST_09  C06   C05  C04  C03  180.00   0.0  0
 TUE  CONST_10  C10   C05  C04  C03    0.00   0.0  0
 TUE  CONST_11  C07   C06  C05  C04  180.00   0.0  0
 TUE  CONST_12  C09   C10  C05  C04  180.00   0.0  0
 TUE  CONST_13  C08   C07  C06  C05    0.00   0.0  0
 TUE  CONST_14  C08   C09  C10  C05    0.00   0.0  0
 TUE  CONST_15  C09   C10  C05  C06    0.00   0.0  0
 TUE  CONST_16  C09   C08  C07  C06    0.00   0.0  0
 TUE  CONST_17  C10   C05  C06  C07    0.00   0.0  0
 TUE  CONST_18  C10   C09  C08  C07    0.00   0.0  0
 TUE  CONST_19  C24   C23  C22  N21    0.00   0.0  0
 TUE  CONST_20  C24   C25  C26  N21    0.00   0.0  0
 TUE  CONST_21  C25   C26  N21  C22    0.00   0.0  0
 TUE  CONST_22  C25   C24  C23  C22    0.00   0.0  0
 TUE  CONST_23  C26   N21  C22  C23    0.00   0.0  0
 TUE  CONST_24  C26   C25  C24  C23    0.00   0.0  0
 TUE  CONST_25  C10   N01  C02  N02  180.00   0.0  0
 TUE  CONST_26  C04   C03  C02  N02  180.00   0.0  0
 TUE  CONST_27  C11   C08  C07  C06  180.00   0.0  0
 TUE  CONST_28  C11   C08  C09  C10  180.00   0.0  0
 TUE  CONST_29  N21   C22  C23  O12  180.00   0.0  0
 TUE  CONST_30  C25   C24  C23  O12  180.00   0.0  0
 TUE  CONST_31  C27   C25  C26  N21  180.00   0.0  0
 TUE  CONST_32  C27   C25  C24  C23  180.00   0.0  0
 TUE  CONST_33  H03   C03  C02  N01  180.00   0.0  0
 TUE  CONST_34  H09   C09  C10  N01    0.00   0.0  0
 TUE  CONST_35  H04   C04  C03  C02  180.00   0.0  0
 TUE  CONST_36  H06   C06  C05  C04    0.00   0.0  0
 TUE  CONST_37  H07   C07  C06  C05  180.00   0.0  0
 TUE  CONST_38  H26   C26  N21  C22  180.00   0.0  0
 TUE  CONST_39  H24   C24  C23  C22  180.00   0.0  0
 TUE  CONST_40  H22   C22  C23  C24  180.00   0.0  0
 TUE  CONST_41  HN02  N02  C02  N01    0.00   0.0  0
 TUE  Var_01    O12   C11  C08  C07   66.10  30.0  2
 TUE  Var_02    C22   C23  O12  C11   -2.12  30.0  2
 TUE  Var_03    N28   C27  C25  C24   58.44  30.0  2
 TUE  Var_04    H29   C29  N28  C27    0.03   0.0  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
 TUE  plan-1  O12   0.020
 TUE  plan-1  N21   0.020
 TUE  plan-1  C22   0.020
 TUE  plan-1  C23   0.020
 TUE  plan-1  C24   0.020
 TUE  plan-1  C25   0.020
 TUE  plan-1  C26   0.020
 TUE  plan-1  C27   0.020
 TUE  plan-1  H24   0.020
 TUE  plan-1  H26   0.020
 TUE  plan-1  H22   0.020
 TUE  plan-2  N01   0.020
 TUE  plan-2  C02   0.020
 TUE  plan-2  N02   0.020
 TUE  plan-2  C03   0.020
 TUE  plan-2  C04   0.020
 TUE  plan-2  C05   0.020
 TUE  plan-2  C06   0.020
 TUE  plan-2  C07   0.020
 TUE  plan-2  C08   0.020
 TUE  plan-2  C09   0.020
 TUE  plan-2  C10   0.020
 TUE  plan-2  C11   0.020
 TUE  plan-2  H03   0.020
 TUE  plan-2  H04   0.020
 TUE  plan-2  H06   0.020
 TUE  plan-2  H07   0.020
 TUE  plan-2  H09   0.020
 TUE  plan-3  C02   0.020
 TUE  plan-3  N02   0.020
 TUE  plan-3  HN02  0.020
 TUE  plan-3  HN0A  0.020
 TUE  plan-4  C27   0.020
 TUE  plan-4  N28   0.020
 TUE  plan-4  C29   0.020
 TUE  plan-4  H29   0.020
 TUE  plan-4  H29A  0.020

