# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr  8 06:41:22 2020
#   Inital geometry file: a 140 line input string
#   Ligand name: 6-[(1~{R})-1-[8-fluoranyl-6-(1-methylpyrazol-4-yl)-[1,2,4]triazolo[4,3-a]pyridin-3-yl]ethyl]-3-(2-methoxyethoxy)-1,6-naphthyridin-5-one
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: COCCOc1cnc2C=CN([C@H](C)c3nnc4n3cc(cc4F)c5cnn(C)c5)C(=O)c2c1
#
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
 5T1  5T1  6-[(1~{R})-1-[8-fluoranyl-6-(1-methylpyrazol-4-yl)-[1,2,4]triazolo[4,3-a]pyridin-3-yl]ethyl]-3-(2-methoxyethoxy)-1,6-naphthyridin-5-one  ligand  56  34  .  2022-07-23  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_5T1
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
 5T1  C23  C  CH3   0  -0.397  -7.3402   4.4445  -0.6040
 5T1  O3   O  O2    0  -0.482  -6.7118   3.2157  -0.3400
 5T1  C22  C  CH2   0  -0.162  -6.1626   3.1608   0.9489
 5T1  C21  C  CH2   0  -0.227  -5.5570   1.8031   1.1837
 5T1  O2   O  O2    0  -0.465  -4.4538   1.6452   0.3025
 5T1  C19  C  CR6   0   0.348  -3.7618   0.4983   0.3245
 5T1  C20  C  CR16  0  -0.270  -2.7044   0.3696  -0.5575
 5T1  C15  C  CR66  0  -0.137  -1.9687  -0.8104  -0.5578
 5T1  C16  C  CR6   0   0.577  -0.8426  -0.9605  -1.4811
 5T1  O1   O  O     0  -0.484  -0.5021  -0.0790  -2.2607
 5T1  C18  C  CR16  0  -0.182  -4.0361  -0.5811   1.1827
 5T1  N7   N  N     0  -0.427  -3.3420  -1.6999   1.1858
 5T1  C14  C  CR66  0   0.311  -2.3192  -1.8336   0.3361
 5T1  C13  C  CR16  0  -0.418  -1.5517  -3.0404   0.3348
 5T1  C12  C  CR16  0   0.035  -0.5237  -3.1561  -0.5198
 5T1  N6   N  NR6   0  -0.541  -0.1716  -2.1599  -1.4035
 5T1  C11  C  CH1   0  -0.273   0.9605  -2.4151  -2.3126
 5T1  C17  C  CH3   0  -0.641   0.6713  -3.5697  -3.2593
 5T1  C10  C  CR5   0   0.461   2.1982  -2.6344  -1.5098
 5T1  N1   N  N     0  -0.569   2.7974  -1.6706  -0.7510
 5T1  C5   C  CR16  0  -0.035   2.5066  -0.3464  -0.5525
 5T1  N5   N  N     0  -0.302   2.8582  -3.7525  -1.3729
 5T1  N4   N  N     0  -0.337   3.8918  -3.5694  -0.5387
 5T1  C4   C  CR56  0   0.292   3.8517  -2.3119  -0.1595
 5T1  C3   C  CR6   0   0.509   4.6587  -1.5523   0.7198
 5T1  F1   F  F     0  -0.284   5.6781  -2.1787   1.2969
 5T1  C2   C  CR16  0  -0.392   4.3808  -0.2546   0.9594
 5T1  C1   C  CR6   0  -0.009   3.2735   0.3779   0.3039
 5T1  C6   C  CR5   0  -0.139   2.9744   1.7798   0.5569
 5T1  C8   C  CR15  0   0.025   3.7808   2.7249   1.1636
 5T1  C7   C  CR15  0  -0.088   1.8006   2.4963   0.2451
 5T1  N2   N  N     0  -0.269   1.8893   3.7535   0.6256
 5T1  N3   N  NR5   0  -0.269   3.0931   3.8746   1.1767
 5T1  C9   C  CH3   0  -0.507   3.5214   5.1463   1.7094
 5T1  H1   H  HCH3  0   0.206  -8.1584   4.6465   0.0976
 5T1  H2   H  HCH3  0   0.206  -6.6389   5.2857  -0.5526
 5T1  H3   H  HCH3  0   0.236  -7.7527   4.4018  -1.6112
 5T1  H4   H  HCH2  0   0.214  -5.4029   3.9420   1.0954
 5T1  H5   H  HCH2  0   0.216  -6.9314   3.3166   1.7186
 5T1  H6   H  HCH2  0   0.242  -5.2331   1.7400   2.2276
 5T1  H7   H  HCH2  0   0.240  -6.3042   1.0203   1.0122
 5T1  H8   H  HCR6  0   0.282  -2.4576   1.1757  -1.2368
 5T1  H9   H  HCR6  0   0.291  -4.8519  -0.5313   1.8942
 5T1  H10  H  HCR6  0   0.278  -1.7924  -3.8434   1.0155
 5T1  H11  H  HCR6  0   0.316   0.0901  -4.0449  -0.5477
 5T1  H12  H  HCH1  0   0.322   1.0808  -1.5121  -2.9116
 5T1  H13  H  HCH3  0   0.261   1.4776  -3.6622  -3.9848
 5T1  H14  H  HCH3  0   0.242   0.5740  -4.5226  -2.7426
 5T1  H15  H  HCH3  0   0.260  -0.2518  -3.3716  -3.8011
 5T1  H16  H  HCR6  0   0.304   1.6860   0.0658  -1.1186
 5T1  H17  H  HCR6  0   0.298   4.9966   0.3041   1.6517
 5T1  H18  H  HCR5  0   0.300   4.7776   2.6584   1.5692
 5T1  H19  H  HCR5  0   0.247   0.8993   2.1374  -0.2308
 5T1  H20  H  HCH3  0   0.265   3.5112   5.9034   0.9286
 5T1  H21  H  HCH3  0   0.264   2.8652   5.4567   2.5198
 5T1  H22  H  HCH3  0   0.261   4.5324   5.0459   2.0928

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
 5T1  C17  C11  single    1.521  0.020  1.521
 5T1  C11  C10  single    1.491  0.020  1.491
 5T1  C11  N6   single    1.474  0.020  1.474
 5T1  N5   C10  aromatic  1.306  0.020  1.306
 5T1  N5   N4   aromatic  1.341  0.020  1.341
 5T1  C10  N1   aromatic  1.365  0.020  1.365
 5T1  N6   C12  single    1.377  0.020  1.377
 5T1  N6   C16  single    1.377  0.020  1.377
 5T1  O1   C16  double    1.225  0.020  1.225
 5T1  C12  C13  double    1.342  0.020  1.342
 5T1  C16  C15  single    1.464  0.020  1.464
 5T1  N4   C4   aromatic  1.314  0.020  1.314
 5T1  N1   C4   aromatic  1.368  0.020  1.368
 5T1  N1   C5   aromatic  1.370  0.020  1.370
 5T1  C13  C14  single    1.430  0.020  1.430
 5T1  C4   C3   aromatic  1.415  0.020  1.415
 5T1  C5   C1   aromatic  1.359  0.020  1.359
 5T1  C15  C14  aromatic  1.403  0.020  1.403
 5T1  C15  C20  aromatic  1.390  0.020  1.390
 5T1  C14  N7   aromatic  1.336  0.020  1.336
 5T1  C20  C19  aromatic  1.383  0.020  1.383
 5T1  C3   F1   single    1.328  0.020  1.328
 5T1  C3   C2   aromatic  1.349  0.020  1.349
 5T1  C1   C6   single    1.456  0.020  1.456
 5T1  C1   C2   aromatic  1.434  0.020  1.434
 5T1  C7   C6   aromatic  1.410  0.020  1.410
 5T1  C7   N2   aromatic  1.317  0.020  1.317
 5T1  N7   C18  aromatic  1.317  0.020  1.317
 5T1  C6   C8   aromatic  1.383  0.020  1.383
 5T1  C19  C18  aromatic  1.406  0.020  1.406
 5T1  C19  O2   single    1.340  0.020  1.340
 5T1  N2   N3   aromatic  1.329  0.020  1.329
 5T1  O2   C21  single    1.421  0.020  1.421
 5T1  C8   N3   aromatic  1.340  0.020  1.340
 5T1  N3   C9   single    1.444  0.020  1.444
 5T1  C21  C22  single    1.505  0.020  1.505
 5T1  C22  O3   single    1.402  0.020  1.402
 5T1  O3   C23  single    1.405  0.020  1.405
 5T1  C23  H1   single    0.970  0.020  1.090
 5T1  C23  H2   single    0.970  0.020  1.090
 5T1  C23  H3   single    0.970  0.020  1.090
 5T1  C22  H4   single    0.970  0.020  1.090
 5T1  C22  H5   single    0.970  0.020  1.090
 5T1  C21  H6   single    0.970  0.020  1.090
 5T1  C21  H7   single    0.970  0.020  1.090
 5T1  C20  H8   single    0.930  0.020  1.080
 5T1  C18  H9   single    0.930  0.020  1.080
 5T1  C13  H10  single    0.930  0.020  1.080
 5T1  C12  H11  single    0.930  0.020  1.080
 5T1  C11  H12  single    0.970  0.020  1.090
 5T1  C17  H13  single    0.970  0.020  1.090
 5T1  C17  H14  single    0.970  0.020  1.090
 5T1  C17  H15  single    0.970  0.020  1.090
 5T1  C5   H16  single    0.930  0.020  1.080
 5T1  C2   H17  single    0.930  0.020  1.080
 5T1  C8   H18  single    0.930  0.020  1.080
 5T1  C7   H19  single    0.930  0.020  1.080
 5T1  C9   H20  single    0.970  0.020  1.090
 5T1  C9   H21  single    0.970  0.020  1.090
 5T1  C9   H22  single    0.970  0.020  1.090

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
 5T1  H3   C23  H2   108.40  3.000
 5T1  H3   C23  H1   108.44  3.000
 5T1  H2   C23  H1   107.82  3.000
 5T1  H3   C23  O3   107.98  3.000
 5T1  H2   C23  O3   112.09  3.000
 5T1  H1   C23  O3   111.99  3.000
 5T1  C22  O3   C23  112.46  3.000
 5T1  H5   C22  H4   106.81  3.000
 5T1  H5   C22  C21  107.46  3.000
 5T1  H4   C22  C21  110.01  3.000
 5T1  H5   C22  O3   111.37  3.000
 5T1  H4   C22  O3   111.42  3.000
 5T1  C21  C22  O3   109.66  3.000
 5T1  H7   C21  H6   108.06  3.000
 5T1  H7   C21  O2   110.67  3.000
 5T1  H6   C21  O2   110.81  3.000
 5T1  H7   C21  C22  110.22  3.000
 5T1  H6   C21  C22  108.65  3.000
 5T1  O2   C21  C22  108.42  3.000
 5T1  C19  O2   C21  119.08  3.000
 5T1  C18  C19  C20  117.84  3.000
 5T1  C18  C19  O2   124.51  3.000
 5T1  C20  C19  O2   117.66  3.000
 5T1  H8   C20  C15  120.74  3.000
 5T1  H8   C20  C19  120.34  3.000
 5T1  C15  C20  C19  118.92  3.000
 5T1  C14  C15  C16  121.28  3.000
 5T1  C14  C15  C20  119.11  3.000
 5T1  C16  C15  C20  119.61  3.000
 5T1  N6   C16  O1   121.83  3.000
 5T1  O1   C16  C15  122.78  3.000
 5T1  N6   C16  C15  115.39  3.000
 5T1  H9   C18  N7   115.74  3.000
 5T1  H9   C18  C19  120.82  3.000
 5T1  N7   C18  C19  123.44  3.000
 5T1  C14  N7   C18  119.14  3.000
 5T1  C13  C14  N7   119.71  3.000
 5T1  N7   C14  C15  121.55  3.000
 5T1  C13  C14  C15  118.73  3.000
 5T1  H10  C13  C12  120.54  3.000
 5T1  H10  C13  C14  120.49  3.000
 5T1  C12  C13  C14  118.98  3.000
 5T1  H11  C12  N6   115.67  3.000
 5T1  H11  C12  C13  121.50  3.000
 5T1  N6   C12  C13  122.83  3.000
 5T1  C11  N6   C12  117.82  3.000
 5T1  C12  N6   C16  122.80  3.000
 5T1  C11  N6   C16  119.37  3.000
 5T1  H12  C11  C10  109.02  3.000
 5T1  H12  C11  C17  107.92  3.000
 5T1  C10  C11  C17  112.41  3.000
 5T1  H12  C11  N6   106.27  3.000
 5T1  C10  C11  N6   109.32  3.000
 5T1  C17  C11  N6   111.67  3.000
 5T1  H15  C17  H14  108.66  3.000
 5T1  H15  C17  H13  108.17  3.000
 5T1  H14  C17  H13  107.96  3.000
 5T1  H15  C17  C11  109.44  3.000
 5T1  H14  C17  C11  112.71  3.000
 5T1  H13  C17  C11  109.79  3.000
 5T1  N5   C10  N1   108.93  3.000
 5T1  N1   C10  C11  124.03  3.000
 5T1  N5   C10  C11  127.00  3.000
 5T1  C4   N1   C5   123.63  3.000
 5T1  C5   N1   C10  132.04  3.000
 5T1  C4   N1   C10  104.33  3.000
 5T1  H16  C5   C1   123.81  3.000
 5T1  H16  C5   N1   117.04  3.000
 5T1  C1   C5   N1   119.12  3.000
 5T1  N4   N5   C10  109.75  3.000
 5T1  C4   N4   N5   106.66  3.000
 5T1  C3   C4   N4   132.51  3.000
 5T1  C3   C4   N1   117.16  3.000
 5T1  N4   C4   N1   110.32  3.000
 5T1  C2   C3   F1   122.32  3.000
 5T1  C2   C3   C4   120.64  3.000
 5T1  F1   C3   C4   117.04  3.000
 5T1  H17  C2   C1   120.28  3.000
 5T1  H17  C2   C3   119.56  3.000
 5T1  C1   C2   C3   120.16  3.000
 5T1  C6   C1   C2   120.27  3.000
 5T1  C2   C1   C5   119.27  3.000
 5T1  C6   C1   C5   120.46  3.000
 5T1  C7   C6   C8   103.60  3.000
 5T1  C8   C6   C1   127.94  3.000
 5T1  C7   C6   C1   128.46  3.000
 5T1  H18  C8   N3   121.59  3.000
 5T1  H18  C8   C6   131.46  3.000
 5T1  N3   C8   C6   106.95  3.000
 5T1  H19  C7   N2   120.05  3.000
 5T1  H19  C7   C6   128.53  3.000
 5T1  N2   C7   C6   111.42  3.000
 5T1  N3   N2   C7   105.53  3.000
 5T1  C9   N3   N2   120.12  3.000
 5T1  C9   N3   C8   127.39  3.000
 5T1  N2   N3   C8   112.49  3.000
 5T1  H22  C9   H21  108.96  3.000
 5T1  H22  C9   H20  109.06  3.000
 5T1  H21  C9   H20  109.30  3.000
 5T1  H22  C9   N3   108.96  3.000
 5T1  H21  C9   N3   110.32  3.000
 5T1  H20  C9   N3   110.21  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
 5T1  CONST_01  C14  C15  C20  C19    0.00   0.0  0
 5T1  CONST_02  C14  N7   C18  C19    0.00   0.0  0
 5T1  CONST_03  N7   C14  C15  C20    0.00   0.0  0
 5T1  CONST_04  N7   C18  C19  C20    0.00   0.0  0
 5T1  CONST_05  C18  N7   C14  C15    0.00   0.0  0
 5T1  CONST_06  C18  C19  C20  C15    0.00   0.0  0
 5T1  CONST_07  C4   N4   N5   C10    0.00   0.0  0
 5T1  CONST_08  N4   C4   N1   C10    0.00   0.0  0
 5T1  CONST_09  C3   C4   N1   C10  180.00   0.0  0
 5T1  CONST_10  C1   C5   N1   C10  180.00   0.0  0
 5T1  CONST_11  N4   N5   C10  N1     0.00   0.0  0
 5T1  CONST_12  N5   N4   C4   N1     0.00   0.0  0
 5T1  CONST_13  C2   C3   C4   N1     0.00   0.0  0
 5T1  CONST_14  C6   C1   C5   N1   180.00   0.0  0
 5T1  CONST_15  C2   C1   C5   N1     0.00   0.0  0
 5T1  CONST_16  N5   C10  N1   C5   180.00   0.0  0
 5T1  CONST_17  N4   C4   N1   C5   180.00   0.0  0
 5T1  CONST_18  C3   C4   N1   C5     0.00   0.0  0
 5T1  CONST_19  C7   C6   C1   C5     0.00   0.0  0
 5T1  CONST_20  C8   C6   C1   C5   180.00   0.0  0
 5T1  CONST_21  C3   C2   C1   C5     0.00   0.0  0
 5T1  CONST_22  C4   N1   C10  N5     0.00   0.0  0
 5T1  CONST_23  C3   C4   N4   N5   180.00   0.0  0
 5T1  CONST_24  C2   C3   C4   N4   180.00   0.0  0
 5T1  CONST_25  C1   C5   N1   C4     0.00   0.0  0
 5T1  CONST_26  C1   C2   C3   C4     0.00   0.0  0
 5T1  CONST_27  C6   C1   C2   C3   180.00   0.0  0
 5T1  CONST_28  C7   C6   C1   C2   180.00   0.0  0
 5T1  CONST_29  C8   C6   C1   C2     0.00   0.0  0
 5T1  CONST_30  N2   C7   C6   C1   180.00   0.0  0
 5T1  CONST_31  N3   C8   C6   C1   180.00   0.0  0
 5T1  CONST_32  N3   N2   C7   C6     0.00   0.0  0
 5T1  CONST_33  N2   N3   C8   C6     0.00   0.0  0
 5T1  CONST_34  N2   C7   C6   C8     0.00   0.0  0
 5T1  CONST_35  C7   N2   N3   C8     0.00   0.0  0
 5T1  CONST_36  N3   C8   C6   C7     0.00   0.0  0
 5T1  CONST_37  C12  N6   C16  C15    0.00   0.0  0
 5T1  CONST_38  C15  C20  C19  O2   180.00   0.0  0
 5T1  CONST_39  N7   C18  C19  O2   180.00   0.0  0
 5T1  CONST_40  N4   N5   C10  C11  180.00   0.0  0
 5T1  CONST_41  C4   N1   C10  C11  180.00   0.0  0
 5T1  CONST_42  C5   N1   C10  C11    0.00   0.0  0
 5T1  CONST_43  F1   C3   C4   N1   180.00   0.0  0
 5T1  CONST_44  F1   C3   C4   N4     0.00   0.0  0
 5T1  CONST_45  C1   C2   C3   F1   180.00   0.0  0
 5T1  CONST_46  C9   N3   C8   C6   180.00   0.0  0
 5T1  CONST_47  C9   N3   N2   C7   180.00   0.0  0
 5T1  CONST_48  C11  N6   C16  C15  180.00   0.0  0
 5T1  CONST_49  C12  N6   C16  O1   180.00   0.0  0
 5T1  CONST_50  H9   C18  C19  C20  180.00   0.0  0
 5T1  CONST_51  H8   C20  C15  C16    0.00   0.0  0
 5T1  CONST_52  H16  C5   N1   C10    0.00   0.0  0
 5T1  CONST_53  H17  C2   C1   C5   180.00   0.0  0
 5T1  CONST_54  H19  C7   C6   C1     0.00   0.0  0
 5T1  CONST_55  H18  C8   C6   C1     0.00   0.0  0
 5T1  CONST_56  C11  N6   C16  O1     0.00   0.0  0
 5T1  Var_01    C20  C19  O2   C21  179.19  30.0  1
 5T1  Var_02    H20  C9   N3   C8   121.13  30.0  2
 5T1  Var_03    H6   C21  O2   C19   61.45  30.0  3
 5T1  Var_04    C21  C22  O3   C23  177.72  30.0  1
 5T1  Var_05    O2   C21  C22  O3    65.68  30.0  1
 5T1  Var_06    H1   C23  O3   C22  -59.74  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
 5T1  chir_01  C11  C17  C10  N6  positiv

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
 5T1  plan-1  C1   0.020
 5T1  plan-1  C6   0.020
 5T1  plan-1  C8   0.020
 5T1  plan-1  C7   0.020
 5T1  plan-1  N2   0.020
 5T1  plan-1  N3   0.020
 5T1  plan-1  C9   0.020
 5T1  plan-1  H18  0.020
 5T1  plan-1  H19  0.020
 5T1  plan-2  C11  0.020
 5T1  plan-2  C10  0.020
 5T1  plan-2  N1   0.020
 5T1  plan-2  C5   0.020
 5T1  plan-2  N5   0.020
 5T1  plan-2  N4   0.020
 5T1  plan-2  C4   0.020
 5T1  plan-2  C3   0.020
 5T1  plan-2  F1   0.020
 5T1  plan-2  C2   0.020
 5T1  plan-2  C1   0.020
 5T1  plan-2  C6   0.020
 5T1  plan-2  H16  0.020
 5T1  plan-2  H17  0.020
 5T1  plan-3  O2   0.020
 5T1  plan-3  C19  0.020
 5T1  plan-3  C20  0.020
 5T1  plan-3  C15  0.020
 5T1  plan-3  C16  0.020
 5T1  plan-3  O1   0.020
 5T1  plan-3  C18  0.020
 5T1  plan-3  N7   0.020
 5T1  plan-3  C14  0.020
 5T1  plan-3  C13  0.020
 5T1  plan-3  C12  0.020
 5T1  plan-3  N6   0.020
 5T1  plan-3  C11  0.020
 5T1  plan-3  H8   0.020
 5T1  plan-3  H9   0.020
 5T1  plan-3  H10  0.020
 5T1  plan-3  H11  0.020

