# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Mar 12 11:10:31 2022
#   Inital geometry file: a 135 line input string
#   Ligand name: ~{N}-[3-[(3~{S})-1-azanyl-5-fluoranyl-3-methyl-4~{H}-2,6-naphthyridin-3-yl]-4-fluoranyl-phenyl]-5-cyano-3-methyl-pyridine-2-carboxamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cc1cc(cnc1C(=O)Nc2ccc(F)c(c2)[C@]3(C)Cc4c(F)nccc4C(=N3)N)C#N
#
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
 GUC  GUC  ~{N}-[3-[(3~{S})-1-azanyl-5-fluoranyl-3-methyl-4~{H}-2,6-naphthyridin-3-yl]-4-fluoranyl-phenyl]-5-cyano-3-methyl-pyridine-2-carboxamide  ligand  50  32  .  2022-08-10  2022-08-10
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_GUC
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
 GUC  C1   C  CH3   0  -0.715  23.5986  43.0215   -4.2211
 GUC  C2   C  CR6   0   0.080  22.2450  42.7755   -3.6251
 GUC  C3   C  CR16  0  -0.159  22.0249  43.1699   -2.3082
 GUC  C4   C  CR6   0  -0.067  20.7946  42.9602   -1.7029
 GUC  C5   C  CR16  0  -0.025  19.7837  42.3470   -2.4396
 GUC  C6   C  CR6   0   0.107  21.1595  42.1700   -4.2732
 GUC  N1   N  N     0  -0.444  19.9830  41.9727   -3.6821
 GUC  N2   N  NH1   0  -0.761  20.1028  41.0866   -6.1148
 GUC  N3   N  N     0  -0.418  15.5626  42.7622  -10.8960
 GUC  C7   C  C     0   0.526  21.2389  41.6832   -5.7007
 GUC  C8   C  CR6   0   0.423  19.8190  40.4814   -7.3410
 GUC  C9   C  CR16  0  -0.316  20.7199  40.3703   -8.3967
 GUC  C10  C  CR16  0  -0.390  20.3215  39.7088   -9.5484
 GUC  C11  C  CR6   0   0.506  19.0541  39.1762   -9.6462
 GUC  C12  C  CR6   0  -0.035  18.1105  39.2921   -8.6299
 GUC  C13  C  CR16  0  -0.423  18.5361  39.9470   -7.4815
 GUC  C14  C  CT    0  -0.018  16.7055  38.6786   -8.7138
 GUC  C15  C  CH3   0  -0.636  16.8330  37.1534   -8.6888
 GUC  N6   N  NS    0  -0.229  20.3637  43.6706    0.7360
 GUC  C23  C  CSP   0   0.052  20.5607  43.3569   -0.3540
 GUC  O    O  O     0  -0.442  22.2406  41.8289   -6.3774
 GUC  F1   F  F     0  -0.315  18.7512  38.5135  -10.7803
 GUC  N5   N  N     0  -0.413  15.9229  39.0511   -7.5442
 GUC  C22  C  C     0   0.403  15.3308  40.1847   -7.5335
 GUC  N4   N  NH2   0  -0.823  14.6540  40.6012   -6.4334
 GUC  C18  C  CR6   0   0.121  15.3951  41.1364   -8.6708
 GUC  C19  C  CR16  0  -0.382  15.2028  42.5098   -8.5538
 GUC  C20  C  CR16  0  -0.048  15.3020  43.2795   -9.6977
 GUC  C21  C  CR6   0   0.555  15.7438  41.4753  -10.9703
 GUC  F2   F  F     0  -0.295  15.9968  40.9975  -12.1923
 GUC  C17  C  CR6   0  -0.147  15.6974  40.5851   -9.9093
 GUC  C16  C  CH2   0  -0.507  15.9590  39.1184   -9.9843
 GUC  H1   H  HCH3  0   0.260  23.5461  43.6851   -5.0820
 GUC  H2   H  HCH3  0   0.249  24.2470  43.4824   -3.4779
 GUC  H3   H  HCH3  0   0.259  24.0683  42.0975   -4.5520
 GUC  H4   H  HCR6  0   0.298  22.8242  43.6438   -1.7529
 GUC  H5   H  HCR6  0   0.298  18.8072  42.1626   -2.0081
 GUC  H6   H  HNH1  0   0.426  19.3647  41.0660   -5.4208
 GUC  H7   H  HCR6  0   0.287  21.7161  40.7751   -8.3380
 GUC  H8   H  HCR6  0   0.278  21.0108  39.6012  -10.3762
 GUC  H9   H  HCR6  0   0.283  17.8499  40.0356   -6.6499
 GUC  H10  H  HCH3  0   0.236  17.3398  36.8341   -7.7783
 GUC  H11  H  HCH3  0   0.234  15.8418  36.6985   -8.7037
 GUC  H12  H  HCH3  0   0.231  17.3914  36.7764   -9.5437
 GUC  H13  H  HNH2  0   0.390  14.5072  39.9122   -5.7127
 GUC  H14  H  HNH2  0   0.398  13.8955  41.2538   -6.5455
 GUC  H15  H  HCR6  0   0.278  14.9973  42.9838   -7.6040
 GUC  H16  H  HCR6  0   0.281  15.1666  44.3530   -9.6536
 GUC  H17  H  HCH2  0   0.275  15.0058  38.5784  -10.0090
 GUC  H18  H  HCH2  0   0.274  16.4885  38.8464  -10.8922

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
 GUC  F2   C21  single    1.336  0.020  1.336
 GUC  F1   C11  single    1.348  0.020  1.348
 GUC  C21  N3   aromatic  1.302  0.020  1.302
 GUC  C21  C17  aromatic  1.386  0.020  1.386
 GUC  C16  C17  single    1.492  0.020  1.492
 GUC  C16  C14  single    1.538  0.020  1.538
 GUC  N3   C20  aromatic  1.331  0.020  1.331
 GUC  C17  C18  aromatic  1.389  0.020  1.389
 GUC  C11  C10  aromatic  1.378  0.020  1.378
 GUC  C11  C12  aromatic  1.392  0.020  1.392
 GUC  C15  C14  single    1.531  0.020  1.531
 GUC  C10  C9   aromatic  1.387  0.020  1.387
 GUC  C14  C12  single    1.535  0.020  1.535
 GUC  C14  N5   single    1.456  0.020  1.456
 GUC  C20  C19  aromatic  1.382  0.020  1.382
 GUC  C12  C13  aromatic  1.389  0.020  1.389
 GUC  C18  C19  aromatic  1.392  0.020  1.392
 GUC  C18  C22  single    1.484  0.020  1.484
 GUC  C9   C8   aromatic  1.392  0.020  1.392
 GUC  N5   C22  double    1.279  0.020  1.279
 GUC  C22  N4   single    1.357  0.020  1.357
 GUC  C13  C8   aromatic  1.397  0.020  1.397
 GUC  C8   N2   single    1.396  0.020  1.396
 GUC  O    C7   double    1.218  0.020  1.218
 GUC  N2   C7   single    1.348  0.020  1.348
 GUC  C7   C6   single    1.510  0.020  1.510
 GUC  C1   C2   single    1.499  0.020  1.499
 GUC  C6   C2   aromatic  1.402  0.020  1.402
 GUC  C6   N1   aromatic  1.331  0.020  1.331
 GUC  C2   C3   aromatic  1.392  0.020  1.392
 GUC  N1   C5   aromatic  1.313  0.020  1.313
 GUC  C3   C4   aromatic  1.387  0.020  1.387
 GUC  C5   C4   aromatic  1.393  0.020  1.393
 GUC  C4   C23  single    1.425  0.020  1.425
 GUC  C23  N6   triple    1.151  0.020  1.151
 GUC  C1   H1   single    0.970  0.020  1.090
 GUC  C1   H2   single    0.970  0.020  1.090
 GUC  C1   H3   single    0.970  0.020  1.090
 GUC  C3   H4   single    0.930  0.020  1.080
 GUC  C5   H5   single    0.930  0.020  1.080
 GUC  N2   H6   single    0.860  0.020  1.020
 GUC  C9   H7   single    0.930  0.020  1.080
 GUC  C10  H8   single    0.930  0.020  1.080
 GUC  C13  H9   single    0.930  0.020  1.080
 GUC  C15  H10  single    0.970  0.020  1.090
 GUC  C15  H11  single    0.970  0.020  1.090
 GUC  C15  H12  single    0.970  0.020  1.090
 GUC  N4   H13  single    0.890  0.020  1.040
 GUC  N4   H14  single    0.890  0.020  1.040
 GUC  C19  H15  single    0.930  0.020  1.080
 GUC  C20  H16  single    0.930  0.020  1.080
 GUC  C16  H17  single    0.970  0.020  1.090
 GUC  C16  H18  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
 GUC  H3   C1   H2   108.06  3.000
 GUC  H3   C1   H1   107.34  3.000
 GUC  H2   C1   H1   108.10  3.000
 GUC  H3   C1   C2   111.80  3.000
 GUC  H2   C1   C2   109.62  3.000
 GUC  H1   C1   C2   111.77  3.000
 GUC  C6   C2   C3   115.93  3.000
 GUC  C3   C2   C1   118.18  3.000
 GUC  C6   C2   C1   125.89  3.000
 GUC  H4   C3   C4   119.82  3.000
 GUC  H4   C3   C2   119.51  3.000
 GUC  C4   C3   C2   120.67  3.000
 GUC  C23  C4   C5   120.26  3.000
 GUC  C23  C4   C3   121.09  3.000
 GUC  C5   C4   C3   118.65  3.000
 GUC  H5   C5   N1   117.73  3.000
 GUC  H5   C5   C4   121.22  3.000
 GUC  N1   C5   C4   121.05  3.000
 GUC  C7   C6   N1   114.73  3.000
 GUC  N1   C6   C2   122.89  3.000
 GUC  C7   C6   C2   122.38  3.000
 GUC  C6   N1   C5   120.80  3.000
 GUC  H6   N2   C8   116.40  3.000
 GUC  H6   N2   C7   114.36  3.000
 GUC  C8   N2   C7   129.24  3.000
 GUC  C21  N3   C20  117.57  3.000
 GUC  O    C7   N2   125.13  3.000
 GUC  N2   C7   C6   112.86  3.000
 GUC  O    C7   C6   122.00  3.000
 GUC  C13  C8   C9   119.17  3.000
 GUC  C13  C8   N2   116.15  3.000
 GUC  C9   C8   N2   124.68  3.000
 GUC  H7   C9   C10  119.36  3.000
 GUC  H7   C9   C8   121.81  3.000
 GUC  C10  C9   C8   118.82  3.000
 GUC  H8   C10  C11  119.53  3.000
 GUC  H8   C10  C9   119.98  3.000
 GUC  C11  C10  C9   120.50  3.000
 GUC  F1   C11  C12  120.19  3.000
 GUC  C12  C11  C10  122.65  3.000
 GUC  F1   C11  C10  117.15  3.000
 GUC  C14  C12  C13  120.93  3.000
 GUC  C13  C12  C11  115.81  3.000
 GUC  C14  C12  C11  123.18  3.000
 GUC  H9   C13  C12  118.68  3.000
 GUC  H9   C13  C8   118.29  3.000
 GUC  C12  C13  C8   123.03  3.000
 GUC  C16  C14  N5   109.25  3.000
 GUC  N5   C14  C15  106.65  3.000
 GUC  C16  C14  C15  109.81  3.000
 GUC  N5   C14  C12  110.23  3.000
 GUC  C15  C14  C12  108.72  3.000
 GUC  C16  C14  C12  112.03  3.000
 GUC  H12  C15  H11  108.12  3.000
 GUC  H12  C15  H10  108.43  3.000
 GUC  H11  C15  H10  108.17  3.000
 GUC  H12  C15  C14  112.02  3.000
 GUC  H11  C15  C14  109.86  3.000
 GUC  H10  C15  C14  110.14  3.000
 GUC  N6   C23  C4   180.00  3.000
 GUC  C22  N5   C14  118.84  3.000
 GUC  C18  C22  N4   116.48  3.000
 GUC  N4   C22  N5   120.65  3.000
 GUC  C18  C22  N5   122.81  3.000
 GUC  H14  N4   H13  114.40  3.000
 GUC  H14  N4   C22  118.97  3.000
 GUC  H13  N4   C22  116.26  3.000
 GUC  C17  C18  C19  119.78  3.000
 GUC  C19  C18  C22  124.21  3.000
 GUC  C17  C18  C22  115.99  3.000
 GUC  H15  C19  C20  119.77  3.000
 GUC  H15  C19  C18  122.19  3.000
 GUC  C20  C19  C18  118.03  3.000
 GUC  H16  C20  C19  120.62  3.000
 GUC  H16  C20  N3   116.51  3.000
 GUC  C19  C20  N3   122.87  3.000
 GUC  C17  C21  F2   118.48  3.000
 GUC  C17  C21  N3   125.93  3.000
 GUC  F2   C21  N3   115.60  3.000
 GUC  C16  C17  C21  125.96  3.000
 GUC  C16  C17  C18  118.25  3.000
 GUC  C21  C17  C18  115.79  3.000
 GUC  H18  C16  H17  106.38  3.000
 GUC  H18  C16  C17  111.96  3.000
 GUC  H17  C16  C17  109.46  3.000
 GUC  H18  C16  C14  112.49  3.000
 GUC  H17  C16  C14  107.45  3.000
 GUC  C17  C16  C14  108.95  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
 GUC  CONST_01  C5   N1   C6   C2      0.00   0.0  0
 GUC  CONST_02  C5   C4   C3   C2      0.00   0.0  0
 GUC  CONST_03  N1   C6   C2   C3      0.00   0.0  0
 GUC  CONST_04  N1   C5   C4   C3      0.00   0.0  0
 GUC  CONST_05  C6   C2   C3   C4      0.00   0.0  0
 GUC  CONST_06  C6   N1   C5   C4      0.00   0.0  0
 GUC  CONST_07  C18  C17  C21  N3      0.00   0.0  0
 GUC  CONST_08  C18  C19  C20  N3      0.00   0.0  0
 GUC  CONST_09  C11  C10  C9   C8      0.00   0.0  0
 GUC  CONST_10  C11  C12  C13  C8      0.00   0.0  0
 GUC  CONST_11  C12  C11  C10  C9      0.00   0.0  0
 GUC  CONST_12  C12  C13  C8   C9      0.00   0.0  0
 GUC  CONST_13  C13  C12  C11  C10     0.00   0.0  0
 GUC  CONST_14  C13  C8   C9   C10     0.00   0.0  0
 GUC  CONST_15  C21  N3   C20  C19     0.00   0.0  0
 GUC  CONST_16  C21  C17  C18  C19     0.00   0.0  0
 GUC  CONST_17  C17  C21  N3   C20     0.00   0.0  0
 GUC  CONST_18  C17  C18  C19  C20     0.00   0.0  0
 GUC  CONST_19  C14  C12  C13  C8    180.00   0.0  0
 GUC  CONST_20  C14  C12  C11  C10   180.00   0.0  0
 GUC  CONST_21  C18  C22  N5   C14     0.00   0.0  0
 GUC  CONST_22  N1   C6   C2   C1    180.00   0.0  0
 GUC  CONST_23  C4   C3   C2   C1    180.00   0.0  0
 GUC  CONST_24  C23  C4   C3   C2    180.00   0.0  0
 GUC  CONST_25  C7   C6   C2   C3    180.00   0.0  0
 GUC  CONST_26  C7   C6   N1   C5    180.00   0.0  0
 GUC  CONST_27  C23  C4   C5   N1    180.00   0.0  0
 GUC  CONST_28  C10  C9   C8   N2    180.00   0.0  0
 GUC  CONST_29  C12  C13  C8   N2    180.00   0.0  0
 GUC  CONST_30  F1   C11  C10  C9    180.00   0.0  0
 GUC  CONST_31  F1   C11  C12  C13   180.00   0.0  0
 GUC  CONST_32  F1   C11  C12  C14     0.00   0.0  0
 GUC  CONST_33  F2   C21  C17  C18   180.00   0.0  0
 GUC  CONST_34  F2   C21  N3   C20   180.00   0.0  0
 GUC  CONST_35  C16  C17  C21  F2      0.00   0.0  0
 GUC  CONST_36  N4   C22  N5   C14   180.00   0.0  0
 GUC  CONST_37  H5   C5   C4   C3    180.00   0.0  0
 GUC  CONST_38  H4   C3   C4   C5    180.00   0.0  0
 GUC  CONST_39  H15  C19  C20  N3    180.00   0.0  0
 GUC  CONST_40  H8   C10  C9   C8    180.00   0.0  0
 GUC  CONST_41  H9   C13  C8   C9    180.00   0.0  0
 GUC  CONST_42  H7   C9   C10  C11   180.00   0.0  0
 GUC  CONST_43  H16  C20  C19  C18   180.00   0.0  0
 GUC  CONST_44  C8   N2   C7   C6    180.00   0.0  0
 GUC  CONST_45  C9   C8   N2   C7      0.00   0.0  0
 GUC  CONST_46  C13  C8   N2   C7    180.00   0.0  0
 GUC  CONST_47  H6   N2   C8   C9    180.00   0.0  0
 GUC  CONST_48  H13  N4   C22  N5      0.00   0.0  0
 GUC  CONST_50  O    C7   N2   C8      0.00   0.0  0
 GUC  Var_01    C21  C17  C16  C14   142.74  30.0  1
 GUC  Var_02    C17  C18  C22  N5     22.62  30.0  1
 GUC  Var_03    O    C7   C6   C2     -2.29  30.0  2
 GUC  Var_04    H1   C1   C2   C3   -118.67  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
 GUC  chir_01  C14  C16  C12  N5  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
 GUC  plan-1  C1   0.020
 GUC  plan-1  C2   0.020
 GUC  plan-1  C3   0.020
 GUC  plan-1  C4   0.020
 GUC  plan-1  C5   0.020
 GUC  plan-1  C6   0.020
 GUC  plan-1  N1   0.020
 GUC  plan-1  C7   0.020
 GUC  plan-1  N6   0.020
 GUC  plan-1  C23  0.020
 GUC  plan-1  H4   0.020
 GUC  plan-1  H5   0.020
 GUC  plan-2  N2   0.020
 GUC  plan-2  C8   0.020
 GUC  plan-2  C9   0.020
 GUC  plan-2  C10  0.020
 GUC  plan-2  C11  0.020
 GUC  plan-2  C12  0.020
 GUC  plan-2  C13  0.020
 GUC  plan-2  C14  0.020
 GUC  plan-2  F1   0.020
 GUC  plan-2  H7   0.020
 GUC  plan-2  H8   0.020
 GUC  plan-2  H9   0.020
 GUC  plan-3  N3   0.020
 GUC  plan-3  C22  0.020
 GUC  plan-3  C18  0.020
 GUC  plan-3  C19  0.020
 GUC  plan-3  C20  0.020
 GUC  plan-3  C21  0.020
 GUC  plan-3  F2   0.020
 GUC  plan-3  C17  0.020
 GUC  plan-3  C16  0.020
 GUC  plan-3  H15  0.020
 GUC  plan-3  H16  0.020
 GUC  plan-4  C6   0.020
 GUC  plan-4  N2   0.020
 GUC  plan-4  C7   0.020
 GUC  plan-4  C8   0.020
 GUC  plan-4  O    0.020
 GUC  plan-4  H6   0.020
 GUC  plan-5  C14  0.020
 GUC  plan-5  N5   0.020
 GUC  plan-5  C22  0.020
 GUC  plan-5  N4   0.020
 GUC  plan-5  C18  0.020
 GUC  plan-5  H13  0.020
 GUC  plan-5  H14  0.020

