# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue May  5 09:38:05 2020
#   Inital geometry file: a 111 line input string
#   Ligand name: N-[3-(5-{[(2-chloro-6-fluorophenyl)methyl]amino}-1H-1,2,4-triazol-3-yl)phenyl]propanamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCC(=O)Nc1cccc(c1)c2n[nH]c(NCc3c(F)cccc3Cl)n2
#
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
 GYL  GYL  N-[3-(5-{[(2-chloro-6-fluorophenyl)methyl]amino}-1H-1,2,4-triazol-3-yl)phenyl]propanamide  ligand  43  26  .  2021-08-10  2021-08-10  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_GYL
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
 GYL  C1   C   CR6   0  -0.072  -5.5353   0.2067   0.9006
 GYL  C2   C   CR6   0  -0.068  -4.6765   0.2497  -0.1960
 GYL  C3   C   CR6   0   0.544  -5.1781  -0.2663  -1.3846
 GYL  C4   C   CR16  0  -0.396  -6.4541  -0.7721  -1.5193
 GYL  C5   C   CR16  0  -0.254  -7.2780  -0.7804  -0.4043
 GYL  C6   C   CR16  0  -0.213  -6.8252  -0.2947   0.8119
 GYL  C37  C   CH3   0  -0.659   8.0319   2.6600  -1.1973
 GYL  C38  C   CH2   0  -0.585   7.7162   1.2131  -0.8634
 GYL  C33  C   C     0   0.551   6.2451   0.9645  -0.6023
 GYL  O35  O   O     0  -0.468   5.3731   1.7326  -0.9651
 GYL  C24  C   CR6   0   0.405   4.7877  -0.7972   0.4029
 GYL  C25  C   CR16  0  -0.375   3.5380  -0.2550   0.1157
 GYL  C23  C   CR16  0  -0.354   4.8617  -2.0163   1.0855
 GYL  C28  C   CR16  0  -0.228   3.7077  -2.6728   1.4706
 GYL  C27  C   CR16  0  -0.325   2.4602  -2.1364   1.1862
 GYL  C26  C   CR6   0   0.038   2.3784  -0.9253   0.5073
 GYL  C19  C   CR5   0   0.339   1.0672  -0.3477   0.1992
 GYL  N18  N   N     0  -0.534  -0.0975  -0.9583   0.5279
 GYL  N20  N   N     0  -0.294   0.9249   0.7987  -0.4187
 GYL  N21  N   NR15  0  -0.501  -0.4138   0.9333  -0.4888
 GYL  C17  C   CR5   0   0.699  -1.0141  -0.1259   0.0754
 GYL  N15  N   NH1   0  -0.680  -2.3528  -0.3220   0.1245
 GYL  C8   C   CH2   0  -0.356  -3.2714   0.7731  -0.1255
 GYL  CL7  CL  CL    0  -0.109  -4.9868   0.7814   2.4400
 GYL  F9   F   F     0  -0.302  -4.3762  -0.2644  -2.4574
 GYL  H1   H   HCR6  0   0.289  -6.7933  -1.1521  -2.4735
 GYL  H2   H   HCR6  0   0.283  -8.2824  -1.1735  -0.4822
 GYL  H3   H   HCR6  0   0.288  -7.4652  -0.3100   1.6826
 GYL  H4   H   HCH3  0   0.237   9.0951   2.7683  -1.4079
 GYL  H5   H   HCH3  0   0.231   7.4829   2.9991  -2.0743
 GYL  H6   H   HCH3  0   0.230   7.7878   3.3255  -0.3695
 GYL  H7   H   HCH2  0   0.278   8.0142   0.5634  -1.6930
 GYL  H8   H   HCH2  0   0.262   8.3045   0.8814  -0.0043
 GYL  H9   H   HNH1  0   0.415   6.8193  -0.7372   0.3075
 GYL  H10  H   HCR6  0   0.276   3.4536   0.6806  -0.4116
 GYL  H11  H   HCR6  0   0.272   5.8289  -2.4496   1.3115
 GYL  H12  H   HCR6  0   0.261   3.7840  -3.6141   1.9990
 GYL  H13  H   HCR6  0   0.252   1.5594  -2.6532   1.4875
 GYL  H15  H   HCH2  0   0.275  -3.0174   1.2375  -1.0789
 GYL  H14  H   HNR5  0   0.432  -0.8197   1.7481  -0.9206
 GYL  H16  H   HNH1  0   0.402  -2.6395  -0.9980   0.8163
 GYL  H17  H   HCH2  0   0.266  -3.1959   1.5560   0.6339
 GYL  N34  N   NH1   0  -0.751   6.0022  -0.2045   0.0496

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
 GYL  F9   C3   single    1.339  0.020  1.339
 GYL  C4   C3   aromatic  1.379  0.020  1.379
 GYL  C4   C5   aromatic  1.386  0.020  1.386
 GYL  C3   C2   aromatic  1.389  0.020  1.389
 GYL  C37  C38  single    1.518  0.020  1.518
 GYL  N21  N20  aromatic  1.347  0.020  1.347
 GYL  N21  C17  aromatic  1.342  0.020  1.342
 GYL  N15  C17  single    1.354  0.020  1.354
 GYL  N15  C8   single    1.451  0.020  1.451
 GYL  C5   C6   aromatic  1.386  0.020  1.386
 GYL  N20  C19  aromatic  1.310  0.020  1.310
 GYL  C17  N18  aromatic  1.318  0.020  1.318
 GYL  C2   C8   single    1.501  0.020  1.501
 GYL  C2   C1   aromatic  1.394  0.020  1.394
 GYL  C19  N18  aromatic  1.356  0.020  1.356
 GYL  C19  C26  single    1.466  0.020  1.466
 GYL  C25  C26  aromatic  1.395  0.020  1.395
 GYL  C25  C24  aromatic  1.392  0.020  1.392
 GYL  C38  C33  single    1.515  0.020  1.515
 GYL  N34  C24  single    1.397  0.020  1.397
 GYL  N34  C33  single    1.360  0.020  1.360
 GYL  C26  C27  aromatic  1.391  0.020  1.391
 GYL  C24  C23  aromatic  1.399  0.020  1.399
 GYL  C33  O35  double    1.217  0.020  1.217
 GYL  C27  C28  aromatic  1.387  0.020  1.387
 GYL  C23  C28  aromatic  1.382  0.020  1.382
 GYL  C6   C1   aromatic  1.387  0.020  1.387
 GYL  C1   CL7  single    1.732  0.020  1.732
 GYL  C4   H1   single    0.930  0.020  1.080
 GYL  C5   H2   single    0.930  0.020  1.080
 GYL  C6   H3   single    0.930  0.020  1.080
 GYL  C37  H4   single    0.970  0.020  1.090
 GYL  C37  H5   single    0.970  0.020  1.090
 GYL  C37  H6   single    0.970  0.020  1.090
 GYL  C38  H7   single    0.970  0.020  1.090
 GYL  C38  H8   single    0.970  0.020  1.090
 GYL  N34  H9   single    0.860  0.020  1.020
 GYL  C25  H10  single    0.930  0.020  1.080
 GYL  C23  H11  single    0.930  0.020  1.080
 GYL  C28  H12  single    0.930  0.020  1.080
 GYL  C27  H13  single    0.930  0.020  1.080
 GYL  C8   H15  single    0.970  0.020  1.090
 GYL  N21  H14  single    0.860  0.020  1.020
 GYL  N15  H16  single    0.890  0.020  1.040
 GYL  C8   H17  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
 GYL  CL7  C1   C6   118.12  3.000
 GYL  CL7  C1   C2   119.60  3.000
 GYL  C6   C1   C2   122.28  3.000
 GYL  C8   C2   C3   120.51  3.000
 GYL  C8   C2   C1   123.41  3.000
 GYL  C3   C2   C1   116.05  3.000
 GYL  F9   C3   C4   118.44  3.000
 GYL  C4   C3   C2   123.63  3.000
 GYL  F9   C3   C2   117.93  3.000
 GYL  H1   C4   C5   121.41  3.000
 GYL  H1   C4   C3   120.34  3.000
 GYL  C5   C4   C3   118.26  3.000
 GYL  H2   C5   C6   119.61  3.000
 GYL  H2   C5   C4   119.75  3.000
 GYL  C6   C5   C4   120.64  3.000
 GYL  H3   C6   C5   120.58  3.000
 GYL  H3   C6   C1   120.29  3.000
 GYL  C5   C6   C1   119.13  3.000
 GYL  H6   C37  H5   107.99  3.000
 GYL  H6   C37  H4   107.74  3.000
 GYL  H5   C37  H4   107.79  3.000
 GYL  H6   C37  C38  111.61  3.000
 GYL  H5   C37  C38  111.66  3.000
 GYL  H4   C37  C38  109.89  3.000
 GYL  H8   C38  H7   105.60  3.000
 GYL  H8   C38  C33  109.73  3.000
 GYL  H7   C38  C33  107.31  3.000
 GYL  H8   C38  C37  110.50  3.000
 GYL  H7   C38  C37  110.01  3.000
 GYL  C33  C38  C37  113.35  3.000
 GYL  N34  C33  O35  123.86  3.000
 GYL  O35  C33  C38  122.73  3.000
 GYL  N34  C33  C38  113.39  3.000
 GYL  C23  C24  C25  119.17  3.000
 GYL  C23  C24  N34  116.56  3.000
 GYL  C25  C24  N34  124.27  3.000
 GYL  H10  C25  C26  119.30  3.000
 GYL  H10  C25  C24  120.63  3.000
 GYL  C26  C25  C24  120.07  3.000
 GYL  H11  C23  C28  119.80  3.000
 GYL  H11  C23  C24  119.82  3.000
 GYL  C28  C23  C24  120.37  3.000
 GYL  H12  C28  C27  119.99  3.000
 GYL  H12  C28  C23  119.36  3.000
 GYL  C27  C28  C23  120.65  3.000
 GYL  H13  C27  C26  120.21  3.000
 GYL  H13  C27  C28  120.47  3.000
 GYL  C26  C27  C28  119.32  3.000
 GYL  C19  C26  C27  119.90  3.000
 GYL  C27  C26  C25  120.42  3.000
 GYL  C19  C26  C25  119.68  3.000
 GYL  N20  C19  N18  114.53  3.000
 GYL  N18  C19  C26  122.70  3.000
 GYL  N20  C19  C26  122.77  3.000
 GYL  C17  N18  C19  103.28  3.000
 GYL  N21  N20  C19  102.70  3.000
 GYL  H14  N21  C17  129.67  3.000
 GYL  H14  N21  N20  120.23  3.000
 GYL  C17  N21  N20  110.10  3.000
 GYL  N15  C17  N21  124.88  3.000
 GYL  N15  C17  N18  125.71  3.000
 GYL  N21  C17  N18  109.37  3.000
 GYL  H16  N15  C8   116.36  3.000
 GYL  H16  N15  C17  113.76  3.000
 GYL  C8   N15  C17  120.69  3.000
 GYL  H17  C8   H15  106.63  3.000
 GYL  H17  C8   N15  112.15  3.000
 GYL  H15  C8   N15  108.94  3.000
 GYL  H17  C8   C2   110.30  3.000
 GYL  H15  C8   C2   108.99  3.000
 GYL  N15  C8   C2   109.73  3.000
 GYL  H9   N34  C24  114.55  3.000
 GYL  H9   N34  C33  115.57  3.000
 GYL  C24  N34  C33  129.87  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
 GYL  CONST_01  C4   C3   C2   C1      0.00   0.0  0
 GYL  CONST_02  C4   C5   C6   C1      0.00   0.0  0
 GYL  CONST_03  C5   C4   C3   C2      0.00   0.0  0
 GYL  CONST_04  C5   C6   C1   C2      0.00   0.0  0
 GYL  CONST_05  C6   C5   C4   C3      0.00   0.0  0
 GYL  CONST_06  C6   C1   C2   C3      0.00   0.0  0
 GYL  CONST_07  C19  C26  C25  C24   180.00   0.0  0
 GYL  CONST_08  C27  C26  C25  C24     0.00   0.0  0
 GYL  CONST_09  C27  C28  C23  C24     0.00   0.0  0
 GYL  CONST_10  N20  C19  C26  C25     0.00   0.0  0
 GYL  CONST_11  N18  C19  C26  C25   180.00   0.0  0
 GYL  CONST_12  C28  C27  C26  C25     0.00   0.0  0
 GYL  CONST_13  C28  C23  C24  C25     0.00   0.0  0
 GYL  CONST_14  C26  C25  C24  C23     0.00   0.0  0
 GYL  CONST_15  C26  C27  C28  C23     0.00   0.0  0
 GYL  CONST_16  C19  C26  C27  C28   180.00   0.0  0
 GYL  CONST_17  N20  C19  C26  C27   180.00   0.0  0
 GYL  CONST_18  N18  C19  C26  C27     0.00   0.0  0
 GYL  CONST_19  N21  N20  C19  C26   180.00   0.0  0
 GYL  CONST_20  C17  N18  C19  C26   180.00   0.0  0
 GYL  CONST_21  C17  N21  N20  C19     0.00   0.0  0
 GYL  CONST_22  N21  C17  N18  C19     0.00   0.0  0
 GYL  CONST_23  N20  N21  C17  N18     0.00   0.0  0
 GYL  CONST_24  N21  N20  C19  N18     0.00   0.0  0
 GYL  CONST_25  C17  N18  C19  N20     0.00   0.0  0
 GYL  CONST_26  F9   C3   C2   C1    180.00   0.0  0
 GYL  CONST_27  CL7  C1   C2   C3    180.00   0.0  0
 GYL  CONST_28  C8   C2   C3   C4    180.00   0.0  0
 GYL  CONST_29  F9   C3   C4   C5    180.00   0.0  0
 GYL  CONST_30  CL7  C1   C6   C5    180.00   0.0  0
 GYL  CONST_31  C8   C2   C1   C6    180.00   0.0  0
 GYL  CONST_32  C26  C25  C24  N34   180.00   0.0  0
 GYL  CONST_33  C28  C23  C24  N34   180.00   0.0  0
 GYL  CONST_34  N15  C17  N18  C19   180.00   0.0  0
 GYL  CONST_35  N15  C17  N21  N20   180.00   0.0  0
 GYL  CONST_36  H2   C5   C6   C1    180.00   0.0  0
 GYL  CONST_37  H1   C4   C3   C2    180.00   0.0  0
 GYL  CONST_38  H3   C6   C1   C2    180.00   0.0  0
 GYL  CONST_39  H12  C28  C23  C24   180.00   0.0  0
 GYL  CONST_40  H13  C27  C26  C25   180.00   0.0  0
 GYL  CONST_41  H11  C23  C24  C25   180.00   0.0  0
 GYL  CONST_42  H10  C25  C24  C23   180.00   0.0  0
 GYL  CONST_43  H14  N21  N20  C19   180.00   0.0  0
 GYL  CONST_44  C25  C24  N34  C33     0.00   0.0  0
 GYL  CONST_45  C23  C24  N34  C33   180.00   0.0  0
 GYL  CONST_46  C8   N15  C17  N18   180.00   0.0  0
 GYL  CONST_48  H9   N34  C24  C25   180.00   0.0  0
 GYL  CONST_50  C24  N34  C33  C38   180.00   0.0  0
 GYL  CONST_51  C24  N34  C33  O35     0.00   0.0  0
 GYL  Var_01    N15  C8   C2   C1     93.31  30.0  2
 GYL  Var_02    C17  N15  C8   C2    172.26  30.0  1
 GYL  Var_03    N34  C33  C38  C37  -162.63  30.0  3
 GYL  Var_04    H4   C37  C38  C33  -178.04  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
 GYL  plan-1  C26  0.020
 GYL  plan-1  C19  0.020
 GYL  plan-1  N18  0.020
 GYL  plan-1  N20  0.020
 GYL  plan-1  N21  0.020
 GYL  plan-1  C17  0.020
 GYL  plan-1  N15  0.020
 GYL  plan-1  H14  0.020
 GYL  plan-2  C1   0.020
 GYL  plan-2  C2   0.020
 GYL  plan-2  C3   0.020
 GYL  plan-2  C4   0.020
 GYL  plan-2  C5   0.020
 GYL  plan-2  C6   0.020
 GYL  plan-2  C8   0.020
 GYL  plan-2  CL7  0.020
 GYL  plan-2  F9   0.020
 GYL  plan-2  H1   0.020
 GYL  plan-2  H2   0.020
 GYL  plan-2  H3   0.020
 GYL  plan-3  C24  0.020
 GYL  plan-3  C25  0.020
 GYL  plan-3  C23  0.020
 GYL  plan-3  C28  0.020
 GYL  plan-3  C27  0.020
 GYL  plan-3  C26  0.020
 GYL  plan-3  C19  0.020
 GYL  plan-3  H10  0.020
 GYL  plan-3  H11  0.020
 GYL  plan-3  H12  0.020
 GYL  plan-3  H13  0.020
 GYL  plan-3  N34  0.020
 GYL  plan-4  C38  0.020
 GYL  plan-4  C33  0.020
 GYL  plan-4  O35  0.020
 GYL  plan-4  C24  0.020
 GYL  plan-4  H9   0.020
 GYL  plan-4  N34  0.020
 GYL  plan-5  C17  0.020
 GYL  plan-5  N15  0.020
 GYL  plan-5  C8   0.020
 GYL  plan-5  H16  0.020

