# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri May  1 10:39:48 2020
#   Inital geometry file: a 141 line input string
#   Ligand name: N-(2,6-difluorobenzyl)-3-({[4-propyl-5-(pyrimidin-4-yl)-4H-1,2,4-triazol-3-yl]methyl}amino)benzamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCCn1c(CNc2cccc(c2)C(=O)NCc3c(F)cccc3F)nnc1c4ccncn4
#
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
 QRX  QRX  N-(2,6-difluorobenzyl)-3-({[4-propyl-5-(pyrimidin-4-yl)-4H-1,2,4-triazol-3-yl]methyl}amino)benzamide  ligand  57  34  .  2021-08-20  2021-08-20  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_QRX
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
 QRX  C1    C  CR6   0   0.214  -6.7711  -0.1429  -0.6965
 QRX  C2    C  CR16  0  -0.311  -7.8115  -0.9353  -1.1740
 QRX  C3    C  CR16  0  -0.024  -8.8483  -0.2766  -1.8047
 QRX  N4    N  N     0  -0.394  -8.8676   1.0444  -1.9600
 QRX  C5    C  CR16  0   0.062  -7.8293   1.7016  -1.4714
 QRX  N6    N  N     0  -0.426  -6.7869   1.1766  -0.8477
 QRX  C7    C  CR5   0   0.436  -5.6398  -0.7640  -0.0095
 QRX  N8    N  N     0  -0.322  -5.5934  -2.0458   0.2533
 QRX  N9    N  N     0  -0.313  -4.4375  -2.3008   0.8808
 QRX  C10   C  CR5   0   0.407  -3.7900  -1.1701   0.9952
 QRX  N11   N  NR5   0  -0.491  -4.5054  -0.1640   0.4406
 QRX  C12   C  CH2   0  -0.313  -4.1186   1.2435   0.4372
 QRX  C13   C  CH2   0  -0.434  -4.7174   2.0096   1.6058
 QRX  C14   C  CH3   0  -0.668  -4.3043   3.4730   1.5613
 QRX  C15   C  CH2   0  -0.390  -2.4558  -1.0217   1.6367
 QRX  N16   N  NH1   0  -0.701  -1.4521  -0.7007   0.6469
 QRX  C17   C  CR6   0   0.399  -0.1353  -0.5146   1.0151
 QRX  C18   C  CR16  0  -0.369   0.8528  -0.5252   0.0237
 QRX  C19   C  CR6   0  -0.026   2.1881  -0.3357   0.3423
 QRX  C20   C  CR16  0  -0.324   2.5669  -0.0970   1.6638
 QRX  C21   C  CR16  0  -0.233   1.5898  -0.0670   2.6452
 QRX  C22   C  CR16  0  -0.340   0.2541  -0.2821   2.3387
 QRX  C23   C  C     0   0.532   3.1803  -0.3516  -0.7773
 QRX  N24   N  NH1   0  -0.638   4.4044  -0.8059  -0.4530
 QRX  O25   O  O     0  -0.486   2.8745   0.0168  -1.9023
 QRX  C26   C  CH2   0  -0.346   5.5271  -0.8185  -1.3633
 QRX  C27   C  CR6   0  -0.292   6.6995  -0.0700  -0.7871
 QRX  C28   C  CR6   0   0.545   7.8695  -0.6891  -0.3729
 QRX  C29   C  CR16  0  -0.418   8.9398  -0.0048   0.1729
 QRX  C30   C  CR16  0  -0.235   8.8402   1.3698   0.3177
 QRX  C31   C  CR16  0  -0.415   7.6917   2.0435  -0.0755
 QRX  C32   C  CR6   0   0.557   6.6565   1.3081  -0.6138
 QRX  F33   F  F     0  -0.303   5.5431   1.9475  -0.9971
 QRX  F34   F  F     0  -0.306   7.9698  -2.0195  -0.5082
 QRX  H2    H  HCR6  0   0.287  -7.8119  -2.0088  -1.0592
 QRX  H3    H  HCR6  0   0.288  -9.6920  -0.8305  -2.1992
 QRX  H5    H  HCR6  0   0.268  -7.8281   2.7792  -1.5894
 QRX  H12   H  HCH2  0   0.277  -3.0300   1.2755   0.4688
 QRX  H12A  H  HCH2  0   0.280  -4.4282   1.6808  -0.5072
 QRX  H13   H  HCH2  0   0.240  -5.8050   1.9262   1.5727
 QRX  H13A  H  HCH2  0   0.231  -4.3903   1.5587   2.5465
 QRX  H14   H  HCH3  0   0.226  -4.6470   3.9537   0.6436
 QRX  H14A  H  HCH3  0   0.239  -4.7279   4.0225   2.4015
 QRX  H14B  H  HCH3  0   0.225  -3.2196   3.5817   1.6093
 QRX  H15   H  HCH2  0   0.269  -2.5032  -0.2267   2.3856
 QRX  H15A  H  HCH2  0   0.276  -2.2440  -1.9522   2.1756
 QRX  HN16  H  HNH1  0   0.391  -1.5629  -1.1993  -0.2234
 QRX  H18   H  HCR6  0   0.263   0.5673  -0.6979  -1.0073
 QRX  H20   H  HCR6  0   0.253   3.5986   0.0926   1.9292
 QRX  H21   H  HCR6  0   0.262   1.8682   0.1261   3.6730
 QRX  H22   H  HCR6  0   0.275  -0.4738  -0.2641   3.1383
 QRX  HN24  H  HNH1  0   0.409   4.5483  -1.2128   0.4572
 QRX  H26   H  HCH2  0   0.278   5.8077  -1.8450  -1.5957
 QRX  H26A  H  HCH2  0   0.281   5.2118  -0.3632  -2.3002
 QRX  H29   H  HCR6  0   0.286   9.8289  -0.5386   0.4797
 QRX  H30   H  HCR6  0   0.282   9.6667   1.9231   0.7416
 QRX  H31   H  HCR6  0   0.285   7.6025   3.1159   0.0327

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
 QRX  C1   C2    aromatic  1.392  0.020  1.392
 QRX  C1   N6    aromatic  1.328  0.020  1.328
 QRX  C1   C7    single    1.462  0.020  1.462
 QRX  C2   C3    aromatic  1.381  0.020  1.381
 QRX  C3   N4    aromatic  1.330  0.020  1.330
 QRX  N4   C5    aromatic  1.322  0.020  1.322
 QRX  C5   N6    aromatic  1.323  0.020  1.323
 QRX  C7   N8    aromatic  1.309  0.020  1.309
 QRX  C7   N11   aromatic  1.360  0.020  1.360
 QRX  N8   N9    aromatic  1.340  0.020  1.340
 QRX  N9   C10   aromatic  1.308  0.020  1.308
 QRX  C10  N11   aromatic  1.353  0.020  1.353
 QRX  C10  C15   single    1.488  0.020  1.488
 QRX  N11  C12   single    1.460  0.020  1.460
 QRX  C12  C13   single    1.520  0.020  1.520
 QRX  C13  C14   single    1.521  0.020  1.521
 QRX  C15  N16   single    1.446  0.020  1.446
 QRX  N16  C17   single    1.380  0.020  1.380
 QRX  C17  C18   aromatic  1.400  0.020  1.400
 QRX  C17  C22   aromatic  1.399  0.020  1.399
 QRX  C18  C19   aromatic  1.386  0.020  1.386
 QRX  C19  C20   aromatic  1.395  0.020  1.395
 QRX  C19  C23   single    1.496  0.020  1.496
 QRX  C20  C21   aromatic  1.385  0.020  1.385
 QRX  C21  C22   aromatic  1.387  0.020  1.387
 QRX  C23  N24   single    1.345  0.020  1.345
 QRX  C23  O25   double    1.223  0.020  1.223
 QRX  N24  C26   single    1.445  0.020  1.445
 QRX  C26  C27   single    1.506  0.020  1.506
 QRX  C27  C28   aromatic  1.387  0.020  1.387
 QRX  C27  C32   aromatic  1.390  0.020  1.390
 QRX  C28  C29   aromatic  1.383  0.020  1.383
 QRX  C28  F34   single    1.341  0.020  1.341
 QRX  C29  C30   aromatic  1.386  0.020  1.386
 QRX  C30  C31   aromatic  1.388  0.020  1.388
 QRX  C31  C32   aromatic  1.379  0.020  1.379
 QRX  C32  F33   single    1.340  0.020  1.340
 QRX  C2   H2    single    0.930  0.020  1.080
 QRX  C3   H3    single    0.930  0.020  1.080
 QRX  C5   H5    single    0.930  0.020  1.080
 QRX  C12  H12   single    0.970  0.020  1.090
 QRX  C12  H12A  single    0.970  0.020  1.090
 QRX  C13  H13   single    0.970  0.020  1.090
 QRX  C13  H13A  single    0.970  0.020  1.090
 QRX  C14  H14   single    0.970  0.020  1.090
 QRX  C14  H14A  single    0.970  0.020  1.090
 QRX  C14  H14B  single    0.970  0.020  1.090
 QRX  C15  H15   single    0.970  0.020  1.090
 QRX  C15  H15A  single    0.970  0.020  1.090
 QRX  N16  HN16  single    0.890  0.020  1.040
 QRX  C18  H18   single    0.930  0.020  1.080
 QRX  C20  H20   single    0.930  0.020  1.080
 QRX  C21  H21   single    0.930  0.020  1.080
 QRX  C22  H22   single    0.930  0.020  1.080
 QRX  N24  HN24  single    0.860  0.020  1.020
 QRX  C26  H26   single    0.970  0.020  1.090
 QRX  C26  H26A  single    0.970  0.020  1.090
 QRX  C29  H29   single    0.930  0.020  1.080
 QRX  C30  H30   single    0.930  0.020  1.080
 QRX  C31  H31   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
 QRX  C7    C1   N6    118.99  3.000
 QRX  C7    C1   C2    119.84  3.000
 QRX  N6    C1   C2    121.17  3.000
 QRX  H2    C2   C3    121.51  3.000
 QRX  H2    C2   C1    121.99  3.000
 QRX  C3    C2   C1    116.50  3.000
 QRX  H3    C3   N4    116.99  3.000
 QRX  H3    C3   C2    120.47  3.000
 QRX  N4    C3   C2    122.55  3.000
 QRX  C5    N4   C3    116.04  3.000
 QRX  H5    C5   N6    116.41  3.000
 QRX  H5    C5   N4    117.04  3.000
 QRX  N6    C5   N4    126.55  3.000
 QRX  C5    N6   C1    117.20  3.000
 QRX  N11   C7   N8    109.63  3.000
 QRX  N11   C7   C1    127.85  3.000
 QRX  N8    C7   C1    122.52  3.000
 QRX  N9    N8   C7    108.12  3.000
 QRX  C10   N9   N8    107.67  3.000
 QRX  C15   C10  N11   125.20  3.000
 QRX  C15   C10  N9    124.60  3.000
 QRX  N11   C10  N9    110.19  3.000
 QRX  C12   N11  C10   125.29  3.000
 QRX  C12   N11  C7    130.22  3.000
 QRX  C10   N11  C7    104.39  3.000
 QRX  H12A  C12  H12   107.35  3.000
 QRX  H12A  C12  C13   110.69  3.000
 QRX  H12   C12  C13   110.88  3.000
 QRX  H12A  C12  N11   108.35  3.000
 QRX  H12   C12  N11   107.04  3.000
 QRX  C13   C12  N11   112.32  3.000
 QRX  H13A  C13  H13   107.02  3.000
 QRX  H13A  C13  C14   109.91  3.000
 QRX  H13   C13  C14   110.07  3.000
 QRX  H13A  C13  C12   109.62  3.000
 QRX  H13   C13  C12   109.31  3.000
 QRX  C14   C13  C12   110.82  3.000
 QRX  H14B  C14  H14A  107.60  3.000
 QRX  H14B  C14  H14   107.77  3.000
 QRX  H14A  C14  H14   107.72  3.000
 QRX  H14B  C14  C13   111.37  3.000
 QRX  H14A  C14  C13   110.92  3.000
 QRX  H14   C14  C13   111.29  3.000
 QRX  H15A  C15  H15   106.80  3.000
 QRX  H15A  C15  N16   113.02  3.000
 QRX  H15   C15  N16   109.73  3.000
 QRX  H15A  C15  C10   107.49  3.000
 QRX  H15   C15  C10   109.21  3.000
 QRX  N16   C15  C10   110.46  3.000
 QRX  HN16  N16  C17   113.68  3.000
 QRX  HN16  N16  C15   113.86  3.000
 QRX  C17   N16  C15   120.65  3.000
 QRX  C22   C17  C18   118.35  3.000
 QRX  C22   C17  N16   122.71  3.000
 QRX  C18   C17  N16   118.92  3.000
 QRX  H18   C18  C19   119.63  3.000
 QRX  H18   C18  C17   119.28  3.000
 QRX  C19   C18  C17   121.08  3.000
 QRX  C23   C19  C20   122.05  3.000
 QRX  C23   C19  C18   117.74  3.000
 QRX  C20   C19  C18   120.18  3.000
 QRX  H20   C20  C21   119.67  3.000
 QRX  H20   C20  C19   121.41  3.000
 QRX  C21   C20  C19   118.90  3.000
 QRX  H21   C21  C22   119.03  3.000
 QRX  H21   C21  C20   119.69  3.000
 QRX  C22   C21  C20   121.28  3.000
 QRX  H22   C22  C21   118.82  3.000
 QRX  H22   C22  C17   120.99  3.000
 QRX  C21   C22  C17   120.18  3.000
 QRX  O25   C23  N24   123.44  3.000
 QRX  O25   C23  C19   121.30  3.000
 QRX  N24   C23  C19   115.25  3.000
 QRX  HN24  N24  C26   117.04  3.000
 QRX  HN24  N24  C23   118.96  3.000
 QRX  C26   N24  C23   123.91  3.000
 QRX  H26A  C26  H26   106.57  3.000
 QRX  H26A  C26  C27   110.31  3.000
 QRX  H26   C26  C27   110.46  3.000
 QRX  H26A  C26  N24   108.26  3.000
 QRX  H26   C26  N24   110.04  3.000
 QRX  C27   C26  N24   111.07  3.000
 QRX  C32   C27  C28   115.57  3.000
 QRX  C32   C27  C26   121.11  3.000
 QRX  C28   C27  C26   123.31  3.000
 QRX  F34   C28  C29   118.23  3.000
 QRX  F34   C28  C27   118.41  3.000
 QRX  C29   C28  C27   123.36  3.000
 QRX  H29   C29  C30   121.27  3.000
 QRX  H29   C29  C28   120.27  3.000
 QRX  C30   C29  C28   118.46  3.000
 QRX  H30   C30  C31   119.67  3.000
 QRX  H30   C30  C29   119.58  3.000
 QRX  C31   C30  C29   120.74  3.000
 QRX  H31   C31  C32   120.39  3.000
 QRX  H31   C31  C30   121.40  3.000
 QRX  C32   C31  C30   118.21  3.000
 QRX  F33   C32  C31   118.75  3.000
 QRX  F33   C32  C27   117.60  3.000
 QRX  C31   C32  C27   123.65  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
 QRX  CONST_01  N4    C3   C2   C1      0.00   0.0  0
 QRX  CONST_02  N4    C5   N6   C1      0.00   0.0  0
 QRX  CONST_03  N9    N8   C7   C1    180.00   0.0  0
 QRX  CONST_04  C10   N11  C7   C1    180.00   0.0  0
 QRX  CONST_05  C5    N6   C1   C2      0.00   0.0  0
 QRX  CONST_06  N8    C7   C1   C2      0.00   0.0  0
 QRX  CONST_07  N11   C7   C1   C2    180.00   0.0  0
 QRX  CONST_08  C5    N4   C3   C2      0.00   0.0  0
 QRX  CONST_09  N6    C1   C2   C3      0.00   0.0  0
 QRX  CONST_10  C7    C1   C2   C3    180.00   0.0  0
 QRX  CONST_11  N6    C5   N4   C3      0.00   0.0  0
 QRX  CONST_12  C7    C1   N6   C5    180.00   0.0  0
 QRX  CONST_13  N8    C7   C1   N6    180.00   0.0  0
 QRX  CONST_14  N11   C7   C1   N6      0.00   0.0  0
 QRX  CONST_15  C10   N9   N8   C7      0.00   0.0  0
 QRX  CONST_16  N9    C10  N11  C7      0.00   0.0  0
 QRX  CONST_17  C10   N11  C7   N8      0.00   0.0  0
 QRX  CONST_18  N11   C10  N9   N8      0.00   0.0  0
 QRX  CONST_19  N11   C7   N8   N9      0.00   0.0  0
 QRX  CONST_20  C20   C19  C18  C17     0.00   0.0  0
 QRX  CONST_21  C20   C21  C22  C17     0.00   0.0  0
 QRX  CONST_22  C21   C22  C17  C18     0.00   0.0  0
 QRX  CONST_23  C21   C20  C19  C18     0.00   0.0  0
 QRX  CONST_24  C22   C17  C18  C19     0.00   0.0  0
 QRX  CONST_25  C22   C21  C20  C19     0.00   0.0  0
 QRX  CONST_26  C30   C29  C28  C27     0.00   0.0  0
 QRX  CONST_27  C30   C31  C32  C27     0.00   0.0  0
 QRX  CONST_28  C31   C32  C27  C28     0.00   0.0  0
 QRX  CONST_29  C31   C30  C29  C28     0.00   0.0  0
 QRX  CONST_30  C32   C27  C28  C29     0.00   0.0  0
 QRX  CONST_31  C32   C31  C30  C29     0.00   0.0  0
 QRX  CONST_32  C12   N11  C7   C1      0.00   0.0  0
 QRX  CONST_33  C15   C10  N11  C7    180.00   0.0  0
 QRX  CONST_34  C12   N11  C7   N8    180.00   0.0  0
 QRX  CONST_35  C15   C10  N9   N8    180.00   0.0  0
 QRX  CONST_36  C12   N11  C10  N9    180.00   0.0  0
 QRX  CONST_37  C19   C18  C17  N16   180.00   0.0  0
 QRX  CONST_38  C21   C22  C17  N16   180.00   0.0  0
 QRX  CONST_39  C23   C19  C18  C17   180.00   0.0  0
 QRX  CONST_40  C23   C19  C20  C21   180.00   0.0  0
 QRX  CONST_41  C29   C28  C27  C26   180.00   0.0  0
 QRX  CONST_42  C31   C32  C27  C26   180.00   0.0  0
 QRX  CONST_43  F33   C32  C27  C28   180.00   0.0  0
 QRX  CONST_44  F34   C28  C29  C30   180.00   0.0  0
 QRX  CONST_45  F33   C32  C31  C30   180.00   0.0  0
 QRX  CONST_46  F34   C28  C27  C32   180.00   0.0  0
 QRX  CONST_47  H3    C3   C2   C1    180.00   0.0  0
 QRX  CONST_48  H5    C5   N6   C1    180.00   0.0  0
 QRX  CONST_49  H2    C2   C3   N4    180.00   0.0  0
 QRX  CONST_50  H21   C21  C22  C17   180.00   0.0  0
 QRX  CONST_51  H22   C22  C17  C18   180.00   0.0  0
 QRX  CONST_52  H20   C20  C19  C18   180.00   0.0  0
 QRX  CONST_53  H18   C18  C19  C20   180.00   0.0  0
 QRX  CONST_54  H29   C29  C28  C27   180.00   0.0  0
 QRX  CONST_55  H31   C31  C32  C27   180.00   0.0  0
 QRX  CONST_56  H30   C30  C29  C28   180.00   0.0  0
 QRX  CONST_60  C26   N24  C23  C19   180.00   0.0  0
 QRX  CONST_61  HN24  N24  C23  C19     0.00   0.0  0
 QRX  CONST_62  C26   N24  C23  O25     0.00   0.0  0
 QRX  Var_01    C13   C12  N11  C7     82.11  30.0  2
 QRX  Var_02    N16   C15  C10  N9    111.07  30.0  2
 QRX  Var_03    C17   N16  C15  C10   179.91  30.0  3
 QRX  Var_04    N24   C23  C19  C18  -149.17  30.0  2
 QRX  Var_05    C28   C27  C26  N24   110.54  30.0  2
 QRX  Var_06    C14   C13  C12  N11  -179.44  30.0  3
 QRX  Var_07    C27   C26  N24  C23   123.94  30.0  3
 QRX  Var_08    H14   C14  C13  C12    60.42  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
 QRX  plan-1  C1    0.020
 QRX  plan-1  C7    0.020
 QRX  plan-1  N8    0.020
 QRX  plan-1  N9    0.020
 QRX  plan-1  C10   0.020
 QRX  plan-1  N11   0.020
 QRX  plan-1  C12   0.020
 QRX  plan-1  C15   0.020
 QRX  plan-2  C1    0.020
 QRX  plan-2  C2    0.020
 QRX  plan-2  C3    0.020
 QRX  plan-2  N4    0.020
 QRX  plan-2  C5    0.020
 QRX  plan-2  N6    0.020
 QRX  plan-2  C7    0.020
 QRX  plan-2  H2    0.020
 QRX  plan-2  H3    0.020
 QRX  plan-2  H5    0.020
 QRX  plan-3  N16   0.020
 QRX  plan-3  C17   0.020
 QRX  plan-3  C18   0.020
 QRX  plan-3  C19   0.020
 QRX  plan-3  C20   0.020
 QRX  plan-3  C21   0.020
 QRX  plan-3  C22   0.020
 QRX  plan-3  C23   0.020
 QRX  plan-3  H18   0.020
 QRX  plan-3  H20   0.020
 QRX  plan-3  H21   0.020
 QRX  plan-3  H22   0.020
 QRX  plan-4  C26   0.020
 QRX  plan-4  C27   0.020
 QRX  plan-4  C28   0.020
 QRX  plan-4  C29   0.020
 QRX  plan-4  C30   0.020
 QRX  plan-4  C31   0.020
 QRX  plan-4  C32   0.020
 QRX  plan-4  F33   0.020
 QRX  plan-4  F34   0.020
 QRX  plan-4  H29   0.020
 QRX  plan-4  H30   0.020
 QRX  plan-4  H31   0.020
 QRX  plan-5  C19   0.020
 QRX  plan-5  C23   0.020
 QRX  plan-5  N24   0.020
 QRX  plan-5  O25   0.020
 QRX  plan-5  C26   0.020
 QRX  plan-5  HN24  0.020
 QRX  plan-6  C15   0.020
 QRX  plan-6  N16   0.020
 QRX  plan-6  C17   0.020
 QRX  plan-6  HN16  0.020

