# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Apr 27 18:37:16 2020
#   Inital geometry file: a 145 line input string
#   Ligand name: (2R,4R)-1-[(3-chloro-2-fluorophenyl)methyl]-4-({3-fluoro-6-[(5-methyl-1H-pyrazol-3-yl)amino]pyridin-2-yl}methyl)-2-methylpiperidine-4-carboxylic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[C@@H]1C[C@](CCN1Cc2cccc(Cl)c2F)(Cc3nc(Nc4cc(C)[nH]n4)ccc3F)C(O)=O
#
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
 EG7  EG7  '(2R,4R)-1-[(3-chloro-2-fluorophenyl)methyl]-4-({3-fluoro-6-[(5-methyl-1H-pyrazol-3-yl)amino]pyridin-2-yl}methyl)-2-methylpiperidine-4-carboxylic acid'  ligand  59  34  .  2022-07-24  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_EG7
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
 EG7  C7   C   CR6    0  -0.102  -3.0722  -0.3766   0.7274
 EG7  C6   C   CR15   0  -0.574   1.1180  -4.1824  -0.4258
 EG7  C1   C   CR16   0  -0.270  -3.8335  -2.4561  -0.2570
 EG7  C5   C   CR16   0  -0.392   4.9350  -1.3160  -0.8988
 EG7  C4   C   CR16   0  -0.223  -4.7693  -1.7777  -1.0212
 EG7  C3   C   CR16   0  -0.304   5.3785  -0.0108  -0.8884
 EG7  C2   C   CR16   0  -0.264  -2.9971  -1.7589   0.6036
 EG7  C8   C   CR6    0   0.438   4.5943   0.9515  -0.2778
 EG7  C9   C   CR6    0   0.621  -4.0176   0.2820  -0.0444
 EG7  C10  C   CR6    0  -0.230  -4.8590  -0.3988  -0.9085
 EG7  C11  C   CR6    0   0.090   3.3901   0.6106   0.3085
 EG7  C12  C   CR5    0   0.413   0.0972  -4.3787   0.4781
 EG7  C13  C   CR6    0   0.464   3.7094  -1.5979  -0.2761
 EG7  C14  C   CR5    0   0.482   2.0212  -3.3252   0.2367
 EG7  C15  C   C      0   0.456   2.1675   3.1694  -0.9701
 EG7  C16  C   CH2    0  -0.406   0.6123   1.1807  -0.7436
 EG7  C17  C   CH2    0  -0.398   0.4236   3.0311   0.8637
 EG7  C18  C   CH2    0  -0.295  -0.2910   0.3672   0.1616
 EG7  C19  C   CH1    0  -0.058  -0.5176   2.1861   1.7267
 EG7  C20  C   CT     0  -0.220   1.4164   2.2334   0.0131
 EG7  C22  C   CH3    0  -0.686  -1.4752   3.1261   2.4544
 EG7  C23  C   CH2    0  -0.333  -2.1604   0.3976   1.6415
 EG7  C24  C   CH2    0  -0.496   2.4780   1.6059   0.9583
 EG7  N25  N   N      0  -0.427   2.9874  -0.6600   0.3075
 EG7  N26  N   N      0  -0.291   1.5979  -3.0188   1.4464
 EG7  N27  N   NR15   0  -0.491   0.4293  -3.6530   1.5601
 EG7  N28  N   NT     0  -0.412  -1.2238   1.2137   0.8941
 EG7  N29  N   NH1    0  -0.774   3.2431  -2.8944  -0.2654
 EG7  F33  F   F      0  -0.287  -4.1429   1.6069   0.0543
 EG7  CL1  CL  CL     0  -0.099  -6.0137   0.4891  -1.8325
 EG7  H40  H   HCR5   0   0.261   1.2017  -4.5910  -1.4197
 EG7  H35  H   HCR6   0   0.265  -3.7569  -3.5317  -0.3414
 EG7  H39  H   HCR6   0   0.273   5.5205  -2.0959  -1.3681
 EG7  H38  H   HCR6   0   0.287  -5.4248  -2.3083  -1.6979
 EG7  H37  H   HCR6   0   0.283   6.3221   0.2582  -1.3461
 EG7  H36  H   HCR6   0   0.248  -2.2569  -2.2916   1.1874
 EG7  H41  H   HCH2   0   0.227   1.2627   0.5060  -1.2980
 EG7  H42  H   HCH2   0   0.207  -0.0149   1.6883  -1.4835
 EG7  H44  H   HCH2   0   0.211  -0.1990   3.6444   0.2022
 EG7  H43  H   HCH2   0   0.218   0.9574   3.7235   1.5179
 EG7  H45  H   HCH2   0   0.228  -0.8627  -0.3249  -0.4610
 EG7  H46  H   HCH2   0   0.213   0.3088  -0.2620   0.8392
 EG7  H47  H   HCH1   0   0.185   0.0784   1.6639   2.4987
 EG7  H49  H   HCH3   0   0.265  -0.9658  -6.2062   0.8103
 EG7  H48  H   HCH3   0   0.248  -1.9559  -4.7639   0.9665
 EG7  H50  H   HCH3   0   0.260  -1.4571  -5.3220  -0.6292
 EG7  H51  H   HCH3   0   0.222  -2.1991   3.5524   1.7568
 EG7  H52  H   HCH3   0   0.230  -2.0246   2.6443   3.2630
 EG7  H53  H   HCH3   0   0.232  -0.9124   3.9467   2.9007
 EG7  H55  H   HCH2   0   0.260  -2.7739   1.0335   2.2794
 EG7  H54  H   HCH2   0   0.215  -1.6487  -0.3143   2.3120
 EG7  H57  H   HCH2   0   0.247   1.9792   1.0811   1.7744
 EG7  H56  H   HCH2   0   0.243   3.0500   2.4194   1.4100
 EG7  H58  H   HNR5   0   0.412  -0.0923  -3.5714   2.4180
 EG7  H59  H   HNH1   0   0.401   3.6814  -3.5205  -0.9204
 EG7  O30  O   O      0  -0.613   2.4081   4.3293  -0.5754
 EG7  O31  O   OC    -1  -0.604   2.4938   2.6903  -2.0739
 EG7  F32  F   F      0  -0.317   5.0291   2.2254  -0.2438
 EG7  C21  C   CH3    0  -0.739  -1.1346  -5.2079   0.4037

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
 EG7  N27  N26  aromatic  1.334  0.020  1.334
 EG7  N27  C12  aromatic  1.344  0.020  1.344
 EG7  N26  C14  aromatic  1.318  0.020  1.318
 EG7  C21  C12  single    1.487  0.020  1.487
 EG7  CL1  C10  single    1.725  0.020  1.725
 EG7  C12  C6   aromatic  1.378  0.020  1.378
 EG7  C14  C6   aromatic  1.410  0.020  1.410
 EG7  C14  N29  single    1.390  0.020  1.390
 EG7  C10  C4   aromatic  1.386  0.020  1.386
 EG7  C10  C9   aromatic  1.385  0.020  1.385
 EG7  C4   C1   aromatic  1.386  0.020  1.386
 EG7  N29  C13  single    1.378  0.020  1.378
 EG7  F33  C9   single    1.335  0.020  1.335
 EG7  C9   C7   aromatic  1.387  0.020  1.387
 EG7  C1   C2   aromatic  1.388  0.020  1.388
 EG7  C13  C5   aromatic  1.403  0.020  1.403
 EG7  C13  N25  aromatic  1.320  0.020  1.320
 EG7  C5   C3   aromatic  1.378  0.020  1.378
 EG7  C7   C2   aromatic  1.390  0.020  1.390
 EG7  C7   C23  single    1.505  0.020  1.505
 EG7  N25  C11  aromatic  1.333  0.020  1.333
 EG7  C18  C16  single    1.516  0.020  1.516
 EG7  C18  N28  single    1.457  0.020  1.457
 EG7  C23  N28  single    1.450  0.020  1.450
 EG7  C3   C8   aromatic  1.383  0.020  1.383
 EG7  C11  C8   aromatic  1.382  0.020  1.382
 EG7  C11  C24  single    1.498  0.020  1.498
 EG7  C16  C20  single    1.526  0.020  1.526
 EG7  N28  C19  single    1.462  0.020  1.462
 EG7  C8   F32  single    1.346  0.020  1.346
 EG7  C24  C20  single    1.554  0.020  1.554
 EG7  C20  C17  single    1.532  0.020  1.532
 EG7  C20  C15  single    1.551  0.020  1.551
 EG7  C19  C17  single    1.531  0.020  1.531
 EG7  C19  C22  single    1.527  0.020  1.527
 EG7  O31  C15  deloc     1.247  0.020  1.247
 EG7  C15  O30  deloc     1.249  0.020  1.249
 EG7  C6   H40  single    0.930  0.020  1.080
 EG7  C1   H35  single    0.930  0.020  1.080
 EG7  C5   H39  single    0.930  0.020  1.080
 EG7  C4   H38  single    0.930  0.020  1.080
 EG7  C3   H37  single    0.930  0.020  1.080
 EG7  C2   H36  single    0.930  0.020  1.080
 EG7  C16  H41  single    0.970  0.020  1.090
 EG7  C16  H42  single    0.970  0.020  1.090
 EG7  C17  H44  single    0.970  0.020  1.090
 EG7  C17  H43  single    0.970  0.020  1.090
 EG7  C18  H45  single    0.970  0.020  1.090
 EG7  C18  H46  single    0.970  0.020  1.090
 EG7  C19  H47  single    0.970  0.020  1.090
 EG7  C21  H49  single    0.970  0.020  1.090
 EG7  C21  H48  single    0.970  0.020  1.090
 EG7  C21  H50  single    0.970  0.020  1.090
 EG7  C22  H51  single    0.970  0.020  1.090
 EG7  C22  H52  single    0.970  0.020  1.090
 EG7  C22  H53  single    0.970  0.020  1.090
 EG7  C23  H55  single    0.970  0.020  1.090
 EG7  C23  H54  single    0.970  0.020  1.090
 EG7  C24  H57  single    0.970  0.020  1.090
 EG7  C24  H56  single    0.970  0.020  1.090
 EG7  N27  H58  single    0.860  0.020  1.020
 EG7  N29  H59  single    0.890  0.020  1.040

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
 EG7  C23  C7   C9   120.44  3.000
 EG7  C23  C7   C2   122.19  3.000
 EG7  C9   C7   C2   117.36  3.000
 EG7  H40  C6   C14  127.86  3.000
 EG7  H40  C6   C12  127.48  3.000
 EG7  C14  C6   C12  104.65  3.000
 EG7  H35  C1   C2   120.35  3.000
 EG7  H35  C1   C4   119.45  3.000
 EG7  C2   C1   C4   120.20  3.000
 EG7  H39  C5   C13  121.34  3.000
 EG7  H39  C5   C3   120.77  3.000
 EG7  C13  C5   C3   117.89  3.000
 EG7  H38  C4   C10  119.98  3.000
 EG7  H38  C4   C1   120.95  3.000
 EG7  C10  C4   C1   119.07  3.000
 EG7  H37  C3   C8   120.52  3.000
 EG7  H37  C3   C5   120.82  3.000
 EG7  C8   C3   C5   118.66  3.000
 EG7  H36  C2   C1   119.94  3.000
 EG7  H36  C2   C7   118.57  3.000
 EG7  C1   C2   C7   121.49  3.000
 EG7  F32  C8   C11  120.27  3.000
 EG7  F32  C8   C3   119.10  3.000
 EG7  C11  C8   C3   120.63  3.000
 EG7  F33  C9   C10  118.50  3.000
 EG7  F33  C9   C7   119.62  3.000
 EG7  C10  C9   C7   121.87  3.000
 EG7  CL1  C10  C9   119.20  3.000
 EG7  C9   C10  C4   120.02  3.000
 EG7  CL1  C10  C4   120.78  3.000
 EG7  N25  C11  C24  116.72  3.000
 EG7  C24  C11  C8   123.40  3.000
 EG7  N25  C11  C8   119.88  3.000
 EG7  N27  C12  C21  123.09  3.000
 EG7  C21  C12  C6   131.34  3.000
 EG7  N27  C12  C6   105.55  3.000
 EG7  N29  C13  N25  118.70  3.000
 EG7  N25  C13  C5   122.09  3.000
 EG7  N29  C13  C5   119.21  3.000
 EG7  N29  C14  N26  122.83  3.000
 EG7  N29  C14  C6   125.58  3.000
 EG7  N26  C14  C6   111.52  3.000
 EG7  O31  C15  O30  125.90  3.000
 EG7  O30  C15  C20  116.96  3.000
 EG7  O31  C15  C20  117.13  3.000
 EG7  H42  C16  H41  106.59  3.000
 EG7  H42  C16  C20  108.49  3.000
 EG7  H41  C16  C20  111.42  3.000
 EG7  H42  C16  C18  108.13  3.000
 EG7  H41  C16  C18  109.12  3.000
 EG7  C20  C16  C18  112.84  3.000
 EG7  H43  C17  H44  106.52  3.000
 EG7  H43  C17  C20  110.25  3.000
 EG7  H44  C17  C20  108.93  3.000
 EG7  H43  C17  C19  108.22  3.000
 EG7  H44  C17  C19  107.45  3.000
 EG7  C20  C17  C19  115.09  3.000
 EG7  H46  C18  H45  105.87  3.000
 EG7  H46  C18  N28  111.78  3.000
 EG7  H45  C18  N28  108.63  3.000
 EG7  H46  C18  C16  110.44  3.000
 EG7  H45  C18  C16  108.15  3.000
 EG7  N28  C18  C16  111.72  3.000
 EG7  H47  C19  N28  110.10  3.000
 EG7  H47  C19  C22  107.22  3.000
 EG7  N28  C19  C22  112.21  3.000
 EG7  H47  C19  C17  108.82  3.000
 EG7  C22  C19  C17  108.33  3.000
 EG7  N28  C19  C17  110.06  3.000
 EG7  C24  C20  C17  108.39  3.000
 EG7  C17  C20  C16  107.05  3.000
 EG7  C24  C20  C16  112.53  3.000
 EG7  C17  C20  C15  110.58  3.000
 EG7  C24  C20  C15  107.36  3.000
 EG7  C16  C20  C15  110.92  3.000
 EG7  H53  C22  H52  106.81  3.000
 EG7  H53  C22  H51  108.05  3.000
 EG7  H52  C22  H51  108.21  3.000
 EG7  H53  C22  C19  109.55  3.000
 EG7  H52  C22  C19  113.43  3.000
 EG7  H51  C22  C19  110.60  3.000
 EG7  H54  C23  H55  106.37  3.000
 EG7  H54  C23  N28  112.13  3.000
 EG7  H55  C23  N28  109.69  3.000
 EG7  H54  C23  C7   108.54  3.000
 EG7  H55  C23  C7   108.33  3.000
 EG7  N28  C23  C7   111.57  3.000
 EG7  H56  C24  H57  106.76  3.000
 EG7  H56  C24  C20  107.97  3.000
 EG7  H57  C24  C20  109.69  3.000
 EG7  H56  C24  C11  110.81  3.000
 EG7  H57  C24  C11  106.45  3.000
 EG7  C20  C24  C11  114.86  3.000
 EG7  C13  N25  C11  120.83  3.000
 EG7  N27  N26  C14  104.42  3.000
 EG7  H58  N27  N26  119.18  3.000
 EG7  H58  N27  C12  126.95  3.000
 EG7  N26  N27  C12  113.85  3.000
 EG7  C23  N28  C19  113.13  3.000
 EG7  C19  N28  C18  111.31  3.000
 EG7  C23  N28  C18  110.23  3.000
 EG7  H59  N29  C14  115.16  3.000
 EG7  H59  N29  C13  115.66  3.000
 EG7  C14  N29  C13  126.31  3.000
 EG7  H50  C21  H48  108.03  3.000
 EG7  H50  C21  H49  107.68  3.000
 EG7  H48  C21  H49  107.26  3.000
 EG7  H50  C21  C12  110.58  3.000
 EG7  H48  C21  C12  111.79  3.000
 EG7  H49  C21  C12  111.31  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
 EG7  CONST_01  C4   C10  C9   C7      0.00   0.0  0
 EG7  CONST_02  C4   C1   C2   C7      0.00   0.0  0
 EG7  CONST_03  N26  N27  C12  C6      0.00   0.0  0
 EG7  CONST_04  N27  N26  C14  C6      0.00   0.0  0
 EG7  CONST_05  C9   C10  C4   C1      0.00   0.0  0
 EG7  CONST_06  C9   C7   C2   C1      0.00   0.0  0
 EG7  CONST_07  C11  N25  C13  C5      0.00   0.0  0
 EG7  CONST_08  C11  C8   C3   C5      0.00   0.0  0
 EG7  CONST_09  N25  C13  C5   C3      0.00   0.0  0
 EG7  CONST_10  N25  C11  C8   C3      0.00   0.0  0
 EG7  CONST_11  C10  C4   C1   C2      0.00   0.0  0
 EG7  CONST_12  C10  C9   C7   C2      0.00   0.0  0
 EG7  CONST_13  C13  C5   C3   C8      0.00   0.0  0
 EG7  CONST_14  C13  N25  C11  C8      0.00   0.0  0
 EG7  CONST_15  C14  N26  N27  C12     0.00   0.0  0
 EG7  CONST_16  N26  C14  C6   C12     0.00   0.0  0
 EG7  CONST_17  N27  C12  C6   C14     0.00   0.0  0
 EG7  CONST_18  CL1  C10  C9   C7    180.00   0.0  0
 EG7  CONST_19  CL1  C10  C4   C1    180.00   0.0  0
 EG7  CONST_20  C23  C7   C2   C1    180.00   0.0  0
 EG7  CONST_21  F32  C8   C3   C5    180.00   0.0  0
 EG7  CONST_22  F33  C9   C10  C4    180.00   0.0  0
 EG7  CONST_23  N29  C13  C5   C3    180.00   0.0  0
 EG7  CONST_24  C24  C11  C8   C3    180.00   0.0  0
 EG7  CONST_25  F33  C9   C7   C2    180.00   0.0  0
 EG7  CONST_26  C23  C7   C9   C10   180.00   0.0  0
 EG7  CONST_27  N29  C13  N25  C11   180.00   0.0  0
 EG7  CONST_28  N29  C14  C6   C12   180.00   0.0  0
 EG7  CONST_29  C24  C11  N25  C13   180.00   0.0  0
 EG7  CONST_30  C21  C12  C6   C14   180.00   0.0  0
 EG7  CONST_31  N26  N27  C12  C21   180.00   0.0  0
 EG7  CONST_32  F32  C8   C11  N25   180.00   0.0  0
 EG7  CONST_33  N29  C14  N26  N27   180.00   0.0  0
 EG7  CONST_34  H35  C1   C2   C7    180.00   0.0  0
 EG7  CONST_35  H58  N27  C12  C6    180.00   0.0  0
 EG7  CONST_36  H36  C2   C1   C4    180.00   0.0  0
 EG7  CONST_37  H38  C4   C1   C2    180.00   0.0  0
 EG7  CONST_38  H39  C5   C3   C8    180.00   0.0  0
 EG7  CONST_39  H37  C3   C8   C11   180.00   0.0  0
 EG7  CONST_40  H40  C6   C14  N26   180.00   0.0  0
 EG7  Var_01    C19  N28  C18  C16   -59.51  30.0  1
 EG7  Var_02    N28  C18  C16  C20    57.79  30.0  1
 EG7  Var_03    C18  N28  C23  C7    -66.83  30.0  3
 EG7  Var_04    C13  N29  C14  C6    132.22  30.0  2
 EG7  Var_05    C14  N29  C13  C5   -176.00  30.0  3
 EG7  Var_06    N28  C23  C7   C2    111.09  30.0  2
 EG7  Var_07    C20  C24  C11  C8     90.46  30.0  2
 EG7  Var_08    H49  C21  C12  C6     91.65  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
 EG7  chir_01  C19  N28  C17  C22  negativ
 EG7  chir_02  C20  C17  C24  C16  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
 EG7  plan-1  C6   0.020
 EG7  plan-1  C12  0.020
 EG7  plan-1  C14  0.020
 EG7  plan-1  N26  0.020
 EG7  plan-1  N27  0.020
 EG7  plan-1  N29  0.020
 EG7  plan-1  H40  0.020
 EG7  plan-1  H58  0.020
 EG7  plan-1  C21  0.020
 EG7  plan-2  C7   0.020
 EG7  plan-2  C1   0.020
 EG7  plan-2  C4   0.020
 EG7  plan-2  C2   0.020
 EG7  plan-2  C9   0.020
 EG7  plan-2  C10  0.020
 EG7  plan-2  C23  0.020
 EG7  plan-2  F33  0.020
 EG7  plan-2  CL1  0.020
 EG7  plan-2  H35  0.020
 EG7  plan-2  H38  0.020
 EG7  plan-2  H36  0.020
 EG7  plan-3  C5   0.020
 EG7  plan-3  C3   0.020
 EG7  plan-3  C8   0.020
 EG7  plan-3  C11  0.020
 EG7  plan-3  C13  0.020
 EG7  plan-3  C24  0.020
 EG7  plan-3  N25  0.020
 EG7  plan-3  N29  0.020
 EG7  plan-3  H39  0.020
 EG7  plan-3  H37  0.020
 EG7  plan-3  F32  0.020
 EG7  plan-4  C15  0.020
 EG7  plan-4  C20  0.020
 EG7  plan-4  O30  0.020
 EG7  plan-4  O31  0.020

