# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Apr 17 03:50:54 2020
#   Inital geometry file: a 126 line input string
#   Ligand name: 4-[4-({[4-chloro-3-(trifluoromethyl)phenyl]carbamoyl}amino)phenoxy]-N-methylpyridine-2-carboxamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CNC(=O)c1cc(Oc2ccc(NC(=O)Nc3ccc(Cl)c(c3)C(F)(F)F)cc2)ccn1
#
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
 BAX  BAX  4-[4-({[4-chloro-3-(trifluoromethyl)phenyl]carbamoyl}amino)phenoxy]-N-methylpyridine-2-carboxamide  ligand  48  32  .  2021-08-06  2021-08-06  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_BAX
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
 BAX  C1    C   CR16  0  -0.417  -1.4144  -0.4048  -4.8417
 BAX  C2    C   CR6   0   0.431  -0.7035  -0.2153  -3.6556
 BAX  C3    C   CR16  0  -0.308   0.6468   0.1218  -3.7315
 BAX  C4    C   CR16  0  -0.189   1.2522   0.2692  -4.9681
 BAX  C13   C   C     0   0.728  -1.0605   0.0357  -1.2203
 BAX  C16   C   CR6   0   0.373  -1.8546  -0.1088   1.1057
 BAX  C17   C   CR16  0  -0.335  -2.2955  -1.0836   2.0000
 BAX  C18   C   CR16  0  -0.290  -2.2890  -0.8514   3.3650
 BAX  C19   C   CR6   0   0.280  -1.8355   0.3654   3.8433
 BAX  C20   C   CR16  0  -0.292  -1.3982   1.3468   2.9700
 BAX  C21   C   CR16  0  -0.295  -1.4134   1.1178   1.6028
 BAX  O22   O   O2    0  -0.499  -1.8684   0.6133   5.1997
 BAX  C24   C   CR16  0  -0.389  -0.8449   0.6924   7.2949
 BAX  C25   C   CR16  0  -0.059   0.2835   0.5116   8.0723
 BAX  C27   C   CR6   0   0.123   1.5255  -0.1392   6.2877
 BAX  C28   C   CR16  0  -0.398   0.4615   0.0019   5.4103
 BAX  N30   N   NH1   0  -0.633   3.8218  -0.7004   6.6524
 BAX  C31   C   CH3   0  -0.515   5.1585  -1.1243   6.3172
 BAX  C5    C   CR6   0  -0.091   0.5405   0.0785  -6.1384
 BAX  C6    C   CR6   0  -0.113  -0.8076  -0.2674  -6.0787
 BAX  C7    C   CT    0   1.075  -1.6060  -0.4957  -7.3295
 BAX  F8    F   F     0  -0.309  -1.6105   0.5813  -8.1224
 BAX  F9    F   F     0  -0.310  -1.1158  -1.5132  -8.0474
 BAX  F10   F   F     0  -0.298  -2.8818  -0.7868  -7.0659
 BAX  CL11  CL  CL    0  -0.110   1.3649   0.2669  -7.6472
 BAX  N12   N   NH1   0  -0.795  -1.3954  -0.4248  -2.4684
 BAX  N14   N   NH1   0  -0.786  -1.9347  -0.3961  -0.2601
 BAX  O15   O   O     0  -0.487  -0.1014   0.7485  -0.9954
 BAX  C23   C   CR6   0   0.473  -0.7538   0.4302   5.9314
 BAX  N26   N   N     0  -0.452   1.4508   0.1052   7.5896
 BAX  O32   O   O     0  -0.488   3.0028  -0.8376   4.5524
 BAX  H1    H   HCR6  0   0.293  -2.4635  -0.6624  -4.7810
 BAX  H3    H   HCR6  0   0.294   1.2419   0.2626  -2.8445
 BAX  H4    H   HCR6  0   0.292   2.3013   0.5267  -5.0136
 BAX  H17   H   HCR6  0   0.279  -2.6466  -2.0377   1.6267
 BAX  H18   H   HCR6  0   0.280  -2.6367  -1.6160   4.0475
 BAX  H20   H   HCR6  0   0.282  -1.0573   2.3020   3.3488
 BAX  H21   H   HCR6  0   0.278  -1.0950   1.9064   0.9386
 BAX  H24   H   HCR6  0   0.290  -1.7727   1.0282   7.7378
 BAX  H25   H   HCR6  0   0.276   0.2386   0.7066   9.1372
 BAX  H28   H   HCR6  0   0.294   0.5971  -0.2163   4.3606
 BAX  H30   H   HNH1  0   0.408   3.5883  -0.4913   7.6104
 BAX  H311  H   HCH3  0   0.253   5.7736  -1.0625   7.2098
 BAX  H312  H   HCH3  0   0.240   5.1779  -2.1535   5.9560
 BAX  H313  H   HCH3  0   0.241   5.5984  -0.4861   5.5508
 BAX  H12   H   HNH1  0   0.420  -2.2967  -0.8665  -2.5714
 BAX  H14   H   HNH1  0   0.416  -2.5574  -1.1524  -0.5024
 BAX  C29   C   C     0   0.539   2.8539  -0.5942   5.7432

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
 BAX  C1   C2    aromatic  1.396  0.020  1.396
 BAX  C1   C6    aromatic  1.385  0.020  1.385
 BAX  C1   H1    single    0.930  0.020  1.080
 BAX  C2   C3    aromatic  1.394  0.020  1.394
 BAX  C2   N12   single    1.390  0.020  1.390
 BAX  C3   C4    aromatic  1.385  0.020  1.385
 BAX  C3   H3    single    0.930  0.020  1.080
 BAX  C4   C5    aromatic  1.383  0.020  1.383
 BAX  C4   H4    single    0.930  0.020  1.080
 BAX  C13  N12   single    1.372  0.020  1.372
 BAX  C13  N14   single    1.368  0.020  1.368
 BAX  C13  O15   double    1.216  0.020  1.216
 BAX  C16  C17   aromatic  1.394  0.020  1.394
 BAX  C16  C21   aromatic  1.395  0.020  1.395
 BAX  C16  N14   single    1.398  0.020  1.398
 BAX  C17  C18   aromatic  1.385  0.020  1.385
 BAX  C17  H17   single    0.930  0.020  1.080
 BAX  C18  C19   aromatic  1.384  0.020  1.384
 BAX  C18  H18   single    0.930  0.020  1.080
 BAX  C19  C20   aromatic  1.385  0.020  1.385
 BAX  C19  O22   single    1.379  0.020  1.379
 BAX  C20  C21   aromatic  1.386  0.020  1.386
 BAX  C20  H20   single    0.930  0.020  1.080
 BAX  C21  H21   single    0.930  0.020  1.080
 BAX  O22  C23   single    1.346  0.020  1.346
 BAX  C24  C25   aromatic  1.382  0.020  1.382
 BAX  C24  C23   aromatic  1.391  0.020  1.391
 BAX  C24  H24   single    0.930  0.020  1.080
 BAX  C25  N26   aromatic  1.327  0.020  1.327
 BAX  C25  H25   single    0.930  0.020  1.080
 BAX  C27  C28   aromatic  1.386  0.020  1.386
 BAX  C27  N26   aromatic  1.327  0.020  1.327
 BAX  C27  C29   single    1.506  0.020  1.506
 BAX  C28  C23   aromatic  1.390  0.020  1.390
 BAX  C28  H28   single    0.930  0.020  1.080
 BAX  N30  C31   single    1.442  0.020  1.442
 BAX  N30  C29   single    1.332  0.020  1.332
 BAX  N30  H30   single    0.860  0.020  1.020
 BAX  C31  H311  single    0.970  0.020  1.090
 BAX  C31  H312  single    0.970  0.020  1.090
 BAX  C31  H313  single    0.970  0.020  1.090
 BAX  C5   C6    aromatic  1.393  0.020  1.393
 BAX  C5   CL11  single    1.730  0.020  1.730
 BAX  C6   C7    single    1.501  0.020  1.501
 BAX  C7   F8    single    1.337  0.020  1.337
 BAX  C7   F9    single    1.338  0.020  1.338
 BAX  C7   F10   single    1.335  0.020  1.335
 BAX  N12  H12   single    0.860  0.020  1.020
 BAX  N14  H14   single    0.860  0.020  1.020
 BAX  C29  O32   double    1.225  0.020  1.225

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
 BAX  H1    C1   C6    119.91  3.000
 BAX  H1    C1   C2    118.59  3.000
 BAX  C6    C1   C2    121.50  3.000
 BAX  N12   C2   C3    124.42  3.000
 BAX  N12   C2   C1    116.86  3.000
 BAX  C3    C2   C1    118.68  3.000
 BAX  H3    C3   C4    118.68  3.000
 BAX  H3    C3   C2    121.45  3.000
 BAX  C4    C3   C2    119.87  3.000
 BAX  H4    C4   C5    119.78  3.000
 BAX  H4    C4   C3    119.15  3.000
 BAX  C5    C4   C3    121.06  3.000
 BAX  O15   C13  N14   124.00  3.000
 BAX  O15   C13  N12   123.89  3.000
 BAX  N14   C13  N12   112.12  3.000
 BAX  N14   C16  C21   123.16  3.000
 BAX  N14   C16  C17   117.70  3.000
 BAX  C21   C16  C17   119.08  3.000
 BAX  H17   C17  C18   119.28  3.000
 BAX  H17   C17  C16   119.82  3.000
 BAX  C18   C17  C16   120.90  3.000
 BAX  H18   C18  C19   120.57  3.000
 BAX  H18   C18  C17   120.11  3.000
 BAX  C19   C18  C17   119.33  3.000
 BAX  O22   C19  C20   120.03  3.000
 BAX  O22   C19  C18   119.35  3.000
 BAX  C20   C19  C18   120.58  3.000
 BAX  H20   C20  C21   119.63  3.000
 BAX  H20   C20  C19   120.27  3.000
 BAX  C21   C20  C19   120.10  3.000
 BAX  H21   C21  C20   118.88  3.000
 BAX  H21   C21  C16   121.10  3.000
 BAX  C20   C21  C16   120.01  3.000
 BAX  C23   O22  C19   119.37  3.000
 BAX  H24   C24  C23   121.06  3.000
 BAX  H24   C24  C25   120.71  3.000
 BAX  C23   C24  C25   118.23  3.000
 BAX  H25   C25  N26   116.69  3.000
 BAX  H25   C25  C24   119.70  3.000
 BAX  N26   C25  C24   123.62  3.000
 BAX  C29   C27  N26   117.39  3.000
 BAX  C29   C27  C28   118.61  3.000
 BAX  N26   C27  C28   123.99  3.000
 BAX  H28   C28  C23   122.42  3.000
 BAX  H28   C28  C27   119.86  3.000
 BAX  C23   C28  C27   117.72  3.000
 BAX  H30   N30  C29   117.63  3.000
 BAX  H30   N30  C31   119.78  3.000
 BAX  C29   N30  C31   122.58  3.000
 BAX  H313  C31  H312  108.21  3.000
 BAX  H313  C31  H311  108.43  3.000
 BAX  H312  C31  H311  108.41  3.000
 BAX  H313  C31  N30   111.43  3.000
 BAX  H312  C31  N30   111.76  3.000
 BAX  H311  C31  N30   108.50  3.000
 BAX  CL11  C5   C6    121.72  3.000
 BAX  CL11  C5   C4    118.54  3.000
 BAX  C6    C5   C4    119.74  3.000
 BAX  C7    C6   C5    121.11  3.000
 BAX  C7    C6   C1    119.75  3.000
 BAX  C5    C6   C1    119.14  3.000
 BAX  F10   C7   F9    106.87  3.000
 BAX  F10   C7   F8    106.82  3.000
 BAX  F9    C7   F8    107.18  3.000
 BAX  F10   C7   C6    112.14  3.000
 BAX  F9    C7   C6    111.58  3.000
 BAX  F8    C7   C6    111.92  3.000
 BAX  H12   N12  C13   117.25  3.000
 BAX  H12   N12  C2    115.06  3.000
 BAX  C13   N12  C2    127.22  3.000
 BAX  H14   N14  C16   115.08  3.000
 BAX  H14   N14  C13   117.53  3.000
 BAX  C16   N14  C13   125.73  3.000
 BAX  C28   C23  C24   118.86  3.000
 BAX  C28   C23  O22   124.21  3.000
 BAX  C24   C23  O22   116.93  3.000
 BAX  C27   N26  C25   117.57  3.000
 BAX  O32   C29  N30   124.02  3.000
 BAX  O32   C29  C27   121.26  3.000
 BAX  N30   C29  C27   114.72  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
 BAX  CONST_01  C4    C3   C2   C1      0.00   0.0  0
 BAX  CONST_02  C4    C5   C6   C1      0.00   0.0  0
 BAX  CONST_03  C5    C6   C1   C2      0.00   0.0  0
 BAX  CONST_04  C5    C4   C3   C2      0.00   0.0  0
 BAX  CONST_05  C6    C1   C2   C3      0.00   0.0  0
 BAX  CONST_06  C6    C5   C4   C3      0.00   0.0  0
 BAX  CONST_07  C19   C18  C17  C16     0.00   0.0  0
 BAX  CONST_08  C19   C20  C21  C16     0.00   0.0  0
 BAX  CONST_09  C20   C21  C16  C17     0.00   0.0  0
 BAX  CONST_10  C20   C19  C18  C17     0.00   0.0  0
 BAX  CONST_11  C21   C16  C17  C18     0.00   0.0  0
 BAX  CONST_12  C21   C20  C19  C18     0.00   0.0  0
 BAX  CONST_13  C27   N26  C25  C24     0.00   0.0  0
 BAX  CONST_14  C27   C28  C23  C24     0.00   0.0  0
 BAX  CONST_15  C28   C23  C24  C25     0.00   0.0  0
 BAX  CONST_16  C28   C27  N26  C25     0.00   0.0  0
 BAX  CONST_17  N26   C25  C24  C23     0.00   0.0  0
 BAX  CONST_18  N26   C27  C28  C23     0.00   0.0  0
 BAX  CONST_19  CL11  C5   C6   C1    180.00   0.0  0
 BAX  CONST_20  C7    C6   C1   C2    180.00   0.0  0
 BAX  CONST_21  CL11  C5   C4   C3    180.00   0.0  0
 BAX  CONST_22  N12   C2   C3   C4    180.00   0.0  0
 BAX  CONST_23  C7    C6   C5   C4    180.00   0.0  0
 BAX  CONST_24  O22   C19  C18  C17   180.00   0.0  0
 BAX  CONST_25  N14   C16  C17  C18   180.00   0.0  0
 BAX  CONST_26  N14   C16  C21  C20   180.00   0.0  0
 BAX  CONST_27  O22   C19  C20  C21   180.00   0.0  0
 BAX  CONST_28  C25   C24  C23  O22   180.00   0.0  0
 BAX  CONST_29  C27   C28  C23  O22   180.00   0.0  0
 BAX  CONST_30  C29   C27  N26  C25   180.00   0.0  0
 BAX  CONST_31  N12   C2   C1   C6    180.00   0.0  0
 BAX  CONST_32  C29   C27  C28  C23   180.00   0.0  0
 BAX  CONST_33  H3    C3   C2   C1    180.00   0.0  0
 BAX  CONST_34  H4    C4   C3   C2    180.00   0.0  0
 BAX  CONST_35  H1    C1   C2   C3    180.00   0.0  0
 BAX  CONST_36  H18   C18  C17  C16   180.00   0.0  0
 BAX  CONST_37  H20   C20  C21  C16   180.00   0.0  0
 BAX  CONST_38  H21   C21  C16  C17   180.00   0.0  0
 BAX  CONST_39  H17   C17  C18  C19   180.00   0.0  0
 BAX  CONST_40  H28   C28  C23  C24   180.00   0.0  0
 BAX  CONST_41  H25   C25  N26  C27   180.00   0.0  0
 BAX  CONST_42  H24   C24  C23  C28   180.00   0.0  0
 BAX  CONST_47  H12   N12  C2   C1      0.00   0.0  0
 BAX  CONST_49  O15   C13  N12  C2      0.00   0.0  0
 BAX  CONST_50  O15   C13  N14  C16     0.00   0.0  0
 BAX  CONST_51  C31   N30  C29  C27   180.00   0.0  0
 BAX  CONST_52  N14   C13  N12  C2    180.00   0.0  0
 BAX  CONST_53  N12   C13  N14  C16   180.00   0.0  0
 BAX  CONST_54  H30   N30  C29  C27     0.00   0.0  0
 BAX  CONST_55  O32   C29  N30  C31     0.00   0.0  0
 BAX  Var_01    C24   C23  O22  C19  -179.86  30.0  2
 BAX  Var_02    F8    C7   C6   C1    121.67  30.0  2
 BAX  Var_03    N30   C29  C27  C28   179.85  30.0  2
 BAX  Var_04    H311  C31  N30  C29   176.06  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
 BAX  plan-1  C1    0.020
 BAX  plan-1  C2    0.020
 BAX  plan-1  C3    0.020
 BAX  plan-1  C4    0.020
 BAX  plan-1  C5    0.020
 BAX  plan-1  C6    0.020
 BAX  plan-1  C7    0.020
 BAX  plan-1  CL11  0.020
 BAX  plan-1  N12   0.020
 BAX  plan-1  H1    0.020
 BAX  plan-1  H3    0.020
 BAX  plan-1  H4    0.020
 BAX  plan-2  C16   0.020
 BAX  plan-2  C17   0.020
 BAX  plan-2  C18   0.020
 BAX  plan-2  C19   0.020
 BAX  plan-2  C20   0.020
 BAX  plan-2  C21   0.020
 BAX  plan-2  O22   0.020
 BAX  plan-2  N14   0.020
 BAX  plan-2  H17   0.020
 BAX  plan-2  H18   0.020
 BAX  plan-2  H20   0.020
 BAX  plan-2  H21   0.020
 BAX  plan-3  O22   0.020
 BAX  plan-3  C24   0.020
 BAX  plan-3  C25   0.020
 BAX  plan-3  C27   0.020
 BAX  plan-3  C28   0.020
 BAX  plan-3  C23   0.020
 BAX  plan-3  N26   0.020
 BAX  plan-3  H24   0.020
 BAX  plan-3  H25   0.020
 BAX  plan-3  H28   0.020
 BAX  plan-3  C29   0.020
 BAX  plan-4  C2    0.020
 BAX  plan-4  C13   0.020
 BAX  plan-4  C16   0.020
 BAX  plan-4  N12   0.020
 BAX  plan-4  N14   0.020
 BAX  plan-4  O15   0.020
 BAX  plan-4  H12   0.020
 BAX  plan-4  H14   0.020
 BAX  plan-5  C27   0.020
 BAX  plan-5  N30   0.020
 BAX  plan-5  C31   0.020
 BAX  plan-5  O32   0.020
 BAX  plan-5  H30   0.020
 BAX  plan-5  C29   0.020

