# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr  8 06:33:09 2020
#   Inital geometry file: a 121 line input string
#   Ligand name: 4-[(2-{[4-chloro-3-(trifluoromethyl)phenyl]amino}-1H-benzimidazol-6-yl)oxy]-N-methylpyridine-2-carboxamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CNC(=O)c1cc(Oc2ccc3nc(Nc4ccc(Cl)c(c4)C(F)(F)F)[nH]c3c2)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
 276  276  4-[(2-{[4-chloro-3-(trifluoromethyl)phenyl]amino}-1H-benzimidazol-6-yl)oxy]-N-methylpyridine-2-carboxamide  ligand  47  32  .  2021-08-04  2021-08-04  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_276
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
 276  C1    C   CR16  0  -0.401   -4.7968   0.5029  -0.9095
 276  C2    C   CR16  0  -0.061   -5.7783   1.2105  -1.5885
 276  N3    N   N     0  -0.452   -7.0622   1.1857  -1.2711
 276  C4    C   CR6   0   0.126   -7.4255   0.4333  -0.2348
 276  C5    C   CR16  0  -0.390   -6.5394  -0.3155   0.5146
 276  C6    C   CR6   0   0.475   -5.1910  -0.2806   0.1679
 276  C10   C   C     0   0.540   -8.8870   0.4083   0.1247
 276  O11   O   O     0  -0.488   -9.3013  -0.2742   1.0532
 276  N12   N   NH1   0  -0.634   -9.6611   1.1783  -0.6388
 276  C13   C   CH3   0  -0.515  -11.0877   1.2758  -0.4535
 276  O17   O   O2    0  -0.503   -4.3558  -1.0197   0.9192
 276  C18   C   CR6   0   0.276   -3.0098  -1.0431   0.6066
 276  C19   C   CR16  0  -0.361   -2.1632  -0.1849   1.2889
 276  C20   C   CR56  0   0.335   -0.8197  -0.2843   0.9702
 276  C21   C   CR56  0   0.204   -0.3251  -1.1866   0.0131
 276  C22   C   CR16  0  -0.341   -1.2043  -2.0304  -0.6551
 276  C23   C   CR16  0  -0.313   -2.5547  -1.9504  -0.3497
 276  N27   N   NR15  0  -0.748    0.2886   0.3772   1.4321
 276  C28   C   CR5   0   0.716    1.3622  -0.1320   0.7622
 276  N29   N   N     0  -0.533    1.0414  -1.0659  -0.0925
 276  N32   N   NH1   0  -0.815    2.6036   0.3491   1.0283
 276  C33   C   CR6   0   0.418    3.8119  -0.0218   0.4637
 276  C34   C   CR16  0  -0.431    4.9560   0.6292   0.9331
 276  C35   C   CR6   0  -0.112    6.2112   0.3308   0.4333
 276  C36   C   CR6   0  -0.094    6.3360  -0.6390  -0.5606
 276  C37   C   CR16  0  -0.185    5.2085  -1.2867  -1.0302
 276  C38   C   CR16  0  -0.317    3.9517  -0.9899  -0.5298
 276  C43   C   CT    0   1.074    7.4141   1.0552   0.9649
 276  CL44  CL  CL    0  -0.113    7.8734  -1.0625  -1.2312
 276  F45   F   F     0  -0.298    7.0919   1.9374   1.9138
 276  F46   F   F     0  -0.309    8.3034   0.2136   1.5041
 276  F47   F   F     0  -0.310    8.0476   1.7350   0.0023
 276  H1    H   HCR6  0   0.298   -3.7669   0.5756  -1.2291
 276  H2    H   HCR6  0   0.276   -5.4978   1.8272  -2.4344
 276  H5    H   HCR6  0   0.284   -6.8812  -0.9108   1.3503
 276  HN12  H   HNH1  0   0.408   -9.2192   1.6846  -1.3904
 276  H131  H   HCH3  0   0.241  -11.3370   1.5566   0.5695
 276  H132  H   HCH3  0   0.253  -11.4698   2.0414  -1.1223
 276  H133  H   HCH3  0   0.240  -11.5925   0.3358  -0.6823
 276  H19   H   HCR6  0   0.284   -2.5390   0.5102   2.0285
 276  H22   H   HCR6  0   0.262   -0.8463  -2.7345  -1.3947
 276  H23   H   HCR6  0   0.273   -3.2629  -2.5984  -0.8500
 276  HN27  H   HNR5  0   0.426    0.3047   1.1051   2.1293
 276  HN32  H   HNH1  0   0.426    2.6545   1.0687   1.7326
 276  H34   H   HCR6  0   0.293    4.8489   1.3803   1.7047
 276  H37   H   HCR6  0   0.291    5.3032  -2.0385  -1.8015
 276  H38   H   HCR6  0   0.307    3.0899  -1.5123  -0.9134

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
 276  C13   N12   single    1.442  0.020  1.442
 276  N12   C10   single    1.332  0.020  1.332
 276  C10   O11   double    1.225  0.020  1.225
 276  C10   C4    single    1.505  0.020  1.505
 276  N3    C4    aromatic  1.331  0.020  1.331
 276  N3    C2    aromatic  1.323  0.020  1.323
 276  C4    C5    aromatic  1.381  0.020  1.381
 276  C2    C1    aromatic  1.387  0.020  1.387
 276  C5    C6    aromatic  1.393  0.020  1.393
 276  C1    C6    aromatic  1.389  0.020  1.389
 276  C6    O17   single    1.345  0.020  1.345
 276  O17   C18   single    1.382  0.020  1.382
 276  C19   C18   aromatic  1.385  0.020  1.385
 276  C19   C20   aromatic  1.384  0.020  1.384
 276  C18   C23   aromatic  1.395  0.020  1.395
 276  C37   C38   aromatic  1.385  0.020  1.385
 276  C37   C36   aromatic  1.382  0.020  1.382
 276  CL44  C36   single    1.730  0.020  1.730
 276  C20   N27   aromatic  1.371  0.020  1.371
 276  C20   C21   aromatic  1.405  0.020  1.405
 276  C38   C33   aromatic  1.394  0.020  1.394
 276  N27   C28   aromatic  1.364  0.020  1.364
 276  C23   C22   aromatic  1.387  0.020  1.387
 276  C36   C35   aromatic  1.394  0.020  1.394
 276  C21   C22   aromatic  1.390  0.020  1.390
 276  C21   N29   aromatic  1.376  0.020  1.376
 276  C28   N32   single    1.358  0.020  1.358
 276  C28   N29   aromatic  1.306  0.020  1.306
 276  C33   N32   single    1.384  0.020  1.384
 276  C33   C34   aromatic  1.398  0.020  1.398
 276  C35   C34   aromatic  1.384  0.020  1.384
 276  C35   C43   single    1.501  0.020  1.501
 276  F46   C43   single    1.338  0.020  1.338
 276  C43   F45   single    1.335  0.020  1.335
 276  C43   F47   single    1.338  0.020  1.338
 276  C1    H1    single    0.930  0.020  1.080
 276  C2    H2    single    0.930  0.020  1.080
 276  C5    H5    single    0.930  0.020  1.080
 276  N12   HN12  single    0.860  0.020  1.020
 276  C13   H131  single    0.970  0.020  1.090
 276  C13   H132  single    0.970  0.020  1.090
 276  C13   H133  single    0.970  0.020  1.090
 276  C19   H19   single    0.930  0.020  1.080
 276  C22   H22   single    0.930  0.020  1.080
 276  C23   H23   single    0.930  0.020  1.080
 276  N27   HN27  single    0.860  0.020  1.020
 276  N32   HN32  single    0.860  0.020  1.020
 276  C34   H34   single    0.930  0.020  1.080
 276  C37   H37   single    0.930  0.020  1.080
 276  C38   H38   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
 276  H1    C1   C6    122.52  3.000
 276  H1    C1   C2    119.68  3.000
 276  C6    C1   C2    117.80  3.000
 276  H2    C2   N3    116.69  3.000
 276  H2    C2   C1    119.28  3.000
 276  N3    C2   C1    124.03  3.000
 276  C4    N3   C2    117.53  3.000
 276  C10   C4   C5    118.97  3.000
 276  C5    C4   N3    123.63  3.000
 276  C10   C4   N3    117.41  3.000
 276  H5    C5   C6    120.81  3.000
 276  H5    C5   C4    121.00  3.000
 276  C6    C5   C4    118.20  3.000
 276  O17   C6   C5    116.65  3.000
 276  O17   C6   C1    124.55  3.000
 276  C5    C6   C1    118.81  3.000
 276  N12   C10  O11   124.06  3.000
 276  O11   C10  C4    121.26  3.000
 276  N12   C10  C4    114.69  3.000
 276  HN12  N12  C13   119.70  3.000
 276  HN12  N12  C10   117.56  3.000
 276  C13   N12  C10   122.70  3.000
 276  H133  C13  H132  108.39  3.000
 276  H133  C13  H131  108.23  3.000
 276  H132  C13  H131  108.42  3.000
 276  H133  C13  N12   111.87  3.000
 276  H132  C13  N12   108.46  3.000
 276  H131  C13  N12   111.37  3.000
 276  C18   O17  C6    119.20  3.000
 276  C23   C18  C19   122.78  3.000
 276  C23   C18  O17   118.95  3.000
 276  C19   C18  O17   118.25  3.000
 276  H19   C19  C20   122.71  3.000
 276  H19   C19  C18   121.48  3.000
 276  C20   C19  C18   115.80  3.000
 276  N27   C20  C21   104.76  3.000
 276  C21   C20  C19   122.99  3.000
 276  N27   C20  C19   132.25  3.000
 276  N29   C21  C22   130.14  3.000
 276  N29   C21  C20   110.21  3.000
 276  C22   C21  C20   119.65  3.000
 276  H22   C22  C23   120.67  3.000
 276  H22   C22  C21   120.96  3.000
 276  C23   C22  C21   118.37  3.000
 276  H23   C23  C22   120.05  3.000
 276  H23   C23  C18   119.53  3.000
 276  C22   C23  C18   120.42  3.000
 276  HN27  N27  C28   126.64  3.000
 276  HN27  N27  C20   126.47  3.000
 276  C28   N27  C20   106.90  3.000
 276  N32   C28  N29   127.32  3.000
 276  N29   C28  N27   113.27  3.000
 276  N32   C28  N27   119.41  3.000
 276  C28   N29  C21   104.86  3.000
 276  HN32  N32  C33   115.60  3.000
 276  HN32  N32  C28   115.85  3.000
 276  C33   N32  C28   128.55  3.000
 276  C38   C33  C34   118.73  3.000
 276  C34   C33  N32   116.92  3.000
 276  C38   C33  N32   124.35  3.000
 276  H34   C34  C35   119.81  3.000
 276  H34   C34  C33   118.80  3.000
 276  C35   C34  C33   121.39  3.000
 276  C43   C35  C36   121.08  3.000
 276  C43   C35  C34   119.66  3.000
 276  C36   C35  C34   119.26  3.000
 276  CL44  C36  C37   118.58  3.000
 276  CL44  C36  C35   121.74  3.000
 276  C37   C36  C35   119.67  3.000
 276  H37   C37  C38   119.09  3.000
 276  H37   C37  C36   119.78  3.000
 276  C38   C37  C36   121.13  3.000
 276  H38   C38  C37   119.54  3.000
 276  H38   C38  C33   120.65  3.000
 276  C37   C38  C33   119.82  3.000
 276  F47   C43  F46   107.15  3.000
 276  F47   C43  F45   106.85  3.000
 276  F46   C43  F45   106.84  3.000
 276  F47   C43  C35   111.70  3.000
 276  F45   C43  C35   112.15  3.000
 276  F46   C43  C35   111.83  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
 276  CONST_01  C4    N3   C2   C1      0.00   0.0  0
 276  CONST_02  C4    C5   C6   C1      0.00   0.0  0
 276  CONST_03  C5    C4   N3   C2      0.00   0.0  0
 276  CONST_04  C5    C6   C1   C2      0.00   0.0  0
 276  CONST_05  C6    C5   C4   N3      0.00   0.0  0
 276  CONST_06  C6    C1   C2   N3      0.00   0.0  0
 276  CONST_07  N27   C20  C19  C18   180.00   0.0  0
 276  CONST_08  C21   C20  C19  C18     0.00   0.0  0
 276  CONST_09  C21   C22  C23  C18     0.00   0.0  0
 276  CONST_10  C22   C23  C18  C19     0.00   0.0  0
 276  CONST_11  C28   N27  C20  C19   180.00   0.0  0
 276  CONST_12  C22   C21  C20  C19     0.00   0.0  0
 276  CONST_13  N29   C21  C20  C19   180.00   0.0  0
 276  CONST_14  C23   C18  C19  C20     0.00   0.0  0
 276  CONST_15  N29   C28  N27  C20     0.00   0.0  0
 276  CONST_16  C23   C22  C21  C20     0.00   0.0  0
 276  CONST_17  C28   N29  C21  C20     0.00   0.0  0
 276  CONST_18  C28   N27  C20  C21     0.00   0.0  0
 276  CONST_19  N27   C28  N29  C21     0.00   0.0  0
 276  CONST_20  N27   C20  C21  C22   180.00   0.0  0
 276  CONST_21  C28   N29  C21  C22   180.00   0.0  0
 276  CONST_22  N29   C21  C22  C23   180.00   0.0  0
 276  CONST_23  N29   C21  C20  N27     0.00   0.0  0
 276  CONST_24  C36   C37  C38  C33     0.00   0.0  0
 276  CONST_25  C36   C35  C34  C33     0.00   0.0  0
 276  CONST_26  C37   C38  C33  C34     0.00   0.0  0
 276  CONST_27  C37   C36  C35  C34     0.00   0.0  0
 276  CONST_28  C38   C37  C36  C35     0.00   0.0  0
 276  CONST_29  C38   C33  C34  C35     0.00   0.0  0
 276  CONST_30  C10   C4   N3   C2    180.00   0.0  0
 276  CONST_31  O17   C6   C1   C2    180.00   0.0  0
 276  CONST_32  O17   C6   C5   C4    180.00   0.0  0
 276  CONST_33  C10   C4   C5   C6    180.00   0.0  0
 276  CONST_34  C20   C19  C18  O17   180.00   0.0  0
 276  CONST_35  C22   C23  C18  O17   180.00   0.0  0
 276  CONST_36  N32   C28  N27  C20   180.00   0.0  0
 276  CONST_37  N32   C28  N29  C21   180.00   0.0  0
 276  CONST_38  C37   C38  C33  N32   180.00   0.0  0
 276  CONST_39  C35   C34  C33  N32   180.00   0.0  0
 276  CONST_40  C43   C35  C34  C33   180.00   0.0  0
 276  CONST_41  CL44  C36  C35  C34   180.00   0.0  0
 276  CONST_42  C43   C35  C36  C37   180.00   0.0  0
 276  CONST_43  CL44  C36  C37  C38   180.00   0.0  0
 276  CONST_44  H5    C5   C6   C1    180.00   0.0  0
 276  CONST_45  H1    C1   C2   N3    180.00   0.0  0
 276  CONST_46  H2    C2   N3   C4    180.00   0.0  0
 276  CONST_47  H22   C22  C23  C18   180.00   0.0  0
 276  CONST_48  H23   C23  C18  C19   180.00   0.0  0
 276  CONST_49  HN27  N27  C20  C19     0.00   0.0  0
 276  CONST_50  H19   C19  C20  C21   180.00   0.0  0
 276  CONST_51  H37   C37  C38  C33   180.00   0.0  0
 276  CONST_52  H38   C38  C33  C34   180.00   0.0  0
 276  CONST_53  H34   C34  C35  C36   180.00   0.0  0
 276  CONST_54  C13   N12  C10  C4    180.00   0.0  0
 276  CONST_55  HN12  N12  C10  C4      0.00   0.0  0
 276  CONST_56  C13   N12  C10  O11     0.00   0.0  0
 276  Var_01    C19   C18  O17  C6     96.22  30.0  2
 276  Var_02    C33   N32  C28  N27  -179.73  30.0  2
 276  Var_03    C38   C33  N32  C28     0.71  30.0  2
 276  Var_04    N12   C10  C4   N3     -1.17  30.0  2
 276  Var_05    F46   C43  C35  C34   120.47  30.0  2
 276  Var_06    H131  C13  N12  C10    54.68  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
 276  plan-1  C1    0.020
 276  plan-1  C2    0.020
 276  plan-1  N3    0.020
 276  plan-1  C4    0.020
 276  plan-1  C5    0.020
 276  plan-1  C6    0.020
 276  plan-1  C10   0.020
 276  plan-1  O17   0.020
 276  plan-1  H1    0.020
 276  plan-1  H2    0.020
 276  plan-1  H5    0.020
 276  plan-2  N32   0.020
 276  plan-2  C33   0.020
 276  plan-2  C34   0.020
 276  plan-2  C35   0.020
 276  plan-2  C36   0.020
 276  plan-2  C37   0.020
 276  plan-2  C38   0.020
 276  plan-2  C43   0.020
 276  plan-2  CL44  0.020
 276  plan-2  H34   0.020
 276  plan-2  H37   0.020
 276  plan-2  H38   0.020
 276  plan-3  O17   0.020
 276  plan-3  C18   0.020
 276  plan-3  C19   0.020
 276  plan-3  C20   0.020
 276  plan-3  C21   0.020
 276  plan-3  C22   0.020
 276  plan-3  C23   0.020
 276  plan-3  N27   0.020
 276  plan-3  C28   0.020
 276  plan-3  N29   0.020
 276  plan-3  N32   0.020
 276  plan-3  H19   0.020
 276  plan-3  H22   0.020
 276  plan-3  H23   0.020
 276  plan-3  HN27  0.020
 276  plan-4  C4    0.020
 276  plan-4  C10   0.020
 276  plan-4  O11   0.020
 276  plan-4  N12   0.020
 276  plan-4  C13   0.020
 276  plan-4  HN12  0.020

