# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Apr  4 00:59:48 2020
#   Inital geometry file: a 154 line input string
#   Ligand name: 1-(3-{[(3Z)-2-oxo-3-(1H-pyrrol-2-ylmethylidene)-2,3-dihydro-1H-indol-6-yl]amino}phenyl)-3-[3-(trifluoromethyl)phenyl]urea
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: FC(F)(F)c1cccc(NC(=O)Nc2cccc(Nc3ccc\4c(NC(=O)C\4=C\c5[nH]ccc5)c3)c2)c1
#
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
 0F4  0F4  1-(3-{[(3Z)-2-oxo-3-(1H-pyrrol-2-ylmethylidene)-2,3-dihydro-1H-indol-6-yl]amino}phenyl)-3-[3-(trifluoromethyl)phenyl]urea  ligand  57  37  .  2021-08-03  2021-08-03  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_0F4
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
 0F4  F1    F  F     0  -0.314    9.7669   1.7399  -1.2108
 0F4  C2    C  CT    0   1.052    9.6979   0.7344  -0.3245
 0F4  F3    F  F     0  -0.304    9.9174  -0.3949  -1.0055
 0F4  F4    F  F     0  -0.310   10.7299   0.8938   0.5133
 0F4  C5    C  CR6   0  -0.181    8.3869   0.7277   0.3977
 0F4  C6    C  CR16  0  -0.292    8.1834   1.6183   1.4455
 0F4  C7    C  CR16  0  -0.238    6.9535   1.6272   2.0816
 0F4  C8    C  CR16  0  -0.293    5.9315   0.7738   1.6932
 0F4  C9    C  CR6   0   0.405    6.1326  -0.1044   0.6286
 0F4  N10   N  NH1   0  -0.793    5.1773  -1.0194   0.1864
 0F4  C11   C  C     0   0.736    3.8147  -0.8671   0.2463
 0F4  O12   O  O     0  -0.492    3.2695   0.0865   0.7704
 0F4  N13   N  NH1   0  -0.794    3.1485  -1.9058  -0.3415
 0F4  C14   C  CR6   0   0.392    1.7691  -2.0645  -0.4955
 0F4  C15   C  CR16  0  -0.374    1.3488  -2.9792  -1.4660
 0F4  C16   C  CR16  0  -0.237   -0.0024  -3.2167  -1.6401
 0F4  C17   C  CR16  0  -0.352   -0.9583  -2.5621  -0.8790
 0F4  C18   C  CR6   0   0.399   -0.5444  -1.6356   0.0802
 0F4  N19   N  NH1   0  -0.806   -1.4260  -0.9703   0.9153
 0F4  C20   C  CR6   0   0.360   -2.7620  -0.6749   0.7166
 0F4  C21   C  CR16  0  -0.355   -3.5540  -0.4247   1.8483
 0F4  C22   C  CR16  0  -0.364   -4.8882  -0.0691   1.7300
 0F4  C23   C  CR56  0   0.054   -5.4619   0.0256   0.4719
 0F4  C24   C  CR56  0   0.408   -4.6601  -0.2258  -0.6462
 0F4  N25   N  NR15  0  -0.769   -5.4323  -0.0572  -1.7837
 0F4  C26   C  CR5   0   0.533   -6.7170   0.2888  -1.4839
 0F4  O27   O  O     0  -0.490   -7.5879   0.4868  -2.3257
 0F4  C28   C  CR5   0  -0.059   -6.7943   0.3572  -0.0065
 0F4  C29   C  C1    0  -0.380   -7.8661   0.6621   0.7707
 0F4  C30   C  CR5   0   0.338   -9.2077   1.0062   0.4572
 0F4  C31   C  CR15  0  -0.334  -10.2223   1.3043   1.3676
 0F4  C32   C  CR15  0  -0.360  -11.3792   1.5907   0.6333
 0F4  C33   C  CR15  0  -0.036  -11.0461   1.4605  -0.7058
 0F4  N34   N  NR15  0  -0.662   -9.7521   1.1121  -0.7937
 0F4  C36   C  CR16  0  -0.392   -3.3258  -0.5629  -0.5620
 0F4  C37   C  CR16  0  -0.433    0.8214  -1.3931   0.2691
 0F4  C38   C  CR16  0  -0.385    7.3711  -0.1188  -0.0151
 0F4  H6    H  HCR6  0   0.273    8.9650   2.2899   1.7746
 0F4  H7    H  HCR6  0   0.271    6.7874   2.3036   2.9093
 0F4  H8    H  HCR6  0   0.281    4.9966   0.7919   2.2295
 0F4  HN10  H  HNH1  0   0.416    5.5404  -1.7747  -0.3752
 0F4  HN13  H  HNH1  0   0.414    3.7013  -2.6076  -0.8101
 0F4  H15   H  HCR6  0   0.265    2.0766  -3.5028  -2.0739
 0F4  H16   H  HCR6  0   0.259   -0.3212  -3.9383  -2.3813
 0F4  H17   H  HCR6  0   0.274   -2.0043  -2.7957  -1.0160
 0F4  HN19  H  HNH1  0   0.401   -1.0379  -0.6485   1.7878
 0F4  H21   H  HCR6  0   0.262   -3.1108  -0.5159   2.8325
 0F4  H22   H  HCR6  0   0.251   -5.4676   0.1215   2.6253
 0F4  HN25  H  HNR5  0   0.412   -5.1031  -0.1846  -2.7285
 0F4  H29   H  H     0   0.266   -7.6859   0.6449   1.8415
 0F4  H31   H  HCR5  0   0.259  -10.1122   1.3087   2.4416
 0F4  H32   H  HCR5  0   0.255  -12.3482   1.8615   1.0200
 0F4  H33   H  HCR5  0   0.280  -11.6500   1.5945  -1.5884
 0F4  H36   H  HCR6  0   0.285   -2.7364  -0.7077  -1.4566
 0F4  H37   H  HCR6  0   0.281    1.1216  -0.6822   1.0234
 0F4  H38   H  HCR6  0   0.284    7.5220  -0.8022  -0.8412
 0F4  HN34  H  HNR5  0   0.431   -9.2085   0.9389  -1.6377

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
 0F4  F1   C2    single    1.342  0.020  1.342
 0F4  C5   C2    single    1.497  0.020  1.497
 0F4  C2   F4    single    1.339  0.020  1.339
 0F4  C2   F3    single    1.337  0.020  1.337
 0F4  C6   C5    aromatic  1.390  0.020  1.390
 0F4  C5   C38   aromatic  1.385  0.020  1.385
 0F4  C7   C6    aromatic  1.385  0.020  1.385
 0F4  C6   H6    single    0.930  0.020  1.080
 0F4  C7   C8    aromatic  1.387  0.020  1.387
 0F4  C7   H7    single    0.930  0.020  1.080
 0F4  C8   C9    aromatic  1.395  0.020  1.395
 0F4  C8   H8    single    0.930  0.020  1.080
 0F4  C9   C38   aromatic  1.396  0.020  1.396
 0F4  C9   N10   single    1.395  0.020  1.395
 0F4  N10  C11   single    1.372  0.020  1.372
 0F4  N10  HN10  single    0.860  0.020  1.020
 0F4  C11  O12   double    1.217  0.020  1.217
 0F4  C11  N13   single    1.367  0.020  1.367
 0F4  N13  C14   single    1.397  0.020  1.397
 0F4  N13  HN13  single    0.860  0.020  1.020
 0F4  C14  C15   aromatic  1.398  0.020  1.398
 0F4  C14  C37   aromatic  1.391  0.020  1.391
 0F4  C15  C16   aromatic  1.383  0.020  1.383
 0F4  C15  H15   single    0.930  0.020  1.080
 0F4  C16  C17   aromatic  1.386  0.020  1.386
 0F4  C16  H16   single    0.930  0.020  1.080
 0F4  C18  C17   aromatic  1.396  0.020  1.396
 0F4  C17  H17   single    0.930  0.020  1.080
 0F4  C37  C18   aromatic  1.400  0.020  1.400
 0F4  C18  N19   single    1.385  0.020  1.385
 0F4  N19  C20   single    1.383  0.020  1.383
 0F4  N19  HN19  single    0.860  0.020  1.020
 0F4  C20  C21   aromatic  1.404  0.020  1.404
 0F4  C20  C36   aromatic  1.402  0.020  1.402
 0F4  C21  C22   aromatic  1.386  0.020  1.386
 0F4  C21  H21   single    0.930  0.020  1.080
 0F4  C22  C23   aromatic  1.386  0.020  1.386
 0F4  C22  H22   single    0.930  0.020  1.080
 0F4  C24  C23   aromatic  1.399  0.020  1.399
 0F4  C23  C28   single    1.454  0.020  1.454
 0F4  C36  C24   aromatic  1.379  0.020  1.379
 0F4  C24  N25   single    1.385  0.020  1.385
 0F4  N25  C26   single    1.364  0.020  1.364
 0F4  N25  HN25  single    0.860  0.020  1.020
 0F4  C28  C26   single    1.481  0.020  1.481
 0F4  C26  O27   double    1.227  0.020  1.227
 0F4  C28  C29   double    1.359  0.020  1.359
 0F4  C29  C30   single    1.420  0.020  1.420
 0F4  C29  H29   single    0.930  0.020  1.080
 0F4  C30  N34   aromatic  1.368  0.020  1.368
 0F4  C30  C31   aromatic  1.395  0.020  1.395
 0F4  C31  C32   aromatic  1.400  0.020  1.400
 0F4  C31  H31   single    0.930  0.020  1.080
 0F4  C33  C32   aromatic  1.386  0.020  1.386
 0F4  C32  H32   single    0.930  0.020  1.080
 0F4  N34  C33   aromatic  1.343  0.020  1.343
 0F4  C33  H33   single    0.930  0.020  1.080
 0F4  C36  H36   single    0.930  0.020  1.080
 0F4  C37  H37   single    0.930  0.020  1.080
 0F4  C38  H38   single    0.930  0.020  1.080
 0F4  N34  HN34  single    0.860  0.020  1.020

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
 0F4  C5    C2   F4   111.95  3.000
 0F4  F4    C2   F3   107.02  3.000
 0F4  C5    C2   F3   112.70  3.000
 0F4  F3    C2   F1   106.74  3.000
 0F4  F4    C2   F1   106.52  3.000
 0F4  C5    C2   F1   111.53  3.000
 0F4  C38   C5   C6   120.58  3.000
 0F4  C38   C5   C2   120.08  3.000
 0F4  C6    C5   C2   119.28  3.000
 0F4  H6    C6   C7   119.86  3.000
 0F4  H6    C6   C5   121.42  3.000
 0F4  C7    C6   C5   118.71  3.000
 0F4  H7    C7   C8   119.07  3.000
 0F4  H7    C7   C6   119.47  3.000
 0F4  C8    C7   C6   121.45  3.000
 0F4  H8    C8   C9   121.03  3.000
 0F4  H8    C8   C7   119.30  3.000
 0F4  C9    C8   C7   119.67  3.000
 0F4  C38   C9   N10  117.05  3.000
 0F4  N10   C9   C8   123.80  3.000
 0F4  C38   C9   C8   119.10  3.000
 0F4  HN10  N10  C11  117.70  3.000
 0F4  HN10  N10  C9   114.90  3.000
 0F4  C11   N10  C9   126.40  3.000
 0F4  N13   C11  O12  124.21  3.000
 0F4  N13   C11  N10  112.39  3.000
 0F4  O12   C11  N10  123.41  3.000
 0F4  HN13  N13  C14  114.26  3.000
 0F4  HN13  N13  C11  117.47  3.000
 0F4  C14   N13  C11  127.95  3.000
 0F4  C37   C14  C15  119.51  3.000
 0F4  C37   C14  N13  123.88  3.000
 0F4  C15   C14  N13  116.59  3.000
 0F4  H15   C15  C16  120.19  3.000
 0F4  H15   C15  C14  120.25  3.000
 0F4  C16   C15  C14  119.56  3.000
 0F4  H16   C16  C17  119.19  3.000
 0F4  H16   C16  C15  119.24  3.000
 0F4  C17   C16  C15  121.57  3.000
 0F4  H17   C17  C18  121.16  3.000
 0F4  H17   C17  C16  119.73  3.000
 0F4  C18   C17  C16  119.09  3.000
 0F4  C37   C18  N19  117.17  3.000
 0F4  N19   C18  C17  122.98  3.000
 0F4  C37   C18  C17  119.79  3.000
 0F4  HN19  N19  C20  115.36  3.000
 0F4  HN19  N19  C18  115.49  3.000
 0F4  C20   N19  C18  129.14  3.000
 0F4  C36   C20  C21  119.61  3.000
 0F4  C36   C20  N19  122.46  3.000
 0F4  C21   C20  N19  117.87  3.000
 0F4  H21   C21  C22  119.54  3.000
 0F4  H21   C21  C20  119.12  3.000
 0F4  C22   C21  C20  121.34  3.000
 0F4  H22   C22  C23  121.11  3.000
 0F4  H22   C22  C21  119.31  3.000
 0F4  C23   C22  C21  119.57  3.000
 0F4  C28   C23  C24  107.65  3.000
 0F4  C28   C23  C22  133.92  3.000
 0F4  C24   C23  C22  118.43  3.000
 0F4  C36   C24  N25  128.27  3.000
 0F4  N25   C24  C23  108.36  3.000
 0F4  C36   C24  C23  123.36  3.000
 0F4  HN25  N25  C26  123.06  3.000
 0F4  HN25  N25  C24  124.89  3.000
 0F4  C26   N25  C24  112.05  3.000
 0F4  C28   C26  O27  129.77  3.000
 0F4  O27   C26  N25  123.96  3.000
 0F4  C28   C26  N25  106.27  3.000
 0F4  C29   C28  C26  128.47  3.000
 0F4  C29   C28  C23  125.87  3.000
 0F4  C26   C28  C23  105.66  3.000
 0F4  H29   C29  C30  112.22  3.000
 0F4  H29   C29  C28  115.44  3.000
 0F4  C30   C29  C28  132.34  3.000
 0F4  N34   C30  C31  106.90  3.000
 0F4  C31   C30  C29  126.49  3.000
 0F4  N34   C30  C29  126.61  3.000
 0F4  H31   C31  C32  127.25  3.000
 0F4  H31   C31  C30  125.15  3.000
 0F4  C32   C31  C30  107.60  3.000
 0F4  H32   C32  C33  125.89  3.000
 0F4  H32   C32  C31  127.32  3.000
 0F4  C33   C32  C31  106.80  3.000
 0F4  H33   C33  N34  121.24  3.000
 0F4  H33   C33  C32  130.15  3.000
 0F4  N34   C33  C32  108.61  3.000
 0F4  HN34  N34  C33  127.77  3.000
 0F4  HN34  N34  C30  122.14  3.000
 0F4  C33   N34  C30  110.10  3.000
 0F4  H36   C36  C24  120.66  3.000
 0F4  H36   C36  C20  121.65  3.000
 0F4  C24   C36  C20  117.67  3.000
 0F4  H37   C37  C18  118.67  3.000
 0F4  H37   C37  C14  120.85  3.000
 0F4  C18   C37  C14  120.47  3.000
 0F4  H38   C38  C9   118.81  3.000
 0F4  H38   C38  C5   120.73  3.000
 0F4  C9    C38  C5   120.46  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
 0F4  CONST_01  C8    C7   C6   C5     0.00   0.0  0
 0F4  CONST_02  C8    C9   C38  C5     0.00   0.0  0
 0F4  CONST_03  C9    C38  C5   C6     0.00   0.0  0
 0F4  CONST_04  C9    C8   C7   C6     0.00   0.0  0
 0F4  CONST_05  C38   C5   C6   C7     0.00   0.0  0
 0F4  CONST_06  C38   C9   C8   C7     0.00   0.0  0
 0F4  CONST_07  C17   C16  C15  C14    0.00   0.0  0
 0F4  CONST_08  C17   C18  C37  C14    0.00   0.0  0
 0F4  CONST_09  C18   C37  C14  C15    0.00   0.0  0
 0F4  CONST_10  C18   C17  C16  C15    0.00   0.0  0
 0F4  CONST_11  C37   C14  C15  C16    0.00   0.0  0
 0F4  CONST_12  C37   C18  C17  C16    0.00   0.0  0
 0F4  CONST_13  C23   C22  C21  C20    0.00   0.0  0
 0F4  CONST_14  C23   C24  C36  C20    0.00   0.0  0
 0F4  CONST_15  C24   C36  C20  C21    0.00   0.0  0
 0F4  CONST_16  C24   C23  C22  C21    0.00   0.0  0
 0F4  CONST_17  C36   C20  C21  C22    0.00   0.0  0
 0F4  CONST_18  C36   C24  C23  C22    0.00   0.0  0
 0F4  CONST_19  C32   C33  N34  C30    0.00   0.0  0
 0F4  CONST_20  C33   C32  C31  C30    0.00   0.0  0
 0F4  CONST_21  C33   N34  C30  C31    0.00   0.0  0
 0F4  CONST_22  N34   C33  C32  C31    0.00   0.0  0
 0F4  CONST_23  N34   C30  C31  C32    0.00   0.0  0
 0F4  CONST_24  C28   C26  N25  C24    0.00   0.0  0
 0F4  CONST_25  C7    C6   C5   C2   180.00   0.0  0
 0F4  CONST_26  C9    C38  C5   C2   180.00   0.0  0
 0F4  CONST_27  N10   C9   C38  C5   180.00   0.0  0
 0F4  CONST_28  N10   C9   C8   C7   180.00   0.0  0
 0F4  CONST_29  C16   C15  C14  N13  180.00   0.0  0
 0F4  CONST_30  C18   C37  C14  N13  180.00   0.0  0
 0F4  CONST_31  N19   C18  C37  C14  180.00   0.0  0
 0F4  CONST_32  N19   C18  C17  C16  180.00   0.0  0
 0F4  CONST_33  C22   C21  C20  N19  180.00   0.0  0
 0F4  CONST_34  C24   C36  C20  N19  180.00   0.0  0
 0F4  CONST_35  C33   N34  C30  C29  180.00   0.0  0
 0F4  CONST_36  C32   C31  C30  C29  180.00   0.0  0
 0F4  CONST_37  O27   C26  N25  C24  180.00   0.0  0
 0F4  CONST_38  H7    C7   C6   C5   180.00   0.0  0
 0F4  CONST_39  H38   C38  C5   C6   180.00   0.0  0
 0F4  CONST_40  H8    C8   C7   C6   180.00   0.0  0
 0F4  CONST_41  H6    C6   C7   C8   180.00   0.0  0
 0F4  CONST_42  H16   C16  C15  C14  180.00   0.0  0
 0F4  CONST_43  H37   C37  C14  C15  180.00   0.0  0
 0F4  CONST_44  H17   C17  C16  C15  180.00   0.0  0
 0F4  CONST_45  H15   C15  C16  C17  180.00   0.0  0
 0F4  CONST_46  H22   C22  C21  C20  180.00   0.0  0
 0F4  CONST_47  H36   C36  C20  C21  180.00   0.0  0
 0F4  CONST_48  H21   C21  C22  C23  180.00   0.0  0
 0F4  CONST_49  H33   C33  N34  C30  180.00   0.0  0
 0F4  CONST_50  H32   C32  C31  C30  180.00   0.0  0
 0F4  CONST_51  HN34  N34  C30  C31  180.00   0.0  0
 0F4  CONST_52  H31   C31  C32  C33  180.00   0.0  0
 0F4  CONST_53  HN25  N25  C26  C28  180.00   0.0  0
 0F4  CONST_59  HN13  N13  C14  C15    0.00   0.0  0
 0F4  CONST_60  O12   C11  N10  C9     0.00   0.0  0
 0F4  CONST_61  C14   N13  C11  O12    0.00   0.0  0
 0F4  CONST_62  N13   C11  N10  C9   180.00   0.0  0
 0F4  CONST_63  C14   N13  C11  N10  180.00   0.0  0
 0F4  Var_01    C20   N19  C18  C17  -25.55  30.0  2
 0F4  Var_02    C21   C20  N19  C18  158.07  30.0  2
 0F4  Var_03    C30   C29  C28  C23  179.75  30.0  2
 0F4  Var_04    N34   C30  C29  C28    0.05  30.0  2
 0F4  Var_05    C6    C5   C2   F1   -79.04  30.0  2

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
 0F4  plan-1  C29   0.020
 0F4  plan-1  C30   0.020
 0F4  plan-1  C31   0.020
 0F4  plan-1  C32   0.020
 0F4  plan-1  C33   0.020
 0F4  plan-1  N34   0.020
 0F4  plan-1  H31   0.020
 0F4  plan-1  H32   0.020
 0F4  plan-1  H33   0.020
 0F4  plan-1  HN34  0.020
 0F4  plan-2  C2    0.020
 0F4  plan-2  C5    0.020
 0F4  plan-2  C6    0.020
 0F4  plan-2  C7    0.020
 0F4  plan-2  C8    0.020
 0F4  plan-2  C9    0.020
 0F4  plan-2  N10   0.020
 0F4  plan-2  C38   0.020
 0F4  plan-2  H6    0.020
 0F4  plan-2  H7    0.020
 0F4  plan-2  H8    0.020
 0F4  plan-2  H38   0.020
 0F4  plan-3  N13   0.020
 0F4  plan-3  C14   0.020
 0F4  plan-3  C15   0.020
 0F4  plan-3  C16   0.020
 0F4  plan-3  C17   0.020
 0F4  plan-3  C18   0.020
 0F4  plan-3  N19   0.020
 0F4  plan-3  C37   0.020
 0F4  plan-3  H15   0.020
 0F4  plan-3  H16   0.020
 0F4  plan-3  H17   0.020
 0F4  plan-3  H37   0.020
 0F4  plan-4  N19   0.020
 0F4  plan-4  C20   0.020
 0F4  plan-4  C21   0.020
 0F4  plan-4  C22   0.020
 0F4  plan-4  C23   0.020
 0F4  plan-4  C24   0.020
 0F4  plan-4  N25   0.020
 0F4  plan-4  C26   0.020
 0F4  plan-4  O27   0.020
 0F4  plan-4  C28   0.020
 0F4  plan-4  C29   0.020
 0F4  plan-4  C36   0.020
 0F4  plan-4  H21   0.020
 0F4  plan-4  H22   0.020
 0F4  plan-4  HN25  0.020
 0F4  plan-4  H36   0.020
 0F4  plan-5  C9    0.020
 0F4  plan-5  N10   0.020
 0F4  plan-5  C11   0.020
 0F4  plan-5  O12   0.020
 0F4  plan-5  N13   0.020
 0F4  plan-5  C14   0.020
 0F4  plan-5  HN10  0.020
 0F4  plan-5  HN13  0.020

