# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Apr 11 22:35:29 2020
#   Inital geometry file: a 111 line input string
#   Ligand name: (2S)-N'-[(3R)-4-chloro-7-methyl-2-oxo-2,3-dihydro-1H-indol-3-yl]-2-(4-hydroxyphenyl)propanehydrazide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[C@H](C(=O)NN[C@H]1C(=O)Nc2c(C)ccc(Cl)c12)c3ccc(O)cc3
#
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
 6XP  6XP  (2S)-N'-[(3R)-4-chloro-7-methyl-2-oxo-2,3-dihydro-1H-indol-3-yl]-2-(4-hydroxyphenyl)propanehydrazide  ligand  43  25  .  2021-08-05  2021-08-05  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_6XP
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
 6XP  C50   C   CH3   0  -0.643  -1.4056   1.9702   1.2455
 6XP  C2    C   CR16  0  -0.293  -3.7543  -0.8926   0.9643
 6XP  C6    C   CR16  0  -0.291  -4.1189   1.2738   0.0422
 6XP  C3    C   CR16  0  -0.325  -5.1059  -1.1812   0.8606
 6XP  C5    C   CR16  0  -0.371  -5.4748   1.0033  -0.0669
 6XP  C19   C   C     0   0.577  -1.0829   0.4696  -0.6947
 6XP  C20   C   CH1   0  -0.492  -1.7516   0.5945   0.6689
 6XP  N13   N   NR15  0  -0.752   2.7486   1.8033  -0.1673
 6XP  N17   N   NH1   0  -0.426   0.8141  -0.4730  -1.7877
 6XP  N18   N   NH1   0  -0.529  -0.0032  -0.3464  -0.6869
 6XP  O21   O   O     0  -0.456  -1.4682   1.0783  -1.6712
 6XP  C1    C   CR6   0   0.148  -3.2329   0.3338   0.5603
 6XP  C4    C   CR6   0   0.340  -5.9780  -0.2300   0.3393
 6XP  C8    C   CR16  0  -0.331   4.0931  -0.7249   2.1636
 6XP  C7    C   CR16  0  -0.218   3.7778  -1.8594   1.4279
 6XP  C11   C   CR56  0   0.116   2.8288  -0.4598  -0.2685
 6XP  C9    C   CR6   0   0.069   3.7950   0.5664   1.7270
 6XP  C15   C   CR15  0  -0.285   2.1558   0.0013  -1.5338
 6XP  C10   C   CR6   0  -0.182   3.1408  -1.7145   0.2011
 6XP  C12   C   CR56  0   0.385   3.1563   0.6528   0.4988
 6XP  C14   C   CR5   0   0.542   2.1510   1.5318  -1.3600
 6XP  H501  H   HCH3  0   0.235  -0.3243   2.0973   1.3201
 6XP  H502  H   HCH3  0   0.237  -1.7918   2.7798   0.6278
 6XP  H503  H   HCH3  0   0.248  -1.8238   2.0763   2.2459
 6XP  H20   H   HCH1  0   0.271  -1.3318  -0.1570   1.3439
 6XP  H2    H   HCR6  0   0.251  -3.0916  -1.6450   1.3764
 6XP  H3    H   HCR6  0   0.261  -5.4857  -2.1415   1.1868
 6XP  H6    H   HCR6  0   0.251  -3.7634   2.2425  -0.2827
 6XP  H5    H   HCR6  0   0.268  -6.1403   1.7583  -0.4712
 6XP  H18   H   HNH1  0   0.404   0.2227  -0.8629   0.1535
 6XP  H241  H   HCH3  0   0.252   4.7241   2.4981   1.9594
 6XP  H242  H   HCH3  0   0.254   3.2252   2.3064   2.8584
 6XP  H243  H   HCH3  0   0.260   4.6953   1.5207   3.4216
 6XP  H13   H   HNR5  0   0.420   2.8828   2.7421   0.1778
 6XP  H17   H   HNH1  0   0.382   0.8170  -1.4286  -2.1193
 6XP  H22   H   HOH1  0   0.473  -7.7860   0.1889  -0.1141
 6XP  H8    H   HCR6  0   0.266   4.5924  -0.8507   3.1164
 6XP  H7    H   HCR6  0   0.279   4.0245  -2.8412   1.8067
 6XP  H15   H   HCR5  0   0.328   2.7589  -0.2475  -2.4134
 6XP  O22   O   OH1   0  -0.634  -7.2864  -0.5476   0.2551
 6XP  O16   O   O     0  -0.428   1.6986   2.3387  -2.1357
 6XP  CL2   CL  CL    0  -0.124   2.7335  -3.1065  -0.7478
 6XP  C24   C   CH3   0  -0.736   4.1275   1.7852   2.5315

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
 6XP  C50  C20   single    1.531  0.020  1.531
 6XP  C2   C3    aromatic  1.386  0.020  1.386
 6XP  C2   C1    aromatic  1.393  0.020  1.393
 6XP  C6   C5    aromatic  1.387  0.020  1.387
 6XP  C6   C1    aromatic  1.392  0.020  1.392
 6XP  C3   C4    aromatic  1.392  0.020  1.392
 6XP  C5   C4    aromatic  1.393  0.020  1.393
 6XP  C19  C20   single    1.524  0.020  1.524
 6XP  C19  N18   single    1.353  0.020  1.353
 6XP  C19  O21   double    1.213  0.020  1.213
 6XP  C24  C9    single    1.498  0.020  1.498
 6XP  C20  C1    single    1.508  0.020  1.508
 6XP  N13  C12   single    1.391  0.020  1.391
 6XP  N13  C14   single    1.361  0.020  1.361
 6XP  N17  N18   single    1.377  0.020  1.377
 6XP  N17  C15   single    1.445  0.020  1.445
 6XP  O16  C14   double    1.207  0.020  1.207
 6XP  O22  C4    single    1.349  0.020  1.349
 6XP  CL2  C10   single    1.733  0.020  1.733
 6XP  C8   C7    aromatic  1.389  0.020  1.389
 6XP  C8   C9    aromatic  1.395  0.020  1.395
 6XP  C7   C10   aromatic  1.390  0.020  1.390
 6XP  C11  C15   single    1.505  0.020  1.505
 6XP  C11  C10   aromatic  1.376  0.020  1.376
 6XP  C11  C12   aromatic  1.391  0.020  1.391
 6XP  C9   C12   aromatic  1.387  0.020  1.387
 6XP  C15  C14   single    1.540  0.020  1.540
 6XP  C50  H501  single    0.970  0.020  1.090
 6XP  C50  H502  single    0.970  0.020  1.090
 6XP  C50  H503  single    0.970  0.020  1.090
 6XP  C20  H20   single    0.970  0.020  1.090
 6XP  C2   H2    single    0.930  0.020  1.080
 6XP  C3   H3    single    0.930  0.020  1.080
 6XP  C6   H6    single    0.930  0.020  1.080
 6XP  C5   H5    single    0.930  0.020  1.080
 6XP  N18  H18   single    0.860  0.020  1.020
 6XP  C24  H241  single    0.970  0.020  1.090
 6XP  C24  H242  single    0.970  0.020  1.090
 6XP  C24  H243  single    0.970  0.020  1.090
 6XP  N13  H13   single    0.860  0.020  1.020
 6XP  N17  H17   single    0.890  0.020  1.040
 6XP  O22  H22   single    0.850  0.020  0.980
 6XP  C8   H8    single    0.930  0.020  1.080
 6XP  C7   H7    single    0.930  0.020  1.080
 6XP  C15  H15   single    0.970  0.020  1.090

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
 6XP  H503  C50  H502  108.20  3.000
 6XP  H503  C50  H501  107.84  3.000
 6XP  H502  C50  H501  107.67  3.000
 6XP  H503  C50  C20   110.27  3.000
 6XP  H502  C50  C20   111.97  3.000
 6XP  H501  C50  C20   110.74  3.000
 6XP  H2    C2   C1    119.51  3.000
 6XP  H2    C2   C3    118.69  3.000
 6XP  C1    C2   C3    121.80  3.000
 6XP  H6    C6   C1    120.49  3.000
 6XP  H6    C6   C5    118.18  3.000
 6XP  C1    C6   C5    121.33  3.000
 6XP  H3    C3   C4    119.94  3.000
 6XP  H3    C3   C2    120.28  3.000
 6XP  C4    C3   C2    119.78  3.000
 6XP  H5    C5   C4    120.23  3.000
 6XP  H5    C5   C6    119.57  3.000
 6XP  C4    C5   C6    120.21  3.000
 6XP  O21   C19  N18   124.08  3.000
 6XP  O21   C19  C20   122.66  3.000
 6XP  N18   C19  C20   113.23  3.000
 6XP  H20   C20  C1    107.61  3.000
 6XP  H20   C20  C19   109.11  3.000
 6XP  C1    C20  C19   110.64  3.000
 6XP  H20   C20  C50   107.34  3.000
 6XP  C1    C20  C50   113.85  3.000
 6XP  C19   C20  C50   108.15  3.000
 6XP  H13   N13  C14   122.92  3.000
 6XP  H13   N13  C12   124.54  3.000
 6XP  C14   N13  C12   112.54  3.000
 6XP  H17   N17  C15   111.40  3.000
 6XP  H17   N17  N18   110.52  3.000
 6XP  C15   N17  N18   112.36  3.000
 6XP  H18   N18  N17   118.98  3.000
 6XP  H18   N18  C19   119.38  3.000
 6XP  N17   N18  C19   121.63  3.000
 6XP  C20   C1   C6    122.37  3.000
 6XP  C20   C1   C2    119.95  3.000
 6XP  C6    C1   C2    117.67  3.000
 6XP  O22   C4   C5    122.74  3.000
 6XP  O22   C4   C3    118.05  3.000
 6XP  C5    C4   C3    119.22  3.000
 6XP  H8    C8   C9    118.77  3.000
 6XP  H8    C8   C7    118.42  3.000
 6XP  C9    C8   C7    122.81  3.000
 6XP  H7    C7   C10   120.58  3.000
 6XP  H7    C7   C8    120.31  3.000
 6XP  C10   C7   C8    119.11  3.000
 6XP  C12   C11  C10   119.21  3.000
 6XP  C12   C11  C15   108.90  3.000
 6XP  C10   C11  C15   131.89  3.000
 6XP  C12   C9   C8    115.66  3.000
 6XP  C12   C9   C24   121.82  3.000
 6XP  C8    C9   C24   122.52  3.000
 6XP  H15   C15  C14   108.54  3.000
 6XP  H15   C15  C11   111.06  3.000
 6XP  C14   C15  C11   102.18  3.000
 6XP  H15   C15  N17   107.19  3.000
 6XP  C14   C15  N17   110.06  3.000
 6XP  C11   C15  N17   117.52  3.000
 6XP  C11   C10  C7    120.03  3.000
 6XP  C11   C10  CL2   119.50  3.000
 6XP  C7    C10  CL2   120.47  3.000
 6XP  C9    C12  C11   123.18  3.000
 6XP  C9    C12  N13   127.64  3.000
 6XP  C11   C12  N13   109.18  3.000
 6XP  C15   C14  O16   126.36  3.000
 6XP  C15   C14  N13   107.19  3.000
 6XP  O16   C14  N13   126.45  3.000
 6XP  H22   O22  C4    110.30  3.000
 6XP  H243  C24  H242  107.59  3.000
 6XP  H243  C24  H241  107.59  3.000
 6XP  H242  C24  H241  107.26  3.000
 6XP  H243  C24  C9    110.94  3.000
 6XP  H242  C24  C9    111.46  3.000
 6XP  H241  C24  C9    111.80  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
 6XP  CONST_01  C5    C4   C3   C2     0.00   0.0  0
 6XP  CONST_02  C5    C6   C1   C2     0.00   0.0  0
 6XP  CONST_03  C3    C4   C5   C6     0.00   0.0  0
 6XP  CONST_04  C3    C2   C1   C6     0.00   0.0  0
 6XP  CONST_05  C4    C3   C2   C1     0.00   0.0  0
 6XP  CONST_06  C4    C5   C6   C1     0.00   0.0  0
 6XP  CONST_07  C11   C10  C7   C8     0.00   0.0  0
 6XP  CONST_08  C11   C12  C9   C8     0.00   0.0  0
 6XP  CONST_09  C12   C9   C8   C7     0.00   0.0  0
 6XP  CONST_10  C12   C11  C10  C7     0.00   0.0  0
 6XP  CONST_11  C10   C7   C8   C9     0.00   0.0  0
 6XP  CONST_12  C10   C11  C12  C9     0.00   0.0  0
 6XP  CONST_13  C12   N13  C14  C15    0.00   0.0  0
 6XP  CONST_14  O22   C4   C3   C2   180.00   0.0  0
 6XP  CONST_15  O22   C4   C5   C6   180.00   0.0  0
 6XP  CONST_16  C20   C1   C2   C3   180.00   0.0  0
 6XP  CONST_17  C20   C1   C6   C5   180.00   0.0  0
 6XP  CONST_18  C7    C8   C9   C24  180.00   0.0  0
 6XP  CONST_19  N13   C12  C9   C24    0.00   0.0  0
 6XP  CONST_20  C11   C12  C9   C24  180.00   0.0  0
 6XP  CONST_21  C8    C7   C10  CL2  180.00   0.0  0
 6XP  CONST_22  C15   C11  C10  CL2    0.00   0.0  0
 6XP  CONST_23  C12   C11  C10  CL2  180.00   0.0  0
 6XP  CONST_24  C12   N13  C14  O16  180.00   0.0  0
 6XP  CONST_25  H6    C6   C1   C2   180.00   0.0  0
 6XP  CONST_26  H2    C2   C1   C6   180.00   0.0  0
 6XP  CONST_27  H5    C5   C4   C3   180.00   0.0  0
 6XP  CONST_28  H3    C3   C4   C5   180.00   0.0  0
 6XP  CONST_29  H7    C7   C10  C11  180.00   0.0  0
 6XP  CONST_30  H8    C8   C7   C10  180.00   0.0  0
 6XP  CONST_31  H13   N13  C14  C15  180.00   0.0  0
 6XP  CONST_32  N17   N18  C19  C20  180.00   0.0  0
 6XP  CONST_33  O21   C19  N18  N17    0.00   0.0  0
 6XP  CONST_34  H18   N18  C19  C20    0.00   0.0  0
 6XP  Var_01    H241  C24  C9   C8   125.27  30.0  2
 6XP  Var_02    C15   N17  N18  C19  115.92  30.0  1

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
 6XP  chir_01  C20  C50  C19  C1   positiv
 6XP  chir_02  C15  N17  C11  C14  positiv

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
 6XP  plan-1  C2   0.020
 6XP  plan-1  C6   0.020
 6XP  plan-1  C3   0.020
 6XP  plan-1  C5   0.020
 6XP  plan-1  C20  0.020
 6XP  plan-1  C1   0.020
 6XP  plan-1  C4   0.020
 6XP  plan-1  H2   0.020
 6XP  plan-1  H3   0.020
 6XP  plan-1  H6   0.020
 6XP  plan-1  H5   0.020
 6XP  plan-1  O22  0.020
 6XP  plan-2  C19  0.020
 6XP  plan-2  C20  0.020
 6XP  plan-2  N17  0.020
 6XP  plan-2  N18  0.020
 6XP  plan-2  O21  0.020
 6XP  plan-2  H18  0.020
 6XP  plan-3  N13  0.020
 6XP  plan-3  C8   0.020
 6XP  plan-3  C7   0.020
 6XP  plan-3  C11  0.020
 6XP  plan-3  C9   0.020
 6XP  plan-3  C15  0.020
 6XP  plan-3  C10  0.020
 6XP  plan-3  C12  0.020
 6XP  plan-3  C14  0.020
 6XP  plan-3  H13  0.020
 6XP  plan-3  H8   0.020
 6XP  plan-3  H7   0.020
 6XP  plan-3  O16  0.020
 6XP  plan-3  CL2  0.020
 6XP  plan-3  C24  0.020

