# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Apr 19 18:04:50 2020
#   Inital geometry file: a 126 line input string
#   Ligand name: ~{N}-[(4-chlorophenyl)methyl]-~{N}-methyl-6-oxidanyl-3-(phenylmethyl)-1~{H}-indazole-5-carboxamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CN(Cc1ccc(Cl)cc1)C(=O)c2cc3c(Cc4ccccc4)n[nH]c3cc2O
#
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
 C4T  C4T  ~{N}-[(4-chlorophenyl)methyl]-~{N}-methyl-6-oxidanyl-3-(phenylmethyl)-1~{H}-indazole-5-carboxamide  ligand  49  29  .  2021-08-07  2021-08-07  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_C4T
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
 C4T  C1   C   CR6   0  -0.211   0.9734   2.3436  -0.3928
 C4T  C2   C   CR6   0   0.359   1.7731   3.5276  -0.3965
 C4T  C3   C   CR16  0  -0.407   3.0254   3.5445   0.1870
 C4T  O5   O   OH1   0  -0.637   1.3325   4.6483  -0.9845
 C4T  C9   C   CR56  0  -0.105   2.6320   1.2352   0.9289
 C4T  C10  C   CR56  0   0.446   3.4432   2.3797   0.8352
 C4T  C13  C   CR5   0   0.246   3.3977   0.3028   1.6911
 C4T  C14  C   CH2   0  -0.593   2.9921  -1.0682   2.1245
 C4T  C15  C   CR6   0   0.102   2.3506  -1.8678   1.0160
 C4T  C16  C   CR16  0  -0.317   1.0454  -2.3346   1.1384
 C4T  C19  C   CR16  0  -0.226   0.4489  -3.0607   0.1143
 C4T  C20  C   CR16  0  -0.283   3.0493  -2.1399  -0.1584
 C4T  C21  C   CH3   0  -0.552   0.0516   0.1783  -2.1229
 C4T  C22  C   CH2   0  -0.392  -2.2243   1.0517  -1.8851
 C4T  C24  C   CR16  0  -0.290  -2.6119  -0.4012   0.1271
 C4T  C27  C   CR16  0  -0.192  -2.9783  -1.5945   0.7259
 C4T  C4   C   CR16  0  -0.323   1.3926   1.2258   0.3015
 C4T  C6   C   C     0   0.562  -0.3632   2.3680  -1.0341
 C4T  N7   N   NT    0  -0.445  -0.8074   1.2360  -1.6153
 C4T  O8   O   O     0  -0.519  -1.0396   3.4022  -0.9953
 C4T  N11  N   NR15  0  -0.562   4.5752   2.0733   1.4996
 C4T  N12  N   N     0  -0.258   4.5509   0.8279   2.0096
 C4T  C17  C   CR16  0  -0.271   1.1548  -3.3300  -1.0491
 C4T  C18  C   CR16  0  -0.235   2.4585  -2.8660  -1.1822
 C4T  C23  C   CR6   0   0.119  -2.6938  -0.2350  -1.2535
 C4T  C25  C   CR6   0  -0.056  -3.4336  -2.6349  -0.0715
 C4T  C26  C   CR16  0  -0.194  -3.5334  -2.4946  -1.4446
 C4T  C28  C   CR16  0  -0.306  -3.1590  -1.2901  -2.0266
 C4T  CL   CL  CL    0  -0.129  -3.8616  -4.1450   0.6667
 C4T  H1   H   HCR6  0   0.276   3.6334   4.4395   0.1633
 C4T  H2   H   HOH1  0   0.473   0.3704   4.5587  -1.1248
 C4T  H3   H   HCH2  0   0.274   3.8710  -1.5896   2.5109
 C4T  H4   H   HCH2  0   0.272   2.2876  -0.9860   2.9572
 C4T  H5   H   HCR6  0   0.252   0.4852  -2.1211   2.0415
 C4T  H6   H   HCR6  0   0.247  -0.5701  -3.4079   0.2261
 C4T  H7   H   HCR6  0   0.248   4.0648  -1.7794  -0.2770
 C4T  H8   H   HCH3  0   0.261   0.0634  -0.7034  -1.4820
 C4T  H9   H   HCH3  0   0.263  -0.3221  -0.1256  -3.1018
 C4T  H10  H   HCH3  0   0.273   1.0700   0.5306  -2.2520
 C4T  H11  H   HCH2  0   0.286  -2.7750   1.9002  -1.4830
 C4T  H12  H   HCH2  0   0.268  -2.4008   1.0308  -2.9639
 C4T  H14  H   HCR6  0   0.279  -2.9055  -1.7144   1.7984
 C4T  H15  H   HCR6  0   0.271   0.7581   0.3521   0.3624
 C4T  H16  H   HNR5  0   0.416   5.3852   2.6530   1.6445
 C4T  H17  H   HCR6  0   0.253   0.6906  -3.8904  -1.8502
 C4T  H18  H   HCR6  0   0.254   3.0161  -3.0685  -2.0877
 C4T  H19  H   HCR6  0   0.279  -3.8868  -3.3119  -2.0584
 C4T  H20  H   HCR6  0   0.265  -3.2234  -1.1843  -3.1027
 C4T  H13  H   HCR6  0   0.262  -2.2507   0.4080   0.7512

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
 C4T  C21  N7   single    1.454  0.020  1.454
 C4T  O8   C6   double    1.236  0.020  1.236
 C4T  N7   C6   single    1.348  0.020  1.348
 C4T  N7   C22  single    1.454  0.020  1.454
 C4T  C6   C1   single    1.483  0.020  1.483
 C4T  C19  C17  aromatic  1.387  0.020  1.387
 C4T  C19  C16  aromatic  1.390  0.020  1.390
 C4T  C17  C18  aromatic  1.390  0.020  1.390
 C4T  C24  C27  aromatic  1.384  0.020  1.384
 C4T  C24  C23  aromatic  1.393  0.020  1.393
 C4T  C22  C23  single    1.508  0.020  1.508
 C4T  C27  C25  aromatic  1.388  0.020  1.388
 C4T  C1   C4   aromatic  1.381  0.020  1.381
 C4T  C1   C2   aromatic  1.429  0.020  1.429
 C4T  C16  C15  aromatic  1.392  0.020  1.392
 C4T  O5   C2   single    1.340  0.020  1.340
 C4T  C23  C28  aromatic  1.388  0.020  1.388
 C4T  C4   C9   aromatic  1.389  0.020  1.389
 C4T  C18  C20  aromatic  1.387  0.020  1.387
 C4T  C2   C3   aromatic  1.382  0.020  1.382
 C4T  C15  C20  aromatic  1.393  0.020  1.393
 C4T  C15  C14  single    1.510  0.020  1.510
 C4T  C25  CL   single    1.735  0.020  1.735
 C4T  C25  C26  aromatic  1.384  0.020  1.384
 C4T  C28  C26  aromatic  1.389  0.020  1.389
 C4T  C9   C10  aromatic  1.406  0.020  1.406
 C4T  C9   C13  aromatic  1.427  0.020  1.427
 C4T  C3   C10  aromatic  1.397  0.020  1.397
 C4T  C14  C13  single    1.494  0.020  1.494
 C4T  C10  N11  aromatic  1.348  0.020  1.348
 C4T  C13  N12  aromatic  1.307  0.020  1.307
 C4T  N11  N12  aromatic  1.346  0.020  1.346
 C4T  C3   H1   single    0.930  0.020  1.080
 C4T  O5   H2   single    0.850  0.020  0.980
 C4T  C14  H3   single    0.970  0.020  1.090
 C4T  C14  H4   single    0.970  0.020  1.090
 C4T  C16  H5   single    0.930  0.020  1.080
 C4T  C19  H6   single    0.930  0.020  1.080
 C4T  C20  H7   single    0.930  0.020  1.080
 C4T  C21  H8   single    0.970  0.020  1.090
 C4T  C21  H9   single    0.970  0.020  1.090
 C4T  C21  H10  single    0.970  0.020  1.090
 C4T  C22  H11  single    0.970  0.020  1.090
 C4T  C22  H12  single    0.970  0.020  1.090
 C4T  C24  H13  single    0.930  0.020  1.080
 C4T  C27  H14  single    0.930  0.020  1.080
 C4T  C4   H15  single    0.930  0.020  1.080
 C4T  N11  H16  single    0.860  0.020  1.020
 C4T  C17  H17  single    0.930  0.020  1.080
 C4T  C18  H18  single    0.930  0.020  1.080
 C4T  C26  H19  single    0.930  0.020  1.080
 C4T  C28  H20  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
 C4T  C6   C1   C4   120.29  3.000
 C4T  C4   C1   C2   120.14  3.000
 C4T  C6   C1   C2   119.33  3.000
 C4T  O5   C2   C3   118.23  3.000
 C4T  C3   C2   C1   121.09  3.000
 C4T  O5   C2   C1   120.67  3.000
 C4T  H1   C3   C10  122.12  3.000
 C4T  H1   C3   C2   120.67  3.000
 C4T  C10  C3   C2   117.18  3.000
 C4T  H2   O5   C2   108.08  3.000
 C4T  C4   C9   C13  135.68  3.000
 C4T  C13  C9   C10  104.95  3.000
 C4T  C4   C9   C10  119.35  3.000
 C4T  N11  C10  C9   105.46  3.000
 C4T  N11  C10  C3   132.02  3.000
 C4T  C9   C10  C3   122.49  3.000
 C4T  N12  C13  C14  122.53  3.000
 C4T  N12  C13  C9   109.95  3.000
 C4T  C14  C13  C9   127.50  3.000
 C4T  H4   C14  H3   106.54  3.000
 C4T  H4   C14  C15  108.97  3.000
 C4T  H3   C14  C15  110.40  3.000
 C4T  H4   C14  C13  109.07  3.000
 C4T  H3   C14  C13  108.79  3.000
 C4T  C15  C14  C13  112.86  3.000
 C4T  C20  C15  C16  118.62  3.000
 C4T  C20  C15  C14  120.61  3.000
 C4T  C16  C15  C14  120.77  3.000
 C4T  H5   C16  C19  119.67  3.000
 C4T  H5   C16  C15  119.47  3.000
 C4T  C19  C16  C15  120.86  3.000
 C4T  H6   C19  C17  120.23  3.000
 C4T  H6   C19  C16  119.71  3.000
 C4T  C17  C19  C16  120.06  3.000
 C4T  H7   C20  C18  119.49  3.000
 C4T  H7   C20  C15  119.80  3.000
 C4T  C18  C20  C15  120.71  3.000
 C4T  H10  C21  H9   107.76  3.000
 C4T  H10  C21  H8   108.80  3.000
 C4T  H9   C21  H8   107.82  3.000
 C4T  H10  C21  N7   111.08  3.000
 C4T  H9   C21  N7   108.27  3.000
 C4T  H8   C21  N7   112.92  3.000
 C4T  H12  C22  H11  107.32  3.000
 C4T  H12  C22  C23  110.28  3.000
 C4T  H11  C22  C23  110.66  3.000
 C4T  H12  C22  N7   110.05  3.000
 C4T  H11  C22  N7   109.00  3.000
 C4T  C23  C22  N7   109.50  3.000
 C4T  H13  C24  C23  120.08  3.000
 C4T  H13  C24  C27  118.86  3.000
 C4T  C23  C24  C27  121.06  3.000
 C4T  H14  C27  C25  120.58  3.000
 C4T  H14  C27  C24  120.43  3.000
 C4T  C25  C27  C24  118.98  3.000
 C4T  H15  C4   C9   120.23  3.000
 C4T  H15  C4   C1   120.27  3.000
 C4T  C9   C4   C1   119.50  3.000
 C4T  O8   C6   N7   122.39  3.000
 C4T  N7   C6   C1   118.02  3.000
 C4T  O8   C6   C1   119.56  3.000
 C4T  C6   N7   C22  120.51  3.000
 C4T  C22  N7   C21  114.75  3.000
 C4T  C6   N7   C21  124.53  3.000
 C4T  H16  N11  N12  119.53  3.000
 C4T  H16  N11  C10  128.01  3.000
 C4T  N12  N11  C10  112.46  3.000
 C4T  N11  N12  C13  107.18  3.000
 C4T  H17  C17  C18  120.28  3.000
 C4T  H17  C17  C19  120.20  3.000
 C4T  C18  C17  C19  119.52  3.000
 C4T  H18  C18  C17  120.04  3.000
 C4T  H18  C18  C20  119.73  3.000
 C4T  C17  C18  C20  120.23  3.000
 C4T  C28  C23  C24  118.75  3.000
 C4T  C28  C23  C22  121.30  3.000
 C4T  C24  C23  C22  119.90  3.000
 C4T  CL   C25  C26  119.52  3.000
 C4T  C26  C25  C27  121.19  3.000
 C4T  CL   C25  C27  119.28  3.000
 C4T  H19  C26  C28  120.37  3.000
 C4T  H19  C26  C25  120.67  3.000
 C4T  C28  C26  C25  118.95  3.000
 C4T  H20  C28  C26  119.00  3.000
 C4T  H20  C28  C23  119.93  3.000
 C4T  C26  C28  C23  121.07  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
 C4T  CONST_01  C10  C9   C4   C1      0.00   0.0  0
 C4T  CONST_02  C13  C9   C4   C1    180.00   0.0  0
 C4T  CONST_03  C10  C3   C2   C1      0.00   0.0  0
 C4T  CONST_04  C9   C4   C1   C2      0.00   0.0  0
 C4T  CONST_05  C9   C10  C3   C2      0.00   0.0  0
 C4T  CONST_06  N11  C10  C3   C2    180.00   0.0  0
 C4T  CONST_07  C4   C1   C2   C3      0.00   0.0  0
 C4T  CONST_08  C4   C9   C10  C3      0.00   0.0  0
 C4T  CONST_09  C13  C9   C10  C3    180.00   0.0  0
 C4T  CONST_10  N12  N11  C10  C3    180.00   0.0  0
 C4T  CONST_11  N12  N11  C10  C9      0.00   0.0  0
 C4T  CONST_12  N11  N12  C13  C9      0.00   0.0  0
 C4T  CONST_13  N12  C13  C9   C10     0.00   0.0  0
 C4T  CONST_14  C13  N12  N11  C10     0.00   0.0  0
 C4T  CONST_15  N11  C10  C9   C13     0.00   0.0  0
 C4T  CONST_16  C17  C19  C16  C15     0.00   0.0  0
 C4T  CONST_17  C17  C18  C20  C15     0.00   0.0  0
 C4T  CONST_18  C18  C17  C19  C16     0.00   0.0  0
 C4T  CONST_19  C18  C20  C15  C16     0.00   0.0  0
 C4T  CONST_20  C20  C18  C17  C19     0.00   0.0  0
 C4T  CONST_21  C20  C15  C16  C19     0.00   0.0  0
 C4T  CONST_22  C26  C25  C27  C24     0.00   0.0  0
 C4T  CONST_23  C26  C28  C23  C24     0.00   0.0  0
 C4T  CONST_24  C28  C23  C24  C27     0.00   0.0  0
 C4T  CONST_25  C28  C26  C25  C27     0.00   0.0  0
 C4T  CONST_26  N11  C10  C9   C4    180.00   0.0  0
 C4T  CONST_27  N12  C13  C9   C4    180.00   0.0  0
 C4T  CONST_28  C25  C27  C24  C23     0.00   0.0  0
 C4T  CONST_29  C25  C26  C28  C23     0.00   0.0  0
 C4T  CONST_30  C6   C1   C2   C3    180.00   0.0  0
 C4T  CONST_31  C4   C1   C2   O5    180.00   0.0  0
 C4T  CONST_32  C10  C3   C2   O5    180.00   0.0  0
 C4T  CONST_33  C6   C1   C4   C9    180.00   0.0  0
 C4T  CONST_34  C14  C13  C9   C10   180.00   0.0  0
 C4T  CONST_35  C19  C16  C15  C14   180.00   0.0  0
 C4T  CONST_36  C18  C20  C15  C14   180.00   0.0  0
 C4T  CONST_37  C4   C9   C13  C14     0.00   0.0  0
 C4T  CONST_38  N11  N12  C13  C14   180.00   0.0  0
 C4T  CONST_39  C27  C24  C23  C22   180.00   0.0  0
 C4T  CONST_40  C26  C28  C23  C22   180.00   0.0  0
 C4T  CONST_41  CL   C25  C27  C24   180.00   0.0  0
 C4T  CONST_42  CL   C25  C26  C28   180.00   0.0  0
 C4T  CONST_43  H1   C3   C2   C1    180.00   0.0  0
 C4T  CONST_44  H15  C4   C1   C2    180.00   0.0  0
 C4T  CONST_45  H16  N11  C10  C3      0.00   0.0  0
 C4T  CONST_46  H6   C19  C16  C15   180.00   0.0  0
 C4T  CONST_47  H18  C18  C20  C15   180.00   0.0  0
 C4T  CONST_48  H17  C17  C19  C16   180.00   0.0  0
 C4T  CONST_49  H7   C20  C15  C16   180.00   0.0  0
 C4T  CONST_50  H5   C16  C15  C20   180.00   0.0  0
 C4T  CONST_51  H20  C28  C23  C24   180.00   0.0  0
 C4T  CONST_52  H19  C26  C25  C27   180.00   0.0  0
 C4T  CONST_53  H14  C27  C24  C23   180.00   0.0  0
 C4T  CONST_54  H13  C24  C27  C25   180.00   0.0  0
 C4T  Var_01    C15  C14  C13  C9     45.71  30.0  2
 C4T  Var_02    C16  C15  C14  C13  -119.45  30.0  2
 C4T  Var_03    O8   C6   C1   C2    -34.02  30.0  2
 C4T  Var_04    N7   C22  C23  C24    61.30  30.0  3
 C4T  Var_05    C23  C22  N7   C21    59.83  30.0  3
 C4T  Var_06    H8   C21  N7   C22   -79.95  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
 C4T  plan-1  C14  0.020
 C4T  plan-1  C15  0.020
 C4T  plan-1  C16  0.020
 C4T  plan-1  C19  0.020
 C4T  plan-1  C20  0.020
 C4T  plan-1  C17  0.020
 C4T  plan-1  C18  0.020
 C4T  plan-1  H5   0.020
 C4T  plan-1  H6   0.020
 C4T  plan-1  H7   0.020
 C4T  plan-1  H17  0.020
 C4T  plan-1  H18  0.020
 C4T  plan-2  C22  0.020
 C4T  plan-2  C24  0.020
 C4T  plan-2  C27  0.020
 C4T  plan-2  C23  0.020
 C4T  plan-2  C25  0.020
 C4T  plan-2  C26  0.020
 C4T  plan-2  C28  0.020
 C4T  plan-2  CL   0.020
 C4T  plan-2  H14  0.020
 C4T  plan-2  H19  0.020
 C4T  plan-2  H20  0.020
 C4T  plan-2  H13  0.020
 C4T  plan-3  C1   0.020
 C4T  plan-3  C2   0.020
 C4T  plan-3  C3   0.020
 C4T  plan-3  O5   0.020
 C4T  plan-3  C9   0.020
 C4T  plan-3  C10  0.020
 C4T  plan-3  C13  0.020
 C4T  plan-3  C14  0.020
 C4T  plan-3  C4   0.020
 C4T  plan-3  C6   0.020
 C4T  plan-3  N11  0.020
 C4T  plan-3  N12  0.020
 C4T  plan-3  H1   0.020
 C4T  plan-3  H15  0.020
 C4T  plan-3  H16  0.020
 C4T  plan-4  C1   0.020
 C4T  plan-4  C21  0.020
 C4T  plan-4  C22  0.020
 C4T  plan-4  C6   0.020
 C4T  plan-4  N7   0.020
 C4T  plan-4  O8   0.020

