# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Apr 11 06:00:08 2020
#   Inital geometry file: a 85 line input string
#   Ligand name: 3-oxidanylidene-2-phenyl-1~{H}-isoindole-4-carboxylic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC(=O)c1cccc2CN(C(=O)c12)c3ccccc3
#
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
 6TJ  6TJ  '3-oxidanylidene-2-phenyl-1~{H}-isoindole-4-carboxylic acid'  ligand  29  19  .  2022-07-23  2022-07-26
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_6TJ
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
 6TJ  O01  O  OC    -1  -0.597  -3.4299  -2.0416  -0.9932
 6TJ  C02  C  C      0   0.342  -3.0460  -1.5543   0.0830
 6TJ  O03  O  O      0  -0.593  -3.0011  -2.0889   1.2018
 6TJ  C04  C  CR6    0  -0.037  -2.6265  -0.0945   0.0364
 6TJ  C05  C  CR16   0  -0.316  -3.5895   0.9121   0.0025
 6TJ  C06  C  CR16   0  -0.232  -3.2354   2.2592  -0.0006
 6TJ  C07  C  CR16   0  -0.351  -1.9032   2.6577   0.0150
 6TJ  C08  C  CR56   0   0.105  -0.9449   1.6627   0.0295
 6TJ  C09  C  CH2    0  -0.303   0.5417   1.7789   0.0359
 6TJ  N10  N  NR5    0  -0.631   0.9852   0.3917   0.0173
 6TJ  C11  C  CR5    0   0.547  -0.0741  -0.4914   0.0236
 6TJ  O12  O  O      0  -0.457  -0.0075  -1.7045   0.0044
 6TJ  C13  C  CR56   0  -0.092  -1.3000   0.3250   0.0421
 6TJ  C14  C  C      0   0.375   2.3506   0.0800  -0.0150
 6TJ  C15  C  C1     0  -0.346   3.2828   1.1207   0.0756
 6TJ  C16  C  C1     0  -0.243   4.6439   0.8596   0.0403
 6TJ  C17  C  C1     0  -0.275   5.1149  -0.4382  -0.0862
 6TJ  C18  C  C1     0  -0.243   4.1948  -1.4724  -0.1783
 6TJ  C19  C  C1     0  -0.321   2.8297  -1.2297  -0.1447
 6TJ  H2   H  HCR6   0   0.256  -4.6402   0.6484  -0.0129
 6TJ  H3   H  HCR6   0   0.261  -4.0155   3.0094  -0.0184
 6TJ  H4   H  HCR6   0   0.255  -1.6352   3.7064   0.0101
 6TJ  H5   H  HCH2   0   0.281   0.9158   2.3203  -0.8367
 6TJ  H6   H  HCH2   0   0.281   0.8999   2.2956   0.9303
 6TJ  H7   H  H      0   0.281   2.9628   2.1481   0.1761
 6TJ  H8   H  H      0   0.259   5.3377   1.6869   0.1134
 6TJ  H9   H  H      0   0.254   6.1776  -0.6386  -0.1138
 6TJ  H10  H  H      0   0.256   4.5369  -2.4944  -0.2817
 6TJ  H11  H  H      0   0.284   2.1499  -2.0607  -0.2199

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
 6TJ  C07  C06  aromatic  1.391  0.020  1.391
 6TJ  C07  C08  aromatic  1.382  0.020  1.382
 6TJ  C06  C05  aromatic  1.393  0.020  1.393
 6TJ  C08  C09  single    1.491  0.020  1.491
 6TJ  C08  C13  aromatic  1.384  0.020  1.384
 6TJ  C09  N10  single    1.457  0.020  1.457
 6TJ  C05  C04  aromatic  1.393  0.020  1.393
 6TJ  C13  C04  aromatic  1.391  0.020  1.391
 6TJ  C13  C11  single    1.473  0.020  1.473
 6TJ  C15  C16  aromatic  1.386  0.020  1.386
 6TJ  C15  C14  aromatic  1.400  0.020  1.400
 6TJ  C04  C02  single    1.520  0.020  1.520
 6TJ  N10  C14  single    1.401  0.020  1.401
 6TJ  N10  C11  single    1.379  0.020  1.379
 6TJ  C16  C17  aromatic  1.386  0.020  1.386
 6TJ  C14  C19  aromatic  1.401  0.020  1.401
 6TJ  C11  O12  double    1.215  0.020  1.215
 6TJ  C02  O03  deloc     1.241  0.020  1.241
 6TJ  C02  O01  deloc     1.242  0.020  1.242
 6TJ  C17  C18  aromatic  1.387  0.020  1.387
 6TJ  C19  C18  aromatic  1.387  0.020  1.387
 6TJ  C05  H2   single    0.930  0.020  1.080
 6TJ  C06  H3   single    0.930  0.020  1.080
 6TJ  C07  H4   single    0.930  0.020  1.080
 6TJ  C09  H5   single    0.970  0.020  1.090
 6TJ  C09  H6   single    0.970  0.020  1.090
 6TJ  C15  H7   single    0.930  0.020  1.080
 6TJ  C16  H8   single    0.930  0.020  1.080
 6TJ  C17  H9   single    0.930  0.020  1.080
 6TJ  C18  H10  single    0.930  0.020  1.080
 6TJ  C19  H11  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
 6TJ  C04  C02  O03  115.57  3.000
 6TJ  O03  C02  O01  128.56  3.000
 6TJ  C04  C02  O01  115.82  3.000
 6TJ  C13  C04  C05  116.18  3.000
 6TJ  C13  C04  C02  123.55  3.000
 6TJ  C05  C04  C02  120.26  3.000
 6TJ  H2   C05  C06  118.81  3.000
 6TJ  H2   C05  C04  119.65  3.000
 6TJ  C06  C05  C04  121.54  3.000
 6TJ  H3   C06  C07  119.47  3.000
 6TJ  H3   C06  C05  119.15  3.000
 6TJ  C07  C06  C05  121.38  3.000
 6TJ  H4   C07  C08  121.74  3.000
 6TJ  H4   C07  C06  120.98  3.000
 6TJ  C08  C07  C06  117.27  3.000
 6TJ  C13  C08  C09  109.34  3.000
 6TJ  C13  C08  C07  121.21  3.000
 6TJ  C09  C08  C07  129.45  3.000
 6TJ  H6   C09  H5   107.87  3.000
 6TJ  H6   C09  N10  111.15  3.000
 6TJ  H5   C09  N10  110.94  3.000
 6TJ  H6   C09  C08  111.53  3.000
 6TJ  H5   C09  C08  112.11  3.000
 6TJ  N10  C09  C08  103.25  3.000
 6TJ  C14  N10  C11  127.32  3.000
 6TJ  C11  N10  C09  112.08  3.000
 6TJ  C14  N10  C09  120.59  3.000
 6TJ  C13  C11  O12  126.81  3.000
 6TJ  O12  C11  N10  126.66  3.000
 6TJ  C13  C11  N10  106.53  3.000
 6TJ  C11  C13  C08  108.78  3.000
 6TJ  C11  C13  C04  128.78  3.000
 6TJ  C08  C13  C04  122.41  3.000
 6TJ  C19  C14  C15  118.25  3.000
 6TJ  C19  C14  N10  122.93  3.000
 6TJ  C15  C14  N10  118.82  3.000
 6TJ  H7   C15  C16  118.17  3.000
 6TJ  H7   C15  C14  121.03  3.000
 6TJ  C16  C15  C14  120.80  3.000
 6TJ  H8   C16  C17  120.26  3.000
 6TJ  H8   C16  C15  118.93  3.000
 6TJ  C17  C16  C15  120.80  3.000
 6TJ  H9   C17  C18  120.77  3.000
 6TJ  H9   C17  C16  120.63  3.000
 6TJ  C18  C17  C16  118.60  3.000
 6TJ  H10  C18  C19  118.59  3.000
 6TJ  H10  C18  C17  120.03  3.000
 6TJ  C19  C18  C17  121.38  3.000
 6TJ  H11  C19  C18  119.00  3.000
 6TJ  H11  C19  C14  120.82  3.000
 6TJ  C18  C19  C14  120.17  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
 6TJ  CONST_01  C07  C06  C05  C04    0.00   0.0  0
 6TJ  CONST_02  C07  C08  C13  C04    0.00   0.0  0
 6TJ  CONST_03  C08  C07  C06  C05    0.00   0.0  0
 6TJ  CONST_04  C08  C13  C04  C05    0.00   0.0  0
 6TJ  CONST_05  C13  C08  C07  C06    0.00   0.0  0
 6TJ  CONST_06  C13  C04  C05  C06    0.00   0.0  0
 6TJ  CONST_07  C17  C16  C15  C14    0.00   0.0  0
 6TJ  CONST_08  C17  C18  C19  C14    0.00   0.0  0
 6TJ  CONST_09  C18  C17  C16  C15    0.00   0.0  0
 6TJ  CONST_10  C18  C19  C14  C15    0.00   0.0  0
 6TJ  CONST_11  C19  C14  C15  C16    0.00   0.0  0
 6TJ  CONST_12  C19  C18  C17  C16    0.00   0.0  0
 6TJ  CONST_13  C16  C15  C14  N10  180.00   0.0  0
 6TJ  CONST_14  C18  C19  C14  N10  180.00   0.0  0
 6TJ  CONST_15  C13  C11  N10  C09    0.00   0.0  0
 6TJ  CONST_16  C14  N10  C11  C13  180.00   0.0  0
 6TJ  CONST_17  C06  C05  C04  C02  180.00   0.0  0
 6TJ  CONST_18  C08  C13  C04  C02  180.00   0.0  0
 6TJ  CONST_19  C11  C13  C04  C02    0.00   0.0  0
 6TJ  CONST_20  O12  C11  N10  C09  180.00   0.0  0
 6TJ  CONST_21  C14  N10  C11  O12    0.00   0.0  0
 6TJ  CONST_22  H3   C06  C05  C04  180.00   0.0  0
 6TJ  CONST_23  H4   C07  C06  C05  180.00   0.0  0
 6TJ  CONST_24  H2   C05  C06  C07  180.00   0.0  0
 6TJ  CONST_25  H7   C15  C14  N10    0.00   0.0  0
 6TJ  CONST_26  H11  C19  C14  N10    0.00   0.0  0
 6TJ  CONST_27  H8   C16  C15  C14  180.00   0.0  0
 6TJ  CONST_28  H10  C18  C19  C14  180.00   0.0  0
 6TJ  CONST_29  H9   C17  C16  C15  180.00   0.0  0
 6TJ  Var_01    C15  C14  N10  C09    4.89  30.0  2
 6TJ  Var_02    H5   C09  C08  C07  -59.14  30.0  1
 6TJ  Var_03    C05  C04  C02  O01   77.31  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
 6TJ  plan-1  N10  0.020
 6TJ  plan-1  C14  0.020
 6TJ  plan-1  C15  0.020
 6TJ  plan-1  C16  0.020
 6TJ  plan-1  C17  0.020
 6TJ  plan-1  C18  0.020
 6TJ  plan-1  C19  0.020
 6TJ  plan-1  H7   0.020
 6TJ  plan-1  H8   0.020
 6TJ  plan-1  H9   0.020
 6TJ  plan-1  H10  0.020
 6TJ  plan-1  H11  0.020
 6TJ  plan-2  C02  0.020
 6TJ  plan-2  C04  0.020
 6TJ  plan-2  C05  0.020
 6TJ  plan-2  C06  0.020
 6TJ  plan-2  C07  0.020
 6TJ  plan-2  C08  0.020
 6TJ  plan-2  C09  0.020
 6TJ  plan-2  N10  0.020
 6TJ  plan-2  C11  0.020
 6TJ  plan-2  O12  0.020
 6TJ  plan-2  C13  0.020
 6TJ  plan-2  C14  0.020
 6TJ  plan-2  H2   0.020
 6TJ  plan-2  H3   0.020
 6TJ  plan-2  H4   0.020
 6TJ  plan-3  O01  0.020
 6TJ  plan-3  C02  0.020
 6TJ  plan-3  O03  0.020
 6TJ  plan-3  C04  0.020

