# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Jul 31 18:58:50 2022
#   Inital geometry file: a 75 line input string
#   Ligand name: (~{E})-3-(1~{H}-indol-3-yl)-2-oxidanyl-but-2-enoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C\C(=C(O)\C(O)=O)c1c[nH]c2ccccc12
#
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
 JAX  JAX  "(E)-3-(1H-indol-3-yl)-2-oxidanyl-but-2-enoic acid"  ligand  26  16  .  2022-08-10  2022-09-22
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_JAX
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
 JAX  C11  C  CR56   0   0.346   3.3418  -32.8773  14.3321
 JAX  C12  C  CR56   0   0.043   2.1504  -32.5859  15.0335
 JAX  C15  C  CR16   0  -0.285   4.6458  -31.8772  16.0451
 JAX  C16  C  CR16   0  -0.308   4.5982  -32.5302  14.8280
 JAX  C02  C  C      0   0.135  -1.1081  -33.7096  15.2989
 JAX  C03  C  C      0   0.365  -0.6534  -34.9612  16.0543
 JAX  C07  C  CH3    0  -0.712  -0.9881  -31.7026  13.8344
 JAX  C08  C  CR5    0   0.017   1.0583  -33.0836  14.2483
 JAX  C09  C  CR15   0  -0.091   1.6224  -33.6191  13.1257
 JAX  C13  C  CR16   0  -0.373   2.2310  -31.9288  16.2655
 JAX  C14  C  CR16   0  -0.271   3.4728  -31.5767  16.7587
 JAX  N10  N  NR15   0  -0.689   2.9874  -33.5097  13.1782
 JAX  O01  O  OH1    0  -0.654  -2.4236  -33.4867  15.5101
 JAX  O04  O  OC    -1  -0.546   0.5211  -35.3359  16.0143
 JAX  O05  O  O      0  -0.618  -1.6091  -35.4992  16.6735
 JAX  H1   H  HCR6   0   0.242   5.6056  -31.5925  16.4573
 JAX  H2   H  HCR6   0   0.252   5.5034  -32.7624  14.2805
 JAX  H3   H  HCH3   0   0.234  -2.0283  -31.5340  14.1057
 JAX  H4   H  HCH3   0   0.227  -0.4280  -30.7963  14.0803
 JAX  H5   H  HCH3   0   0.227  -0.9394  -31.8050  12.7466
 JAX  H6   H  HCR5   0   0.270   1.1441  -34.0858  12.2784
 JAX  H7   H  HCR6   0   0.231   1.3296  -31.6991  16.8214
 JAX  H8   H  HCR6   0   0.238   3.5492  -31.0645  17.7094
 JAX  H9   H  HNR5   0   0.402   3.6213  -33.8333  12.4675
 JAX  H10  H  HOH1   0   0.441  -2.6483  -34.2440  16.1010
 JAX  C06  C  C      0  -0.124  -0.3804  -32.9022  14.5129

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
 JAX  C09  N10  aromatic  1.370  0.020  1.370
 JAX  C09  C08  aromatic  1.366  0.020  1.366
 JAX  N10  C11  aromatic  1.363  0.020  1.363
 JAX  C07  C06  single    1.506  0.020  1.506
 JAX  C11  C16  aromatic  1.395  0.020  1.395
 JAX  C11  C12  aromatic  1.413  0.020  1.413
 JAX  C08  C06  single    1.474  0.020  1.474
 JAX  C08  C12  aromatic  1.434  0.020  1.434
 JAX  C06  C02  double    1.341  0.020  1.341
 JAX  C16  C15  aromatic  1.382  0.020  1.382
 JAX  C12  C13  aromatic  1.399  0.020  1.399
 JAX  C02  O01  single    1.351  0.020  1.351
 JAX  C02  C03  single    1.531  0.020  1.531
 JAX  O05  C03  deloc     1.260  0.020  1.260
 JAX  C03  O04  deloc     1.233  0.020  1.233
 JAX  C15  C14  aromatic  1.406  0.020  1.406
 JAX  C13  C14  aromatic  1.382  0.020  1.382
 JAX  C15  H1   single    0.930  0.020  1.080
 JAX  C16  H2   single    0.930  0.020  1.080
 JAX  C07  H3   single    0.970  0.020  1.090
 JAX  C07  H4   single    0.970  0.020  1.090
 JAX  C07  H5   single    0.970  0.020  1.090
 JAX  C09  H6   single    0.930  0.020  1.080
 JAX  C13  H7   single    0.930  0.020  1.080
 JAX  C14  H8   single    0.930  0.020  1.080
 JAX  N10  H9   single    0.860  0.020  1.020
 JAX  O01  H10  single    0.850  0.020  0.980

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
 JAX  N10  C11  C16  130.61  3.000
 JAX  C16  C11  C12  122.13  3.000
 JAX  N10  C11  C12  107.26  3.000
 JAX  C13  C12  C08  133.57  3.000
 JAX  C13  C12  C11  119.05  3.000
 JAX  C08  C12  C11  107.38  3.000
 JAX  H1   C15  C14  119.36  3.000
 JAX  H1   C15  C16  119.35  3.000
 JAX  C14  C15  C16  121.29  3.000
 JAX  H2   C16  C15  121.17  3.000
 JAX  H2   C16  C11  121.33  3.000
 JAX  C15  C16  C11  117.50  3.000
 JAX  O01  C02  C06  121.37  3.000
 JAX  O01  C02  C03  110.31  3.000
 JAX  C06  C02  C03  128.32  3.000
 JAX  O05  C03  O04  127.50  3.000
 JAX  O04  C03  C02  121.01  3.000
 JAX  O05  C03  C02  111.49  3.000
 JAX  H5   C07  H4   106.17  3.000
 JAX  H5   C07  H3   107.76  3.000
 JAX  H4   C07  H3   107.77  3.000
 JAX  H5   C07  C06  110.82  3.000
 JAX  H4   C07  C06  110.62  3.000
 JAX  H3   C07  C06  113.37  3.000
 JAX  C09  C08  C06  126.79  3.000
 JAX  C06  C08  C12  127.03  3.000
 JAX  C09  C08  C12  105.76  3.000
 JAX  H6   C09  N10  120.40  3.000
 JAX  H6   C09  C08  129.20  3.000
 JAX  N10  C09  C08  110.40  3.000
 JAX  H7   C13  C14  120.69  3.000
 JAX  H7   C13  C12  120.24  3.000
 JAX  C14  C13  C12  119.07  3.000
 JAX  H8   C14  C13  119.83  3.000
 JAX  H8   C14  C15  119.22  3.000
 JAX  C13  C14  C15  120.95  3.000
 JAX  H9   N10  C09  125.10  3.000
 JAX  H9   N10  C11  125.71  3.000
 JAX  C09  N10  C11  109.18  3.000
 JAX  H10  O01  C02  100.88  3.000
 JAX  C08  C06  C07  114.26  3.000
 JAX  C08  C06  C02  124.10  3.000
 JAX  C07  C06  C02  121.63  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
 JAX  CONST_01  C08  C09  N10  C11     0.00   0.0  0
 JAX  CONST_02  C14  C15  C16  C11     0.00   0.0  0
 JAX  CONST_03  C09  C08  C12  C11     0.00   0.0  0
 JAX  CONST_04  C14  C13  C12  C11     0.00   0.0  0
 JAX  CONST_05  C09  N10  C11  C12     0.00   0.0  0
 JAX  CONST_06  C15  C16  C11  C12     0.00   0.0  0
 JAX  CONST_07  N10  C09  C08  C12     0.00   0.0  0
 JAX  CONST_08  C15  C14  C13  C12     0.00   0.0  0
 JAX  CONST_09  N10  C11  C16  C15   180.00   0.0  0
 JAX  CONST_10  C09  N10  C11  C16   180.00   0.0  0
 JAX  CONST_11  C08  C12  C11  C16   180.00   0.0  0
 JAX  CONST_12  C13  C12  C11  C16     0.00   0.0  0
 JAX  CONST_13  C13  C14  C15  C16     0.00   0.0  0
 JAX  CONST_14  N10  C11  C12  C08     0.00   0.0  0
 JAX  CONST_15  C14  C13  C12  C08   180.00   0.0  0
 JAX  CONST_16  C13  C12  C08  C09   180.00   0.0  0
 JAX  CONST_17  N10  C11  C12  C13   180.00   0.0  0
 JAX  CONST_18  C06  C08  C12  C11   180.00   0.0  0
 JAX  CONST_19  N10  C09  C08  C06   180.00   0.0  0
 JAX  CONST_20  C13  C12  C08  C06     0.00   0.0  0
 JAX  CONST_21  H6   C09  N10  C11   180.00   0.0  0
 JAX  CONST_22  H1   C15  C16  C11   180.00   0.0  0
 JAX  CONST_23  H7   C13  C12  C11   180.00   0.0  0
 JAX  CONST_24  H9   N10  C11  C12   180.00   0.0  0
 JAX  CONST_25  H2   C16  C11  C12   180.00   0.0  0
 JAX  CONST_26  H6   C09  C08  C12   180.00   0.0  0
 JAX  CONST_27  H8   C14  C13  C12   180.00   0.0  0
 JAX  CONST_28  H7   C13  C14  C15   180.00   0.0  0
 JAX  CONST_29  H9   N10  C11  C16     0.00   0.0  0
 JAX  CONST_30  H8   C14  C15  C16   180.00   0.0  0
 JAX  CONST_31  H9   N10  C09  C08   180.00   0.0  0
 JAX  CONST_32  H7   C13  C12  C08     0.00   0.0  0
 JAX  CONST_33  H1   C15  C14  C13   180.00   0.0  0
 JAX  CONST_34  H2   C16  C15  C14   180.00   0.0  0
 JAX  CONST_35  H2   C16  C11  N10     0.00   0.0  0
 JAX  Var_01    C07  C06  C08  C12    92.36  30.0  2
 JAX  Var_02    C02  C06  C08  C12   -86.84  30.0  2
 JAX  Var_03    C09  C08  C06  C02   101.65  30.0  2
 JAX  Var_04    C09  C08  C06  C07   -79.15  30.0  2
 JAX  Var_05    C08  C06  C02  C03    -1.03   0.0  2
 JAX  Var_06    O01  C02  C06  C08   179.59   0.0  2
 JAX  Var_07    H3   C07  C06  C08  -175.13  30.0  3
 JAX  Var_08    H4   C07  C06  C08   -53.94  30.0  3
 JAX  Var_09    H5   C07  C06  C08    63.55  30.0  3
 JAX  Var_10    C07  C06  C02  C03   179.83   0.0  2
 JAX  Var_11    O01  C02  C06  C07     0.44   0.0  2
 JAX  Var_12    O05  C03  C02  C06  -178.36  30.0  2
 JAX  Var_13    O04  C03  C02  C06     1.63  30.0  2
 JAX  Var_14    O05  C03  C02  O01     1.08  30.0  2
 JAX  Var_15    O04  C03  C02  O01  -178.93  30.0  2
 JAX  Var_16    H3   C07  C06  C02     4.09  30.0  3
 JAX  Var_17    H4   C07  C06  C02   125.28  30.0  3
 JAX  Var_18    H5   C07  C06  C02  -117.23  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
 JAX  plan-1  C11  0.020
 JAX  plan-1  C12  0.020
 JAX  plan-1  C15  0.020
 JAX  plan-1  C16  0.020
 JAX  plan-1  C08  0.020
 JAX  plan-1  C09  0.020
 JAX  plan-1  C13  0.020
 JAX  plan-1  C14  0.020
 JAX  plan-1  N10  0.020
 JAX  plan-1  H1   0.020
 JAX  plan-1  H2   0.020
 JAX  plan-1  H6   0.020
 JAX  plan-1  H7   0.020
 JAX  plan-1  H8   0.020
 JAX  plan-1  H9   0.020
 JAX  plan-1  C06  0.020
 JAX  plan-2  C02  0.020
 JAX  plan-2  C03  0.020
 JAX  plan-2  O04  0.020
 JAX  plan-2  O05  0.020
 JAX  plan-3  C02  0.020
 JAX  plan-3  C03  0.020
 JAX  plan-3  C07  0.020
 JAX  plan-3  C08  0.020
 JAX  plan-3  O01  0.020
 JAX  plan-3  C06  0.020

