# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Mar 31 18:50:30 2020
#   Inital geometry file: a 108 line input string
#   Ligand name: [1-(2-methoxy-5-nitrobenzyl)-1H-indol-3-yl]acetic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: COc1ccc(cc1Cn2cc(CC(O)=O)c3ccccc23)[N+]([O-])=O
#
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
 2T7  2T7  '[1-(2-methoxy-5-nitrobenzyl)-1H-indol-3-yl]acetic acid'  ligand  40  25  .  2021-08-04  2021-08-04  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_2T7
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
 2T7  O25  O  O      0  -0.390  -4.8346  -2.0087  -1.0828
 2T7  N23  N  N      1   0.324  -4.9527  -1.1084  -0.2816
 2T7  O24  O  O     -1  -0.389  -5.9184  -0.9764   0.4373
 2T7  C20  C  C      0   0.244  -3.8868  -0.1411  -0.1775
 2T7  C21  C  C1     0  -0.261  -3.9909   0.8975   0.7333
 2T7  C18  C  C1     0  -0.377  -2.9707   1.8250   0.8251
 2T7  C16  C  C      0   0.407  -1.8450   1.7132   0.0079
 2T7  O19  O  O2     0  -0.446  -0.8348   2.5757   0.0163
 2T7  C22  C  CH3    0  -0.443  -0.8388   3.6543   0.9375
 2T7  C17  C  C1     0  -0.335  -2.7635  -0.2668  -0.9906
 2T7  C15  C  C      0   0.048  -1.7327   0.6436  -0.9020
 2T7  C3   C  CH2    0  -0.407  -0.5008   0.4948  -1.7594
 2T7  N2   N  NR5    0  -0.525   0.6849   0.1817  -0.9962
 2T7  C10  C  CR56   0   0.371   0.9399  -1.0059  -0.3656
 2T7  C5   C  CR16   0  -0.302   0.2137  -2.1965  -0.3432
 2T7  C4   C  CR16   0  -0.284   0.7331  -3.2512   0.3862
 2T7  C9   C  CR56   0   0.034   2.1699  -0.8709   0.3170
 2T7  C6   C  CR16   0  -0.369   2.6724  -1.9552   1.0411
 2T7  C1   C  CR16   0  -0.275   1.9487  -3.1323   1.0777
 2T7  C8   C  CR5    0   0.054   2.6525   0.4555   0.0732
 2T7  C7   C  CR15   0  -0.076   1.7152   1.0497  -0.7169
 2T7  C11  C  CH2    0  -0.732   3.9018   1.0574   0.6094
 2T7  C12  C  C      0   0.415   5.2206   0.4647   0.0607
 2T7  O13  O  OC    -1  -0.631   6.2607   0.8703   0.6212
 2T7  O14  O  O      0  -0.595   5.1504  -0.3402  -0.8841
 2T7  H1   H  H      0   0.301  -4.8558   0.9994   1.3723
 2T7  H2   H  H      0   0.301  -3.0710   2.6315   1.5372
 2T7  H3   H  HCH3   0   0.241  -1.6831   4.3256   0.7681
 2T7  H4   H  HCH3   0   0.241  -0.8617   3.2980   1.9690
 2T7  H5   H  HCH3   0   0.269   0.0861   4.1986   0.7707
 2T7  H6   H  H      0   0.295  -2.6919  -1.0775  -1.7029
 2T7  H7   H  HCH2   0   0.284  -0.6694  -0.2898  -2.4993
 2T7  H8   H  HCH2   0   0.289  -0.3044   1.4100  -2.3183
 2T7  H9   H  HCR6   0   0.249  -0.7218  -2.3111  -0.8747
 2T7  H10  H  HCR6   0   0.246   0.1902  -4.1871   0.4208
 2T7  H11  H  HCR6   0   0.237   3.6128  -1.8735   1.5726
 2T7  H12  H  HCR6   0   0.242   2.3230  -3.9781   1.6404
 2T7  H13  H  HCR5   0   0.271   1.6988   2.0528  -1.1148
 2T7  H14  H  HCH2   0   0.245   3.9074   2.1334   0.4052
 2T7  H15  H  HCH2   0   0.230   3.9205   0.9740   1.7017

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
 2T7  O25  N23  double    1.211  0.020  1.211
 2T7  O24  N23  single    1.211  0.020  1.211
 2T7  N23  C20  single    1.443  0.020  1.443
 2T7  C21  C20  aromatic  1.385  0.020  1.385
 2T7  C21  C18  aromatic  1.382  0.020  1.382
 2T7  C20  C17  aromatic  1.392  0.020  1.392
 2T7  C18  C16  aromatic  1.396  0.020  1.396
 2T7  C17  C15  aromatic  1.378  0.020  1.378
 2T7  C16  C15  aromatic  1.409  0.020  1.409
 2T7  C16  O19  single    1.328  0.020  1.328
 2T7  C15  C3   single    1.508  0.020  1.508
 2T7  O19  C22  single    1.418  0.020  1.418
 2T7  C3   N2   single    1.444  0.020  1.444
 2T7  N2   C7   aromatic  1.376  0.020  1.376
 2T7  N2   C10  aromatic  1.369  0.020  1.369
 2T7  C7   C8   aromatic  1.362  0.020  1.362
 2T7  C10  C5   aromatic  1.395  0.020  1.395
 2T7  C10  C9   aromatic  1.413  0.020  1.413
 2T7  C5   C4   aromatic  1.384  0.020  1.384
 2T7  C8   C9   aromatic  1.432  0.020  1.432
 2T7  C8   C11  single    1.487  0.020  1.487
 2T7  C9   C6   aromatic  1.397  0.020  1.397
 2T7  C11  C12  single    1.547  0.020  1.547
 2T7  C4   C1   aromatic  1.404  0.020  1.404
 2T7  O14  C12  deloc     1.243  0.020  1.243
 2T7  C12  O13  deloc     1.249  0.020  1.249
 2T7  C6   C1   aromatic  1.382  0.020  1.382
 2T7  C21  H1   single    0.930  0.020  1.080
 2T7  C18  H2   single    0.930  0.020  1.080
 2T7  C22  H3   single    0.970  0.020  1.090
 2T7  C22  H4   single    0.970  0.020  1.090
 2T7  C22  H5   single    0.970  0.020  1.090
 2T7  C17  H6   single    0.930  0.020  1.080
 2T7  C3   H7   single    0.970  0.020  1.090
 2T7  C3   H8   single    0.970  0.020  1.090
 2T7  C5   H9   single    0.930  0.020  1.080
 2T7  C4   H10  single    0.930  0.020  1.080
 2T7  C6   H11  single    0.930  0.020  1.080
 2T7  C1   H12  single    0.930  0.020  1.080
 2T7  C7   H13  single    0.930  0.020  1.080
 2T7  C11  H14  single    0.970  0.020  1.090
 2T7  C11  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
 2T7  C20  N23  O24  118.23  3.000
 2T7  C20  N23  O25  118.29  3.000
 2T7  O24  N23  O25  123.48  3.000
 2T7  C17  C20  C21  120.81  3.000
 2T7  C17  C20  N23  119.56  3.000
 2T7  C21  C20  N23  119.63  3.000
 2T7  H1   C21  C18  119.25  3.000
 2T7  H1   C21  C20  121.32  3.000
 2T7  C18  C21  C20  119.44  3.000
 2T7  H2   C18  C16  121.37  3.000
 2T7  H2   C18  C21  118.44  3.000
 2T7  C16  C18  C21  120.19  3.000
 2T7  C15  C16  O19  115.88  3.000
 2T7  O19  C16  C18  123.90  3.000
 2T7  C15  C16  C18  120.22  3.000
 2T7  C22  O19  C16  119.71  3.000
 2T7  H5   C22  H4   109.06  3.000
 2T7  H5   C22  H3   109.06  3.000
 2T7  H4   C22  H3   109.34  3.000
 2T7  H5   C22  O19  106.20  3.000
 2T7  H4   C22  O19  111.45  3.000
 2T7  H3   C22  O19  111.65  3.000
 2T7  H6   C17  C15  119.21  3.000
 2T7  H6   C17  C20  120.37  3.000
 2T7  C15  C17  C20  120.41  3.000
 2T7  C3   C15  C17  120.61  3.000
 2T7  C3   C15  C16  120.48  3.000
 2T7  C17  C15  C16  118.91  3.000
 2T7  H8   C3   H7   106.49  3.000
 2T7  H8   C3   N2   107.76  3.000
 2T7  H7   C3   N2   109.22  3.000
 2T7  H8   C3   C15  110.84  3.000
 2T7  H7   C3   C15  109.27  3.000
 2T7  N2   C3   C15  113.04  3.000
 2T7  C7   N2   C10  108.33  3.000
 2T7  C10  N2   C3   125.77  3.000
 2T7  C7   N2   C3   125.81  3.000
 2T7  C9   C10  C5   121.80  3.000
 2T7  C9   C10  N2   107.57  3.000
 2T7  C5   C10  N2   130.62  3.000
 2T7  H9   C5   C4   120.19  3.000
 2T7  H9   C5   C10  122.19  3.000
 2T7  C4   C5   C10  117.63  3.000
 2T7  H10  C4   C1   119.46  3.000
 2T7  H10  C4   C5   119.19  3.000
 2T7  C1   C4   C5   121.36  3.000
 2T7  C8   C9   C6   133.29  3.000
 2T7  C6   C9   C10  119.29  3.000
 2T7  C8   C9   C10  107.43  3.000
 2T7  H11  C6   C1   120.38  3.000
 2T7  H11  C6   C9   120.53  3.000
 2T7  C1   C6   C9   119.10  3.000
 2T7  H12  C1   C6   119.87  3.000
 2T7  H12  C1   C4   119.30  3.000
 2T7  C6   C1   C4   120.83  3.000
 2T7  C11  C8   C7   127.64  3.000
 2T7  C11  C8   C9   126.63  3.000
 2T7  C7   C8   C9   105.72  3.000
 2T7  H13  C7   C8   129.03  3.000
 2T7  H13  C7   N2   120.01  3.000
 2T7  C8   C7   N2   110.96  3.000
 2T7  H15  C11  H14  105.11  3.000
 2T7  H15  C11  C12  108.06  3.000
 2T7  H14  C11  C12  107.82  3.000
 2T7  H15  C11  C8   110.06  3.000
 2T7  H14  C11  C8   109.56  3.000
 2T7  C12  C11  C8   115.69  3.000
 2T7  O14  C12  O13  126.75  3.000
 2T7  O13  C12  C11  115.24  3.000
 2T7  O14  C12  C11  118.01  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
 2T7  CONST_01  C16  C18  C21  C20     0.00   0.0  0
 2T7  CONST_02  C16  C15  C17  C20     0.00   0.0  0
 2T7  CONST_03  C15  C17  C20  C21     0.00   0.0  0
 2T7  CONST_04  C15  C16  C18  C21     0.00   0.0  0
 2T7  CONST_05  C17  C20  C21  C18     0.00   0.0  0
 2T7  CONST_06  C17  C15  C16  C18     0.00   0.0  0
 2T7  CONST_07  C9   C8   C7   N2      0.00   0.0  0
 2T7  CONST_08  C4   C5   C10  N2    180.00   0.0  0
 2T7  CONST_09  C8   C9   C10  N2      0.00   0.0  0
 2T7  CONST_10  C6   C9   C10  N2    180.00   0.0  0
 2T7  CONST_11  C8   C7   N2   C10     0.00   0.0  0
 2T7  CONST_12  C1   C4   C5   C10     0.00   0.0  0
 2T7  CONST_13  C7   C8   C9   C10     0.00   0.0  0
 2T7  CONST_14  C1   C6   C9   C10     0.00   0.0  0
 2T7  CONST_15  C7   N2   C10  C5    180.00   0.0  0
 2T7  CONST_16  C8   C9   C10  C5    180.00   0.0  0
 2T7  CONST_17  C6   C9   C10  C5      0.00   0.0  0
 2T7  CONST_18  C6   C1   C4   C5      0.00   0.0  0
 2T7  CONST_19  C9   C10  C5   C4      0.00   0.0  0
 2T7  CONST_20  C9   C6   C1   C4      0.00   0.0  0
 2T7  CONST_21  C7   N2   C10  C9      0.00   0.0  0
 2T7  CONST_22  C7   C8   C9   C6    180.00   0.0  0
 2T7  CONST_23  C8   C9   C6   C1    180.00   0.0  0
 2T7  CONST_24  C18  C21  C20  N23   180.00   0.0  0
 2T7  CONST_25  C15  C17  C20  N23   180.00   0.0  0
 2T7  CONST_26  C3   C15  C17  C20   180.00   0.0  0
 2T7  CONST_27  O19  C16  C18  C21   180.00   0.0  0
 2T7  CONST_28  C3   C15  C16  C18   180.00   0.0  0
 2T7  CONST_29  C17  C15  C16  O19   180.00   0.0  0
 2T7  CONST_30  C8   C7   N2   C3    180.00   0.0  0
 2T7  CONST_31  C5   C10  N2   C3      0.00   0.0  0
 2T7  CONST_32  C9   C10  N2   C3    180.00   0.0  0
 2T7  CONST_33  C11  C8   C7   N2    180.00   0.0  0
 2T7  CONST_34  C11  C8   C9   C10   180.00   0.0  0
 2T7  CONST_35  C11  C8   C9   C6      0.00   0.0  0
 2T7  CONST_36  H2   C18  C21  C20   180.00   0.0  0
 2T7  CONST_37  H6   C17  C20  C21   180.00   0.0  0
 2T7  CONST_38  H1   C21  C18  C16   180.00   0.0  0
 2T7  CONST_39  H9   C5   C10  N2      0.00   0.0  0
 2T7  CONST_40  H13  C7   N2   C10   180.00   0.0  0
 2T7  CONST_41  H10  C4   C5   C10   180.00   0.0  0
 2T7  CONST_42  H11  C6   C9   C10   180.00   0.0  0
 2T7  CONST_43  H12  C1   C4   C5    180.00   0.0  0
 2T7  CONST_44  C21  C20  N23  O25   180.00   0.0  0
 2T7  CONST_45  C17  C20  N23  O25     0.00   0.0  0
 2T7  CONST_46  C21  C20  N23  O24     0.00   0.0  0
 2T7  CONST_47  C17  C20  N23  O24   180.00   0.0  0
 2T7  Var_01    N2   C3   C15  C16    67.00  30.0  2
 2T7  Var_02    C7   N2   C3   C15  -105.94  30.0  2
 2T7  Var_03    C15  C16  O19  C22  -177.54  30.0  1
 2T7  Var_04    C12  C11  C8   C9     68.43  30.0  2
 2T7  Var_05    O14  C12  C11  C8      8.34  30.0  3
 2T7  Var_06    H3   C22  O19  C16   -62.51  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
 2T7  plan-1  N23  0.020
 2T7  plan-1  C20  0.020
 2T7  plan-1  C21  0.020
 2T7  plan-1  C18  0.020
 2T7  plan-1  C16  0.020
 2T7  plan-1  O19  0.020
 2T7  plan-1  C17  0.020
 2T7  plan-1  C15  0.020
 2T7  plan-1  C3   0.020
 2T7  plan-1  H1   0.020
 2T7  plan-1  H2   0.020
 2T7  plan-1  H6   0.020
 2T7  plan-2  C3   0.020
 2T7  plan-2  N2   0.020
 2T7  plan-2  C10  0.020
 2T7  plan-2  C5   0.020
 2T7  plan-2  C4   0.020
 2T7  plan-2  C9   0.020
 2T7  plan-2  C6   0.020
 2T7  plan-2  C1   0.020
 2T7  plan-2  C8   0.020
 2T7  plan-2  C7   0.020
 2T7  plan-2  C11  0.020
 2T7  plan-2  H9   0.020
 2T7  plan-2  H10  0.020
 2T7  plan-2  H11  0.020
 2T7  plan-2  H12  0.020
 2T7  plan-2  H13  0.020
 2T7  plan-3  O25  0.020
 2T7  plan-3  N23  0.020
 2T7  plan-3  O24  0.020
 2T7  plan-3  C20  0.020
 2T7  plan-4  C11  0.020
 2T7  plan-4  C12  0.020
 2T7  plan-4  O13  0.020
 2T7  plan-4  O14  0.020

