# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Mar 31 23:36:00 2020
#   Inital geometry file: a 142 line input string
#   Ligand name: [6-(3,5-diaminophenyl)-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)c3ccc(cc23)c4cc(N)cc(N)c4)[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
 2T9  2T9  '[6-(3,5-diaminophenyl)-1-(2-methoxy-5-nitrobenzyl)-1H-indol-3-yl]acetic acid'  ligand  54  33  .  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_2T9
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
 2T9  O33  O  O     -1  -0.397  -2.1122  -3.7161   1.2375
 2T9  N31  N  N      1   0.331  -1.3068  -4.2418   0.4963
 2T9  O32  O  O      0  -0.381  -1.5501  -5.2264  -0.1625
 2T9  C6   C  CR6    0   0.241   0.0049  -3.6536   0.3932
 2T9  C5   C  CR16   0  -0.259   0.9150  -4.1557  -0.5234
 2T9  C4   C  CR16   0  -0.377   2.1594  -3.5659  -0.6358
 2T9  C7   C  CR16   0  -0.335   0.3348  -2.5707   1.2030
 2T9  C8   C  CR6    0   0.047   1.5660  -1.9626   1.0919
 2T9  C3   C  CR6    0   0.406   2.4944  -2.4704   0.1628
 2T9  O2   O  O2     0  -0.446   3.6676  -1.8501   0.1152
 2T9  C1   C  CH3    0  -0.443   4.6466  -2.2679  -0.8234
 2T9  C9   C  CH2    0  -0.408   1.8913  -0.7464   1.9226
 2T9  N10  N  NR5    0  -0.534   1.9241   0.4641   1.1335
 2T9  C22  C  CR56   0   0.407   0.8461   1.0323   0.5109
 2T9  C17  C  CR56   0   0.029   1.3187   2.1102  -0.2670
 2T9  C12  C  CR5    0   0.052   2.7387   2.1735  -0.0958
 2T9  C13  C  CH2    0  -0.731   3.6721   3.1275  -0.7516
 2T9  C14  C  C      0   0.417   3.4922   4.6157  -0.3705
 2T9  O16  O  O      0  -0.596   2.6875   4.8941   0.5356
 2T9  O15  O  OC    -1  -0.629   4.1963   5.4182  -1.0178
 2T9  C11  C  CR15   0  -0.079   3.0535   1.1495   0.7474
 2T9  C21  C  CR16   0  -0.368  -0.5034   0.7025   0.5739
 2T9  C20  C  CR6    0   0.061  -1.4072   1.4411  -0.1794
 2T9  C19  C  CR16   0  -0.330  -0.9401   2.5186  -0.9609
 2T9  C18  C  CR16   0  -0.357   0.3966   2.8617  -0.9996
 2T9  C23  C  CR6    0   0.118  -2.8420   1.0810  -0.1672
 2T9  C30  C  CR16   0  -0.439  -3.8174   2.0715  -0.2490
 2T9  C28  C  CR6    0   0.339  -5.1741   1.7280  -0.2366
 2T9  N29  N  NH2    0  -0.866  -6.1401   2.7146  -0.2547
 2T9  C27  C  CR16   0  -0.422  -5.5413   0.3845  -0.1421
 2T9  C25  C  CR6    0   0.341  -4.5703  -0.6156  -0.0638
 2T9  N26  N  NH2    0  -0.869  -4.9374  -1.9454  -0.0436
 2T9  C24  C  CR16   0  -0.432  -3.2181  -0.2579  -0.0771
 2T9  H1   H  HCR6   0   0.302   0.6708  -4.9967  -1.1558
 2T9  H2   H  HCR6   0   0.302   2.8583  -3.9726  -1.3524
 2T9  H3   H  HCR6   0   0.301  -0.3726  -2.1942   1.9289
 2T9  H4   H  HCH3   0   0.269   5.4957  -1.6043  -0.6885
 2T9  H5   H  HCH3   0   0.241   4.9656  -3.2965  -0.6427
 2T9  H6   H  HCH3   0   0.242   4.2821  -2.1774  -1.8485
 2T9  H7   H  HCH2   0   0.285   1.1458  -0.6447   2.7140
 2T9  H8   H  HCH2   0   0.290   2.8564  -0.8499   2.4180
 2T9  H9   H  HCH2   0   0.245   4.7052   2.8432  -0.5246
 2T9  H10  H  HCH2   0   0.231   3.5865   3.0462  -1.8410
 2T9  H12  H  HCR5   0   0.273   4.0219   0.8451   1.1137
 2T9  H13  H  HCR6   0   0.243  -0.8610  -0.0953   1.2099
 2T9  H14  H  HCR6   0   0.239  -1.6465   3.0795  -1.5598
 2T9  H15  H  HCR6   0   0.237   0.7248   3.6957  -1.6072
 2T9  H16  H  HCR6   0   0.241  -3.5334   3.1163  -0.2958
 2T9  H17  H  HNH2   0   0.376  -5.8584   3.5852  -0.6762
 2T9  H18  H  HNH2   0   0.375  -7.0488   2.4259  -0.5802
 2T9  H19  H  HCR6   0   0.249  -6.5926   0.1153  -0.1327
 2T9  H20  H  HNH2   0   0.376  -5.8681  -2.1391   0.2889
 2T9  H21  H  HNH2   0   0.366  -4.2619  -2.5806   0.3500
 2T9  H22  H  HCR6   0   0.225  -2.4639  -1.0352  -0.0545

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
 2T9  O32  N31  double    1.209  0.020  1.209
 2T9  N31  O33  single    1.214  0.020  1.214
 2T9  N31  C6   single    1.441  0.020  1.441
 2T9  C5   C6   aromatic  1.386  0.020  1.386
 2T9  C5   C4   aromatic  1.382  0.020  1.382
 2T9  C6   C7   aromatic  1.392  0.020  1.392
 2T9  C4   C3   aromatic  1.396  0.020  1.396
 2T9  C7   C8   aromatic  1.378  0.020  1.378
 2T9  C3   C8   aromatic  1.408  0.020  1.408
 2T9  C3   O2   single    1.328  0.020  1.328
 2T9  C1   O2   single    1.419  0.020  1.419
 2T9  C8   C9   single    1.508  0.020  1.508
 2T9  C9   N10  single    1.445  0.020  1.445
 2T9  N10  C11  aromatic  1.376  0.020  1.376
 2T9  N10  C22  aromatic  1.368  0.020  1.368
 2T9  C11  C12  aromatic  1.363  0.020  1.363
 2T9  C22  C21  aromatic  1.391  0.020  1.391
 2T9  C22  C17  aromatic  1.411  0.020  1.411
 2T9  N26  C25  single    1.380  0.020  1.380
 2T9  C21  C20  aromatic  1.389  0.020  1.389
 2T9  C12  C17  aromatic  1.432  0.020  1.432
 2T9  C12  C13  single    1.487  0.020  1.487
 2T9  C24  C25  aromatic  1.399  0.020  1.399
 2T9  C24  C23  aromatic  1.394  0.020  1.394
 2T9  C25  C27  aromatic  1.396  0.020  1.396
 2T9  C17  C18  aromatic  1.397  0.020  1.397
 2T9  C13  C14  single    1.547  0.020  1.547
 2T9  C20  C23  single    1.479  0.020  1.479
 2T9  C20  C19  aromatic  1.411  0.020  1.411
 2T9  C23  C30  aromatic  1.393  0.020  1.393
 2T9  O16  C14  deloc     1.243  0.020  1.243
 2T9  C27  C28  aromatic  1.396  0.020  1.396
 2T9  C14  O15  deloc     1.249  0.020  1.249
 2T9  C18  C19  aromatic  1.381  0.020  1.381
 2T9  C30  C28  aromatic  1.400  0.020  1.400
 2T9  C28  N29  single    1.381  0.020  1.381
 2T9  C5   H1   single    0.930  0.020  1.080
 2T9  C4   H2   single    0.930  0.020  1.080
 2T9  C7   H3   single    0.930  0.020  1.080
 2T9  C1   H4   single    0.970  0.020  1.090
 2T9  C1   H5   single    0.970  0.020  1.090
 2T9  C1   H6   single    0.970  0.020  1.090
 2T9  C9   H7   single    0.970  0.020  1.090
 2T9  C9   H8   single    0.970  0.020  1.090
 2T9  C13  H9   single    0.970  0.020  1.090
 2T9  C13  H10  single    0.970  0.020  1.090
 2T9  C11  H12  single    0.930  0.020  1.080
 2T9  C21  H13  single    0.930  0.020  1.080
 2T9  C19  H14  single    0.930  0.020  1.080
 2T9  C18  H15  single    0.930  0.020  1.080
 2T9  C30  H16  single    0.930  0.020  1.080
 2T9  N29  H17  single    0.890  0.020  1.040
 2T9  N29  H18  single    0.890  0.020  1.040
 2T9  C27  H19  single    0.930  0.020  1.080
 2T9  N26  H20  single    0.890  0.020  1.040
 2T9  N26  H21  single    0.890  0.020  1.040
 2T9  C24  H22  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
 2T9  C6   N31  O32  118.45  3.000
 2T9  C6   N31  O33  118.08  3.000
 2T9  O32  N31  O33  123.47  3.000
 2T9  C7   C6   C5   120.73  3.000
 2T9  C7   C6   N31  119.44  3.000
 2T9  C5   C6   N31  119.81  3.000
 2T9  H1   C5   C4   119.23  3.000
 2T9  H1   C5   C6   121.39  3.000
 2T9  C4   C5   C6   119.38  3.000
 2T9  H2   C4   C3   121.29  3.000
 2T9  H2   C4   C5   118.42  3.000
 2T9  C3   C4   C5   120.29  3.000
 2T9  H3   C7   C8   119.02  3.000
 2T9  H3   C7   C6   120.42  3.000
 2T9  C8   C7   C6   120.55  3.000
 2T9  C9   C8   C3   120.80  3.000
 2T9  C9   C8   C7   120.28  3.000
 2T9  C3   C8   C7   118.89  3.000
 2T9  O2   C3   C8   115.95  3.000
 2T9  O2   C3   C4   123.91  3.000
 2T9  C8   C3   C4   120.14  3.000
 2T9  C1   O2   C3   119.71  3.000
 2T9  H6   C1   H5   109.33  3.000
 2T9  H6   C1   H4   109.09  3.000
 2T9  H5   C1   H4   109.06  3.000
 2T9  H6   C1   O2   111.49  3.000
 2T9  H5   C1   O2   111.68  3.000
 2T9  H4   C1   O2   106.10  3.000
 2T9  H8   C9   H7   106.50  3.000
 2T9  H8   C9   N10  107.92  3.000
 2T9  H7   C9   N10  109.46  3.000
 2T9  H8   C9   C8   111.40  3.000
 2T9  H7   C9   C8   109.09  3.000
 2T9  N10  C9   C8   112.30  3.000
 2T9  C11  N10  C22  108.18  3.000
 2T9  C22  N10  C9   125.33  3.000
 2T9  C11  N10  C9   126.07  3.000
 2T9  C21  C22  C17  122.09  3.000
 2T9  C17  C22  N10  107.71  3.000
 2T9  C21  C22  N10  130.19  3.000
 2T9  C18  C17  C12  133.92  3.000
 2T9  C18  C17  C22  118.62  3.000
 2T9  C12  C17  C22  107.46  3.000
 2T9  C11  C12  C13  127.56  3.000
 2T9  C13  C12  C17  126.74  3.000
 2T9  C11  C12  C17  105.65  3.000
 2T9  H10  C13  H9   105.10  3.000
 2T9  H10  C13  C14  107.89  3.000
 2T9  H9   C13  C14  107.96  3.000
 2T9  H10  C13  C12  109.99  3.000
 2T9  H9   C13  C12  109.52  3.000
 2T9  C14  C13  C12  115.82  3.000
 2T9  O15  C14  O16  126.79  3.000
 2T9  O15  C14  C13  115.16  3.000
 2T9  O16  C14  C13  118.05  3.000
 2T9  H12  C11  C12  128.98  3.000
 2T9  H12  C11  N10  120.04  3.000
 2T9  C12  C11  N10  110.98  3.000
 2T9  H13  C21  C20  119.74  3.000
 2T9  H13  C21  C22  121.51  3.000
 2T9  C20  C21  C22  118.73  3.000
 2T9  C23  C20  C19  120.77  3.000
 2T9  C19  C20  C21  119.41  3.000
 2T9  C23  C20  C21  119.81  3.000
 2T9  H14  C19  C18  119.18  3.000
 2T9  H14  C19  C20  119.08  3.000
 2T9  C18  C19  C20  121.73  3.000
 2T9  H15  C18  C19  120.04  3.000
 2T9  H15  C18  C17  120.56  3.000
 2T9  C19  C18  C17  119.39  3.000
 2T9  C24  C23  C30  119.88  3.000
 2T9  C30  C23  C20  120.38  3.000
 2T9  C24  C23  C20  119.74  3.000
 2T9  H16  C30  C28  119.41  3.000
 2T9  H16  C30  C23  120.31  3.000
 2T9  C28  C30  C23  120.26  3.000
 2T9  C27  C28  N29  120.30  3.000
 2T9  N29  C28  C30  120.18  3.000
 2T9  C27  C28  C30  119.46  3.000
 2T9  H18  N29  H17  111.39  3.000
 2T9  H18  N29  C28  115.50  3.000
 2T9  H17  N29  C28  115.29  3.000
 2T9  H19  C27  C25  119.71  3.000
 2T9  H19  C27  C28  119.61  3.000
 2T9  C25  C27  C28  120.68  3.000
 2T9  C24  C25  N26  120.25  3.000
 2T9  C24  C25  C27  119.25  3.000
 2T9  N26  C25  C27  120.41  3.000
 2T9  H21  N26  H20  111.68  3.000
 2T9  H21  N26  C25  115.79  3.000
 2T9  H20  N26  C25  115.85  3.000
 2T9  H22  C24  C25  119.30  3.000
 2T9  H22  C24  C23  120.19  3.000
 2T9  C25  C24  C23  120.47  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
 2T9  CONST_01  C3   C4   C5   C6      0.00   0.0  0
 2T9  CONST_02  C3   C8   C7   C6      0.00   0.0  0
 2T9  CONST_03  C8   C7   C6   C5      0.00   0.0  0
 2T9  CONST_04  C8   C3   C4   C5      0.00   0.0  0
 2T9  CONST_05  C7   C6   C5   C4      0.00   0.0  0
 2T9  CONST_06  C7   C8   C3   C4      0.00   0.0  0
 2T9  CONST_07  C17  C12  C11  N10     0.00   0.0  0
 2T9  CONST_08  C20  C21  C22  N10   180.00   0.0  0
 2T9  CONST_09  C12  C17  C22  N10     0.00   0.0  0
 2T9  CONST_10  C18  C17  C22  N10   180.00   0.0  0
 2T9  CONST_11  C12  C11  N10  C22     0.00   0.0  0
 2T9  CONST_12  C23  C20  C21  C22   180.00   0.0  0
 2T9  CONST_13  C19  C20  C21  C22     0.00   0.0  0
 2T9  CONST_14  C11  C12  C17  C22     0.00   0.0  0
 2T9  CONST_15  C19  C18  C17  C22     0.00   0.0  0
 2T9  CONST_16  C11  N10  C22  C17     0.00   0.0  0
 2T9  CONST_17  C20  C21  C22  C17     0.00   0.0  0
 2T9  CONST_18  C20  C19  C18  C17     0.00   0.0  0
 2T9  CONST_19  C21  C22  C17  C12   180.00   0.0  0
 2T9  CONST_20  C19  C18  C17  C12   180.00   0.0  0
 2T9  CONST_21  C21  C22  N10  C11   180.00   0.0  0
 2T9  CONST_22  C18  C17  C12  C11   180.00   0.0  0
 2T9  CONST_23  C18  C17  C22  C21     0.00   0.0  0
 2T9  CONST_26  C18  C19  C20  C21     0.00   0.0  0
 2T9  CONST_27  C25  C24  C23  C20   180.00   0.0  0
 2T9  CONST_28  C28  C30  C23  C20   180.00   0.0  0
 2T9  CONST_31  C23  C20  C19  C18   180.00   0.0  0
 2T9  CONST_32  C27  C25  C24  C23     0.00   0.0  0
 2T9  CONST_33  C27  C28  C30  C23     0.00   0.0  0
 2T9  CONST_34  C25  C24  C23  C30     0.00   0.0  0
 2T9  CONST_35  C25  C27  C28  C30     0.00   0.0  0
 2T9  CONST_36  C24  C25  C27  C28     0.00   0.0  0
 2T9  CONST_37  C24  C23  C30  C28     0.00   0.0  0
 2T9  CONST_38  C4   C5   C6   N31   180.00   0.0  0
 2T9  CONST_39  C8   C7   C6   N31   180.00   0.0  0
 2T9  CONST_40  C9   C8   C7   C6    180.00   0.0  0
 2T9  CONST_41  O2   C3   C4   C5    180.00   0.0  0
 2T9  CONST_42  C9   C8   C3   C4    180.00   0.0  0
 2T9  CONST_43  O2   C3   C8   C7    180.00   0.0  0
 2T9  CONST_44  C12  C11  N10  C9    180.00   0.0  0
 2T9  CONST_45  C21  C22  N10  C9      0.00   0.0  0
 2T9  CONST_46  C17  C22  N10  C9    180.00   0.0  0
 2T9  CONST_47  C13  C12  C11  N10   180.00   0.0  0
 2T9  CONST_48  C13  C12  C17  C22   180.00   0.0  0
 2T9  CONST_49  C18  C17  C12  C13     0.00   0.0  0
 2T9  CONST_50  N26  C25  C24  C23   180.00   0.0  0
 2T9  CONST_51  N29  C28  C30  C23   180.00   0.0  0
 2T9  CONST_52  N26  C25  C27  C28   180.00   0.0  0
 2T9  CONST_53  C25  C27  C28  N29   180.00   0.0  0
 2T9  CONST_54  H2   C4   C5   C6    180.00   0.0  0
 2T9  CONST_55  H3   C7   C6   C5    180.00   0.0  0
 2T9  CONST_56  H1   C5   C6   C7    180.00   0.0  0
 2T9  CONST_57  H13  C21  C22  N10     0.00   0.0  0
 2T9  CONST_58  H12  C11  N10  C22   180.00   0.0  0
 2T9  CONST_59  H15  C18  C17  C22   180.00   0.0  0
 2T9  CONST_60  H14  C19  C18  C17   180.00   0.0  0
 2T9  CONST_61  H22  C24  C23  C20     0.00   0.0  0
 2T9  CONST_62  H16  C30  C23  C20     0.00   0.0  0
 2T9  CONST_63  H19  C27  C28  C30   180.00   0.0  0
 2T9  CONST_64  C5   C6   N31  O33   180.00   0.0  0
 2T9  CONST_65  C7   C6   N31  O33     0.00   0.0  0
 2T9  CONST_66  C5   C6   N31  O32     0.00   0.0  0
 2T9  CONST_67  C7   C6   N31  O32   180.00   0.0  0
 2T9  Var_01    N10  C9   C8   C7   -107.68  30.0  2
 2T9  Var_02    C11  N10  C9   C8   -105.56  30.0  2
 2T9  Var_03    C14  C13  C12  C17    65.08  30.0  2
 2T9  Var_04    O16  C14  C13  C12     6.84  30.0  3
 2T9  Var_05    H4   C1   O2   C3    178.64  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
 2T9  plan-1  N31  0.020
 2T9  plan-1  C6   0.020
 2T9  plan-1  C5   0.020
 2T9  plan-1  C4   0.020
 2T9  plan-1  C7   0.020
 2T9  plan-1  C8   0.020
 2T9  plan-1  C3   0.020
 2T9  plan-1  O2   0.020
 2T9  plan-1  C9   0.020
 2T9  plan-1  H1   0.020
 2T9  plan-1  H2   0.020
 2T9  plan-1  H3   0.020
 2T9  plan-2  C20  0.020
 2T9  plan-2  C23  0.020
 2T9  plan-2  C30  0.020
 2T9  plan-2  C28  0.020
 2T9  plan-2  N29  0.020
 2T9  plan-2  C27  0.020
 2T9  plan-2  C25  0.020
 2T9  plan-2  N26  0.020
 2T9  plan-2  C24  0.020
 2T9  plan-2  H16  0.020
 2T9  plan-2  H19  0.020
 2T9  plan-2  H22  0.020
 2T9  plan-3  C9   0.020
 2T9  plan-3  N10  0.020
 2T9  plan-3  C22  0.020
 2T9  plan-3  C17  0.020
 2T9  plan-3  C12  0.020
 2T9  plan-3  C13  0.020
 2T9  plan-3  C11  0.020
 2T9  plan-3  C21  0.020
 2T9  plan-3  C20  0.020
 2T9  plan-3  C19  0.020
 2T9  plan-3  C18  0.020
 2T9  plan-3  C23  0.020
 2T9  plan-3  H12  0.020
 2T9  plan-3  H13  0.020
 2T9  plan-3  H14  0.020
 2T9  plan-3  H15  0.020
 2T9  plan-4  O33  0.020
 2T9  plan-4  N31  0.020
 2T9  plan-4  O32  0.020
 2T9  plan-4  C6   0.020
 2T9  plan-5  C28  0.020
 2T9  plan-5  N29  0.020
 2T9  plan-5  H17  0.020
 2T9  plan-5  H18  0.020
 2T9  plan-6  C25  0.020
 2T9  plan-6  N26  0.020
 2T9  plan-6  H20  0.020
 2T9  plan-6  H21  0.020
 2T9  plan-7  C13  0.020
 2T9  plan-7  C14  0.020
 2T9  plan-7  O16  0.020
 2T9  plan-7  O15  0.020

