# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Mar  9 08:51:54 2022
#   Inital geometry file: a 114 line input string
#   Ligand name: 2-{5-[amino(iminio)methyl]-6-chloro-1H-indol-2-yl}-6-(cyclopentyloxy)phenolate
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: NC(=[NH2+])c1cc2cc([nH]c2cc1Cl)c3cccc(OC4CCCC4)c3[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
 991  991  2-{5-[amino(iminio)methyl]-6-chloro-1H-indol-2-yl}-6-(cyclopentyloxy)phenolate  ligand  46  26  .  2022-03-11  2022-03-11
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_991
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
 991  C1    C   CR6    0   0.041   4.4803   0.0455  -0.0253
 991  C2    C   CR6    0  -0.106   3.9503  -1.2331  -0.2918
 991  CL2   CL  CL     0  -0.118   4.9923  -2.6185  -0.3930
 991  C3    C   CR16   0  -0.260   2.5919  -1.4403  -0.4147
 991  C4    C   CR56   0   0.362   1.7568  -0.3372  -0.2822
 991  C5    C   CR56   0   0.105   2.2540   0.9652  -0.0085
 991  C6    C   CR16   0  -0.383   3.6280   1.1353   0.1280
 991  C7    C   C      0   0.545   5.9248   0.3007   0.0888
 991  N1    N   NH2    0  -0.744   6.7400  -0.0745  -0.8653
 991  N2    N   NC2    1  -0.746   6.3614   0.9477   1.1425
 991  N3    N   NR15   0  -0.763   0.4121  -0.2435  -0.3654
 991  CN4   C   CR15   0  -0.478   1.1319   1.8308   0.0617
 991  C8    C   CR5    0   0.412   0.0098   1.0535  -0.1613
 991  C1'   C   CR6    0  -0.211  -1.3976   1.4002  -0.2039
 991  C2'   C   CR16   0  -0.339  -1.7769   2.7432  -0.0211
 991  C3'   C   CR16   0  -0.296  -3.0947   3.1196  -0.0493
 991  C4'   C   CR16   0  -0.383  -4.0884   2.1453  -0.2597
 991  C5'   C   CR6    0   0.244  -3.7497   0.8244  -0.4405
 991  O5'   O   O2     0  -0.478  -4.6306  -0.1801  -0.6645
 991  C6'   C   CR6    0   0.244  -2.3735   0.3800  -0.4269
 991  O6'   O   OC    -1  -0.607  -2.0980  -0.8482  -0.6073
 991  C1B   C   CH2    0  -0.452  -6.7276  -1.1895  -1.0543
 991  C2B   C   CR15   0  -0.014  -6.0228   0.0816  -0.6041
 991  C3B   C   CH2    0  -0.475  -6.5093   0.2415   0.8369
 991  C4B   C   CH2    0  -0.439  -6.6459  -1.1940   1.3829
 991  C5B   C   CH2    0  -0.450  -6.6146  -2.1254   0.1514
 991  HC3   H   HCR6   0   0.287   2.1968  -2.4299  -0.6004
 991  HC6   H   HCR6   0   0.275   4.0404   2.1176   0.3230
 991  HH11  H   HNH2   0   0.440   6.3875  -0.4806  -1.7161
 991  HH12  H   HNH2   0   0.437   7.7391   0.0536  -0.8009
 991  HH21  H   HNC2   0   0.436   7.3231   1.2388   1.2365
 991  HH22  H   HNC2   0   0.446   5.7433   1.1434   1.9129
 991  HN3   H   HNR5   0   0.414  -0.3089  -0.9497  -0.5359
 991  HCN4  H   HCR5   0   0.243   1.1532   2.8915   0.2534
 991  HC2'  H   HCR6   0   0.227  -1.0112   3.4928   0.1416
 991  HC3'  H   HCR6   0   0.230  -3.3794   4.1536   0.0931
 991  HC4'  H   HCR6   0   0.257  -5.1241   2.4610  -0.2724
 991  H1A   H   HCH2   0   0.231  -7.7742  -0.9448  -1.2513
 991  H1B   H   HCH2   0   0.239  -6.3122  -1.6017  -1.9756
 991  H2A   H   HCR5   0   0.233  -6.2801   0.9399  -1.2361
 991  H3A   H   HCH2   0   0.246  -5.8517   0.8668   1.4416
 991  H3B   H   HCH2   0   0.234  -7.4815   0.7394   0.8151
 991  H4A   H   HCH2   0   0.228  -7.5751  -1.3029   1.9434
 991  H4B   H   HCH2   0   0.229  -5.8379  -1.4338   2.0749
 991  H5A   H   HCH2   0   0.229  -7.4137  -2.8666   0.1706
 991  H5B   H   HCH2   0   0.228  -5.6736  -2.6762   0.1127

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
 991  C1   C2    aromatic  1.410  0.020  1.410
 991  C1   C6    aromatic  1.392  0.020  1.392
 991  C1   C7    single    1.471  0.020  1.471
 991  C2   CL2   single    1.736  0.020  1.736
 991  C2   C3    aromatic  1.380  0.020  1.380
 991  C3   C4    aromatic  1.390  0.020  1.390
 991  C3   HC3   single    0.930  0.020  1.080
 991  C4   C5    aromatic  1.421  0.020  1.421
 991  C4   N3    aromatic  1.350  0.020  1.350
 991  C5   C6    aromatic  1.391  0.020  1.391
 991  C5   CN4   aromatic  1.419  0.020  1.419
 991  C6   HC6   single    0.930  0.020  1.080
 991  C7   N1    single    1.310  0.020  1.310
 991  C7   N2    double    1.311  0.020  1.311
 991  N1   HH11  single    0.860  0.020  1.020
 991  N1   HH12  single    0.860  0.020  1.020
 991  N2   HH21  single    0.860  0.020  1.020
 991  N2   HH22  single    0.860  0.020  1.020
 991  N3   C8    aromatic  1.373  0.020  1.373
 991  N3   HN3   single    0.860  0.020  1.020
 991  CN4  C8    aromatic  1.383  0.020  1.383
 991  CN4  HCN4  single    0.930  0.020  1.080
 991  C8   C1'   single    1.450  0.020  1.450
 991  C1'  C2'   aromatic  1.407  0.020  1.407
 991  C1'  C6'   aromatic  1.429  0.020  1.429
 991  C2'  C3'   aromatic  1.371  0.020  1.371
 991  C2'  HC2'  single    0.930  0.020  1.080
 991  C3'  C4'   aromatic  1.407  0.020  1.407
 991  C3'  HC3'  single    0.930  0.020  1.080
 991  C4'  C5'   aromatic  1.376  0.020  1.376
 991  C4'  HC4'  single    0.930  0.020  1.080
 991  C5'  O5'   single    1.355  0.020  1.355
 991  C5'  C6'   aromatic  1.446  0.020  1.446
 991  O5'  C2B   single    1.418  0.020  1.418
 991  C6'  O6'   single    1.272  0.020  1.272
 991  C1B  C2B   single    1.522  0.020  1.522
 991  C1B  C5B   single    1.530  0.020  1.530
 991  C1B  H1A   single    0.970  0.020  1.090
 991  C1B  H1B   single    0.970  0.020  1.090
 991  C2B  C3B   single    1.529  0.020  1.529
 991  C2B  H2A   single    0.970  0.020  1.090
 991  C3B  C4B   single    1.542  0.020  1.542
 991  C3B  H3A   single    0.970  0.020  1.090
 991  C3B  H3B   single    0.970  0.020  1.090
 991  C4B  C5B   single    1.544  0.020  1.544
 991  C4B  H4A   single    0.970  0.020  1.090
 991  C4B  H4B   single    0.970  0.020  1.090
 991  C5B  H5A   single    0.970  0.020  1.090
 991  C5B  H5B   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
 991  C7    C1   C6    117.18  3.000
 991  C7    C1   C2    122.77  3.000
 991  C6    C1   C2    120.05  3.000
 991  C3    C2   CL2   117.76  3.000
 991  C3    C2   C1    121.56  3.000
 991  CL2   C2   C1    120.60  3.000
 991  HC3   C3   C4    121.54  3.000
 991  HC3   C3   C2    120.82  3.000
 991  C4    C3   C2    117.64  3.000
 991  N3    C4   C5    107.26  3.000
 991  N3    C4   C3    130.35  3.000
 991  C5    C4   C3    122.39  3.000
 991  CN4   C5   C6    134.56  3.000
 991  CN4   C5   C4    106.98  3.000
 991  C6    C5   C4    118.46  3.000
 991  HC6   C6   C5    120.31  3.000
 991  HC6   C6   C1    119.79  3.000
 991  C5    C6   C1    119.88  3.000
 991  N2    C7   N1    121.30  3.000
 991  N2    C7   C1    118.34  3.000
 991  N1    C7   C1    120.32  3.000
 991  HH12  N1   HH11  116.87  3.000
 991  HH12  N1   C7    122.22  3.000
 991  HH11  N1   C7    120.88  3.000
 991  HH22  N2   HH21  117.23  3.000
 991  HH22  N2   C7    120.42  3.000
 991  HH21  N2   C7    122.30  3.000
 991  HN3   N3   C8    118.04  3.000
 991  HN3   N3   C4    131.59  3.000
 991  C8    N3   C4    110.37  3.000
 991  HCN4  CN4  C8    126.70  3.000
 991  HCN4  CN4  C5    126.40  3.000
 991  C8    CN4  C5    106.90  3.000
 991  C1'   C8   CN4   131.12  3.000
 991  C1'   C8   N3    120.39  3.000
 991  CN4   C8   N3    108.49  3.000
 991  C6'   C1'  C2'   121.15  3.000
 991  C6'   C1'  C8    119.77  3.000
 991  C2'   C1'  C8    119.07  3.000
 991  HC2'  C2'  C3'   119.50  3.000
 991  HC2'  C2'  C1'   119.28  3.000
 991  C3'   C2'  C1'   121.23  3.000
 991  HC3'  C3'  C4'   119.70  3.000
 991  HC3'  C3'  C2'   120.84  3.000
 991  C4'   C3'  C2'   119.46  3.000
 991  HC4'  C4'  C5'   120.93  3.000
 991  HC4'  C4'  C3'   118.37  3.000
 991  C5'   C4'  C3'   120.70  3.000
 991  C6'   C5'  O5'   113.11  3.000
 991  C6'   C5'  C4'   121.88  3.000
 991  O5'   C5'  C4'   125.00  3.000
 991  C2B   O5'  C5'   119.64  3.000
 991  O6'   C6'  C5'   120.10  3.000
 991  O6'   C6'  C1'   124.31  3.000
 991  C5'   C6'  C1'   115.58  3.000
 991  H1B   C1B  H1A   107.27  3.000
 991  H1B   C1B  C5B   113.95  3.000
 991  H1A   C1B  C5B   110.47  3.000
 991  H1B   C1B  C2B   112.89  3.000
 991  H1A   C1B  C2B   108.05  3.000
 991  C5B   C1B  C2B   104.10  3.000
 991  H2A   C2B  C3B   112.74  3.000
 991  H2A   C2B  C1B   112.00  3.000
 991  C3B   C2B  C1B   102.63  3.000
 991  H2A   C2B  O5'   110.51  3.000
 991  C3B   C2B  O5'   111.83  3.000
 991  C1B   C2B  O5'   106.74  3.000
 991  H3B   C3B  H3A   106.64  3.000
 991  H3B   C3B  C4B   110.64  3.000
 991  H3A   C3B  C4B   113.01  3.000
 991  H3B   C3B  C2B   108.18  3.000
 991  H3A   C3B  C2B   112.99  3.000
 991  C4B   C3B  C2B   105.34  3.000
 991  H4B   C4B  H4A   106.45  3.000
 991  H4B   C4B  C5B   111.00  3.000
 991  H4A   C4B  C5B   111.52  3.000
 991  H4B   C4B  C3B   111.33  3.000
 991  H4A   C4B  C3B   110.51  3.000
 991  C5B   C4B  C3B   106.10  3.000
 991  H5B   C5B  H5A   106.84  3.000
 991  H5B   C5B  C4B   110.51  3.000
 991  H5A   C5B  C4B   112.41  3.000
 991  H5B   C5B  C1B   110.14  3.000
 991  H5A   C5B  C1B   112.05  3.000
 991  C4B   C5B  C1B   104.94  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
 991  CONST_01  C4    C3   C2   C1     0.00   0.0  0
 991  CONST_02  C4    C5   C6   C1     0.00   0.0  0
 991  CONST_03  CN4   C5   C6   C1   180.00   0.0  0
 991  CONST_04  C5    C6   C1   C2     0.00   0.0  0
 991  CONST_05  C5    C4   C3   C2     0.00   0.0  0
 991  CONST_06  N3    C4   C3   C2   180.00   0.0  0
 991  CONST_07  C6    C1   C2   C3     0.00   0.0  0
 991  CONST_08  C6    C5   C4   C3     0.00   0.0  0
 991  CONST_09  CN4   C5   C4   C3   180.00   0.0  0
 991  CONST_10  C8    N3   C4   C3   180.00   0.0  0
 991  CONST_11  C8    CN4  C5   C4     0.00   0.0  0
 991  CONST_12  CN4   C8   N3   C4     0.00   0.0  0
 991  CONST_13  C1'   C8   N3   C4   180.00   0.0  0
 991  CONST_14  C8    N3   C4   C5     0.00   0.0  0
 991  CONST_15  N3    C8   CN4  C5     0.00   0.0  0
 991  CONST_16  C1'   C8   CN4  C5   180.00   0.0  0
 991  CONST_17  N3    C4   C5   C6   180.00   0.0  0
 991  CONST_18  C8    CN4  C5   C6   180.00   0.0  0
 991  CONST_19  CN4   C5   C4   N3     0.00   0.0  0
 991  CONST_20  C2'   C1'  C8   N3   180.00   0.0  0
 991  CONST_21  C6'   C1'  C8   N3     0.00   0.0  0
 991  CONST_22  C2'   C1'  C8   CN4    0.00   0.0  0
 991  CONST_23  C6'   C1'  C8   CN4  180.00   0.0  0
 991  CONST_24  C3'   C2'  C1'  C8   180.00   0.0  0
 991  CONST_25  C5'   C6'  C1'  C8   180.00   0.0  0
 991  CONST_26  C4'   C3'  C2'  C1'    0.00   0.0  0
 991  CONST_27  C4'   C5'  C6'  C1'    0.00   0.0  0
 991  CONST_28  C5'   C6'  C1'  C2'    0.00   0.0  0
 991  CONST_29  C5'   C4'  C3'  C2'    0.00   0.0  0
 991  CONST_30  C6'   C1'  C2'  C3'    0.00   0.0  0
 991  CONST_31  C6'   C5'  C4'  C3'    0.00   0.0  0
 991  CONST_32  C6    C1   C2   CL2  180.00   0.0  0
 991  CONST_33  C4    C3   C2   CL2  180.00   0.0  0
 991  CONST_34  C7    C1   C2   C3   180.00   0.0  0
 991  CONST_35  C7    C1   C6   C5   180.00   0.0  0
 991  CONST_36  O6'   C6'  C1'  C8     0.00   0.0  0
 991  CONST_37  O5'   C5'  C6'  C1'  180.00   0.0  0
 991  CONST_38  O6'   C6'  C1'  C2'  180.00   0.0  0
 991  CONST_39  O5'   C5'  C4'  C3'  180.00   0.0  0
 991  CONST_40  O6'   C6'  C5'  C4'  180.00   0.0  0
 991  CONST_41  HC3   C3   C2   C1   180.00   0.0  0
 991  CONST_42  HC6   C6   C1   C2   180.00   0.0  0
 991  CONST_43  HN3   N3   C4   C3     0.00   0.0  0
 991  CONST_44  HCN4  CN4  C5   C4   180.00   0.0  0
 991  CONST_45  HC2'  C2'  C1'  C8     0.00   0.0  0
 991  CONST_46  HC3'  C3'  C2'  C1'  180.00   0.0  0
 991  CONST_47  HC4'  C4'  C3'  C2'  180.00   0.0  0
 991  CONST_48  HH11  N1   C7   C1     0.00   0.0  0
 991  CONST_49  HH12  N1   C7   C1   180.00   0.0  0
 991  CONST_50  HH21  N2   C7   C1   180.00   0.0  0
 991  CONST_51  HH22  N2   C7   C1     0.00   0.0  0
 991  Var_01    C3B   C4B  C5B  C1B  -10.32  30.0  1
 991  Var_02    C4B   C5B  C1B  C2B   32.17  30.0  1
 991  Var_03    C5B   C4B  C3B  C2B  -15.18  30.0  1
 991  Var_04    N1    C7   C1   C2    53.00  30.0  2

loop_
_chem_comp_chir.comp_id
_chem_comp_chir.id
_chem_comp_chir.atom_id_centre
_chem_comp_chir.atom_id_1
_chem_comp_chir.atom_id_2
_chem_comp_chir.atom_id_3
_chem_comp_chir.volume_sign
 991  chir_01  C2B  O5'  C1B  C3B  negativ

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
 991  plan-1  C8    0.020
 991  plan-1  C1'   0.020
 991  plan-1  C2'   0.020
 991  plan-1  C3'   0.020
 991  plan-1  C4'   0.020
 991  plan-1  C5'   0.020
 991  plan-1  O5'   0.020
 991  plan-1  C6'   0.020
 991  plan-1  O6'   0.020
 991  plan-1  HC2'  0.020
 991  plan-1  HC3'  0.020
 991  plan-1  HC4'  0.020
 991  plan-2  C1    0.020
 991  plan-2  C2    0.020
 991  plan-2  CL2   0.020
 991  plan-2  C3    0.020
 991  plan-2  C4    0.020
 991  plan-2  C5    0.020
 991  plan-2  C6    0.020
 991  plan-2  C7    0.020
 991  plan-2  N3    0.020
 991  plan-2  CN4   0.020
 991  plan-2  C8    0.020
 991  plan-2  C1'   0.020
 991  plan-2  HC3   0.020
 991  plan-2  HC6   0.020
 991  plan-2  HN3   0.020
 991  plan-2  HCN4  0.020
 991  plan-3  C1    0.020
 991  plan-3  C7    0.020
 991  plan-3  N1    0.020
 991  plan-3  N2    0.020
 991  plan-3  HH11  0.020
 991  plan-3  HH12  0.020
 991  plan-3  HH21  0.020
 991  plan-3  HH22  0.020

