# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Apr 21 06:09:44 2020
#   Inital geometry file: a 114 line input string
#   Ligand name: 2-{5-[amino(iminio)methyl]-1H-indol-2-yl}-6-(cyclopentyloxy)phenolate
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: NC(=[NH2+])c1ccc2[nH]c(cc2c1)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
 CR3  CR3  2-{5-[amino(iminio)methyl]-1H-indol-2-yl}-6-(cyclopentyloxy)phenolate  ligand  46  25  .  2021-08-07  2021-08-07  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_CR3
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
 CR3  C1    C  CR6    0   0.002  -5.0495   0.4303   0.1796
 CR3  C2    C  CR16   0  -0.311  -4.4567   1.7032   0.0538
 CR3  C3    C  CR16   0  -0.303  -3.0919   1.8364  -0.0924
 CR3  C4    C  CR56   0   0.364  -2.3224   0.6767  -0.1209
 CR3  C5    C  CR56   0   0.096  -2.8982  -0.6187  -0.0032
 CR3  C6    C  CR16   0  -0.393  -4.2774  -0.7286   0.1537
 CR3  C7    C  C      0   0.578  -6.5000   0.3277   0.3407
 CR3  N1    N  NH2    0  -0.772  -7.0084  -0.6346   1.0779
 CR3  N2    N  NC2    1  -0.773  -7.2857   1.1988  -0.2523
 CR3  N3    N  NR15   0  -0.760  -0.9886   0.5101  -0.2542
 CR3  CN4   C  CR15   0  -0.481  -1.8305  -1.5536  -0.0812
 CR3  C8    C  CR5    0   0.412  -0.6659  -0.8240  -0.2311
 CR3  C1'   C  CR6    0  -0.211   0.7192  -1.2416  -0.3488
 CR3  C2'   C  CR16   0  -0.341   1.0245  -2.6151  -0.3412
 CR3  C3'   C  CR16   0  -0.297   2.3190  -3.0576  -0.4386
 CR3  C4'   C  CR16   0  -0.383   3.3639  -2.1210  -0.5426
 CR3  C5'   C  CR6    0   0.246   3.0976  -0.7711  -0.5530
 CR3  O5'   O  O2     0  -0.477   4.0319   0.2036  -0.6659
 CR3  C6'   C  CR6    0   0.244   1.7497  -0.2569  -0.4631
 CR3  O6'   O  OC    -1  -0.608   1.5434   0.9982  -0.4874
 CR3  C1B   C  CH2    0  -0.452   6.1757   1.1448  -0.9370
 CR3  C2B   C  CR15   0  -0.015   5.4091  -0.1333  -0.6332
 CR3  C3B   C  CH2    0  -0.475   5.8755  -0.4697   0.7822
 CR3  C4B   C  CH2    0  -0.439   6.0170   0.8920   1.4883
 CR3  C5B   C  CH2    0  -0.449   6.0896   1.9502   0.3640
 CR3  HC2   H  HCR6   0   0.265  -5.0666   2.5951   0.1110
 CR3  HC3   H  HCR6   0   0.266  -2.6390   2.8158  -0.1730
 CR3  HC6   H  HCR6   0   0.263  -4.7366  -1.7076   0.2212
 CR3  HH11  H  HNH2   0   0.433  -8.0030  -0.7827   1.1555
 CR3  HH12  H  HNH2   0   0.442  -6.4144  -1.2092   1.6522
 CR3  HH21  H  HNC2   0   0.441  -6.9170   1.8502  -0.9252
 CR3  HH22  H  HNC2   0   0.433  -8.2836   1.2058  -0.1085
 CR3  HN3   H  HNR5   0   0.412  -0.2257   1.1854  -0.3532
 CR3  HCN4  H  HCR5   0   0.240  -1.9153  -2.6271  -0.0254
 CR3  HC2'  H  HCR6   0   0.227   0.2198  -3.3364  -0.2580
 CR3  HC3'  H  HCR6   0   0.229   2.5450  -4.1157  -0.4323
 CR3  HC4'  H  HCR6   0   0.256   4.3809  -2.4866  -0.6120
 CR3  H1A   H  HCH2   0   0.231   7.2126   0.8759  -1.1524
 CR3  H1B   H  HCH2   0   0.238   5.7897   1.6737  -1.8102
 CR3  H2A   H  HCR5   0   0.233   5.6277  -0.9278  -1.3562
 CR3  H3A   H  HCH2   0   0.246   5.2053  -1.1537   1.3041
 CR3  H3B   H  HCH2   0   0.234   6.8449  -0.9691   0.7119
 CR3  H4A   H  HCH2   0   0.227   6.9063   0.9106   2.1188
 CR3  H4B   H  HCH2   0   0.229   5.1673   1.0806   2.1455
 CR3  H5A   H  HCH2   0   0.228   6.9384   2.6245   0.4806
 CR3  H5B   H  HCH2   0   0.229   5.1917   2.5690   0.3638

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
 CR3  C1   C2    aromatic  1.410  0.020  1.410
 CR3  C1   C6    aromatic  1.393  0.020  1.393
 CR3  C1   C7    single    1.463  0.020  1.463
 CR3  C2   C3    aromatic  1.379  0.020  1.379
 CR3  C2   HC2   single    0.930  0.020  1.080
 CR3  C3   C4    aromatic  1.392  0.020  1.392
 CR3  C3   HC3   single    0.930  0.020  1.080
 CR3  C4   C5    aromatic  1.423  0.020  1.423
 CR3  C4   N3    aromatic  1.351  0.020  1.351
 CR3  C5   C6    aromatic  1.392  0.020  1.392
 CR3  C5   CN4   aromatic  1.421  0.020  1.421
 CR3  C6   HC6   single    0.930  0.020  1.080
 CR3  C7   N1    single    1.315  0.020  1.315
 CR3  C7   N2    double    1.314  0.020  1.314
 CR3  N1   HH11  single    0.860  0.020  1.020
 CR3  N1   HH12  single    0.860  0.020  1.020
 CR3  N2   HH21  single    0.860  0.020  1.020
 CR3  N2   HH22  single    0.860  0.020  1.020
 CR3  N3   C8    aromatic  1.373  0.020  1.373
 CR3  N3   HN3   single    0.860  0.020  1.020
 CR3  CN4  C8    aromatic  1.382  0.020  1.382
 CR3  CN4  HCN4  single    0.930  0.020  1.080
 CR3  C8   C1'   single    1.451  0.020  1.451
 CR3  C1'  C2'   aromatic  1.407  0.020  1.407
 CR3  C1'  C6'   aromatic  1.430  0.020  1.430
 CR3  C2'  C3'   aromatic  1.372  0.020  1.372
 CR3  C2'  HC2'  single    0.930  0.020  1.080
 CR3  C3'  C4'   aromatic  1.407  0.020  1.407
 CR3  C3'  HC3'  single    0.930  0.020  1.080
 CR3  C4'  C5'   aromatic  1.376  0.020  1.376
 CR3  C4'  HC4'  single    0.930  0.020  1.080
 CR3  C5'  O5'   single    1.355  0.020  1.355
 CR3  C5'  C6'   aromatic  1.445  0.020  1.445
 CR3  O5'  C2B   single    1.418  0.020  1.418
 CR3  C6'  O6'   single    1.272  0.020  1.272
 CR3  C1B  C2B   single    1.521  0.020  1.521
 CR3  C1B  C5B   single    1.532  0.020  1.532
 CR3  C1B  H1A   single    0.970  0.020  1.090
 CR3  C1B  H1B   single    0.970  0.020  1.090
 CR3  C2B  C3B   single    1.528  0.020  1.528
 CR3  C2B  H2A   single    0.970  0.020  1.090
 CR3  C3B  C4B   single    1.540  0.020  1.540
 CR3  C3B  H3A   single    0.970  0.020  1.090
 CR3  C3B  H3B   single    0.970  0.020  1.090
 CR3  C4B  C5B   single    1.546  0.020  1.546
 CR3  C4B  H4A   single    0.970  0.020  1.090
 CR3  C4B  H4B   single    0.970  0.020  1.090
 CR3  C5B  H5A   single    0.970  0.020  1.090
 CR3  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
 CR3  C7    C1   C6    119.56  3.000
 CR3  C7    C1   C2    119.34  3.000
 CR3  C6    C1   C2    121.10  3.000
 CR3  HC2   C2   C3    118.93  3.000
 CR3  HC2   C2   C1    120.17  3.000
 CR3  C3    C2   C1    120.85  3.000
 CR3  HC3   C3   C4    121.40  3.000
 CR3  HC3   C3   C2    120.64  3.000
 CR3  C4    C3   C2    117.95  3.000
 CR3  N3    C4   C5    107.19  3.000
 CR3  N3    C4   C3    130.59  3.000
 CR3  C5    C4   C3    122.22  3.000
 CR3  CN4   C5   C6    134.29  3.000
 CR3  CN4   C5   C4    106.88  3.000
 CR3  C6    C5   C4    118.83  3.000
 CR3  HC6   C6   C5    119.88  3.000
 CR3  HC6   C6   C1    121.04  3.000
 CR3  C5    C6   C1    119.05  3.000
 CR3  N2    C7   N1    120.46  3.000
 CR3  N2    C7   C1    119.77  3.000
 CR3  N1    C7   C1    119.77  3.000
 CR3  HH12  N1   HH11  117.02  3.000
 CR3  HH12  N1   C7    120.64  3.000
 CR3  HH11  N1   C7    122.15  3.000
 CR3  HH22  N2   HH21  116.96  3.000
 CR3  HH22  N2   C7    122.13  3.000
 CR3  HH21  N2   C7    120.77  3.000
 CR3  HN3   N3   C8    117.87  3.000
 CR3  HN3   N3   C4    131.62  3.000
 CR3  C8    N3   C4    110.51  3.000
 CR3  HCN4  CN4  C8    126.67  3.000
 CR3  HCN4  CN4  C5    126.37  3.000
 CR3  C8    CN4  C5    106.96  3.000
 CR3  C1'   C8   CN4   131.37  3.000
 CR3  C1'   C8   N3    120.18  3.000
 CR3  CN4   C8   N3    108.46  3.000
 CR3  C6'   C1'  C2'   121.08  3.000
 CR3  C6'   C1'  C8    119.74  3.000
 CR3  C2'   C1'  C8    119.18  3.000
 CR3  HC2'  C2'  C3'   119.44  3.000
 CR3  HC2'  C2'  C1'   119.27  3.000
 CR3  C3'   C2'  C1'   121.29  3.000
 CR3  HC3'  C3'  C4'   119.75  3.000
 CR3  HC3'  C3'  C2'   120.81  3.000
 CR3  C4'   C3'  C2'   119.44  3.000
 CR3  HC4'  C4'  C5'   120.83  3.000
 CR3  HC4'  C4'  C3'   118.52  3.000
 CR3  C5'   C4'  C3'   120.65  3.000
 CR3  C6'   C5'  O5'   113.10  3.000
 CR3  C6'   C5'  C4'   121.94  3.000
 CR3  O5'   C5'  C4'   124.95  3.000
 CR3  C2B   O5'  C5'   119.79  3.000
 CR3  O6'   C6'  C5'   120.06  3.000
 CR3  O6'   C6'  C1'   124.34  3.000
 CR3  C5'   C6'  C1'   115.60  3.000
 CR3  H1B   C1B  H1A   107.29  3.000
 CR3  H1B   C1B  C5B   113.87  3.000
 CR3  H1A   C1B  C5B   110.49  3.000
 CR3  H1B   C1B  C2B   112.87  3.000
 CR3  H1A   C1B  C2B   108.12  3.000
 CR3  C5B   C1B  C2B   104.11  3.000
 CR3  H2A   C2B  C3B   112.98  3.000
 CR3  H2A   C2B  C1B   112.13  3.000
 CR3  C3B   C2B  C1B   102.49  3.000
 CR3  H2A   C2B  O5'   110.52  3.000
 CR3  C3B   C2B  O5'   111.73  3.000
 CR3  C1B   C2B  O5'   106.58  3.000
 CR3  H3B   C3B  H3A   106.82  3.000
 CR3  H3B   C3B  C4B   110.61  3.000
 CR3  H3A   C3B  C4B   113.05  3.000
 CR3  H3B   C3B  C2B   108.17  3.000
 CR3  H3A   C3B  C2B   113.19  3.000
 CR3  C4B   C3B  C2B   104.95  3.000
 CR3  H4B   C4B  H4A   106.50  3.000
 CR3  H4B   C4B  C5B   110.89  3.000
 CR3  H4A   C4B  C5B   111.76  3.000
 CR3  H4B   C4B  C3B   110.95  3.000
 CR3  H4A   C4B  C3B   110.80  3.000
 CR3  C5B   C4B  C3B   106.02  3.000
 CR3  H5B   C5B  H5A   106.86  3.000
 CR3  H5B   C5B  C4B   110.48  3.000
 CR3  H5A   C5B  C4B   112.47  3.000
 CR3  H5B   C5B  C1B   110.14  3.000
 CR3  H5A   C5B  C1B   111.84  3.000
 CR3  C4B   C5B  C1B   105.09  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
 CR3  CONST_01  C4    C3   C2   C1      0.00   0.0  0
 CR3  CONST_02  C4    C5   C6   C1      0.00   0.0  0
 CR3  CONST_03  CN4   C5   C6   C1    180.00   0.0  0
 CR3  CONST_04  C5    C6   C1   C2      0.00   0.0  0
 CR3  CONST_05  C5    C4   C3   C2      0.00   0.0  0
 CR3  CONST_06  N3    C4   C3   C2    180.00   0.0  0
 CR3  CONST_07  C6    C1   C2   C3      0.00   0.0  0
 CR3  CONST_08  C6    C5   C4   C3      0.00   0.0  0
 CR3  CONST_09  CN4   C5   C4   C3    180.00   0.0  0
 CR3  CONST_10  C8    N3   C4   C3    180.00   0.0  0
 CR3  CONST_11  C8    CN4  C5   C4      0.00   0.0  0
 CR3  CONST_12  CN4   C8   N3   C4      0.00   0.0  0
 CR3  CONST_13  C1'   C8   N3   C4    180.00   0.0  0
 CR3  CONST_14  C8    N3   C4   C5      0.00   0.0  0
 CR3  CONST_15  N3    C8   CN4  C5      0.00   0.0  0
 CR3  CONST_16  C1'   C8   CN4  C5    180.00   0.0  0
 CR3  CONST_17  N3    C4   C5   C6    180.00   0.0  0
 CR3  CONST_18  C8    CN4  C5   C6    180.00   0.0  0
 CR3  CONST_19  CN4   C5   C4   N3      0.00   0.0  0
 CR3  CONST_20  C2'   C1'  C8   N3    180.00   0.0  0
 CR3  CONST_21  C6'   C1'  C8   N3      0.00   0.0  0
 CR3  CONST_22  C2'   C1'  C8   CN4     0.00   0.0  0
 CR3  CONST_23  C6'   C1'  C8   CN4   180.00   0.0  0
 CR3  CONST_24  C3'   C2'  C1'  C8    180.00   0.0  0
 CR3  CONST_25  C5'   C6'  C1'  C8    180.00   0.0  0
 CR3  CONST_26  C4'   C3'  C2'  C1'     0.00   0.0  0
 CR3  CONST_27  C4'   C5'  C6'  C1'     0.00   0.0  0
 CR3  CONST_28  C5'   C6'  C1'  C2'     0.00   0.0  0
 CR3  CONST_29  C5'   C4'  C3'  C2'     0.00   0.0  0
 CR3  CONST_30  C6'   C1'  C2'  C3'     0.00   0.0  0
 CR3  CONST_31  C6'   C5'  C4'  C3'     0.00   0.0  0
 CR3  CONST_32  C7    C1   C2   C3    180.00   0.0  0
 CR3  CONST_33  C7    C1   C6   C5    180.00   0.0  0
 CR3  CONST_34  O6'   C6'  C1'  C8      0.00   0.0  0
 CR3  CONST_35  O5'   C5'  C6'  C1'   180.00   0.0  0
 CR3  CONST_36  O6'   C6'  C1'  C2'   180.00   0.0  0
 CR3  CONST_37  O5'   C5'  C4'  C3'   180.00   0.0  0
 CR3  CONST_38  O6'   C6'  C5'  C4'   180.00   0.0  0
 CR3  CONST_39  HC3   C3   C2   C1    180.00   0.0  0
 CR3  CONST_40  HC6   C6   C1   C2    180.00   0.0  0
 CR3  CONST_41  HN3   N3   C4   C3      0.00   0.0  0
 CR3  CONST_42  HC2   C2   C3   C4    180.00   0.0  0
 CR3  CONST_43  HCN4  CN4  C5   C4    180.00   0.0  0
 CR3  CONST_44  HC2'  C2'  C1'  C8      0.00   0.0  0
 CR3  CONST_45  HC3'  C3'  C2'  C1'   180.00   0.0  0
 CR3  CONST_46  HC4'  C4'  C3'  C2'   180.00   0.0  0
 CR3  CONST_47  HH11  N1   C7   C1    180.00   0.0  0
 CR3  CONST_48  HH12  N1   C7   C1      0.00   0.0  0
 CR3  CONST_49  HH21  N2   C7   C1      0.00   0.0  0
 CR3  CONST_50  HH22  N2   C7   C1    180.00   0.0  0
 CR3  Var_01    C3B   C4B  C5B  C1B    -7.32  30.0  1
 CR3  Var_02    C4B   C5B  C1B  C2B    30.40  30.0  1
 CR3  Var_03    C5B   C4B  C3B  C2B   -18.32  30.0  1
 CR3  Var_04    N1    C7   C1   C2   -146.41  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
 CR3  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
 CR3  plan-1  C8    0.020
 CR3  plan-1  C1'   0.020
 CR3  plan-1  C2'   0.020
 CR3  plan-1  C3'   0.020
 CR3  plan-1  C4'   0.020
 CR3  plan-1  C5'   0.020
 CR3  plan-1  O5'   0.020
 CR3  plan-1  C6'   0.020
 CR3  plan-1  O6'   0.020
 CR3  plan-1  HC2'  0.020
 CR3  plan-1  HC3'  0.020
 CR3  plan-1  HC4'  0.020
 CR3  plan-2  C1    0.020
 CR3  plan-2  C2    0.020
 CR3  plan-2  C3    0.020
 CR3  plan-2  C4    0.020
 CR3  plan-2  C5    0.020
 CR3  plan-2  C6    0.020
 CR3  plan-2  C7    0.020
 CR3  plan-2  N3    0.020
 CR3  plan-2  CN4   0.020
 CR3  plan-2  C8    0.020
 CR3  plan-2  C1'   0.020
 CR3  plan-2  HC2   0.020
 CR3  plan-2  HC3   0.020
 CR3  plan-2  HC6   0.020
 CR3  plan-2  HN3   0.020
 CR3  plan-2  HCN4  0.020
 CR3  plan-3  C1    0.020
 CR3  plan-3  C7    0.020
 CR3  plan-3  N1    0.020
 CR3  plan-3  N2    0.020
 CR3  plan-3  HH11  0.020
 CR3  plan-3  HH12  0.020
 CR3  plan-3  HH21  0.020
 CR3  plan-3  HH22  0.020

