# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Mar  9 08:48:51 2022
#   Inital geometry file: a 92 line input string
#   Ligand name: 2-{5-[amino(iminio)methyl]-1H-indol-2-yl}-6-bromo-4-methylphenolate
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cc1cc(Br)c([O-])c(c1)c2[nH]c3ccc(cc3c2)C(N)=[NH2+]
#
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
 907  907  2-{5-[amino(iminio)methyl]-1H-indol-2-yl}-6-bromo-4-methylphenolate  ligand  35  21  .  2022-03-11  2022-03-11
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_907
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
 907  C1    C   CR6    0   0.004  -4.8976  -0.2343  -0.0067
 907  C2    C   CR16   0  -0.305  -4.9005   1.1696   0.1191
 907  C3    C   CR16   0  -0.300  -3.7225   1.8858   0.0941
 907  C4    C   CR56   0   0.362  -2.5357   1.1767  -0.0681
 907  C5    C   CR56   0   0.111  -2.5082  -0.2319  -0.2134
 907  C6    C   CR16   0  -0.389  -3.7073  -0.9364  -0.1736
 907  C7    C   C      0   0.581  -6.1651  -0.9639   0.0425
 907  N1    N   NH2    0  -0.773  -7.2559  -0.4109  -0.4384
 907  N2    N   NC2    1  -0.771  -6.2035  -2.1672   0.5698
 907  N3    N   NR15   0  -0.761  -1.2542   1.6087  -0.1285
 907  CN4   C   CR15   0  -0.470  -1.1455  -0.6059  -0.3825
 907  C8    C   CR5    0   0.390  -0.3886   0.5449  -0.3165
 907  C1'   C   CR6    0  -0.158   1.0476   0.7588  -0.3846
 907  C2'   C   CR16   0  -0.346   1.5952   1.9714   0.0490
 907  C3'   C   CR6    0   0.052   2.9498   2.2565   0.0043
 907  CV'   C   CH3    0  -0.720   3.4950   3.5818   0.4594
 907  C4'   C   CR16   0  -0.272   3.7949   1.2623  -0.4983
 907  C5'   C   CR6    0  -0.276   3.2813   0.0584  -0.9218
 907  C6'   C   CR6    0   0.325   1.8911  -0.2975  -0.8923
 907  O6'   O   OC    -1  -0.554   1.4706  -1.4149  -1.2732
 907  BR5'  BR  BR     0  -0.125   4.4635  -1.2728  -1.5795
 907  HC2   H   HCR6   0   0.267  -5.8302   1.7002   0.2777
 907  HC3   H   HCR6   0   0.271  -3.7279   2.9618   0.2079
 907  HC6   H   HCR6   0   0.267  -3.7071  -2.0116  -0.3036
 907  HH11  H   HNH2   0   0.442  -7.2103   0.4459  -0.9649
 907  HH12  H   HNH2   0   0.434  -8.1595  -0.8517  -0.3599
 907  HH21  H   HNC2   0   0.434  -7.0447  -2.7233   0.5745
 907  HH22  H   HNC2   0   0.443  -5.4132  -2.5337   1.0741
 907  HN3   H   HNR5   0   0.414  -0.9854   2.5788  -0.1206
 907  HCN4  H   HCR5   0   0.248  -0.7660  -1.6024  -0.5136
 907  HC2'  H   HCR6   0   0.224   0.9440   2.7315   0.4696
 907  H32'  H   HCH3   0   0.233   3.5997   4.2889  -0.3675
 907  H33'  H   HCH3   0   0.234   2.8403   4.0469   1.1971
 907  H34'  H   HCH3   0   0.233   4.4805   3.4773   0.9154
 907  HC4'  H   HCR6   0   0.252   4.8627   1.4453  -0.5427

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
 907  C1   C2    aromatic  1.410  0.020  1.410
 907  C1   C6    aromatic  1.392  0.020  1.392
 907  C1   C7    single    1.463  0.020  1.463
 907  C2   C3    aromatic  1.379  0.020  1.379
 907  C2   HC2   single    0.930  0.020  1.080
 907  C3   C4    aromatic  1.392  0.020  1.392
 907  C3   HC3   single    0.930  0.020  1.080
 907  C4   C5    aromatic  1.416  0.020  1.416
 907  C4   N3    aromatic  1.354  0.020  1.354
 907  C5   C6    aromatic  1.391  0.020  1.391
 907  C5   CN4   aromatic  1.423  0.020  1.423
 907  C6   HC6   single    0.930  0.020  1.080
 907  C7   N1    single    1.314  0.020  1.314
 907  C7   N2    double    1.314  0.020  1.314
 907  N1   HH11  single    0.860  0.020  1.020
 907  N1   HH12  single    0.860  0.020  1.020
 907  N2   HH21  single    0.860  0.020  1.020
 907  N2   HH22  single    0.860  0.020  1.020
 907  N3   C8    aromatic  1.384  0.020  1.384
 907  N3   HN3   single    0.860  0.020  1.020
 907  CN4  C8    aromatic  1.379  0.020  1.379
 907  CN4  HCN4  single    0.930  0.020  1.080
 907  C8   C1'   single    1.454  0.020  1.454
 907  C1'  C2'   aromatic  1.399  0.020  1.399
 907  C1'  C6'   aromatic  1.444  0.020  1.444
 907  C2'  C3'   aromatic  1.385  0.020  1.385
 907  C2'  HC2'  single    0.930  0.020  1.080
 907  C3'  CV'   single    1.504  0.020  1.504
 907  C3'  C4'   aromatic  1.398  0.020  1.398
 907  CV'  H32'  single    0.970  0.020  1.090
 907  CV'  H33'  single    0.970  0.020  1.090
 907  CV'  H34'  single    0.970  0.020  1.090
 907  C4'  C5'   aromatic  1.376  0.020  1.376
 907  C4'  HC4'  single    0.930  0.020  1.080
 907  C5'  C6'   aromatic  1.435  0.020  1.435
 907  C5'  BR5'  single    1.898  0.020  1.898
 907  C6'  O6'   single    1.253  0.020  1.253

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
 907  C7    C1   C6    119.55  3.000
 907  C7    C1   C2    119.46  3.000
 907  C6    C1   C2    120.99  3.000
 907  HC2   C2   C3    118.81  3.000
 907  HC2   C2   C1    120.21  3.000
 907  C3    C2   C1    120.93  3.000
 907  HC3   C3   C4    121.54  3.000
 907  HC3   C3   C2    120.69  3.000
 907  C4    C3   C2    117.77  3.000
 907  N3    C4   C5    107.12  3.000
 907  N3    C4   C3    130.52  3.000
 907  C5    C4   C3    122.36  3.000
 907  CN4   C5   C6    134.07  3.000
 907  CN4   C5   C4    106.99  3.000
 907  C6    C5   C4    118.94  3.000
 907  HC6   C6   C5    119.94  3.000
 907  HC6   C6   C1    121.02  3.000
 907  C5    C6   C1    119.01  3.000
 907  N2    C7   N1    120.52  3.000
 907  N2    C7   C1    119.68  3.000
 907  N1    C7   C1    119.79  3.000
 907  HH12  N1   HH11  116.96  3.000
 907  HH12  N1   C7    122.09  3.000
 907  HH11  N1   C7    120.79  3.000
 907  HH22  N2   HH21  116.86  3.000
 907  HH22  N2   C7    120.76  3.000
 907  HH21  N2   C7    122.08  3.000
 907  HN3   N3   C8    125.08  3.000
 907  HN3   N3   C4    124.05  3.000
 907  C8    N3   C4    110.65  3.000
 907  HCN4  CN4  C8    125.87  3.000
 907  HCN4  CN4  C5    126.62  3.000
 907  C8    CN4  C5    107.49  3.000
 907  C1'   C8   CN4   131.52  3.000
 907  C1'   C8   N3    120.73  3.000
 907  CN4   C8   N3    107.74  3.000
 907  C6'   C1'  C2'   120.95  3.000
 907  C6'   C1'  C8    119.08  3.000
 907  C2'   C1'  C8    119.97  3.000
 907  HC2'  C2'  C3'   117.07  3.000
 907  HC2'  C2'  C1'   119.47  3.000
 907  C3'   C2'  C1'   123.44  3.000
 907  C4'   C3'  CV'   121.09  3.000
 907  C4'   C3'  C2'   117.15  3.000
 907  CV'   C3'  C2'   121.76  3.000
 907  H34'  CV'  H33'  107.49  3.000
 907  H34'  CV'  H32'  106.96  3.000
 907  H33'  CV'  H32'  107.06  3.000
 907  H34'  CV'  C3'   111.70  3.000
 907  H33'  CV'  C3'   111.29  3.000
 907  H32'  CV'  C3'   112.08  3.000
 907  HC4'  C4'  C5'   120.18  3.000
 907  HC4'  C4'  C3'   119.34  3.000
 907  C5'   C4'  C3'   120.48  3.000
 907  BR5'  C5'  C6'   115.88  3.000
 907  BR5'  C5'  C4'   119.21  3.000
 907  C6'   C5'  C4'   124.91  3.000
 907  O6'   C6'  C5'   122.67  3.000
 907  O6'   C6'  C1'   124.27  3.000
 907  C5'   C6'  C1'   113.06  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
 907  CONST_01  C4    C3   C2   C1     0.00   0.0  0
 907  CONST_02  C4    C5   C6   C1     0.00   0.0  0
 907  CONST_03  CN4   C5   C6   C1   180.00   0.0  0
 907  CONST_04  C5    C6   C1   C2     0.00   0.0  0
 907  CONST_05  C5    C4   C3   C2     0.00   0.0  0
 907  CONST_06  N3    C4   C3   C2   180.00   0.0  0
 907  CONST_07  C6    C1   C2   C3     0.00   0.0  0
 907  CONST_08  C6    C5   C4   C3     0.00   0.0  0
 907  CONST_09  CN4   C5   C4   C3   180.00   0.0  0
 907  CONST_10  C8    N3   C4   C3   180.00   0.0  0
 907  CONST_11  C8    CN4  C5   C4     0.00   0.0  0
 907  CONST_12  CN4   C8   N3   C4     0.00   0.0  0
 907  CONST_13  C1'   C8   N3   C4   180.00   0.0  0
 907  CONST_14  C8    N3   C4   C5     0.00   0.0  0
 907  CONST_15  N3    C8   CN4  C5     0.00   0.0  0
 907  CONST_16  C1'   C8   CN4  C5   180.00   0.0  0
 907  CONST_17  N3    C4   C5   C6   180.00   0.0  0
 907  CONST_18  C8    CN4  C5   C6   180.00   0.0  0
 907  CONST_19  CN4   C5   C4   N3     0.00   0.0  0
 907  CONST_21  C6'   C1'  C8   N3   180.00   0.0  0
 907  CONST_24  C3'   C2'  C1'  C8   180.00   0.0  0
 907  CONST_25  C5'   C6'  C1'  C8   180.00   0.0  0
 907  CONST_26  C4'   C3'  C2'  C1'    0.00   0.0  0
 907  CONST_27  C4'   C5'  C6'  C1'    0.00   0.0  0
 907  CONST_28  C5'   C6'  C1'  C2'    0.00   0.0  0
 907  CONST_29  C5'   C4'  C3'  C2'    0.00   0.0  0
 907  CONST_30  C6'   C1'  C2'  C3'    0.00   0.0  0
 907  CONST_31  C6'   C5'  C4'  C3'    0.00   0.0  0
 907  CONST_32  C7    C1   C2   C3   180.00   0.0  0
 907  CONST_33  C7    C1   C6   C5   180.00   0.0  0
 907  CONST_34  O6'   C6'  C1'  C8     0.00   0.0  0
 907  CONST_35  CV'   C3'  C2'  C1'  180.00   0.0  0
 907  CONST_36  BR5'  C5'  C6'  C1'  180.00   0.0  0
 907  CONST_37  O6'   C6'  C1'  C2'  180.00   0.0  0
 907  CONST_38  BR5'  C5'  C4'  C3'  180.00   0.0  0
 907  CONST_39  C5'   C4'  C3'  CV'  180.00   0.0  0
 907  CONST_40  O6'   C6'  C5'  C4'  180.00   0.0  0
 907  CONST_41  HC3   C3   C2   C1   180.00   0.0  0
 907  CONST_42  HC6   C6   C1   C2   180.00   0.0  0
 907  CONST_43  HN3   N3   C4   C3     0.00   0.0  0
 907  CONST_44  HC2   C2   C3   C4   180.00   0.0  0
 907  CONST_45  HCN4  CN4  C5   C4   180.00   0.0  0
 907  CONST_46  HC2'  C2'  C1'  C8     0.00   0.0  0
 907  CONST_47  HC4'  C4'  C3'  C2'  180.00   0.0  0
 907  CONST_48  HH11  N1   C7   C1     0.00   0.0  0
 907  CONST_49  HH12  N1   C7   C1   180.00   0.0  0
 907  CONST_50  HH21  N2   C7   C1   180.00   0.0  0
 907  CONST_51  HH22  N2   C7   C1     0.00   0.0  0
 907  Var_01    N1    C7   C1   C2    33.16  30.0  2
 907  Var_02    H32'  CV'  C3'  C2'  -93.89  30.0  2

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
 907  plan-1  C8    0.020
 907  plan-1  C1'   0.020
 907  plan-1  C2'   0.020
 907  plan-1  C3'   0.020
 907  plan-1  CV'   0.020
 907  plan-1  C4'   0.020
 907  plan-1  C5'   0.020
 907  plan-1  C6'   0.020
 907  plan-1  O6'   0.020
 907  plan-1  BR5'  0.020
 907  plan-1  HC2'  0.020
 907  plan-1  HC4'  0.020
 907  plan-2  C1    0.020
 907  plan-2  C2    0.020
 907  plan-2  C3    0.020
 907  plan-2  C4    0.020
 907  plan-2  C5    0.020
 907  plan-2  C6    0.020
 907  plan-2  C7    0.020
 907  plan-2  N3    0.020
 907  plan-2  CN4   0.020
 907  plan-2  C8    0.020
 907  plan-2  C1'   0.020
 907  plan-2  HC2   0.020
 907  plan-2  HC3   0.020
 907  plan-2  HC6   0.020
 907  plan-2  HN3   0.020
 907  plan-2  HCN4  0.020
 907  plan-3  C1    0.020
 907  plan-3  C7    0.020
 907  plan-3  N1    0.020
 907  plan-3  N2    0.020
 907  plan-3  HH11  0.020
 907  plan-3  HH12  0.020
 907  plan-3  HH21  0.020
 907  plan-3  HH22  0.020

