# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Apr  9 10:16:23 2020
#   Inital geometry file: a 99 line input string
#   Ligand name: (3-{5-[amino(iminio)methyl]-1H-indol-2-yl}-5-bromo-4-oxidophenyl)acetate
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: NC(=[NH2+])c1ccc2[nH]c(cc2c1)c3cc(CC([O-])=O)cc(Br)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
 678  678  (3-{5-[amino(iminio)methyl]-1H-indol-2-yl}-5-bromo-4-oxidophenyl)acetate  ligand  37  24  .  2021-08-05  2022-09-22
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_678
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
 678  C1    C   CR6    0   0.002   5.3845   0.0958  -0.0255
 678  C2    C   CR16   0  -0.305   5.1586   1.4577  -0.3084
 678  C3    C   CR16   0  -0.300   3.8785   1.9694  -0.3496
 678  C4    C   CR56   0   0.360   2.8245   1.0987  -0.0909
 678  C5    C   CR56   0   0.115   3.0247  -0.2748   0.1927
 678  C6    C   CR16   0  -0.391   4.3239  -0.7728   0.2197
 678  C7    C   C      0   0.579   6.7569  -0.4113   0.0095
 678  N1    N   NH2    0  -0.770   7.0094  -1.6358  -0.3944
 678  N2    N   NC2    1  -0.772   7.7264   0.3633   0.4427
 678  N3    N   NR15   0  -0.764   1.4906   1.3241  -0.0475
 678  CN4   C   CR15   0  -0.478   1.7384  -0.8477   0.3990
 678  C8    C   CR5    0   0.392   0.8052   0.1583   0.2498
 678  C1'   C   CR6    0  -0.156  -0.6421   0.1597   0.3739
 678  C2'   C   CR16   0  -0.368  -1.3389   1.3751   0.4443
 678  C3'   C   CR6    0   0.141  -2.7137   1.4669   0.5507
 678  CV'   C   CH2    0  -0.693  -3.4167   2.7867   0.6325
 678  CW'   C   C      0   0.416  -4.2367   3.1990  -0.6132
 678  OX'   O   O      0  -0.598  -4.3925   2.3612  -1.5189
 678  OY'   O   OC    -1  -0.632  -4.6925   4.3617  -0.5870
 678  C4'   C   CR16   0  -0.274  -3.4279   0.2641   0.5933
 678  C5'   C   CR6    0  -0.279  -2.7692  -0.9403   0.5414
 678  C6'   C   CR6    0   0.319  -1.3450  -1.0980   0.4342
 678  O6'   O   OC    -1  -0.557  -0.7909  -2.2231   0.3986
 678  BR5'  BR  BR     0  -0.131  -3.7762  -2.5489   0.6257
 678  HC2   H   HCR6   0   0.267   5.9899   2.1134  -0.5321
 678  HC3   H   HCR6   0   0.270   3.7068   3.0128  -0.5789
 678  HC6   H   HCR6   0   0.266   4.4987  -1.8143   0.4614
 678  HH11  H   HNH2   0   0.434   7.9286  -2.0450  -0.3254
 678  HH12  H   HNH2   0   0.443   6.2992  -2.1832  -0.8518
 678  HH21  H   HNC2   0   0.442   7.5225   1.2398   0.8938
 678  HH22  H   HNC2   0   0.434   8.6926   0.0746   0.4227
 678  HN3   H   HNR5   0   0.412   1.0627   2.2048  -0.2781
 678  HCN4  H   HCR5   0   0.248   1.5232  -1.8715   0.6418
 678  HC2'  H   HCR6   0   0.215  -0.7854   2.3091   0.4398
 678  H31B  H   HCH2   0   0.233  -2.6905   3.5782   0.8420
 678  H31A  H   HCH2   0   0.235  -4.1054   2.7968   1.4858
 678  HC4'  H   HCR6   0   0.246  -4.5075   0.2913   0.6850

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
 678  C1   C2    aromatic  1.409  0.020  1.409
 678  C1   C6    aromatic  1.393  0.020  1.393
 678  C1   C7    single    1.464  0.020  1.464
 678  C2   C3    aromatic  1.379  0.020  1.379
 678  C2   HC2   single    0.930  0.020  1.080
 678  C3   C4    aromatic  1.391  0.020  1.391
 678  C3   HC3   single    0.930  0.020  1.080
 678  C4   C5    aromatic  1.417  0.020  1.417
 678  C4   N3    aromatic  1.354  0.020  1.354
 678  C5   C6    aromatic  1.392  0.020  1.392
 678  C5   CN4   aromatic  1.423  0.020  1.423
 678  C6   HC6   single    0.930  0.020  1.080
 678  C7   N1    single    1.314  0.020  1.314
 678  C7   N2    double    1.314  0.020  1.314
 678  N1   HH11  single    0.860  0.020  1.020
 678  N1   HH12  single    0.860  0.020  1.020
 678  N2   HH21  single    0.860  0.020  1.020
 678  N2   HH22  single    0.860  0.020  1.020
 678  N3   C8    aromatic  1.385  0.020  1.385
 678  N3   HN3   single    0.860  0.020  1.020
 678  CN4  C8    aromatic  1.380  0.020  1.380
 678  CN4  HCN4  single    0.930  0.020  1.080
 678  C8   C1'   single    1.453  0.020  1.453
 678  C1'  C2'   aromatic  1.403  0.020  1.403
 678  C1'  C6'   aromatic  1.442  0.020  1.442
 678  C2'  C3'   aromatic  1.382  0.020  1.382
 678  C2'  HC2'  single    0.930  0.020  1.080
 678  C3'  CV'   single    1.498  0.020  1.498
 678  C3'  C4'   aromatic  1.399  0.020  1.399
 678  CV'  CW'   single    1.547  0.020  1.547
 678  CV'  H31B  single    0.970  0.020  1.090
 678  CV'  H31A  single    0.970  0.020  1.090
 678  CW'  OX'   deloc     1.244  0.020  1.244
 678  CW'  OY'   deloc     1.249  0.020  1.249
 678  C4'  C5'   aromatic  1.374  0.020  1.374
 678  C4'  HC4'  single    0.930  0.020  1.080
 678  C5'  C6'   aromatic  1.437  0.020  1.437
 678  C5'  BR5'  single    1.900  0.020  1.900
 678  C6'  O6'   single    1.255  0.020  1.255

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
 678  C7    C1   C6    119.60  3.000
 678  C7    C1   C2    119.34  3.000
 678  C6    C1   C2    121.06  3.000
 678  HC2   C2   C3    118.82  3.000
 678  HC2   C2   C1    120.26  3.000
 678  C3    C2   C1    120.89  3.000
 678  HC3   C3   C4    121.51  3.000
 678  HC3   C3   C2    120.76  3.000
 678  C4    C3   C2    117.73  3.000
 678  N3    C4   C5    107.12  3.000
 678  N3    C4   C3    130.41  3.000
 678  C5    C4   C3    122.47  3.000
 678  CN4   C5   C6    134.18  3.000
 678  CN4   C5   C4    106.95  3.000
 678  C6    C5   C4    118.87  3.000
 678  HC6   C6   C5    119.94  3.000
 678  HC6   C6   C1    121.06  3.000
 678  C5    C6   C1    118.97  3.000
 678  N2    C7   N1    120.59  3.000
 678  N2    C7   C1    119.70  3.000
 678  N1    C7   C1    119.72  3.000
 678  HH12  N1   HH11  116.97  3.000
 678  HH12  N1   C7    120.73  3.000
 678  HH11  N1   C7    122.15  3.000
 678  HH22  N2   HH21  116.89  3.000
 678  HH22  N2   C7    122.10  3.000
 678  HH21  N2   C7    120.75  3.000
 678  HN3   N3   C8    125.16  3.000
 678  HN3   N3   C4    123.89  3.000
 678  C8    N3   C4    110.76  3.000
 678  HCN4  CN4  C8    125.72  3.000
 678  HCN4  CN4  C5    126.70  3.000
 678  C8    CN4  C5    107.58  3.000
 678  C1'   C8   CN4   131.69  3.000
 678  C1'   C8   N3    120.71  3.000
 678  CN4   C8   N3    107.59  3.000
 678  C6'   C1'  C2'   120.76  3.000
 678  C6'   C1'  C8    119.23  3.000
 678  C2'   C1'  C8    120.01  3.000
 678  HC2'  C2'  C3'   116.76  3.000
 678  HC2'  C2'  C1'   119.47  3.000
 678  C3'   C2'  C1'   123.75  3.000
 678  C4'   C3'  CV'   121.08  3.000
 678  C4'   C3'  C2'   116.93  3.000
 678  CV'   C3'  C2'   121.99  3.000
 678  H31A  CV'  H31B  105.14  3.000
 678  H31A  CV'  CW'   106.92  3.000
 678  H31B  CV'  CW'   108.24  3.000
 678  H31A  CV'  C3'   110.21  3.000
 678  H31B  CV'  C3'   109.65  3.000
 678  CW'   CV'  C3'   116.08  3.000
 678  OY'   CW'  OX'   126.64  3.000
 678  OY'   CW'  CV'   115.12  3.000
 678  OX'   CW'  CV'   118.24  3.000
 678  HC4'  C4'  C5'   120.18  3.000
 678  HC4'  C4'  C3'   119.30  3.000
 678  C5'   C4'  C3'   120.51  3.000
 678  BR5'  C5'  C6'   115.84  3.000
 678  BR5'  C5'  C4'   119.11  3.000
 678  C6'   C5'  C4'   125.05  3.000
 678  O6'   C6'  C5'   122.57  3.000
 678  O6'   C6'  C1'   124.45  3.000
 678  C5'   C6'  C1'   112.98  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
 678  CONST_01  C4    C3   C2   C1      0.00   0.0  0
 678  CONST_02  C4    C5   C6   C1      0.00   0.0  0
 678  CONST_03  CN4   C5   C6   C1    180.00   0.0  0
 678  CONST_04  C5    C6   C1   C2      0.00   0.0  0
 678  CONST_05  C5    C4   C3   C2      0.00   0.0  0
 678  CONST_06  N3    C4   C3   C2    180.00   0.0  0
 678  CONST_07  C6    C1   C2   C3      0.00   0.0  0
 678  CONST_08  C6    C5   C4   C3      0.00   0.0  0
 678  CONST_09  CN4   C5   C4   C3    180.00   0.0  0
 678  CONST_10  C8    N3   C4   C3    180.00   0.0  0
 678  CONST_11  C8    CN4  C5   C4      0.00   0.0  0
 678  CONST_12  CN4   C8   N3   C4      0.00   0.0  0
 678  CONST_13  C1'   C8   N3   C4    180.00   0.0  0
 678  CONST_14  C8    N3   C4   C5      0.00   0.0  0
 678  CONST_15  N3    C8   CN4  C5      0.00   0.0  0
 678  CONST_16  C1'   C8   CN4  C5    180.00   0.0  0
 678  CONST_17  N3    C4   C5   C6    180.00   0.0  0
 678  CONST_18  C8    CN4  C5   C6    180.00   0.0  0
 678  CONST_19  CN4   C5   C4   N3      0.00   0.0  0
 678  CONST_20  C2'   C1'  C8   N3      0.00   0.0  0
 678  CONST_21  C6'   C1'  C8   N3    180.00   0.0  0
 678  CONST_22  C2'   C1'  C8   CN4   180.00   0.0  0
 678  CONST_23  C6'   C1'  C8   CN4     0.00   0.0  0
 678  CONST_24  C3'   C2'  C1'  C8    180.00   0.0  0
 678  CONST_25  C5'   C6'  C1'  C8    180.00   0.0  0
 678  CONST_26  C4'   C3'  C2'  C1'     0.00   0.0  0
 678  CONST_27  C4'   C5'  C6'  C1'     0.00   0.0  0
 678  CONST_28  C5'   C6'  C1'  C2'     0.00   0.0  0
 678  CONST_29  C5'   C4'  C3'  C2'     0.00   0.0  0
 678  CONST_30  C6'   C1'  C2'  C3'     0.00   0.0  0
 678  CONST_31  C6'   C5'  C4'  C3'     0.00   0.0  0
 678  CONST_32  C7    C1   C2   C3    180.00   0.0  0
 678  CONST_33  C7    C1   C6   C5    180.00   0.0  0
 678  CONST_34  O6'   C6'  C1'  C8      0.00   0.0  0
 678  CONST_35  CV'   C3'  C2'  C1'   180.00   0.0  0
 678  CONST_36  BR5'  C5'  C6'  C1'   180.00   0.0  0
 678  CONST_37  O6'   C6'  C1'  C2'   180.00   0.0  0
 678  CONST_38  BR5'  C5'  C4'  C3'   180.00   0.0  0
 678  CONST_39  C5'   C4'  C3'  CV'   180.00   0.0  0
 678  CONST_40  O6'   C6'  C5'  C4'   180.00   0.0  0
 678  CONST_41  HC3   C3   C2   C1    180.00   0.0  0
 678  CONST_42  HC6   C6   C1   C2    180.00   0.0  0
 678  CONST_43  HN3   N3   C4   C3      0.00   0.0  0
 678  CONST_44  HC2   C2   C3   C4    180.00   0.0  0
 678  CONST_45  HCN4  CN4  C5   C4    180.00   0.0  0
 678  CONST_46  HC2'  C2'  C1'  C8      0.00   0.0  0
 678  CONST_47  HC4'  C4'  C3'  C2'   180.00   0.0  0
 678  CONST_48  HH11  N1   C7   C1    180.00   0.0  0
 678  CONST_49  HH12  N1   C7   C1      0.00   0.0  0
 678  CONST_50  HH21  N2   C7   C1      0.00   0.0  0
 678  CONST_51  HH22  N2   C7   C1    180.00   0.0  0
 678  Var_01    N1    C7   C1   C2   -145.90  30.0  2
 678  Var_02    CW'   CV'  C3'  C2'   109.16  30.0  2
 678  Var_03    OX'   CW'  CV'  C3'     8.42  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
 678  plan-1  C8    0.020
 678  plan-1  C1'   0.020
 678  plan-1  C2'   0.020
 678  plan-1  C3'   0.020
 678  plan-1  CV'   0.020
 678  plan-1  C4'   0.020
 678  plan-1  C5'   0.020
 678  plan-1  C6'   0.020
 678  plan-1  O6'   0.020
 678  plan-1  BR5'  0.020
 678  plan-1  HC2'  0.020
 678  plan-1  HC4'  0.020
 678  plan-2  C1    0.020
 678  plan-2  C2    0.020
 678  plan-2  C3    0.020
 678  plan-2  C4    0.020
 678  plan-2  C5    0.020
 678  plan-2  C6    0.020
 678  plan-2  C7    0.020
 678  plan-2  N3    0.020
 678  plan-2  CN4   0.020
 678  plan-2  C8    0.020
 678  plan-2  C1'   0.020
 678  plan-2  HC2   0.020
 678  plan-2  HC3   0.020
 678  plan-2  HC6   0.020
 678  plan-2  HN3   0.020
 678  plan-2  HCN4  0.020
 678  plan-3  C1    0.020
 678  plan-3  C7    0.020
 678  plan-3  N1    0.020
 678  plan-3  N2    0.020
 678  plan-3  HH11  0.020
 678  plan-3  HH12  0.020
 678  plan-3  HH21  0.020
 678  plan-3  HH22  0.020
 678  plan-4  CV'   0.020
 678  plan-4  CW'   0.020
 678  plan-4  OX'   0.020
 678  plan-4  OY'   0.020

