# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Mar 18 17:25:23 2022
#   Inital geometry file: a 78 line input string
#   Ligand name: N-[(6-bromo-1H-indol-1-yl)acetyl]glycine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC(=O)CNC(=O)Cn1ccc2ccc(Br)cc12
#
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
 LB6  LB6  N-[(6-bromo-1H-indol-1-yl)acetyl]glycine  ligand  28  18  .  2022-03-22  2022-03-22
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_LB6
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
 LB6  C10  C   CH2    0  -0.441  32.3448  51.3450  -29.0281
 LB6  C11  C   C      0   0.497  31.3714  51.8853  -27.9811
 LB6  C12  C   CH2    0  -0.459  31.7367  54.2468  -28.6946
 LB6  C13  C   C      0   0.407  33.1801  54.4884  -28.1809
 LB6  C2   C   CR15   0  -0.037  32.7213  52.2918  -31.3174
 LB6  C3   C   CR15   0  -0.412  32.0778  52.3251  -32.5179
 LB6  C4   C   CR16   0  -0.340  29.7755  51.2978  -33.1744
 LB6  C5   C   CR16   0  -0.247  28.7203  50.5616  -32.6724
 LB6  C6   C   CR6    0  -0.135  28.7363  50.1381  -31.3357
 LB6  C7   C   CR16   0  -0.271  29.7716  50.4327  -30.4718
 LB6  C8   C   CR56   0   0.376  30.8225  51.1828  -30.9969
 LB6  C9   C   CR56   0   0.060  30.8499  51.6176  -32.3401
 LB6  N1   N   NR5    0  -0.523  31.9700  51.6125  -30.3929
 LB6  N2   N   NH1    0  -0.588  31.0117  53.1770  -28.0466
 LB6  O1   O   O      0  -0.489  30.9175  51.1203  -27.1398
 LB6  O2   O   OC    -1  -0.588  33.6170  53.7217  -27.3053
 LB6  O3   O   O      0  -0.602  33.7580  55.4472  -28.7241
 LB6  H1   H   HCH2   0   0.285  32.4196  50.2683  -28.8684
 LB6  H2   H   HCH2   0   0.302  33.3315  51.7718  -28.8545
 LB6  H3   H   HCH2   0   0.257  31.7611  54.1062  -29.7763
 LB6  H4   H   HCH2   0   0.267  31.1567  55.1572  -28.5381
 LB6  H5   H   HCR5   0   0.295  33.6748  52.7104  -31.0324
 LB6  H6   H   HCR5   0   0.251  32.4353  52.7972  -33.4187
 LB6  H7   H   HCR6   0   0.257  29.7638  51.6182  -34.2085
 LB6  H8   H   HCR6   0   0.269  27.8868  50.3111  -33.3145
 LB6  H9   H   HCR6   0   0.284  29.7687  50.0948  -29.4438
 LB6  H10  H   HNH1   0   0.387  30.3986  53.4593  -27.2954
 LB6  BR   BR  BR     0  -0.062  27.2779  49.1163  -30.6916

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
 LB6  C4   C5   aromatic  1.381  0.020  1.381
 LB6  C4   C9   aromatic  1.397  0.020  1.397
 LB6  C3   C9   aromatic  1.428  0.020  1.428
 LB6  C3   C2   aromatic  1.362  0.020  1.362
 LB6  C5   C6   aromatic  1.402  0.020  1.402
 LB6  C9   C8   aromatic  1.412  0.020  1.412
 LB6  C2   N1   aromatic  1.371  0.020  1.371
 LB6  C6   C7   aromatic  1.380  0.020  1.380
 LB6  C6   BR   single    1.894  0.020  1.894
 LB6  C8   N1   aromatic  1.366  0.020  1.366
 LB6  C8   C7   aromatic  1.394  0.020  1.394
 LB6  N1   C10  single    1.440  0.020  1.440
 LB6  C10  C11  single    1.528  0.020  1.528
 LB6  C12  N2   single    1.446  0.020  1.446
 LB6  C12  C13  single    1.551  0.020  1.551
 LB6  N2   C11  single    1.342  0.020  1.342
 LB6  C11  O1   double    1.224  0.020  1.224
 LB6  C13  O3   deloc     1.244  0.020  1.244
 LB6  C13  O2   deloc     1.243  0.020  1.243
 LB6  C10  H1   single    0.970  0.020  1.090
 LB6  C10  H2   single    0.970  0.020  1.090
 LB6  C12  H3   single    0.970  0.020  1.090
 LB6  C12  H4   single    0.970  0.020  1.090
 LB6  C2   H5   single    0.930  0.020  1.080
 LB6  C3   H6   single    0.930  0.020  1.080
 LB6  C4   H7   single    0.930  0.020  1.080
 LB6  C5   H8   single    0.930  0.020  1.080
 LB6  C7   H9   single    0.930  0.020  1.080
 LB6  N2   H10  single    0.890  0.020  1.040

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
 LB6  H2   C10  H1   107.54  3.000
 LB6  H2   C10  N1   108.30  3.000
 LB6  H1   C10  N1   109.86  3.000
 LB6  H2   C10  C11  109.23  3.000
 LB6  H1   C10  C11  106.99  3.000
 LB6  N1   C10  C11  114.69  3.000
 LB6  O1   C11  N2   122.37  3.000
 LB6  O1   C11  C10  119.08  3.000
 LB6  N2   C11  C10  118.52  3.000
 LB6  H4   C12  H3   105.17  3.000
 LB6  H4   C12  N2   106.65  3.000
 LB6  H3   C12  N2   111.12  3.000
 LB6  H4   C12  C13  108.50  3.000
 LB6  H3   C12  C13  109.13  3.000
 LB6  N2   C12  C13  115.69  3.000
 LB6  O3   C13  O2   128.28  3.000
 LB6  O2   C13  C12  117.66  3.000
 LB6  O3   C13  C12  114.06  3.000
 LB6  H5   C2   N1   119.86  3.000
 LB6  H5   C2   C3   129.81  3.000
 LB6  N1   C2   C3   110.32  3.000
 LB6  H6   C3   C9   127.30  3.000
 LB6  H6   C3   C2   126.18  3.000
 LB6  C9   C3   C2   106.52  3.000
 LB6  H7   C4   C9   120.72  3.000
 LB6  H7   C4   C5   119.78  3.000
 LB6  C9   C4   C5   119.50  3.000
 LB6  H8   C5   C6   120.32  3.000
 LB6  H8   C5   C4   119.77  3.000
 LB6  C6   C5   C4   119.92  3.000
 LB6  BR   C6   C7   118.68  3.000
 LB6  BR   C6   C5   118.58  3.000
 LB6  C7   C6   C5   122.74  3.000
 LB6  H9   C7   C8   121.87  3.000
 LB6  H9   C7   C6   121.74  3.000
 LB6  C8   C7   C6   116.40  3.000
 LB6  N1   C8   C9   107.90  3.000
 LB6  N1   C8   C7   129.49  3.000
 LB6  C9   C8   C7   122.60  3.000
 LB6  C8   C9   C4   118.85  3.000
 LB6  C8   C9   C3   106.71  3.000
 LB6  C4   C9   C3   134.44  3.000
 LB6  C8   N1   C2   108.54  3.000
 LB6  C8   N1   C10  125.39  3.000
 LB6  C2   N1   C10  126.03  3.000
 LB6  H10  N2   C12  115.54  3.000
 LB6  H10  N2   C11  113.29  3.000
 LB6  C12  N2   C11  126.83  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
 LB6  CONST_01  C4   C9   C3   C2    180.00   0.0  0
 LB6  CONST_02  C8   C9   C3   C2      0.00   0.0  0
 LB6  CONST_03  C9   C8   N1   C2      0.00   0.0  0
 LB6  CONST_04  C7   C8   N1   C2    180.00   0.0  0
 LB6  CONST_05  C5   C4   C9   C3    180.00   0.0  0
 LB6  CONST_06  N1   C8   C9   C3      0.00   0.0  0
 LB6  CONST_07  C7   C8   C9   C3    180.00   0.0  0
 LB6  CONST_08  C8   N1   C2   C3      0.00   0.0  0
 LB6  CONST_09  C7   C6   C5   C4      0.00   0.0  0
 LB6  CONST_10  N1   C8   C9   C4    180.00   0.0  0
 LB6  CONST_11  C7   C8   C9   C4      0.00   0.0  0
 LB6  CONST_12  C8   C9   C4   C5      0.00   0.0  0
 LB6  CONST_13  C8   C7   C6   C5      0.00   0.0  0
 LB6  CONST_14  C9   C4   C5   C6      0.00   0.0  0
 LB6  CONST_15  C9   C8   C7   C6      0.00   0.0  0
 LB6  CONST_16  N1   C8   C7   C6    180.00   0.0  0
 LB6  CONST_17  N1   C2   C3   C9      0.00   0.0  0
 LB6  CONST_18  C3   C2   N1   C10   180.00   0.0  0
 LB6  CONST_19  C9   C8   N1   C10   180.00   0.0  0
 LB6  CONST_20  C7   C8   N1   C10     0.00   0.0  0
 LB6  CONST_21  BR   C6   C5   C4    180.00   0.0  0
 LB6  CONST_22  BR   C6   C7   C8    180.00   0.0  0
 LB6  CONST_23  H7   C4   C9   C3      0.00   0.0  0
 LB6  CONST_24  H6   C3   C9   C4      0.00   0.0  0
 LB6  CONST_25  H9   C7   C6   C5    180.00   0.0  0
 LB6  CONST_26  H8   C5   C6   C7    180.00   0.0  0
 LB6  CONST_27  H5   C2   N1   C8    180.00   0.0  0
 LB6  CONST_30  H10  N2   C11  C10   180.00   0.0  0
 LB6  Var_01    C2   N1   C10  C11   122.05  30.0  2
 LB6  Var_02    N2   C11  C10  N1    -51.77  30.0  3
 LB6  Var_03    C13  C12  N2   C11   -58.63  30.0  1
 LB6  Var_04    O3   C13  C12  N2   -177.44  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
 LB6  plan-1  C10  0.020
 LB6  plan-1  C2   0.020
 LB6  plan-1  C3   0.020
 LB6  plan-1  C4   0.020
 LB6  plan-1  C5   0.020
 LB6  plan-1  C6   0.020
 LB6  plan-1  C7   0.020
 LB6  plan-1  C8   0.020
 LB6  plan-1  C9   0.020
 LB6  plan-1  N1   0.020
 LB6  plan-1  H5   0.020
 LB6  plan-1  H6   0.020
 LB6  plan-1  H7   0.020
 LB6  plan-1  H8   0.020
 LB6  plan-1  H9   0.020
 LB6  plan-1  BR   0.020
 LB6  plan-2  C10  0.020
 LB6  plan-2  C11  0.020
 LB6  plan-2  C12  0.020
 LB6  plan-2  N2   0.020
 LB6  plan-2  O1   0.020
 LB6  plan-2  H10  0.020
 LB6  plan-3  C12  0.020
 LB6  plan-3  C13  0.020
 LB6  plan-3  O2   0.020
 LB6  plan-3  O3   0.020

