# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr  1 09:16:38 2020
#   Inital geometry file: a 67 line input string
#   Ligand name: (1-methyl-1H-indol-3-yl)acetic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cn1cc(CC(O)=O)c2ccccc12
#
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
 3VY  3VY  '(1-methyl-1H-indol-3-yl)acetic acid'  ligand  24  14  .  2021-08-04  2021-08-04  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_3VY
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
 3VY  C8   C  CR15   0  -0.107   0.0127   1.7727   0.4038
 3VY  C4   C  CR16   0  -0.320  -2.7986  -0.3210  -0.3654
 3VY  C5   C  CR56   0   0.364  -1.6010   0.3151  -0.0384
 3VY  C2   C  CR16   0  -0.276  -1.6567  -2.4404  -0.0359
 3VY  C9   C  CR5    0   0.060   0.5965   0.5498   0.5671
 3VY  C11  C  CH2    0  -0.729   1.9971   0.2596   0.9737
 3VY  C12  C  C      0   0.416   2.8846  -0.3981  -0.1107
 3VY  C3   C  CR16   0  -0.284  -2.8085  -1.7039  -0.3584
 3VY  O14  O  OC    -1  -0.631   4.0223  -0.7441   0.2711
 3VY  O13  O  O      0  -0.596   2.4143  -0.5190  -1.2550
 3VY  C6   C  CR56   0   0.042  -0.4307  -0.4071   0.2893
 3VY  C1   C  CR16   0  -0.371  -0.4711  -1.8045   0.2812
 3VY  N7   N  NR5    0  -0.521  -1.3041   1.6444   0.0332
 3VY  H1   H  HCR5   0   0.274   0.4445   2.7551   0.5272
 3VY  H2   H  HCR6   0   0.258  -3.6912   0.2381  -0.6175
 3VY  H3   H  HCR6   0   0.241  -1.7024  -3.5220  -0.0426
 3VY  H4   H  HCH3   0   0.247  -2.6564   2.6500  -1.2124
 3VY  H5   H  HCH3   0   0.246  -3.0394   2.7257   0.5140
 3VY  H6   H  HCH3   0   0.260  -1.6971   3.6690  -0.1390
 3VY  H7   H  HCH2   0   0.244   2.4862   1.1865   1.2920
 3VY  H8   H  HCH2   0   0.230   2.0074  -0.3876   1.8581
 3VY  H9   H  HCR6   0   0.245  -3.7216  -2.2288  -0.6088
 3VY  H11  H  HCR6   0   0.236   0.4122  -2.3822   0.5254
 3VY  C10  C  CH3    0  -0.527  -2.2263   2.7225  -0.2131

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
 3VY  C10  N7   single    1.440  0.020  1.440
 3VY  N7   C8   aromatic  1.374  0.020  1.374
 3VY  N7   C5   aromatic  1.364  0.020  1.364
 3VY  C8   C9   aromatic  1.365  0.020  1.365
 3VY  C5   C4   aromatic  1.395  0.020  1.395
 3VY  C5   C6   aromatic  1.414  0.020  1.414
 3VY  C4   C3   aromatic  1.383  0.020  1.383
 3VY  C9   C6   aromatic  1.431  0.020  1.431
 3VY  C9   C11  single    1.487  0.020  1.487
 3VY  C6   C1   aromatic  1.398  0.020  1.398
 3VY  C11  C12  single    1.548  0.020  1.548
 3VY  C3   C2   aromatic  1.405  0.020  1.405
 3VY  O13  C12  deloc     1.243  0.020  1.243
 3VY  C1   C2   aromatic  1.382  0.020  1.382
 3VY  C12  O14  deloc     1.249  0.020  1.249
 3VY  C8   H1   single    0.930  0.020  1.080
 3VY  C4   H2   single    0.930  0.020  1.080
 3VY  C2   H3   single    0.930  0.020  1.080
 3VY  C10  H4   single    0.970  0.020  1.090
 3VY  C10  H5   single    0.970  0.020  1.090
 3VY  C10  H6   single    0.970  0.020  1.090
 3VY  C11  H7   single    0.970  0.020  1.090
 3VY  C11  H8   single    0.970  0.020  1.090
 3VY  C3   H9   single    0.930  0.020  1.080
 3VY  C1   H11  single    0.930  0.020  1.080

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
 3VY  H1   C8   N7   119.92  3.000
 3VY  H1   C8   C9   129.07  3.000
 3VY  N7   C8   C9   111.01  3.000
 3VY  H2   C4   C3   120.76  3.000
 3VY  H2   C4   C5   121.78  3.000
 3VY  C3   C4   C5   117.45  3.000
 3VY  N7   C5   C6   107.79  3.000
 3VY  C6   C5   C4   122.15  3.000
 3VY  N7   C5   C4   130.07  3.000
 3VY  H3   C2   C1   119.82  3.000
 3VY  H3   C2   C3   119.20  3.000
 3VY  C1   C2   C3   120.98  3.000
 3VY  C6   C9   C11  126.77  3.000
 3VY  C11  C9   C8   127.62  3.000
 3VY  C6   C9   C8   105.60  3.000
 3VY  H8   C11  H7   105.13  3.000
 3VY  H8   C11  C12  108.00  3.000
 3VY  H7   C11  C12  107.89  3.000
 3VY  H8   C11  C9   110.16  3.000
 3VY  H7   C11  C9   109.56  3.000
 3VY  C12  C11  C9   115.56  3.000
 3VY  O13  C12  O14  126.81  3.000
 3VY  O14  C12  C11  115.20  3.000
 3VY  O13  C12  C11  117.99  3.000
 3VY  H9   C3   C2   119.37  3.000
 3VY  H9   C3   C4   119.33  3.000
 3VY  C2   C3   C4   121.30  3.000
 3VY  C1   C6   C9   133.65  3.000
 3VY  C1   C6   C5   119.04  3.000
 3VY  C9   C6   C5   107.31  3.000
 3VY  H11  C1   C6   120.54  3.000
 3VY  H11  C1   C2   120.38  3.000
 3VY  C6   C1   C2   119.07  3.000
 3VY  C10  N7   C5   125.54  3.000
 3VY  C5   N7   C8   108.29  3.000
 3VY  C10  N7   C8   126.16  3.000
 3VY  H6   C10  H5   108.36  3.000
 3VY  H6   C10  H4   108.21  3.000
 3VY  H5   C10  H4   108.49  3.000
 3VY  H6   C10  N7   109.18  3.000
 3VY  H5   C10  N7   111.44  3.000
 3VY  H4   C10  N7   111.08  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
 3VY  CONST_01  C4   C5   N7   C8    180.00   0.0  0
 3VY  CONST_02  C6   C5   N7   C8      0.00   0.0  0
 3VY  CONST_03  C5   C6   C9   C8      0.00   0.0  0
 3VY  CONST_04  C1   C6   C9   C8    180.00   0.0  0
 3VY  CONST_05  C9   C6   C5   C4    180.00   0.0  0
 3VY  CONST_06  C1   C6   C5   C4      0.00   0.0  0
 3VY  CONST_07  C1   C2   C3   C4      0.00   0.0  0
 3VY  CONST_08  C9   C8   N7   C5      0.00   0.0  0
 3VY  CONST_09  C2   C3   C4   C5      0.00   0.0  0
 3VY  CONST_10  C2   C1   C6   C5      0.00   0.0  0
 3VY  CONST_11  C9   C6   C1   C2    180.00   0.0  0
 3VY  CONST_12  N7   C5   C6   C9      0.00   0.0  0
 3VY  CONST_13  N7   C5   C4   C3    180.00   0.0  0
 3VY  CONST_14  C6   C5   C4   C3      0.00   0.0  0
 3VY  CONST_15  C6   C1   C2   C3      0.00   0.0  0
 3VY  CONST_16  N7   C8   C9   C6      0.00   0.0  0
 3VY  CONST_17  N7   C5   C6   C1    180.00   0.0  0
 3VY  CONST_18  C10  N7   C5   C4      0.00   0.0  0
 3VY  CONST_19  C11  C9   C6   C5    180.00   0.0  0
 3VY  CONST_20  C10  N7   C8   C9    180.00   0.0  0
 3VY  CONST_21  C6   C5   N7   C10   180.00   0.0  0
 3VY  CONST_22  N7   C8   C9   C11   180.00   0.0  0
 3VY  CONST_23  C1   C6   C9   C11     0.00   0.0  0
 3VY  CONST_24  H3   C2   C3   C4    180.00   0.0  0
 3VY  CONST_25  H1   C8   N7   C5    180.00   0.0  0
 3VY  CONST_26  H9   C3   C4   C5    180.00   0.0  0
 3VY  CONST_27  H11  C1   C6   C5    180.00   0.0  0
 3VY  CONST_28  H2   C4   C3   C2    180.00   0.0  0
 3VY  Var_01    C12  C11  C9   C8   -112.96  30.0  2
 3VY  Var_02    H4   C10  N7   C8    123.81  30.0  2
 3VY  Var_03    O13  C12  C11  C9      6.51  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
 3VY  plan-1  C8   0.020
 3VY  plan-1  C4   0.020
 3VY  plan-1  C5   0.020
 3VY  plan-1  C2   0.020
 3VY  plan-1  C9   0.020
 3VY  plan-1  C11  0.020
 3VY  plan-1  C3   0.020
 3VY  plan-1  C6   0.020
 3VY  plan-1  C1   0.020
 3VY  plan-1  N7   0.020
 3VY  plan-1  H1   0.020
 3VY  plan-1  H2   0.020
 3VY  plan-1  H3   0.020
 3VY  plan-1  H9   0.020
 3VY  plan-1  H11  0.020
 3VY  plan-1  C10  0.020
 3VY  plan-2  C11  0.020
 3VY  plan-2  C12  0.020
 3VY  plan-2  O14  0.020
 3VY  plan-2  O13  0.020

