# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Apr 25 17:31:04 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  25  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 GRAND
;

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  -0.079   0.0273   1.7654   0.3729
 3VY  C4   C  CR16  0  -0.315  -2.7982  -0.3264  -0.3368
 3VY  C5   C  CR56  0   0.369  -1.5928   0.3049  -0.0320
 3VY  C2   C  CR16  0  -0.271  -1.6614  -2.4489  -0.0118
 3VY  C9   C  CR5   0   0.029   0.6064   0.5396   0.5343
 3VY  C11  C  CH2   0  -0.722   2.0156   0.2657   0.9212
 3VY  C12  C  C     0   0.553   2.8478  -0.3121  -0.1986
 3VY  C3   C  CR16  0  -0.282  -2.8142  -1.7086  -0.3218
 3VY  O14  O  OH1   0  -0.596   4.1036  -0.5184   0.1879
 3VY  O13  O  O     0  -0.435   2.4491  -0.5641  -1.3061
 3VY  C6   C  CR56  0   0.048  -0.4221  -0.4210   0.2805
 3VY  C1   C  CR16  0  -0.373  -0.4681  -1.8189   0.2852
 3VY  N7   N  NR5   0  -0.522  -1.2904   1.6354   0.0295
 3VY  H1   H  HCR5  0   0.286   0.4663   2.7457   0.4839
 3VY  H2   H  HCR6  0   0.263  -3.6915   0.2363  -0.5777
 3VY  H3   H  HCR6  0   0.246  -1.7124  -3.5301  -0.0106
 3VY  H4   H  HCH3  0   0.252  -2.6563   2.6372  -1.2039
 3VY  H5   H  HCH3  0   0.251  -3.0190   2.7168   0.5278
 3VY  H6   H  HCH3  0   0.263  -1.6855   3.6601  -0.1442
 3VY  H7   H  HCH2  0   0.302   2.5042   1.1796   1.2709
 3VY  H8   H  HCH2  0   0.293   2.0648  -0.4307   1.7660
 3VY  H9   H  HCR6  0   0.249  -3.7330  -2.2308  -0.5555
 3VY  H10  H  HOH1  0   0.479   4.6185  -0.8846  -0.5466
 3VY  H11  H  HCR6  0   0.240   0.4143  -2.4020   0.5207
 3VY  C10  C  CH3   0  -0.528  -2.2160   2.7140  -0.2097

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    1.441  0.020  1.441
 3VY  N7   C8   aromatic  1.368  0.020  1.368
 3VY  N7   C5   aromatic  1.366  0.020  1.366
 3VY  C8   C9   aromatic  1.365  0.020  1.365
 3VY  C5   C4   aromatic  1.394  0.020  1.394
 3VY  C5   C6   aromatic  1.413  0.020  1.413
 3VY  C4   C3   aromatic  1.382  0.020  1.382
 3VY  C9   C6   aromatic  1.430  0.020  1.430
 3VY  C9   C11  single    1.487  0.020  1.487
 3VY  C6   C1   aromatic  1.399  0.020  1.399
 3VY  C11  C12  single    1.510  0.020  1.510
 3VY  C3   C2   aromatic  1.405  0.020  1.405
 3VY  O13  C12  double    1.204  0.020  1.204
 3VY  C1   C2   aromatic  1.382  0.020  1.382
 3VY  C12  O14  single    1.330  0.020  1.330
 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  O14  H10  single    0.850  0.020  0.980
 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   120.24  3.000
 3VY  H1   C8   C9   129.08  3.000
 3VY  N7   C8   C9   110.67  3.000
 3VY  H2   C4   C3   120.83  3.000
 3VY  H2   C4   C5   121.77  3.000
 3VY  C3   C4   C5   117.41  3.000
 3VY  N7   C5   C6   107.89  3.000
 3VY  C6   C5   C4   122.15  3.000
 3VY  N7   C5   C4   129.96  3.000
 3VY  H3   C2   C1   119.73  3.000
 3VY  H3   C2   C3   119.21  3.000
 3VY  C1   C2   C3   121.06  3.000
 3VY  C6   C9   C11  127.16  3.000
 3VY  C11  C9   C8   126.75  3.000
 3VY  C6   C9   C8   106.09  3.000
 3VY  H8   C11  H7   105.33  3.000
 3VY  H8   C11  C12  107.68  3.000
 3VY  H7   C11  C12  108.09  3.000
 3VY  H8   C11  C9   111.12  3.000
 3VY  H7   C11  C9   110.65  3.000
 3VY  C12  C11  C9   113.57  3.000
 3VY  O13  C12  O14  123.21  3.000
 3VY  O14  C12  C11  111.36  3.000
 3VY  O13  C12  C11  125.43  3.000
 3VY  H9   C3   C2   119.35  3.000
 3VY  H9   C3   C4   119.33  3.000
 3VY  C2   C3   C4   121.32  3.000
 3VY  H10  O14  C12  109.88  3.000
 3VY  C1   C6   C9   133.99  3.000
 3VY  C1   C6   C5   119.15  3.000
 3VY  C9   C6   C5   106.86  3.000
 3VY  H11  C1   C6   120.78  3.000
 3VY  H11  C1   C2   120.31  3.000
 3VY  C6   C1   C2   118.91  3.000
 3VY  C10  N7   C5   125.40  3.000
 3VY  C5   N7   C8   108.49  3.000
 3VY  C10  N7   C8   126.10  3.000
 3VY  H6   C10  H5   108.45  3.000
 3VY  H6   C10  H4   108.27  3.000
 3VY  H5   C10  H4   108.64  3.000
 3VY  H6   C10  N7   109.15  3.000
 3VY  H5   C10  N7   111.26  3.000
 3VY  H4   C10  N7   110.99  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  CONST_29  H10  O14  C12  C11   180.00   0.0  0
 3VY  Var_01    C12  C11  C9   C8   -109.93  30.0  2
 3VY  Var_02    H4   C10  N7   C8    123.26  30.0  2
 3VY  Var_03    O13  C12  C11  C9     -1.17  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
 3VY  plan-2  H10  0.020

