# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Apr  2 22:31:40 2020
#   Inital geometry file: a 61 line input string
#   Ligand name: 5-methyl-1H-indole-2-carboxylic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cc1ccc2[nH]c(cc2c1)C(O)=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
 4BY  4BY  '5-methyl-1H-indole-2-carboxylic acid'  ligand  21  13  .  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_4BY
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
 4BY  C1    C  CR5    0   0.167  -1.5732  -0.1137  -0.0063
 4BY  N2    N  NR15   0  -0.710  -0.8603   1.0535  -0.0384
 4BY  C3    C  CR15   0  -0.441  -0.6980  -1.1688   0.0270
 4BY  C4    C  CR56   0   0.083   0.6193  -0.6227   0.0150
 4BY  C5    C  CR56   0   0.324   0.4734   0.7825  -0.0262
 4BY  C6    C  C      0   0.360  -3.0764  -0.0953  -0.0089
 4BY  C7    C  CR16   0  -0.408   1.9098  -1.1735   0.0352
 4BY  O8    O  O      0  -0.587  -3.6404  -1.2032   0.0244
 4BY  C9    C  CR16   0  -0.298   1.5795   1.6328  -0.0464
 4BY  O10   O  OC    -1  -0.604  -3.6053   1.0337  -0.0434
 4BY  C11   C  CR6    0   0.085   3.0157  -0.3449   0.0159
 4BY  C12   C  CR16   0  -0.319   2.8315   1.0549  -0.0250
 4BY  C13   C  CH3    0  -0.723   4.4100  -0.9062   0.0396
 4BY  H3    H  HCR5   0   0.238  -0.9670  -2.2128   0.0570
 4BY  H7    H  HCR6   0   0.235   2.0399  -2.2497   0.0656
 4BY  H9    H  HCR6   0   0.253   1.4632   2.7090  -0.0769
 4BY  H12   H  HCR6   0   0.239   3.7042   1.6976  -0.0403
 4BY  H13   H  HCH3   0   0.237   4.9850  -0.5858  -0.8312
 4BY  H13A  H  HCH3   0   0.238   4.9599  -0.5727   0.9219
 4BY  H13B  H  HCH3   0   0.239   4.4027  -1.9959   0.0481
 4BY  HN2   H  HNR5   0   0.393  -1.2885   1.9644  -0.0660

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
 4BY  N2   C1    aromatic  1.368  0.020  1.368
 4BY  C6   C1    single    1.503  0.020  1.503
 4BY  C1   C3    aromatic  1.371  0.020  1.371
 4BY  N2   C5    aromatic  1.361  0.020  1.361
 4BY  C4   C3    aromatic  1.426  0.020  1.426
 4BY  C3   H3    single    0.930  0.020  1.080
 4BY  C5   C4    aromatic  1.413  0.020  1.413
 4BY  C4   C7    aromatic  1.403  0.020  1.403
 4BY  C9   C5    aromatic  1.395  0.020  1.395
 4BY  O8   C6    deloc     1.244  0.020  1.244
 4BY  C6   O10   deloc     1.247  0.020  1.247
 4BY  C11  C7    aromatic  1.382  0.020  1.382
 4BY  C7   H7    single    0.930  0.020  1.080
 4BY  C9   C12   aromatic  1.379  0.020  1.379
 4BY  C9   H9    single    0.930  0.020  1.080
 4BY  C12  C11   aromatic  1.412  0.020  1.412
 4BY  C11  C13   single    1.503  0.020  1.503
 4BY  C12  H12   single    0.930  0.020  1.080
 4BY  C13  H13   single    0.970  0.020  1.090
 4BY  C13  H13A  single    0.970  0.020  1.090
 4BY  C13  H13B  single    0.970  0.020  1.090
 4BY  N2   HN2   single    0.860  0.020  1.020

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
 4BY  C6    C1   C3    130.36  3.000
 4BY  C3    C1   N2    108.93  3.000
 4BY  C6    C1   N2    120.71  3.000
 4BY  HN2   N2   C5    126.67  3.000
 4BY  HN2   N2   C1    123.42  3.000
 4BY  C5    N2   C1    109.91  3.000
 4BY  H3    C3   C4    126.96  3.000
 4BY  H3    C3   C1    125.89  3.000
 4BY  C4    C3   C1    107.14  3.000
 4BY  C7    C4   C5    119.05  3.000
 4BY  C7    C4   C3    134.35  3.000
 4BY  C5    C4   C3    106.59  3.000
 4BY  C9    C5   C4    121.63  3.000
 4BY  C9    C5   N2    130.94  3.000
 4BY  C4    C5   N2    107.42  3.000
 4BY  O10   C6   O8    127.94  3.000
 4BY  O10   C6   C1    115.79  3.000
 4BY  O8    C6   C1    116.27  3.000
 4BY  H7    C7   C11   119.95  3.000
 4BY  H7    C7   C4    120.02  3.000
 4BY  C11   C7   C4    120.03  3.000
 4BY  H9    C9   C12   120.95  3.000
 4BY  H9    C9   C5    121.40  3.000
 4BY  C12   C9   C5    117.65  3.000
 4BY  C13   C11  C12   119.43  3.000
 4BY  C13   C11  C7    121.21  3.000
 4BY  C12   C11  C7    119.35  3.000
 4BY  H12   C12  C11   118.88  3.000
 4BY  H12   C12  C9    118.83  3.000
 4BY  C11   C12  C9    122.28  3.000
 4BY  H13B  C13  H13A  107.61  3.000
 4BY  H13B  C13  H13   107.65  3.000
 4BY  H13A  C13  H13   106.85  3.000
 4BY  H13B  C13  C11   111.54  3.000
 4BY  H13A  C13  C11   111.46  3.000
 4BY  H13   C13  C11   111.49  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
 4BY  CONST_01  C4   C5   N2   C1     0.00   0.0  0
 4BY  CONST_02  C9   C5   N2   C1   180.00   0.0  0
 4BY  CONST_03  C5   C4   C3   C1     0.00   0.0  0
 4BY  CONST_04  C7   C4   C3   C1   180.00   0.0  0
 4BY  CONST_05  C4   C3   C1   N2     0.00   0.0  0
 4BY  CONST_06  C3   C4   C5   N2     0.00   0.0  0
 4BY  CONST_07  C7   C4   C5   N2   180.00   0.0  0
 4BY  CONST_08  C12  C9   C5   N2   180.00   0.0  0
 4BY  CONST_09  C5   N2   C1   C3     0.00   0.0  0
 4BY  CONST_10  C9   C5   C4   C3   180.00   0.0  0
 4BY  CONST_11  C11  C7   C4   C3   180.00   0.0  0
 4BY  CONST_12  C12  C9   C5   C4     0.00   0.0  0
 4BY  CONST_13  C12  C11  C7   C4     0.00   0.0  0
 4BY  CONST_14  C11  C7   C4   C5     0.00   0.0  0
 4BY  CONST_15  C11  C12  C9   C5     0.00   0.0  0
 4BY  CONST_16  C9   C5   C4   C7     0.00   0.0  0
 4BY  CONST_17  C9   C12  C11  C7     0.00   0.0  0
 4BY  CONST_18  C6   C1   C3   C4   180.00   0.0  0
 4BY  CONST_19  C13  C11  C7   C4   180.00   0.0  0
 4BY  CONST_20  C6   C1   N2   C5   180.00   0.0  0
 4BY  CONST_21  C13  C11  C12  C9   180.00   0.0  0
 4BY  CONST_22  H3   C3   C1   N2   180.00   0.0  0
 4BY  CONST_23  H9   C9   C5   N2     0.00   0.0  0
 4BY  CONST_24  HN2  N2   C1   C3   180.00   0.0  0
 4BY  CONST_25  H7   C7   C4   C3     0.00   0.0  0
 4BY  CONST_26  H12  C12  C9   C5   180.00   0.0  0
 4BY  Var_01    O8   C6   C1   N2  -179.87  30.0  2
 4BY  Var_02    H13  C13  C11  C7   121.75  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
 4BY  plan-1  C1   0.020
 4BY  plan-1  N2   0.020
 4BY  plan-1  C3   0.020
 4BY  plan-1  C4   0.020
 4BY  plan-1  C5   0.020
 4BY  plan-1  C6   0.020
 4BY  plan-1  C7   0.020
 4BY  plan-1  C9   0.020
 4BY  plan-1  C11  0.020
 4BY  plan-1  C12  0.020
 4BY  plan-1  C13  0.020
 4BY  plan-1  H3   0.020
 4BY  plan-1  H7   0.020
 4BY  plan-1  H9   0.020
 4BY  plan-1  H12  0.020
 4BY  plan-1  HN2  0.020
 4BY  plan-2  C1   0.020
 4BY  plan-2  C6   0.020
 4BY  plan-2  O8   0.020
 4BY  plan-2  O10  0.020

