# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Apr 25 12:17:49 2020
#   Inital geometry file: a 73 line input string
#   Ligand name: 4-(1H-indol-3-yl)butanoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC(=O)CCCc1c[nH]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
 3IB  3IB  '4-(1H-indol-3-yl)butanoic acid'  ligand  28  15  .  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_3IB
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
 3IB  N1    N  NR15  0  -0.688   1.9522   0.2714  -2.5729
 3IB  C2    C  CR15  0  -0.094   2.1997  -0.1961  -1.3108
 3IB  C3    C  CR5   0   0.027   1.0313  -0.5542  -0.7003
 3IB  C4    C  CR16  0  -0.376  -1.3979  -0.4511  -1.6381
 3IB  C5    C  CR16  0  -0.269  -2.1258  -0.0971  -2.7573
 3IB  C6    C  CR16  0  -0.285  -1.4904   0.4177  -3.9002
 3IB  C7    C  CR16  0  -0.307  -0.1194   0.5842  -3.9466
 3IB  C8    C  CR56  0   0.354   0.6116   0.2250  -2.8147
 3IB  C9    C  CR56  0   0.025  -0.0071  -0.2904  -1.6533
 3IB  C10   C  CH2   0  -0.533   0.8577  -1.0826   0.6847
 3IB  C11   C  CH2   0  -0.417   0.2482  -0.0579   1.6442
 3IB  C12   C  CH2   0  -0.584   0.0567  -0.6487   3.0308
 3IB  C13   C  C     0   0.548  -0.5303   0.3113   4.0272
 3IB  O1    O  OH1   0  -0.598  -0.6755  -0.2481   5.2258
 3IB  O2    O  O     0  -0.445  -0.8410   1.4535   3.7963
 3IB  HN1   H  HNR5  0   0.407   2.6567   0.5785  -3.2221
 3IB  H2    H  HCR5  0   0.278   3.2096  -0.2425  -0.9331
 3IB  H4    H  HCR6  0   0.239  -1.8969  -0.8503  -0.7628
 3IB  H5    H  HCR6  0   0.244  -3.2017  -0.2159  -2.7587
 3IB  H6    H  HCR6  0   0.248  -2.0868   0.6899  -4.7616
 3IB  H7    H  HCR6  0   0.257   0.3666   0.9790  -4.8298
 3IB  H101  H  HCH2  0   0.240   1.8254  -1.4098   1.0750
 3IB  H102  H  HCH2  0   0.230   0.2206  -1.9736   0.6620
 3IB  H111  H  HCH2  0   0.234  -0.7107   0.2889   1.2515
 3IB  H112  H  HCH2  0   0.233   0.9005   0.8168   1.6923
 3IB  H121  H  HCH2  0   0.277   1.0098  -1.0110   3.4295
 3IB  H122  H  HCH2  0   0.277  -0.5927  -1.5293   2.9864
 3IB  HO1   H  HOH1  0   0.478  -1.0545   0.3936   5.8445

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
 3IB  N1   C2    aromatic  1.368  0.020  1.368
 3IB  N1   C8    aromatic  1.363  0.020  1.363
 3IB  N1   HN1   single    0.860  0.020  1.020
 3IB  C2   C3    aromatic  1.366  0.020  1.366
 3IB  C2   H2    single    0.930  0.020  1.080
 3IB  C3   C9    aromatic  1.434  0.020  1.434
 3IB  C3   C10   single    1.492  0.020  1.492
 3IB  C4   C5    aromatic  1.381  0.020  1.381
 3IB  C4   C9    aromatic  1.400  0.020  1.400
 3IB  C4   H4    single    0.930  0.020  1.080
 3IB  C5   C6    aromatic  1.405  0.020  1.405
 3IB  C5   H5    single    0.930  0.020  1.080
 3IB  C6   C7    aromatic  1.382  0.020  1.382
 3IB  C6   H6    single    0.930  0.020  1.080
 3IB  C7   C8    aromatic  1.394  0.020  1.394
 3IB  C7   H7    single    0.930  0.020  1.080
 3IB  C8   C9    aromatic  1.413  0.020  1.413
 3IB  C10  C11   single    1.530  0.020  1.530
 3IB  C10  H101  single    0.970  0.020  1.090
 3IB  C10  H102  single    0.970  0.020  1.090
 3IB  C11  C12   single    1.519  0.020  1.519
 3IB  C11  H111  single    0.970  0.020  1.090
 3IB  C11  H112  single    0.970  0.020  1.090
 3IB  C12  C13   single    1.503  0.020  1.503
 3IB  C12  H121  single    0.970  0.020  1.090
 3IB  C12  H122  single    0.970  0.020  1.090
 3IB  C13  O1    single    1.331  0.020  1.331
 3IB  C13  O2    double    1.206  0.020  1.206
 3IB  O1   HO1   single    0.850  0.020  0.980

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
 3IB  HN1   N1   C8    125.78  3.000
 3IB  HN1   N1   C2    124.95  3.000
 3IB  C8    N1   C2    109.26  3.000
 3IB  H2    C2   C3    129.25  3.000
 3IB  H2    C2   N1    120.44  3.000
 3IB  C3    C2   N1    110.30  3.000
 3IB  C10   C3   C9    126.70  3.000
 3IB  C10   C3   C2    127.37  3.000
 3IB  C9    C3   C2    105.92  3.000
 3IB  H4    C4   C9    120.56  3.000
 3IB  H4    C4   C5    120.41  3.000
 3IB  C9    C4   C5    119.03  3.000
 3IB  H5    C5   C6    119.25  3.000
 3IB  H5    C5   C4    119.78  3.000
 3IB  C6    C5   C4    120.97  3.000
 3IB  H6    C6   C7    119.32  3.000
 3IB  H6    C6   C5    119.35  3.000
 3IB  C7    C6   C5    121.34  3.000
 3IB  H7    C7   C8    121.38  3.000
 3IB  H7    C7   C6    121.11  3.000
 3IB  C8    C7   C6    117.50  3.000
 3IB  C9    C8   C7    122.11  3.000
 3IB  C9    C8   N1    107.29  3.000
 3IB  C7    C8   N1    130.60  3.000
 3IB  C8    C9   C4    119.05  3.000
 3IB  C8    C9   C3    107.23  3.000
 3IB  C4    C9   C3    133.71  3.000
 3IB  H102  C10  H101  106.17  3.000
 3IB  H102  C10  C11   109.02  3.000
 3IB  H101  C10  C11   109.21  3.000
 3IB  H102  C10  C3    109.66  3.000
 3IB  H101  C10  C3    109.53  3.000
 3IB  C11   C10  C3    113.02  3.000
 3IB  H112  C11  H111  106.61  3.000
 3IB  H112  C11  C12   110.27  3.000
 3IB  H111  C11  C12   109.92  3.000
 3IB  H112  C11  C10   109.02  3.000
 3IB  H111  C11  C10   109.68  3.000
 3IB  C12   C11  C10   111.23  3.000
 3IB  H122  C12  H121  105.37  3.000
 3IB  H122  C12  C13   108.00  3.000
 3IB  H121  C12  C13   108.06  3.000
 3IB  H122  C12  C11   110.51  3.000
 3IB  H121  C12  C11   110.56  3.000
 3IB  C13   C12  C11   113.94  3.000
 3IB  O2    C13  O1    122.86  3.000
 3IB  O2    C13  C12   125.36  3.000
 3IB  O1    C13  C12   111.79  3.000
 3IB  HO1   O1   C13   109.84  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
 3IB  CONST_01  C9   C3   C2   N1      0.00   0.0  0
 3IB  CONST_02  C6   C7   C8   N1    180.00   0.0  0
 3IB  CONST_03  C3   C9   C8   N1      0.00   0.0  0
 3IB  CONST_04  C4   C9   C8   N1    180.00   0.0  0
 3IB  CONST_05  C7   C8   N1   C2    180.00   0.0  0
 3IB  CONST_06  C9   C8   N1   C2      0.00   0.0  0
 3IB  CONST_07  C4   C9   C3   C2    180.00   0.0  0
 3IB  CONST_08  C8   C9   C3   C2      0.00   0.0  0
 3IB  CONST_09  C8   N1   C2   C3      0.00   0.0  0
 3IB  CONST_10  C5   C4   C9   C3    180.00   0.0  0
 3IB  CONST_11  C7   C8   C9   C3    180.00   0.0  0
 3IB  CONST_12  C7   C6   C5   C4      0.00   0.0  0
 3IB  CONST_13  C7   C8   C9   C4      0.00   0.0  0
 3IB  CONST_14  C8   C9   C4   C5      0.00   0.0  0
 3IB  CONST_15  C8   C7   C6   C5      0.00   0.0  0
 3IB  CONST_16  C9   C4   C5   C6      0.00   0.0  0
 3IB  CONST_17  C9   C8   C7   C6      0.00   0.0  0
 3IB  CONST_18  C10  C3   C2   N1    180.00   0.0  0
 3IB  CONST_19  C10  C3   C9   C4      0.00   0.0  0
 3IB  CONST_20  C10  C3   C9   C8    180.00   0.0  0
 3IB  CONST_21  H7   C7   C8   N1      0.00   0.0  0
 3IB  CONST_22  HN1  N1   C2   C3    180.00   0.0  0
 3IB  CONST_23  H4   C4   C9   C3      0.00   0.0  0
 3IB  CONST_24  H6   C6   C5   C4    180.00   0.0  0
 3IB  CONST_25  H5   C5   C6   C7    180.00   0.0  0
 3IB  CONST_26  H2   C2   N1   C8    180.00   0.0  0
 3IB  CONST_27  HO1  O1   C13  C12   180.00   0.0  0
 3IB  Var_01    C11  C10  C3   C2    106.52  30.0  2
 3IB  Var_02    C12  C11  C10  C3    178.54  30.0  3
 3IB  Var_03    C13  C12  C11  C10   179.56  30.0  3
 3IB  Var_04    O1   C13  C12  C11  -179.81  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
 3IB  plan-1  N1   0.020
 3IB  plan-1  C2   0.020
 3IB  plan-1  C3   0.020
 3IB  plan-1  C4   0.020
 3IB  plan-1  C5   0.020
 3IB  plan-1  C6   0.020
 3IB  plan-1  C7   0.020
 3IB  plan-1  C8   0.020
 3IB  plan-1  C9   0.020
 3IB  plan-1  C10  0.020
 3IB  plan-1  HN1  0.020
 3IB  plan-1  H2   0.020
 3IB  plan-1  H4   0.020
 3IB  plan-1  H5   0.020
 3IB  plan-1  H6   0.020
 3IB  plan-1  H7   0.020
 3IB  plan-2  C12  0.020
 3IB  plan-2  C13  0.020
 3IB  plan-2  O1   0.020
 3IB  plan-2  O2   0.020
 3IB  plan-2  HO1  0.020

