# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Apr 28 20:37:11 2020
#   Inital geometry file: a 73 line input string
#   Ligand name: 3-(3-methylindol-1-yl)propanoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cc1cn(CCC(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
 9F8  9F8  '3-(3-methylindol-1-yl)propanoic acid'  ligand  28  15  .  2021-08-06  2021-08-06  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_9F8
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
 9F8  C10  C  CH2   0  -0.311   1.3693  -0.3618  -0.8488
 9F8  C15  C  CH3   0  -0.749  -2.8953  -2.7375   0.3464
 9F8  C01  C  CR15  0  -0.080  -0.6113  -1.8032  -0.3384
 9F8  C02  C  CR5   0  -0.031  -1.9141  -1.6580   0.0398
 9F8  C03  C  CR56  0   0.037  -2.1559  -0.2463   0.0725
 9F8  C04  C  CR56  0   0.371  -0.9519   0.3927  -0.2986
 9F8  C05  C  CR16  0  -0.311  -0.8416   1.7816  -0.3604
 9F8  C06  C  CR16  0  -0.282  -1.9639   2.5260  -0.0474
 9F8  C07  C  CR16  0  -0.270  -3.1710   1.9094   0.3201
 9F8  C08  C  CR16  0  -0.368  -3.2757   0.5329   0.3811
 9F8  N09  N  NR5   0  -0.531  -0.0269  -0.5796  -0.5572
 9F8  C11  C  CH2   0  -0.593   2.1722  -0.0994   0.4200
 9F8  C12  C  C     0   0.557   3.6322   0.1206   0.1424
 9F8  O13  O  OH1   0  -0.593   4.3197   0.3383   1.2568
 9F8  O14  O  O     0  -0.444   4.1345   0.1035  -0.9539
 9F8  H1   H  HCH2  0   0.276   1.7467  -1.2439  -1.3645
 9F8  H2   H  HCH2  0   0.269   1.4601   0.4725  -1.5450
 9F8  H3   H  HCH3  0   0.235  -3.3089  -2.6328   1.3517
 9F8  H4   H  HCH3  0   0.235  -3.7396  -2.7264  -0.3464
 9F8  H5   H  HCH3  0   0.242  -2.4322  -3.7218   0.2824
 9F8  H6   H  HCR5  0   0.281  -0.0404  -2.7089  -0.4827
 9F8  H7   H  HCR6  0   0.259   0.0831   2.2694  -0.6432
 9F8  H8   H  HCR6  0   0.249  -1.9098   3.6063  -0.0848
 9F8  H9   H  HCR6  0   0.245  -4.0280   2.5252   0.5611
 9F8  H10  H  HCR6  0   0.242  -4.2100   0.0659   0.6689
 9F8  H11  H  HCH2  0   0.291   1.7837   0.7757   0.9491
 9F8  H12  H  HCH2  0   0.295   2.0697  -0.9395   1.1127
 9F8  H13  H  HOH1  0   0.481   5.2561   0.4745   1.0484

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
 9F8  C15  C02  single    1.491  0.020  1.491
 9F8  C01  C02  aromatic  1.364  0.020  1.364
 9F8  C01  N09  aromatic  1.374  0.020  1.374
 9F8  C02  C03  aromatic  1.433  0.020  1.433
 9F8  N09  C10  single    1.443  0.020  1.443
 9F8  N09  C04  aromatic  1.367  0.020  1.367
 9F8  C03  C04  aromatic  1.413  0.020  1.413
 9F8  C03  C08  aromatic  1.399  0.020  1.399
 9F8  C10  C11  single    1.524  0.020  1.524
 9F8  C04  C05  aromatic  1.395  0.020  1.395
 9F8  O14  C12  double    1.206  0.020  1.206
 9F8  O13  C12  single    1.327  0.020  1.327
 9F8  C12  C11  single    1.502  0.020  1.502
 9F8  C08  C07  aromatic  1.382  0.020  1.382
 9F8  C05  C06  aromatic  1.383  0.020  1.383
 9F8  C07  C06  aromatic  1.404  0.020  1.404
 9F8  C10  H1   single    0.970  0.020  1.090
 9F8  C10  H2   single    0.970  0.020  1.090
 9F8  C15  H3   single    0.970  0.020  1.090
 9F8  C15  H4   single    0.970  0.020  1.090
 9F8  C15  H5   single    0.970  0.020  1.090
 9F8  C01  H6   single    0.930  0.020  1.080
 9F8  C05  H7   single    0.930  0.020  1.080
 9F8  C06  H8   single    0.930  0.020  1.080
 9F8  C07  H9   single    0.930  0.020  1.080
 9F8  C08  H10  single    0.930  0.020  1.080
 9F8  C11  H11  single    0.970  0.020  1.090
 9F8  C11  H12  single    0.970  0.020  1.090
 9F8  O13  H13  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
 9F8  H2   C10  H1   106.76  3.000
 9F8  H2   C10  C11  110.85  3.000
 9F8  H1   C10  C11  110.55  3.000
 9F8  H2   C10  N09  108.97  3.000
 9F8  H1   C10  N09  107.98  3.000
 9F8  C11  C10  N09  111.56  3.000
 9F8  H5   C15  H4   107.49  3.000
 9F8  H5   C15  H3   107.55  3.000
 9F8  H4   C15  H3   106.87  3.000
 9F8  H5   C15  C02  111.24  3.000
 9F8  H4   C15  C02  111.78  3.000
 9F8  H3   C15  C02  111.66  3.000
 9F8  H6   C01  N09  120.05  3.000
 9F8  H6   C01  C02  129.11  3.000
 9F8  N09  C01  C02  110.83  3.000
 9F8  C03  C02  C01  105.80  3.000
 9F8  C03  C02  C15  126.71  3.000
 9F8  C01  C02  C15  127.48  3.000
 9F8  C08  C03  C04  119.23  3.000
 9F8  C08  C03  C02  133.56  3.000
 9F8  C04  C03  C02  107.21  3.000
 9F8  N09  C04  C05  130.28  3.000
 9F8  C05  C04  C03  121.97  3.000
 9F8  N09  C04  C03  107.74  3.000
 9F8  H7   C05  C06  120.65  3.000
 9F8  H7   C05  C04  121.84  3.000
 9F8  C06  C05  C04  117.51  3.000
 9F8  H8   C06  C07  119.36  3.000
 9F8  H8   C06  C05  119.27  3.000
 9F8  C07  C06  C05  121.37  3.000
 9F8  H9   C07  C08  119.79  3.000
 9F8  H9   C07  C06  119.27  3.000
 9F8  C08  C07  C06  120.93  3.000
 9F8  H10  C08  C07  120.43  3.000
 9F8  H10  C08  C03  120.59  3.000
 9F8  C07  C08  C03  118.98  3.000
 9F8  C04  N09  C01  108.40  3.000
 9F8  C04  N09  C10  125.86  3.000
 9F8  C01  N09  C10  125.33  3.000
 9F8  H12  C11  H11  105.95  3.000
 9F8  H12  C11  C12  108.70  3.000
 9F8  H11  C11  C12  108.50  3.000
 9F8  H12  C11  C10  110.22  3.000
 9F8  H11  C11  C10  110.69  3.000
 9F8  C12  C11  C10  112.54  3.000
 9F8  O14  C12  O13  123.36  3.000
 9F8  O13  C12  C11  111.85  3.000
 9F8  O14  C12  C11  124.79  3.000
 9F8  H13  O13  C12  110.06  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
 9F8  CONST_01  C04  C03  C02  C01    0.00   0.0  0
 9F8  CONST_02  C08  C03  C02  C01  180.00   0.0  0
 9F8  CONST_03  C03  C04  N09  C01    0.00   0.0  0
 9F8  CONST_04  C05  C04  N09  C01  180.00   0.0  0
 9F8  CONST_05  C04  N09  C01  C02    0.00   0.0  0
 9F8  CONST_06  N09  C04  C03  C02    0.00   0.0  0
 9F8  CONST_07  C05  C04  C03  C02  180.00   0.0  0
 9F8  CONST_08  C07  C08  C03  C02  180.00   0.0  0
 9F8  CONST_09  N09  C01  C02  C03    0.00   0.0  0
 9F8  CONST_10  C06  C05  C04  C03    0.00   0.0  0
 9F8  CONST_11  C06  C07  C08  C03    0.00   0.0  0
 9F8  CONST_12  C07  C08  C03  C04    0.00   0.0  0
 9F8  CONST_13  C07  C06  C05  C04    0.00   0.0  0
 9F8  CONST_14  C08  C03  C04  C05    0.00   0.0  0
 9F8  CONST_15  C08  C07  C06  C05    0.00   0.0  0
 9F8  CONST_16  N09  C04  C05  C06  180.00   0.0  0
 9F8  CONST_17  N09  C04  C03  C08  180.00   0.0  0
 9F8  CONST_18  C02  C01  N09  C10  180.00   0.0  0
 9F8  CONST_19  C03  C04  N09  C10  180.00   0.0  0
 9F8  CONST_20  C05  C04  N09  C10    0.00   0.0  0
 9F8  CONST_21  N09  C01  C02  C15  180.00   0.0  0
 9F8  CONST_22  C04  C03  C02  C15  180.00   0.0  0
 9F8  CONST_23  C08  C03  C02  C15    0.00   0.0  0
 9F8  CONST_24  H10  C08  C03  C02    0.00   0.0  0
 9F8  CONST_25  H6   C01  C02  C03  180.00   0.0  0
 9F8  CONST_26  H7   C05  C04  C03  180.00   0.0  0
 9F8  CONST_27  H9   C07  C08  C03  180.00   0.0  0
 9F8  CONST_28  H8   C06  C05  C04  180.00   0.0  0
 9F8  CONST_29  H13  O13  C12  C11  180.00   0.0  0
 9F8  Var_01    C11  C10  N09  C01  -92.44  30.0  2
 9F8  Var_02    H3   C15  C02  C01  123.06  30.0  2
 9F8  Var_03    C12  C11  C10  N09  179.58  30.0  3
 9F8  Var_04    O14  C12  C11  C10    0.38  30.0  1

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
 9F8  plan-1  C10  0.020
 9F8  plan-1  C15  0.020
 9F8  plan-1  C01  0.020
 9F8  plan-1  C02  0.020
 9F8  plan-1  C03  0.020
 9F8  plan-1  C04  0.020
 9F8  plan-1  C05  0.020
 9F8  plan-1  C06  0.020
 9F8  plan-1  C07  0.020
 9F8  plan-1  C08  0.020
 9F8  plan-1  N09  0.020
 9F8  plan-1  H6   0.020
 9F8  plan-1  H7   0.020
 9F8  plan-1  H8   0.020
 9F8  plan-1  H9   0.020
 9F8  plan-1  H10  0.020
 9F8  plan-2  C11  0.020
 9F8  plan-2  C12  0.020
 9F8  plan-2  O13  0.020
 9F8  plan-2  O14  0.020
 9F8  plan-2  H13  0.020

