# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Aug  3 08:07:05 2022
#   Inital geometry file: a 58 line input string
#   Ligand name: 3-butylpyridine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCCCc1cccnc1
#
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
 Y8J  Y8J  "3-butylpyridine"
  ligand  23  10  .  2022-08-11  2022-08-11
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_Y8J
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
 Y8J  C10  C  CR16  0  -0.101  -33.9827   7.1562   4.9112
 Y8J  C01  C  CH3   0  -0.657  -33.3867   9.7913   0.3672
 Y8J  C02  C  CH2   0  -0.421  -32.8560   8.7586   1.3517
 Y8J  C03  C  CH2   0  -0.411  -32.7015   9.3211   2.7583
 Y8J  C04  C  CH2   0  -0.517  -32.0833   8.3396   3.7591
 Y8J  C05  C  CR6   0   0.035  -32.9314   7.1242   3.9974
 Y8J  C06  C  CR16  0  -0.193  -32.7341   5.9305   3.3126
 Y8J  C07  C  CR16  0  -0.318  -33.5723   4.8537   3.5586
 Y8J  C08  C  CR16  0  -0.078  -34.5888   5.0057   4.4888
 Y8J  N09  N  N     0  -0.399  -34.7928   6.1349   5.1582
 Y8J  H1   H  HCR6  0   0.252  -34.1691   8.0650   5.4773
 Y8J  H2   H  HCH3  0   0.226  -33.4999   9.3696  -0.6319
 Y8J  H3   H  HCH3  0   0.216  -34.3625  10.1690   0.6784
 Y8J  H4   H  HCH3  0   0.216  -32.7130  10.6466   0.2913
 Y8J  H5   H  HCH2  0   0.218  -33.5252   7.8940   1.3677
 Y8J  H6   H  HCH2  0   0.211  -31.8873   8.3839   1.0062
 Y8J  H7   H  HCH2  0   0.224  -32.0692  10.2133   2.7211
 Y8J  H8   H  HCH2  0   0.218  -33.6759   9.6542   3.1304
 Y8J  H9   H  HCH2  0   0.242  -31.0981   8.0312   3.3993
 Y8J  H10  H  HCH2  0   0.249  -31.9208   8.8577   4.7073
 Y8J  H11  H  HCR6  0   0.264  -31.9271   5.8421   2.5947
 Y8J  H12  H  HCR6  0   0.266  -33.4416   3.9125   3.0418
 Y8J  H13  H  HCR6  0   0.257  -35.2623   4.1836   4.7054

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
 Y8J  C01  C02  single    1.522  0.020  1.522
 Y8J  C02  C03  single    1.523  0.020  1.523
 Y8J  C03  C04  single    1.532  0.020  1.532
 Y8J  C06  C07  aromatic  1.387  0.020  1.387
 Y8J  C06  C05  aromatic  1.390  0.020  1.390
 Y8J  C07  C08  aromatic  1.386  0.020  1.386
 Y8J  C04  C05  single    1.501  0.020  1.501
 Y8J  C05  C10  aromatic  1.393  0.020  1.393
 Y8J  C08  N09  aromatic  1.328  0.020  1.328
 Y8J  C10  N09  aromatic  1.327  0.020  1.327
 Y8J  C10  H1   single    0.930  0.020  1.080
 Y8J  C01  H2   single    0.970  0.020  1.090
 Y8J  C01  H3   single    0.970  0.020  1.090
 Y8J  C01  H4   single    0.970  0.020  1.090
 Y8J  C02  H5   single    0.970  0.020  1.090
 Y8J  C02  H6   single    0.970  0.020  1.090
 Y8J  C03  H7   single    0.970  0.020  1.090
 Y8J  C03  H8   single    0.970  0.020  1.090
 Y8J  C04  H9   single    0.970  0.020  1.090
 Y8J  C04  H10  single    0.970  0.020  1.090
 Y8J  C06  H11  single    0.930  0.020  1.080
 Y8J  C07  H12  single    0.930  0.020  1.080
 Y8J  C08  H13  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
 Y8J  H1   C10  N09  116.24  3.000
 Y8J  H1   C10  C05  119.36  3.000
 Y8J  N09  C10  C05  124.41  3.000
 Y8J  H4   C01  H3   107.49  3.000
 Y8J  H4   C01  H2   107.66  3.000
 Y8J  H3   C01  H2   107.59  3.000
 Y8J  H4   C01  C02  111.19  3.000
 Y8J  H3   C01  C02  111.22  3.000
 Y8J  H2   C01  C02  111.49  3.000
 Y8J  H6   C02  H5   105.99  3.000
 Y8J  H6   C02  C03  109.16  3.000
 Y8J  H5   C02  C03  109.91  3.000
 Y8J  H6   C02  C01  109.68  3.000
 Y8J  H5   C02  C01  109.43  3.000
 Y8J  C03  C02  C01  112.47  3.000
 Y8J  H8   C03  H7   106.12  3.000
 Y8J  H8   C03  C04  109.39  3.000
 Y8J  H7   C03  C04  108.14  3.000
 Y8J  H8   C03  C02  109.64  3.000
 Y8J  H7   C03  C02  109.17  3.000
 Y8J  C04  C03  C02  114.07  3.000
 Y8J  H10  C04  H9   106.58  3.000
 Y8J  H10  C04  C05  109.28  3.000
 Y8J  H9   C04  C05  109.45  3.000
 Y8J  H10  C04  C03  108.85  3.000
 Y8J  H9   C04  C03  109.23  3.000
 Y8J  C05  C04  C03  113.23  3.000
 Y8J  C06  C05  C04  122.47  3.000
 Y8J  C04  C05  C10  120.78  3.000
 Y8J  C06  C05  C10  116.74  3.000
 Y8J  H11  C06  C07  120.28  3.000
 Y8J  H11  C06  C05  120.14  3.000
 Y8J  C07  C06  C05  119.58  3.000
 Y8J  H12  C07  C08  120.30  3.000
 Y8J  H12  C07  C06  121.19  3.000
 Y8J  C08  C07  C06  118.50  3.000
 Y8J  H13  C08  N09  116.63  3.000
 Y8J  H13  C08  C07  120.42  3.000
 Y8J  N09  C08  C07  122.95  3.000
 Y8J  C08  N09  C10  117.83  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
 Y8J  CONST_01  C07  C06  C05  C10     0.00   0.0  0
 Y8J  CONST_02  C07  C08  N09  C10     0.00   0.0  0
 Y8J  CONST_03  C08  C07  C06  C05     0.00   0.0  0
 Y8J  CONST_04  C08  N09  C10  C05     0.00   0.0  0
 Y8J  CONST_05  N09  C08  C07  C06     0.00   0.0  0
 Y8J  CONST_06  N09  C10  C05  C06     0.00   0.0  0
 Y8J  CONST_07  C07  C06  C05  C04   180.00   0.0  0
 Y8J  CONST_08  N09  C10  C05  C04   180.00   0.0  0
 Y8J  CONST_09  H11  C06  C05  C10   180.00   0.0  0
 Y8J  CONST_10  H13  C08  N09  C10   180.00   0.0  0
 Y8J  CONST_11  H12  C07  C06  C05   180.00   0.0  0
 Y8J  CONST_12  H13  C08  C07  C06   180.00   0.0  0
 Y8J  CONST_13  H1   C10  C05  C06   180.00   0.0  0
 Y8J  CONST_14  H11  C06  C07  C08   180.00   0.0  0
 Y8J  CONST_15  H1   C10  N09  C08   180.00   0.0  0
 Y8J  CONST_16  H12  C07  C08  N09   180.00   0.0  0
 Y8J  Var_01    C03  C04  C05  C10   -83.27  30.0  2
 Y8J  Var_02    C06  C05  C04  C03    95.46  30.0  2
 Y8J  Var_03    H9   C04  C05  C10   154.62  30.0  2
 Y8J  Var_04    H10  C04  C05  C10    38.24  30.0  2
 Y8J  Var_05    H9   C04  C05  C06   -26.65  30.0  2
 Y8J  Var_06    H10  C04  C05  C06  -143.03  30.0  2
 Y8J  Var_07    C05  C04  C03  C02   -63.79  30.0  3
 Y8J  Var_08    H7   C03  C04  C05   174.55  30.0  2
 Y8J  Var_09    H8   C03  C04  C05    59.39  30.0  2
 Y8J  Var_10    C04  C03  C02  C01  -176.20  30.0  3
 Y8J  Var_11    H7   C03  C02  C01   -55.12  30.0  3
 Y8J  Var_12    H8   C03  C02  C01    60.75  30.0  3
 Y8J  Var_13    H9   C04  C03  C02    58.45  30.0  3
 Y8J  Var_14    H10  C04  C03  C02   174.46  30.0  3
 Y8J  Var_15    H2   C01  C02  C03  -179.47  30.0  3
 Y8J  Var_16    H3   C01  C02  C03   -59.38  30.0  3
 Y8J  Var_17    H4   C01  C02  C03    60.38  30.0  3
 Y8J  Var_18    H5   C02  C03  C04    61.62  30.0  1
 Y8J  Var_19    H6   C02  C03  C04   -54.23  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
 Y8J  plan-1  C10  0.020
 Y8J  plan-1  C04  0.020
 Y8J  plan-1  C05  0.020
 Y8J  plan-1  C06  0.020
 Y8J  plan-1  C07  0.020
 Y8J  plan-1  C08  0.020
 Y8J  plan-1  N09  0.020
 Y8J  plan-1  H1   0.020
 Y8J  plan-1  H11  0.020
 Y8J  plan-1  H12  0.020
 Y8J  plan-1  H13  0.020

