# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu May 28 19:46:58 2020
#   Inital geometry file: a 92 line input string
#   Ligand name: tridecanoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCCCCCCCCCCCC(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
 TDA  TDA  'tridecanoic acid         '  ligand  41  15  .  2021-08-24  2021-08-24  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_TDA
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
 TDA  O21   O  OH1   0  -0.599   0.6582  -0.0026  -7.5412
 TDA  O22   O  O     0  -0.446  -1.3531   0.0558  -6.5830
 TDA  C21   C  C     0   0.549  -0.1514   0.0242  -6.4852
 TDA  C22   C  CH2   0  -0.580   0.6159   0.0116  -5.1927
 TDA  C23   C  CH2   0  -0.418  -0.2623   0.0183  -3.9523
 TDA  C24   C  CH2   0  -0.415   0.5656   0.0042  -2.6732
 TDA  C25   C  CH2   0  -0.413  -0.2912   0.0103  -1.4136
 TDA  C26   C  CH2   0  -0.412   0.5298  -0.0057  -0.1303
 TDA  C27   C  CH2   0  -0.412  -0.3260  -0.0010   1.1304
 TDA  C28   C  CH2   0  -0.412   0.4935  -0.0122   2.4148
 TDA  C29   C  CH2   0  -0.411  -0.3638  -0.0076   3.6746
 TDA  C30   C  CH2   0  -0.412   0.4531  -0.0184   4.9607
 TDA  C31   C  CH2   0  -0.406  -0.4072  -0.0118   6.2182
 TDA  C32   C  CH2   0  -0.419   0.4043  -0.0294   7.5081
 TDA  C33   C  CH3   0  -0.662  -0.4714  -0.0215   8.7538
 TDA  H21   H  HOH1  0   0.478   0.1368   0.0086  -8.3577
 TDA  H222  H  HCH2  0   0.275   1.2885   0.8761  -5.1901
 TDA  H221  H  HCH2  0   0.274   1.2716  -0.8653  -5.1946
 TDA  H232  H  HCH2  0   0.224  -0.9270  -0.8499  -3.9634
 TDA  H231  H  HCH2  0   0.224  -0.9069   0.9015  -3.9582
 TDA  H242  H  HCH2  0   0.212   1.2351   0.8715  -2.6611
 TDA  H241  H  HCH2  0   0.212   1.2139  -0.8794  -2.6671
 TDA  H252  H  HCH2  0   0.209  -0.9613  -0.8567  -1.4266
 TDA  H251  H  HCH2  0   0.209  -0.9392   0.8941  -1.4195
 TDA  H262  H  HCH2  0   0.207   1.1998   0.8615  -0.1174
 TDA  H261  H  HCH2  0   0.207   1.1785  -0.8889  -0.1251
 TDA  H272  H  HCH2  0   0.207  -0.9938  -0.8699   1.1182
 TDA  H271  H  HCH2  0   0.206  -0.9771   0.8805   1.1234
 TDA  H282  H  HCH2  0   0.206   1.1610   0.8569   2.4273
 TDA  H281  H  HCH2  0   0.206   1.1448  -0.8937   2.4225
 TDA  H292  H  HCH2  0   0.206  -1.0318  -0.8765   3.6615
 TDA  H291  H  HCH2  0   0.206  -1.0150   0.8739   3.6663
 TDA  H302  H  HCH2  0   0.206   1.1204   0.8508   4.9736
 TDA  H301  H  HCH2  0   0.206   1.1043  -0.8999   4.9702
 TDA  H312  H  HCH2  0   0.205  -1.0809  -0.8762   6.2025
 TDA  H311  H  HCH2  0   0.205  -1.0530   0.8738   6.2105
 TDA  H322  H  HCH2  0   0.210   1.0747   0.8357   7.5247
 TDA  H321  H  HCH2  0   0.210   1.0503  -0.9130   7.5178
 TDA  H333  H  HCH3  0   0.225   0.1243  -0.0339   9.6673
 TDA  H332  H  HCH3  0   0.215  -1.1026   0.8689   8.7837
 TDA  H331  H  HCH3  0   0.215  -1.1295  -0.8922   8.7765

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
 TDA  O21  C21   single  1.331  0.020  1.331
 TDA  O21  H21   single  0.850  0.020  0.980
 TDA  O22  C21   double  1.206  0.020  1.206
 TDA  C21  C22   single  1.503  0.020  1.503
 TDA  C22  C23   single  1.520  0.020  1.520
 TDA  C22  H222  single  0.970  0.020  1.090
 TDA  C22  H221  single  0.970  0.020  1.090
 TDA  C23  C24   single  1.524  0.020  1.524
 TDA  C23  H232  single  0.970  0.020  1.090
 TDA  C23  H231  single  0.970  0.020  1.090
 TDA  C24  C25   single  1.523  0.020  1.523
 TDA  C24  H242  single  0.970  0.020  1.090
 TDA  C24  H241  single  0.970  0.020  1.090
 TDA  C25  C26   single  1.524  0.020  1.524
 TDA  C25  H252  single  0.970  0.020  1.090
 TDA  C25  H251  single  0.970  0.020  1.090
 TDA  C26  C27   single  1.524  0.020  1.524
 TDA  C26  H262  single  0.970  0.020  1.090
 TDA  C26  H261  single  0.970  0.020  1.090
 TDA  C27  C28   single  1.524  0.020  1.524
 TDA  C27  H272  single  0.970  0.020  1.090
 TDA  C27  H271  single  0.970  0.020  1.090
 TDA  C28  C29   single  1.524  0.020  1.524
 TDA  C28  H282  single  0.970  0.020  1.090
 TDA  C28  H281  single  0.970  0.020  1.090
 TDA  C29  C30   single  1.524  0.020  1.524
 TDA  C29  H292  single  0.970  0.020  1.090
 TDA  C29  H291  single  0.970  0.020  1.090
 TDA  C30  C31   single  1.524  0.020  1.524
 TDA  C30  H302  single  0.970  0.020  1.090
 TDA  C30  H301  single  0.970  0.020  1.090
 TDA  C31  C32   single  1.524  0.020  1.524
 TDA  C31  H312  single  0.970  0.020  1.090
 TDA  C31  H311  single  0.970  0.020  1.090
 TDA  C32  C33   single  1.523  0.020  1.523
 TDA  C32  H322  single  0.970  0.020  1.090
 TDA  C32  H321  single  0.970  0.020  1.090
 TDA  C33  H333  single  0.970  0.020  1.090
 TDA  C33  H332  single  0.970  0.020  1.090
 TDA  C33  H331  single  0.970  0.020  1.090

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
 TDA  H21   O21  C21   109.94  3.000
 TDA  C22   C21  O22   125.35  3.000
 TDA  C22   C21  O21   111.81  3.000
 TDA  O22   C21  O21   122.84  3.000
 TDA  H221  C22  H222  105.33  3.000
 TDA  H221  C22  C23   110.55  3.000
 TDA  H222  C22  C23   110.45  3.000
 TDA  H221  C22  C21   108.12  3.000
 TDA  H222  C22  C21   107.99  3.000
 TDA  C23   C22  C21   114.00  3.000
 TDA  H231  C23  H232  106.43  3.000
 TDA  H231  C23  C24   109.41  3.000
 TDA  H232  C23  C24   109.36  3.000
 TDA  H231  C23  C22   109.86  3.000
 TDA  H232  C23  C22   109.85  3.000
 TDA  C24   C23  C22   111.78  3.000
 TDA  H241  C24  H242  106.06  3.000
 TDA  H241  C24  C25   109.35  3.000
 TDA  H242  C24  C25   109.35  3.000
 TDA  H241  C24  C23   109.49  3.000
 TDA  H242  C24  C23   109.51  3.000
 TDA  C25   C24  C23   112.86  3.000
 TDA  H251  C25  H252  106.05  3.000
 TDA  H251  C25  C26   109.36  3.000
 TDA  H252  C25  C26   109.35  3.000
 TDA  H251  C25  C24   109.35  3.000
 TDA  H252  C25  C24   109.33  3.000
 TDA  C26   C25  C24   113.16  3.000
 TDA  H261  C26  H262  106.02  3.000
 TDA  H261  C26  C27   109.33  3.000
 TDA  H262  C26  C27   109.34  3.000
 TDA  H261  C26  C25   109.35  3.000
 TDA  H262  C26  C25   109.34  3.000
 TDA  C27   C26  C25   113.21  3.000
 TDA  H271  C27  H272  106.00  3.000
 TDA  H271  C27  C28   109.32  3.000
 TDA  H272  C27  C28   109.35  3.000
 TDA  H271  C27  C26   109.32  3.000
 TDA  H272  C27  C26   109.30  3.000
 TDA  C28   C27  C26   113.29  3.000
 TDA  H281  C28  H282  106.01  3.000
 TDA  H281  C28  C29   109.33  3.000
 TDA  H282  C28  C29   109.32  3.000
 TDA  H281  C28  C27   109.36  3.000
 TDA  H282  C28  C27   109.35  3.000
 TDA  C29   C28  C27   113.22  3.000
 TDA  H291  C29  H292  105.99  3.000
 TDA  H291  C29  C30   109.31  3.000
 TDA  H292  C29  C30   109.34  3.000
 TDA  H291  C29  C28   109.30  3.000
 TDA  H292  C29  C28   109.31  3.000
 TDA  C30   C29  C28   113.34  3.000
 TDA  H301  C30  H302  106.02  3.000
 TDA  H301  C30  C31   109.38  3.000
 TDA  H302  C30  C31   109.31  3.000
 TDA  H301  C30  C29   109.37  3.000
 TDA  H302  C30  C29   109.31  3.000
 TDA  C31   C30  C29   113.20  3.000
 TDA  H311  C31  H312  105.96  3.000
 TDA  H311  C31  C32   109.21  3.000
 TDA  H312  C31  C32   109.29  3.000
 TDA  H311  C31  C30   109.29  3.000
 TDA  H312  C31  C30   109.38  3.000
 TDA  C32   C31  C30   113.44  3.000
 TDA  H321  C32  H322  106.05  3.000
 TDA  H321  C32  C33   109.66  3.000
 TDA  H322  C32  C33   109.62  3.000
 TDA  H321  C32  C31   109.33  3.000
 TDA  H322  C32  C31   109.26  3.000
 TDA  C33   C32  C31   112.71  3.000
 TDA  H331  C33  H332  107.54  3.000
 TDA  H331  C33  H333  107.62  3.000
 TDA  H332  C33  H333  107.59  3.000
 TDA  H331  C33  C32   111.07  3.000
 TDA  H332  C33  C32   111.05  3.000
 TDA  H333  C33  C32   111.78  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
 TDA  CONST_01  H21   O21  C21  O22     0.00   0.0  0
 TDA  Var_01    C23   C22  C21  O21  -179.06  30.0  3
 TDA  Var_02    C24   C23  C22  C21   179.97  30.0  3
 TDA  Var_03    C25   C24  C23  C22  -179.99  30.0  3
 TDA  Var_04    C26   C25  C24  C23   179.92  30.0  3
 TDA  Var_05    C27   C26  C25  C24  -179.94  30.0  3
 TDA  Var_06    C28   C27  C26  C25  -179.81  30.0  3
 TDA  Var_07    C29   C28  C27  C26   180.00  30.0  3
 TDA  Var_08    C30   C29  C28  C27  -179.99  30.0  3
 TDA  Var_09    C31   C30  C29  C28   179.92  30.0  3
 TDA  Var_10    C32   C31  C30  C29   179.72  30.0  3
 TDA  Var_11    C33   C32  C31  C30   179.96  30.0  3
 TDA  Var_12    H333  C33  C32  C31  -179.98  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
 TDA  plan-1  O21  0.020
 TDA  plan-1  O22  0.020
 TDA  plan-1  C21  0.020
 TDA  plan-1  C22  0.020
 TDA  plan-1  H21  0.020

