# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr  1 15:11:31 2020
#   Inital geometry file: a 62 line input string
#   Ligand name: 3-cyclopentyl-N-hydroxypropanamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: ONC(=O)CCC1CCCC1
#
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
 3YP  3YP  3-cyclopentyl-N-hydroxypropanamide  ligand  26  11  .  2021-08-04  2022-09-22
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_3YP
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
 3YP  CAF   C  CH2   0  -0.440  -2.6323  -1.0717  -0.5350
 3YP  CAC   C  CH2   0  -0.443  -3.8037  -0.5776   0.3282
 3YP  CAD   C  CH2   0  -0.442  -3.6524   0.9419   0.3341
 3YP  CAG   C  CH2   0  -0.441  -2.1415   1.1271   0.4289
 3YP  CAK   C  CH1   0  -0.218  -1.5667   0.0551  -0.5116
 3YP  CAH   C  CH2   0  -0.430  -0.1872  -0.4457  -0.1036
 3YP  CAE   C  CH2   0  -0.586   0.8685   0.6556  -0.1093
 3YP  CAJ   C  C     0   0.530   2.2238   0.1514   0.3252
 3YP  OAA   O  O     0  -0.483   2.3986  -0.5097   1.3347
 3YP  NAI   N  NH1   0  -0.377   3.2191   0.4822  -0.5207
 3YP  OAB   O  OH1   0  -0.546   4.5168   0.2708  -0.1631
 3YP  HAF1  H  HCH2  0   0.226  -2.9598  -1.2625  -1.5585
 3YP  HAF2  H  HCH2  0   0.225  -2.2289  -2.0150  -0.1601
 3YP  HAC1  H  HCH2  0   0.227  -4.7735  -0.9140  -0.0413
 3YP  HAC2  H  HCH2  0   0.217  -3.7025  -0.9516   1.3506
 3YP  HAD1  H  HCH2  0   0.214  -4.0241   1.3644  -0.6043
 3YP  HAD2  H  HCH2  0   0.227  -4.1963   1.4248   1.1479
 3YP  HAG1  H  HCH2  0   0.213  -1.8144   0.9334   1.4575
 3YP  HAG2  H  HCH2  0   0.231  -1.8155   2.1364   0.1724
 3YP  HAK   H  HCH1  0   0.224  -1.4914   0.4858  -1.5162
 3YP  HAH1  H  HCH2  0   0.235   0.1246  -1.2451  -0.7831
 3YP  HAH2  H  HCH2  0   0.224  -0.2481  -0.8919   0.8931
 3YP  HAE1  H  HCH2  0   0.273   0.5864   1.4512   0.5871
 3YP  HAE2  H  HCH2  0   0.249   0.9176   1.1180  -1.0989
 3YP  HAI   H  HNH1  0   0.414   3.0909   1.1513  -1.2657
 3YP  HAB   H  HOH1  0   0.477   4.7842  -0.5516  -0.5928

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
 3YP  CAF  CAC   single  1.537  0.020  1.537
 3YP  CAF  CAK   single  1.551  0.020  1.551
 3YP  CAF  HAF1  single  0.970  0.020  1.090
 3YP  CAF  HAF2  single  0.970  0.020  1.090
 3YP  CAC  CAD   single  1.527  0.020  1.527
 3YP  CAC  HAC1  single  0.970  0.020  1.090
 3YP  CAC  HAC2  single  0.970  0.020  1.090
 3YP  CAD  CAG   single  1.525  0.020  1.525
 3YP  CAD  HAD1  single  0.970  0.020  1.090
 3YP  CAD  HAD2  single  0.970  0.020  1.090
 3YP  CAG  CAK   single  1.538  0.020  1.538
 3YP  CAG  HAG1  single  0.970  0.020  1.090
 3YP  CAG  HAG2  single  0.970  0.020  1.090
 3YP  CAK  CAH   single  1.523  0.020  1.523
 3YP  CAK  HAK   single  0.970  0.020  1.090
 3YP  CAH  CAE   single  1.526  0.020  1.526
 3YP  CAH  HAH1  single  0.970  0.020  1.090
 3YP  CAH  HAH2  single  0.970  0.020  1.090
 3YP  CAE  CAJ   single  1.510  0.020  1.510
 3YP  CAE  HAE1  single  0.970  0.020  1.090
 3YP  CAE  HAE2  single  0.970  0.020  1.090
 3YP  CAJ  OAA   double  1.219  0.020  1.219
 3YP  CAJ  NAI   single  1.347  0.020  1.347
 3YP  NAI  OAB   single  1.363  0.020  1.363
 3YP  NAI  HAI   single  0.890  0.020  1.040
 3YP  OAB  HAB   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
 3YP  HAF2  CAF  HAF1  106.36  3.000
 3YP  HAF2  CAF  CAK   111.62  3.000
 3YP  HAF1  CAF  CAK   110.32  3.000
 3YP  HAF2  CAF  CAC   111.49  3.000
 3YP  HAF1  CAF  CAC   110.75  3.000
 3YP  CAK   CAF  CAC   106.36  3.000
 3YP  HAC2  CAC  HAC1  107.07  3.000
 3YP  HAC2  CAC  CAD   109.12  3.000
 3YP  HAC1  CAC  CAD   113.34  3.000
 3YP  HAC2  CAC  CAF   110.17  3.000
 3YP  HAC1  CAC  CAF   112.84  3.000
 3YP  CAD   CAC  CAF   104.28  3.000
 3YP  HAD2  CAD  HAD1  107.42  3.000
 3YP  HAD2  CAD  CAG   113.18  3.000
 3YP  HAD1  CAD  CAG   110.05  3.000
 3YP  HAD2  CAD  CAC   113.19  3.000
 3YP  HAD1  CAD  CAC   110.32  3.000
 3YP  CAG   CAD  CAC   102.66  3.000
 3YP  HAG2  CAG  HAG1  107.14  3.000
 3YP  HAG2  CAG  CAK   112.92  3.000
 3YP  HAG1  CAG  CAK   109.82  3.000
 3YP  HAG2  CAG  CAD   113.18  3.000
 3YP  HAG1  CAG  CAD   109.41  3.000
 3YP  CAK   CAG  CAD   104.34  3.000
 3YP  HAK   CAK  CAH   108.22  3.000
 3YP  HAK   CAK  CAG   108.21  3.000
 3YP  CAH   CAK  CAG   113.83  3.000
 3YP  HAK   CAK  CAF   108.60  3.000
 3YP  CAH   CAK  CAF   112.79  3.000
 3YP  CAG   CAK  CAF   105.00  3.000
 3YP  HAH2  CAH  HAH1  106.48  3.000
 3YP  HAH2  CAH  CAE   109.66  3.000
 3YP  HAH1  CAH  CAE   109.14  3.000
 3YP  HAH2  CAH  CAK   109.13  3.000
 3YP  HAH1  CAH  CAK   109.38  3.000
 3YP  CAE   CAH  CAK   112.85  3.000
 3YP  HAE2  CAE  HAE1  106.27  3.000
 3YP  HAE2  CAE  CAJ   111.18  3.000
 3YP  HAE1  CAE  CAJ   106.92  3.000
 3YP  HAE2  CAE  CAH   109.86  3.000
 3YP  HAE1  CAE  CAH   110.12  3.000
 3YP  CAJ   CAE  CAH   112.27  3.000
 3YP  NAI   CAJ  OAA   123.16  3.000
 3YP  NAI   CAJ  CAE   113.60  3.000
 3YP  OAA   CAJ  CAE   123.23  3.000
 3YP  HAI   NAI  OAB   114.67  3.000
 3YP  HAI   NAI  CAJ   122.16  3.000
 3YP  OAB   NAI  CAJ   120.04  3.000
 3YP  HAB   OAB  NAI   106.21  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
 3YP  CONST_01  OAB  NAI  CAJ  CAE  180.00   0.0  0
 3YP  CONST_02  OAB  NAI  CAJ  OAA    0.00   0.0  0
 3YP  CONST_03  HAI  NAI  CAJ  CAE    0.00   0.0  0
 3YP  Var_01    CAG  CAD  CAC  CAF  -38.96  30.0  1
 3YP  Var_02    CAK  CAG  CAD  CAC   41.00  30.0  1
 3YP  Var_03    CAK  CAF  CAC  CAD   22.28  30.0  1
 3YP  Var_04    CAJ  CAE  CAH  CAK  178.78  30.0  3
 3YP  Var_05    OAA  CAJ  CAE  CAH  -49.48  30.0  3

loop_
_chem_comp_chir.comp_id
_chem_comp_chir.id
_chem_comp_chir.atom_id_centre
_chem_comp_chir.atom_id_1
_chem_comp_chir.atom_id_2
_chem_comp_chir.atom_id_3
_chem_comp_chir.volume_sign
 3YP  chir_01  CAK  CAF  CAG  CAH  negativ

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
 3YP  plan-1  CAE  0.020
 3YP  plan-1  CAJ  0.020
 3YP  plan-1  OAA  0.020
 3YP  plan-1  NAI  0.020
 3YP  plan-1  OAB  0.020
 3YP  plan-1  HAI  0.020

