# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Apr 24 21:53:18 2020
#   Inital geometry file: a 56 line input string
#   Ligand name: (2S)-amino(cyclopentyl)ethanoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: N[C@@H](C1CCCC1)C(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
 2KY  2KY  '(2S)-amino(cyclopentyl)ethanoic acid'  L-peptide  23  10  .  2022-03-10  2022-11-17
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_2KY
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
 2KY  C5    C  C     0   0.550   1.8452  -0.3293  -0.0403
 2KY  C6    C  CH1   0  -0.201   0.7466   0.6100   0.4096
 2KY  N7    N  NH2   0  -0.788   1.1840   1.9719   0.1546
 2KY  O32   O  O     0  -0.447   2.4786  -0.1793  -1.0563
 2KY  C33   C  CR15  0  -0.251  -0.5683   0.2162  -0.2823
 2KY  C34   C  CH2   0  -0.448  -1.7412   1.1209   0.1426
 2KY  C35   C  CH2   0  -0.444  -3.0105   0.2443   0.0637
 2KY  C36   C  CH2   0  -0.447  -2.5382  -1.1300  -0.4297
 2KY  C37   C  CH2   0  -0.434  -1.0765  -1.1993  -0.0001
 2KY  H6    H  HCH1  0   0.257   0.6075   0.4979   1.4891
 2KY  H7    H  HNH2  0   0.344   1.2241   2.1368  -0.8445
 2KY  H33   H  HCR5  0   0.234  -0.4191   0.3170  -1.3650
 2KY  H341  H  HCH2  0   0.227  -1.5901   1.4754   1.1665
 2KY  H342  H  HCH2  0   0.237  -1.8098   2.0074  -0.4882
 2KY  H352  H  HCH2  0   0.226  -3.4644   0.1532   1.0520
 2KY  H351  H  HCH2  0   0.231  -3.7698   0.6739  -0.5904
 2KY  H361  H  HCH2  0   0.231  -3.1390  -1.9505  -0.0342
 2KY  H362  H  HCH2  0   0.220  -2.6009  -1.1846  -1.5198
 2KY  H371  H  HCH2  0   0.235  -0.5177  -1.9745  -0.5272
 2KY  H372  H  HCH2  0   0.218  -1.0068  -1.4164   1.0713
 2KY  H2    H  HNH2  0   0.360   0.4891   2.6134   0.5154
 2KY  OXT   O  OH1   0  -0.588   2.0173  -1.3577   0.7795
 2KY  HXT   H  HOH1  0   0.479   2.6813  -1.9632   0.4158

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
 2KY  O32  C5    double  1.207  0.020  1.207
 2KY  C5   C6    single  1.514  0.020  1.514
 2KY  N7   C6    single  1.453  0.020  1.453
 2KY  C6   C33   single  1.537  0.020  1.537
 2KY  C33  C34   single  1.541  0.020  1.541
 2KY  C33  C37   single  1.530  0.020  1.530
 2KY  C34  C35   single  1.545  0.020  1.545
 2KY  C37  C36   single  1.525  0.020  1.525
 2KY  C35  C36   single  1.535  0.020  1.535
 2KY  C6   H6    single  0.970  0.020  1.090
 2KY  N7   H7    single  0.890  0.020  1.040
 2KY  C33  H33   single  0.970  0.020  1.090
 2KY  C34  H341  single  0.970  0.020  1.090
 2KY  C34  H342  single  0.970  0.020  1.090
 2KY  C35  H352  single  0.970  0.020  1.090
 2KY  C35  H351  single  0.970  0.020  1.090
 2KY  C36  H361  single  0.970  0.020  1.090
 2KY  C36  H362  single  0.970  0.020  1.090
 2KY  C37  H371  single  0.970  0.020  1.090
 2KY  C37  H372  single  0.970  0.020  1.090
 2KY  N7   H2    single  0.890  0.020  1.040
 2KY  C5   OXT   single  1.326  0.020  1.326
 2KY  OXT  HXT   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
 2KY  OXT   C5   O32   123.27  3.000
 2KY  OXT   C5   C6    113.05  3.000
 2KY  O32   C5   C6    123.65  3.000
 2KY  H6    C6   C33   108.01  3.000
 2KY  H6    C6   N7    107.90  3.000
 2KY  C33   C6   N7    114.75  3.000
 2KY  H6    C6   C5    108.77  3.000
 2KY  C33   C6   C5    109.15  3.000
 2KY  N7    C6   C5    108.12  3.000
 2KY  H2    N7   H7    105.99  3.000
 2KY  H2    N7   C6    108.96  3.000
 2KY  H7    N7   C6    109.72  3.000
 2KY  H33   C33  C37   108.18  3.000
 2KY  H33   C33  C34   108.75  3.000
 2KY  C37   C33  C34   103.86  3.000
 2KY  H33   C33  C6    107.71  3.000
 2KY  C37   C33  C6    115.98  3.000
 2KY  C34   C33  C6    112.12  3.000
 2KY  H342  C34  H341  106.66  3.000
 2KY  H342  C34  C35   112.35  3.000
 2KY  H341  C34  C35   110.19  3.000
 2KY  H342  C34  C33   111.46  3.000
 2KY  H341  C34  C33   110.07  3.000
 2KY  C35   C34  C33   106.15  3.000
 2KY  H351  C35  H352  106.65  3.000
 2KY  H351  C35  C36   111.98  3.000
 2KY  H352  C35  C36   110.14  3.000
 2KY  H351  C35  C34   112.29  3.000
 2KY  H352  C35  C34   110.06  3.000
 2KY  C36   C35  C34   105.77  3.000
 2KY  H362  C36  H361  106.99  3.000
 2KY  H362  C36  C37   109.49  3.000
 2KY  H361  C36  C37   113.05  3.000
 2KY  H362  C36  C35   110.34  3.000
 2KY  H361  C36  C35   112.79  3.000
 2KY  C37   C36  C35   104.19  3.000
 2KY  H372  C37  H371  107.41  3.000
 2KY  H372  C37  C36   110.21  3.000
 2KY  H371  C37  C36   112.76  3.000
 2KY  H372  C37  C33   110.04  3.000
 2KY  H371  C37  C33   113.45  3.000
 2KY  C36   C37  C33   102.96  3.000
 2KY  HXT   OXT  C5    109.95  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
 2KY  CONST_01  HXT  OXT  C5   C6   180.00   0.0  0
 2KY  Var_01    C36  C35  C34  C33   -1.08  30.0  1
 2KY  Var_02    C35  C36  C37  C33  -40.18  30.0  1
 2KY  Var_03    C37  C36  C35  C34   25.41  30.0  1

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
 2KY  chir_01  C6   C5   N7   C33  negativ
 2KY  chir_02  C33  C37  C34  C6   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
 2KY  plan-1  C5   0.020
 2KY  plan-1  C6   0.020
 2KY  plan-1  O32  0.020
 2KY  plan-1  OXT  0.020
 2KY  plan-1  HXT  0.020

