# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Apr 30 02:34:29 2020
#   Inital geometry file: a 95 line input string
#   Ligand name: N~6~-{[(2R,3R)-3-methyl-3,4-dihydro-2H-pyrrol-2-yl]carbonyl}-L-lysine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[C@@H]1CC=N[C@H]1C(=O)NCCCC[C@H](N)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
 PYH  PYH  N~6~-{[(2R,3R)-3-methyl-3,4-dihydro-2H-pyrrol-2-yl]carbonyl}-L-lysine  L-peptide  38  18  .  2022-07-22  2022-07-22
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_PYH
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
 PYH  CAA   C  CH3    0  -0.663   3.9815   2.4644   0.0976
 PYH  CAP   C  CR15   0  -0.269   4.5442   1.0845   0.3824
 PYH  CAJ   C  CH2    0  -0.509   6.0400   0.9141   0.0938
 PYH  CAF   C  CR15   0  -0.040   6.0859  -0.4865  -0.4318
 PYH  NAL   N  N      0  -0.337   4.9758  -1.0098  -0.7418
 PYH  CAR   C  CR15   0  -0.229   3.9215  -0.0359  -0.4869
 PYH  CAO   C  C      0   0.554   2.7483  -0.6988   0.2102
 PYH  OAD   O  O      0  -0.497   2.9144  -1.5085   1.1117
 PYH  NZ    N  NH1    0  -0.644   1.5396  -0.2938  -0.1970
 PYH  CE    C  CH2    0  -0.233   0.3017  -0.7772   0.3810
 PYH  CD    C  CH2    0  -0.476  -0.8901  -0.0576  -0.2281
 PYH  CG    C  CH2    0  -0.408  -2.2142  -0.5596   0.3315
 PYH  CB    C  CH2    0  -0.416  -3.4096   0.1769  -0.2569
 PYH  CA    C  CH1    0  -0.212  -4.7603  -0.3065   0.2767
 PYH  C     C  C      0   0.383  -5.8770   0.6503  -0.2099
 PYH  OXT   O  OC    -1  -0.625  -5.8526   1.8050   0.2672
 PYH  O     O  O      0  -0.609  -6.6949   0.2125  -1.0434
 PYH  N     N  NH2    0  -0.786  -4.9525  -1.7109  -0.0529
 PYH  HA    H  HCH1   0   0.206  -4.7226  -0.2293   1.3704
 PYH  H     H  HNH2   0   0.333  -5.7986  -2.0373   0.3986
 PYH  HN2   H  HNH2   0   0.321  -5.1605  -1.7711  -1.0437
 PYH  HB1   H  HCH2   0   0.217  -3.3141   1.2454  -0.0494
 PYH  HB2   H  HCH2   0   0.204  -3.3977   0.0759  -1.3498
 PYH  HG1   H  HCH2   0   0.219  -2.3136  -1.6307   0.1410
 PYH  HG2   H  HCH2   0   0.208  -2.2201  -0.4399   1.4207
 PYH  HD1   H  HCH2   0   0.227  -0.7964   1.0183  -0.0483
 PYH  HD2   H  HCH2   0   0.226  -0.8804  -0.1942  -1.3147
 PYH  HE1   H  HCH2   0   0.230   0.2080  -1.8551   0.2165
 PYH  HE2   H  HCH2   0   0.232   0.3174  -0.6232   1.4631
 PYH  HZ    H  HNH1   0   0.400   1.4792   0.3383  -0.9789
 PYH  HAR   H  HCR5   0   0.262   3.6001   0.3729  -1.4543
 PYH  HAF   H  HCR5   0   0.258   7.0143  -1.0321  -0.5784
 PYH  HAJ1  H  HCH2   0   0.260   6.3963   1.6046  -0.6792
 PYH  HAJ2  H  HCH2   0   0.264   6.6776   1.0596   0.9667
 PYH  HAP   H  HCR5   0   0.257   4.3760   0.8380   1.4354
 PYH  HAA1  H  HCH3   0   0.225   4.1410   2.7452  -0.9455
 PYH  HAA2  H  HCH3   0   0.229   2.9085   2.5041   0.2932
 PYH  HAA3  H  HCH3   0   0.238   4.4550   3.2209   0.7241

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
 PYH  CAA  CAP   single  1.517  0.020  1.517
 PYH  CAA  HAA1  single  0.970  0.020  1.090
 PYH  CAA  HAA2  single  0.970  0.020  1.090
 PYH  CAA  HAA3  single  0.970  0.020  1.090
 PYH  CAP  CAJ   single  1.533  0.020  1.533
 PYH  CAP  CAR   single  1.549  0.020  1.549
 PYH  CAP  HAP   single  0.970  0.020  1.090
 PYH  CAJ  CAF   single  1.497  0.020  1.497
 PYH  CAJ  HAJ1  single  0.970  0.020  1.090
 PYH  CAJ  HAJ2  single  0.970  0.020  1.090
 PYH  CAF  NAL   double  1.266  0.020  1.266
 PYH  CAF  HAF   single  0.930  0.020  1.080
 PYH  NAL  CAR   single  1.458  0.020  1.458
 PYH  CAR  CAO   single  1.517  0.020  1.517
 PYH  CAR  HAR   single  0.970  0.020  1.090
 PYH  CAO  NZ    single  1.338  0.020  1.338
 PYH  CAO  OAD   double  1.223  0.020  1.223
 PYH  NZ   CE    single  1.449  0.020  1.449
 PYH  NZ   HZ    single  0.860  0.020  1.020
 PYH  CE   CD    single  1.520  0.020  1.520
 PYH  CE   HE1   single  0.970  0.020  1.090
 PYH  CE   HE2   single  0.970  0.020  1.090
 PYH  CD   CG    single  1.523  0.020  1.523
 PYH  CD   HD1   single  0.970  0.020  1.090
 PYH  CD   HD2   single  0.970  0.020  1.090
 PYH  CG   CB    single  1.522  0.020  1.522
 PYH  CG   HG1   single  0.970  0.020  1.090
 PYH  CG   HG2   single  0.970  0.020  1.090
 PYH  CB   CA    single  1.530  0.020  1.530
 PYH  CB   HB1   single  0.970  0.020  1.090
 PYH  CB   HB2   single  0.970  0.020  1.090
 PYH  CA   C     single  1.525  0.021  1.525
 PYH  CA   HA    single  0.970  0.020  0.970
 PYH  CA   N     single  1.458  0.019  1.458
 PYH  C    OXT   deloc   1.250  0.020  1.250
 PYH  C    O     deloc   1.231  0.020  1.231
 PYH  N    H     single  0.860  0.020  0.860
 PYH  N    HN2   single  0.890  0.020  1.040

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
 PYH  HAA3  CAA  HAA2  107.38  3.000
 PYH  HAA3  CAA  HAA1  107.88  3.000
 PYH  HAA2  CAA  HAA1  107.79  3.000
 PYH  HAA3  CAA  CAP   111.23  3.000
 PYH  HAA2  CAA  CAP   111.35  3.000
 PYH  HAA1  CAA  CAP   111.04  3.000
 PYH  HAP   CAP  CAR   108.38  3.000
 PYH  HAP   CAP  CAJ   107.82  3.000
 PYH  CAR   CAP  CAJ   101.90  3.000
 PYH  HAP   CAP  CAA   109.18  3.000
 PYH  CAR   CAP  CAA   113.79  3.000
 PYH  CAJ   CAP  CAA   115.32  3.000
 PYH  HAJ2  CAJ  HAJ1  106.88  3.000
 PYH  HAJ2  CAJ  CAF   112.83  3.000
 PYH  HAJ1  CAJ  CAF   109.39  3.000
 PYH  HAJ2  CAJ  CAP   113.88  3.000
 PYH  HAJ1  CAJ  CAP   112.33  3.000
 PYH  CAF   CAJ  CAP   101.54  3.000
 PYH  HAF   CAF  NAL   120.58  3.000
 PYH  HAF   CAF  CAJ   122.91  3.000
 PYH  NAL   CAF  CAJ   116.48  3.000
 PYH  CAR   NAL  CAF   108.38  3.000
 PYH  HAR   CAR  CAO   109.95  3.000
 PYH  HAR   CAR  NAL   107.83  3.000
 PYH  CAO   CAR  NAL   110.34  3.000
 PYH  HAR   CAR  CAP   110.05  3.000
 PYH  CAO   CAR  CAP   111.66  3.000
 PYH  NAL   CAR  CAP   106.89  3.000
 PYH  NZ    CAO  OAD   123.18  3.000
 PYH  OAD   CAO  CAR   121.53  3.000
 PYH  NZ    CAO  CAR   115.24  3.000
 PYH  HZ    NZ   CE    117.89  3.000
 PYH  HZ    NZ   CAO   118.70  3.000
 PYH  CE    NZ   CAO   123.31  3.000
 PYH  HE2   CE   HE1   106.79  3.000
 PYH  HE2   CE   CD    109.95  3.000
 PYH  HE1   CE   CD    109.82  3.000
 PYH  HE2   CE   NZ    109.61  3.000
 PYH  HE1   CE   NZ    109.99  3.000
 PYH  CD    CE   NZ    110.61  3.000
 PYH  HD2   CD   HD1   106.54  3.000
 PYH  HD2   CD   CG    109.34  3.000
 PYH  HD1   CD   CG    109.76  3.000
 PYH  HD2   CD   CE    109.37  3.000
 PYH  HD1   CD   CE    109.42  3.000
 PYH  CG    CD   CE    112.25  3.000
 PYH  HG2   CG   HG1   106.25  3.000
 PYH  HG2   CG   CB    109.09  3.000
 PYH  HG1   CG   CB    109.60  3.000
 PYH  HG2   CG   CD    109.51  3.000
 PYH  HG1   CG   CD    109.78  3.000
 PYH  CB    CG   CD    112.42  3.000
 PYH  HB2   CB   HB1   106.15  3.000
 PYH  HB2   CB   CA    109.12  3.000
 PYH  HB1   CB   CA    108.65  3.000
 PYH  HB2   CB   CG    109.38  3.000
 PYH  HB1   CB   CG    109.34  3.000
 PYH  CA    CB   CG    113.92  3.000
 PYH  HA    CA   N     110.00  3.000
 PYH  N     CA   C     111.00  2.800
 PYH  HA    CA   C     109.00  3.000
 PYH  N     CA   CB    110.50  1.700
 PYH  HA    CA   CB    109.00  3.000
 PYH  C     CA   CB    110.10  1.900
 PYH  O     C    OXT   126.33  3.000
 PYH  O     C    CA    120.80  1.700
 PYH  OXT   C    CA    115.90  3.000
 PYH  HN2   N    H     104.18  3.000
 PYH  HN2   N    CA    107.79  3.000
 PYH  H     N    CA    114.00  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
 PYH  CONST_01  CE   NZ   CAO  CAR  180.00   0.0  0
 PYH  CONST_02  HZ   NZ   CAO  CAR    0.00   0.0  0
 PYH  CONST_03  CE   NZ   CAO  OAD    0.00   0.0  0
 PYH  Var_01    NAL  CAF  CAJ  CAP   13.44  30.0  1
 PYH  Var_02    CD   CE   NZ   CAO  176.02  30.0  3
 PYH  Var_03    CG   CD   CE   NZ   178.73  30.0  3
 PYH  Var_04    CB   CG   CD   CE   178.92  30.0  3
 PYH  Var_05    CA   CB   CG   CD   179.67  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
 PYH  chir_01  CAP  CAA  CAJ  CAR  positiv
 PYH  chir_02  CAR  NAL  CAP  CAO  positiv
 PYH  chir_03  CA   CB   C    N    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
 PYH  plan-1  CAR  0.020
 PYH  plan-1  CAO  0.020
 PYH  plan-1  OAD  0.020
 PYH  plan-1  NZ   0.020
 PYH  plan-1  CE   0.020
 PYH  plan-1  HZ   0.020
 PYH  plan-2  CA   0.020
 PYH  plan-2  C    0.020
 PYH  plan-2  OXT  0.020
 PYH  plan-2  O    0.020

