# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Mar  4 18:41:12 2022
#   Inital geometry file: a 80 line input string
#   Ligand name: 1-[(4S,5S)-4-amino-5-hydroxy-5-(1,3-thiazol-2-yl)pentyl]guanidine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: N[C@@H](CCCNC(N)=N)[C@H](O)c1sccn1
#
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
 00Y  00Y  1-[(4S,5S)-4-amino-5-hydroxy-5-(1,3-thiazol-2-yl)pentyl]guanidine  peptide  33  16  .  2019-03-22  2022-09-22
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND (side chain)
;

data_comp_00Y
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
 00Y  C     C  CH1   0   0.023  14.5342  -10.4268  18.8124
 00Y  N     N  NH2   0  -0.811  15.3661  -11.9554  20.5069
 00Y  O     O  OH1   0  -0.653  13.3551   -9.9744  18.1977
 00Y  CA    C  CH1   0  -0.097  14.1515  -11.4945  19.8542
 00Y  CB    C  CH2   0  -0.416  13.1930  -10.9118  20.8900
 00Y  CD    C  CH2   0  -0.223  11.6108  -11.3475  22.7954
 00Y  NE    N  NH1   0  -0.645  11.1477  -12.3276  23.7506
 00Y  CG    C  CH2   0  -0.476  12.6887  -11.9384  21.8990
 00Y  CZ    C  C     0   0.547  10.2505  -11.9774  24.7251
 00Y  C1X   C  CR5   0   0.017  15.4552  -10.9883  17.7648
 00Y  N1X   N  N     0  -0.377  16.7427  -11.0850  17.8402
 00Y  S1X   S  S2    0   0.227  14.7752  -11.6310  16.3101
 00Y  C2X   C  CR15  0  -0.030  17.2577  -11.6963  16.7318
 00Y  C3X   C  CR15  0  -0.502  16.3491  -12.0667  15.7939
 00Y  NH1   N  N     0  -0.715   9.9502  -10.7468  24.9250
 00Y  NH2   N  NH2   0  -0.839   9.7250  -13.0608  25.4004
 00Y  HN    H  HNH2  0   0.355  15.1355  -12.6495  21.2058
 00Y  HA    H  HCH1  0   0.204  13.6225  -12.2983  19.3147
 00Y  HB    H  HCH2  0   0.218  13.6932  -10.0920  21.4168
 00Y  HBA   H  HCH2  0   0.233  12.3337  -10.4809  20.3743
 00Y  HD    H  HCH2  0   0.207  10.7889  -10.9603  22.1791
 00Y  HDA   H  HCH2  0   0.225  12.0166  -10.4932  23.3398
 00Y  HNE   H  HNH1  0   0.377  11.0429  -13.2604  23.3810
 00Y  HG    H  HCH2  0   0.224  12.2878  -12.8061  21.3631
 00Y  HGA   H  HCH2  0   0.226  13.5029  -12.3047  22.5299
 00Y  H2X   H  HCR5  0   0.269  18.3250  -11.8456  16.6501
 00Y  H3X   H  HCR5  0   0.303  16.5271  -12.5460  14.8444
 00Y  HNH1  H  H     0   0.315   9.3419  -10.6536  25.7301
 00Y  HNH2  H  HNH2  0   0.383   9.2780  -12.8427  26.2766
 00Y  HNHA  H  HNH2  0   0.380  10.3230  -13.8694  25.4782
 00Y  H33   H  HCH1  0   0.240  15.0687   -9.6262  19.3407
 00Y  H34   H  HOH1  0   0.460  13.5419   -9.1526  17.7320
 00Y  H2    H  HNH2  0   0.352  15.9651  -12.4325  19.8452

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
 00Y  C    CA    single    1.525  0.021  1.525
 00Y  N    HN    single    0.890  0.020  1.040
 00Y  O    C     single    1.231  0.020  1.231
 00Y  CA   N     single    1.458  0.019  1.458
 00Y  CA   CB    single    1.521  0.033  1.521
 00Y  CA   HA    single    0.970  0.020  0.970
 00Y  CB   CG    single    1.525  0.020  1.525
 00Y  CB   HB    single    0.970  0.020  1.090
 00Y  CB   HBA   single    0.970  0.020  1.090
 00Y  CD   NE    single    1.445  0.020  1.445
 00Y  CD   HD    single    0.970  0.020  1.090
 00Y  CD   HDA   single    0.970  0.020  1.090
 00Y  NE   CZ    single    1.370  0.020  1.370
 00Y  NE   HNE   single    0.890  0.020  1.040
 00Y  CG   CD    single    1.521  0.020  1.521
 00Y  CG   HG    single    0.970  0.020  1.090
 00Y  CG   HGA   single    0.970  0.020  1.090
 00Y  CZ   NH1   double    1.282  0.020  1.282
 00Y  CZ   NH2   single    1.381  0.020  1.381
 00Y  C1X  C     single    1.504  0.020  1.504
 00Y  N1X  C1X   aromatic  1.293  0.020  1.293
 00Y  S1X  C1X   aromatic  1.730  0.020  1.730
 00Y  C2X  N1X   aromatic  1.367  0.020  1.367
 00Y  C2X  H2X   single    0.930  0.020  1.080
 00Y  C3X  S1X   aromatic  1.713  0.020  1.713
 00Y  C3X  C2X   aromatic  1.357  0.020  1.357
 00Y  C3X  H3X   single    0.930  0.020  1.080
 00Y  NH1  HNH1  single    0.890  0.020  1.040
 00Y  NH2  HNH2  single    0.890  0.020  1.040
 00Y  NH2  HNHA  single    0.890  0.020  1.040
 00Y  C    H33   single    0.970  0.020  1.090
 00Y  O    H34   single    0.850  0.020  0.980
 00Y  N    H2    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
 00Y  H33   C    C1X   108.01  3.000
 00Y  H33   C    CA    107.52  3.000
 00Y  C1X   C    CA    111.38  3.000
 00Y  H33   C    O     112.60  3.000
 00Y  C1X   C    O     109.24  3.000
 00Y  CA    C    O     120.80  1.700
 00Y  H2    N    HN    105.26  3.000
 00Y  H2    N    CA    110.51  3.000
 00Y  HN    N    CA    109.71  3.000
 00Y  H34   O    C     108.89  3.000
 00Y  HA    CA   CB    109.00  3.000
 00Y  HA    CA   N     110.00  3.000
 00Y  CB    CA   N     110.40  1.500
 00Y  HA    CA   C     110.00  3.000
 00Y  CB    CA   C     110.50  1.500
 00Y  N     CA   C     111.00  2.800
 00Y  HBA   CB   HB    106.94  3.000
 00Y  HBA   CB   CG    108.55  3.000
 00Y  HB    CB   CG    109.67  3.000
 00Y  HBA   CB   CA    108.94  3.000
 00Y  HB    CB   CA    108.98  3.000
 00Y  CG    CB   CA    113.55  3.000
 00Y  HDA   CD   HD    106.40  3.000
 00Y  HDA   CD   CG    109.55  3.000
 00Y  HD    CD   CG    109.67  3.000
 00Y  CG    CD   NE    110.68  3.000
 00Y  HDA   CD   NE    108.69  3.000
 00Y  HD    CD   NE    111.74  3.000
 00Y  HNE   NE   CZ    115.39  3.000
 00Y  HNE   NE   CD    114.73  3.000
 00Y  CZ    NE   CD    120.44  3.000
 00Y  HGA   CG   HG    106.82  3.000
 00Y  HGA   CG   CD    108.53  3.000
 00Y  HG    CG   CD    109.66  3.000
 00Y  HGA   CG   CB    111.17  3.000
 00Y  HG    CG   CB    109.30  3.000
 00Y  CD    CG   CB    111.26  3.000
 00Y  NH2   CZ   NH1   126.00  3.000
 00Y  NH2   CZ   NE    113.36  3.000
 00Y  NH1   CZ   NE    120.63  3.000
 00Y  S1X   C1X  N1X   114.37  3.000
 00Y  S1X   C1X  C     118.94  3.000
 00Y  N1X   C1X  C     126.66  3.000
 00Y  C2X   N1X  C1X   111.19  3.000
 00Y  C3X   S1X  C1X    89.24  3.000
 00Y  H2X   C2X  C3X   124.83  3.000
 00Y  C3X   C2X  N1X   115.48  3.000
 00Y  H2X   C2X  N1X   119.69  3.000
 00Y  H3X   C3X  C2X   128.26  3.000
 00Y  H3X   C3X  S1X   122.01  3.000
 00Y  C2X   C3X  S1X   109.72  3.000
 00Y  HNH1  NH1  CZ    110.65  3.000
 00Y  HNHA  NH2  HNH2  111.69  3.000
 00Y  HNHA  NH2  CZ    116.18  3.000
 00Y  HNH2  NH2  CZ    115.11  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
 00Y  CONST_01  C3X   C2X  N1X  C1X     0.00   0.0  0
 00Y  CONST_02  C2X   C3X  S1X  C1X     0.00   0.0  0
 00Y  CONST_03  C3X   S1X  C1X  N1X     0.00   0.0  0
 00Y  CONST_04  S1X   C3X  C2X  N1X     0.00   0.0  0
 00Y  CONST_05  C2X   N1X  C1X  S1X     0.00   0.0  0
 00Y  CONST_06  C2X   N1X  C1X  C     180.00   0.0  0
 00Y  CONST_07  C3X   S1X  C1X  C     180.00   0.0  0
 00Y  CONST_08  H2X   C2X  N1X  C1X   180.00   0.0  0
 00Y  CONST_09  H3X   C3X  S1X  C1X   180.00   0.0  0
 00Y  CONST_10  NH1   CZ   NE   CD      0.00   0.0  0
 00Y  CONST_11  NH2   CZ   NE   CD    180.00   0.0  0
 00Y  CONST_12  HNH1  NH1  CZ   NE    180.00   0.0  0
 00Y  Var_01    CD    CG   CB   CA   -172.95  30.0  3
 00Y  Var_02    NE    CD   CG   CB   -179.67  30.0  3
 00Y  Var_03    CZ    NE   CD   CG    174.88  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
 00Y  chir_01  C   CA  O  C1X  positiv
 00Y  chir_02  CA  N   C  CB   positiv

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
 00Y  plan-1  C     0.020
 00Y  plan-1  C1X   0.020
 00Y  plan-1  N1X   0.020
 00Y  plan-1  S1X   0.020
 00Y  plan-1  C2X   0.020
 00Y  plan-1  C3X   0.020
 00Y  plan-1  H2X   0.020
 00Y  plan-1  H3X   0.020
 00Y  plan-2  CD    0.020
 00Y  plan-2  NE    0.020
 00Y  plan-2  CZ    0.020
 00Y  plan-2  NH1   0.020
 00Y  plan-2  NH2   0.020
 00Y  plan-2  HNE   0.020
 00Y  plan-2  HNH1  0.020
 00Y  plan-2  HNH2  0.020
 00Y  plan-2  HNHA  0.020

