# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Mar  8 16:38:31 2022
#   Inital geometry file: a 64 line input string
#   Ligand name: (2S)-2-azanyl-2-[(4S,6R)-2-azanyl-4-hydroxy-1,4,5,6-tetrahydropyrimidin-6-yl]ethanoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: N[C@@H]([C@H]1C[C@H](O)N=C(N)N1)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
 5OH  5OH  '(2S)-2-azanyl-2-[(4S,6R)-2-azanyl-4-hydroxy-1,4,5,6-tetrahydropyrimidin-6-yl]ethanoic acid'  L-peptide  24  13  .  2012-08-28  2022-03-10
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_5OH
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
 5OH  C     C  C      0   0.418  103.2843   9.6497  23.5616
 5OH  N     N  NH2    0  -0.812  104.4834   7.9621  24.9131
 5OH  O     O  O      0  -0.601  102.9365  10.8422  23.4492
 5OH  CA    C  CH1    0  -0.223  103.6857   9.1725  24.9857
 5OH  CB    C  CH1    0  -0.029  104.3861  10.2918  25.7604
 5OH  NP    N  NH1    0  -0.660  105.5394  10.8050  25.0461
 5OH  CQ    C  C      0   0.581  106.8015  10.7348  25.5353
 5OH  NQ    N  NH2    0  -0.837  107.7231  11.5232  24.8741
 5OH  CR    C  CH2    0  -0.540  104.8095   9.9210  27.1799
 5OH  NR    N  N      0  -0.523  107.1836  10.0433  26.5492
 5OH  CS    C  CH1    0   0.180  106.1951   9.2768  27.2331
 5OH  OS    O  OH1    0  -0.672  106.6406   9.1582  28.5731
 5OH  OXT   O  OC    -1  -0.593  103.3069   8.7915  22.6585
 5OH  HN    H  HNH2   0   0.334  104.2832   7.3573  25.6978
 5OH  HNA   H  HNH2   0   0.338  104.2021   7.4668  24.0762
 5OH  HA    H  HCH1   0   0.203  102.7312   9.0019  25.5149
 5OH  HP    H  HCH1   0   0.234  103.6615  11.1043  25.8417
 5OH  HNP   H  HNH1   0   0.379  105.3459  11.4731  24.3182
 5OH  HNQ   H  HNH2   0   0.372  108.6756  11.2473  25.0522
 5OH  HNQA  H  HNH2   0   0.376  107.5564  11.6679  23.8899
 5OH  HR    H  HCH2   0   0.231  104.8456  10.8299  27.7883
 5OH  HRA   H  HCH2   0   0.231  104.0583   9.2664  27.6307
 5OH  HS    H  HCH1   0   0.175  106.1340   8.2736  26.7874
 5OH  HOS   H  HOH1   0   0.437  106.0676   8.5239  29.0152

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
 5OH  C   CA    single  1.525  0.021  1.525
 5OH  C   OXT   deloc   1.246  0.020  1.246
 5OH  N   CA    single  1.458  0.019  1.458
 5OH  N   HN    single  0.890  0.020  1.040
 5OH  N   HNA   single  0.890  0.020  1.040
 5OH  O   C     deloc   1.231  0.020  1.231
 5OH  CA  CB    single  1.521  0.033  1.521
 5OH  CA  HA    single  0.970  0.020  0.970
 5OH  CB  CR    single  1.527  0.020  1.527
 5OH  CB  HP    single  0.970  0.020  1.090
 5OH  NP  CB    single  1.450  0.020  1.450
 5OH  NP  CQ    single  1.355  0.020  1.355
 5OH  NP  HNP   single  0.860  0.020  1.020
 5OH  CQ  NR    double  1.285  0.020  1.285
 5OH  NQ  CQ    single  1.381  0.020  1.381
 5OH  NQ  HNQ   single  0.890  0.020  1.040
 5OH  NQ  HNQA  single  0.890  0.020  1.040
 5OH  CR  HR    single  0.970  0.020  1.090
 5OH  CR  HRA   single  0.970  0.020  1.090
 5OH  NR  CS    single  1.426  0.020  1.426
 5OH  CS  CR    single  1.529  0.020  1.529
 5OH  CS  OS    single  1.417  0.020  1.417
 5OH  CS  HS    single  0.970  0.020  1.090
 5OH  OS  HOS   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
 5OH  OXT   C   CA   116.61  3.000
 5OH  OXT   C   O    126.75  3.000
 5OH  CA    C   O    120.80  1.700
 5OH  HNA   N   HN   107.10  3.000
 5OH  HNA   N   CA   107.26  3.000
 5OH  HN    N   CA   110.57  3.000
 5OH  HA    CA  CB   109.00  3.000
 5OH  HA    CA  N    110.00  3.000
 5OH  CB    CA  N    110.40  1.500
 5OH  HA    CA  C    109.00  3.000
 5OH  CB    CA  C    110.50  1.500
 5OH  N     CA  C    111.00  2.800
 5OH  HP    CB  CR   107.19  3.000
 5OH  HP    CB  NP   107.52  3.000
 5OH  CR    CB  NP   108.86  3.000
 5OH  NP    CB  CA   111.92  3.000
 5OH  HP    CB  CA   106.15  3.000
 5OH  CR    CB  CA   114.82  3.000
 5OH  HNP   NP  CQ   118.31  3.000
 5OH  HNP   NP  CB   115.98  3.000
 5OH  CQ    NP  CB   122.98  3.000
 5OH  NR    CQ  NQ   119.10  3.000
 5OH  NQ    CQ  NP   114.77  3.000
 5OH  NR    CQ  NP   126.11  3.000
 5OH  HNQA  NQ  HNQ  111.59  3.000
 5OH  HNQA  NQ  CQ   116.01  3.000
 5OH  HNQ   NQ  CQ   112.94  3.000
 5OH  HRA   CR  HR   106.89  3.000
 5OH  HRA   CR  CS   110.85  3.000
 5OH  HR    CR  CS   107.50  3.000
 5OH  CS    CR  CB   112.70  3.000
 5OH  HRA   CR  CB   109.76  3.000
 5OH  HR    CR  CB   108.93  3.000
 5OH  CS    NR  CQ   117.49  3.000
 5OH  HS    CS  OS   108.93  3.000
 5OH  HS    CS  NR   109.55  3.000
 5OH  OS    CS  NR   106.30  3.000
 5OH  HS    CS  CR   108.66  3.000
 5OH  OS    CS  CR   110.68  3.000
 5OH  NR    CS  CR   112.65  3.000
 5OH  HOS   OS  CS   107.61  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
 5OH  CONST_01  NR   CQ  NP  CB    0.00  0.0  0
 5OH  CONST_02  CS   NR  CQ  NP    0.00  0.0  0
 5OH  CONST_03  NQ   CQ  NP  CB  180.00  0.0  0
 5OH  CONST_04  CS   NR  CQ  NQ  180.00  0.0  0
 5OH  CONST_05  HNP  NP  CQ  NR  180.00  0.0  0

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
 5OH  chir_01  CA  C   N   CB  negativ
 5OH  chir_02  CB  NP  CR  CA  positiv
 5OH  chir_03  CS  OS  NR  CR  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
 5OH  plan-1  CB    0.020
 5OH  plan-1  NP    0.020
 5OH  plan-1  CQ    0.020
 5OH  plan-1  NQ    0.020
 5OH  plan-1  NR    0.020
 5OH  plan-1  CS    0.020
 5OH  plan-1  HNP   0.020
 5OH  plan-1  HNQ   0.020
 5OH  plan-1  HNQA  0.020
 5OH  plan-2  C     0.020
 5OH  plan-2  O     0.020
 5OH  plan-2  CA    0.020
 5OH  plan-2  OXT   0.020

