# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Mar 18 23:09:00 2022
#   Inital geometry file: a 62 line input string
#   Ligand name: (2S)-2-azanyl-2-[(4R)-2-azanyl-1,4,5,6-tetrahydropyrimidin-4-yl]ethanoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: N[C@@H]([C@H]1CCNC(=N1)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
 MYN  MYN  '(2S)-2-azanyl-2-[(4R)-2-azanyl-1,4,5,6-tetrahydropyrimidin-4-yl]ethanoic acid'  L-peptide  23  12  .  2012-08-28  2022-03-22
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_MYN
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
 MYN  CA    C  CH1    0  -0.211  -102.5557   8.9286  -24.3576
 MYN  N     N  NH2    0  -0.800  -103.1888   7.6190  -24.3634
 MYN  C     C  C      0   0.390  -102.1589   9.4759  -22.9580
 MYN  CB    C  CH1    0  -0.086  -103.4488   9.9404  -25.0827
 MYN  CG    C  CH2    0  -0.471  -103.7008   9.5813  -26.5444
 MYN  CD    C  CH2    0  -0.258  -104.6410  10.6068  -27.1534
 MYN  NE    N  NH1    0  -0.662  -105.7921  10.7998  -26.2904
 MYN  CZ    C  C      0   0.574  -105.7349  10.4447  -24.9747
 MYN  N1    N  N      0  -0.502  -104.6832  10.0864  -24.3367
 MYN  NZ    N  NH2    0  -0.837  -106.9566  10.4746  -24.3272
 MYN  O     O  O      0  -0.618  -101.6159  10.6015  -22.9463
 MYN  H4    H  HCH1   0   0.201  -101.6241   8.8570  -24.9367
 MYN  HN5   H  HNH2   0   0.326  -102.7054   7.0313  -23.6955
 MYN  HNT   H  HNH2   0   0.318  -104.1173   7.7337  -23.9701
 MYN  OXT   O  OC    -1  -0.604  -102.3803   8.7512  -21.9674
 MYN  H20   H  HCH1   0   0.203  -102.8996  10.8902  -25.0707
 MYN  H21   H  HCH2   0   0.227  -102.7629   9.5656  -27.1038
 MYN  H21A  H  HCH2   0   0.222  -104.1412   8.5841  -26.6166
 MYN  H22   H  HCH2   0   0.217  -104.1141  11.5547  -27.3037
 MYN  H22A  H  HCH2   0   0.243  -104.9929  10.2820  -28.1330
 MYN  HN23  H  HNH1   0   0.385  -106.6990  10.8037  -26.7264
 MYN  HN26  H  HNH2   0   0.370  -106.8617  10.4420  -23.3242
 MYN  HN2A  H  HNH2   0   0.374  -107.5811  11.2134  -24.6142

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
 MYN  CA  N     single  1.458  0.019  1.458
 MYN  CA  C     single  1.525  0.021  1.525
 MYN  CA  H4    single  0.970  0.020  1.090
 MYN  N   HN5   single  0.890  0.020  1.040
 MYN  N   HNT   single  0.890  0.020  1.040
 MYN  C   O     deloc   1.231  0.020  1.231
 MYN  C   OXT   deloc   1.247  0.020  1.247
 MYN  CB  CA    single  1.530  0.020  1.530
 MYN  CB  N1    single  1.450  0.020  1.450
 MYN  CB  H20   single  0.970  0.020  1.090
 MYN  CG  CB    single  1.526  0.020  1.526
 MYN  CG  H21   single  0.970  0.020  1.090
 MYN  CG  H21A  single  0.970  0.020  1.090
 MYN  CD  CG    single  1.519  0.020  1.519
 MYN  CD  NE    single  1.452  0.020  1.452
 MYN  CD  H22   single  0.970  0.020  1.090
 MYN  CD  H22A  single  0.970  0.020  1.090
 MYN  NE  CZ    single  1.364  0.020  1.364
 MYN  NE  HN23  single  0.890  0.020  1.040
 MYN  CZ  NZ    single  1.383  0.020  1.383
 MYN  CZ  N1    double  1.281  0.020  1.281
 MYN  NZ  HN26  single  0.890  0.020  1.040
 MYN  NZ  HN2A  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
 MYN  H4    CA  CB    106.72  3.000
 MYN  CB    CA  C     110.10  1.900
 MYN  H4    CA  C     106.32  3.000
 MYN  CB    CA  N     110.50  1.700
 MYN  H4    CA  N     107.95  3.000
 MYN  C     CA  N     111.00  2.800
 MYN  HNT   N   HN5   104.29  3.000
 MYN  HNT   N   CA    107.15  3.000
 MYN  HN5   N   CA    108.19  3.000
 MYN  OXT   C   O     126.37  3.000
 MYN  OXT   C   CA    117.73  3.000
 MYN  O     C   CA    120.80  1.700
 MYN  H20   CB  N1    109.47  3.000
 MYN  H20   CB  CG    107.27  3.000
 MYN  N1    CB  CG    112.09  3.000
 MYN  CG    CB  CA    113.22  3.000
 MYN  H20   CB  CA    105.95  3.000
 MYN  N1    CB  CA    108.62  3.000
 MYN  H21A  CG  H21   107.41  3.000
 MYN  H21A  CG  CD    109.89  3.000
 MYN  H21   CG  CD    109.62  3.000
 MYN  CD    CG  CB    109.11  3.000
 MYN  H21A  CG  CB    110.16  3.000
 MYN  H21   CG  CB    110.62  3.000
 MYN  H22A  CD  H22   106.85  3.000
 MYN  H22A  CD  NE    108.53  3.000
 MYN  H22   CD  NE    110.37  3.000
 MYN  H22A  CD  CG    111.04  3.000
 MYN  H22   CD  CG    109.98  3.000
 MYN  NE    CD  CG    110.02  3.000
 MYN  HN23  NE  CZ    117.17  3.000
 MYN  HN23  NE  CD    117.24  3.000
 MYN  CZ    NE  CD    120.38  3.000
 MYN  NZ    CZ  N1    119.86  3.000
 MYN  N1    CZ  NE    125.98  3.000
 MYN  NZ    CZ  NE    114.15  3.000
 MYN  CZ    N1  CB    118.09  3.000
 MYN  HN2A  NZ  HN26  111.41  3.000
 MYN  HN2A  NZ  CZ    115.43  3.000
 MYN  HN26  NZ  CZ    112.46  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
 MYN  CONST_01  NE    CZ  N1  CB    0.00   0.0  0
 MYN  CONST_02  N1    CZ  NE  CD    0.00   0.0  0
 MYN  CONST_03  NZ    CZ  N1  CB  180.00   0.0  0
 MYN  CONST_04  NZ    CZ  NE  CD  180.00   0.0  0
 MYN  CONST_06  HN26  NZ  CZ  NE  180.00   0.0  0
 MYN  Var_01    NE    CD  CG  CB  -49.05  30.0  1
 MYN  Var_02    CZ    NE  CD  CG   20.03  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
 MYN  chir_01  CA  N   C   CB  positiv
 MYN  chir_02  CB  N1  CG  CA  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
 MYN  plan-1  CB    0.020
 MYN  plan-1  CD    0.020
 MYN  plan-1  NE    0.020
 MYN  plan-1  CZ    0.020
 MYN  plan-1  N1    0.020
 MYN  plan-1  NZ    0.020
 MYN  plan-1  HN23  0.020
 MYN  plan-1  HN26  0.020
 MYN  plan-1  HN2A  0.020
 MYN  plan-2  CA    0.020
 MYN  plan-2  C     0.020
 MYN  plan-2  O     0.020
 MYN  plan-2  OXT   0.020

