# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Mar 12 05:09:36 2022
#   Inital geometry file: a 81 line input string
#   Ligand name: (2S)-2-amino-4-(2-amino-6-oxo-1,6-dihydro-9H-purin-9-yl)butanoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: N[C@@H](CCn1cnc2C(=O)NC(=Nc12)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
 HGL  HGL  '(2S)-2-amino-4-(2-amino-6-oxo-1,6-dihydro-9H-purin-9-yl)butanoic acid'  L-peptide  29  18  .  2012-08-28  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_HGL
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
 HGL  C2    C  CR6    0   0.677  -2.0562  -15.5608   6.1146
 HGL  O6    O  O      0  -0.467  -0.6972  -17.2918   3.3236
 HGL  C4    C  CR56   0   0.493  -3.3334  -17.3305   5.7490
 HGL  C5    C  CR56   0  -0.088  -2.6045  -17.7978   4.6690
 HGL  C6    C  CR6    0   0.495  -1.4604  -17.0607   4.2459
 HGL  C8    C  CR15   0   0.089  -4.1898  -19.1632   4.9373
 HGL  N     N  NH2    0  -0.797  -5.2363  -18.8761  10.7295
 HGL  CA    C  CH1    0  -0.179  -5.8084  -18.4775   9.4522
 HGL  CB    C  CH2    0  -0.460  -4.8498  -18.7092   8.2726
 HGL  CG    C  CH2    0  -0.312  -5.3704  -18.1801   6.9417
 HGL  N9    N  NR5    0  -0.488  -4.3518  -18.2125   5.9076
 HGL  N3    N  N      0  -0.511  -3.1082  -16.2387   6.4967
 HGL  N2    N  NH2    0  -0.832  -1.7287  -14.4199   6.7437
 HGL  N1    N  NR16   0  -0.726  -1.2713  -15.9353   5.0608
 HGL  N7    N  N      0  -0.447  -3.1595  -18.9496   4.1744
 HGL  C     C  C      0   0.403  -7.1340  -19.2327   9.2018
 HGL  O     O  O      0  -0.600  -7.1845  -20.4110   9.6077
 HGL  OXT   O  OC    -1  -0.606  -8.0202  -18.6157   8.5775
 HGL  HN1   H  HNR6   0   0.422  -0.4771  -15.3542   4.8219
 HGL  HA    H  HCH1   0   0.200  -6.0253  -17.4042   9.4931
 HGL  HB    H  HCH2   0   0.223  -4.6311  -19.7780   8.1826
 HGL  HBA   H  HCH2   0   0.233  -3.9020  -18.2105   8.4993
 HGL  HG    H  HCH2   0   0.267  -6.2162  -18.7631   6.5827
 HGL  HGA   H  HCH2   0   0.254  -5.7125  -17.1497   7.0456
 HGL  HN2   H  HNH2   0   0.409  -2.1953  -14.2232   7.6133
 HGL  HN2A  H  HNH2   0   0.412  -0.8162  -14.0116   6.6307
 HGL  H8    H  HCR5   0   0.282  -4.8798  -19.9897   4.8479
 HGL  HN    H  HNH2   0   0.326  -5.2215  -19.8883  10.7643
 HGL  HNA   H  HNH2   0   0.329  -4.2722  -18.5701  10.7900

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
 HGL  N1    C2   single    1.366  0.020  1.366
 HGL  C2    N3   double    1.308  0.020  1.308
 HGL  C2    N2   single    1.343  0.020  1.343
 HGL  O6    C6   double    1.219  0.020  1.219
 HGL  C5    C4   aromatic  1.384  0.020  1.384
 HGL  C4    N9   aromatic  1.357  0.020  1.357
 HGL  C4    N3   single    1.342  0.020  1.342
 HGL  N7    C5   aromatic  1.371  0.020  1.371
 HGL  C6    C5   single    1.425  0.020  1.425
 HGL  C6    N1   single    1.402  0.020  1.402
 HGL  N7    C8   aromatic  1.300  0.020  1.300
 HGL  C8    H8   single    0.930  0.020  1.080
 HGL  C8    N9   aromatic  1.368  0.020  1.368
 HGL  CA    N    single    1.458  0.019  1.458
 HGL  HN    N    single    0.890  0.020  1.040
 HGL  N     HNA  single    0.890  0.020  1.040
 HGL  CB    CA   single    1.521  0.033  1.521
 HGL  C     CA   single    1.525  0.021  1.525
 HGL  CA    HA   single    0.970  0.020  0.970
 HGL  CG    CB   single    1.524  0.020  1.524
 HGL  HBA   CB   single    0.970  0.020  1.090
 HGL  CB    HB   single    0.970  0.020  1.090
 HGL  N9    CG   single    1.452  0.020  1.452
 HGL  HG    CG   single    0.970  0.020  1.090
 HGL  CG    HGA  single    0.970  0.020  1.090
 HGL  HN2A  N2   single    0.890  0.020  1.040
 HGL  N2    HN2  single    0.890  0.020  1.040
 HGL  HN1   N1   single    0.860  0.020  1.020
 HGL  OXT   C    deloc     1.247  0.020  1.247
 HGL  O     C    deloc     1.231  0.020  1.231

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
 HGL  N1    C2  N2   116.99  3.000
 HGL  N2    C2  N3   119.95  3.000
 HGL  N1    C2  N3   123.03  3.000
 HGL  N3    C4  N9   126.13  3.000
 HGL  N3    C4  C5   128.38  3.000
 HGL  N9    C4  C5   105.49  3.000
 HGL  N7    C5  C6   130.72  3.000
 HGL  C6    C5  C4   118.67  3.000
 HGL  N7    C5  C4   110.61  3.000
 HGL  N1    C6  C5   110.54  3.000
 HGL  N1    C6  O6   120.48  3.000
 HGL  C5    C6  O6   128.98  3.000
 HGL  H8    C8  N7   125.70  3.000
 HGL  H8    C8  N9   120.98  3.000
 HGL  N7    C8  N9   113.33  3.000
 HGL  HNA   N   HN   106.61  3.000
 HGL  HNA   N   CA   110.11  3.000
 HGL  HN    N   CA   108.04  3.000
 HGL  HA    CA  C    110.00  3.000
 HGL  HA    CA  CB   109.00  3.000
 HGL  C     CA  CB   110.50  1.500
 HGL  HA    CA  N    110.00  3.000
 HGL  C     CA  N    111.00  2.800
 HGL  CB    CA  N    110.40  1.500
 HGL  HBA   CB  HB   106.79  3.000
 HGL  HB    CB  CG   109.60  3.000
 HGL  HBA   CB  CG   108.57  3.000
 HGL  HB    CB  CA   109.56  3.000
 HGL  HBA   CB  CA   108.19  3.000
 HGL  CG    CB  CA   113.88  3.000
 HGL  HGA   CG  HG   107.09  3.000
 HGL  HGA   CG  N9   108.00  3.000
 HGL  HG    CG  N9   107.36  3.000
 HGL  HGA   CG  CB   110.60  3.000
 HGL  HG    CG  CB   111.56  3.000
 HGL  N9    CG  CB   112.00  3.000
 HGL  CG    N9  C8   127.14  3.000
 HGL  CG    N9  C4   126.55  3.000
 HGL  C8    N9  C4   106.26  3.000
 HGL  C4    N3  C2   113.18  3.000
 HGL  HN2A  N2  HN2  116.00  3.000
 HGL  HN2   N2  C2   117.24  3.000
 HGL  HN2A  N2  C2   120.87  3.000
 HGL  HN1   N1  C6   115.42  3.000
 HGL  HN1   N1  C2   118.37  3.000
 HGL  C6    N1  C2   126.20  3.000
 HGL  C8    N7  C5   104.31  3.000
 HGL  OXT   C   O    126.97  3.000
 HGL  O     C   CA   120.80  1.700
 HGL  OXT   C   CA   120.80  1.700

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
 HGL  CONST_01  C8   N7  C5  C4    0.00   0.0  0
 HGL  CONST_02  N7   C8  N9  C4    0.00   0.0  0
 HGL  CONST_03  C8   N9  C4  C5    0.00   0.0  0
 HGL  CONST_04  N9   C8  N7  C5    0.00   0.0  0
 HGL  CONST_05  N7   C5  C4  N9    0.00   0.0  0
 HGL  CONST_06  C5   C6  N1  C2    0.00   0.0  0
 HGL  CONST_07  N1   C2  N3  C4    0.00   0.0  0
 HGL  CONST_08  N3   C2  N1  C6    0.00   0.0  0
 HGL  CONST_09  CG   N9  C4  C5  180.00   0.0  0
 HGL  CONST_10  N3   C4  N9  CG    0.00   0.0  0
 HGL  CONST_11  N7   C8  N9  CG  180.00   0.0  0
 HGL  CONST_12  O6   C6  N1  C2  180.00   0.0  0
 HGL  CONST_13  N2   C2  N3  C4  180.00   0.0  0
 HGL  CONST_14  N2   C2  N1  C6  180.00   0.0  0
 HGL  CONST_15  H8   C8  N9  C4  180.00   0.0  0
 HGL  CONST_16  HN1  N1  C6  C5  180.00   0.0  0
 HGL  CONST_18  HN2  N2  C2  N3    0.00   0.0  0
 HGL  Var_01    CB   CG  N9  C4  -78.25  30.0  2
 HGL  Var_02    N9   CG  CB  CA  170.24  30.0  2

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
 HGL  chir_01  CA  N  CB  C  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
 HGL  plan-1  C2    0.020
 HGL  plan-1  O6    0.020
 HGL  plan-1  C4    0.020
 HGL  plan-1  C5    0.020
 HGL  plan-1  C6    0.020
 HGL  plan-1  C8    0.020
 HGL  plan-1  CG    0.020
 HGL  plan-1  N9    0.020
 HGL  plan-1  N3    0.020
 HGL  plan-1  N2    0.020
 HGL  plan-1  N1    0.020
 HGL  plan-1  N7    0.020
 HGL  plan-1  HN1   0.020
 HGL  plan-1  HN2   0.020
 HGL  plan-1  HN2A  0.020
 HGL  plan-1  H8    0.020
 HGL  plan-2  CA    0.020
 HGL  plan-2  C     0.020
 HGL  plan-2  O     0.020
 HGL  plan-2  OXT   0.020

