# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Mar  9 11:18:17 2022
#   Inital geometry file: a 75 line input string
#   Ligand name: 3-(2-amino-6-oxo-1,6-dihydro-9H-purin-9-yl)-D-alanine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: N[C@H](Cn1cnc2C(=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
 AGD  AGD  3-(2-amino-6-oxo-1,6-dihydro-9H-purin-9-yl)-D-alanine  D-peptide  26  17  .  2016-04-22  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_AGD
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
 AGD  C2    C  CR6    0   0.680   -6.7145  -15.2120   5.5319
 AGD  C4    C  CR56   0   0.474   -8.1107  -16.9207   5.7224
 AGD  C5    C  CR56   0  -0.089   -7.6117  -17.6155   4.6336
 AGD  C6    C  CR6    0   0.495   -6.5271  -17.0545   3.9004
 AGD  N     N  NH2    0  -0.783   -8.0098  -17.9871   8.9460
 AGD  CA    C  CH1    0  -0.227   -9.4001  -18.2223   8.6226
 AGD  N9    N  NR5    0  -0.488   -9.1180  -17.6892   6.2102
 AGD  N3    N  N      0  -0.506   -7.7059  -15.7355   6.2060
 AGD  N2    N  NH2    0  -0.833   -6.2331  -14.0060   5.8769
 AGD  N1    N  NR16   0  -0.726   -6.1476  -15.8208   4.4473
 AGD  O6    O  O      0  -0.468   -5.9464  -17.5056   2.9277
 AGD  N7    N  N      0  -0.444   -8.2933  -18.7906   4.4558
 AGD  C8    C  CR15   0   0.088   -9.1741  -18.7995   5.4108
 AGD  C     C  C      0   0.407  -10.3456  -17.8911   9.8080
 AGD  O     O  O      0  -0.610  -11.5310  -18.2471   9.6515
 AGD  OXT   O  OC    -1  -0.588   -9.8600  -17.2844  10.7782
 AGD  HN1   H  HNR6   0   0.422   -5.3832  -15.3537   3.9758
 AGD  HA    H  HCH1   0   0.226   -9.5139  -19.2896   8.3989
 AGD  HN2   H  HNH2   0   0.412   -5.3445  -13.6837   5.5321
 AGD  HN2A  H  HNH2   0   0.409   -6.5315  -13.6254   6.7593
 AGD  H8    H  HCR5   0   0.283   -9.9020  -19.5776   5.5899
 AGD  CB    C  CH2    0  -0.323   -9.9157  -17.4469   7.3972
 AGD  HN    H  HNH2   0   0.339   -7.4200  -18.1456   8.1387
 AGD  HB    H  HCH2   0   0.262  -10.9451  -17.7263   7.1795
 AGD  HBA   H  HCH2   0   0.258   -9.8941  -16.3731   7.5890
 AGD  HNA   H  HNH2   0   0.329   -7.8784  -17.0227   9.2234

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
 AGD  N1    C2   single    1.367  0.020  1.367
 AGD  C2    N2   single    1.344  0.020  1.344
 AGD  C2    N3   double    1.308  0.020  1.308
 AGD  C5    C4   aromatic  1.385  0.020  1.385
 AGD  C4    N3   single    1.343  0.020  1.343
 AGD  C4    N9   aromatic  1.358  0.020  1.358
 AGD  C6    C5   single    1.424  0.020  1.424
 AGD  N7    C5   aromatic  1.370  0.020  1.370
 AGD  O6    C6   double    1.219  0.020  1.219
 AGD  C6    N1   single    1.402  0.020  1.402
 AGD  CA    N    single    1.458  0.019  1.458
 AGD  N     HN   single    0.890  0.020  1.040
 AGD  N     HNA  single    0.890  0.020  1.040
 AGD  CB    CA   single    1.521  0.033  1.521
 AGD  HA    CA   single    0.970  0.020  0.970
 AGD  CA    C    single    1.525  0.021  1.525
 AGD  N9    CB   single    1.451  0.020  1.451
 AGD  HB    CB   single    0.970  0.020  1.090
 AGD  CB    HBA  single    0.970  0.020  1.090
 AGD  C8    N9   aromatic  1.369  0.020  1.369
 AGD  HN2A  N2   single    0.890  0.020  1.040
 AGD  N2    HN2  single    0.890  0.020  1.040
 AGD  HN1   N1   single    0.860  0.020  1.020
 AGD  N7    C8   aromatic  1.299  0.020  1.299
 AGD  C8    H8   single    0.930  0.020  1.080
 AGD  O     C    deloc     1.231  0.020  1.231
 AGD  C     OXT  deloc     1.243  0.020  1.243

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
 AGD  N1    C2  N2   117.06  3.000
 AGD  N2    C2  N3   119.90  3.000
 AGD  N1    C2  N3   123.02  3.000
 AGD  N3    C4  N9   126.44  3.000
 AGD  N9    C4  C5   105.42  3.000
 AGD  N3    C4  C5   128.14  3.000
 AGD  N7    C5  C6   130.53  3.000
 AGD  N7    C5  C4   110.68  3.000
 AGD  C6    C5  C4   118.79  3.000
 AGD  O6    C6  N1   120.53  3.000
 AGD  N1    C6  C5   110.60  3.000
 AGD  O6    C6  C5   128.87  3.000
 AGD  HNA   N   HN   106.99  3.000
 AGD  HNA   N   CA   109.93  3.000
 AGD  HN    N   CA   110.87  3.000
 AGD  HA    CA  C    110.00  3.000
 AGD  C     CA  CB   110.50  1.500
 AGD  HA    CA  CB   109.00  3.000
 AGD  C     CA  N    111.00  2.800
 AGD  HA    CA  N    110.00  3.000
 AGD  CB    CA  N    110.40  1.500
 AGD  C8    N9  CB   126.20  3.000
 AGD  C8    N9  C4   106.24  3.000
 AGD  CB    N9  C4   127.41  3.000
 AGD  C4    N3  C2   113.34  3.000
 AGD  HN2A  N2  HN2  116.19  3.000
 AGD  HN2   N2  C2   121.06  3.000
 AGD  HN2A  N2  C2   117.28  3.000
 AGD  HN1   N1  C6   115.39  3.000
 AGD  HN1   N1  C2   118.50  3.000
 AGD  C6    N1  C2   126.11  3.000
 AGD  C8    N7  C5   104.34  3.000
 AGD  H8    C8  N7   125.70  3.000
 AGD  H8    C8  N9   120.98  3.000
 AGD  N7    C8  N9   113.32  3.000
 AGD  OXT   C   O    127.47  3.000
 AGD  OXT   C   CA   120.80  1.700
 AGD  O     C   CA   120.80  1.700
 AGD  HBA   CB  HB   107.85  3.000
 AGD  HBA   CB  N9   107.30  3.000
 AGD  HB    CB  N9   108.27  3.000
 AGD  HBA   CB  CA   110.44  3.000
 AGD  HB    CB  CA   110.29  3.000
 AGD  N9    CB  CA   112.53  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
 AGD  CONST_01  C8    N7  C5  C4    0.00   0.0  0
 AGD  CONST_02  N7    C8  N9  C4    0.00   0.0  0
 AGD  CONST_03  C8    N9  C4  C5    0.00   0.0  0
 AGD  CONST_04  N9    C8  N7  C5    0.00   0.0  0
 AGD  CONST_05  N7    C5  C4  N9    0.00   0.0  0
 AGD  CONST_06  C5    C6  N1  C2    0.00   0.0  0
 AGD  CONST_07  N1    C2  N3  C4    0.00   0.0  0
 AGD  CONST_08  N3    C2  N1  C6    0.00   0.0  0
 AGD  CONST_09  CB    N9  C4  C5  180.00   0.0  0
 AGD  CONST_10  N3    C4  N9  CB    0.00   0.0  0
 AGD  CONST_11  N7    C8  N9  CB  180.00   0.0  0
 AGD  CONST_12  O6    C6  N1  C2  180.00   0.0  0
 AGD  CONST_13  N2    C2  N3  C4  180.00   0.0  0
 AGD  CONST_14  N2    C2  N1  C6  180.00   0.0  0
 AGD  CONST_15  H8    C8  N9  C4  180.00   0.0  0
 AGD  CONST_16  HN1   N1  C6  C5  180.00   0.0  0
 AGD  CONST_17  HN2A  N2  C2  N3    0.00   0.0  0
 AGD  Var_01    CA    CB  N9  C4  -97.04  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
 AGD  chir_01  CA  N  CB  C  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
 AGD  plan-1  C2    0.020
 AGD  plan-1  C4    0.020
 AGD  plan-1  C5    0.020
 AGD  plan-1  C6    0.020
 AGD  plan-1  N9    0.020
 AGD  plan-1  N3    0.020
 AGD  plan-1  N2    0.020
 AGD  plan-1  N1    0.020
 AGD  plan-1  O6    0.020
 AGD  plan-1  N7    0.020
 AGD  plan-1  C8    0.020
 AGD  plan-1  HN1   0.020
 AGD  plan-1  HN2   0.020
 AGD  plan-1  HN2A  0.020
 AGD  plan-1  H8    0.020
 AGD  plan-1  CB    0.020
 AGD  plan-2  CA    0.020
 AGD  plan-2  C     0.020
 AGD  plan-2  O     0.020
 AGD  plan-2  OXT   0.020

