# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon May  4 14:09:49 2020
#   Inital geometry file: a 100 line input string
#   Ligand name: 2-{[(2-amino-6-oxo-1,6-dihydro-9H-purin-9-yl)acetyl](carboxymethyl)amino}ethanaminium
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: NC1=Nc2n(CC(=O)N(CC[NH3+])CC(O)=O)cnc2C(=O)N1
#
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
 GPN  GPN  2-{[(2-amino-6-oxo-1,6-dihydro-9H-purin-9-yl)acetyl](carboxymethyl)amino}ethanaminium  peptide  38  22  .  2022-03-18  2022-11-17
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_GPN
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
 GPN  C8'   C  CH2   0  -0.458  -0.4956   0.2290  -1.5621
 GPN  C7'   C  C     0   0.574  -1.2971   0.6308  -0.3267
 GPN  O7'   O  O     0  -0.465  -0.9885   1.6275   0.2983
 GPN  C5'   C  CH2   0  -0.452  -3.1068   0.2754   1.1818
 GPN  C'    C  C     0   0.553  -3.9919   1.4630   0.8662
 GPN  O1'   O  O     0  -0.431  -4.2069   1.8765  -0.2416
 GPN  OXT   O  OH1   0  -0.588  -4.5174   1.9650   1.9721
 GPN  N4'   N  NT    0  -0.453  -2.3475  -0.1394   0.0296
 GPN  C3'   C  CH2   0  -0.378  -2.7690  -1.3293  -0.6780
 GPN  C2'   C  CH2   0  -0.316  -2.0677  -2.5532  -0.1023
 GPN  N1'   N  NT3   1  -0.776  -2.5482  -3.7933  -0.7570
 GPN  N9    N  NR5   0  -0.483   0.8697   0.6307  -1.3959
 GPN  C8    C  CR15  0   0.097   1.5033   1.7386  -1.8927
 GPN  N7    N  N     0  -0.445   2.7214   1.8580  -1.4616
 GPN  C5    C  CR56  0  -0.090   2.8986   0.7866  -0.6222
 GPN  C6    C  CR6   0   0.506   4.0186   0.3850   0.1618
 GPN  O6    O  O     0  -0.472   5.1147   0.9094   0.2598
 GPN  N1    N  NR16  0  -0.728   3.7192  -0.7788   0.8853
 GPN  C2    C  CR6   0   0.694   2.5354  -1.4594   0.8732
 GPN  N2    N  NH2   0  -0.832   2.4628  -2.5696   1.6191
 GPN  N3    N  N     0  -0.513   1.5078  -1.0860   0.1498
 GPN  C4    C  CR56  0   0.508   1.7508   0.0208  -0.5646
 GPN  H8'1  H  HCH2  0   0.294  -0.5189  -0.8374  -1.7731
 GPN  H8'2  H  HCH2  0   0.335  -0.9187   0.7359  -2.4316
 GPN  H5'1  H  HCH2  0   0.309  -2.4544   0.5104   2.0236
 GPN  H5'2  H  HCH2  0   0.317  -3.7429  -0.5496   1.5086
 GPN  HXT   H  HOH1  0   0.487  -5.1058   2.7062   1.7623
 GPN  H3'1  H  HCH2  0   0.308  -3.8499  -1.4283  -0.5714
 GPN  H3'2  H  HCH2  0   0.302  -2.5856  -1.2354  -1.7479
 GPN  H2'1  H  HCH2  0   0.301  -0.9892  -2.5048  -0.2452
 GPN  H2'2  H  HCH2  0   0.312  -2.2690  -2.6566   0.9618
 GPN  H1'1  H  HNT3  0   0.486  -2.0846  -4.6153  -0.3711
 GPN  H1'2  H  HNT3  0   0.475  -3.5506  -3.9319  -0.6279
 GPN  H1'3  H  HNT3  0   0.475  -2.3688  -3.7989  -1.7611
 GPN  H8    H  HCR5  0   0.291   1.0051   2.4067  -2.5795
 GPN  HN1   H  HNR6  0   0.426   4.4657  -1.1309   1.4711
 GPN  HN21  H  HNH2  0   0.416   3.1489  -2.7657   2.3279
 GPN  HN22  H  HNH2  0   0.412   1.5599  -2.9967   1.7370

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
 GPN  C8'  C7'   single    1.526  0.020  1.526
 GPN  C8'  N9    single    1.433  0.020  1.433
 GPN  C8'  H8'1  single    0.970  0.020  1.090
 GPN  C8'  H8'2  single    0.970  0.020  1.090
 GPN  C7'  O7'   double    1.216  0.020  1.216
 GPN  C7'  N4'   single    1.350  0.020  1.350
 GPN  C5'  C'    single    1.514  0.020  1.514
 GPN  C5'  N4'   single    1.441  0.020  1.441
 GPN  C5'  H5'1  single    0.970  0.020  1.090
 GPN  C5'  H5'2  single    0.970  0.020  1.090
 GPN  C'   O1'   double    1.202  0.020  1.202
 GPN  C'   OXT   single    1.323  0.020  1.323
 GPN  OXT  HXT   single    0.850  0.020  0.980
 GPN  N4'  C3'   single    1.447  0.020  1.447
 GPN  C3'  C2'   single    1.524  0.020  1.524
 GPN  C3'  H3'1  single    0.970  0.020  1.090
 GPN  C3'  H3'2  single    0.970  0.020  1.090
 GPN  C2'  N1'   single    1.482  0.020  1.482
 GPN  C2'  H2'1  single    0.970  0.020  1.090
 GPN  C2'  H2'2  single    0.970  0.020  1.090
 GPN  N1'  H1'1  single    0.890  0.020  1.040
 GPN  N1'  H1'2  single    0.890  0.020  1.040
 GPN  N1'  H1'3  single    0.890  0.020  1.040
 GPN  N9   C8    aromatic  1.370  0.020  1.370
 GPN  N9   C4    aromatic  1.356  0.020  1.356
 GPN  C8   N7    aromatic  1.298  0.020  1.298
 GPN  C8   H8    single    0.930  0.020  1.080
 GPN  N7   C5    aromatic  1.373  0.020  1.373
 GPN  C5   C6    single    1.425  0.020  1.425
 GPN  C5   C4    aromatic  1.381  0.020  1.381
 GPN  C6   O6    double    1.219  0.020  1.219
 GPN  C6   N1    single    1.403  0.020  1.403
 GPN  N1   C2    single    1.365  0.020  1.365
 GPN  N1   HN1   single    0.860  0.020  1.020
 GPN  C2   N2    single    1.339  0.020  1.339
 GPN  C2   N3    double    1.311  0.020  1.311
 GPN  N2   HN21  single    0.890  0.020  1.040
 GPN  N2   HN22  single    0.890  0.020  1.040
 GPN  N3   C4    single    1.340  0.020  1.340

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
 GPN  H8'2  C8'  H8'1  107.01  3.000
 GPN  H8'2  C8'  N9    109.36  3.000
 GPN  H8'1  C8'  N9    108.54  3.000
 GPN  H8'2  C8'  C7'   108.59  3.000
 GPN  H8'1  C8'  C7'   113.82  3.000
 GPN  N9    C8'  C7'   109.43  3.000
 GPN  N4'   C7'  O7'   121.95  3.000
 GPN  N4'   C7'  C8'   118.16  3.000
 GPN  O7'   C7'  C8'   119.89  3.000
 GPN  H5'2  C5'  H5'1  106.28  3.000
 GPN  H5'2  C5'  N4'   109.20  3.000
 GPN  H5'1  C5'  N4'   111.34  3.000
 GPN  H5'2  C5'  C'    108.33  3.000
 GPN  H5'1  C5'  C'    109.97  3.000
 GPN  N4'   C5'  C'    111.53  3.000
 GPN  OXT   C'   O1'   124.66  3.000
 GPN  OXT   C'   C5'   110.82  3.000
 GPN  O1'   C'   C5'   124.51  3.000
 GPN  HXT   OXT  C'    110.50  3.000
 GPN  C3'   N4'  C5'   118.31  3.000
 GPN  C3'   N4'  C7'   124.51  3.000
 GPN  C5'   N4'  C7'   117.18  3.000
 GPN  H3'2  C3'  H3'1  105.70  3.000
 GPN  H3'2  C3'  C2'   111.27  3.000
 GPN  H3'1  C3'  C2'   110.26  3.000
 GPN  H3'2  C3'  N4'   111.12  3.000
 GPN  H3'1  C3'  N4'   108.39  3.000
 GPN  C2'   C3'  N4'   109.98  3.000
 GPN  H2'2  C2'  H2'1  108.41  3.000
 GPN  H2'2  C2'  N1'   107.00  3.000
 GPN  H2'1  C2'  N1'   107.47  3.000
 GPN  H2'2  C2'  C3'   111.15  3.000
 GPN  H2'1  C2'  C3'   111.75  3.000
 GPN  N1'   C2'  C3'   110.85  3.000
 GPN  H1'3  N1'  H1'2  107.26  3.000
 GPN  H1'3  N1'  H1'1  106.75  3.000
 GPN  H1'2  N1'  H1'1  106.82  3.000
 GPN  H1'3  N1'  C2'   112.48  3.000
 GPN  H1'2  N1'  C2'   112.10  3.000
 GPN  H1'1  N1'  C2'   111.09  3.000
 GPN  C4    N9   C8    106.59  3.000
 GPN  C4    N9   C8'   124.33  3.000
 GPN  C8    N9   C8'   128.72  3.000
 GPN  H8    C8   N7    125.97  3.000
 GPN  H8    C8   N9    121.18  3.000
 GPN  N7    C8   N9    112.84  3.000
 GPN  C5    N7   C8    104.63  3.000
 GPN  C4    C5   C6    118.30  3.000
 GPN  C4    C5   N7    110.55  3.000
 GPN  C6    C5   N7    131.14  3.000
 GPN  N1    C6   O6    120.49  3.000
 GPN  N1    C6   C5    110.48  3.000
 GPN  O6    C6   C5    129.03  3.000
 GPN  HN1   N1   C2    118.11  3.000
 GPN  HN1   N1   C6    115.45  3.000
 GPN  C2    N1   C6    126.44  3.000
 GPN  N3    C2   N2    120.05  3.000
 GPN  N3    C2   N1    122.85  3.000
 GPN  N2    C2   N1    117.08  3.000
 GPN  HN22  N2   HN21  116.55  3.000
 GPN  HN22  N2   C2    117.77  3.000
 GPN  HN21  N2   C2    121.14  3.000
 GPN  C4    N3   C2    112.79  3.000
 GPN  N3    C4   C5    129.14  3.000
 GPN  N3    C4   N9    125.50  3.000
 GPN  C5    C4   N9    105.36  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
 GPN  CONST_01  C5    N7   C8   N9      0.00   0.0  0
 GPN  CONST_02  N7    C5   C4   N9      0.00   0.0  0
 GPN  CONST_03  C5    C4   N9   C8      0.00   0.0  0
 GPN  CONST_04  C4    C5   N7   C8      0.00   0.0  0
 GPN  CONST_05  C4    N9   C8   N7      0.00   0.0  0
 GPN  CONST_06  C2    N1   C6   C5      0.00   0.0  0
 GPN  CONST_07  N3    C2   N1   C6      0.00   0.0  0
 GPN  CONST_08  C4    N3   C2   N1      0.00   0.0  0
 GPN  CONST_09  N7    C8   N9   C8'   180.00   0.0  0
 GPN  CONST_10  C5    C4   N9   C8'   180.00   0.0  0
 GPN  CONST_11  N3    C4   N9   C8'     0.00   0.0  0
 GPN  CONST_12  N2    C2   N1   C6    180.00   0.0  0
 GPN  CONST_13  C2    N1   C6   O6    180.00   0.0  0
 GPN  CONST_14  C4    N3   C2   N2    180.00   0.0  0
 GPN  CONST_15  H8    C8   N7   C5    180.00   0.0  0
 GPN  CONST_16  HN1   N1   C6   C5    180.00   0.0  0
 GPN  CONST_18  HN22  N2   C2   N1    180.00   0.0  0
 GPN  CONST_19  C5'   N4'  C7'  C8'   180.00   0.0  0
 GPN  CONST_20  C3'   N4'  C7'  C8'     0.00   0.0  0
 GPN  CONST_21  C5'   N4'  C7'  O7'     0.00   0.0  0
 GPN  CONST_22  C3'   N4'  C7'  O7'   180.00   0.0  0
 GPN  CONST_23  HXT   OXT  C'   C5'   180.00   0.0  0
 GPN  Var_01    C8    N9   C8'  C7'   -99.03  30.0  2
 GPN  Var_02    N9    C8'  C7'  O7'    31.53  30.0  2
 GPN  Var_03    C'    C5'  N4'  C7'    74.92  30.0  2
 GPN  Var_04    C2'   C3'  N4'  C7'    90.46  30.0  3
 GPN  Var_05    N4'   C5'  C'   O1'    11.29  30.0  2
 GPN  Var_06    N1'   C2'  C3'  N4'   176.49  30.0  3
 GPN  Var_07    H1'1  N1'  C2'  C3'  -179.71  30.0  3

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
 GPN  plan-1  C8'   0.020
 GPN  plan-1  N9    0.020
 GPN  plan-1  C8    0.020
 GPN  plan-1  N7    0.020
 GPN  plan-1  C5    0.020
 GPN  plan-1  C6    0.020
 GPN  plan-1  O6    0.020
 GPN  plan-1  N1    0.020
 GPN  plan-1  C2    0.020
 GPN  plan-1  N2    0.020
 GPN  plan-1  N3    0.020
 GPN  plan-1  C4    0.020
 GPN  plan-1  H8    0.020
 GPN  plan-1  HN1   0.020
 GPN  plan-1  HN21  0.020
 GPN  plan-1  HN22  0.020
 GPN  plan-2  C8'   0.020
 GPN  plan-2  C7'   0.020
 GPN  plan-2  O7'   0.020
 GPN  plan-2  C5'   0.020
 GPN  plan-2  N4'   0.020
 GPN  plan-2  C3'   0.020
 GPN  plan-3  C5'   0.020
 GPN  plan-3  C'    0.020
 GPN  plan-3  O1'   0.020
 GPN  plan-3  OXT   0.020
 GPN  plan-3  HXT   0.020

