# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Apr 26 00:26:16 2020
#   Inital geometry file: a 104 line input string
#   Ligand name: N-[(2-amino-6-oxo-1,6-dihydro-9H-purin-9-yl)acetyl]-N-[(2S)-2-aminopropyl]glycine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[C@H](N)CN(CC(O)=O)C(=O)Cn1cnc2C(=O)NC(=Nc12)N
#
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
 40G  40G  N-[(2-amino-6-oxo-1,6-dihydro-9H-purin-9-yl)acetyl]-N-[(2S)-2-aminopropyl]glycine  peptide  40  23  .  2022-03-10  2022-11-17
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_40G
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
 40G  C'    C  C     0   0.551   3.6383   1.6467   0.6959
 40G  N1    N  NR16  0  -0.728  -4.4705  -0.5484   0.4596
 40G  C2    C  CR6   0   0.694  -3.4316  -0.9944   1.2267
 40G  N2    N  NH2   0  -0.836  -3.6950  -1.9804   2.0913
 40G  N3    N  N     0  -0.511  -2.2259  -0.4847   1.1603
 40G  C4    C  CR56  0   0.502  -2.1291   0.5177   0.2779
 40G  C5    C  CR56  0  -0.094  -3.1119   1.0485  -0.5376
 40G  C6    C  CR6   0   0.501  -4.4211   0.4924  -0.4772
 40G  O6    O  O     0  -0.476  -5.4172   0.8049  -1.1086
 40G  N7    N  N     0  -0.444  -2.6082   2.0714  -1.3008
 40G  C8    C  CR15  0   0.095  -1.3614   2.1523  -0.9529
 40G  N9    N  NR5   0  -0.486  -1.0157   1.2484   0.0170
 40G  N1'   N  NH2   0  -0.773   1.9648  -3.1425  -0.0538
 40G  O1'   O  O     0  -0.430   3.4728   2.2224  -0.3469
 40G  C2'   C  CH1   0  -0.103   3.2700  -2.5593  -0.3158
 40G  C2M   C  CH3   0  -0.667   4.1580  -3.3876  -1.2417
 40G  C3'   C  CH2   0  -0.308   3.1047  -1.1587  -0.9012
 40G  N4'   N  NT    0  -0.438   2.3138  -0.2734  -0.0646
 40G  C5'   C  CH2   0  -0.479   2.9914   0.3221   1.0528
 40G  C7'   C  C     0   0.565   1.0402   0.0167  -0.3964
 40G  O7'   O  O     0  -0.475   0.4746  -0.4452  -1.3702
 40G  C8'   C  CH2   0  -0.465   0.3015   0.9951   0.5192
 40G  HN1   H  HNR6  0   0.424  -5.3711  -0.9980   0.5651
 40G  H8    H  HCR5  0   0.287  -0.6404   2.8530  -1.3478
 40G  H22'  H  HCH1  0   0.224   3.7805  -2.4731   0.6505
 40G  HN2   H  HNH2  0   0.417  -4.5662  -2.4817   2.0808
 40G  HN2A  H  HNH2  0   0.414  -2.9301  -2.3911   2.5978
 40G  H13'  H  HCH2  0   0.256   4.0886  -0.7077  -1.0537
 40G  H23'  H  HCH2  0   0.257   2.6375  -1.2253  -1.8835
 40G  H15'  H  HCH2  0   0.322   3.7634  -0.3603   1.4151
 40G  H25'  H  HCH2  0   0.319   2.3304   0.4698   1.9093
 40G  H18'  H  HCH2  0   0.310   0.8330   1.9442   0.5944
 40G  H28'  H  HCH2  0   0.313   0.2163   0.5927   1.5299
 40G  H2M   H  HCH3  0   0.234   4.3445  -4.3732  -0.8134
 40G  H2MA  H  HCH3  0   0.220   3.6780  -3.5305  -2.2128
 40G  H2MB  H  HCH3  0   0.222   5.1255  -2.9119  -1.4126
 40G  OXT   O  OH1   0  -0.585   4.3971   2.0876   1.6860
 40G  HNXT  H  HNH2  0   0.345   2.0859  -4.0723   0.3294
 40G  HXT   H  HOH1  0   0.488   4.7856   2.9454   1.4566
 40G  HN1'  H  HNH2  0   0.334   1.4671  -3.2657  -0.9284

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
 40G  C'    C5'   single    1.517  0.020  1.517
 40G  C'    O1'   double    1.203  0.020  1.203
 40G  C'    OXT   single    1.323  0.020  1.323
 40G  N1    C2    single    1.366  0.020  1.366
 40G  C2    N3    double    1.311  0.020  1.311
 40G  N2    C2    single    1.338  0.020  1.338
 40G  N2    HN2   single    0.860  0.020  1.020
 40G  C4    N3    single    1.339  0.020  1.339
 40G  C4    N9    aromatic  1.357  0.020  1.357
 40G  C5    C4    aromatic  1.383  0.020  1.383
 40G  C5    N7    aromatic  1.372  0.020  1.372
 40G  C6    N1    single    1.401  0.020  1.401
 40G  C6    C5    single    1.424  0.020  1.424
 40G  O6    C6    double    1.220  0.020  1.220
 40G  N7    C8    aromatic  1.297  0.020  1.297
 40G  C8    N9    aromatic  1.370  0.020  1.370
 40G  C8    H8    single    0.930  0.020  1.080
 40G  N9    C8'   single    1.432  0.020  1.432
 40G  N1'   C2'   single    1.453  0.020  1.453
 40G  N1'   HNXT  single    0.890  0.020  1.040
 40G  C2'   H22'  single    0.970  0.020  1.090
 40G  C2'   C2M   single    1.527  0.020  1.527
 40G  C2M   H2MA  single    0.970  0.020  1.090
 40G  C2M   H2M   single    0.970  0.020  1.090
 40G  C3'   C2'   single    1.527  0.020  1.527
 40G  C3'   H23'  single    0.970  0.020  1.090
 40G  N4'   C3'   single    1.452  0.020  1.452
 40G  N4'   C5'   single    1.436  0.020  1.436
 40G  C5'   H25'  single    0.970  0.020  1.090
 40G  C7'   N4'   single    1.348  0.020  1.348
 40G  O7'   C7'   double    1.217  0.020  1.217
 40G  C8'   C7'   single    1.530  0.020  1.530
 40G  C8'   H28'  single    0.970  0.020  1.090
 40G  C8'   H18'  single    0.970  0.020  1.090
 40G  HN1   N1    single    0.860  0.020  1.020
 40G  HN1'  N1'   single    0.890  0.020  1.040
 40G  HN2A  N2    single    0.860  0.020  1.020
 40G  H13'  C3'   single    0.970  0.020  1.090
 40G  H15'  C5'   single    0.970  0.020  1.090
 40G  H2MB  C2M   single    0.970  0.020  1.090
 40G  OXT   HXT   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
 40G  OXT   C'   C5'   111.07  3.000
 40G  OXT   C'   O1'   124.63  3.000
 40G  C5'   C'   O1'   124.29  3.000
 40G  HN1   N1   C6    115.53  3.000
 40G  HN1   N1   C2    118.23  3.000
 40G  C6    N1   C2    126.23  3.000
 40G  N3    C2   N2    120.04  3.000
 40G  N2    C2   N1    116.99  3.000
 40G  N3    C2   N1    122.96  3.000
 40G  HN2A  N2   HN2   117.46  3.000
 40G  HN2A  N2   C2    118.49  3.000
 40G  HN2   N2   C2    122.11  3.000
 40G  C4    N3   C2    113.02  3.000
 40G  N9    C4   C5    105.25  3.000
 40G  C5    C4   N3    128.65  3.000
 40G  N9    C4   N3    126.09  3.000
 40G  N7    C5   C6    130.73  3.000
 40G  C6    C5   C4    118.59  3.000
 40G  N7    C5   C4    110.69  3.000
 40G  O6    C6   C5    128.96  3.000
 40G  O6    C6   N1    120.49  3.000
 40G  C5    C6   N1    110.54  3.000
 40G  C8    N7   C5    104.49  3.000
 40G  H8    C8   N9    121.22  3.000
 40G  H8    C8   N7    125.74  3.000
 40G  N9    C8   N7    113.04  3.000
 40G  C8'   N9   C8    126.65  3.000
 40G  C8'   N9   C4    126.29  3.000
 40G  C8    N9   C4    106.52  3.000
 40G  HNXT  N1'  HN1'  105.87  3.000
 40G  HN1'  N1'  C2'   109.52  3.000
 40G  HNXT  N1'  C2'   109.22  3.000
 40G  H22'  C2'  C3'   108.43  3.000
 40G  C3'   C2'  C2M   109.15  3.000
 40G  H22'  C2'  C2M   107.84  3.000
 40G  C3'   C2'  N1'   109.87  3.000
 40G  C2M   C2'  N1'   114.45  3.000
 40G  H22'  C2'  N1'   106.91  3.000
 40G  H2MB  C2M  H2MA  107.89  3.000
 40G  H2MB  C2M  H2M   107.68  3.000
 40G  H2MA  C2M  H2M   107.81  3.000
 40G  H2MB  C2M  C2'   111.96  3.000
 40G  H2M   C2M  C2'   110.58  3.000
 40G  H2MA  C2M  C2'   110.76  3.000
 40G  H23'  C3'  H13'  106.58  3.000
 40G  H13'  C3'  N4'   108.60  3.000
 40G  H23'  C3'  N4'   108.85  3.000
 40G  H13'  C3'  C2'   109.54  3.000
 40G  N4'   C3'  C2'   113.41  3.000
 40G  H23'  C3'  C2'   109.63  3.000
 40G  C7'   N4'  C5'   123.24  3.000
 40G  C7'   N4'  C3'   120.27  3.000
 40G  C5'   N4'  C3'   116.36  3.000
 40G  H25'  C5'  H15'  104.61  3.000
 40G  H15'  C5'  N4'   109.42  3.000
 40G  H25'  C5'  N4'   112.39  3.000
 40G  H15'  C5'  C'    108.79  3.000
 40G  H25'  C5'  C'    108.94  3.000
 40G  N4'   C5'  C'    112.35  3.000
 40G  C8'   C7'  O7'   119.80  3.000
 40G  C8'   C7'  N4'   116.52  3.000
 40G  O7'   C7'  N4'   123.67  3.000
 40G  H28'  C8'  H18'  107.17  3.000
 40G  H18'  C8'  C7'   111.26  3.000
 40G  H28'  C8'  C7'   110.86  3.000
 40G  H18'  C8'  N9    108.57  3.000
 40G  H28'  C8'  N9    108.55  3.000
 40G  C7'   C8'  N9    110.32  3.000
 40G  HXT   OXT  C'    110.35  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
 40G  CONST_01  N7    C8   N9   C4     0.00   0.0  0
 40G  CONST_02  C8    N7   C5   C4     0.00   0.0  0
 40G  CONST_03  C8    N9   C4   C5     0.00   0.0  0
 40G  CONST_04  N9    C8   N7   C5     0.00   0.0  0
 40G  CONST_05  N9    C4   C5   N7     0.00   0.0  0
 40G  CONST_06  C4    N3   C2   N1     0.00   0.0  0
 40G  CONST_07  C5    C6   N1   C2     0.00   0.0  0
 40G  CONST_08  C6    N1   C2   N3     0.00   0.0  0
 40G  CONST_09  C8'   N9   C4   N3     0.00   0.0  0
 40G  CONST_10  C8'   N9   C4   C5   180.00   0.0  0
 40G  CONST_11  C8'   N9   C8   N7   180.00   0.0  0
 40G  CONST_12  O6    C6   N1   C2   180.00   0.0  0
 40G  CONST_13  C6    N1   C2   N2   180.00   0.0  0
 40G  CONST_14  C4    N3   C2   N2   180.00   0.0  0
 40G  CONST_15  H8    C8   N9   C4   180.00   0.0  0
 40G  CONST_16  HN1   N1   C2   N3   180.00   0.0  0
 40G  CONST_17  HN2   N2   C2   N1     0.00   0.0  0
 40G  CONST_18  HN2A  N2   C2   N1   180.00   0.0  0
 40G  CONST_19  O7'   C7'  N4'  C3'    0.00   0.0  0
 40G  CONST_20  C8'   C7'  N4'  C3'  180.00   0.0  0
 40G  CONST_21  O7'   C7'  N4'  C5'  180.00   0.0  0
 40G  CONST_22  C8'   C7'  N4'  C5'    0.00   0.0  0
 40G  CONST_23  HXT   OXT  C'   O1'    0.00   0.0  0
 40G  Var_01    C7'   C8'  N9   C4    87.07  30.0  2
 40G  Var_02    N4'   C7'  C8'  N9   177.73  30.0  3
 40G  Var_03    C3'   N4'  C5'  C'    89.70  30.0  2
 40G  Var_04    N4'   C5'  C'   O1'    8.66  30.0  3
 40G  Var_05    C5'   N4'  C3'  C2'   79.81  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
 40G  chir_01  C2'  N1'  C2M  C3'  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
 40G  plan-1  N1    0.020
 40G  plan-1  C2    0.020
 40G  plan-1  N2    0.020
 40G  plan-1  N3    0.020
 40G  plan-1  C4    0.020
 40G  plan-1  C5    0.020
 40G  plan-1  C6    0.020
 40G  plan-1  O6    0.020
 40G  plan-1  N7    0.020
 40G  plan-1  C8    0.020
 40G  plan-1  N9    0.020
 40G  plan-1  C8'   0.020
 40G  plan-1  HN1   0.020
 40G  plan-1  H8    0.020
 40G  plan-1  HN2   0.020
 40G  plan-1  HN2A  0.020
 40G  plan-2  C3'   0.020
 40G  plan-2  N4'   0.020
 40G  plan-2  C5'   0.020
 40G  plan-2  C7'   0.020
 40G  plan-2  O7'   0.020
 40G  plan-2  C8'   0.020
 40G  plan-3  C'    0.020
 40G  plan-3  O1'   0.020
 40G  plan-3  C5'   0.020
 40G  plan-3  OXT   0.020
 40G  plan-3  HXT   0.020

