# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Mar 25 06:51:25 2022
#   Inital geometry file: a 112 line input string
#   Ligand name: N-[(1S,2S)-2-aminocyclopentyl]-N-[(2-amino-6-oxo-1,6-dihydro-9H-purin-9-yl)acetyl]glycine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: N[C@H]1CCC[C@@H]1N(CC(O)=O)C(=O)Cn2cnc3C(=O)NC(=Nc23)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
 XDJ  XDJ  N-[(1S,2S)-2-aminocyclopentyl]-N-[(2-amino-6-oxo-1,6-dihydro-9H-purin-9-yl)acetyl]glycine  peptide  43  25  .  2022-03-29  2022-03-29
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_XDJ
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
 XDJ  C02   C  C      0   0.417  -33.7772  3.1747  -15.3526
 XDJ  C03   C  CH2    0  -0.469  -35.0176  3.9160  -15.9083
 XDJ  C05   C  CH1    0  -0.126  -34.8394  6.3604  -16.3997
 XDJ  C06   C  CH1    0  -0.076  -35.8306  6.4945  -17.5683
 XDJ  C08   C  CH2    0  -0.447  -35.1186  7.5088  -18.4560
 XDJ  C09   C  CH2    0  -0.447  -33.6225  7.1613  -18.3425
 XDJ  C10   C  CH2    0  -0.435  -33.4718  6.2802  -17.0824
 XDJ  C11   C  C      0   0.542  -35.5408  5.4864  -14.2006
 XDJ  C12   C  CH2    0  -0.467  -35.6630  6.9317  -13.7007
 XDJ  C14   C  CR15   0   0.093  -37.3607  6.9708  -11.8528
 XDJ  C16   C  CR56   0   0.497  -35.2720  6.7744  -11.2492
 XDJ  C17   C  CR56   0  -0.092  -36.1228  6.7330  -10.1601
 XDJ  C18   C  CR6    0   0.497  -35.5599  6.5738   -8.8608
 XDJ  C20   C  CR6    0   0.683  -33.4117  6.5339  -10.0790
 XDJ  N04   N  NT     0  -0.438  -35.1540  5.2913  -15.4714
 XDJ  N07   N  NH2    0  -0.789  -37.1860  6.8728  -17.2369
 XDJ  N13   N  NR5    0  -0.482  -36.0765  6.9484  -12.3272
 XDJ  N15   N  N      0  -0.444  -37.4288  6.8575  -10.5618
 XDJ  N19   N  NR16   0  -0.726  -34.1625  6.4800   -8.9390
 XDJ  N22   N  N      0  -0.509  -33.9354  6.6778  -11.2704
 XDJ  O01   O  O      0  -0.614  -33.7744  1.9485  -15.5764
 XDJ  O24   O  O      0  -0.490  -35.8185  4.5692  -13.4428
 XDJ  H031  H  HCH2   0   0.252  -34.9621  3.9024  -16.9986
 XDJ  H032  H  HCH2   0   0.248  -35.9176  3.3547  -15.6521
 XDJ  H051  H  HCH1   0   0.266  -34.8783  7.3082  -15.8596
 XDJ  H061  H  HCH1   0   0.226  -35.8718  5.5359  -18.0996
 XDJ  H081  H  HCH2   0   0.222  -35.3078  8.5141  -18.0659
 XDJ  H082  H  HCH2   0   0.237  -35.4827  7.4912  -19.4832
 XDJ  H092  H  HCH2   0   0.232  -33.2806  6.6221  -19.2261
 XDJ  H091  H  HCH2   0   0.232  -33.0157  8.0645  -18.2771
 XDJ  H102  H  HCH2   0   0.236  -33.2423  5.2528  -17.3649
 XDJ  H101  H  HCH2   0   0.237  -32.6703  6.6130  -16.4239
 XDJ  H122  H  HCH2   0   0.302  -34.7140  7.4630  -13.7835
 XDJ  H121  H  HCH2   0   0.307  -36.3955  7.4873  -14.2878
 XDJ  H141  H  HCR5   0   0.284  -38.2000  7.0885  -12.5226
 XDJ  H071  H  HNH2   0   0.344  -37.5996  6.1837  -16.6201
 XDJ  H3    H  HNH2   0   0.339  -37.1813  7.7470  -16.7224
 XDJ  H191  H  HNR6   0   0.423  -33.6854  6.3722   -8.0525
 XDJ  H211  H  HNH2   0   0.410  -31.5326  6.3446  -10.7742
 XDJ  H212  H  HNH2   0   0.412  -31.6625  6.1358   -9.0845
 XDJ  O1    O  OC    -1  -0.592  -32.9064  3.8471  -14.7762
 XDJ  N21   N  NH2    0  -0.832  -32.0779  6.4694   -9.9378
 XDJ  O23   O  O      0  -0.467  -36.1233  6.5143   -7.7814

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
 XDJ  C08  C09   single    1.540  0.020  1.540
 XDJ  C08  C06   single    1.524  0.020  1.524
 XDJ  C09  C10   single    1.545  0.020  1.545
 XDJ  C06  N07   single    1.446  0.020  1.446
 XDJ  C06  C05   single    1.538  0.020  1.538
 XDJ  C10  C05   single    1.531  0.020  1.531
 XDJ  O01  C02   deloc     1.246  0.020  1.246
 XDJ  C05  N04   single    1.450  0.020  1.450
 XDJ  C03  C02   single    1.548  0.020  1.548
 XDJ  C03  N04   single    1.449  0.020  1.449
 XDJ  N04  C11   single    1.343  0.020  1.343
 XDJ  C11  C12   single    1.534  0.020  1.534
 XDJ  C11  O24   double    1.222  0.020  1.222
 XDJ  C12  N13   single    1.435  0.020  1.435
 XDJ  N13  C14   aromatic  1.369  0.020  1.369
 XDJ  N13  C16   aromatic  1.356  0.020  1.356
 XDJ  C14  N15   aromatic  1.298  0.020  1.298
 XDJ  N22  C16   single    1.340  0.020  1.340
 XDJ  N22  C20   double    1.309  0.020  1.309
 XDJ  C16  C17   aromatic  1.383  0.020  1.383
 XDJ  N15  C17   aromatic  1.372  0.020  1.372
 XDJ  C17  C18   single    1.425  0.020  1.425
 XDJ  C20  N21   single    1.343  0.020  1.343
 XDJ  C20  N19   single    1.366  0.020  1.366
 XDJ  N19  C18   single    1.403  0.020  1.403
 XDJ  C18  O23   double    1.219  0.020  1.219
 XDJ  C03  H031  single    0.970  0.020  1.090
 XDJ  C03  H032  single    0.970  0.020  1.090
 XDJ  C05  H051  single    0.970  0.020  1.090
 XDJ  C06  H061  single    0.970  0.020  1.090
 XDJ  C08  H081  single    0.970  0.020  1.090
 XDJ  C08  H082  single    0.970  0.020  1.090
 XDJ  C09  H092  single    0.970  0.020  1.090
 XDJ  C09  H091  single    0.970  0.020  1.090
 XDJ  C10  H102  single    0.970  0.020  1.090
 XDJ  C10  H101  single    0.970  0.020  1.090
 XDJ  C12  H122  single    0.970  0.020  1.090
 XDJ  C12  H121  single    0.970  0.020  1.090
 XDJ  C14  H141  single    0.930  0.020  1.080
 XDJ  N07  H071  single    0.890  0.020  1.040
 XDJ  N07  H3    single    0.890  0.020  1.040
 XDJ  N19  H191  single    0.860  0.020  1.020
 XDJ  N21  H211  single    0.890  0.020  1.040
 XDJ  N21  H212  single    0.890  0.020  1.040
 XDJ  C02  O1    deloc     1.242  0.020  1.242

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
 XDJ  O1    C02  O01   127.90  3.000
 XDJ  O1    C02  C03   117.97  3.000
 XDJ  O01   C02  C03   114.10  3.000
 XDJ  H032  C03  H031  105.66  3.000
 XDJ  H032  C03  N04   109.85  3.000
 XDJ  H031  C03  N04   108.52  3.000
 XDJ  H032  C03  C02   109.28  3.000
 XDJ  H031  C03  C02   108.17  3.000
 XDJ  N04   C03  C02   114.93  3.000
 XDJ  H051  C05  N04   108.40  3.000
 XDJ  H051  C05  C10   107.34  3.000
 XDJ  N04   C05  C10   116.15  3.000
 XDJ  H051  C05  C06   106.10  3.000
 XDJ  N04   C05  C06   114.25  3.000
 XDJ  C10   C05  C06   103.97  3.000
 XDJ  H061  C06  N07   107.73  3.000
 XDJ  H061  C06  C08   108.48  3.000
 XDJ  N07   C06  C08   113.41  3.000
 XDJ  H061  C06  C05   108.43  3.000
 XDJ  N07   C06  C05   116.93  3.000
 XDJ  C08   C06  C05   101.50  3.000
 XDJ  H082  C08  H081  107.03  3.000
 XDJ  H082  C08  C09   112.98  3.000
 XDJ  H081  C08  C09   110.41  3.000
 XDJ  H082  C08  C06   112.46  3.000
 XDJ  H081  C08  C06   108.83  3.000
 XDJ  C09   C08  C06   105.11  3.000
 XDJ  H091  C09  H092  106.49  3.000
 XDJ  H091  C09  C10   111.68  3.000
 XDJ  H092  C09  C10   110.39  3.000
 XDJ  H091  C09  C08   110.99  3.000
 XDJ  H092  C09  C08   110.89  3.000
 XDJ  C10   C09  C08   106.47  3.000
 XDJ  H101  C10  H102  106.84  3.000
 XDJ  H101  C10  C09   112.98  3.000
 XDJ  H102  C10  C09   110.29  3.000
 XDJ  H101  C10  C05   111.82  3.000
 XDJ  H102  C10  C05   110.68  3.000
 XDJ  C09   C10  C05   104.29  3.000
 XDJ  O24   C11  N04   122.92  3.000
 XDJ  O24   C11  C12   119.14  3.000
 XDJ  N04   C11  C12   117.93  3.000
 XDJ  H121  C12  H122  107.17  3.000
 XDJ  H121  C12  N13   108.41  3.000
 XDJ  H122  C12  N13   108.53  3.000
 XDJ  H121  C12  C11   110.97  3.000
 XDJ  H122  C12  C11   111.40  3.000
 XDJ  N13   C12  C11   110.24  3.000
 XDJ  H141  C14  N15   125.84  3.000
 XDJ  H141  C14  N13   121.04  3.000
 XDJ  N15   C14  N13   113.11  3.000
 XDJ  N22   C16  N13   126.03  3.000
 XDJ  N22   C16  C17   128.61  3.000
 XDJ  N13   C16  C17   105.36  3.000
 XDJ  N15   C17  C18   130.78  3.000
 XDJ  C18   C17  C16   118.59  3.000
 XDJ  N15   C17  C16   110.63  3.000
 XDJ  O23   C18  N19   120.43  3.000
 XDJ  O23   C18  C17   129.07  3.000
 XDJ  N19   C18  C17   110.50  3.000
 XDJ  N22   C20  N21   119.88  3.000
 XDJ  N21   C20  N19   117.14  3.000
 XDJ  N22   C20  N19   122.95  3.000
 XDJ  C11   N04  C05   124.13  3.000
 XDJ  C11   N04  C03   116.77  3.000
 XDJ  C05   N04  C03   119.08  3.000
 XDJ  H3    N07  H071  106.22  3.000
 XDJ  H3    N07  C06   109.72  3.000
 XDJ  H071  N07  C06   110.15  3.000
 XDJ  C16   N13  C14   106.44  3.000
 XDJ  C16   N13  C12   126.05  3.000
 XDJ  C14   N13  C12   127.04  3.000
 XDJ  C17   N15  C14   104.43  3.000
 XDJ  H191  N19  C20   118.42  3.000
 XDJ  H191  N19  C18   115.33  3.000
 XDJ  C20   N19  C18   126.25  3.000
 XDJ  C20   N22  C16   113.10  3.000
 XDJ  H212  N21  H211  116.11  3.000
 XDJ  H212  N21  C20   121.02  3.000
 XDJ  H211  N21  C20   117.19  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
 XDJ  CONST_01  C17   C16  N13  C14     0.00   0.0  0
 XDJ  CONST_02  C16   C17  N15  C14     0.00   0.0  0
 XDJ  CONST_03  N15   C14  N13  C16     0.00   0.0  0
 XDJ  CONST_04  N13   C14  N15  C17     0.00   0.0  0
 XDJ  CONST_05  N15   C17  C16  N13     0.00   0.0  0
 XDJ  CONST_06  N19   C20  N22  C16     0.00   0.0  0
 XDJ  CONST_07  C20   N19  C18  C17     0.00   0.0  0
 XDJ  CONST_08  N22   C20  N19  C18     0.00   0.0  0
 XDJ  CONST_09  N15   C14  N13  C12   180.00   0.0  0
 XDJ  CONST_10  N22   C16  N13  C12     0.00   0.0  0
 XDJ  CONST_11  C17   C16  N13  C12   180.00   0.0  0
 XDJ  CONST_12  N21   C20  N22  C16   180.00   0.0  0
 XDJ  CONST_13  N21   C20  N19  C18   180.00   0.0  0
 XDJ  CONST_14  O23   C18  N19  C20   180.00   0.0  0
 XDJ  CONST_15  H141  C14  N13  C16   180.00   0.0  0
 XDJ  CONST_16  H191  N19  C18  C17   180.00   0.0  0
 XDJ  CONST_17  H211  N21  C20  N19   180.00   0.0  0
 XDJ  CONST_19  C12   C11  N04  C05     0.00   0.0  0
 XDJ  CONST_20  O24   C11  N04  C05   180.00   0.0  0
 XDJ  CONST_21  C12   C11  N04  C03   180.00   0.0  0
 XDJ  CONST_22  O24   C11  N04  C03     0.00   0.0  0
 XDJ  Var_01    C08   C09  C10  C05    -9.39  30.0  1
 XDJ  Var_02    C10   C09  C08  C06   -17.53  30.0  1
 XDJ  Var_03    C14   N13  C12  C11   -89.59  30.0  2
 XDJ  Var_04    C05   N04  C03  C02   104.91  30.0  3
 XDJ  Var_05    N13   C12  C11  N04  -179.64  30.0  3
 XDJ  Var_06    O01   C02  C03  N04   170.16  30.0  3

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
 XDJ  chir_01  C05  C06  C10  N04  positiv
 XDJ  chir_02  C06  N07  C05  C08  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
 XDJ  plan-1  C12   0.020
 XDJ  plan-1  C14   0.020
 XDJ  plan-1  C16   0.020
 XDJ  plan-1  C17   0.020
 XDJ  plan-1  C18   0.020
 XDJ  plan-1  C20   0.020
 XDJ  plan-1  N13   0.020
 XDJ  plan-1  N15   0.020
 XDJ  plan-1  N19   0.020
 XDJ  plan-1  N22   0.020
 XDJ  plan-1  H141  0.020
 XDJ  plan-1  H191  0.020
 XDJ  plan-1  H211  0.020
 XDJ  plan-1  H212  0.020
 XDJ  plan-1  N21   0.020
 XDJ  plan-1  O23   0.020
 XDJ  plan-2  C03   0.020
 XDJ  plan-2  C05   0.020
 XDJ  plan-2  C11   0.020
 XDJ  plan-2  C12   0.020
 XDJ  plan-2  N04   0.020
 XDJ  plan-2  O24   0.020
 XDJ  plan-3  C02   0.020
 XDJ  plan-3  C03   0.020
 XDJ  plan-3  O01   0.020
 XDJ  plan-3  O1    0.020

