# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Jul 23 16:35:46 2021
#   Inital geometry file: a 103 line input string
#   Ligand name: N-[(1S,2S)-2-aminocyclopentyl]-N-[(6-amino-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(N)ncnc23
#
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
 XDD  XDD  N-[(1S,2S)-2-aminocyclopentyl]-N-[(6-amino-9H-purin-9-yl)acetyl]glycine  peptide  43  24  .  2022-03-29  2022-11-18
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_XDD
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
 XDD  C12   C  CH2   0  -0.468  -41.9549  13.7481  -12.9297
 XDD  C14   C  CR15  0   0.112  -41.3296  13.1900  -10.5690
 XDD  C16   C  CR56  0   0.484  -39.6824  13.3458  -11.9924
 XDD  C10   C  CH2   0  -0.439  -43.6299  13.8904  -16.6753
 XDD  C11   C  C     0   0.568  -42.4043  12.4345  -13.5663
 XDD  C02   C  C     0   0.548  -42.6120  10.4065  -15.7688
 XDD  C05   C  CH1   0  -0.139  -43.7999  13.7255  -15.1643
 XDD  C06   C  CH1   0  -0.078  -45.3043  13.9304  -14.9245
 XDD  C08   C  CH2   0  -0.449  -45.5917  15.1301  -15.8206
 XDD  C09   C  CH2   0  -0.448  -44.7083  14.9260  -17.0660
 XDD  C17   C  CR56  0  -0.006  -39.2370  12.9858  -10.7302
 XDD  C18   C  CR6   0   0.455  -37.8497  12.7963  -10.5929
 XDD  C21   C  CR16  0   0.041  -37.6548  13.3149  -12.8273
 XDD  N04   N  NT    0  -0.466  -43.2695  12.4971  -14.5969
 XDD  N07   N  NH2   0  -0.790  -45.7295  14.1175  -13.5558
 XDD  N13   N  NR5   0  -0.488  -41.0303  13.4938  -11.8658
 XDD  N15   N  N     0  -0.451  -40.2864  12.8931   -9.8519
 XDD  N20   N  N     0  -0.475  -37.0835  12.9707  -11.6759
 XDD  N22   N  N     0  -0.453  -38.9355  13.5229  -13.0792
 XDD  O01   O  O     0  -0.447  -42.6686   9.2072  -15.8712
 XDD  O23   O  O     0  -0.477  -41.9902  11.3703  -13.1381
 XDD  H121  H  HCH2  0   0.316  -41.4673  14.3910  -13.6635
 XDD  H122  H  HCH2  0   0.307  -42.8090  14.3013  -12.5359
 XDD  H141  H  HCR5  0   0.294  -42.3479  13.2210  -10.2098
 XDD  H101  H  HCH2  0   0.237  -43.8085  12.9479  -17.1948
 XDD  H102  H  HCH2  0   0.251  -42.6203  14.2069  -16.9346
 XDD  H032  H  HCH2  0   0.304  -44.4717  11.3983  -15.8841
 XDD  H031  H  HCH2  0   0.304  -44.1777  10.6139  -14.3527
 XDD  H051  H  HCH1  0   0.278  -43.2909  14.5638  -14.6867
 XDD  H061  H  HCH1  0   0.232  -45.8425  13.0597  -15.3203
 XDD  H082  H  HCH2  0   0.228  -45.3014  16.0438  -15.2929
 XDD  H081  H  HCH2  0   0.244  -46.6503  15.2225  -16.0622
 XDD  H092  H  HCH2  0   0.238  -44.2606  15.8661  -17.3864
 XDD  H091  H  HCH2  0   0.237  -45.2974  14.5591  -17.9063
 XDD  H211  H  HCR6  0   0.251  -36.9758  13.4401  -13.6642
 XDD  H2    H  HNH2  0   0.347  -45.5048  13.3037  -12.9969
 XDD  H3    H  HNH2  0   0.341  -45.2417  14.9023  -13.1387
 XDD  H192  H  HNH2  0   0.403  -36.2797  12.3533   -9.3748
 XDD  H191  H  HNH2  0   0.411  -37.8231  12.3320   -8.6025
 XDD  O1    O  OH1   0  -0.576  -41.6321  11.1475  -16.2562
 XDD  H1    H  HOH1  0   0.485  -40.9706  10.5832  -16.6843
 XDD  N19   N  NH2   0  -0.817  -37.2782  12.4511   -9.4381
 XDD  C03   C  CH2   0  -0.449  -43.7080  11.2266  -15.1231

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
 XDD  C09  C10   single    1.545  0.020  1.545
 XDD  C09  C08   single    1.540  0.020  1.540
 XDD  C10  C05   single    1.529  0.020  1.529
 XDD  O01  C02   double    1.205  0.020  1.205
 XDD  C02  C03   single    1.514  0.020  1.514
 XDD  C08  C06   single    1.525  0.020  1.525
 XDD  C03  N04   single    1.443  0.020  1.443
 XDD  C05  C06   single    1.537  0.020  1.537
 XDD  C05  N04   single    1.453  0.020  1.453
 XDD  C06  N07   single    1.445  0.020  1.445
 XDD  N04  C11   single    1.347  0.020  1.347
 XDD  C11  O23   double    1.220  0.020  1.220
 XDD  C11  C12   single    1.527  0.020  1.527
 XDD  N22  C21   aromatic  1.322  0.020  1.322
 XDD  N22  C16   aromatic  1.331  0.020  1.331
 XDD  C12  N13   single    1.432  0.020  1.432
 XDD  C21  N20   aromatic  1.331  0.020  1.331
 XDD  C16  N13   aromatic  1.362  0.020  1.362
 XDD  C16  C17   aromatic  1.386  0.020  1.386
 XDD  N13  C14   aromatic  1.365  0.020  1.365
 XDD  N20  C18   aromatic  1.338  0.020  1.338
 XDD  C17  C18   aromatic  1.407  0.020  1.407
 XDD  C17  N15   aromatic  1.372  0.020  1.372
 XDD  C18  N19   single    1.334  0.020  1.334
 XDD  C14  N15   aromatic  1.300  0.020  1.300
 XDD  C12  H121  single    0.970  0.020  1.090
 XDD  C12  H122  single    0.970  0.020  1.090
 XDD  C14  H141  single    0.930  0.020  1.080
 XDD  C10  H101  single    0.970  0.020  1.090
 XDD  C10  H102  single    0.970  0.020  1.090
 XDD  C03  H032  single    0.970  0.020  1.090
 XDD  C03  H031  single    0.970  0.020  1.090
 XDD  C05  H051  single    0.970  0.020  1.090
 XDD  C06  H061  single    0.970  0.020  1.090
 XDD  C08  H082  single    0.970  0.020  1.090
 XDD  C08  H081  single    0.970  0.020  1.090
 XDD  C09  H092  single    0.970  0.020  1.090
 XDD  C09  H091  single    0.970  0.020  1.090
 XDD  C21  H211  single    0.930  0.020  1.080
 XDD  N07  H2    single    0.890  0.020  1.040
 XDD  N07  H3    single    0.890  0.020  1.040
 XDD  N19  H192  single    0.860  0.020  1.020
 XDD  N19  H191  single    0.860  0.020  1.020
 XDD  C02  O1    single    1.322  0.020  1.322
 XDD  O1   H1    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
 XDD  H122  C12  H121  107.09  3.000
 XDD  H122  C12  N13   109.10  3.000
 XDD  H121  C12  N13   108.41  3.000
 XDD  H122  C12  C11   110.87  3.000
 XDD  H121  C12  C11   110.98  3.000
 XDD  N13   C12  C11   110.29  3.000
 XDD  H141  C14  N15   125.41  3.000
 XDD  H141  C14  N13   121.08  3.000
 XDD  N15   C14  N13   113.51  3.000
 XDD  N22   C16  N13   128.10  3.000
 XDD  N13   C16  C17   105.16  3.000
 XDD  N22   C16  C17   126.73  3.000
 XDD  H102  C10  H101  106.82  3.000
 XDD  H102  C10  C09   113.07  3.000
 XDD  H101  C10  C09   110.14  3.000
 XDD  H102  C10  C05   111.69  3.000
 XDD  H101  C10  C05   111.05  3.000
 XDD  C09   C10  C05   104.15  3.000
 XDD  O23   C11  N04   121.82  3.000
 XDD  O23   C11  C12   120.28  3.000
 XDD  N04   C11  C12   117.90  3.000
 XDD  O1    C02  O01   124.16  3.000
 XDD  O1    C02  C03   112.98  3.000
 XDD  O01   C02  C03   122.79  3.000
 XDD  H051  C05  N04   107.95  3.000
 XDD  H051  C05  C06   106.61  3.000
 XDD  N04   C05  C06   114.14  3.000
 XDD  H051  C05  C10   107.33  3.000
 XDD  N04   C05  C10   115.87  3.000
 XDD  C06   C05  C10   104.40  3.000
 XDD  H061  C06  N07   107.46  3.000
 XDD  H061  C06  C08   108.65  3.000
 XDD  N07   C06  C08   113.53  3.000
 XDD  H061  C06  C05   108.53  3.000
 XDD  N07   C06  C05   116.93  3.000
 XDD  C08   C06  C05   101.40  3.000
 XDD  H081  C08  H082  107.08  3.000
 XDD  H081  C08  C09   112.90  3.000
 XDD  H082  C08  C09   110.38  3.000
 XDD  H081  C08  C06   112.34  3.000
 XDD  H082  C08  C06   108.88  3.000
 XDD  C09   C08  C06   105.24  3.000
 XDD  H091  C09  H092  106.61  3.000
 XDD  H091  C09  C08   110.98  3.000
 XDD  H092  C09  C08   111.04  3.000
 XDD  H091  C09  C10   110.28  3.000
 XDD  H092  C09  C10   111.46  3.000
 XDD  C08   C09  C10   106.53  3.000
 XDD  N15   C17  C18   133.07  3.000
 XDD  N15   C17  C16   110.78  3.000
 XDD  C18   C17  C16   116.15  3.000
 XDD  N20   C18  N19   119.28  3.000
 XDD  N19   C18  C17   122.81  3.000
 XDD  N20   C18  C17   117.91  3.000
 XDD  H211  C21  N22   116.19  3.000
 XDD  H211  C21  N20   115.38  3.000
 XDD  N22   C21  N20   128.44  3.000
 XDD  C05   N04  C03   119.39  3.000
 XDD  C05   N04  C11   124.92  3.000
 XDD  C03   N04  C11   115.67  3.000
 XDD  H3    N07  H2    106.76  3.000
 XDD  H3    N07  C06   110.38  3.000
 XDD  H2    N07  C06   110.70  3.000
 XDD  C16   N13  C14   106.33  3.000
 XDD  C14   N13  C12   127.13  3.000
 XDD  C16   N13  C12   126.10  3.000
 XDD  C17   N15  C14   104.19  3.000
 XDD  C21   N20  C18   119.22  3.000
 XDD  C21   N22  C16   111.55  3.000
 XDD  H1    O1   C02   110.03  3.000
 XDD  H191  N19  H192  118.35  3.000
 XDD  H191  N19  C18   121.22  3.000
 XDD  H192  N19  C18   120.35  3.000
 XDD  H031  C03  H032  106.23  3.000
 XDD  H031  C03  N04   111.58  3.000
 XDD  H032  C03  N04   109.16  3.000
 XDD  H031  C03  C02   107.99  3.000
 XDD  H032  C03  C02   107.12  3.000
 XDD  N04   C03  C02   114.37  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
 XDD  CONST_01  N22   C16  N13  C14   180.00   0.0  0
 XDD  CONST_02  C17   C16  N13  C14     0.00   0.0  0
 XDD  CONST_03  C16   C17  N15  C14     0.00   0.0  0
 XDD  CONST_04  C18   C17  N15  C14   180.00   0.0  0
 XDD  CONST_05  N20   C21  N22  C16     0.00   0.0  0
 XDD  CONST_06  N15   C14  N13  C16     0.00   0.0  0
 XDD  CONST_07  N20   C18  C17  C16     0.00   0.0  0
 XDD  CONST_08  C21   N22  C16  C17     0.00   0.0  0
 XDD  CONST_09  C21   N20  C18  C17     0.00   0.0  0
 XDD  CONST_10  N13   C14  N15  C17     0.00   0.0  0
 XDD  CONST_11  N22   C21  N20  C18     0.00   0.0  0
 XDD  CONST_12  N22   C16  C17  C18     0.00   0.0  0
 XDD  CONST_13  N13   C16  C17  C18   180.00   0.0  0
 XDD  CONST_14  N13   C16  N22  C21   180.00   0.0  0
 XDD  CONST_15  N15   C17  C16  N13     0.00   0.0  0
 XDD  CONST_16  N22   C16  C17  N15   180.00   0.0  0
 XDD  CONST_17  N20   C18  C17  N15   180.00   0.0  0
 XDD  CONST_18  N22   C16  N13  C12     0.00   0.0  0
 XDD  CONST_19  C17   C16  N13  C12   180.00   0.0  0
 XDD  CONST_20  N15   C14  N13  C12   180.00   0.0  0
 XDD  CONST_21  N19   C18  C17  C16   180.00   0.0  0
 XDD  CONST_22  N19   C18  N20  C21   180.00   0.0  0
 XDD  CONST_23  N19   C18  C17  N15     0.00   0.0  0
 XDD  CONST_24  H211  C21  N22  C16   180.00   0.0  0
 XDD  CONST_25  H141  C14  N13  C16   180.00   0.0  0
 XDD  CONST_26  H192  N19  C18  C17   180.00   0.0  0
 XDD  CONST_27  H191  N19  C18  C17     0.00   0.0  0
 XDD  CONST_28  C05   N04  C11  C12     0.00   0.0  0
 XDD  CONST_29  O23   C11  N04  C05   180.00   0.0  0
 XDD  CONST_30  C03   N04  C11  C12   180.00   0.0  0
 XDD  CONST_31  O23   C11  N04  C03     0.00   0.0  0
 XDD  CONST_32  H1    O1   C02  C03   180.00   0.0  0
 XDD  Var_01    C06   C08  C09  C10   -17.49  30.0  1
 XDD  Var_02    C08   C09  C10  C05    -9.15  30.0  1
 XDD  Var_03    C11   C12  N13  C14   -84.68  30.0  2
 XDD  Var_04    C05   N04  C03  C02   116.43  30.0  3
 XDD  Var_05    N13   C12  C11  N04  -179.36  30.0  3
 XDD  Var_06    O01   C02  C03  N04   155.69  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
 XDD  chir_01  C05  C10  C06  N04  negativ
 XDD  chir_02  C06  N07  C08  C05  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
 XDD  plan-1  C12   0.020
 XDD  plan-1  C14   0.020
 XDD  plan-1  C16   0.020
 XDD  plan-1  C17   0.020
 XDD  plan-1  C18   0.020
 XDD  plan-1  C21   0.020
 XDD  plan-1  N13   0.020
 XDD  plan-1  N15   0.020
 XDD  plan-1  N20   0.020
 XDD  plan-1  N22   0.020
 XDD  plan-1  H141  0.020
 XDD  plan-1  H211  0.020
 XDD  plan-1  N19   0.020
 XDD  plan-2  C18   0.020
 XDD  plan-2  H192  0.020
 XDD  plan-2  H191  0.020
 XDD  plan-2  N19   0.020
 XDD  plan-3  C12   0.020
 XDD  plan-3  C11   0.020
 XDD  plan-3  C05   0.020
 XDD  plan-3  N04   0.020
 XDD  plan-3  O23   0.020
 XDD  plan-3  C03   0.020
 XDD  plan-4  C02   0.020
 XDD  plan-4  O01   0.020
 XDD  plan-4  O1    0.020
 XDD  plan-4  H1    0.020
 XDD  plan-4  C03   0.020

