# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Mar 25 01:40:27 2022
#   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  42  24  .  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_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  -0.470  -41.8932  13.8414  -12.9914
 XDD  C14   C  CR15   0   0.108  -41.3051  13.4650  -10.5891
 XDD  C16   C  CR56   0   0.482  -39.6486  13.3774  -12.0039
 XDD  C10   C  CH2    0  -0.435  -43.6989  13.8512  -16.6604
 XDD  C11   C  C      0   0.542  -42.3288  12.4891  -13.5702
 XDD  C02   C  C      0   0.417  -42.5338  10.6008  -16.1130
 XDD  C05   C  CH1    0  -0.129  -43.7966  13.7003  -15.1423
 XDD  C06   C  CH1    0  -0.073  -45.2987  13.8716  -14.8594
 XDD  C08   C  CH2    0  -0.448  -45.6490  15.0633  -15.7462
 XDD  C09   C  CH2    0  -0.446  -44.7524  14.9272  -16.9947
 XDD  C17   C  CR56   0  -0.007  -39.2360  13.0868  -10.7123
 XDD  C18   C  CR6    0   0.451  -37.8719  12.7868  -10.5481
 XDD  C21   C  CR16   0   0.039  -37.6270  13.1078  -12.8134
 XDD  N04   N  NT     0  -0.437  -43.2178  12.4950  -14.5765
 XDD  N07   N  NH2    0  -0.790  -45.6921  14.0517  -13.4786
 XDD  N13   N  NR5    0  -0.484  -40.9807  13.6399  -11.9028
 XDD  N15   N  N      0  -0.449  -40.2912  13.1475   -9.8387
 XDD  N20   N  N      0  -0.471  -37.0899  12.8079  -11.6329
 XDD  N22   N  N      0  -0.452  -38.8842  13.4020  -13.0938
 XDD  O01   O  O      0  -0.614  -42.8348   9.4637  -16.5253
 XDD  O23   O  O      0  -0.489  -41.8675  11.4643  -13.0912
 XDD  H121  H  HCH2   0   0.305  -41.4033  14.4531  -13.7505
 XDD  H122  H  HCH2   0   0.307  -42.7484  14.4090  -12.6236
 XDD  H141  H  HCR5   0   0.290  -42.3201  13.6020  -10.2439
 XDD  H101  H  HCH2   0   0.233  -43.9520  12.9131  -17.1550
 XDD  H102  H  HCH2   0   0.239  -42.6945  14.1213  -16.9837
 XDD  H032  H  HCH2   0   0.251  -44.5220  11.3273  -15.6877
 XDD  H031  H  HCH2   0   0.252  -43.7850  10.5000  -14.3484
 XDD  H051  H  HCH1   0   0.266  -43.2993  14.5647  -14.6982
 XDD  H061  H  HCH1   0   0.226  -45.8227  12.9852  -15.2368
 XDD  H082  H  HCH2   0   0.224  -45.4125  15.9864  -15.2088
 XDD  H081  H  HCH2   0   0.237  -46.7112  15.0991  -15.9878
 XDD  H092  H  HCH2   0   0.232  -44.2803  15.8795  -17.2363
 XDD  H091  H  HCH2   0   0.232  -45.3313  14.6379  -17.8716
 XDD  H211  H  HCR6   0   0.247  -36.9376  13.1065  -13.6513
 XDD  H2    H  HNH2   0   0.344  -45.4055  13.2502  -12.9290
 XDD  H3    H  HNH2   0   0.339  -45.2075  14.8516  -13.0863
 XDD  H192  H  HNH2   0   0.401  -36.3711  12.2137   -9.2989
 XDD  H191  H  HNH2   0   0.408  -37.9110  12.3947   -8.5434
 XDD  O1    O  OC    -1  -0.590  -41.5285  11.2734  -16.3939
 XDD  C03   C  CH2    0  -0.473  -43.5799  11.2132  -15.1482
 XDD  N19   N  NH2    0  -0.818  -37.3347  12.4944   -9.3605

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    1.543  0.020  1.543
 XDD  C09  C08   single    1.543  0.020  1.543
 XDD  C10  C05   single    1.529  0.020  1.529
 XDD  O01  C02   deloc     1.246  0.020  1.246
 XDD  C02  C03   single    1.549  0.020  1.549
 XDD  C08  C06   single    1.526  0.020  1.526
 XDD  C03  N04   single    1.450  0.020  1.450
 XDD  C05  C06   single    1.538  0.020  1.538
 XDD  C05  N04   single    1.452  0.020  1.452
 XDD  C06  N07   single    1.447  0.020  1.447
 XDD  N04  C11   single    1.343  0.020  1.343
 XDD  C11  O23   double    1.222  0.020  1.222
 XDD  C11  C12   single    1.534  0.020  1.534
 XDD  N22  C21   aromatic  1.321  0.020  1.321
 XDD  N22  C16   aromatic  1.331  0.020  1.331
 XDD  C12  N13   single    1.435  0.020  1.435
 XDD  C21  N20   aromatic  1.331  0.020  1.331
 XDD  C16  N13   aromatic  1.362  0.020  1.362
 XDD  C16  C17   aromatic  1.387  0.020  1.387
 XDD  N13  C14   aromatic  1.364  0.020  1.364
 XDD  N20  C18   aromatic  1.337  0.020  1.337
 XDD  C17  C18   aromatic  1.406  0.020  1.406
 XDD  C17  N15   aromatic  1.371  0.020  1.371
 XDD  C18  N19   single    1.336  0.020  1.336
 XDD  C14  N15   aromatic  1.301  0.020  1.301
 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    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
 XDD  H122  C12  H121  107.16  3.000
 XDD  H122  C12  N13   108.42  3.000
 XDD  H121  C12  N13   108.73  3.000
 XDD  H122  C12  C11   111.31  3.000
 XDD  H121  C12  C11   111.05  3.000
 XDD  N13   C12  C11   110.06  3.000
 XDD  H141  C14  N15   125.36  3.000
 XDD  H141  C14  N13   120.96  3.000
 XDD  N15   C14  N13   113.67  3.000
 XDD  N22   C16  N13   128.23  3.000
 XDD  N13   C16  C17   105.21  3.000
 XDD  N22   C16  C17   126.55  3.000
 XDD  H102  C10  H101  107.02  3.000
 XDD  H102  C10  C09   113.11  3.000
 XDD  H101  C10  C09   110.08  3.000
 XDD  H102  C10  C05   112.23  3.000
 XDD  H101  C10  C05   110.53  3.000
 XDD  C09   C10  C05   103.91  3.000
 XDD  O23   C11  N04   123.20  3.000
 XDD  O23   C11  C12   118.97  3.000
 XDD  N04   C11  C12   117.83  3.000
 XDD  O1    C02  O01   127.93  3.000
 XDD  O1    C02  C03   118.26  3.000
 XDD  O01   C02  C03   113.80  3.000
 XDD  H051  C05  N04   108.49  3.000
 XDD  H051  C05  C06   106.38  3.000
 XDD  N04   C05  C06   114.22  3.000
 XDD  H051  C05  C10   107.25  3.000
 XDD  N04   C05  C10   116.32  3.000
 XDD  C06   C05  C10   103.54  3.000
 XDD  H061  C06  N07   107.40  3.000
 XDD  H061  C06  C08   108.75  3.000
 XDD  N07   C06  C08   113.26  3.000
 XDD  H061  C06  C05   108.26  3.000
 XDD  N07   C06  C05   117.06  3.000
 XDD  C08   C06  C05   101.79  3.000
 XDD  H081  C08  H082  106.97  3.000
 XDD  H081  C08  C09   112.94  3.000
 XDD  H082  C08  C09   110.26  3.000
 XDD  H081  C08  C06   112.22  3.000
 XDD  H082  C08  C06   108.89  3.000
 XDD  C09   C08  C06   105.54  3.000
 XDD  H091  C09  H092  106.48  3.000
 XDD  H091  C09  C08   111.46  3.000
 XDD  H092  C09  C08   110.72  3.000
 XDD  H091  C09  C10   110.61  3.000
 XDD  H092  C09  C10   111.20  3.000
 XDD  C08   C09  C10   106.44  3.000
 XDD  N15   C17  C18   132.96  3.000
 XDD  N15   C17  C16   110.81  3.000
 XDD  C18   C17  C16   116.23  3.000
 XDD  N20   C18  N19   119.30  3.000
 XDD  N19   C18  C17   122.73  3.000
 XDD  N20   C18  C17   117.98  3.000
 XDD  H211  C21  N22   116.16  3.000
 XDD  H211  C21  N20   115.35  3.000
 XDD  N22   C21  N20   128.49  3.000
 XDD  C05   N04  C03   118.74  3.000
 XDD  C05   N04  C11   124.04  3.000
 XDD  C03   N04  C11   117.20  3.000
 XDD  H3    N07  H2    106.21  3.000
 XDD  H3    N07  C06   109.71  3.000
 XDD  H2    N07  C06   110.02  3.000
 XDD  C16   N13  C14   106.22  3.000
 XDD  C14   N13  C12   126.68  3.000
 XDD  C16   N13  C12   126.38  3.000
 XDD  C17   N15  C14   104.07  3.000
 XDD  C21   N20  C18   119.13  3.000
 XDD  C21   N22  C16   111.61  3.000
 XDD  H031  C03  H032  105.57  3.000
 XDD  H031  C03  N04   109.63  3.000
 XDD  H032  C03  N04   108.55  3.000
 XDD  H031  C03  C02   108.97  3.000
 XDD  H032  C03  C02   108.44  3.000
 XDD  N04   C03  C02   115.24  3.000
 XDD  H191  N19  H192  118.17  3.000
 XDD  H191  N19  C18   120.93  3.000
 XDD  H192  N19  C18   120.07  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  Var_01    C06   C08  C09  C10  -12.21  30.0  1
 XDD  Var_02    C08   C09  C10  C05  -14.83  30.0  1
 XDD  Var_03    C11   C12  N13  C14  -88.32  30.0  1
 XDD  Var_04    C05   N04  C03  C02  100.88  30.0  3
 XDD  Var_05    N13   C12  C11  N04  178.09  30.0  3
 XDD  Var_06    O01   C02  C03  N04  175.89  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  C03   0.020

