# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Apr 14 00:21:30 2020
#   Inital geometry file: a 117 line input string
#   Ligand name: N~2~-(2-aminoethyl)-N~2~-[(6-amino-9H-purin-9-yl)acetyl]-D-lysine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: NCCCC[C@@H](N(CCN)C(=O)Cn1cnc2c(N)ncnc12)C(O)=O
#
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
 A66  A66  N~2~-(2-aminoethyl)-N~2~-[(6-amino-9H-purin-9-yl)acetyl]-D-lysine  L-peptide  49  26  .  2022-03-11  2022-07-24
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_A66
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
 A66  C8'   C  CH2    0  -0.463   2.9493   0.3338  -3.8971
 A66  C7'   C  C      0   0.555   2.4295  -0.4541  -2.6922
 A66  O7'   O  O      0  -0.495   2.7823  -1.6146  -2.5404
 A66  C5'   C  CH1    0  -0.291   0.9992   1.4756  -2.1531
 A66  C'    C  C      0   0.438  -0.4077   1.2804  -2.7942
 A66  O1'   O  O      0  -0.594  -0.5769   0.2151  -3.4138
 A66  OXT   O  OC    -1  -0.592  -1.2102   2.2239  -2.6788
 A66  N4'   N  NT     0  -0.427   1.6034   0.1843  -1.8498
 A66  C3'   C  CH2    0  -0.315   0.9738  -0.6065  -0.8014
 A66  C2'   C  CH2    0  -0.288   1.8421  -0.7813   0.4389
 A66  N1'   N  NH2    0  -0.800   1.1307  -1.5974   1.4108
 A66  N9    N  NR5    0  -0.485   3.9207  -0.4347  -4.6192
 A66  C8    C  CR15   0   0.110   3.6845  -1.3229  -5.6265
 A66  N7    N  N      0  -0.454   4.7500  -1.9550  -6.0243
 A66  C5    C  CR56   0  -0.007   5.7471  -1.4695  -5.2177
 A66  C6    C  CR6    0   0.451   7.1261  -1.7327  -5.1315
 A66  N6    N  NH2    0  -0.817   7.7485  -2.5949  -5.9391
 A66  N1    N  N      0  -0.474   7.8333  -1.0742  -4.2061
 A66  C2    C  CR16   0   0.039   7.2133  -0.2012  -3.4153
 A66  N3    N  N      0  -0.451   5.9351   0.1335  -3.4031
 A66  C4    C  CR56   0   0.481   5.2463  -0.5318  -4.3275
 A66  CB    C  CH2    0  -0.413   1.0409   2.4250  -0.9619
 A66  CG    C  CH2    0  -0.424   2.4555   2.7994  -0.5373
 A66  CD    C  CH2    0  -0.424   2.4758   3.7838   0.6246
 A66  CE    C  CH2    0  -0.271   3.8842   4.1497   1.0659
 A66  NZ    N  NH2    0  -0.801   3.8569   5.0904   2.1774
 A66  H8'1  H  HCH2   0   0.310   2.1252   0.5776  -4.5692
 A66  H8'2  H  HCH2   0   0.299   3.4130   1.2726  -3.5933
 A66  H5'1  H  HCH1   0   0.269   1.5976   1.9575  -2.9307
 A66  H3'1  H  HCH2   0   0.244   0.6996  -1.5889  -1.1883
 A66  H3'2  H  HCH2   0   0.241   0.0437  -0.1088  -0.5206
 A66  H2'1  H  HCH2   0   0.201   2.1347   0.2053   0.8226
 A66  H2'2  H  HCH2   0   0.228   2.7634  -1.2953   0.1614
 A66  H1'1  H  HNH2   0   0.351   1.7396  -1.7922   2.1946
 A66  H1'2  H  HNH2   0   0.340   0.3586  -1.0651   1.7932
 A66  H8    H  HCR5   0   0.292   2.6940  -1.4475  -6.0394
 A66  HN61  H  HNH2   0   0.410   7.2287  -3.1600  -6.5874
 A66  HN62  H  HNH2   0   0.402   8.7192  -2.8118  -5.7937
 A66  H2    H  HCR6   0   0.250   7.8448   0.2966  -2.6871
 A66  HB1   H  HCH2   0   0.234   0.5007   3.3273  -1.2510
 A66  HB2   H  HCH2   0   0.217   0.4915   2.0084  -0.1102
 A66  HG1   H  HCH2   0   0.213   2.9858   3.2314  -1.3935
 A66  HG2   H  HCH2   0   0.215   3.0155   1.9013  -0.2594
 A66  HD1   H  HCH2   0   0.211   1.9351   3.3609   1.4774
 A66  HD2   H  HCH2   0   0.210   1.9375   4.6943   0.3371
 A66  HE1   H  HCH2   0   0.210   4.3993   3.2442   1.3993
 A66  HE2   H  HCH2   0   0.186   4.4461   4.5170   0.1942
 A66  HZ1   H  HNH2   0   0.336   3.4764   5.9730   1.8580
 A66  HZ2   H  HNH2   0   0.344   4.8033   5.2937   2.4726

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
 A66  C8'  C7'   single    1.531  0.020  1.531
 A66  C8'  N9    single    1.434  0.020  1.434
 A66  C8'  H8'1  single    0.970  0.020  1.090
 A66  C8'  H8'2  single    0.970  0.020  1.090
 A66  C7'  O7'   double    1.222  0.020  1.222
 A66  C7'  N4'   single    1.341  0.020  1.341
 A66  C5'  C'    single    1.558  0.020  1.558
 A66  C5'  N4'   single    1.458  0.020  1.458
 A66  C5'  CB    single    1.524  0.020  1.524
 A66  C5'  H5'1  single    0.970  0.020  1.090
 A66  C'   O1'   deloc     1.244  0.020  1.244
 A66  C'   OXT   deloc     1.244  0.020  1.244
 A66  N4'  C3'   single    1.456  0.020  1.456
 A66  C3'  C2'   single    1.524  0.020  1.524
 A66  C3'  H3'1  single    0.970  0.020  1.090
 A66  C3'  H3'2  single    0.970  0.020  1.090
 A66  C2'  N1'   single    1.455  0.020  1.455
 A66  C2'  H2'1  single    0.970  0.020  1.090
 A66  C2'  H2'2  single    0.970  0.020  1.090
 A66  N1'  H1'1  single    0.890  0.020  1.040
 A66  N1'  H1'2  single    0.890  0.020  1.040
 A66  N9   C8    aromatic  1.364  0.020  1.364
 A66  N9   C4    aromatic  1.361  0.020  1.361
 A66  C8   N7    aromatic  1.301  0.020  1.301
 A66  C8   H8    single    0.930  0.020  1.080
 A66  N7   C5    aromatic  1.371  0.020  1.371
 A66  C5   C6    aromatic  1.407  0.020  1.407
 A66  C5   C4    aromatic  1.387  0.020  1.387
 A66  C6   N6    single    1.335  0.020  1.335
 A66  C6   N1    aromatic  1.338  0.020  1.338
 A66  N6   HN61  single    0.860  0.020  1.020
 A66  N6   HN62  single    0.860  0.020  1.020
 A66  N1   C2    aromatic  1.331  0.020  1.331
 A66  C2   N3    aromatic  1.321  0.020  1.321
 A66  C2   H2    single    0.930  0.020  1.080
 A66  N3   C4    aromatic  1.331  0.020  1.331
 A66  CB   CG    single    1.524  0.020  1.524
 A66  CB   HB1   single    0.970  0.020  1.090
 A66  CB   HB2   single    0.970  0.020  1.090
 A66  CG   CD    single    1.523  0.020  1.523
 A66  CG   HG1   single    0.970  0.020  1.090
 A66  CG   HG2   single    0.970  0.020  1.090
 A66  CD   CE    single    1.521  0.020  1.521
 A66  CD   HD1   single    0.970  0.020  1.090
 A66  CD   HD2   single    0.970  0.020  1.090
 A66  CE   NZ    single    1.456  0.020  1.456
 A66  CE   HE1   single    0.970  0.020  1.090
 A66  CE   HE2   single    0.970  0.020  1.090
 A66  NZ   HZ1   single    0.890  0.020  1.040
 A66  NZ   HZ2   single    0.890  0.020  1.040

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
 A66  H8'2  C8'  H8'1  107.49  3.000
 A66  H8'2  C8'  N9    108.29  3.000
 A66  H8'1  C8'  N9    108.74  3.000
 A66  H8'2  C8'  C7'   111.61  3.000
 A66  H8'1  C8'  C7'   110.08  3.000
 A66  N9    C8'  C7'   110.52  3.000
 A66  N4'   C7'  O7'   123.47  3.000
 A66  N4'   C7'  C8'   117.29  3.000
 A66  O7'   C7'  C8'   119.24  3.000
 A66  H5'1  C5'  CB    105.45  3.000
 A66  H5'1  C5'  N4'   108.16  3.000
 A66  CB    C5'  N4'   112.21  3.000
 A66  H5'1  C5'  C'    104.88  3.000
 A66  CB    C5'  C'    115.11  3.000
 A66  N4'   C5'  C'    110.42  3.000
 A66  OXT   C'   O1'   127.44  3.000
 A66  OXT   C'   C5'   116.70  3.000
 A66  O1'   C'   C5'   115.79  3.000
 A66  C3'   N4'  C5'   116.85  3.000
 A66  C3'   N4'  C7'   117.38  3.000
 A66  C5'   N4'  C7'   123.11  3.000
 A66  H3'2  C3'  H3'1  106.72  3.000
 A66  H3'2  C3'  C2'   109.17  3.000
 A66  H3'1  C3'  C2'   109.18  3.000
 A66  H3'2  C3'  N4'   107.82  3.000
 A66  H3'1  C3'  N4'   110.02  3.000
 A66  C2'   C3'  N4'   113.69  3.000
 A66  H2'2  C2'  H2'1  106.68  3.000
 A66  H2'2  C2'  N1'   108.58  3.000
 A66  H2'1  C2'  N1'   113.62  3.000
 A66  H2'2  C2'  C3'   109.16  3.000
 A66  H2'1  C2'  C3'   109.46  3.000
 A66  N1'   C2'  C3'   109.23  3.000
 A66  H1'2  N1'  H1'1  105.52  3.000
 A66  H1'2  N1'  C2'   109.28  3.000
 A66  H1'1  N1'  C2'   109.35  3.000
 A66  C4    N9   C8    106.30  3.000
 A66  C4    N9   C8'   126.17  3.000
 A66  C8    N9   C8'   127.14  3.000
 A66  H8    C8   N7    125.31  3.000
 A66  H8    C8   N9    121.08  3.000
 A66  N7    C8   N9    113.60  3.000
 A66  C5    N7   C8    104.10  3.000
 A66  C4    C5   C6    116.19  3.000
 A66  C4    C5   N7    110.76  3.000
 A66  C6    C5   N7    133.05  3.000
 A66  N1    C6   N6    119.33  3.000
 A66  N1    C6   C5    117.94  3.000
 A66  N6    C6   C5    122.73  3.000
 A66  HN62  N6   HN61  118.13  3.000
 A66  HN62  N6   C6    120.13  3.000
 A66  HN61  N6   C6    120.81  3.000
 A66  C2    N1   C6    119.17  3.000
 A66  H2    C2   N3    116.15  3.000
 A66  H2    C2   N1    115.38  3.000
 A66  N3    C2   N1    128.48  3.000
 A66  C4    N3   C2    111.57  3.000
 A66  N3    C4   C5    126.65  3.000
 A66  N3    C4   N9    128.13  3.000
 A66  C5    C4   N9    105.21  3.000
 A66  HB2   CB   HB1   105.80  3.000
 A66  HB2   CB   CG    110.02  3.000
 A66  HB1   CB   CG    109.30  3.000
 A66  HB2   CB   C5'   110.91  3.000
 A66  HB1   CB   C5'   107.13  3.000
 A66  CG    CB   C5'   113.35  3.000
 A66  HG2   CG   HG1   105.92  3.000
 A66  HG2   CG   CD    109.27  3.000
 A66  HG1   CG   CD    109.56  3.000
 A66  HG2   CG   CB    110.14  3.000
 A66  HG1   CG   CB    109.17  3.000
 A66  CD    CG   CB    112.57  3.000
 A66  HD2   CD   HD1   106.42  3.000
 A66  HD2   CD   CE    109.33  3.000
 A66  HD1   CD   CE    108.93  3.000
 A66  HD2   CD   CG    109.28  3.000
 A66  HD1   CD   CG    109.75  3.000
 A66  CE    CD   CG    112.91  3.000
 A66  HE2   CE   HE1   106.10  3.000
 A66  HE2   CE   NZ    113.49  3.000
 A66  HE1   CE   NZ    108.11  3.000
 A66  HE2   CE   CD    108.87  3.000
 A66  HE1   CE   CD    108.99  3.000
 A66  NZ    CE   CD    111.07  3.000
 A66  HZ2   NZ   HZ1   105.55  3.000
 A66  HZ2   NZ   CE    109.56  3.000
 A66  HZ1   NZ   CE    109.22  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
 A66  CONST_01  C5    N7   C8   N9      0.00   0.0  0
 A66  CONST_02  N7    C5   C4   N9      0.00   0.0  0
 A66  CONST_03  C6    C5   C4   N9    180.00   0.0  0
 A66  CONST_04  C2    N3   C4   N9    180.00   0.0  0
 A66  CONST_05  C5    C4   N9   C8      0.00   0.0  0
 A66  CONST_06  N3    C4   N9   C8    180.00   0.0  0
 A66  CONST_07  C6    C5   N7   C8    180.00   0.0  0
 A66  CONST_08  C4    C5   N7   C8      0.00   0.0  0
 A66  CONST_09  C4    N9   C8   N7      0.00   0.0  0
 A66  CONST_10  N1    C6   C5   N7    180.00   0.0  0
 A66  CONST_11  N3    C4   C5   N7    180.00   0.0  0
 A66  CONST_12  C2    N1   C6   C5      0.00   0.0  0
 A66  CONST_13  C2    N3   C4   C5      0.00   0.0  0
 A66  CONST_14  N3    C4   C5   C6      0.00   0.0  0
 A66  CONST_15  N3    C2   N1   C6      0.00   0.0  0
 A66  CONST_16  C4    C5   C6   N1      0.00   0.0  0
 A66  CONST_17  C4    N3   C2   N1      0.00   0.0  0
 A66  CONST_18  N7    C8   N9   C8'   180.00   0.0  0
 A66  CONST_19  C5    C4   N9   C8'   180.00   0.0  0
 A66  CONST_20  N3    C4   N9   C8'     0.00   0.0  0
 A66  CONST_21  N6    C6   C5   N7      0.00   0.0  0
 A66  CONST_22  C4    C5   C6   N6    180.00   0.0  0
 A66  CONST_23  C2    N1   C6   N6    180.00   0.0  0
 A66  CONST_24  H8    C8   N7   C5    180.00   0.0  0
 A66  CONST_25  H2    C2   N1   C6    180.00   0.0  0
 A66  CONST_26  HN61  N6   C6   C5      0.00   0.0  0
 A66  CONST_27  HN62  N6   C6   C5    180.00   0.0  0
 A66  CONST_28  C5'   N4'  C7'  C8'     0.00   0.0  0
 A66  CONST_29  C3'   N4'  C7'  C8'   180.00   0.0  0
 A66  CONST_30  C5'   N4'  C7'  O7'   180.00   0.0  0
 A66  CONST_31  C3'   N4'  C7'  O7'     0.00   0.0  0
 A66  Var_01    C8    N9   C8'  C7'    88.13  30.0  2
 A66  Var_02    N9    C8'  C7'  O7'    -5.71  30.0  2
 A66  Var_03    C2'   C3'  N4'  C7'    84.41  30.0  3
 A66  Var_04    CD    CG   CB   C5'   178.12  30.0  3
 A66  Var_05    N1'   C2'  C3'  N4'  -179.21  30.0  3
 A66  Var_06    CE    CD   CG   CB    179.30  30.0  3
 A66  Var_07    NZ    CE   CD   CG   -179.95  30.0  3
 A66  Var_08    H1'1  N1'  C2'  C3'   174.36  30.0  3
 A66  Var_09    HZ1   NZ   CE   CD    -66.73  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
 A66  chir_01  C5'  C'  N4'  CB  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
 A66  plan-1  C8'   0.020
 A66  plan-1  N9    0.020
 A66  plan-1  C8    0.020
 A66  plan-1  N7    0.020
 A66  plan-1  C5    0.020
 A66  plan-1  C6    0.020
 A66  plan-1  N6    0.020
 A66  plan-1  N1    0.020
 A66  plan-1  C2    0.020
 A66  plan-1  N3    0.020
 A66  plan-1  C4    0.020
 A66  plan-1  H8    0.020
 A66  plan-1  H2    0.020
 A66  plan-2  C8'   0.020
 A66  plan-2  C7'   0.020
 A66  plan-2  O7'   0.020
 A66  plan-2  C5'   0.020
 A66  plan-2  N4'   0.020
 A66  plan-2  C3'   0.020
 A66  plan-3  C6    0.020
 A66  plan-3  N6    0.020
 A66  plan-3  HN61  0.020
 A66  plan-3  HN62  0.020
 A66  plan-4  C5'   0.020
 A66  plan-4  C'    0.020
 A66  plan-4  O1'   0.020
 A66  plan-4  OXT   0.020

