# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Apr 30 23:08:44 2020
#   Inital geometry file: a 120 line input string
#   Ligand name: N~2~-(2-aminoethyl)-N~2~-[(4-amino-2-oxopyrimidin-1(2H)-yl)acetyl]-D-lysine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: NCCCC[C@@H](N(CCN)C(=O)CN1C=CC(=NC1=O)N)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
 C66  C66  N~2~-(2-aminoethyl)-N~2~-[(4-amino-2-oxopyrimidin-1(2H)-yl)acetyl]-D-lysine  L-peptide  48  24  .  2022-03-15  2022-11-17
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_C66
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
 C66  C8'   C  CH2   0  -0.455   2.6111  -1.5300  -0.3950
 C66  C7'   C  C     0   0.587   2.0785  -0.1146  -0.5958
 C66  O7'   O  O     0  -0.483   2.1703   0.7127   0.2967
 C66  C5'   C  CH1   0  -0.243   0.9936   1.5173  -1.9693
 C66  C'    C  C     0   0.568   0.0197   1.8643  -0.8479
 C66  O1'   O  O     0  -0.442  -0.7599   1.0723  -0.3836
 C66  OXT   O  OH1   0  -0.584   0.0564   3.1414  -0.5049
 C66  N4'   N  NT    0  -0.455   1.4992   0.1679  -1.7779
 C66  C3'   C  CH2   0  -0.371   1.2182  -0.8249  -2.8031
 C66  C2'   C  CH2   0  -0.284  -0.1441  -1.5027  -2.6307
 C66  N1'   N  NH2   0  -0.785  -0.4591  -2.4666  -3.6657
 C66  N1    N  NR6   0  -0.499   3.3254  -1.6162   0.8515
 C66  C2    C  CR6   0   0.591   4.6105  -1.0575   0.9125
 C66  N3    N  N     0  -0.541   5.2451  -1.0524   2.1019
 C66  C4    C  CR6   0   0.511   4.6547  -1.5165   3.1866
 C66  C5    C  CR16  0  -0.472   3.3290  -2.0497   3.1655
 C66  C6    C  CR16  0   0.099   2.7096  -2.0620   1.9682
 C66  O2    O  O     0  -0.516   5.1041  -0.6092  -0.1133
 C66  N4    N  NH2   0  -0.809   5.3308  -1.4836   4.3348
 C66  CB    C  CH2   0  -0.409   2.1043   2.5358  -2.2336
 C66  CG    C  CH2   0  -0.426   2.9753   2.1477  -3.4223
 C66  CD    C  CH2   0  -0.424   4.0667   3.1741  -3.6966
 C66  CE    C  CH2   0  -0.270   4.9249   2.8071  -4.8970
 C66  NZ    N  NH2   0  -0.800   5.9797   3.7891  -5.1062
 C66  H8'1  H  HCH2  0   0.304   1.7831  -2.2415  -0.3762
 C66  H8'2  H  HCH2  0   0.307   3.2666  -1.8260  -1.2123
 C66  H5'1  H  HCH1  0   0.306   0.3643   1.4825  -2.8671
 C66  HXT   H  HOH1  0   0.483  -0.6242   3.3223   0.1611
 C66  H3'1  H  HCH2  0   0.264   2.0092  -1.5757  -2.8265
 C66  H3'2  H  HCH2  0   0.266   1.2554  -0.3285  -3.7753
 C66  H2'1  H  HCH2  0   0.231  -0.9261  -0.7406  -2.6084
 C66  H2'2  H  HCH2  0   0.224  -0.1817  -2.0042  -1.6599
 C66  H1'1  H  HNH2  0   0.345   0.2514  -3.1873  -3.6988
 C66  H1'2  H  HNH2  0   0.345  -0.4472  -2.0168  -4.5727
 C66  H5    H  HCR6  0   0.288   2.8418  -2.4196   4.0546
 C66  H6    H  HCR6  0   0.313   1.7046  -2.4422   1.8471
 C66  HN41  H  HNH2  0   0.402   6.2476  -1.0715   4.3679
 C66  HN42  H  HNH2  0   0.413   4.9146  -1.7814   5.1992
 C66  HB1   H  HCH2  0   0.240   1.6445   3.5051  -2.4372
 C66  HB2   H  HCH2  0   0.238   2.7246   2.6606  -1.3446
 C66  HG1   H  HCH2  0   0.215   2.3497   2.0326  -4.3145
 C66  HG2   H  HCH2  0   0.223   3.4399   1.1737  -3.2433
 C66  HD1   H  HCH2  0   0.215   4.7075   3.2753  -2.8153
 C66  HD2   H  HCH2  0   0.213   3.6117   4.1569  -3.8639
 C66  HE1   H  HCH2  0   0.211   5.3935   1.8357  -4.7160
 C66  HE2   H  HCH2  0   0.186   4.2720   2.6723  -5.7722
 C66  HZ1   H  HNH2  0   0.336   5.5629   4.6723  -5.3752
 C66  HZ2   H  HNH2  0   0.345   6.5487   3.5086  -5.8946

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
 C66  C8'  C7'   single  1.526  0.020  1.526
 C66  C8'  N1    single  1.439  0.020  1.439
 C66  C8'  H8'1  single  0.970  0.020  1.090
 C66  C8'  H8'2  single  0.970  0.020  1.090
 C66  C7'  O7'   double  1.220  0.020  1.220
 C66  C7'  N4'   single  1.346  0.020  1.346
 C66  C5'  C'    single  1.525  0.020  1.525
 C66  C5'  N4'   single  1.454  0.020  1.454
 C66  C5'  CB    single  1.530  0.020  1.530
 C66  C5'  H5'1  single  0.970  0.020  1.090
 C66  C'   O1'   double  1.204  0.020  1.204
 C66  C'   OXT   single  1.323  0.020  1.323
 C66  OXT  HXT   single  0.850  0.020  0.980
 C66  N4'  C3'   single  1.455  0.020  1.455
 C66  C3'  C2'   single  1.531  0.020  1.531
 C66  C3'  H3'1  single  0.970  0.020  1.090
 C66  C3'  H3'2  single  0.970  0.020  1.090
 C66  C2'  N1'   single  1.449  0.020  1.449
 C66  C2'  H2'1  single  0.970  0.020  1.090
 C66  C2'  H2'2  single  0.970  0.020  1.090
 C66  N1'  H1'1  single  0.890  0.020  1.040
 C66  N1'  H1'2  single  0.890  0.020  1.040
 C66  N1   C2    single  1.403  0.020  1.403
 C66  N1   C6    single  1.351  0.020  1.351
 C66  C2   N3    single  1.348  0.020  1.348
 C66  C2   O2    double  1.223  0.020  1.223
 C66  N3   C4    double  1.319  0.020  1.319
 C66  C4   C5    single  1.429  0.020  1.429
 C66  C4   N4    single  1.333  0.020  1.333
 C66  C5   C6    double  1.348  0.020  1.348
 C66  C5   H5    single  0.930  0.020  1.080
 C66  C6   H6    single  0.930  0.020  1.080
 C66  N4   HN41  single  0.860  0.020  1.020
 C66  N4   HN42  single  0.860  0.020  1.020
 C66  CB   CG    single  1.524  0.020  1.524
 C66  CB   HB1   single  0.970  0.020  1.090
 C66  CB   HB2   single  0.970  0.020  1.090
 C66  CG   CD    single  1.523  0.020  1.523
 C66  CG   HG1   single  0.970  0.020  1.090
 C66  CG   HG2   single  0.970  0.020  1.090
 C66  CD   CE    single  1.521  0.020  1.521
 C66  CD   HD1   single  0.970  0.020  1.090
 C66  CD   HD2   single  0.970  0.020  1.090
 C66  CE   NZ    single  1.456  0.020  1.456
 C66  CE   HE1   single  0.970  0.020  1.090
 C66  CE   HE2   single  0.970  0.020  1.090
 C66  NZ   HZ1   single  0.890  0.020  1.040
 C66  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
 C66  H8'2  C8'  H8'1  107.00  3.000
 C66  H8'2  C8'  N1    109.58  3.000
 C66  H8'1  C8'  N1    108.81  3.000
 C66  H8'2  C8'  C7'   111.32  3.000
 C66  H8'1  C8'  C7'   110.01  3.000
 C66  N1    C8'  C7'   110.05  3.000
 C66  N4'   C7'  O7'   122.16  3.000
 C66  N4'   C7'  C8'   117.41  3.000
 C66  O7'   C7'  C8'   120.43  3.000
 C66  H5'1  C5'  CB    107.23  3.000
 C66  H5'1  C5'  N4'   106.13  3.000
 C66  CB    C5'  N4'   112.84  3.000
 C66  H5'1  C5'  C'    104.04  3.000
 C66  CB    C5'  C'    116.05  3.000
 C66  N4'   C5'  C'    109.65  3.000
 C66  OXT   C'   O1'   123.56  3.000
 C66  OXT   C'   C5'   113.11  3.000
 C66  O1'   C'   C5'   123.18  3.000
 C66  HXT   OXT  C'    109.81  3.000
 C66  C3'   N4'  C5'   118.27  3.000
 C66  C3'   N4'  C7'   123.97  3.000
 C66  C5'   N4'  C7'   117.39  3.000
 C66  H3'2  C3'  H3'1  105.61  3.000
 C66  H3'2  C3'  C2'   109.37  3.000
 C66  H3'1  C3'  C2'   110.05  3.000
 C66  H3'2  C3'  N4'   108.09  3.000
 C66  H3'1  C3'  N4'   110.17  3.000
 C66  C2'   C3'  N4'   113.24  3.000
 C66  H2'2  C2'  H2'1  106.10  3.000
 C66  H2'2  C2'  N1'   108.76  3.000
 C66  H2'1  C2'  N1'   108.85  3.000
 C66  H2'2  C2'  C3'   109.49  3.000
 C66  H2'1  C2'  C3'   109.30  3.000
 C66  N1'   C2'  C3'   114.04  3.000
 C66  H1'2  N1'  H1'1  106.18  3.000
 C66  H1'2  N1'  C2'   109.99  3.000
 C66  H1'1  N1'  C2'   110.14  3.000
 C66  C6    N1   C2    120.88  3.000
 C66  C6    N1   C8'   120.62  3.000
 C66  C2    N1   C8'   117.94  3.000
 C66  O2    C2   N3    123.26  3.000
 C66  O2    C2   N1    118.63  3.000
 C66  N3    C2   N1    118.11  3.000
 C66  C4    N3   C2    120.89  3.000
 C66  N4    C4   C5    119.51  3.000
 C66  N4    C4   N3    118.20  3.000
 C66  C5    C4   N3    122.30  3.000
 C66  H5    C5   C6    121.40  3.000
 C66  H5    C5   C4    122.32  3.000
 C66  C6    C5   C4    116.28  3.000
 C66  H6    C6   C5    121.99  3.000
 C66  H6    C6   N1    116.56  3.000
 C66  C5    C6   N1    121.44  3.000
 C66  HN42  N4   HN41  118.09  3.000
 C66  HN42  N4   C4    121.58  3.000
 C66  HN41  N4   C4    120.06  3.000
 C66  HB2   CB   HB1   106.84  3.000
 C66  HB2   CB   CG    109.86  3.000
 C66  HB1   CB   CG    108.74  3.000
 C66  HB2   CB   C5'   110.37  3.000
 C66  HB1   CB   C5'   108.51  3.000
 C66  CG    CB   C5'   112.34  3.000
 C66  HG2   CG   HG1   106.39  3.000
 C66  HG2   CG   CD    108.97  3.000
 C66  HG1   CG   CD    109.46  3.000
 C66  HG2   CG   CB    109.99  3.000
 C66  HG1   CG   CB    109.61  3.000
 C66  CD    CG   CB    112.24  3.000
 C66  HD2   CD   HD1   106.44  3.000
 C66  HD2   CD   CE    109.29  3.000
 C66  HD1   CD   CE    109.12  3.000
 C66  HD2   CD   CG    109.53  3.000
 C66  HD1   CD   CG    109.69  3.000
 C66  CE    CD   CG    112.58  3.000
 C66  HE2   CE   HE1   106.09  3.000
 C66  HE2   CE   NZ    113.46  3.000
 C66  HE1   CE   NZ    108.20  3.000
 C66  HE2   CE   CD    108.82  3.000
 C66  HE1   CE   CD    109.00  3.000
 C66  NZ    CE   CD    111.07  3.000
 C66  HZ2   NZ   HZ1   105.44  3.000
 C66  HZ2   NZ   CE    109.41  3.000
 C66  HZ1   NZ   CE    109.16  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
 C66  CONST_01  C4    N3   C2   N1      0.00   0.0  0
 C66  CONST_02  C5    C4   N3   C2      0.00   0.0  0
 C66  CONST_03  C6    N1   C2   N3      0.00   0.0  0
 C66  CONST_04  N3    C2   N1   C8'   180.00   0.0  0
 C66  CONST_05  N4    C4   N3   C2    180.00   0.0  0
 C66  CONST_06  O2    C2   N3   C4    180.00   0.0  0
 C66  CONST_07  O2    C2   N1   C6    180.00   0.0  0
 C66  CONST_08  O2    C2   N1   C8'     0.00   0.0  0
 C66  CONST_09  HN41  N4   C4   N3      0.00   0.0  0
 C66  CONST_10  HN42  N4   C4   N3    180.00   0.0  0
 C66  CONST_11  C5'   N4'  C7'  C8'   180.00   0.0  0
 C66  CONST_12  C3'   N4'  C7'  C8'     0.00   0.0  0
 C66  CONST_13  C5'   N4'  C7'  O7'     0.00   0.0  0
 C66  CONST_14  C3'   N4'  C7'  O7'   180.00   0.0  0
 C66  CONST_15  HXT   OXT  C'   C5'   180.00   0.0  0
 C66  Var_01    C2    N1   C8'  C7'   -75.73  30.0  3
 C66  Var_02    N1    C8'  C7'  O7'    -7.15  30.0  2
 C66  Var_03    C2'   C3'  N4'  C7'    87.79  30.0  3
 C66  Var_04    CD    CG   CB   C5'   179.11  30.0  3
 C66  Var_05    N1'   C2'  C3'  N4'   178.25  30.0  3
 C66  Var_06    CE    CD   CG   CB   -178.96  30.0  3
 C66  Var_07    NZ    CE   CD   CG   -178.38  30.0  3
 C66  Var_08    H1'1  N1'  C2'  C3'    58.10  30.0  3
 C66  Var_09    HZ1   NZ   CE   CD    -66.54  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
 C66  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
 C66  plan-1  C8'   0.020
 C66  plan-1  N1    0.020
 C66  plan-1  C2    0.020
 C66  plan-1  N3    0.020
 C66  plan-1  C4    0.020
 C66  plan-1  C5    0.020
 C66  plan-1  C6    0.020
 C66  plan-1  O2    0.020
 C66  plan-1  N4    0.020
 C66  plan-1  H5    0.020
 C66  plan-1  H6    0.020
 C66  plan-1  HN41  0.020
 C66  plan-1  HN42  0.020
 C66  plan-2  C8'   0.020
 C66  plan-2  C7'   0.020
 C66  plan-2  O7'   0.020
 C66  plan-2  C5'   0.020
 C66  plan-2  N4'   0.020
 C66  plan-2  C3'   0.020
 C66  plan-3  C5'   0.020
 C66  plan-3  C'    0.020
 C66  plan-3  O1'   0.020
 C66  plan-3  OXT   0.020
 C66  plan-3  HXT   0.020

