# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Apr 19 13:53:54 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  47  24  .  2022-03-15  2022-07-24
;
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  -0.459   2.6543  -1.5631  -0.3808
 C66  C7'   C  C      0   0.577   2.2297  -0.1102  -0.6116
 C66  O7'   O  O      0  -0.498   2.4413   0.7208   0.2587
 C66  C5'   C  CH1    0  -0.242   1.0979   1.5229  -1.9682
 C66  C'    C  C      0   0.431   0.1104   1.9184  -0.8349
 C66  O1'   O  O      0  -0.597  -0.5752   0.9989  -0.3541
 C66  OXT   O  OC    -1  -0.602   0.0376   3.1306  -0.5575
 C66  N4'   N  NT     0  -0.440   1.6329   0.1774  -1.7772
 C66  C3'   C  CH2    0  -0.366   1.2965  -0.8306  -2.7662
 C66  C2'   C  CH2    0  -0.285  -0.0827  -1.4650  -2.5643
 C66  N1'   N  NH2    0  -0.787  -0.4359  -2.4365  -3.5828
 C66  N1    N  NR6    0  -0.494   3.3361  -1.6816   0.8830
 C66  C2    C  CR6    0   0.587   4.6767  -1.2806   0.9557
 C66  N3    N  N      0  -0.541   5.2752  -1.2778   2.1647
 C66  C4    C  CR6    0   0.510   4.6030  -1.5956   3.2541
 C66  C5    C  CR16   0  -0.474   3.2227  -1.9613   3.2194
 C66  C6    C  CR16   0   0.099   2.6401  -1.9710   2.0033
 C66  O2    O  O      0  -0.519   5.2551  -0.9625  -0.0749
 C66  N4    N  NH2    0  -0.810   5.2459  -1.5711   4.4222
 C66  CB    C  CH2    0  -0.399   2.1890   2.5480  -2.2630
 C66  CG    C  CH2    0  -0.419   3.0269   2.2074  -3.4889
 C66  CD    C  CH2    0  -0.423   4.0887   3.2592  -3.7835
 C66  CE    C  CH2    0  -0.269   4.8858   2.9598  -5.0430
 C66  NZ    N  NH2    0  -0.801   5.9120   3.9695  -5.2670
 C66  H8'1  H  HCH2   0   0.294   1.7793  -2.2154  -0.3660
 C66  H8'2  H  HCH2   0   0.302   3.3044  -1.9232  -1.1760
 C66  H5'1  H  HCH1   0   0.246   0.4742   1.4569  -2.8692
 C66  H3'1  H  HCH2   0   0.250   2.0601  -1.6102  -2.7933
 C66  H3'2  H  HCH2   0   0.255   1.3287  -0.3574  -3.7507
 C66  H2'1  H  HCH2   0   0.231  -0.8414  -0.6815  -2.5402
 C66  H2'2  H  HCH2   0   0.217  -0.1245  -1.9503  -1.5859
 C66  H1'1  H  HNH2   0   0.342   0.2616  -3.1700  -3.6206
 C66  H1'2  H  HNH2   0   0.342  -0.4256  -1.9962  -4.4947
 C66  H5    H  HCR6   0   0.286   2.6683  -2.2100   4.1114
 C66  H6    H  HCR6   0   0.310   1.5975  -2.2257   1.8711
 C66  HN41  H  HNH2   0   0.401   6.2113  -1.2929   4.4634
 C66  HN42  H  HNH2   0   0.412   4.7742  -1.7730   5.2857
 C66  HB1   H  HCH2   0   0.215   1.7047   3.5136  -2.4202
 C66  HB2   H  HCH2   0   0.215   2.8387   2.6693  -1.3933
 C66  HG1   H  HCH2   0   0.203   2.3709   2.0999  -4.3608
 C66  HG2   H  HCH2   0   0.212   3.5149   1.2368  -3.3533
 C66  HD1   H  HCH2   0   0.210   4.7760   3.3383  -2.9351
 C66  HD2   H  HCH2   0   0.207   3.6107   4.2406  -3.8845
 C66  HE1   H  HCH2   0   0.208   5.3791   1.9896  -4.9319
 C66  HE2   H  HCH2   0   0.184   4.1879   2.8522  -5.8867
 C66  HZ1   H  HNH2   0   0.335   5.4643   4.8611  -5.4432
 C66  HZ2   H  HNH2   0   0.344   6.4180   3.7519  -6.1160

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  1.531  0.020  1.531
 C66  C8'  N1    single  1.441  0.020  1.441
 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  1.222  0.020  1.222
 C66  C7'  N4'   single  1.341  0.020  1.341
 C66  C5'  C'    single  1.554  0.020  1.554
 C66  C5'  N4'   single  1.461  0.020  1.461
 C66  C5'  CB    single  1.526  0.020  1.526
 C66  C5'  H5'1  single  0.970  0.020  1.090
 C66  C'   O1'   deloc   1.244  0.020  1.244
 C66  C'   OXT   deloc   1.246  0.020  1.246
 C66  N4'  C3'   single  1.452  0.020  1.452
 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  1.451  0.020  1.451
 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  1.401  0.020  1.401
 C66  N1   C6    single  1.350  0.020  1.350
 C66  C2   N3    single  1.349  0.020  1.349
 C66  C2   O2    double  1.224  0.020  1.224
 C66  N3   C4    double  1.319  0.020  1.319
 C66  C4   C5    single  1.428  0.020  1.428
 C66  C4   N4    single  1.334  0.020  1.334
 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  1.520  0.020  1.520
 C66  CD   HD1   single  0.970  0.020  1.090
 C66  CD   HD2   single  0.970  0.020  1.090
 C66  CE   NZ    single  1.457  0.020  1.457
 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  106.92  3.000
 C66  H8'2  C8'  N1    109.33  3.000
 C66  H8'1  C8'  N1    108.56  3.000
 C66  H8'2  C8'  C7'   111.68  3.000
 C66  H8'1  C8'  C7'   110.29  3.000
 C66  N1    C8'  C7'   109.96  3.000
 C66  N4'   C7'  O7'   123.41  3.000
 C66  N4'   C7'  C8'   117.26  3.000
 C66  O7'   C7'  C8'   119.34  3.000
 C66  H5'1  C5'  CB    106.75  3.000
 C66  H5'1  C5'  N4'   105.07  3.000
 C66  CB    C5'  N4'   112.47  3.000
 C66  H5'1  C5'  C'    104.64  3.000
 C66  CB    C5'  C'    115.10  3.000
 C66  N4'   C5'  C'    111.83  3.000
 C66  OXT   C'   O1'   126.96  3.000
 C66  OXT   C'   C5'   116.56  3.000
 C66  O1'   C'   C5'   116.36  3.000
 C66  C3'   N4'  C5'   117.75  3.000
 C66  C3'   N4'  C7'   123.13  3.000
 C66  C5'   N4'  C7'   118.32  3.000
 C66  H3'2  C3'  H3'1  105.44  3.000
 C66  H3'2  C3'  C2'   108.94  3.000
 C66  H3'1  C3'  C2'   109.71  3.000
 C66  H3'2  C3'  N4'   107.84  3.000
 C66  H3'1  C3'  N4'   110.53  3.000
 C66  C2'   C3'  N4'   113.99  3.000
 C66  H2'2  C2'  H2'1  105.81  3.000
 C66  H2'2  C2'  N1'   108.77  3.000
 C66  H2'1  C2'  N1'   109.09  3.000
 C66  H2'2  C2'  C3'   109.66  3.000
 C66  H2'1  C2'  C3'   109.37  3.000
 C66  N1'   C2'  C3'   113.83  3.000
 C66  H1'2  N1'  H1'1  105.92  3.000
 C66  H1'2  N1'  C2'   109.78  3.000
 C66  H1'1  N1'  C2'   110.08  3.000
 C66  C6    N1   C2    120.76  3.000
 C66  C6    N1   C8'   120.10  3.000
 C66  C2    N1   C8'   118.34  3.000
 C66  O2    C2   N3    122.99  3.000
 C66  O2    C2   N1    118.87  3.000
 C66  N3    C2   N1    118.14  3.000
 C66  C4    N3   C2    120.91  3.000
 C66  N4    C4   C5    119.46  3.000
 C66  N4    C4   N3    118.26  3.000
 C66  C5    C4   N3    122.28  3.000
 C66  H5    C5   C6    121.45  3.000
 C66  H5    C5   C4    122.36  3.000
 C66  C6    C5   C4    116.19  3.000
 C66  H6    C6   C5    121.90  3.000
 C66  H6    C6   N1    116.49  3.000
 C66  C5    C6   N1    121.60  3.000
 C66  HN42  N4   HN41  118.11  3.000
 C66  HN42  N4   C4    121.53  3.000
 C66  HN41  N4   C4    120.25  3.000
 C66  HB2   CB   HB1   106.28  3.000
 C66  HB2   CB   CG    109.77  3.000
 C66  HB1   CB   CG    109.02  3.000
 C66  HB2   CB   C5'   110.25  3.000
 C66  HB1   CB   C5'   107.75  3.000
 C66  CG    CB   C5'   113.49  3.000
 C66  HG2   CG   HG1   106.16  3.000
 C66  HG2   CG   CD    108.99  3.000
 C66  HG1   CG   CD    109.33  3.000
 C66  HG2   CG   CB    110.10  3.000
 C66  HG1   CG   CB    109.43  3.000
 C66  CD    CG   CB    112.62  3.000
 C66  HD2   CD   HD1   106.29  3.000
 C66  HD2   CD   CE    109.19  3.000
 C66  HD1   CD   CE    109.09  3.000
 C66  HD2   CD   CG    109.39  3.000
 C66  HD1   CD   CG    109.73  3.000
 C66  CE    CD   CG    112.93  3.000
 C66  HE2   CE   HE1   106.09  3.000
 C66  HE2   CE   NZ    113.37  3.000
 C66  HE1   CE   NZ    108.22  3.000
 C66  HE2   CE   CD    108.79  3.000
 C66  HE1   CE   CD    109.08  3.000
 C66  NZ    CE   CD    111.11  3.000
 C66  HZ2   NZ   HZ1   105.33  3.000
 C66  HZ2   NZ   CE    109.40  3.000
 C66  HZ1   NZ   CE    108.99  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  Var_01    C2    N1   C8'  C7'   -78.82  30.0  3
 C66  Var_02    N1    C8'  C7'  O7'    -3.12  30.0  1
 C66  Var_03    C2'   C3'  N4'  C7'    88.14  30.0  3
 C66  Var_04    CD    CG   CB   C5'   178.69  30.0  3
 C66  Var_05    N1'   C2'  C3'  N4'   177.85  30.0  3
 C66  Var_06    CE    CD   CG   CB   -177.29  30.0  3
 C66  Var_07    NZ    CE   CD   CG   -178.47  30.0  3
 C66  Var_08    H1'1  N1'  C2'  C3'    57.33  30.0  3
 C66  Var_09    HZ1   NZ   CE   CD    -64.62  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

