# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon May  4 23:16:09 2020
#   Inital geometry file: a 123 line input string
#   Ligand name: N~2~-(2-aminoethyl)-N~2~-[(5-methyl-2,4-dioxo-3,4-dihydropyrimidin-1(2H)-yl)acetyl]-D-lysine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC1=CN(CC(=O)N(CCN)[C@H](CCCCN)C(O)=O)C(=O)NC1=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
 T66  T66  N~2~-(2-aminoethyl)-N~2~-[(5-methyl-2,4-dioxo-3,4-dihydropyrimidin-1(2H)-yl)acetyl]-D-lysine  L-peptide  49  25  .  2022-03-23  2022-03-23
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_T66
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
 T66  C8'   C  CH2    0  -0.471   2.7607  -1.5690  -0.4115
 T66  C7'   C  C      0   0.579   2.3656  -0.1078  -0.6467
 T66  O7'   O  O      0  -0.497   2.6634   0.7312   0.1904
 T66  C5'   C  CH1    0  -0.245   1.1613   1.5157  -1.9484
 T66  C'    C  C      0   0.432   0.2370   1.9114  -0.7617
 T66  O1'   O  O      0  -0.594  -0.3742   0.9847  -0.2025
 T66  OXT   O  OC    -1  -0.603   0.1363   3.1297  -0.5216
 T66  N4'   N  NT     0  -0.438   1.7080   0.1729  -1.7789
 T66  C3'   C  CH2    0  -0.369   1.3152  -0.8443  -2.7377
 T66  C2'   C  CH2    0  -0.285  -0.0669  -1.4504  -2.4784
 T66  N1'   N  NH2    0  -0.787  -0.4649  -2.4399  -3.4624
 T66  N1    N  NR6    0  -0.506   3.4130  -1.6993   0.8691
 T66  C6    C  CR16   0   0.062   2.6582  -1.8829   1.9943
 T66  C2    C  CR6    0   0.720   4.7479  -1.3917   0.9488
 T66  O2    O  O      0  -0.483   5.4327  -1.1469  -0.0237
 T66  N3    N  NR16   0  -0.731   5.2551  -1.4065   2.2218
 T66  C4    C  CR6    0   0.558   4.5727  -1.6254   3.4054
 T66  O4    O  O      0  -0.457   5.1591  -1.5961   4.4726
 T66  C5    C  CR6    0  -0.181   3.1546  -1.8756   3.2438
 T66  C5M   C  CH3    0  -0.706   2.3185  -2.1077   4.4593
 T66  CB    C  CH2    0  -0.399   2.2269   2.5467  -2.3058
 T66  CG    C  CH2    0  -0.419   3.0001   2.2149  -3.5762
 T66  CD    C  CH2    0  -0.434   4.0219   3.2867  -3.9350
 T66  CE    C  CH2    0  -0.282   4.7583   3.0010  -5.2402
 T66  NZ    N  NH2    0  -0.792   5.7454   3.9936  -5.6392
 T66  H8'1  H  HCH2   0   0.300   1.8826  -2.2161  -0.4143
 T66  H8'2  H  HCH2   0   0.314   3.4230  -1.9368  -1.1937
 T66  H5'1  H  HCH1   0   0.247   0.4887   1.4429  -2.8128
 T66  H3'1  H  HCH2   0   0.252   2.0647  -1.6368  -2.7785
 T66  H3'2  H  HCH2   0   0.257   1.3216  -0.3875  -3.7305
 T66  H2'1  H  HCH2   0   0.231  -0.8133  -0.6551  -2.4540
 T66  H2'2  H  HCH2   0   0.217  -0.0884  -1.9088  -1.4867
 T66  H1'1  H  HNH2   0   0.342   0.2199  -3.1849  -3.5047
 T66  H1'2  H  HNH2   0   0.343  -0.4771  -2.0213  -4.3843
 T66  H6    H  HCR6   0   0.308   1.6067  -2.0617   1.8131
 T66  HN3   H  HNR6   0   0.424   6.2460  -1.2127   2.2972
 T66  HM51  H  HCH3   0   0.246   2.6496  -2.9912   5.0069
 T66  HM52  H  HCH3   0   0.247   1.2735  -2.2532   4.1908
 T66  HM53  H  HCH3   0   0.247   2.3740  -1.2624   5.1461
 T66  HB1   H  HCH2   0   0.216   1.7254   3.5070  -2.4366
 T66  HB2   H  HCH2   0   0.216   2.9229   2.6755  -1.4738
 T66  HG1   H  HCH2   0   0.203   2.2974   2.0926  -4.4092
 T66  HG2   H  HCH2   0   0.212   3.5134   1.2538  -3.4671
 T66  HD1   H  HCH2   0   0.208   4.7526   3.3816  -3.1237
 T66  HD2   H  HCH2   0   0.206   3.5221   4.2591  -4.0128
 T66  HE1   H  HCH2   0   0.210   5.2587   2.0305  -5.1689
 T66  HE2   H  HCH2   0   0.209   4.0285   2.9034  -6.0500
 T66  HZ1   H  HNH2   0   0.336   5.2999   4.9022  -5.6903
 T66  HZ2   H  HNH2   0   0.336   6.4469   4.0799  -4.9134

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
 T66  C8'  C7'   single  1.532  0.020  1.532
 T66  C8'  N1    single  1.443  0.020  1.443
 T66  C8'  H8'1  single  0.970  0.020  1.090
 T66  C8'  H8'2  single  0.970  0.020  1.090
 T66  C7'  O7'   double  1.222  0.020  1.222
 T66  C7'  N4'   single  1.339  0.020  1.339
 T66  C5'  C'    single  1.555  0.020  1.555
 T66  C5'  N4'   single  1.460  0.020  1.460
 T66  C5'  CB    single  1.525  0.020  1.525
 T66  C5'  H5'1  single  0.970  0.020  1.090
 T66  C'   O1'   deloc   1.243  0.020  1.243
 T66  C'   OXT   deloc   1.246  0.020  1.246
 T66  N4'  C3'   single  1.452  0.020  1.452
 T66  C3'  C2'   single  1.531  0.020  1.531
 T66  C3'  H3'1  single  0.970  0.020  1.090
 T66  C3'  H3'2  single  0.970  0.020  1.090
 T66  C2'  N1'   single  1.451  0.020  1.451
 T66  C2'  H2'1  single  0.970  0.020  1.090
 T66  C2'  H2'2  single  0.970  0.020  1.090
 T66  N1'  H1'1  single  0.890  0.020  1.040
 T66  N1'  H1'2  single  0.890  0.020  1.040
 T66  N1   C6    single  1.367  0.020  1.367
 T66  N1   C2    single  1.372  0.020  1.372
 T66  C6   C5    double  1.344  0.020  1.344
 T66  C6   H6    single  0.930  0.020  1.080
 T66  C2   O2    double  1.214  0.020  1.214
 T66  C2   N3    single  1.370  0.020  1.370
 T66  N3   C4    single  1.384  0.020  1.384
 T66  N3   HN3   single  0.860  0.020  1.020
 T66  C4   O4    double  1.218  0.020  1.218
 T66  C4   C5    single  1.449  0.020  1.449
 T66  C5   C5M   single  1.493  0.020  1.493
 T66  C5M  HM51  single  0.970  0.020  1.090
 T66  C5M  HM52  single  0.970  0.020  1.090
 T66  C5M  HM53  single  0.970  0.020  1.090
 T66  CB   CG    single  1.524  0.020  1.524
 T66  CB   HB1   single  0.970  0.020  1.090
 T66  CB   HB2   single  0.970  0.020  1.090
 T66  CG   CD    single  1.524  0.020  1.524
 T66  CG   HG1   single  0.970  0.020  1.090
 T66  CG   HG2   single  0.970  0.020  1.090
 T66  CD   CE    single  1.526  0.020  1.526
 T66  CD   HD1   single  0.970  0.020  1.090
 T66  CD   HD2   single  0.970  0.020  1.090
 T66  CE   NZ    single  1.456  0.020  1.456
 T66  CE   HE1   single  0.970  0.020  1.090
 T66  CE   HE2   single  0.970  0.020  1.090
 T66  NZ   HZ1   single  0.890  0.020  1.040
 T66  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
 T66  H8'2  C8'  H8'1  106.70  3.000
 T66  H8'2  C8'  N1    109.39  3.000
 T66  H8'1  C8'  N1    108.22  3.000
 T66  H8'2  C8'  C7'   111.64  3.000
 T66  H8'1  C8'  C7'   110.97  3.000
 T66  N1    C8'  C7'   109.81  3.000
 T66  N4'   C7'  O7'   123.71  3.000
 T66  N4'   C7'  C8'   117.16  3.000
 T66  O7'   C7'  C8'   119.14  3.000
 T66  H5'1  C5'  CB    106.76  3.000
 T66  H5'1  C5'  N4'   105.06  3.000
 T66  CB    C5'  N4'   112.79  3.000
 T66  H5'1  C5'  C'    104.69  3.000
 T66  CB    C5'  C'    114.96  3.000
 T66  N4'   C5'  C'    111.59  3.000
 T66  OXT   C'   O1'   127.06  3.000
 T66  OXT   C'   C5'   116.35  3.000
 T66  O1'   C'   C5'   116.48  3.000
 T66  C3'   N4'  C5'   117.81  3.000
 T66  C3'   N4'  C7'   122.98  3.000
 T66  C5'   N4'  C7'   118.35  3.000
 T66  H3'2  C3'  H3'1  105.40  3.000
 T66  H3'2  C3'  C2'   108.94  3.000
 T66  H3'1  C3'  C2'   109.79  3.000
 T66  H3'2  C3'  N4'   107.79  3.000
 T66  H3'1  C3'  N4'   110.34  3.000
 T66  C2'   C3'  N4'   114.18  3.000
 T66  H2'2  C2'  H2'1  105.78  3.000
 T66  H2'2  C2'  N1'   108.91  3.000
 T66  H2'1  C2'  N1'   108.94  3.000
 T66  H2'2  C2'  C3'   109.72  3.000
 T66  H2'1  C2'  C3'   109.43  3.000
 T66  N1'   C2'  C3'   113.74  3.000
 T66  H1'2  N1'  H1'1  105.92  3.000
 T66  H1'2  N1'  C2'   109.80  3.000
 T66  H1'1  N1'  C2'   110.15  3.000
 T66  C2    N1   C6    121.29  3.000
 T66  C2    N1   C8'   118.10  3.000
 T66  C6    N1   C8'   119.53  3.000
 T66  H6    C6   C5    121.02  3.000
 T66  H6    C6   N1    114.89  3.000
 T66  C5    C6   N1    124.08  3.000
 T66  N3    C2   O2    122.51  3.000
 T66  N3    C2   N1    114.30  3.000
 T66  O2    C2   N1    123.18  3.000
 T66  HN3   N3   C4    116.70  3.000
 T66  HN3   N3   C2    115.42  3.000
 T66  C4    N3   C2    127.87  3.000
 T66  C5    C4   O4    124.96  3.000
 T66  C5    C4   N3    114.49  3.000
 T66  O4    C4   N3    120.55  3.000
 T66  C5M   C5   C4    118.94  3.000
 T66  C5M   C5   C6    123.29  3.000
 T66  C4    C5   C6    117.77  3.000
 T66  HM53  C5M  HM52  107.93  3.000
 T66  HM53  C5M  HM51  107.23  3.000
 T66  HM52  C5M  HM51  107.87  3.000
 T66  HM53  C5M  C5    111.33  3.000
 T66  HM52  C5M  C5    110.93  3.000
 T66  HM51  C5M  C5    111.38  3.000
 T66  HB2   CB   HB1   106.28  3.000
 T66  HB2   CB   CG    109.71  3.000
 T66  HB1   CB   CG    108.96  3.000
 T66  HB2   CB   C5'   110.27  3.000
 T66  HB1   CB   C5'   107.58  3.000
 T66  CG    CB   C5'   113.75  3.000
 T66  HG2   CG   HG1   106.15  3.000
 T66  HG2   CG   CD    109.05  3.000
 T66  HG1   CG   CD    109.22  3.000
 T66  HG2   CG   CB    110.24  3.000
 T66  HG1   CG   CB    109.42  3.000
 T66  CD    CG   CB    112.55  3.000
 T66  HD2   CD   HD1   106.24  3.000
 T66  HD2   CD   CE    108.99  3.000
 T66  HD1   CD   CE    109.13  3.000
 T66  HD2   CD   CG    109.57  3.000
 T66  HD1   CD   CG    109.50  3.000
 T66  CE    CD   CG    113.17  3.000
 T66  HE2   CE   HE1   105.90  3.000
 T66  HE2   CE   NZ    108.07  3.000
 T66  HE1   CE   NZ    108.22  3.000
 T66  HE2   CE   CD    109.14  3.000
 T66  HE1   CE   CD    109.33  3.000
 T66  NZ    CE   CD    115.73  3.000
 T66  HZ2   NZ   HZ1   105.32  3.000
 T66  HZ2   NZ   CE    109.34  3.000
 T66  HZ1   NZ   CE    109.09  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
 T66  CONST_01  C4    N3   C2   N1      0.00   0.0  0
 T66  CONST_02  N3    C2   N1   C6      0.00   0.0  0
 T66  CONST_03  C5    C4   N3   C2      0.00   0.0  0
 T66  CONST_04  N3    C2   N1   C8'   180.00   0.0  0
 T66  CONST_05  O2    C2   N1   C6    180.00   0.0  0
 T66  CONST_06  O4    C4   N3   C2    180.00   0.0  0
 T66  CONST_07  C4    N3   C2   O2    180.00   0.0  0
 T66  CONST_08  HN3   N3   C2   N1    180.00   0.0  0
 T66  CONST_09  O2    C2   N1   C8'     0.00   0.0  0
 T66  CONST_10  C5'   N4'  C7'  C8'   180.00   0.0  0
 T66  CONST_11  C3'   N4'  C7'  C8'     0.00   0.0  0
 T66  CONST_12  C5'   N4'  C7'  O7'     0.00   0.0  0
 T66  CONST_13  C3'   N4'  C7'  O7'   180.00   0.0  0
 T66  Var_01    C6    N1   C8'  C7'    86.15  30.0  3
 T66  Var_02    HM51  C5M  C5   C6    118.72  30.0  3
 T66  Var_03    N1    C8'  C7'  O7'     2.29  30.0  1
 T66  Var_04    C2'   C3'  N4'  C7'    89.56  30.0  3
 T66  Var_05    CD    CG   CB   C5'   177.93  30.0  3
 T66  Var_06    N1'   C2'  C3'  N4'   178.44  30.0  3
 T66  Var_07    CE    CD   CG   CB   -177.29  30.0  3
 T66  Var_08    NZ    CE   CD   CG    179.78  30.0  3
 T66  Var_09    H1'1  N1'  C2'  C3'    57.25  30.0  3
 T66  Var_10    HZ1   NZ   CE   CD    -55.76  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
 T66  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
 T66  plan-1  C8'  0.020
 T66  plan-1  N1   0.020
 T66  plan-1  C6   0.020
 T66  plan-1  C2   0.020
 T66  plan-1  O2   0.020
 T66  plan-1  N3   0.020
 T66  plan-1  C4   0.020
 T66  plan-1  O4   0.020
 T66  plan-1  C5   0.020
 T66  plan-1  C5M  0.020
 T66  plan-1  H6   0.020
 T66  plan-1  HN3  0.020
 T66  plan-2  C8'  0.020
 T66  plan-2  C7'  0.020
 T66  plan-2  O7'  0.020
 T66  plan-2  C5'  0.020
 T66  plan-2  N4'  0.020
 T66  plan-2  C3'  0.020
 T66  plan-3  C5'  0.020
 T66  plan-3  C'   0.020
 T66  plan-3  O1'  0.020
 T66  plan-3  OXT  0.020

