# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Mar 25 06:36:25 2022
#   Inital geometry file: a 84 line input string
#   Ligand name: N~6~-7H-purin-6-yl-L-lysine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: N[C@@H](CCCCNc1ncnc2nc[nH]c12)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
 XX1  XX1  N~6~-7H-purin-6-yl-L-lysine  L-peptide  34  19  .  2012-08-28  2022-09-22
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND (side chain)
;

data_comp_XX1
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
 XX1  O    O  O      0  -0.615  -20.1988   -9.1822  19.4489
 XX1  C    C  C      0   0.383  -19.5641   -9.3865  18.3935
 XX1  CA   C  CH1    0  -0.220  -20.2196   -8.8455  17.0965
 XX1  N    N  NH2    0  -0.796  -19.3397   -8.7777  15.9342
 XX1  CB   C  CH2    0  -0.402  -21.4671   -9.6760  16.7718
 XX1  CG   C  CH2    0  -0.432  -21.1784  -11.1299  16.4164
 XX1  CD   C  CH2    0  -0.467  -22.4512  -11.8976  16.0762
 XX1  CE   C  CH2    0  -0.291  -22.2200  -13.3625  15.7380
 XX1  NZ   N  NH1    0  -0.646  -21.4209  -13.4930  14.5382
 XX1  C6   C  CR6    0   0.515  -20.9202  -14.6250  14.0295
 XX1  C5   C  CR56   0   0.141  -21.1115  -15.9179  14.5505
 XX1  N7   N  NR15   0  -0.649  -21.7922  -16.4862  15.6001
 XX1  C8   C  CR15   0   0.113  -21.5684  -17.8108  15.5325
 XX1  N1   N  N      0  -0.475  -20.1690  -14.5258  12.9273
 XX1  C2   C  CR16   0   0.024  -19.6387  -15.6217  12.3912
 XX1  N3   N  N      0  -0.445  -19.7476  -16.8680  12.8001
 XX1  C4   C  CR56   0   0.275  -20.5048  -16.9935  13.8978
 XX1  N9   N  N      0  -0.458  -20.8025  -18.1627  14.5310
 XX1  OXT  O  OC    -1  -0.604  -18.4847  -10.0019  18.2770
 XX1  HA   H  HCH1   0   0.213  -20.5666   -7.8272  17.3019
 XX1  H    H  HNH2   0   0.332  -18.6811   -8.0211  16.0763
 XX1  H2   H  HNH2   0   0.325  -18.7597   -9.6092  15.9452
 XX1  HB2  H  HCH2   0   0.208  -22.1472   -9.6383  17.6269
 XX1  HB3  H  HCH2   0   0.207  -21.9943   -9.2068  15.9345
 XX1  HG2  H  HCH2   0   0.215  -20.4868  -11.1653  15.5700
 XX1  HG3  H  HCH2   0   0.219  -20.6724  -11.6317  17.2472
 XX1  HD2  H  HCH2   0   0.243  -23.1370  -11.8605  16.9258
 XX1  HD3  H  HCH2   0   0.231  -22.9718  -11.4139  15.2430
 XX1  HE2  H  HCH2   0   0.238  -21.7091  -13.8401  16.5803
 XX1  HE3  H  HCH2   0   0.250  -23.1871  -13.8600  15.6096
 XX1  HZ   H  HNH1   0   0.397  -21.2232  -12.6603  14.0044
 XX1  HN7  H  HNR5   0   0.435  -22.3526  -16.0293  16.3021
 XX1  H8   H  HCR5   0   0.292  -21.9995  -18.4877  16.2548
 XX1  HC2  H  HCR6   0   0.245  -19.0390  -15.4554  11.5017

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
 XX1  O   C    deloc     1.231  0.020  1.231
 XX1  C   CA   single    1.525  0.021  1.525
 XX1  C   OXT  deloc     1.248  0.020  1.248
 XX1  CA  N    single    1.458  0.019  1.458
 XX1  CA  CB   single    1.530  0.020  1.530
 XX1  CA  HA   single    0.970  0.020  0.970
 XX1  N   H    single    0.860  0.020  0.860
 XX1  N   H2   single    0.890  0.020  1.040
 XX1  CB  CG   single    1.524  0.020  1.524
 XX1  CB  HB2  single    0.970  0.020  1.090
 XX1  CB  HB3  single    0.970  0.020  1.090
 XX1  CG  CD   single    1.525  0.020  1.525
 XX1  CG  HG2  single    0.970  0.020  1.090
 XX1  CG  HG3  single    0.970  0.020  1.090
 XX1  CD  CE   single    1.521  0.020  1.521
 XX1  CD  HD2  single    0.970  0.020  1.090
 XX1  CD  HD3  single    0.970  0.020  1.090
 XX1  CE  NZ   single    1.447  0.020  1.447
 XX1  CE  HE2  single    0.970  0.020  1.090
 XX1  CE  HE3  single    0.970  0.020  1.090
 XX1  NZ  C6   single    1.338  0.020  1.338
 XX1  NZ  HZ   single    0.860  0.020  1.020
 XX1  C6  N1   aromatic  1.337  0.020  1.337
 XX1  C6  C5   aromatic  1.407  0.020  1.407
 XX1  C5  C4   aromatic  1.397  0.020  1.397
 XX1  C5  N7   aromatic  1.374  0.020  1.374
 XX1  N7  C8   aromatic  1.345  0.020  1.345
 XX1  N7  HN7  single    0.860  0.020  1.020
 XX1  C8  N9   aromatic  1.309  0.020  1.309
 XX1  C8  H8   single    0.930  0.020  1.080
 XX1  N1  C2   aromatic  1.330  0.020  1.330
 XX1  C2  N3   aromatic  1.316  0.020  1.316
 XX1  C2  HC2  single    0.930  0.020  1.080
 XX1  N3  C4   aromatic  1.339  0.020  1.339
 XX1  C4  N9   aromatic  1.363  0.020  1.363

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
 XX1  OXT  C   CA   117.36  3.000
 XX1  OXT  C   O    126.82  3.000
 XX1  CA   C   O    120.80  1.700
 XX1  HA   CA  CB   109.00  3.000
 XX1  HA   CA  N    110.00  3.000
 XX1  CB   CA  N    110.50  1.700
 XX1  HA   CA  C    109.00  3.000
 XX1  CB   CA  C    110.10  1.900
 XX1  N    CA  C    111.00  2.800
 XX1  H2   N   H    103.83  3.000
 XX1  H2   N   CA   107.35  3.000
 XX1  H    N   CA   114.00  3.000
 XX1  HB3  CB  HB2  106.49  3.000
 XX1  HB3  CB  CG   108.76  3.000
 XX1  HB2  CB  CG   109.45  3.000
 XX1  HB3  CB  CA   108.76  3.000
 XX1  HB2  CB  CA   108.77  3.000
 XX1  CG   CB  CA   114.32  3.000
 XX1  HG3  CG  HG2  106.28  3.000
 XX1  HG3  CG  CD   108.93  3.000
 XX1  HG2  CG  CD   109.81  3.000
 XX1  HG3  CG  CB   110.36  3.000
 XX1  HG2  CG  CB   109.33  3.000
 XX1  CD   CG  CB   111.97  3.000
 XX1  HD3  CD  HD2  106.16  3.000
 XX1  HD3  CD  CE   109.18  3.000
 XX1  HD2  CD  CE   107.52  3.000
 XX1  HD3  CD  CG   110.14  3.000
 XX1  HD2  CD  CG   109.48  3.000
 XX1  CE   CD  CG   114.05  3.000
 XX1  HE3  CE  HE2  107.71  3.000
 XX1  HE3  CE  NZ   110.45  3.000
 XX1  HE2  CE  NZ   109.93  3.000
 XX1  HE3  CE  CD   109.23  3.000
 XX1  HE2  CE  CD   108.67  3.000
 XX1  NZ   CE  CD   110.79  3.000
 XX1  HZ   NZ  C6   115.07  3.000
 XX1  HZ   NZ  CE   118.20  3.000
 XX1  C6   NZ  CE   126.72  3.000
 XX1  N1   C6  C5   116.72  3.000
 XX1  C5   C6  NZ   125.85  3.000
 XX1  N1   C6  NZ   117.43  3.000
 XX1  C4   C5  N7   104.70  3.000
 XX1  N7   C5  C6   136.91  3.000
 XX1  C4   C5  C6   118.39  3.000
 XX1  HN7  N7  C8   125.03  3.000
 XX1  HN7  N7  C5   128.32  3.000
 XX1  C8   N7  C5   106.65  3.000
 XX1  H8   C8  N9   125.24  3.000
 XX1  H8   C8  N7   121.16  3.000
 XX1  N9   C8  N7   113.61  3.000
 XX1  C2   N1  C6   119.66  3.000
 XX1  HC2  C2  N3   116.44  3.000
 XX1  HC2  C2  N1   115.10  3.000
 XX1  N3   C2  N1   128.46  3.000
 XX1  C4   N3  C2   112.96  3.000
 XX1  N9   C4  N3   125.79  3.000
 XX1  N9   C4  C5   110.41  3.000
 XX1  N3   C4  C5   123.80  3.000
 XX1  C4   N9  C8   104.64  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
 XX1  CONST_01  N3   C2  N1  C6     0.00   0.0  0
 XX1  CONST_02  N3   C4  C5  C6     0.00   0.0  0
 XX1  CONST_03  N9   C4  C5  C6   180.00   0.0  0
 XX1  CONST_04  C8   N7  C5  C6   180.00   0.0  0
 XX1  CONST_05  C2   N1  C6  C5     0.00   0.0  0
 XX1  CONST_06  C2   N3  C4  C5     0.00   0.0  0
 XX1  CONST_07  C8   N9  C4  C5     0.00   0.0  0
 XX1  CONST_08  N9   C8  N7  C5     0.00   0.0  0
 XX1  CONST_09  N1   C6  C5  N7   180.00   0.0  0
 XX1  CONST_10  N3   C4  C5  N7   180.00   0.0  0
 XX1  CONST_11  N9   C4  C5  N7     0.00   0.0  0
 XX1  CONST_12  C4   N9  C8  N7     0.00   0.0  0
 XX1  CONST_13  C4   C5  N7  C8     0.00   0.0  0
 XX1  CONST_14  N3   C4  N9  C8   180.00   0.0  0
 XX1  CONST_15  C4   C5  C6  N1     0.00   0.0  0
 XX1  CONST_16  C4   N3  C2  N1     0.00   0.0  0
 XX1  CONST_17  N9   C4  N3  C2   180.00   0.0  0
 XX1  CONST_18  C2   N1  C6  NZ   180.00   0.0  0
 XX1  CONST_19  C4   C5  C6  NZ   180.00   0.0  0
 XX1  CONST_20  N7   C5  C6  NZ     0.00   0.0  0
 XX1  CONST_21  HC2  C2  N1  C6   180.00   0.0  0
 XX1  CONST_22  HN7  N7  C5  C6     0.00   0.0  0
 XX1  CONST_23  H8   C8  N7  C5   180.00   0.0  0
 XX1  CONST_24  N1   C6  NZ  CE   180.00   0.0  0
 XX1  CONST_25  C5   C6  NZ  CE     0.00   0.0  0
 XX1  CONST_26  HZ   NZ  C6  C5   180.00   0.0  0
 XX1  Var_01    C6   NZ  CE  CD   172.98  30.0  3
 XX1  Var_02    CD   CG  CB  CA  -178.84  30.0  3
 XX1  Var_03    CE   CD  CG  CB  -178.96  30.0  3
 XX1  Var_04    NZ   CE  CD  CG   -63.93  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
 XX1  chir_01  CA  C  N  CB  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
 XX1  plan-1  NZ   0.020
 XX1  plan-1  C6   0.020
 XX1  plan-1  C5   0.020
 XX1  plan-1  N7   0.020
 XX1  plan-1  C8   0.020
 XX1  plan-1  N1   0.020
 XX1  plan-1  C2   0.020
 XX1  plan-1  N3   0.020
 XX1  plan-1  C4   0.020
 XX1  plan-1  N9   0.020
 XX1  plan-1  HN7  0.020
 XX1  plan-1  H8   0.020
 XX1  plan-1  HC2  0.020
 XX1  plan-2  CE   0.020
 XX1  plan-2  NZ   0.020
 XX1  plan-2  C6   0.020
 XX1  plan-2  HZ   0.020
 XX1  plan-3  O    0.020
 XX1  plan-3  C    0.020
 XX1  plan-3  CA   0.020
 XX1  plan-3  OXT  0.020

