# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Mar 18 21:08:11 2022
#   Inital geometry file: a 116 line input string
#   Ligand name: (E)-N~6~-({3-hydroxy-2-methyl-5-[(phosphonooxy)methyl]pyridin-4-yl}methylidene)-L-lysine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cc1ncc(CO[P](O)(O)=O)c(C=NCCCC[C@H](N)C(O)=O)c1O
#
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
 LLP  LLP  (E)-N~6~-({3-hydroxy-2-methyl-5-[(phosphonooxy)methyl]pyridin-4-yl}methylidene)-L-lysine  L-peptide  44  25  .  2013-08-26  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_LLP
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
 LLP  N1    N  N      0  -0.400  -28.6180  -11.8105  3.4180
 LLP  C2    C  CR6    0   0.122  -27.6387  -12.6941  3.3830
 LLP  C2'   C  CH3    0  -0.719  -27.8781  -14.0165  2.7206
 LLP  C3    C  CR6    0   0.290  -26.3822  -12.4095  3.9527
 LLP  O3    O  OH1    0  -0.635  -25.4332  -13.3379  3.8799
 LLP  C4    C  CR6    0  -0.043  -26.1785  -11.1714  4.5789
 LLP  C4'   C  C1     0   0.032  -24.8863  -10.8698  5.1974
 LLP  C5    C  CR6    0  -0.013  -27.2363  -10.2472  4.6005
 LLP  C6    C  CR16   0  -0.172  -28.4219  -10.6278  4.0018
 LLP  C5'   C  CH2    0  -0.239  -27.1050   -8.8865  5.2374
 LLP  OP4   O  O2     0  -0.654  -26.0947   -8.1522  4.6143
 LLP  P     P  P      0   1.240  -25.2326   -7.0097  5.5786
 LLP  OP1   O  O      0  -0.878  -24.2255   -6.4941  4.5622
 LLP  OP2   O  OP    -1  -0.880  -24.6387   -7.8459  6.7170
 LLP  OP3   O  OP    -1  -0.889  -26.2854   -6.0086  6.0391
 LLP  N     N  NH2    0  -0.786  -18.4679  -11.6268  4.0738
 LLP  CA    C  CH1    0  -0.200  -18.9269  -12.5368  3.0162
 LLP  CB    C  CH2    0  -0.418  -20.3555  -12.2122  2.5994
 LLP  CG    C  CH2    0  -0.419  -21.4140  -12.3840  3.6932
 LLP  CD    C  CH2    0  -0.430  -21.6090  -11.1683  4.5927
 LLP  CE    C  CH2    0  -0.305  -22.6493  -11.3717  5.6919
 LLP  NZ    N  N      0  -0.469  -23.9350  -11.7134  5.1320
 LLP  C     C  C      0   0.396  -17.9207  -12.5566  1.8380
 LLP  O     O  O      0  -0.623  -16.8656  -13.1943  2.0473
 LLP  OXT   O  OC    -1  -0.605  -18.2019  -11.9072  0.8100
 LLP  H2'1  H  HCH3   0   0.244  -28.8937  -14.0623  2.3332
 LLP  H2'2  H  HCH3   0   0.244  -27.1869  -14.1838  1.8927
 LLP  H2'3  H  HCH3   0   0.243  -27.7407  -14.8455  3.4178
 LLP  HO3   H  HOH1   0   0.475  -24.6184  -12.9529  4.3289
 LLP  H4'1  H  H      0   0.285  -24.7635   -9.9142  5.7130
 LLP  H6    H  HCR6   0   0.244  -29.2639   -9.9432  3.9880
 LLP  H5'1  H  HCH2   0   0.198  -28.0810   -8.3844  5.1687
 LLP  H5'2  H  HCH2   0   0.186  -26.9118   -9.0227  6.3103
 LLP  HA    H  HCH1   0   0.191  -18.9327  -13.5407  3.4588
 LLP  HB2   H  HCH2   0   0.200  -20.4044  -11.1962  2.1932
 LLP  HB3   H  HCH2   0   0.214  -20.6106  -12.8714  1.7659
 LLP  HG2   H  HCH2   0   0.216  -22.3687  -12.6200  3.2156
 LLP  HG3   H  HCH2   0   0.202  -21.1684  -13.2567  4.3095
 LLP  HD2   H  HCH2   0   0.235  -20.6627  -10.9088  5.0687
 LLP  HD3   H  HCH2   0   0.211  -21.9037  -10.3051  3.9865
 LLP  HE2   H  HCH2   0   0.233  -22.3321  -12.1929  6.3408
 LLP  HE3   H  HCH2   0   0.217  -22.7151  -10.4671  6.3082
 LLP  H     H  HNH2   0   0.333  -17.5043  -11.8500  4.2959
 LLP  HN2   H  HNH2   0   0.327  -18.4485  -10.6817  3.7050

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
 LLP  N1   C2    aromatic  1.319  0.020  1.319
 LLP  N1   C6    aromatic  1.333  0.020  1.333
 LLP  C2   C2'   single    1.498  0.020  1.498
 LLP  C2   C3    aromatic  1.409  0.020  1.409
 LLP  C3   O3    single    1.330  0.020  1.330
 LLP  C3   C4    aromatic  1.402  0.020  1.402
 LLP  C4   C4'   single    1.464  0.020  1.464
 LLP  C4   C5    aromatic  1.405  0.020  1.405
 LLP  C4'  NZ    double    1.273  0.020  1.273
 LLP  C5   C6    aromatic  1.382  0.020  1.382
 LLP  C5   C5'   single    1.508  0.020  1.508
 LLP  C5'  OP4   single    1.396  0.020  1.396
 LLP  OP4  P     single    1.726  0.020  1.726
 LLP  P    OP1   deloc     1.521  0.020  1.521
 LLP  P    OP2   deloc     1.532  0.020  1.532
 LLP  P    OP3   deloc     1.524  0.020  1.524
 LLP  N    CA    single    1.458  0.019  1.458
 LLP  CA   CB    single    1.530  0.020  1.530
 LLP  CA   C     single    1.525  0.021  1.525
 LLP  CB   CG    single    1.532  0.020  1.532
 LLP  CG   CD    single    1.525  0.020  1.525
 LLP  CD   CE    single    1.527  0.020  1.527
 LLP  CE   NZ    single    1.443  0.020  1.443
 LLP  C    O     deloc     1.231  0.020  1.231
 LLP  C    OXT   deloc     1.248  0.020  1.248
 LLP  C2'  H2'1  single    0.970  0.020  1.090
 LLP  C2'  H2'2  single    0.970  0.020  1.090
 LLP  C2'  H2'3  single    0.970  0.020  1.090
 LLP  O3   HO3   single    0.850  0.020  0.980
 LLP  C4'  H4'1  single    0.930  0.020  1.080
 LLP  C6   H6    single    0.930  0.020  1.080
 LLP  C5'  H5'1  single    0.970  0.020  1.090
 LLP  C5'  H5'2  single    0.970  0.020  1.090
 LLP  N    H     single    0.860  0.020  0.860
 LLP  N    HN2   single    0.890  0.020  1.040
 LLP  CA   HA    single    0.970  0.020  0.970
 LLP  CB   HB2   single    0.970  0.020  1.090
 LLP  CB   HB3   single    0.970  0.020  1.090
 LLP  CG   HG2   single    0.970  0.020  1.090
 LLP  CG   HG3   single    0.970  0.020  1.090
 LLP  CD   HD2   single    0.970  0.020  1.090
 LLP  CD   HD3   single    0.970  0.020  1.090
 LLP  CE   HE2   single    0.970  0.020  1.090
 LLP  CE   HE3   single    0.970  0.020  1.090

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
 LLP  C6    N1   C2    119.76  3.000
 LLP  C3    C2   C2'   119.98  3.000
 LLP  C3    C2   N1    121.06  3.000
 LLP  C2'   C2   N1    118.96  3.000
 LLP  H2'3  C2'  H2'2  106.75  3.000
 LLP  H2'3  C2'  H2'1  108.24  3.000
 LLP  H2'2  C2'  H2'1  108.34  3.000
 LLP  H2'3  C2'  C2    111.58  3.000
 LLP  H2'2  C2'  C2    111.68  3.000
 LLP  H2'1  C2'  C2    110.11  3.000
 LLP  C4    C3   O3    122.50  3.000
 LLP  C4    C3   C2    119.25  3.000
 LLP  O3    C3   C2    118.26  3.000
 LLP  HO3   O3   C3    106.63  3.000
 LLP  C5    C4   C4'   121.51  3.000
 LLP  C5    C4   C3    118.58  3.000
 LLP  C4'   C4   C3    119.92  3.000
 LLP  H4'1  C4'  NZ    121.32  3.000
 LLP  H4'1  C4'  C4    118.60  3.000
 LLP  NZ    C4'  C4    120.09  3.000
 LLP  C5'   C5   C6    120.42  3.000
 LLP  C5'   C5   C4    122.31  3.000
 LLP  C6    C5   C4    117.27  3.000
 LLP  H6    C6   C5    119.83  3.000
 LLP  H6    C6   N1    116.10  3.000
 LLP  C5    C6   N1    124.08  3.000
 LLP  H5'2  C5'  H5'1  105.88  3.000
 LLP  H5'2  C5'  OP4   111.96  3.000
 LLP  H5'1  C5'  OP4   111.98  3.000
 LLP  H5'2  C5'  C5    108.42  3.000
 LLP  H5'1  C5'  C5    107.96  3.000
 LLP  OP4   C5'  C5    110.44  3.000
 LLP  P     OP4  C5'   117.41  3.000
 LLP  OP3   P    OP2   113.69  3.000
 LLP  OP3   P    OP1   115.89  3.000
 LLP  OP2   P    OP1   115.14  3.000
 LLP  OP3   P    OP4   104.99  3.000
 LLP  OP2   P    OP4   104.33  3.000
 LLP  OP1   P    OP4   100.47  3.000
 LLP  HN2   N    H     105.45  3.000
 LLP  HN2   N    CA    108.75  3.000
 LLP  H     N    CA    114.00  3.000
 LLP  HA    CA   C     109.00  3.000
 LLP  HA    CA   CB    109.00  3.000
 LLP  C     CA   CB    110.10  1.900
 LLP  HA    CA   N     110.00  3.000
 LLP  C     CA   N     111.00  2.800
 LLP  CB    CA   N     110.50  1.700
 LLP  HB3   CB   HB2   105.44  3.000
 LLP  HB3   CB   CG    108.40  3.000
 LLP  HB2   CB   CG    109.76  3.000
 LLP  HB3   CB   CA    107.40  3.000
 LLP  HB2   CB   CA    109.94  3.000
 LLP  CG    CB   CA    115.40  3.000
 LLP  HG3   CG   HG2   105.63  3.000
 LLP  HG3   CG   CD    109.37  3.000
 LLP  HG2   CG   CD    108.55  3.000
 LLP  HG3   CG   CB    109.63  3.000
 LLP  HG2   CG   CB    108.40  3.000
 LLP  CD    CG   CB    114.85  3.000
 LLP  HD3   CD   HD2   106.71  3.000
 LLP  HD3   CD   CE    108.67  3.000
 LLP  HD2   CD   CE    107.98  3.000
 LLP  HD3   CD   CG    109.65  3.000
 LLP  HD2   CD   CG    109.64  3.000
 LLP  CE    CD   CG    113.93  3.000
 LLP  HE3   CE   HE2   107.66  3.000
 LLP  HE3   CE   NZ    111.09  3.000
 LLP  HE2   CE   NZ    108.11  3.000
 LLP  HE3   CE   CD    109.61  3.000
 LLP  HE2   CE   CD    109.24  3.000
 LLP  NZ    CE   CD    111.05  3.000
 LLP  CE    NZ   C4'   119.26  3.000
 LLP  OXT   C    O     126.39  3.000
 LLP  OXT   C    CA    118.25  3.000
 LLP  O     C    CA    120.80  1.700

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
 LLP  CONST_01  C4    C3   C2   N1      0.00   0.0  0
 LLP  CONST_02  C4    C5   C6   N1      0.00   0.0  0
 LLP  CONST_03  C5    C6   N1   C2      0.00   0.0  0
 LLP  CONST_04  C5    C4   C3   C2      0.00   0.0  0
 LLP  CONST_05  C6    N1   C2   C3      0.00   0.0  0
 LLP  CONST_06  C6    C5   C4   C3      0.00   0.0  0
 LLP  CONST_07  O3    C3   C2   N1    180.00   0.0  0
 LLP  CONST_08  C5'   C5   C6   N1    180.00   0.0  0
 LLP  CONST_09  C4'   C4   C3   C2    180.00   0.0  0
 LLP  CONST_10  C6    N1   C2   C2'   180.00   0.0  0
 LLP  CONST_11  C4    C3   C2   C2'   180.00   0.0  0
 LLP  CONST_12  C5'   C5   C4   C3    180.00   0.0  0
 LLP  CONST_13  C5    C4   C3   O3    180.00   0.0  0
 LLP  CONST_14  C6    C5   C4   C4'   180.00   0.0  0
 LLP  CONST_15  H6    C6   N1   C2    180.00   0.0  0
 LLP  Var_01    NZ    C4'  C4   C3      2.14  30.0  2
 LLP  Var_02    OP4   C5'  C5   C4     60.30  30.0  2
 LLP  Var_03    H2'1  C2'  C2   N1      0.21  30.0  2
 LLP  Var_04    CD    CE   NZ   C4'  -110.28  30.0  1
 LLP  Var_05    OP1   P    OP4  C5'   177.83  30.0  3
 LLP  Var_06    CD    CG   CB   CA     86.38  30.0  3
 LLP  Var_07    CE    CD   CG   CB   -178.88  30.0  3
 LLP  Var_08    NZ    CE   CD   CG    -58.22  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
 LLP  chir_01  CA  N  CB  C  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
 LLP  plan-1  N1    0.020
 LLP  plan-1  C2    0.020
 LLP  plan-1  C2'   0.020
 LLP  plan-1  C3    0.020
 LLP  plan-1  O3    0.020
 LLP  plan-1  C4    0.020
 LLP  plan-1  C4'   0.020
 LLP  plan-1  C5    0.020
 LLP  plan-1  C6    0.020
 LLP  plan-1  C5'   0.020
 LLP  plan-1  H6    0.020
 LLP  plan-2  CA    0.020
 LLP  plan-2  C     0.020
 LLP  plan-2  O     0.020
 LLP  plan-2  OXT   0.020
 LLP  plan-3  C4    0.020
 LLP  plan-3  C4'   0.020
 LLP  plan-3  CE    0.020
 LLP  plan-3  NZ    0.020
 LLP  plan-3  H4'1  0.020

