# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri May 15 08:03:06 2020
#   Inital geometry file: a 108 line input string
#   Ligand name: N-({3-hydroxy-2-methyl-5-[(phosphonooxy)methyl]pyridin-4-yl}methyl)-L-methionine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CSCC[C@H](NCc1c(O)c(C)ncc1CO[P](O)(O)=O)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
 LPI  LPI  N-({3-hydroxy-2-methyl-5-[(phosphonooxy)methyl]pyridin-4-yl}methyl)-L-methionine  ligand  45  24  .  2022-11-17  2022-11-17
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_LPI
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
 LPI  OP1  O  O     0  -0.709   4.2805  -2.1255   0.4857
 LPI  P    P  P     0   1.465   4.0229  -1.3392  -0.7340
 LPI  OP3  O  OH1   0  -0.730   5.2719  -0.7110  -1.4978
 LPI  OP2  O  OH1   0  -0.741   3.1998  -2.2226  -1.7794
 LPI  OP4  O  O2    0  -0.595   3.2195   0.0281  -0.5428
 LPI  C5'  C  CH2   0  -0.211   2.0047   0.0287   0.2024
 LPI  C5   C  CR6   0  -0.062   1.4321   1.4156   0.2294
 LPI  C6   C  CR16  0  -0.138   2.0855   2.5042  -0.3252
 LPI  N1   N  N     0  -0.406   1.5901   3.7369  -0.2997
 LPI  C2   C  CR6   0   0.127   0.4178   3.9629   0.2682
 LPI  C2'  C  CH3   0  -0.785  -0.1115   5.3662   0.2702
 LPI  C3   C  CR6   0   0.251  -0.3170   2.9187   0.8497
 LPI  O3   O  OH1   0  -0.620  -1.5231   3.1218   1.4137
 LPI  C4   C  CR6   0   0.069   0.1969   1.6267   0.8484
 LPI  C4'  C  CH2   0  -0.363  -0.5817   0.4847   1.4444
 LPI  C1   C  CH1   0  -0.171  -2.0558  -1.3548   0.8659
 LPI  C8   C  CH2   0  -0.454  -3.0561  -1.8180  -0.2042
 LPI  C9   C  CH2   0  -0.557  -4.1994  -0.8290  -0.3935
 LPI  S10  S  S2    0  -0.034  -5.3801  -1.5042  -1.5942
 LPI  C11  C  CH3   0  -0.764  -6.6062  -0.1788  -1.5983
 LPI  C7   C  C     0   0.540  -1.1512  -2.5292   1.2073
 LPI  O9   O  OH1   0  -0.592  -1.7526  -3.3695   2.0416
 LPI  O8   O  O     0  -0.421  -0.0461  -2.7075   0.7659
 LPI  N3   N  NH1   0  -0.591  -1.2653  -0.2465   0.3862
 LPI  H1   H  HOH1  0   0.504   5.9985  -1.3325  -1.6399
 LPI  H2   H  HOH1  0   0.496   3.0250  -1.8077  -2.6349
 LPI  H3   H  HCH2  0   0.267   1.2791  -0.6592  -0.2396
 LPI  H4   H  HCH2  0   0.255   2.1988  -0.3128   1.2241
 LPI  H5   H  HCR6  0   0.257   3.0447   2.3903  -0.8137
 LPI  H6   H  HCH3  0   0.258  -1.0434   5.4540  -0.2943
 LPI  H7   H  HCH3  0   0.256  -0.3030   5.7345   1.2815
 LPI  H8   H  HCH3  0   0.272   0.6145   6.0332  -0.1889
 LPI  H9   H  HOH1  0   0.486  -1.7794   4.0493   1.3715
 LPI  H10  H  HCH2  0   0.253   0.1054  -0.1955   1.9529
 LPI  H11  H  HCH2  0   0.247  -1.2682   0.8475   2.2178
 LPI  H12  H  HCH1  0   0.247  -2.6252  -1.1060   1.7762
 LPI  H13  H  HCH2  0   0.257  -2.5226  -1.9685  -1.1461
 LPI  H14  H  HCH2  0   0.266  -3.4751  -2.7827   0.0884
 LPI  H15  H  HCH2  0   0.269  -4.7104  -0.6593   0.5568
 LPI  H16  H  HCH2  0   0.261  -3.8474   0.1370  -0.7618
 LPI  H17  H  HCH3  0   0.275  -7.4086  -0.4752  -2.2714
 LPI  H18  H  HCH3  0   0.262  -7.0244  -0.0288  -0.6040
 LPI  H19  H  HCH3  0   0.262  -6.1778   0.7559  -1.9569
 LPI  H20  H  HOH1  0   0.483  -1.1864  -4.1385   2.2046
 LPI  H21  H  HNH1  0   0.359  -1.8554   0.3982  -0.1236

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
 LPI  C2'  C2   single    1.500  0.020  1.500
 LPI  C2   N1   aromatic  1.322  0.020  1.322
 LPI  C2   C3   aromatic  1.403  0.020  1.403
 LPI  N1   C6   aromatic  1.329  0.020  1.329
 LPI  O3   C3   single    1.347  0.020  1.347
 LPI  C3   C4   aromatic  1.390  0.020  1.390
 LPI  O8   C7   double    1.203  0.020  1.203
 LPI  C6   C5   aromatic  1.385  0.020  1.385
 LPI  C4   C5   aromatic  1.398  0.020  1.398
 LPI  C4   C4'  single    1.505  0.020  1.505
 LPI  C5   C5'  single    1.501  0.020  1.501
 LPI  C7   O9   single    1.328  0.020  1.328
 LPI  C7   C1   single    1.521  0.020  1.521
 LPI  N3   C4'  single    1.457  0.020  1.457
 LPI  N3   C1   single    1.443  0.020  1.443
 LPI  C1   C8   single    1.536  0.020  1.536
 LPI  C5'  OP4  single    1.425  0.020  1.425
 LPI  C8   C9   single    1.524  0.020  1.524
 LPI  OP4  P    single    1.597  0.020  1.597
 LPI  C9   S10  single    1.814  0.020  1.814
 LPI  C11  S10  single    1.806  0.020  1.806
 LPI  P    OP1  double    1.474  0.020  1.474
 LPI  P    OP3  single    1.593  0.020  1.593
 LPI  P    OP2  single    1.597  0.020  1.597
 LPI  OP3  H1   single    0.850  0.020  0.980
 LPI  OP2  H2   single    0.850  0.020  0.980
 LPI  C5'  H3   single    0.970  0.020  1.090
 LPI  C5'  H4   single    0.970  0.020  1.090
 LPI  C6   H5   single    0.930  0.020  1.080
 LPI  C2'  H6   single    0.970  0.020  1.090
 LPI  C2'  H7   single    0.970  0.020  1.090
 LPI  C2'  H8   single    0.970  0.020  1.090
 LPI  O3   H9   single    0.850  0.020  0.980
 LPI  C4'  H10  single    0.970  0.020  1.090
 LPI  C4'  H11  single    0.970  0.020  1.090
 LPI  C1   H12  single    0.970  0.020  1.090
 LPI  C8   H13  single    0.970  0.020  1.090
 LPI  C8   H14  single    0.970  0.020  1.090
 LPI  C9   H15  single    0.970  0.020  1.090
 LPI  C9   H16  single    0.970  0.020  1.090
 LPI  C11  H17  single    0.970  0.020  1.090
 LPI  C11  H18  single    0.970  0.020  1.090
 LPI  C11  H19  single    0.970  0.020  1.090
 LPI  O9   H20  single    0.850  0.020  0.980
 LPI  N3   H21  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
 LPI  OP4  P    OP2  107.02  3.000
 LPI  OP2  P    OP3  107.96  3.000
 LPI  OP4  P    OP3   96.55  3.000
 LPI  OP2  P    OP1  109.67  3.000
 LPI  OP3  P    OP1  118.04  3.000
 LPI  OP4  P    OP1  116.46  3.000
 LPI  H1   OP3  P    113.97  3.000
 LPI  H2   OP2  P    115.79  3.000
 LPI  C5'  OP4  P    119.45  3.000
 LPI  H4   C5'  H3   107.38  3.000
 LPI  H4   C5'  C5   109.83  3.000
 LPI  H3   C5'  C5   109.61  3.000
 LPI  H4   C5'  OP4  109.68  3.000
 LPI  H3   C5'  OP4  110.74  3.000
 LPI  C5   C5'  OP4  109.57  3.000
 LPI  C4   C5   C6   118.38  3.000
 LPI  C4   C5   C5'  119.00  3.000
 LPI  C6   C5   C5'  122.62  3.000
 LPI  H5   C6   N1   115.89  3.000
 LPI  H5   C6   C5   121.06  3.000
 LPI  N1   C6   C5   123.05  3.000
 LPI  C2   N1   C6   119.83  3.000
 LPI  C3   C2   C2'  120.73  3.000
 LPI  C3   C2   N1   121.01  3.000
 LPI  C2'  C2   N1   118.26  3.000
 LPI  H8   C2'  H7   107.51  3.000
 LPI  H8   C2'  H6   107.57  3.000
 LPI  H7   C2'  H6   107.54  3.000
 LPI  H8   C2'  C2   109.74  3.000
 LPI  H7   C2'  C2   112.23  3.000
 LPI  H6   C2'  C2   112.04  3.000
 LPI  C4   C3   O3   118.13  3.000
 LPI  C4   C3   C2   119.84  3.000
 LPI  O3   C3   C2   122.03  3.000
 LPI  H9   O3   C3   111.41  3.000
 LPI  C4'  C4   C3   120.89  3.000
 LPI  C4'  C4   C5   121.19  3.000
 LPI  C3   C4   C5   117.87  3.000
 LPI  H11  C4'  H10  105.76  3.000
 LPI  H11  C4'  N3   112.63  3.000
 LPI  H10  C4'  N3   108.71  3.000
 LPI  H11  C4'  C4   110.62  3.000
 LPI  H10  C4'  C4   109.35  3.000
 LPI  N3   C4'  C4   109.63  3.000
 LPI  H12  C1   N3   112.59  3.000
 LPI  H12  C1   C7   107.22  3.000
 LPI  N3   C1   C7   109.98  3.000
 LPI  H12  C1   C8   107.88  3.000
 LPI  N3   C1   C8   110.89  3.000
 LPI  C7   C1   C8   108.10  3.000
 LPI  H14  C8   H13  107.26  3.000
 LPI  H14  C8   C9   108.60  3.000
 LPI  H13  C8   C9   110.40  3.000
 LPI  H14  C8   C1   109.25  3.000
 LPI  H13  C8   C1   108.91  3.000
 LPI  C9   C8   C1   112.30  3.000
 LPI  H16  C9   H15  107.87  3.000
 LPI  H16  C9   S10  108.41  3.000
 LPI  H15  C9   S10  109.22  3.000
 LPI  H16  C9   C8   111.98  3.000
 LPI  H15  C9   C8   110.11  3.000
 LPI  S10  C9   C8   109.21  3.000
 LPI  C11  S10  C9    99.80  3.000
 LPI  H19  C11  H18  109.48  3.000
 LPI  H19  C11  H17  108.67  3.000
 LPI  H18  C11  H17  108.60  3.000
 LPI  H19  C11  S10  111.33  3.000
 LPI  H18  C11  S10  111.09  3.000
 LPI  H17  C11  S10  107.58  3.000
 LPI  O8   C7   O9   123.54  3.000
 LPI  O9   C7   C1   111.11  3.000
 LPI  O8   C7   C1   125.33  3.000
 LPI  H20  O9   C7   110.08  3.000
 LPI  H21  N3   C1   109.72  3.000
 LPI  H21  N3   C4'  108.66  3.000
 LPI  C1   N3   C4'  113.64  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
 LPI  CONST_01  C2   N1   C6   C5      0.00   0.0  0
 LPI  CONST_02  C2   C3   C4   C5      0.00   0.0  0
 LPI  CONST_03  C3   C2   N1   C6      0.00   0.0  0
 LPI  CONST_04  C3   C4   C5   C6      0.00   0.0  0
 LPI  CONST_05  C4   C3   C2   N1      0.00   0.0  0
 LPI  CONST_06  C4   C5   C6   N1      0.00   0.0  0
 LPI  CONST_07  N1   C6   C5   C5'   180.00   0.0  0
 LPI  CONST_08  C3   C4   C5   C5'   180.00   0.0  0
 LPI  CONST_09  O3   C3   C4   C5    180.00   0.0  0
 LPI  CONST_10  C2'  C2   N1   C6    180.00   0.0  0
 LPI  CONST_11  C4'  C4   C5   C6    180.00   0.0  0
 LPI  CONST_12  O3   C3   C2   N1    180.00   0.0  0
 LPI  CONST_13  C4'  C4   C3   C2    180.00   0.0  0
 LPI  CONST_14  C4   C3   C2   C2'   180.00   0.0  0
 LPI  CONST_15  H5   C6   N1   C2    180.00   0.0  0
 LPI  CONST_16  H20  O9   C7   C1    180.00   0.0  0
 LPI  Var_01    C6   C5   C5'  OP4    -4.14  30.0  1
 LPI  Var_02    N3   C4'  C4   C5    -78.78  30.0  2
 LPI  Var_03    H6   C2'  C2   N1    116.97  30.0  2
 LPI  Var_04    C5   C5'  OP4  P    -179.38  30.0  1
 LPI  Var_05    C1   N3   C4'  C4   -179.23  30.0  1
 LPI  Var_06    S10  C9   C8   C1   -176.48  30.0  3
 LPI  Var_07    H17  C11  S10  C9   -178.23  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
 LPI  chir_01  C1  C7  N3  C8  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
 LPI  plan-1  C5'  0.020
 LPI  plan-1  C5   0.020
 LPI  plan-1  C6   0.020
 LPI  plan-1  N1   0.020
 LPI  plan-1  C2   0.020
 LPI  plan-1  C2'  0.020
 LPI  plan-1  C3   0.020
 LPI  plan-1  O3   0.020
 LPI  plan-1  C4   0.020
 LPI  plan-1  C4'  0.020
 LPI  plan-1  H5   0.020
 LPI  plan-2  C1   0.020
 LPI  plan-2  C7   0.020
 LPI  plan-2  O9   0.020
 LPI  plan-2  O8   0.020
 LPI  plan-2  H20  0.020

