# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Mar  8 05:31:58 2022
#   Inital geometry file: a 122 line input string
#   Ligand name: N-({3-hydroxy-2-methyl-5-[(phosphonooxy)methyl]pyridin-4-yl}methyl)-L-tyrosine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cc1ncc(CO[P](O)(O)=O)c(CN[C@@H](Cc2ccc(O)cc2)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
 0PR  0PR  N-({3-hydroxy-2-methyl-5-[(phosphonooxy)methyl]pyridin-4-yl}methyl)-L-tyrosine  L-peptide  46  28  .  2019-03-22  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_0PR
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
 0PR  N1    N  N      0  -0.409   -3.9664  56.5046  27.0074
 0PR  C2    C  CR6    0   0.124   -4.9775  57.3343  26.7923
 0PR  C2A   C  CH3    0  -0.780   -5.0823  58.5574  27.6559
 0PR  C3    C  CR6    0   0.250   -5.9160  57.0815  25.7845
 0PR  O3    O  OH1    0  -0.628   -6.9532  57.9131  25.5432
 0PR  C4    C  CR6    0   0.089   -5.8051  55.9463  24.9830
 0PR  C4A   C  CH2    0  -0.374   -6.8338  55.6895  23.9099
 0PR  C5    C  CR6    0  -0.026   -4.7265  55.0906  25.2244
 0PR  C6    C  CR16   0  -0.157   -3.8482  55.4251  26.2458
 0PR  C5A   C  CH2    0  -0.235   -4.4710  53.8621  24.3905
 0PR  O4P   O  O2     0  -0.650   -4.0970  54.2452  23.1014
 0PR  P     P  P      0   1.237   -4.2732  53.0953  21.8333
 0PR  O1P   O  O      0  -0.896   -3.2445  52.0128  22.1455
 0PR  O2P   O  OP    -1  -0.884   -3.9601  53.9638  20.6238
 0PR  O3P   O  OP    -1  -0.880   -5.7230  52.6162  21.9313
 0PR  N     N  NH1    0  -0.601   -8.1342  55.3669  24.4693
 0PR  CA    C  CH1    0  -0.200   -9.0979  54.9663  23.4633
 0PR  C     C  C      0   0.417  -10.5240  55.4806  23.7806
 0PR  O     O  O      0  -0.595  -10.6723  56.1760  24.8052
 0PR  CB    C  CH2    0  -0.506   -9.0930  53.4387  23.2800
 0PR  CG    C  C      0   0.114   -9.5864  52.6974  24.4889
 0PR  CD1   C  C1     0  -0.287  -10.9143  52.2853  24.5928
 0PR  CD2   C  C1     0  -0.298   -8.7476  52.4212  25.5662
 0PR  CE1   C  C1     0  -0.327  -11.3931  51.6315  25.7182
 0PR  CE2   C  C1     0  -0.373   -9.2075  51.7676  26.7016
 0PR  CZ    C  C      0   0.331  -10.5393  51.3710  26.7862
 0PR  OH    O  OH1    0  -0.637  -11.0495  50.7340  27.8644
 0PR  OXT   O  OC    -1  -0.606  -11.4055  55.1623  22.9583
 0PR  H2A1  H  HCH3   0   0.266   -4.2589  58.5783  28.3660
 0PR  H2A2  H  HCH3   0   0.252   -5.0371  59.4798  27.0707
 0PR  H2A3  H  HCH3   0   0.253   -6.0137  58.5796  28.2280
 0PR  HO3   H  HOH1   0   0.482   -6.9470  58.6759  26.1317
 0PR  H4A   H  HCH2   0   0.201   -6.8664  56.5617  23.2358
 0PR  H6    H  HCR6   0   0.241   -3.0001  54.7799  26.4557
 0PR  H5A1  H  HCH2   0   0.191   -3.6894  53.2659  24.8853
 0PR  H5A2  H  HCH2   0   0.188   -5.3740  53.2368  24.3858
 0PR  H     H  HNH1   0   0.340   -8.5211  56.1588  24.9657
 0PR  HA    H  HCH1   0   0.197   -8.8382  55.4011  22.4818
 0PR  HB2   H  HCH2   0   0.221   -9.7105  53.1901  22.4154
 0PR  HB3   H  HCH2   0   0.236   -8.0761  53.1211  23.0351
 0PR  HD1   H  H      0   0.235  -11.5961  52.4853  23.7758
 0PR  HD2   H  H      0   0.247   -7.7085  52.7229  25.5193
 0PR  HE1   H  H      0   0.249  -12.4300  51.3217  25.7710
 0PR  HE2   H  H      0   0.257   -8.5261  51.5675  27.5218
 0PR  HH    H  HOH1   0   0.468  -10.3646  50.6036  28.5294
 0PR  HA1   H  HCH2   0   0.263   -6.5059  54.8549  23.2946

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
 0PR  N1   C2    aromatic  1.326  0.020  1.326
 0PR  N1   C6    aromatic  1.326  0.020  1.326
 0PR  C2   C2A   single    1.501  0.020  1.501
 0PR  C2   C3    aromatic  1.400  0.020  1.400
 0PR  C2A  H2A1  single    0.970  0.020  1.090
 0PR  C2A  H2A2  single    0.970  0.020  1.090
 0PR  C2A  H2A3  single    0.970  0.020  1.090
 0PR  C3   O3    single    1.351  0.020  1.351
 0PR  C3   C4    aromatic  1.394  0.020  1.394
 0PR  O3   HO3   single    0.850  0.020  0.980
 0PR  C4   C4A   single    1.509  0.020  1.509
 0PR  C4   C5    aromatic  1.398  0.020  1.398
 0PR  C4A  H4A   single    0.970  0.020  1.090
 0PR  C5   C6    aromatic  1.388  0.020  1.388
 0PR  C5   C5A   single    1.507  0.020  1.507
 0PR  C6   H6    single    0.930  0.020  1.080
 0PR  C5A  O4P   single    1.396  0.020  1.396
 0PR  C5A  H5A1  single    0.970  0.020  1.090
 0PR  C5A  H5A2  single    0.970  0.020  1.090
 0PR  O4P  P     single    1.721  0.020  1.721
 0PR  P    O1P   deloc     1.526  0.020  1.526
 0PR  P    O2P   deloc     1.522  0.020  1.522
 0PR  P    O3P   deloc     1.530  0.020  1.530
 0PR  N    CA    single    1.458  0.019  1.458
 0PR  N    H     single    0.860  0.020  0.860
 0PR  CA   C     single    1.525  0.021  1.525
 0PR  CA   CB    single    1.530  0.020  1.530
 0PR  CA   HA    single    0.970  0.020  0.970
 0PR  C    O     deloc     1.231  0.020  1.231
 0PR  C    OXT   deloc     1.247  0.020  1.247
 0PR  CB   CG    single    1.501  0.020  1.501
 0PR  CB   HB2   single    0.970  0.020  1.090
 0PR  CB   HB3   single    0.970  0.020  1.090
 0PR  CG   CD1   aromatic  1.394  0.020  1.394
 0PR  CG   CD2   aromatic  1.393  0.020  1.393
 0PR  CD1  CE1   aromatic  1.387  0.020  1.387
 0PR  CD1  HD1   single    0.930  0.020  1.080
 0PR  CD2  CE2   aromatic  1.389  0.020  1.389
 0PR  CD2  HD2   single    0.930  0.020  1.080
 0PR  CE1  CZ    aromatic  1.392  0.020  1.392
 0PR  CE1  HE1   single    0.930  0.020  1.080
 0PR  CE2  CZ    aromatic  1.392  0.020  1.392
 0PR  CE2  HE2   single    0.930  0.020  1.080
 0PR  CZ   OH    single    1.352  0.020  1.352
 0PR  OH   HH    single    0.850  0.020  0.980
 0PR  C4A  N     single    1.452  0.020  1.452
 0PR  C4A  HA1   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
 0PR  C6    N1   C2    118.96  3.000
 0PR  C3    C2   C2A   120.97  3.000
 0PR  C3    C2   N1    121.00  3.000
 0PR  C2A   C2   N1    118.03  3.000
 0PR  H2A3  C2A  H2A2  107.35  3.000
 0PR  H2A3  C2A  H2A1  107.64  3.000
 0PR  H2A2  C2A  H2A1  107.58  3.000
 0PR  H2A3  C2A  C2    112.16  3.000
 0PR  H2A2  C2A  C2    112.12  3.000
 0PR  H2A1  C2A  C2    109.79  3.000
 0PR  C4    C3   O3    117.37  3.000
 0PR  C4    C3   C2    120.50  3.000
 0PR  O3    C3   C2    122.14  3.000
 0PR  HO3   O3   C3    111.92  3.000
 0PR  C5    C4   C4A   123.01  3.000
 0PR  C5    C4   C3    117.43  3.000
 0PR  C4A   C4   C3    119.56  3.000
 0PR  HA1   C4A  H4A   105.67  3.000
 0PR  HA1   C4A  N     108.51  3.000
 0PR  H4A   C4A  N     112.62  3.000
 0PR  HA1   C4A  C4    109.12  3.000
 0PR  N     C4A  C4    111.99  3.000
 0PR  H4A   C4A  C4    108.68  3.000
 0PR  C5A   C5   C6    119.77  3.000
 0PR  C5A   C5   C4    122.31  3.000
 0PR  C6    C5   C4    117.89  3.000
 0PR  H6    C6   C5    119.55  3.000
 0PR  H6    C6   N1    116.23  3.000
 0PR  C5    C6   N1    124.22  3.000
 0PR  H5A2  C5A  H5A1  106.10  3.000
 0PR  H5A2  C5A  O4P   111.87  3.000
 0PR  H5A1  C5A  O4P   111.94  3.000
 0PR  H5A2  C5A  C5    109.10  3.000
 0PR  H5A1  C5A  C5    108.26  3.000
 0PR  O4P   C5A  C5    109.44  3.000
 0PR  P     O4P  C5A   118.01  3.000
 0PR  O3P   P    O2P   115.13  3.000
 0PR  O3P   P    O1P   113.80  3.000
 0PR  O2P   P    O1P   115.40  3.000
 0PR  O3P   P    O4P   105.02  3.000
 0PR  O2P   P    O4P   100.56  3.000
 0PR  O1P   P    O4P   104.73  3.000
 0PR  H     N    CA    114.00  3.000
 0PR  H     N    C4A   110.96  3.000
 0PR  CA    N    C4A   112.92  3.000
 0PR  HA    CA   CB    109.00  3.000
 0PR  HA    CA   C     109.00  3.000
 0PR  CB    CA   C     110.10  1.900
 0PR  HA    CA   N     110.00  3.000
 0PR  CB    CA   N     110.50  1.700
 0PR  C     CA   N     111.00  2.800
 0PR  OXT   C    O     126.88  3.000
 0PR  OXT   C    CA    115.53  3.000
 0PR  O     C    CA    120.80  1.700
 0PR  HB3   CB   HB2   106.43  3.000
 0PR  HB3   CB   CG    110.04  3.000
 0PR  HB2   CB   CG    109.85  3.000
 0PR  HB3   CB   CA    108.55  3.000
 0PR  HB2   CB   CA    108.59  3.000
 0PR  CG    CB   CA    113.15  3.000
 0PR  CD2   CG   CD1   117.21  3.000
 0PR  CD2   CG   CB    121.51  3.000
 0PR  CD1   CG   CB    121.26  3.000
 0PR  HD1   CD1  CE1   118.81  3.000
 0PR  HD1   CD1  CG    119.27  3.000
 0PR  CE1   CD1  CG    121.92  3.000
 0PR  HD2   CD2  CE2   118.97  3.000
 0PR  HD2   CD2  CG    119.28  3.000
 0PR  CE2   CD2  CG    121.75  3.000
 0PR  HE1   CE1  CZ    119.74  3.000
 0PR  HE1   CE1  CD1   120.32  3.000
 0PR  CZ    CE1  CD1   119.94  3.000
 0PR  HE2   CE2  CZ    120.16  3.000
 0PR  HE2   CE2  CD2   119.80  3.000
 0PR  CZ    CE2  CD2   120.04  3.000
 0PR  OH    CZ   CE2   122.93  3.000
 0PR  OH    CZ   CE1   117.94  3.000
 0PR  CE2   CZ   CE1   119.14  3.000
 0PR  HH    OH   CZ    110.24  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
 0PR  CONST_01  C4    C3   C2   N1      0.00   0.0  0
 0PR  CONST_02  C4    C5   C6   N1      0.00   0.0  0
 0PR  CONST_03  C5    C6   N1   C2      0.00   0.0  0
 0PR  CONST_04  C5    C4   C3   C2      0.00   0.0  0
 0PR  CONST_05  C6    N1   C2   C3      0.00   0.0  0
 0PR  CONST_06  C6    C5   C4   C3      0.00   0.0  0
 0PR  CONST_07  CZ    CE1  CD1  CG      0.00   0.0  0
 0PR  CONST_08  CZ    CE2  CD2  CG      0.00   0.0  0
 0PR  CONST_09  CE2   CD2  CG   CD1     0.00   0.0  0
 0PR  CONST_10  CE2   CZ   CE1  CD1     0.00   0.0  0
 0PR  CONST_11  CE1   CD1  CG   CD2     0.00   0.0  0
 0PR  CONST_12  CE1   CZ   CE2  CD2     0.00   0.0  0
 0PR  CONST_13  O3    C3   C2   N1    180.00   0.0  0
 0PR  CONST_14  C5A   C5   C6   N1    180.00   0.0  0
 0PR  CONST_15  C4A   C4   C3   C2    180.00   0.0  0
 0PR  CONST_16  C6    N1   C2   C2A   180.00   0.0  0
 0PR  CONST_17  C4    C3   C2   C2A   180.00   0.0  0
 0PR  CONST_18  C5A   C5   C4   C3    180.00   0.0  0
 0PR  CONST_19  C5    C4   C3   O3    180.00   0.0  0
 0PR  CONST_20  C6    C5   C4   C4A   180.00   0.0  0
 0PR  CONST_21  CE1   CD1  CG   CB    180.00   0.0  0
 0PR  CONST_22  CE2   CD2  CG   CB    180.00   0.0  0
 0PR  CONST_23  OH    CZ   CE1  CD1   180.00   0.0  0
 0PR  CONST_24  OH    CZ   CE2  CD2   180.00   0.0  0
 0PR  CONST_25  H6    C6   N1   C2    180.00   0.0  0
 0PR  CONST_26  HE1   CE1  CD1  CG    180.00   0.0  0
 0PR  CONST_27  HE2   CE2  CD2  CG    180.00   0.0  0
 0PR  CONST_28  HD2   CD2  CG   CD1   180.00   0.0  0
 0PR  CONST_29  HD1   CD1  CG   CD2   180.00   0.0  0
 0PR  Var_01    N     C4A  C4   C3    -68.42  30.0  2
 0PR  Var_02    O4P   C5A  C5   C4     68.00  30.0  2
 0PR  Var_03    CD1   CG   CB   CA     95.66  30.0  2
 0PR  Var_04    H2A1  C2A  C2   N1      0.29  30.0  2
 0PR  Var_05    CA    N    C4A  C4   -173.32  30.0  3
 0PR  Var_06    O1P   P    O4P  C5A   -67.81  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
 0PR  chir_01  CA  N  C  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
 0PR  plan-1  N1   0.020
 0PR  plan-1  C2   0.020
 0PR  plan-1  C2A  0.020
 0PR  plan-1  C3   0.020
 0PR  plan-1  O3   0.020
 0PR  plan-1  C4   0.020
 0PR  plan-1  C4A  0.020
 0PR  plan-1  C5   0.020
 0PR  plan-1  C6   0.020
 0PR  plan-1  C5A  0.020
 0PR  plan-1  H6   0.020
 0PR  plan-2  CB   0.020
 0PR  plan-2  CG   0.020
 0PR  plan-2  CD1  0.020
 0PR  plan-2  CD2  0.020
 0PR  plan-2  CE1  0.020
 0PR  plan-2  CE2  0.020
 0PR  plan-2  CZ   0.020
 0PR  plan-2  OH   0.020
 0PR  plan-2  HD1  0.020
 0PR  plan-2  HD2  0.020
 0PR  plan-2  HE1  0.020
 0PR  plan-2  HE2  0.020
 0PR  plan-3  CA   0.020
 0PR  plan-3  C    0.020
 0PR  plan-3  O    0.020
 0PR  plan-3  OXT  0.020

