# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu May 21 18:44:56 2020
#   Inital geometry file: a 94 line input string
#   Ligand name: 2-[({3-hydroxy-2-methyl-5-[(phosphonooxy)methyl]pyridin-4-yl}methyl)amino]prop-2-enoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cc1ncc(CO[P](O)(O)=O)c(CNC(=C)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
 P1T  P1T  '2-[({3-hydroxy-2-methyl-5-[(phosphonooxy)methyl]pyridin-4-yl}methyl)amino]prop-2-enoic acid'  ligand  36  21  .  2021-08-20  2021-08-20  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_P1T
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
 P1T  OP1   O  OH1   0  -0.748   0.7186   1.1979  -3.0953
 P1T  P     P  P     0   1.476   0.0272  -0.2366  -2.9325
 P1T  OP2   O  O     0  -0.697   0.5889  -1.3134  -3.7674
 P1T  OP3   O  OH1   0  -0.745  -1.5167   0.1175  -3.0948
 P1T  OP4   O  O2    0  -0.581   0.1032  -0.6123  -1.3844
 P1T  C5A   C  CH2   0  -0.290  -0.4170   0.2375  -0.3493
 P1T  C5    C  CR6   0  -0.033   0.1526  -0.2165   0.9586
 P1T  C6    C  CR16  0  -0.131  -0.6464  -0.9500   1.8213
 P1T  N1    N  N     0  -0.408  -0.2344  -1.4024   2.9973
 P1T  C2    C  CR6   0   0.136   1.0083  -1.1569   3.3830
 P1T  C2A   C  CH3   0  -0.786   1.4567  -1.6788   4.7148
 P1T  C3    C  CR6   0   0.281   1.8904  -0.4277   2.5728
 P1T  O3A   O  OH1   0  -0.623   3.1594  -0.1770   2.9450
 P1T  C4    C  CR6   0   0.106   1.4689   0.0572   1.3383
 P1T  C4A   C  CH2   0  -0.431   2.3949   0.9152   0.5091
 P1T  N     N  NH1   0  -0.625   2.3283   2.3285   0.8705
 P1T  CA    C  C     0   0.213   2.7496   2.7297   2.1367
 P1T  CB    C  C2    0  -0.587   1.9794   3.4066   2.9934
 P1T  C     C  C     0   0.527   4.1994   2.5051   2.4161
 P1T  OXT   O  OH1   0  -0.590   4.5040   2.6107   3.7005
 P1T  O     O  O     0  -0.443   5.0148   2.2819   1.5552
 P1T  HOP1  H  HOH1  0   0.500   1.6480   1.1589  -3.3575
 P1T  HOP3  H  HOH1  0   0.504  -1.7903   0.3801  -3.9838
 P1T  H5A1  H  HCH2  0   0.273  -1.5050   0.1559  -0.3264
 P1T  H5A2  H  HCH2  0   0.247  -0.1719   1.2830  -0.5503
 P1T  H6    H  HCR6  0   0.259  -1.6712  -1.1785   1.5466
 P1T  H2A1  H  HCH3  0   0.259   1.7343  -0.8709   5.3972
 P1T  H2A2  H  HCH3  0   0.274   0.6532  -2.2421   5.1830
 P1T  H2A3  H  HCH3  0   0.260   2.3197  -2.3432   4.6247
 P1T  HO3A  H  HOH1  0   0.487   3.3437  -0.5105   3.8302
 P1T  H4A1  H  HCH2  0   0.281   3.4212   0.5658   0.5920
 P1T  H4A2  H  HCH2  0   0.262   2.1453   0.8409  -0.5472
 P1T  HN    H  HNH1  0   0.371   1.4121   2.7059   0.6684
 P1T  HB1   H  H     0   0.256   0.9388   3.6008   2.7671
 P1T  HB2   H  H     0   0.262   2.3646   3.8256   3.9098
 P1T  HO    H  HOH1  0   0.484   5.4606   2.5129   3.8169

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
 P1T  OP1  P     single    1.601  0.020  1.601
 P1T  OP1  HOP1  single    0.850  0.020  0.980
 P1T  P    OP2   double    1.474  0.020  1.474
 P1T  P    OP4   single    1.595  0.020  1.595
 P1T  P    OP3   single    1.592  0.020  1.592
 P1T  OP3  HOP3  single    0.850  0.020  0.980
 P1T  OP4  C5A   single    1.437  0.020  1.437
 P1T  C5A  C5    single    1.497  0.020  1.497
 P1T  C5A  H5A1  single    0.970  0.020  1.090
 P1T  C5A  H5A2  single    0.970  0.020  1.090
 P1T  C5   C4    aromatic  1.397  0.020  1.397
 P1T  C5   C6    aromatic  1.386  0.020  1.386
 P1T  C6   N1    aromatic  1.326  0.020  1.326
 P1T  C6   H6    single    0.930  0.020  1.080
 P1T  N1   C2    aromatic  1.324  0.020  1.324
 P1T  C2   C3    aromatic  1.402  0.020  1.402
 P1T  C2   C2A   single    1.499  0.020  1.499
 P1T  C2A  H2A1  single    0.970  0.020  1.090
 P1T  C2A  H2A2  single    0.970  0.020  1.090
 P1T  C2A  H2A3  single    0.970  0.020  1.090
 P1T  C3   O3A   single    1.346  0.020  1.346
 P1T  C3   C4    aromatic  1.392  0.020  1.392
 P1T  O3A  HO3A  single    0.850  0.020  0.980
 P1T  C4   C4A   single    1.510  0.020  1.510
 P1T  C4A  N     single    1.460  0.020  1.460
 P1T  C4A  H4A1  single    0.970  0.020  1.090
 P1T  C4A  H4A2  single    0.970  0.020  1.090
 P1T  N    CA    single    1.393  0.020  1.393
 P1T  N    HN    single    0.890  0.020  1.040
 P1T  CA   C     single    1.493  0.020  1.493
 P1T  CA   CB    double    1.336  0.020  1.336
 P1T  CB   HB1   single    0.930  0.020  1.080
 P1T  CB   HB2   single    0.930  0.020  1.080
 P1T  C    O     double    1.207  0.020  1.207
 P1T  C    OXT   single    1.324  0.020  1.324
 P1T  OXT  HO    single    0.850  0.020  0.980

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
 P1T  HOP1  OP1  P     114.01  3.000
 P1T  OP4   P    OP3   101.39  3.000
 P1T  OP3   P    OP2   118.31  3.000
 P1T  OP4   P    OP2   111.08  3.000
 P1T  OP3   P    OP1   102.07  3.000
 P1T  OP4   P    OP1   106.81  3.000
 P1T  OP2   P    OP1   115.63  3.000
 P1T  HOP3  OP3  P     115.39  3.000
 P1T  C5A   OP4  P     122.87  3.000
 P1T  H5A2  C5A  H5A1  107.40  3.000
 P1T  H5A2  C5A  C5    111.45  3.000
 P1T  H5A1  C5A  C5    109.78  3.000
 P1T  H5A2  C5A  OP4   110.63  3.000
 P1T  H5A1  C5A  OP4   109.38  3.000
 P1T  C5    C5A  OP4   108.20  3.000
 P1T  C4    C5   C6    118.54  3.000
 P1T  C6    C5   C5A   119.01  3.000
 P1T  C4    C5   C5A   122.45  3.000
 P1T  H6    C6   N1    116.50  3.000
 P1T  H6    C6   C5    119.89  3.000
 P1T  N1    C6   C5    123.61  3.000
 P1T  C2    N1   C6    119.13  3.000
 P1T  C3    C2   C2A   120.41  3.000
 P1T  C2A   C2   N1    118.36  3.000
 P1T  C3    C2   N1    121.23  3.000
 P1T  H2A3  C2A  H2A2  107.71  3.000
 P1T  H2A3  C2A  H2A1  107.47  3.000
 P1T  H2A2  C2A  H2A1  107.56  3.000
 P1T  H2A3  C2A  C2    112.00  3.000
 P1T  H2A2  C2A  C2    109.99  3.000
 P1T  H2A1  C2A  C2    111.91  3.000
 P1T  C4    C3   O3A   117.77  3.000
 P1T  C4    C3   C2    120.21  3.000
 P1T  O3A   C3   C2    122.02  3.000
 P1T  HO3A  O3A  C3    111.71  3.000
 P1T  C4A   C4   C3    119.95  3.000
 P1T  C4A   C4   C5    122.66  3.000
 P1T  C3    C4   C5    117.27  3.000
 P1T  H4A2  C4A  H4A1  105.58  3.000
 P1T  H4A2  C4A  N     107.21  3.000
 P1T  H4A1  C4A  N     109.58  3.000
 P1T  H4A2  C4A  C4    110.71  3.000
 P1T  H4A1  C4A  C4    110.75  3.000
 P1T  N     C4A  C4    112.70  3.000
 P1T  HN    N    CA    110.37  3.000
 P1T  HN    N    C4A   110.67  3.000
 P1T  CA    N    C4A   119.32  3.000
 P1T  C     CA   CB    121.05  3.000
 P1T  CB    CA   N     123.65  3.000
 P1T  C     CA   N     114.85  3.000
 P1T  HB2   CB   HB1   116.83  3.000
 P1T  HB2   CB   CA    122.38  3.000
 P1T  HB1   CB   CA    120.72  3.000
 P1T  O     C    OXT   123.46  3.000
 P1T  OXT   C    CA    113.13  3.000
 P1T  O     C    CA    123.39  3.000
 P1T  HO    OXT  C     109.61  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
 P1T  CONST_01  C2    C3   C4   C5      0.00   0.0  0
 P1T  CONST_02  C2    N1   C6   C5      0.00   0.0  0
 P1T  CONST_03  C3    C4   C5   C6      0.00   0.0  0
 P1T  CONST_04  C3    C2   N1   C6      0.00   0.0  0
 P1T  CONST_05  C4    C5   C6   N1      0.00   0.0  0
 P1T  CONST_06  C4    C3   C2   N1      0.00   0.0  0
 P1T  CONST_07  C3    C4   C5   C5A   180.00   0.0  0
 P1T  CONST_08  N1    C6   C5   C5A   180.00   0.0  0
 P1T  CONST_09  O3A   C3   C4   C5    180.00   0.0  0
 P1T  CONST_10  C4A   C4   C5   C6    180.00   0.0  0
 P1T  CONST_11  C2A   C2   N1   C6    180.00   0.0  0
 P1T  CONST_12  O3A   C3   C2   N1    180.00   0.0  0
 P1T  CONST_13  C4A   C4   C3   C2    180.00   0.0  0
 P1T  CONST_14  C4    C3   C2   C2A   180.00   0.0  0
 P1T  CONST_15  H6    C6   N1   C2    180.00   0.0  0
 P1T  CONST_16  HO    OXT  C    CA    180.00   0.0  0
 P1T  Var_01    C4    C5   C5A  OP4    75.78  30.0  2
 P1T  Var_02    N     C4A  C4   C5     90.41  30.0  2
 P1T  Var_03    H2A1  C2A  C2   N1   -117.73  30.0  2
 P1T  Var_04    C5    C5A  OP4  P    -164.30  30.0  3
 P1T  Var_05    CA    N    C4A  C4     65.08  30.0  3
 P1T  Var_06    C     CA   N    C4A    63.79  30.0  2
 P1T  Var_07    O     C    CA   N      15.93  30.0  2
 P1T  Var_08    HB1   CB   CA   N       5.57   0.0  2

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
 P1T  plan-1  C5A  0.020
 P1T  plan-1  C5   0.020
 P1T  plan-1  C6   0.020
 P1T  plan-1  N1   0.020
 P1T  plan-1  C2   0.020
 P1T  plan-1  C2A  0.020
 P1T  plan-1  C3   0.020
 P1T  plan-1  O3A  0.020
 P1T  plan-1  C4   0.020
 P1T  plan-1  C4A  0.020
 P1T  plan-1  H6   0.020
 P1T  plan-2  CA   0.020
 P1T  plan-2  C    0.020
 P1T  plan-2  OXT  0.020
 P1T  plan-2  O    0.020
 P1T  plan-2  HO   0.020
 P1T  plan-3  N    0.020
 P1T  plan-3  CA   0.020
 P1T  plan-3  CB   0.020
 P1T  plan-3  C    0.020
 P1T  plan-3  HB1  0.020
 P1T  plan-3  HB2  0.020

