# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Mar  9 13:30:07 2022
#   Inital geometry file: a 96 line input string
#   Ligand name: N-({3-hydroxy-2-methyl-5-[(phosphonooxy)methyl]pyridin-4-yl}methyl)-L-cysteine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cc1ncc(CO[P](O)(O)=O)c(CN[C@@H](CS)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
 C6P  C6P  N-({3-hydroxy-2-methyl-5-[(phosphonooxy)methyl]pyridin-4-yl}methyl)-L-cysteine  ligand  36  22  .  2022-03-15  2022-03-15
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_C6P
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
 C6P  N     N  NH1    0  -0.588   4.0631  -1.6404  -1.1105
 C6P  C     C  C      0   0.392   2.3943  -1.8434  -2.9147
 C6P  O     O  O      0  -0.598   1.3708  -2.0760  -2.2416
 C6P  P     P  P      0   1.227   0.1676   0.6831   2.5433
 C6P  OP3   O  OP    -1  -0.891   1.0210   0.5517   3.8051
 C6P  OP1   O  OP    -1  -0.902  -0.5851  -0.5938   2.1799
 C6P  OP2   O  O      0  -0.897  -0.6475   1.9662   2.4488
 C6P  OP4   O  O2     0  -0.656   1.2740   0.9238   1.2703
 C6P  C5    C  CR6    0  -0.019   3.6101   0.4759   1.0919
 C6P  C6    C  CR16   0  -0.144   4.0052   1.0811   2.2800
 C6P  N1    N  N      0  -0.414   5.2037   1.6130   2.4735
 C6P  C2    C  CR6    0   0.111   6.0943   1.5775   1.4895
 C6P  C2A   C  CH3    0  -0.788   7.4451   2.1850   1.7370
 C6P  C3    C  CR6    0   0.239   5.7883   0.9916   0.2572
 C6P  O3    O  OH1    0  -0.627   6.6910   0.9444  -0.7487
 C6P  C4    C  CR6    0   0.055   4.5255   0.4377   0.0399
 C6P  C4A   C  CH2    0  -0.359   4.1684  -0.2004  -1.2756
 C6P  CA    C  CH1    0  -0.111   3.7340  -2.3610  -2.3320
 C6P  OXT   O  OC    -1  -0.605   2.4500  -1.2398  -4.0026
 C6P  CB    C  CH2    0  -0.581   3.6347  -3.8350  -1.9683
 C6P  SG    S  S2     0  -0.263   3.2711  -4.9164  -3.3851
 C6P  HN    H  HNH1   0   0.339   4.9515  -1.9845  -0.7629
 C6P  H5M1  H  HCH2   0   0.231   2.0283  -0.5388   0.0310
 C6P  H5M2  H  HCH2   0   0.187   2.1423  -0.9113   1.7302
 C6P  H6    H  HCR6   0   0.257   3.3031   1.1262   3.1066
 C6P  H2A1  H  HCH3   0   0.267   7.4889   2.5849   2.7474
 C6P  H2A2  H  HCH3   0   0.252   8.2530   1.4551   1.6370
 C6P  H2A3  H  HCH3   0   0.253   7.6620   3.0071   1.0494
 C6P  HO3   H  HOH1   0   0.482   7.5231   1.3493  -0.4823
 C6P  H4A1  H  HCH2   0   0.243   3.1973   0.1907  -1.5883
 C6P  H4A2  H  HCH2   0   0.228   4.8784   0.0899  -2.0588
 C6P  HA    H  HCH1   0   0.179   4.5121  -2.2403  -3.1020
 C6P  HB1   H  HCH2   0   0.267   2.8801  -3.9795  -1.1969
 C6P  HB2   H  HCH2   0   0.268   4.5873  -4.1972  -1.5755
 C6P  HSG   H  HSH1   0   0.215   1.9786  -4.5991  -3.5192
 C6P  C5M   C  CH2    0  -0.247   2.2105  -0.0864   1.0097

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
 C6P  N    CA    single    1.456  0.020  1.456
 C6P  N    C4A   single    1.453  0.020  1.453
 C6P  N    HN    single    0.890  0.020  1.040
 C6P  C    O     deloc     1.247  0.020  1.247
 C6P  C    CA    single    1.550  0.020  1.550
 C6P  C    OXT   deloc     1.245  0.020  1.245
 C6P  P    OP2   deloc     1.523  0.020  1.523
 C6P  P    OP1   deloc     1.526  0.020  1.526
 C6P  P    OP3   deloc     1.529  0.020  1.529
 C6P  P    OP4   single    1.704  0.020  1.704
 C6P  OP4  C5M   single    1.402  0.020  1.402
 C6P  C5M  C5    single    1.511  0.020  1.511
 C6P  C5M  H5M1  single    0.970  0.020  1.090
 C6P  C5M  H5M2  single    0.970  0.020  1.090
 C6P  C5   C4    aromatic  1.395  0.020  1.395
 C6P  C5   C6    aromatic  1.391  0.020  1.391
 C6P  C6   N1    aromatic  1.325  0.020  1.325
 C6P  C6   H6    single    0.930  0.020  1.080
 C6P  N1   C2    aromatic  1.328  0.020  1.328
 C6P  C2   C3    aromatic  1.398  0.020  1.398
 C6P  C2   C2A   single    1.502  0.020  1.502
 C6P  C2A  H2A1  single    0.970  0.020  1.090
 C6P  C2A  H2A2  single    0.970  0.020  1.090
 C6P  C2A  H2A3  single    0.970  0.020  1.090
 C6P  C3   C4    aromatic  1.396  0.020  1.396
 C6P  C3   O3    single    1.352  0.020  1.352
 C6P  O3   HO3   single    0.850  0.020  0.980
 C6P  C4   C4A   single    1.505  0.020  1.505
 C6P  C4A  H4A1  single    0.970  0.020  1.090
 C6P  C4A  H4A2  single    0.970  0.020  1.090
 C6P  CA   CB    single    1.521  0.020  1.521
 C6P  CA   HA    single    0.970  0.020  1.090
 C6P  CB   SG    single    1.819  0.020  1.819
 C6P  CB   HB1   single    0.970  0.020  1.090
 C6P  CB   HB2   single    0.970  0.020  1.090
 C6P  SG   HSG   single    1.200  0.020  1.300

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
 C6P  HN    N    CA    108.52  3.000
 C6P  HN    N    C4A   108.16  3.000
 C6P  CA    N    C4A   114.30  3.000
 C6P  OXT   C    CA    116.85  3.000
 C6P  OXT   C    O     126.77  3.000
 C6P  CA    C    O     116.38  3.000
 C6P  OP4   P    OP2   100.50  3.000
 C6P  OP4   P    OP1   105.10  3.000
 C6P  OP2   P    OP1   115.22  3.000
 C6P  OP4   P    OP3   105.45  3.000
 C6P  OP1   P    OP3   113.57  3.000
 C6P  OP2   P    OP3   114.98  3.000
 C6P  C5M   OP4  P     118.09  3.000
 C6P  C4    C5   C6    118.02  3.000
 C6P  C6    C5   C5M   118.14  3.000
 C6P  C4    C5   C5M   123.84  3.000
 C6P  H6    C6   N1    117.20  3.000
 C6P  H6    C6   C5    119.00  3.000
 C6P  N1    C6   C5    123.80  3.000
 C6P  C2    N1   C6    119.19  3.000
 C6P  C3    C2   C2A   120.77  3.000
 C6P  C2A   C2   N1    118.06  3.000
 C6P  C3    C2   N1    121.17  3.000
 C6P  H2A3  C2A  H2A2  107.32  3.000
 C6P  H2A3  C2A  H2A1  107.44  3.000
 C6P  H2A2  C2A  H2A1  107.50  3.000
 C6P  H2A3  C2A  C2    112.27  3.000
 C6P  H2A2  C2A  C2    112.31  3.000
 C6P  H2A1  C2A  C2    109.76  3.000
 C6P  C4    C3   O3    118.31  3.000
 C6P  O3    C3   C2    121.60  3.000
 C6P  C4    C3   C2    120.09  3.000
 C6P  HO3   O3   C3    110.87  3.000
 C6P  C4A   C4   C3    121.26  3.000
 C6P  C4A   C4   C5    121.00  3.000
 C6P  C3    C4   C5    117.74  3.000
 C6P  H4A2  C4A  H4A1  106.05  3.000
 C6P  H4A2  C4A  C4    111.01  3.000
 C6P  H4A1  C4A  C4    108.01  3.000
 C6P  H4A2  C4A  N     112.98  3.000
 C6P  H4A1  C4A  N     108.83  3.000
 C6P  C4    C4A  N     109.75  3.000
 C6P  HA    CA   CB    108.63  3.000
 C6P  HA    CA   C     108.13  3.000
 C6P  CB    CA   C     110.91  3.000
 C6P  HA    CA   N     111.88  3.000
 C6P  CB    CA   N     107.08  3.000
 C6P  C     CA   N     110.21  3.000
 C6P  HB2   CB   HB1   107.80  3.000
 C6P  HB2   CB   SG    104.91  3.000
 C6P  HB1   CB   SG    109.54  3.000
 C6P  HB2   CB   CA    110.51  3.000
 C6P  HB1   CB   CA    110.07  3.000
 C6P  SG    CB   CA    113.75  3.000
 C6P  HSG   SG   CB     97.48  3.000
 C6P  H5M2  C5M  H5M1  105.45  3.000
 C6P  H5M2  C5M  C5    107.56  3.000
 C6P  H5M1  C5M  C5    110.92  3.000
 C6P  H5M2  C5M  OP4   112.22  3.000
 C6P  H5M1  C5M  OP4   110.68  3.000
 C6P  C5    C5M  OP4   109.91  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
 C6P  CONST_01  C2    C3   C4   C5      0.00   0.0  0
 C6P  CONST_02  C2    N1   C6   C5      0.00   0.0  0
 C6P  CONST_03  C3    C4   C5   C6      0.00   0.0  0
 C6P  CONST_04  C3    C2   N1   C6      0.00   0.0  0
 C6P  CONST_05  C4    C5   C6   N1      0.00   0.0  0
 C6P  CONST_06  C4    C3   C2   N1      0.00   0.0  0
 C6P  CONST_07  C3    C4   C5   C5M   180.00   0.0  0
 C6P  CONST_08  N1    C6   C5   C5M   180.00   0.0  0
 C6P  CONST_09  O3    C3   C4   C5    180.00   0.0  0
 C6P  CONST_10  C4A   C4   C5   C6    180.00   0.0  0
 C6P  CONST_11  C2A   C2   N1   C6    180.00   0.0  0
 C6P  CONST_12  O3    C3   C2   N1    180.00   0.0  0
 C6P  CONST_13  C4A   C4   C3   C2    180.00   0.0  0
 C6P  CONST_14  C4    C3   C2   C2A   180.00   0.0  0
 C6P  CONST_15  H6    C6   N1   C2    180.00   0.0  0
 C6P  Var_01    C5    C4   C4A  N     -69.68  30.0  1
 C6P  Var_02    C4    C5   C5M  OP4  -121.54  30.0  2
 C6P  Var_03    H2A1  C2A  C2   N1      0.05  30.0  2
 C6P  Var_04    C5    C5M  OP4  P    -123.13  30.0  3
 C6P  Var_05    CA    N    C4A  C4   -179.37  30.0  2

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
 C6P  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
 C6P  plan-1  C5   0.020
 C6P  plan-1  C6   0.020
 C6P  plan-1  N1   0.020
 C6P  plan-1  C2   0.020
 C6P  plan-1  C2A  0.020
 C6P  plan-1  C3   0.020
 C6P  plan-1  O3   0.020
 C6P  plan-1  C4   0.020
 C6P  plan-1  C4A  0.020
 C6P  plan-1  H6   0.020
 C6P  plan-1  C5M  0.020
 C6P  plan-2  C    0.020
 C6P  plan-2  O    0.020
 C6P  plan-2  CA   0.020
 C6P  plan-2  OXT  0.020

