# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon May 18 10:22:23 2020
#   Inital geometry file: a 73 line input string
#   Ligand name: (4-formyl-5-hydroxy-6-methyl-1-oxidopyridin-3-yl)methyl dihydrogen phosphate
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cc1c(O)c(C=O)c(CO[P](O)(O)=O)c[n+]1[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
 NOP  NOP  '(4-formyl-5-hydroxy-6-methyl-1-oxidopyridin-3-yl)methyl dihydrogen phosphate'  ligand  27  17  .  2021-08-15  2021-08-15  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_NOP
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
 NOP  N1    N  NR6    1  -0.047  -130.6401  4.0870  63.5550
 NOP  O1    O  O     -1  -0.513  -129.5201  3.5658  63.3192
 NOP  C2    C  CR6    0   0.209  -131.3451  4.6604  62.5528
 NOP  C2A   C  CH3    0  -0.707  -130.7340  4.6428  61.1982
 NOP  C3    C  CR6    0   0.304  -132.5874  5.2348  62.8462
 NOP  O3    O  OH1    0  -0.604  -133.2431  5.7902  61.8416
 NOP  C4    C  CR6    0  -0.080  -133.1015  5.2225  64.1547
 NOP  C4A   C  C1     0   0.161  -134.3797  5.8538  64.4289
 NOP  O4A   O  O      0  -0.435  -135.0591  6.3885  63.5622
 NOP  C5    C  CR6    0  -0.011  -132.3271  4.6094  65.1555
 NOP  C6    C  CR16   0  -0.081  -131.1246  4.0559  64.8339
 NOP  C5A   C  CH2    0  -0.305  -132.7731  4.5233  66.5856
 NOP  O4P   O  O2     0  -0.578  -133.8895  3.6309  66.6447
 NOP  P     P  P      0   1.459  -134.9618  3.7865  67.8213
 NOP  O1P   O  O      0  -0.702  -135.7123  5.0579  67.8749
 NOP  O2P   O  OH1    0  -0.722  -135.7909  2.4666  67.5080
 NOP  O3P   O  OH1    0  -0.738  -134.0889  3.4719  69.1228
 NOP  H2A1  H  HCH3   0   0.262  -131.3870  5.1105  60.4687
 NOP  H2A2  H  HCH3   0   0.265  -129.7814  5.1751  61.1953
 NOP  H2A3  H  HCH3   0   0.265  -130.5336  3.6208  60.8731
 NOP  HO3   H  HOH1   0   0.485  -134.0902  6.1535  62.1914
 NOP  H4A   H  H      0   0.227  -134.7410  5.8504  65.4642
 NOP  H6    H  HCR6   0   0.318  -130.4831  3.5641  65.5492
 NOP  H5A1  H  HCH2   0   0.287  -131.9623  4.1367  67.2042
 NOP  H5A2  H  HCH2   0   0.271  -133.0321  5.5154  66.9648
 NOP  HOP2  H  HOH1   0   0.507  -136.7141  2.5092  67.7905
 NOP  HOP3  H  HOH1   0   0.502  -134.3243  4.0061  69.8924

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
 NOP  N1   O1    single    1.258  0.020  1.258
 NOP  N1   C2    aromatic  1.353  0.020  1.353
 NOP  N1   C6    aromatic  1.368  0.020  1.368
 NOP  C2   C2A   single    1.486  0.020  1.486
 NOP  C2   C3    aromatic  1.400  0.020  1.400
 NOP  C2A  H2A1  single    0.970  0.020  1.090
 NOP  C2A  H2A2  single    0.970  0.020  1.090
 NOP  C2A  H2A3  single    0.970  0.020  1.090
 NOP  C3   O3    single    1.322  0.020  1.322
 NOP  C3   C4    aromatic  1.406  0.020  1.406
 NOP  O3   HO3   single    0.850  0.020  0.980
 NOP  C4   C4A   single    1.452  0.020  1.452
 NOP  C4   C5    aromatic  1.406  0.020  1.406
 NOP  C4A  O4A   double    1.224  0.020  1.224
 NOP  C4A  H4A   single    0.930  0.020  1.080
 NOP  C5   C6    aromatic  1.362  0.020  1.362
 NOP  C5   C5A   single    1.501  0.020  1.501
 NOP  C6   H6    single    0.930  0.020  1.080
 NOP  C5A  O4P   single    1.430  0.020  1.430
 NOP  C5A  H5A1  single    0.970  0.020  1.090
 NOP  C5A  H5A2  single    0.970  0.020  1.090
 NOP  O4P  P     single    1.599  0.020  1.599
 NOP  P    O1P   double    1.477  0.020  1.477
 NOP  P    O2P   single    1.590  0.020  1.590
 NOP  P    O3P   single    1.598  0.020  1.598
 NOP  O2P  HOP2  single    0.850  0.020  0.980
 NOP  O3P  HOP3  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
 NOP  C6    N1   C2    121.17  3.000
 NOP  C6    N1   O1    118.77  3.000
 NOP  C2    N1   O1    120.05  3.000
 NOP  C3    C2   C2A   124.11  3.000
 NOP  C3    C2   N1    118.76  3.000
 NOP  C2A   C2   N1    117.13  3.000
 NOP  H2A3  C2A  H2A2  107.21  3.000
 NOP  H2A3  C2A  H2A1  108.30  3.000
 NOP  H2A2  C2A  H2A1  108.26  3.000
 NOP  H2A3  C2A  C2    110.99  3.000
 NOP  H2A2  C2A  C2    110.83  3.000
 NOP  H2A1  C2A  C2    111.12  3.000
 NOP  C4    C3   O3    121.97  3.000
 NOP  C4    C3   C2    121.07  3.000
 NOP  O3    C3   C2    116.96  3.000
 NOP  HO3   O3   C3    108.14  3.000
 NOP  C5    C4   C4A   122.69  3.000
 NOP  C5    C4   C3    117.70  3.000
 NOP  C4A   C4   C3    119.60  3.000
 NOP  H4A   C4A  O4A   119.13  3.000
 NOP  H4A   C4A  C4    117.85  3.000
 NOP  O4A   C4A  C4    123.02  3.000
 NOP  C5A   C5   C6    117.65  3.000
 NOP  C5A   C5   C4    122.66  3.000
 NOP  C6    C5   C4    119.69  3.000
 NOP  H6    C6   C5    123.59  3.000
 NOP  H6    C6   N1    114.80  3.000
 NOP  C5    C6   N1    121.61  3.000
 NOP  H5A2  C5A  H5A1  107.52  3.000
 NOP  H5A2  C5A  O4P   111.53  3.000
 NOP  H5A1  C5A  O4P   109.62  3.000
 NOP  H5A2  C5A  C5    110.42  3.000
 NOP  H5A1  C5A  C5    109.87  3.000
 NOP  O4P   C5A  C5    107.89  3.000
 NOP  P     O4P  C5A   119.53  3.000
 NOP  O3P   P    O2P   106.37  3.000
 NOP  O3P   P    O1P   114.66  3.000
 NOP  O2P   P    O1P   117.17  3.000
 NOP  O3P   P    O4P   102.34  3.000
 NOP  O2P   P    O4P    97.12  3.000
 NOP  O1P   P    O4P   116.80  3.000
 NOP  HOP2  O2P  P     113.83  3.000
 NOP  HOP3  O3P  P     114.01  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
 NOP  CONST_01  C4    C3   C2   N1     0.00   0.0  0
 NOP  CONST_02  C4    C5   C6   N1     0.00   0.0  0
 NOP  CONST_03  C5    C6   N1   C2     0.00   0.0  0
 NOP  CONST_04  C5    C4   C3   C2     0.00   0.0  0
 NOP  CONST_05  C6    N1   C2   C3     0.00   0.0  0
 NOP  CONST_06  C6    C5   C4   C3     0.00   0.0  0
 NOP  CONST_07  O3    C3   C2   N1   180.00   0.0  0
 NOP  CONST_08  C5A   C5   C6   N1   180.00   0.0  0
 NOP  CONST_09  C3    C2   N1   O1   180.00   0.0  0
 NOP  CONST_10  C5    C6   N1   O1   180.00   0.0  0
 NOP  CONST_11  C4A   C4   C3   C2   180.00   0.0  0
 NOP  CONST_12  C6    N1   C2   C2A  180.00   0.0  0
 NOP  CONST_13  C4    C3   C2   C2A  180.00   0.0  0
 NOP  CONST_14  C5A   C5   C4   C3   180.00   0.0  0
 NOP  CONST_15  C5    C4   C3   O3   180.00   0.0  0
 NOP  CONST_16  C6    C5   C4   C4A  180.00   0.0  0
 NOP  CONST_17  H6    C6   N1   C2   180.00   0.0  0
 NOP  Var_01    O4A   C4A  C4   C3     1.25  30.0  2
 NOP  Var_02    O4P   C5A  C5   C4    68.46  30.0  2
 NOP  Var_03    H2A1  C2A  C2   N1   178.98  30.0  2
 NOP  Var_04    O1P   P    O4P  C5A   62.29  30.0  3

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
 NOP  plan-1  N1   0.020
 NOP  plan-1  O1   0.020
 NOP  plan-1  C2   0.020
 NOP  plan-1  C2A  0.020
 NOP  plan-1  C3   0.020
 NOP  plan-1  O3   0.020
 NOP  plan-1  C4   0.020
 NOP  plan-1  C4A  0.020
 NOP  plan-1  C5   0.020
 NOP  plan-1  C6   0.020
 NOP  plan-1  C5A  0.020
 NOP  plan-1  H6   0.020
 NOP  plan-2  C4   0.020
 NOP  plan-2  C4A  0.020
 NOP  plan-2  O4A  0.020
 NOP  plan-2  H4A  0.020

