# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Apr 25 16:29:22 2020
#   Inital geometry file: a 68 line input string
#   Ligand name: 4-methyl-5-[2-(phosphonooxy)ethyl]-1,3-thiazole-2-carboxylic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cc1nc(sc1CCO[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
 3NM  3NM  '4-methyl-5-[2-(phosphonooxy)ethyl]-1,3-thiazole-2-carboxylic acid'  ligand  26  16  .  2021-08-04  2021-08-04  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_3NM
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
 3NM  N    N  N     0  -0.363   2.8835  -1.2028   0.2276
 3NM  P    P  P     0   1.456  -3.9481   0.2732   0.3589
 3NM  S    S  S2    0   0.302   2.0380   0.9697  -0.7980
 3NM  C1   C  CH3   0  -0.733   0.9979  -2.7812   0.0922
 3NM  O1   O  O     0  -0.428   4.8124   1.7540  -0.0563
 3NM  C2   C  CR5   0   0.316   1.6003  -1.4398  -0.1543
 3NM  O2   O  OH1   0  -0.576   5.3933  -0.2376   0.7994
 3NM  C3   C  CR5   0  -0.074   3.2422   0.0110  -0.0450
 3NM  O3   O  O2    0  -0.587  -2.6958   0.1651  -0.6264
 3NM  C4   C  C     0   0.515   4.5611   0.6087   0.2281
 3NM  O4   O  O     0  -0.709  -3.8714   1.2924   1.4212
 3NM  C5   C  CR5   0  -0.265   0.9721  -0.3697  -0.7434
 3NM  O5   O  OH1   0  -0.731  -5.0593   0.4523  -0.7688
 3NM  C6   C  CH2   0  -0.556  -0.4346  -0.2751  -1.2335
 3NM  O6   O  OH1   0  -0.741  -4.1411  -1.1717   1.0133
 3NM  C7   C  CH2   0  -0.144  -1.3737   0.0700  -0.0879
 3NM  H1   H  HCH3  0   0.260   0.9320  -2.9829   1.1620
 3NM  H1A  H  HCH3  0   0.247  -0.0050  -2.8616  -0.3219
 3NM  H1B  H  HCH3  0   0.260   1.6091  -3.5668  -0.3527
 3NM  HO2  H  HOH1  0   0.495   6.2468   0.1931   0.9603
 3NM  HO5  H  HOH1  0   0.505  -5.9166   0.7482  -0.4346
 3NM  H6   H  HCH2  0   0.285  -0.5182   0.4800  -2.0171
 3NM  H6A  H  HCH2  0   0.280  -0.7281  -1.2282  -1.6778
 3NM  HO6  H  HOH1  0   0.496  -4.2623  -1.9022   0.3919
 3NM  H7   H  HCH2  0   0.249  -1.0862   1.0210   0.3657
 3NM  H7A  H  HCH2  0   0.241  -1.3225  -0.7032   0.6846

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
 3NM  C3  N    aromatic  1.295  0.020  1.295
 3NM  N   C2   aromatic  1.360  0.020  1.360
 3NM  O4  P    double    1.474  0.020  1.474
 3NM  O6  P    single    1.598  0.020  1.598
 3NM  P   O3   single    1.597  0.020  1.597
 3NM  P   O5   single    1.593  0.020  1.593
 3NM  C3  S    aromatic  1.714  0.020  1.714
 3NM  S   C5   aromatic  1.713  0.020  1.713
 3NM  C2  C1   single    1.491  0.020  1.491
 3NM  C1  H1   single    0.970  0.020  1.090
 3NM  C1  H1A  single    0.970  0.020  1.090
 3NM  C1  H1B  single    0.970  0.020  1.090
 3NM  O1  C4   double    1.207  0.020  1.207
 3NM  C5  C2   aromatic  1.374  0.020  1.374
 3NM  O2  C4   single    1.317  0.020  1.317
 3NM  O2  HO2  single    0.850  0.020  0.980
 3NM  C4  C3   single    1.474  0.020  1.474
 3NM  C7  O3   single    1.431  0.020  1.431
 3NM  C5  C6   single    1.493  0.020  1.493
 3NM  O5  HO5  single    0.850  0.020  0.980
 3NM  C7  C6   single    1.521  0.020  1.521
 3NM  C6  H6   single    0.970  0.020  1.090
 3NM  C6  H6A  single    0.970  0.020  1.090
 3NM  O6  HO6  single    0.850  0.020  0.980
 3NM  C7  H7   single    0.970  0.020  1.090
 3NM  C7  H7A  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
 3NM  C3   N   C2   111.46  3.000
 3NM  O6   P   O5   107.89  3.000
 3NM  O5   P   O4   117.95  3.000
 3NM  O6   P   O4   109.66  3.000
 3NM  O5   P   O3    96.77  3.000
 3NM  O6   P   O3   106.63  3.000
 3NM  O4   P   O3   116.78  3.000
 3NM  C5   S   C3    89.19  3.000
 3NM  H1B  C1  H1A  107.95  3.000
 3NM  H1B  C1  H1   107.52  3.000
 3NM  H1A  C1  H1   107.69  3.000
 3NM  H1B  C1  C2   110.75  3.000
 3NM  H1A  C1  C2   112.08  3.000
 3NM  H1   C1  C2   110.67  3.000
 3NM  C5   C2  C1   125.95  3.000
 3NM  C5   C2  N    114.60  3.000
 3NM  C1   C2  N    119.45  3.000
 3NM  HO2  O2  C4   110.04  3.000
 3NM  C4   C3  S    118.92  3.000
 3NM  C4   C3  N    126.10  3.000
 3NM  S    C3  N    114.98  3.000
 3NM  C7   O3  P    119.79  3.000
 3NM  C3   C4  O2   112.66  3.000
 3NM  C3   C4  O1   121.85  3.000
 3NM  O2   C4  O1   125.49  3.000
 3NM  C6   C5  C2   128.40  3.000
 3NM  C6   C5  S    121.77  3.000
 3NM  C2   C5  S    109.77  3.000
 3NM  HO5  O5  P    114.10  3.000
 3NM  H6A  C6  H6   106.93  3.000
 3NM  H6A  C6  C7   109.79  3.000
 3NM  H6   C6  C7   109.66  3.000
 3NM  H6A  C6  C5   109.37  3.000
 3NM  H6   C6  C5   110.59  3.000
 3NM  C7   C6  C5   110.42  3.000
 3NM  HO6  O6  P    115.80  3.000
 3NM  H7A  C7  H7   108.05  3.000
 3NM  H7A  C7  C6   110.03  3.000
 3NM  H7   C7  C6   110.36  3.000
 3NM  H7A  C7  O3   110.85  3.000
 3NM  H7   C7  O3   109.98  3.000
 3NM  C6   C7  O3   107.59  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
 3NM  CONST_01  C5   S   C3  N      0.00   0.0  0
 3NM  CONST_02  S    C5  C2  N      0.00   0.0  0
 3NM  CONST_03  C2   N   C3  S      0.00   0.0  0
 3NM  CONST_04  C3   S   C5  C2     0.00   0.0  0
 3NM  CONST_05  C5   C2  N   C3     0.00   0.0  0
 3NM  CONST_06  C6   C5  C2  N    180.00   0.0  0
 3NM  CONST_07  C1   C2  C5  S    180.00   0.0  0
 3NM  CONST_08  C3   N   C2  C1   180.00   0.0  0
 3NM  CONST_09  C4   C3  N   C2   180.00   0.0  0
 3NM  CONST_10  C6   C5  S   C3   180.00   0.0  0
 3NM  CONST_11  C5   S   C3  C4   180.00   0.0  0
 3NM  CONST_12  HO2  O2  C4  C3   180.00   0.0  0
 3NM  Var_01    O1   C4  C3  N   -179.80  30.0  2
 3NM  Var_02    C7   C6  C5  S    -93.39  30.0  2
 3NM  Var_03    H1   C1  C2  N     63.80  30.0  2
 3NM  Var_04    C5   C6  C7  O3   179.13  30.0  3
 3NM  Var_05    C6   C7  O3  P    169.73  30.0  1

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
 3NM  plan-1  N    0.020
 3NM  plan-1  S    0.020
 3NM  plan-1  C1   0.020
 3NM  plan-1  C2   0.020
 3NM  plan-1  C3   0.020
 3NM  plan-1  C4   0.020
 3NM  plan-1  C5   0.020
 3NM  plan-1  C6   0.020
 3NM  plan-2  O1   0.020
 3NM  plan-2  O2   0.020
 3NM  plan-2  C3   0.020
 3NM  plan-2  C4   0.020
 3NM  plan-2  HO2  0.020

