# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Jul 22 10:01:20 2021
#   Inital geometry file: a 113 line input string
#   Ligand name: 2-[3-[(4-azanyl-2-methoxy-pyrimidin-5-yl)methyl]-4-methyl-1,3-thiazol-3-ium-5-yl]ethyl phosphono hydrogen phosphate
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: COc1ncc(C[n+]2csc(CCO[P](O)(=O)O[P](O)(O)=O)c2C)c(N)n1
#
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
 NDQ  NDQ  '2-[3-[(4-azanyl-2-methoxy-pyrimidin-5-yl)methyl]-4-methyl-1,3-thiazol-3-ium-5-yl]ethyl phosphono hydrogen phosphate'  ligand  46  27  .  2022-11-17  2022-11-17
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_NDQ
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
 NDQ  C4   C  CR5   0   0.519  25.7983  11.2981   0.4584
 NDQ  C5   C  CR5   0  -0.296  25.7929  10.5813  -0.6940
 NDQ  C2   C  CR15  0  -0.154  24.0562  12.2663  -0.6237
 NDQ  C2'  C  CR6   0   0.598  23.0966  11.0484   4.8966
 NDQ  C4'  C  CR6   0   0.485  22.6796  11.8167   2.8069
 NDQ  C4A  C  CH3   0  -0.744  26.7648  11.1640   1.5773
 NDQ  C5'  C  CR6   0  -0.055  23.9609  12.4209   2.7849
 NDQ  C6'  C  CR16  0  -0.039  24.6881  12.2987   3.9463
 NDQ  N1'  N  N     0  -0.483  24.2790  11.6267   5.0177
 NDQ  N3   N  NR5   1  -0.382  24.7858  12.2438   0.4699
 NDQ  N3'  N  N     0  -0.481  22.2769  11.1165   3.8615
 NDQ  O2'  O  O2    0  -0.446  22.6278  10.3207   5.8969
 NDQ  S1   S  S2    0   0.391  24.5399  11.1232  -1.7390
 NDQ  C5A  C  CH2   0  -0.555  26.7526   9.5336  -1.1479
 NDQ  C5B  C  CH2   0  -0.183  27.9524  10.1353  -1.8645
 NDQ  O21  O  OH1   0  -0.722  25.5735  14.8497  -1.3784
 NDQ  O22  O  O     0  -0.678  27.9700  15.5485  -2.1973
 NDQ  O23  O  OH1   0  -0.718  27.3561  14.6431   0.2066
 NDQ  O5G  O  O2    0  -0.575  27.4847  10.9329  -2.9617
 NDQ  P1   P  P     0   1.498  27.8314  12.4698  -3.1488
 NDQ  P2   P  P     0   1.484  27.1466  14.6624  -1.3622
 NDQ  H1   H  HCR5  0   0.378  23.2447  12.9578  -0.7853
 NDQ  H2   H  HCH2  0   0.329  25.4435  13.6469   1.8697
 NDQ  H3   H  HCH2  0   0.326  23.8465  13.9284   1.2302
 NDQ  H4   H  HCH3  0   0.271  27.1437  12.1318   1.9031
 NDQ  H5   H  HCH3  0   0.289  26.3225  10.6604   2.4362
 NDQ  H6   H  HCH3  0   0.288  27.6210  10.5753   1.2586
 NDQ  H7   H  HCR6  0   0.280  25.6628  12.7716   4.0203
 NDQ  H8   H  HCH3  0   0.251  22.8551   9.5439   7.7386
 NDQ  H9   H  HCH3  0   0.235  24.3806   9.6926   6.8408
 NDQ  H10  H  HCH3  0   0.235  23.6232  11.1338   7.5431
 NDQ  H11  H  HNH2  0   0.406  20.9022  11.5429   1.9028
 NDQ  H12  H  HNH2  0   0.403  21.8931  12.6693   1.1258
 NDQ  H13  H  HCH2  0   0.300  26.2483   8.8195  -1.8005
 NDQ  H14  H  HCH2  0   0.302  27.1132   8.9643  -0.2905
 NDQ  H15  H  HCH2  0   0.283  28.5794   9.3434  -2.2716
 NDQ  H16  H  HCH2  0   0.253  28.5585  10.7198  -1.1702
 NDQ  H17  H  HOH1  0   0.509  29.9187  12.4124  -3.7697
 NDQ  H18  H  HOH1  0   0.514  25.2157  15.2361  -2.1898
 NDQ  H19  H  HOH1  0   0.515  28.2789  14.6467   0.4978
 NDQ  C35  C  CH2   0  -0.485  24.5114  13.1496   1.6054
 NDQ  N4'  N  NH2   0  -0.820  21.8371  11.8914   1.7600
 NDQ  O11  O  O2    0  -0.710  27.3495  13.0885  -1.7339
 NDQ  C7'  C  CH3   0  -0.417  23.4289  10.1740   7.0647
 NDQ  O12  O  O     0  -0.672  27.1873  13.0379  -4.3398
 NDQ  O13  O  OH1   0  -0.729  29.4017  12.6376  -2.9832

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
 NDQ  O22  P2   double    1.470  0.020  1.470
 NDQ  O21  P2   single    1.584  0.020  1.584
 NDQ  P2   O23  single    1.583  0.020  1.583
 NDQ  P2   O11  single    1.630  0.020  1.630
 NDQ  O12  P1   double    1.468  0.020  1.468
 NDQ  O13  P1   single    1.588  0.020  1.588
 NDQ  P1   O11  single    1.618  0.020  1.618
 NDQ  P1   O5G  single    1.587  0.020  1.587
 NDQ  O5G  C5B  single    1.435  0.020  1.435
 NDQ  C5B  C5A  single    1.522  0.020  1.522
 NDQ  S1   C5   aromatic  1.719  0.020  1.719
 NDQ  S1   C2   aromatic  1.669  0.020  1.669
 NDQ  C5A  C5   single    1.492  0.020  1.492
 NDQ  C5   C4   aromatic  1.357  0.020  1.357
 NDQ  C2   N3   aromatic  1.315  0.020  1.315
 NDQ  C4   N3   aromatic  1.385  0.020  1.385
 NDQ  C4   C4A  single    1.485  0.020  1.485
 NDQ  N3   C35  single    1.478  0.020  1.478
 NDQ  N4'  C4'  single    1.346  0.020  1.346
 NDQ  C4'  N3'  aromatic  1.328  0.020  1.328
 NDQ  C4'  C5'  aromatic  1.417  0.020  1.417
 NDQ  N3'  C2'  aromatic  1.322  0.020  1.322
 NDQ  C35  C5'  single    1.492  0.020  1.492
 NDQ  C5'  C6'  aromatic  1.376  0.020  1.376
 NDQ  C2'  O2'  single    1.323  0.020  1.323
 NDQ  C2'  N1'  aromatic  1.322  0.020  1.322
 NDQ  O2'  C7'  single    1.424  0.020  1.424
 NDQ  C6'  N1'  aromatic  1.329  0.020  1.329
 NDQ  C2   H1   single    0.930  0.020  1.080
 NDQ  C35  H2   single    0.970  0.020  1.090
 NDQ  C35  H3   single    0.970  0.020  1.090
 NDQ  C4A  H4   single    0.970  0.020  1.090
 NDQ  C4A  H5   single    0.970  0.020  1.090
 NDQ  C4A  H6   single    0.970  0.020  1.090
 NDQ  C6'  H7   single    0.930  0.020  1.080
 NDQ  C7'  H8   single    0.970  0.020  1.090
 NDQ  C7'  H9   single    0.970  0.020  1.090
 NDQ  C7'  H10  single    0.970  0.020  1.090
 NDQ  N4'  H11  single    0.890  0.020  1.040
 NDQ  N4'  H12  single    0.890  0.020  1.040
 NDQ  C5A  H13  single    0.970  0.020  1.090
 NDQ  C5A  H14  single    0.970  0.020  1.090
 NDQ  C5B  H15  single    0.970  0.020  1.090
 NDQ  C5B  H16  single    0.970  0.020  1.090
 NDQ  O13  H17  single    0.850  0.020  0.980
 NDQ  O21  H18  single    0.850  0.020  0.980
 NDQ  O23  H19  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
 NDQ  N3   C4   C4A  122.09  3.000
 NDQ  C4A  C4   C5   126.50  3.000
 NDQ  N3   C4   C5   111.38  3.000
 NDQ  C5A  C5   S1   120.36  3.000
 NDQ  C5A  C5   C4   128.81  3.000
 NDQ  S1   C5   C4   110.64  3.000
 NDQ  H1   C2   S1   123.87  3.000
 NDQ  H1   C2   N3   123.59  3.000
 NDQ  S1   C2   N3   112.54  3.000
 NDQ  O2'  C2'  N3'  113.62  3.000
 NDQ  O2'  C2'  N1'  119.23  3.000
 NDQ  N3'  C2'  N1'  127.14  3.000
 NDQ  N4'  C4'  N3'  117.20  3.000
 NDQ  N3'  C4'  C5'  120.75  3.000
 NDQ  N4'  C4'  C5'  122.03  3.000
 NDQ  H6   C4A  H5   107.49  3.000
 NDQ  H6   C4A  H4   107.15  3.000
 NDQ  H5   C4A  H4   108.43  3.000
 NDQ  H6   C4A  C4   109.93  3.000
 NDQ  H5   C4A  C4   111.82  3.000
 NDQ  H4   C4A  C4   111.82  3.000
 NDQ  C6'  C5'  C4'  115.29  3.000
 NDQ  C6'  C5'  C35  121.05  3.000
 NDQ  C4'  C5'  C35  123.67  3.000
 NDQ  H7   C6'  N1'  116.19  3.000
 NDQ  H7   C6'  C5'  119.56  3.000
 NDQ  N1'  C6'  C5'  124.24  3.000
 NDQ  C6'  N1'  C2'  115.00  3.000
 NDQ  C35  N3   C2   121.70  3.000
 NDQ  C35  N3   C4   124.07  3.000
 NDQ  C2   N3   C4   114.23  3.000
 NDQ  C4'  N3'  C2'  117.44  3.000
 NDQ  C7'  O2'  C2'  118.52  3.000
 NDQ  C2   S1   C5    91.20  3.000
 NDQ  H14  C5A  H13  106.34  3.000
 NDQ  H14  C5A  C5B  108.43  3.000
 NDQ  H13  C5A  C5B  109.98  3.000
 NDQ  H14  C5A  C5   109.89  3.000
 NDQ  H13  C5A  C5   110.14  3.000
 NDQ  C5B  C5A  C5   111.90  3.000
 NDQ  H16  C5B  H15  107.90  3.000
 NDQ  H16  C5B  O5G  111.71  3.000
 NDQ  H15  C5B  O5G  107.82  3.000
 NDQ  H16  C5B  C5A  110.49  3.000
 NDQ  H15  C5B  C5A  110.03  3.000
 NDQ  O5G  C5B  C5A  108.85  3.000
 NDQ  H18  O21  P2   115.03  3.000
 NDQ  H19  O23  P2   115.12  3.000
 NDQ  P1   O5G  C5B  123.88  3.000
 NDQ  O5G  P1   O13  107.83  3.000
 NDQ  O5G  P1   O12  112.00  3.000
 NDQ  O13  P1   O12  118.52  3.000
 NDQ  O5G  P1   O11  101.67  3.000
 NDQ  O13  P1   O11   99.38  3.000
 NDQ  O12  P1   O11  115.52  3.000
 NDQ  O23  P2   O22  119.75  3.000
 NDQ  O23  P2   O21   98.22  3.000
 NDQ  O22  P2   O21  118.63  3.000
 NDQ  O23  P2   O11  101.41  3.000
 NDQ  O21  P2   O11  103.62  3.000
 NDQ  O22  P2   O11  112.51  3.000
 NDQ  H3   C35  H2   106.22  3.000
 NDQ  H3   C35  N3   106.64  3.000
 NDQ  H2   C35  N3   107.90  3.000
 NDQ  H3   C35  C5'  113.32  3.000
 NDQ  H2   C35  C5'  110.31  3.000
 NDQ  N3   C35  C5'  112.12  3.000
 NDQ  H12  N4'  H11  114.12  3.000
 NDQ  H12  N4'  C4'  119.92  3.000
 NDQ  H11  N4'  C4'  116.82  3.000
 NDQ  P2   O11  P1   127.29  3.000
 NDQ  H10  C7'  H9   108.88  3.000
 NDQ  H10  C7'  H8   109.43  3.000
 NDQ  H9   C7'  H8   109.41  3.000
 NDQ  H10  C7'  O2'  111.69  3.000
 NDQ  H9   C7'  O2'  111.61  3.000
 NDQ  H8   C7'  O2'  105.74  3.000
 NDQ  H17  O13  P1   114.77  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
 NDQ  CONST_01  C2   S1   C5   C4      0.00   0.0  0
 NDQ  CONST_02  S1   C2   N3   C4      0.00   0.0  0
 NDQ  CONST_03  N3   C2   S1   C5      0.00   0.0  0
 NDQ  CONST_04  C2   N3   C4   C5      0.00   0.0  0
 NDQ  CONST_05  C5'  C4'  N3'  C2'     0.00   0.0  0
 NDQ  CONST_06  C5'  C6'  N1'  C2'     0.00   0.0  0
 NDQ  CONST_07  N1'  C2'  N3'  C4'     0.00   0.0  0
 NDQ  CONST_08  N1'  C6'  C5'  C4'     0.00   0.0  0
 NDQ  CONST_09  N3'  C4'  C5'  C6'     0.00   0.0  0
 NDQ  CONST_10  N3'  C2'  N1'  C6'     0.00   0.0  0
 NDQ  CONST_11  S1   C5   C4   N3      0.00   0.0  0
 NDQ  CONST_12  C35  N3   C4   C5    180.00   0.0  0
 NDQ  CONST_13  C5A  C5   S1   C2    180.00   0.0  0
 NDQ  CONST_14  C4A  C4   N3   C2    180.00   0.0  0
 NDQ  CONST_15  N4'  C4'  N3'  C2'   180.00   0.0  0
 NDQ  CONST_16  S1   C2   N3   C35   180.00   0.0  0
 NDQ  CONST_17  N3'  C4'  C5'  C35   180.00   0.0  0
 NDQ  CONST_18  N1'  C6'  C5'  C35   180.00   0.0  0
 NDQ  CONST_19  O2'  C2'  N3'  C4'   180.00   0.0  0
 NDQ  CONST_20  S1   C5   C4   C4A   180.00   0.0  0
 NDQ  CONST_21  N4'  C4'  C5'  C6'   180.00   0.0  0
 NDQ  CONST_22  O2'  C2'  N1'  C6'   180.00   0.0  0
 NDQ  CONST_23  C5A  C5   C4   N3    180.00   0.0  0
 NDQ  CONST_24  H1   C2   N3   C4    180.00   0.0  0
 NDQ  CONST_25  H7   C6'  N1'  C2'   180.00   0.0  0
 NDQ  CONST_26  H11  N4'  C4'  C5'   180.00   0.0  0
 NDQ  Var_01    C5'  C35  N3   C4    -69.55  30.0  2
 NDQ  Var_02    N3   C35  C5'  C4'   -67.89  30.0  2
 NDQ  Var_03    C5B  C5A  C5   C4    -86.36  30.0  1
 NDQ  Var_04    N3'  C2'  O2'  C7'   179.82  30.0  1
 NDQ  Var_05    H4   C4A  C4   C5    132.44  30.0  2
 NDQ  Var_06    O5G  C5B  C5A  C5    -56.25  30.0  1
 NDQ  Var_07    H8   C7'  O2'  C2'  -179.76  30.0  3
 NDQ  Var_08    O12  P1   O5G  C5B  -178.43  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
 NDQ  chir_01  P1  O13  O11  O5G  both

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
 NDQ  plan-1  C4   0.020
 NDQ  plan-1  C5   0.020
 NDQ  plan-1  C2   0.020
 NDQ  plan-1  C4A  0.020
 NDQ  plan-1  N3   0.020
 NDQ  plan-1  S1   0.020
 NDQ  plan-1  C5A  0.020
 NDQ  plan-1  H1   0.020
 NDQ  plan-1  C35  0.020
 NDQ  plan-2  C2'  0.020
 NDQ  plan-2  C4'  0.020
 NDQ  plan-2  C5'  0.020
 NDQ  plan-2  C6'  0.020
 NDQ  plan-2  N1'  0.020
 NDQ  plan-2  N3'  0.020
 NDQ  plan-2  O2'  0.020
 NDQ  plan-2  H7   0.020
 NDQ  plan-2  C35  0.020
 NDQ  plan-2  N4'  0.020
 NDQ  plan-3  C4'  0.020
 NDQ  plan-3  H11  0.020
 NDQ  plan-3  H12  0.020
 NDQ  plan-3  N4'  0.020

