# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Jul 31 07:33:51 2022
#   Inital geometry file: a 115 line input string
#   Ligand name: 3-[(4-amino-2-methylpyrimidin-5-yl)methyl]-5-(2-{[(S)-hydroxy(phosphonomethyl)phosphoryl]oxy}ethyl)-4-methyl-1,3-thiazol-3-ium
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cc1ncc(C[n+]2csc(CCO[P](O)(=O)C[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
 GMI  GMI  "[2-[3-[(4-azanyl-2-methyl-pyrimidin-5-yl)methyl]-4-methyl-1,3-thiazol-5-yl]ethoxy-oxidanyl-phosphoryl]methylphosphonic acid"  ligand  44  26  .  2022-08-10  2022-09-22
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_GMI
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
 GMI  N1'  N  N      0  -0.439   8.5785  17.7422  -2.7039
 GMI  C2'  C  CR6    0   0.356   7.3445  17.2516  -2.6884
 GMI  CM2  C  CH3    0  -0.728   7.1828  15.8056  -3.0367
 GMI  N3'  N  N      0  -0.462   6.2513  17.9343  -2.3871
 GMI  C4'  C  CR6    0   0.494   6.3765  19.2199  -2.0526
 GMI  N4'  N  NH2    0  -0.833   5.2491  19.8837  -1.7554
 GMI  C5'  C  CR6    0  -0.093   7.6511  19.8284  -1.9980
 GMI  C6'  C  CR16   0  -0.056   8.7055  19.0210  -2.3562
 GMI  C7'  C  CH2    0  -0.378   7.7822  21.2661  -1.5867
 GMI  N3   N  NR5    1  -0.407   9.1661  21.6478  -1.3176
 GMI  C2   C  CR15   0  -0.133   9.8790  22.3396  -2.1790
 GMI  S1   S  S2     0   0.391  11.4343  22.6111  -1.6392
 GMI  C5   C  CR5    0  -0.274  11.1265  21.7423  -0.1807
 GMI  C4   C  CR5    0   0.477   9.8450  21.2908  -0.1625
 GMI  CM4  C  CH3    0  -0.736   9.1631  20.5228   0.9112
 GMI  C6   C  CH2    0  -0.529  12.2097  21.5307   0.8262
 GMI  C7   C  CH2    0  -0.166  13.1866  22.6917   0.9402
 GMI  O7   O  O2     0  -0.626  12.4839  23.8443   1.3023
 GMI  PA   P  P      0   1.255  13.2614  25.3460   1.2351
 GMI  O1A  O  O      0  -0.807  12.3567  26.2326   2.0492
 GMI  O2A  O  OP    -1  -0.819  14.6881  25.1215   1.6734
 GMI  PB   P  P      0   1.159  13.8807  27.3106  -1.2362
 GMI  O1B  O  OP    -1  -0.905  15.3871  27.2418  -0.9543
 GMI  O2B  O  OP    -1  -0.904  13.1584  28.4497  -0.5062
 GMI  O3B  O  O      0  -0.909  13.5336  27.2159  -2.7295
 GMI  C3A  C  CH2    0  -1.005  13.1526  25.7086  -0.5405
 GMI  H1   H  HCH3   0   0.247   6.1341  15.5223  -3.0707
 GMI  H2   H  HCH3   0   0.254   7.6395  15.5905  -4.0029
 GMI  H3   H  HCH3   0   0.256   7.6879  15.1804  -2.2988
 GMI  H4   H  HNH2   0   0.403   4.3685  19.4188  -1.9021
 GMI  H5   H  HNH2   0   0.417   5.2153  20.8848  -1.6765
 GMI  H6   H  HCR6   0   0.264   9.7204  19.4076  -2.3641
 GMI  H7   H  HCH2   0   0.327   7.4047  21.9395  -2.3586
 GMI  H8   H  HCH2   0   0.313   7.2052  21.4728  -0.6830
 GMI  H9   H  HCR5   0   0.376   9.4854  22.6902  -3.1220
 GMI  H10  H  HCH3   0   0.280   8.8507  19.5370   0.5658
 GMI  H11  H  HCH3   0   0.286   9.8328  20.3819   1.7544
 GMI  H12  H  HCH3   0   0.281   8.2802  21.0498   1.2743
 GMI  H13  H  HCH2   0   0.271  11.7542  21.3420   1.7994
 GMI  H14  H  HCH2   0   0.281  12.7667  20.6278   0.5610
 GMI  H15  H  HCH2   0   0.229  13.9463  22.4191   1.6807
 GMI  H16  H  HCH2   0   0.194  13.7249  22.8091  -0.0133
 GMI  H20  H  HCH2   0   0.198  12.0925  25.6751  -0.8148
 GMI  H21  H  HCH2   0   0.199  13.6257  24.8819  -1.0841

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
 GMI  CM2  C2'  single    1.496  0.020  1.496
 GMI  C2'  N3'  aromatic  1.324  0.020  1.324
 GMI  C2'  N1'  aromatic  1.328  0.020  1.328
 GMI  N3'  C4'  aromatic  1.334  0.020  1.334
 GMI  O3B  PB   deloc     1.536  0.020  1.536
 GMI  N1'  C6'  aromatic  1.331  0.020  1.331
 GMI  C4'  N4'  single    1.342  0.020  1.342
 GMI  C4'  C5'  aromatic  1.413  0.020  1.413
 GMI  C2   S1   aromatic  1.669  0.020  1.669
 GMI  C2   N3   aromatic  1.315  0.020  1.315
 GMI  C6'  C5'  aromatic  1.375  0.020  1.375
 GMI  S1   C5   aromatic  1.725  0.020  1.725
 GMI  C5'  C7'  single    1.501  0.020  1.501
 GMI  C7'  N3   single    1.461  0.020  1.461
 GMI  N3   C4   aromatic  1.387  0.020  1.387
 GMI  PB   C3A  single    1.892  0.020  1.892
 GMI  PB   O1B  deloc     1.534  0.020  1.534
 GMI  PB   O2B  deloc     1.534  0.020  1.534
 GMI  C3A  PA   single    1.815  0.020  1.815
 GMI  C5   C4   aromatic  1.359  0.020  1.359
 GMI  C5   C6   single    1.494  0.020  1.494
 GMI  C4   CM4  single    1.486  0.020  1.486
 GMI  C7   C6   single    1.522  0.020  1.522
 GMI  C7   O7   single    1.398  0.020  1.398
 GMI  PA   O7   single    1.692  0.020  1.692
 GMI  PA   O1A  deloc     1.506  0.020  1.506
 GMI  PA   O2A  deloc     1.509  0.020  1.509
 GMI  CM2  H1   single    0.970  0.020  1.090
 GMI  CM2  H2   single    0.970  0.020  1.090
 GMI  CM2  H3   single    0.970  0.020  1.090
 GMI  N4'  H4   single    0.860  0.020  1.020
 GMI  N4'  H5   single    0.860  0.020  1.020
 GMI  C6'  H6   single    0.930  0.020  1.080
 GMI  C7'  H7   single    0.970  0.020  1.090
 GMI  C7'  H8   single    0.970  0.020  1.090
 GMI  C2   H9   single    0.930  0.020  1.080
 GMI  CM4  H10  single    0.970  0.020  1.090
 GMI  CM4  H11  single    0.970  0.020  1.090
 GMI  CM4  H12  single    0.970  0.020  1.090
 GMI  C6   H13  single    0.970  0.020  1.090
 GMI  C6   H14  single    0.970  0.020  1.090
 GMI  C7   H15  single    0.970  0.020  1.090
 GMI  C7   H16  single    0.970  0.020  1.090
 GMI  C3A  H20  single    0.970  0.020  1.090
 GMI  C3A  H21  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
 GMI  C6'  N1'  C2'  116.13  3.000
 GMI  N3'  C2'  CM2  117.53  3.000
 GMI  N3'  C2'  N1'  125.42  3.000
 GMI  CM2  C2'  N1'  117.05  3.000
 GMI  H3   CM2  H2   107.00  3.000
 GMI  H3   CM2  H1   108.57  3.000
 GMI  H2   CM2  H1   108.97  3.000
 GMI  H3   CM2  C2'  110.27  3.000
 GMI  H2   CM2  C2'  110.60  3.000
 GMI  H1   CM2  C2'  111.32  3.000
 GMI  C4'  N3'  C2'  118.46  3.000
 GMI  C5'  C4'  N4'  122.43  3.000
 GMI  C5'  C4'  N3'  120.60  3.000
 GMI  N4'  C4'  N3'  116.96  3.000
 GMI  H5   N4'  H4   116.25  3.000
 GMI  H5   N4'  C4'  122.59  3.000
 GMI  H4   N4'  C4'  118.32  3.000
 GMI  C7'  C5'  C6'  124.51  3.000
 GMI  C7'  C5'  C4'  120.11  3.000
 GMI  C6'  C5'  C4'  115.37  3.000
 GMI  H6   C6'  C5'  120.62  3.000
 GMI  H6   C6'  N1'  115.42  3.000
 GMI  C5'  C6'  N1'  123.97  3.000
 GMI  H8   C7'  H7   106.60  3.000
 GMI  H8   C7'  N3   107.38  3.000
 GMI  H7   C7'  N3   107.26  3.000
 GMI  H8   C7'  C5'  111.22  3.000
 GMI  H7   C7'  C5'  111.52  3.000
 GMI  N3   C7'  C5'  112.55  3.000
 GMI  C4   N3   C2   114.57  3.000
 GMI  C4   N3   C7'  123.37  3.000
 GMI  C2   N3   C7'  122.04  3.000
 GMI  H9   C2   S1   124.69  3.000
 GMI  H9   C2   N3   123.03  3.000
 GMI  S1   C2   N3   112.28  3.000
 GMI  C5   S1   C2    91.45  3.000
 GMI  C6   C5   C4   128.88  3.000
 GMI  C6   C5   S1   120.78  3.000
 GMI  C4   C5   S1   110.30  3.000
 GMI  CM4  C4   C5   127.90  3.000
 GMI  CM4  C4   N3   120.69  3.000
 GMI  C5   C4   N3   111.41  3.000
 GMI  H12  CM4  H11  107.66  3.000
 GMI  H12  CM4  H10  108.09  3.000
 GMI  H11  CM4  H10  107.78  3.000
 GMI  H12  CM4  C4   111.25  3.000
 GMI  H11  CM4  C4   110.19  3.000
 GMI  H10  CM4  C4   111.71  3.000
 GMI  H14  C6   H13  106.63  3.000
 GMI  H14  C6   C7   108.73  3.000
 GMI  H13  C6   C7   109.47  3.000
 GMI  H14  C6   C5   108.83  3.000
 GMI  H13  C6   C5   108.84  3.000
 GMI  C7   C6   C5   114.08  3.000
 GMI  H16  C7   H15  105.83  3.000
 GMI  H16  C7   O7   112.47  3.000
 GMI  H15  C7   O7   112.26  3.000
 GMI  H16  C7   C6   109.29  3.000
 GMI  H15  C7   C6   107.82  3.000
 GMI  O7   C7   C6   109.02  3.000
 GMI  PA   O7   C7   119.38  3.000
 GMI  C3A  PA   O2A  111.74  3.000
 GMI  O2A  PA   O1A  119.90  3.000
 GMI  C3A  PA   O1A  112.04  3.000
 GMI  O2A  PA   O7   106.90  3.000
 GMI  O1A  PA   O7   103.00  3.000
 GMI  C3A  PA   O7   100.87  3.000
 GMI  C3A  PB   O3B  102.61  3.000
 GMI  C3A  PB   O2B  105.82  3.000
 GMI  O3B  PB   O2B  113.71  3.000
 GMI  O2B  PB   O1B  114.10  3.000
 GMI  C3A  PB   O1B  105.80  3.000
 GMI  O3B  PB   O1B  113.44  3.000
 GMI  H21  C3A  H20  105.68  3.000
 GMI  H21  C3A  PB   106.85  3.000
 GMI  H20  C3A  PB   107.83  3.000
 GMI  H21  C3A  PA   107.96  3.000
 GMI  H20  C3A  PA   107.27  3.000
 GMI  PB   C3A  PA   120.37  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
 GMI  CONST_01  C4'  N3'  C2'  N1'     0.00   0.0  0
 GMI  CONST_02  C4'  C5'  C6'  N1'     0.00   0.0  0
 GMI  CONST_03  C5'  C4'  N3'  C2'     0.00   0.0  0
 GMI  CONST_04  C5'  C6'  N1'  C2'     0.00   0.0  0
 GMI  CONST_05  C6'  N1'  C2'  N3'     0.00   0.0  0
 GMI  CONST_06  C6'  C5'  C4'  N3'     0.00   0.0  0
 GMI  CONST_07  C5   S1   C2   N3      0.00   0.0  0
 GMI  CONST_08  S1   C5   C4   N3      0.00   0.0  0
 GMI  CONST_09  C4   C5   S1   C2      0.00   0.0  0
 GMI  CONST_10  C5   C4   N3   C2      0.00   0.0  0
 GMI  CONST_11  C4   N3   C2   S1      0.00   0.0  0
 GMI  CONST_12  C7'  C5'  C6'  N1'   180.00   0.0  0
 GMI  CONST_13  N4'  C4'  N3'  C2'   180.00   0.0  0
 GMI  CONST_14  C4'  N3'  C2'  CM2   180.00   0.0  0
 GMI  CONST_15  C6'  N1'  C2'  CM2   180.00   0.0  0
 GMI  CONST_16  C7'  C5'  C4'  N3'   180.00   0.0  0
 GMI  CONST_17  C6'  C5'  C4'  N4'   180.00   0.0  0
 GMI  CONST_18  S1   C2   N3   C7'   180.00   0.0  0
 GMI  CONST_19  C5   C4   N3   C7'   180.00   0.0  0
 GMI  CONST_20  C6   C5   C4   N3    180.00   0.0  0
 GMI  CONST_21  C6   C5   S1   C2    180.00   0.0  0
 GMI  CONST_22  CM4  C4   N3   C2    180.00   0.0  0
 GMI  CONST_23  CM4  C4   C5   S1    180.00   0.0  0
 GMI  CONST_24  H6   C6'  N1'  C2'   180.00   0.0  0
 GMI  CONST_25  H6   C6'  C5'  C4'   180.00   0.0  0
 GMI  CONST_26  H9   C2   S1   C5    180.00   0.0  0
 GMI  CONST_27  H9   C2   N3   C4    180.00   0.0  0
 GMI  CONST_28  H4   N4'  C4'  N3'     0.00   0.0  0
 GMI  CONST_29  H5   N4'  C4'  N3'   180.00   0.0  0
 GMI  CONST_30  H4   N4'  C4'  C5'   180.00   0.0  0
 GMI  CONST_31  H5   N4'  C4'  C5'     0.00   0.0  0
 GMI  Var_01    N3   C7'  C5'  C4'   168.07  30.0  2
 GMI  Var_02    C2   N3   C7'  C5'   102.41  30.0  2
 GMI  Var_03    C4   N3   C7'  C5'   -76.00  30.0  2
 GMI  Var_04    N3   C7'  C5'  C6'   -12.74  30.0  2
 GMI  Var_05    C7   C6   C5   S1     34.80  30.0  2
 GMI  Var_06    C7   C6   C5   C4   -147.88  30.0  2
 GMI  Var_07    H1   CM2  C2'  N1'  -175.57  30.0  2
 GMI  Var_08    H2   CM2  C2'  N1'   -54.28  30.0  2
 GMI  Var_09    H3   CM2  C2'  N1'    63.86  30.0  2
 GMI  Var_10    H1   CM2  C2'  N3'     4.63  30.0  2
 GMI  Var_11    H2   CM2  C2'  N3'   125.92  30.0  2
 GMI  Var_12    H3   CM2  C2'  N3'  -115.93  30.0  2
 GMI  Var_13    H7   C7'  C5'  C4'   -71.33  30.0  2
 GMI  Var_14    H8   C7'  C5'  C4'    47.52  30.0  2
 GMI  Var_15    H7   C7'  C5'  C6'   107.86  30.0  2
 GMI  Var_16    H8   C7'  C5'  C6'  -133.29  30.0  2
 GMI  Var_17    H10  CM4  C4   N3     63.20  30.0  2
 GMI  Var_18    H11  CM4  C4   N3   -177.02  30.0  2
 GMI  Var_19    H12  CM4  C4   N3    -57.69  30.0  2
 GMI  Var_20    H7   C7'  N3   C2    -20.61  30.0  2
 GMI  Var_21    H8   C7'  N3   C2   -134.86  30.0  2
 GMI  Var_22    H13  C6   C5   S1    157.35  30.0  2
 GMI  Var_23    H14  C6   C5   S1    -86.81  30.0  2
 GMI  Var_24    H10  CM4  C4   C5   -117.56  30.0  2
 GMI  Var_25    H11  CM4  C4   C5      2.22  30.0  2
 GMI  Var_26    H12  CM4  C4   C5    121.55  30.0  2
 GMI  Var_27    H7   C7'  N3   C4    160.98  30.0  2
 GMI  Var_28    H8   C7'  N3   C4     46.73  30.0  2
 GMI  Var_29    H13  C6   C5   C4    -25.32  30.0  2
 GMI  Var_30    H14  C6   C5   C4     90.51  30.0  2
 GMI  Var_31    O7   C7   C6   C5     59.38  30.0  1
 GMI  Var_32    H15  C7   C6   C5   -178.50  30.0  1
 GMI  Var_33    H16  C7   C6   C5    -63.91  30.0  1
 GMI  Var_34    PA   O7   C7   C6   -169.17  30.0  3
 GMI  Var_35    C3A  PA   O7   C7     79.83  30.0  1
 GMI  Var_36    O1A  PA   O7   C7   -164.29  30.0  1
 GMI  Var_37    O2A  PA   O7   C7    -37.07  30.0  1
 GMI  Var_38    PB   C3A  PA   O7   -179.88  30.0  2
 GMI  Var_39    O3B  PB   C3A  PA   -178.51  30.0  3
 GMI  Var_40    O1B  PB   C3A  PA     62.35  30.0  3
 GMI  Var_41    O2B  PB   C3A  PA    -59.06  30.0  3
 GMI  Var_42    PB   C3A  PA   O1A    71.16  30.0  2
 GMI  Var_43    PB   C3A  PA   O2A   -66.60  30.0  2
 GMI  Var_44    H13  C6   C7   O7    -62.83  30.0  3
 GMI  Var_45    H14  C6   C7   O7   -178.96  30.0  3
 GMI  Var_46    H20  C3A  PA   O7     56.50  30.0  2
 GMI  Var_47    H21  C3A  PA   O7    -56.98  30.0  2
 GMI  Var_48    H15  C7   O7   PA     71.44  30.0  1
 GMI  Var_49    H16  C7   O7   PA    -47.79  30.0  1
 GMI  Var_50    H20  C3A  PA   O1A   -52.46  30.0  2
 GMI  Var_51    H21  C3A  PA   O1A  -165.93  30.0  2
 GMI  Var_52    H20  C3A  PA   O2A   169.78  30.0  2
 GMI  Var_53    H21  C3A  PA   O2A    56.31  30.0  2
 GMI  Var_54    H20  C3A  PB   O1B  -174.29  30.0  3
 GMI  Var_55    H21  C3A  PB   O1B   -61.08  30.0  3
 GMI  Var_56    H20  C3A  PB   O2B    64.29  30.0  3
 GMI  Var_57    H21  C3A  PB   O2B   177.50  30.0  3
 GMI  Var_58    H20  C3A  PB   O3B   -55.15  30.0  3
 GMI  Var_59    H21  C3A  PB   O3B    58.06  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
 GMI  plan-1  C7'  0.020
 GMI  plan-1  N3   0.020
 GMI  plan-1  C2   0.020
 GMI  plan-1  S1   0.020
 GMI  plan-1  C5   0.020
 GMI  plan-1  C4   0.020
 GMI  plan-1  CM4  0.020
 GMI  plan-1  C6   0.020
 GMI  plan-1  H9   0.020
 GMI  plan-2  N1'  0.020
 GMI  plan-2  C2'  0.020
 GMI  plan-2  CM2  0.020
 GMI  plan-2  N3'  0.020
 GMI  plan-2  C4'  0.020
 GMI  plan-2  N4'  0.020
 GMI  plan-2  C5'  0.020
 GMI  plan-2  C6'  0.020
 GMI  plan-2  C7'  0.020
 GMI  plan-2  H6   0.020
 GMI  plan-3  C4'  0.020
 GMI  plan-3  N4'  0.020
 GMI  plan-3  H4   0.020
 GMI  plan-3  H5   0.020

