# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue May 19 06:43:16 2020
#   Inital geometry file: a 112 line input string
#   Ligand name: [2-[3-[(2-amino-6-methyl-pyridin-3-yl)methyl]-4-methyl-1,3-thiazol-3-ium-5-yl]ethoxy-hydroxy-phosphoryl] hydrogen phosphate
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cc1ccc(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
 N1T  N1T  '[2-[3-[(2-amino-6-methyl-pyridin-3-yl)methyl]-4-methyl-1,3-thiazol-3-ium-5-yl]ethoxy-hydroxy-phosphoryl] hydrogen phosphate'  ligand  45  26  .  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_N1T
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
 N1T  C1'   C  CR16   0  -0.357  16.8710  71.9545  27.3477
 N1T  C2'   C  CR6    0   0.263  15.5491  72.3183  27.1287
 N1T  CM2   C  CH3    0  -0.744  14.4200  71.3866  27.4414
 N1T  N3'   N  N      0  -0.484  15.2184  73.5101  26.6345
 N1T  C4'   C  CR6    0   0.361  16.1673  74.3786  26.3103
 N1T  N4'   N  NH2    0  -0.778  15.7581  75.5887  25.8128
 N1T  C5'   C  CR6    0  -0.063  17.5382  74.0689  26.4177
 N1T  C6'   C  CR16   0  -0.156  17.8651  72.8462  26.9738
 N1T  C7'   C  CH2    0  -0.454  18.6002  75.0053  25.9301
 N1T  N3    N  NR5    1  -0.397  18.5587  75.1594  24.4631
 N1T  C2    C  CR15   0  -0.067  18.1457  76.2694  23.8927
 N1T  S1    S  S2     0   0.382  18.1530  76.1736  22.2274
 N1T  C5    C  CR5    0  -0.234  18.7345  74.5555  22.2874
 N1T  C4    C  CR5    0   0.478  18.9164  74.1613  23.5733
 N1T  CM4   C  CH3    0  -0.759  19.4538  72.8583  24.0401
 N1T  C6    C  CH2    0  -0.512  19.0534  73.8164  21.0336
 N1T  C7    C  CH2    0  -0.238  20.3975  74.2385  20.4657
 N1T  O7    O  O2     0  -0.523  20.3222  75.6175  20.1065
 N1T  PA    P  P      0   1.438  21.4954  76.6613  20.4379
 N1T  O1A   O  O      0  -0.812  21.2438  77.9191  19.7129
 N1T  O2A   O  OH1    0  -0.609  22.8593  75.9328  20.1463
 N1T  O3A   O  O2     0  -0.638  21.4277  76.8233  22.0399
 N1T  PB    P  P      0   1.233  22.5774  76.4113  23.1827
 N1T  O1B   O  O      0  -0.828  23.1126  77.6535  23.7927
 N1T  O2B   O  OP    -1  -0.864  23.4768  75.4152  22.4746
 N1T  O3B   O  OH1    0  -0.709  21.6543  75.5857  24.2190
 N1T  H1'   H  HCR6   0   0.234  17.1196  70.9954  27.7796
 N1T  HM21  H  HCH3   0   0.276  13.6649  71.8824  28.0515
 N1T  HM22  H  HCH3   0   0.245  13.9292  71.0620  26.5219
 N1T  HM23  H  HCH3   0   0.258  14.7641  70.4998  27.9704
 N1T  HN41  H  HNH2   0   0.368  16.2849  76.3974  26.1042
 N1T  HN42  H  HNH2   0   0.402  14.7655  75.7478  25.8993
 N1T  H6'   H  HCR6   0   0.279  18.9071  72.5797  27.1062
 N1T  H7'1  H  HCH2   0   0.335  18.5161  76.0080  26.3504
 N1T  H7'2  H  HCH2   0   0.339  19.5878  74.6329  26.1980
 N1T  H2    H  HCR5   0   0.326  17.8627  77.1520  24.4436
 N1T  HM41  H  HCH3   0   0.299  19.9059  72.3195  23.2117
 N1T  HM42  H  HCH3   0   0.265  20.2262  72.9957  24.7959
 N1T  HM43  H  HCH3   0   0.288  18.6707  72.2291  24.4618
 N1T  H61   H  HCH2   0   0.310  19.0815  72.7454  21.2341
 N1T  H62   H  HCH2   0   0.281  18.2691  73.9678  20.2899
 N1T  H71   H  HCH2   0   0.257  21.1826  74.0472  21.2018
 N1T  H72   H  HCH2   0   0.262  20.6274  73.6551  19.5735
 N1T  HOA2  H  HOH1   0   0.543  23.2887  75.6076  21.0322
 N1T  HOB3  H  HOH1   0   0.505  21.5372  76.0655  25.0476

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
 N1T  C1'  C2'   aromatic  1.388  0.020  1.388
 N1T  C1'  C6'   aromatic  1.387  0.020  1.387
 N1T  C1'  H1'   single    0.930  0.020  1.080
 N1T  C2'  CM2   single    1.497  0.020  1.497
 N1T  C2'  N3'   aromatic  1.332  0.020  1.332
 N1T  CM2  HM21  single    0.970  0.020  1.090
 N1T  CM2  HM22  single    0.970  0.020  1.090
 N1T  CM2  HM23  single    0.970  0.020  1.090
 N1T  N3'  C4'   aromatic  1.327  0.020  1.327
 N1T  C4'  N4'   single    1.371  0.020  1.371
 N1T  C4'  C5'   aromatic  1.410  0.020  1.410
 N1T  N4'  HN41  single    0.890  0.020  1.040
 N1T  N4'  HN42  single    0.890  0.020  1.040
 N1T  C5'  C6'   aromatic  1.382  0.020  1.382
 N1T  C5'  C7'   single    1.497  0.020  1.497
 N1T  C6'  H6'   single    0.930  0.020  1.080
 N1T  C7'  N3    single    1.476  0.020  1.476
 N1T  C7'  H7'1  single    0.970  0.020  1.090
 N1T  C7'  H7'2  single    0.970  0.020  1.090
 N1T  N3   C2    aromatic  1.315  0.020  1.315
 N1T  N3   C4    aromatic  1.384  0.020  1.384
 N1T  C2   S1    aromatic  1.668  0.020  1.668
 N1T  C2   H2    single    0.930  0.020  1.080
 N1T  S1   C5    aromatic  1.720  0.020  1.720
 N1T  C5   C4    aromatic  1.357  0.020  1.357
 N1T  C5   C6    single    1.490  0.020  1.490
 N1T  C4   CM4   single    1.485  0.020  1.485
 N1T  CM4  HM41  single    0.970  0.020  1.090
 N1T  CM4  HM42  single    0.970  0.020  1.090
 N1T  CM4  HM43  single    0.970  0.020  1.090
 N1T  C6   C7    single    1.519  0.020  1.519
 N1T  C6   H61   single    0.970  0.020  1.090
 N1T  C6   H62   single    0.970  0.020  1.090
 N1T  C7   O7    single    1.427  0.020  1.427
 N1T  C7   H71   single    0.970  0.020  1.090
 N1T  C7   H72   single    0.970  0.020  1.090
 N1T  O7   PA    single    1.605  0.020  1.605
 N1T  PA   O1A   double    1.473  0.020  1.473
 N1T  PA   O2A   single    1.574  0.020  1.574
 N1T  PA   O3A   single    1.612  0.020  1.612
 N1T  O2A  HOA2  single    0.850  0.020  0.980
 N1T  O3A  PB    single    1.673  0.020  1.673
 N1T  PB   O1B   double    1.484  0.020  1.484
 N1T  PB   O2B   single    1.517  0.020  1.517
 N1T  PB   O3B   single    1.615  0.020  1.615
 N1T  O3B  HOB3  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
 N1T  H1'   C1'  C6'   120.89  3.000
 N1T  H1'   C1'  C2'   120.97  3.000
 N1T  C6'   C1'  C2'   118.13  3.000
 N1T  N3'   C2'  CM2   116.56  3.000
 N1T  N3'   C2'  C1'   121.97  3.000
 N1T  CM2   C2'  C1'   121.48  3.000
 N1T  HM23  CM2  HM22  108.01  3.000
 N1T  HM23  CM2  HM21  108.51  3.000
 N1T  HM22  CM2  HM21  107.18  3.000
 N1T  HM23  CM2  C2'   111.72  3.000
 N1T  HM22  CM2  C2'   110.38  3.000
 N1T  HM21  CM2  C2'   110.88  3.000
 N1T  C4'   N3'  C2'   119.92  3.000
 N1T  C5'   C4'  N4'   120.79  3.000
 N1T  C5'   C4'  N3'   122.23  3.000
 N1T  N4'   C4'  N3'   116.94  3.000
 N1T  HN42  N4'  HN41  111.27  3.000
 N1T  HN42  N4'  C4'   113.69  3.000
 N1T  HN41  N4'  C4'   116.56  3.000
 N1T  C7'   C5'  C6'   121.09  3.000
 N1T  C7'   C5'  C4'   121.84  3.000
 N1T  C6'   C5'  C4'   117.06  3.000
 N1T  H6'   C6'  C5'   119.61  3.000
 N1T  H6'   C6'  C1'   119.88  3.000
 N1T  C5'   C6'  C1'   120.51  3.000
 N1T  H7'2  C7'  H7'1  106.83  3.000
 N1T  H7'2  C7'  N3    107.81  3.000
 N1T  H7'1  C7'  N3    106.55  3.000
 N1T  H7'2  C7'  C5'   110.44  3.000
 N1T  H7'1  C7'  C5'   113.25  3.000
 N1T  N3    C7'  C5'   111.66  3.000
 N1T  C4    N3   C2    114.27  3.000
 N1T  C4    N3   C7'   123.82  3.000
 N1T  C2    N3   C7'   121.90  3.000
 N1T  H2    C2   S1    123.94  3.000
 N1T  H2    C2   N3    123.50  3.000
 N1T  S1    C2   N3    112.54  3.000
 N1T  C5    S1   C2     91.19  3.000
 N1T  C6    C5   C4    128.65  3.000
 N1T  C6    C5   S1    120.63  3.000
 N1T  C4    C5   S1    110.58  3.000
 N1T  CM4   C4   C5    126.96  3.000
 N1T  CM4   C4   N3    121.62  3.000
 N1T  C5    C4   N3    111.41  3.000
 N1T  HM43  CM4  HM42  108.29  3.000
 N1T  HM43  CM4  HM41  107.92  3.000
 N1T  HM42  CM4  HM41  107.24  3.000
 N1T  HM43  CM4  C4    111.62  3.000
 N1T  HM42  CM4  C4    111.35  3.000
 N1T  HM41  CM4  C4    110.25  3.000
 N1T  H62   C6   H61   106.27  3.000
 N1T  H62   C6   C7    110.03  3.000
 N1T  H61   C6   C7    108.60  3.000
 N1T  H62   C6   C5    110.54  3.000
 N1T  H61   C6   C5    109.76  3.000
 N1T  C7    C6   C5    111.48  3.000
 N1T  H72   C7   H71   107.81  3.000
 N1T  H72   C7   O7    108.79  3.000
 N1T  H71   C7   O7    112.11  3.000
 N1T  H72   C7   C6    110.11  3.000
 N1T  H71   C7   C6    109.58  3.000
 N1T  O7    C7   C6    108.42  3.000
 N1T  PA    O7   C7    122.55  3.000
 N1T  O3A   PA   O2A   105.50  3.000
 N1T  O3A   PA   O1A   113.34  3.000
 N1T  O2A   PA   O1A   116.88  3.000
 N1T  O3A   PA   O7    103.88  3.000
 N1T  O2A   PA   O7    107.11  3.000
 N1T  O1A   PA   O7    109.19  3.000
 N1T  HOA2  O2A  PA    110.23  3.000
 N1T  PB    O3A  PA    128.72  3.000
 N1T  O3B   PB   O2B   107.62  3.000
 N1T  O3B   PB   O1B   111.74  3.000
 N1T  O2B   PB   O1B   121.85  3.000
 N1T  O3B   PB   O3A    99.87  3.000
 N1T  O2B   PB   O3A   104.50  3.000
 N1T  O1B   PB   O3A   108.82  3.000
 N1T  HOB3  O3B  PB    111.49  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
 N1T  CONST_01  C4'   N3'  C2'  C1'     0.00   0.0  0
 N1T  CONST_02  C4'   C5'  C6'  C1'     0.00   0.0  0
 N1T  CONST_03  C5'   C6'  C1'  C2'     0.00   0.0  0
 N1T  CONST_04  C5'   C4'  N3'  C2'     0.00   0.0  0
 N1T  CONST_05  C6'   C1'  C2'  N3'     0.00   0.0  0
 N1T  CONST_06  C6'   C5'  C4'  N3'     0.00   0.0  0
 N1T  CONST_07  C5    S1   C2   N3      0.00   0.0  0
 N1T  CONST_08  S1    C5   C4   N3      0.00   0.0  0
 N1T  CONST_09  C5    C4   N3   C2      0.00   0.0  0
 N1T  CONST_10  C4    C5   S1   C2      0.00   0.0  0
 N1T  CONST_11  C4    N3   C2   S1      0.00   0.0  0
 N1T  CONST_12  C7'   C5'  C6'  C1'   180.00   0.0  0
 N1T  CONST_13  N4'   C4'  N3'  C2'   180.00   0.0  0
 N1T  CONST_14  C6'   C1'  C2'  CM2   180.00   0.0  0
 N1T  CONST_15  C4'   N3'  C2'  CM2   180.00   0.0  0
 N1T  CONST_16  C7'   C5'  C4'  N3'   180.00   0.0  0
 N1T  CONST_17  C6'   C5'  C4'  N4'   180.00   0.0  0
 N1T  CONST_18  S1    C2   N3   C7'   180.00   0.0  0
 N1T  CONST_19  C5    C4   N3   C7'   180.00   0.0  0
 N1T  CONST_20  C6    C5   C4   N3    180.00   0.0  0
 N1T  CONST_21  CM4   C4   N3   C2    180.00   0.0  0
 N1T  CONST_22  C6    C5   S1   C2    180.00   0.0  0
 N1T  CONST_23  CM4   C4   C5   S1    180.00   0.0  0
 N1T  CONST_24  H6'   C6'  C1'  C2'   180.00   0.0  0
 N1T  CONST_25  H1'   C1'  C2'  N3'   180.00   0.0  0
 N1T  CONST_26  H2    C2   S1   C5    180.00   0.0  0
 N1T  CONST_28  HN42  N4'  C4'  N3'     0.00   0.0  0
 N1T  Var_01    N3    C7'  C5'  C4'   -66.03  30.0  2
 N1T  Var_02    C2    N3   C7'  C5'   108.58  30.0  2
 N1T  Var_03    C7    C6   C5   S1     78.34  30.0  2
 N1T  Var_04    HM21  CM2  C2'  C1'   129.26  30.0  2
 N1T  Var_05    HM41  CM4  C4   N3   -165.55  30.0  2
 N1T  Var_06    O7    C7   C6   C5    -63.45  30.0  3
 N1T  Var_07    O1A   PA   O7   C7    168.80  30.0  3
 N1T  Var_08    O1B   PB   O3A  PA    111.94  30.0  3

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
 N1T  chir_01  PA  O1A  O2A  O3A  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
 N1T  plan-1  C7'   0.020
 N1T  plan-1  N3    0.020
 N1T  plan-1  C2    0.020
 N1T  plan-1  S1    0.020
 N1T  plan-1  C5    0.020
 N1T  plan-1  C4    0.020
 N1T  plan-1  CM4   0.020
 N1T  plan-1  C6    0.020
 N1T  plan-1  H2    0.020
 N1T  plan-2  C1'   0.020
 N1T  plan-2  C2'   0.020
 N1T  plan-2  CM2   0.020
 N1T  plan-2  N3'   0.020
 N1T  plan-2  C4'   0.020
 N1T  plan-2  N4'   0.020
 N1T  plan-2  C5'   0.020
 N1T  plan-2  C6'   0.020
 N1T  plan-2  C7'   0.020
 N1T  plan-2  H1'   0.020
 N1T  plan-2  H6'   0.020
 N1T  plan-3  C4'   0.020
 N1T  plan-3  N4'   0.020
 N1T  plan-3  HN41  0.020
 N1T  plan-3  HN42  0.020

