# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon May 18 11:21:18 2020
#   Inital geometry file: a 112 line input string
#   Ligand name: [2-[3-[(4-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: Cc1cc(N)c(C[n+]2csc(CCO[P@@](O)(=O)O[P](O)([O-])=O)c2C)cn1
#
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
 N3T  N3T  '[2-[3-[(4-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_N3T
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
 N3T  N1'   N  N      0  -0.447  17.1539  71.9504  27.1871
 N3T  C2'   C  CR6    0   0.242  15.8525  72.2586  27.1627
 N3T  CM2   C  CH3    0  -0.718  14.8988  71.1861  27.5894
 N3T  C3'   C  CR16   0  -0.407  15.3934  73.5032  26.7723
 N3T  C4'   C  CR6    0   0.399  16.2949  74.4970  26.3729
 N3T  N4'   N  NH2    0  -0.851  15.8564  75.7281  25.9865
 N3T  C5'   C  CR6    0  -0.006  17.6570  74.1489  26.3455
 N3T  C6'   C  CR16   0  -0.120  18.0033  72.8787  26.7822
 N3T  C7'   C  CH2    0  -0.478  18.7162  75.0897  25.8642
 N3T  N3    N  NR5    1  -0.383  18.5987  75.3635  24.4185
 N3T  C2    C  CR15   0  -0.150  18.2055  76.5337  23.9656
 N3T  S1    S  S2     0   0.391  18.1018  76.5746  22.3020
 N3T  C5    C  CR5    0  -0.301  18.6144  74.9368  22.1950
 N3T  C4    C  CR5    0   0.537  18.8533  74.4279  23.4309
 N3T  CM4   C  CH3    0  -0.745  19.3404  73.0610  23.7453
 N3T  C6    C  CH2    0  -0.553  18.8433  74.3013  20.8667
 N3T  C7    C  CH2    0  -0.171  20.2045  74.6767  20.3015
 N3T  O7    O  O2     0  -0.589  20.2558  76.0933  20.1423
 N3T  PA    P  P      0   1.459  21.4505  76.9913  20.7168
 N3T  O1A   O  O      0  -0.695  21.2419  78.3920  20.3061
 N3T  O2A   O  OH1    0  -0.786  22.7927  76.2991  20.2806
 N3T  O3A   O  O2     0  -0.730  21.3578  76.7634  22.3130
 N3T  PB    P  P      0   1.385  22.6025  76.4346  23.3751
 N3T  O1B   O  O      0  -0.740  22.8784  77.6323  24.2061
 N3T  O2B   O  OP    -1  -0.792  23.6837  75.8079  22.5129
 N3T  O3B   O  OH1    0  -0.753  21.8794  75.2674  24.2285
 N3T  HM21  H  HCH3   0   0.245  13.8803  71.5594  27.6760
 N3T  HM22  H  HCH3   0   0.254  14.8972  70.3681  26.8667
 N3T  HM23  H  HCH3   0   0.251  15.1958  70.7659  28.5504
 N3T  H3'   H  HCR6   0   0.271  14.3325  73.7201  26.7938
 N3T  HN41  H  HNH2   0   0.388  16.4485  76.5185  26.1837
 N3T  HN42  H  HNH2   0   0.400  14.8882  75.9335  26.1779
 N3T  H6'   H  HCR6   0   0.263  19.0549  72.6047  26.8000
 N3T  H7'1  H  HCH2   0   0.323  18.6895  76.0564  26.3691
 N3T  H7'2  H  HCH2   0   0.320  19.7069  74.6759  26.0458
 N3T  H2    H  HCR5   0   0.371  17.9999  77.3794  24.6022
 N3T  HM41  H  HCH3   0   0.284  19.7224  72.5870  22.8448
 N3T  HM42  H  HCH3   0   0.273  20.1557  73.0764  24.4669
 N3T  HM43  H  HCH3   0   0.285  18.5424  72.4332  24.1402
 N3T  H61   H  HCH2   0   0.291  18.7904  73.2166  20.9597
 N3T  H62   H  HCH2   0   0.295  18.0566  74.5861  20.1657
 N3T  H71   H  HCH2   0   0.238  20.9948  74.3090  20.9604
 N3T  H72   H  HCH2   0   0.270  20.3440  74.2136  19.3243
 N3T  HOA2  H  HOH1   0   0.493  23.3362  76.0113  21.1212
 N3T  HOB3  H  HOH1   0   0.487  21.9347  75.4357  25.1767

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
 N3T  N1'  C2'   aromatic  1.338  0.020  1.338
 N3T  N1'  C6'   aromatic  1.322  0.020  1.322
 N3T  C2'  CM2   single    1.497  0.020  1.497
 N3T  C2'  C3'   aromatic  1.383  0.020  1.383
 N3T  CM2  HM21  single    0.970  0.020  1.090
 N3T  CM2  HM22  single    0.970  0.020  1.090
 N3T  CM2  HM23  single    0.970  0.020  1.090
 N3T  C3'  C4'   aromatic  1.400  0.020  1.400
 N3T  C3'  H3'   single    0.930  0.020  1.080
 N3T  C4'  N4'   single    1.363  0.020  1.363
 N3T  C4'  C5'   aromatic  1.406  0.020  1.406
 N3T  N4'  HN41  single    0.890  0.020  1.040
 N3T  N4'  HN42  single    0.890  0.020  1.040
 N3T  C5'  C6'   aromatic  1.387  0.020  1.387
 N3T  C5'  C7'   single    1.496  0.020  1.496
 N3T  C6'  H6'   single    0.930  0.020  1.080
 N3T  C7'  N3    single    1.476  0.020  1.476
 N3T  C7'  H7'1  single    0.970  0.020  1.090
 N3T  C7'  H7'2  single    0.970  0.020  1.090
 N3T  N3   C2    aromatic  1.315  0.020  1.315
 N3T  N3   C4    aromatic  1.384  0.020  1.384
 N3T  C2   S1    aromatic  1.667  0.020  1.667
 N3T  C2   H2    single    0.930  0.020  1.080
 N3T  S1   C5    aromatic  1.719  0.020  1.719
 N3T  C5   C4    aromatic  1.358  0.020  1.358
 N3T  C5   C6    single    1.490  0.020  1.490
 N3T  C4   CM4   single    1.485  0.020  1.485
 N3T  CM4  HM41  single    0.970  0.020  1.090
 N3T  CM4  HM42  single    0.970  0.020  1.090
 N3T  CM4  HM43  single    0.970  0.020  1.090
 N3T  C6   C7    single    1.521  0.020  1.521
 N3T  C6   H61   single    0.970  0.020  1.090
 N3T  C6   H62   single    0.970  0.020  1.090
 N3T  C7   O7    single    1.427  0.020  1.427
 N3T  C7   H71   single    0.970  0.020  1.090
 N3T  C7   H72   single    0.970  0.020  1.090
 N3T  O7   PA    single    1.601  0.020  1.601
 N3T  PA   O1A   double    1.474  0.020  1.474
 N3T  PA   O2A   single    1.572  0.020  1.572
 N3T  PA   O3A   single    1.615  0.020  1.615
 N3T  O2A  HOA2  single    0.850  0.020  0.980
 N3T  O3A  PB    single    1.669  0.020  1.669
 N3T  PB   O1B   double    1.484  0.020  1.484
 N3T  PB   O2B   single    1.518  0.020  1.518
 N3T  PB   O3B   single    1.617  0.020  1.617
 N3T  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
 N3T  C6'   N1'  C2'   117.25  3.000
 N3T  C3'   C2'  CM2   120.91  3.000
 N3T  C3'   C2'  N1'   122.38  3.000
 N3T  CM2   C2'  N1'   116.71  3.000
 N3T  HM23  CM2  HM22  107.17  3.000
 N3T  HM23  CM2  HM21  108.48  3.000
 N3T  HM22  CM2  HM21  107.97  3.000
 N3T  HM23  CM2  C2'   110.72  3.000
 N3T  HM22  CM2  C2'   110.43  3.000
 N3T  HM21  CM2  C2'   111.91  3.000
 N3T  H3'   C3'  C4'   119.62  3.000
 N3T  H3'   C3'  C2'   119.99  3.000
 N3T  C4'   C3'  C2'   120.37  3.000
 N3T  C5'   C4'  N4'   121.99  3.000
 N3T  C5'   C4'  C3'   116.97  3.000
 N3T  N4'   C4'  C3'   120.99  3.000
 N3T  HN42  N4'  HN41  111.57  3.000
 N3T  HN42  N4'  C4'   116.06  3.000
 N3T  HN41  N4'  C4'   117.67  3.000
 N3T  C7'   C5'  C6'   120.02  3.000
 N3T  C7'   C5'  C4'   122.43  3.000
 N3T  C6'   C5'  C4'   117.54  3.000
 N3T  H6'   C6'  C5'   118.53  3.000
 N3T  H6'   C6'  N1'   116.08  3.000
 N3T  C5'   C6'  N1'   125.39  3.000
 N3T  H7'2  C7'  H7'1  106.37  3.000
 N3T  H7'2  C7'  N3    107.83  3.000
 N3T  H7'1  C7'  N3    106.67  3.000
 N3T  H7'2  C7'  C5'   110.58  3.000
 N3T  H7'1  C7'  C5'   113.02  3.000
 N3T  N3    C7'  C5'   112.05  3.000
 N3T  C4    N3   C2    114.26  3.000
 N3T  C4    N3   C7'   123.97  3.000
 N3T  C2    N3   C7'   121.75  3.000
 N3T  H2    C2   S1    123.92  3.000
 N3T  H2    C2   N3    123.48  3.000
 N3T  S1    C2   N3    112.58  3.000
 N3T  C5    S1   C2     91.16  3.000
 N3T  C6    C5   C4    128.64  3.000
 N3T  C6    C5   S1    120.50  3.000
 N3T  C4    C5   S1    110.66  3.000
 N3T  CM4   C4   C5    126.55  3.000
 N3T  CM4   C4   N3    122.11  3.000
 N3T  C5    C4   N3    111.33  3.000
 N3T  HM43  CM4  HM42  108.45  3.000
 N3T  HM43  CM4  HM41  107.84  3.000
 N3T  HM42  CM4  HM41  106.98  3.000
 N3T  HM43  CM4  C4    111.53  3.000
 N3T  HM42  CM4  C4    111.90  3.000
 N3T  HM41  CM4  C4    109.96  3.000
 N3T  H62   C6   H61   106.23  3.000
 N3T  H62   C6   C7    110.00  3.000
 N3T  H61   C6   C7    108.71  3.000
 N3T  H62   C6   C5    110.51  3.000
 N3T  H61   C6   C5    109.93  3.000
 N3T  C7    C6   C5    111.32  3.000
 N3T  H72   C7   H71   107.76  3.000
 N3T  H72   C7   O7    108.49  3.000
 N3T  H71   C7   O7    112.05  3.000
 N3T  H72   C7   C6    110.05  3.000
 N3T  H71   C7   C6    109.89  3.000
 N3T  O7    C7   C6    108.59  3.000
 N3T  PA    O7   C7    122.94  3.000
 N3T  O3A   PA   O2A   105.14  3.000
 N3T  O3A   PA   O1A   113.65  3.000
 N3T  O2A   PA   O1A   117.50  3.000
 N3T  O3A   PA   O7    103.46  3.000
 N3T  O2A   PA   O7    106.89  3.000
 N3T  O1A   PA   O7    109.10  3.000
 N3T  HOA2  O2A  PA    110.08  3.000
 N3T  PB    O3A  PA    127.88  3.000
 N3T  O3B   PB   O2B   108.68  3.000
 N3T  O3B   PB   O1B   111.74  3.000
 N3T  O2B   PB   O1B   121.25  3.000
 N3T  O3B   PB   O3A    98.32  3.000
 N3T  O2B   PB   O3A   104.54  3.000
 N3T  O1B   PB   O3A   109.64  3.000
 N3T  HOB3  O3B  PB    111.55  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
 N3T  CONST_01  C4'   C3'  C2'  N1'     0.00   0.0  0
 N3T  CONST_02  C4'   C5'  C6'  N1'     0.00   0.0  0
 N3T  CONST_03  C5'   C6'  N1'  C2'     0.00   0.0  0
 N3T  CONST_04  C5'   C4'  C3'  C2'     0.00   0.0  0
 N3T  CONST_05  C6'   N1'  C2'  C3'     0.00   0.0  0
 N3T  CONST_06  C6'   C5'  C4'  C3'     0.00   0.0  0
 N3T  CONST_07  C5    S1   C2   N3      0.00   0.0  0
 N3T  CONST_08  S1    C5   C4   N3      0.00   0.0  0
 N3T  CONST_09  C5    C4   N3   C2      0.00   0.0  0
 N3T  CONST_10  C4    C5   S1   C2      0.00   0.0  0
 N3T  CONST_11  C4    N3   C2   S1      0.00   0.0  0
 N3T  CONST_12  C7'   C5'  C6'  N1'   180.00   0.0  0
 N3T  CONST_13  N4'   C4'  C3'  C2'   180.00   0.0  0
 N3T  CONST_14  C6'   N1'  C2'  CM2   180.00   0.0  0
 N3T  CONST_15  C4'   C3'  C2'  CM2   180.00   0.0  0
 N3T  CONST_16  C7'   C5'  C4'  C3'   180.00   0.0  0
 N3T  CONST_17  C6'   C5'  C4'  N4'   180.00   0.0  0
 N3T  CONST_18  S1    C2   N3   C7'   180.00   0.0  0
 N3T  CONST_19  C5    C4   N3   C7'   180.00   0.0  0
 N3T  CONST_20  C6    C5   C4   N3    180.00   0.0  0
 N3T  CONST_21  CM4   C4   N3   C2    180.00   0.0  0
 N3T  CONST_22  C6    C5   S1   C2    180.00   0.0  0
 N3T  CONST_23  CM4   C4   C5   S1    180.00   0.0  0
 N3T  CONST_24  H3'   C3'  C2'  N1'   180.00   0.0  0
 N3T  CONST_25  H6'   C6'  N1'  C2'   180.00   0.0  0
 N3T  CONST_26  H2    C2   S1   C5    180.00   0.0  0
 N3T  CONST_28  HN42  N4'  C4'  C3'     0.00   0.0  0
 N3T  Var_01    N3    C7'  C5'  C4'   -67.04  30.0  2
 N3T  Var_02    C2    N3   C7'  C5'   109.35  30.0  2
 N3T  Var_03    C7    C6   C5   S1     80.71  30.0  2
 N3T  Var_04    HM21  CM2  C2'  N1'   171.88  30.0  2
 N3T  Var_05    HM41  CM4  C4   N3   -165.04  30.0  2
 N3T  Var_06    O7    C7   C6   C5    -60.53  30.0  3
 N3T  Var_07    O1A   PA   O7   C7    176.37  30.0  3
 N3T  Var_08    O1B   PB   O3A  PA    107.42  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
 N3T  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
 N3T  plan-1  C7'   0.020
 N3T  plan-1  N3    0.020
 N3T  plan-1  C2    0.020
 N3T  plan-1  S1    0.020
 N3T  plan-1  C5    0.020
 N3T  plan-1  C4    0.020
 N3T  plan-1  CM4   0.020
 N3T  plan-1  C6    0.020
 N3T  plan-1  H2    0.020
 N3T  plan-2  N1'   0.020
 N3T  plan-2  C2'   0.020
 N3T  plan-2  CM2   0.020
 N3T  plan-2  C3'   0.020
 N3T  plan-2  C4'   0.020
 N3T  plan-2  N4'   0.020
 N3T  plan-2  C5'   0.020
 N3T  plan-2  C6'   0.020
 N3T  plan-2  C7'   0.020
 N3T  plan-2  H3'   0.020
 N3T  plan-2  H6'   0.020
 N3T  plan-3  C4'   0.020
 N3T  plan-3  N4'   0.020
 N3T  plan-3  HN41  0.020
 N3T  plan-3  HN42  0.020

