# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat May 30 09:36:15 2020
#   Inital geometry file: a 107 line input string
#   Ligand name: [[(Z)-4-[(4-amino-2-methyl-pyrimidin-5-yl)methylamino]-3-sulfanyl-pent-3-enoxy]-oxido-phosphoryl] hydrogen phosphate
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC(/NCc1cnc(C)nc1N)=C(/S)CCO[P]([O-])(=O)O[P](O)([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
 TP9  TP9  '[[(Z)-4-[(4-amino-2-methyl-pyrimidin-5-yl)methylamino]-3-sulfanyl-pent-3-enoxy]-oxido-phosphoryl] hydrogen phosphate'  ligand  43  25  .  2021-08-24  2021-08-24  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_TP9
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
 TP9  N1'   N  N      0  -0.457  -11.6150   5.1640  6.4955
 TP9  C2'   C  CR6    0   0.345  -12.0871   4.0053  6.9341
 TP9  CM2   C  CH3    0  -0.728  -13.1278   4.0400  8.0117
 TP9  N3'   N  N      0  -0.466  -11.7132   2.8051  6.5160
 TP9  C4'   C  CR6    0   0.440  -10.7801   2.7158  5.5595
 TP9  N4'   N  NH2    0  -0.879  -10.4235   1.4870  5.1780
 TP9  C5'   C  CR6    0  -0.055  -10.2456   3.9003  4.9817
 TP9  C6'   C  CR16   0  -0.094  -10.7061   5.0758  5.5187
 TP9  C7'   C  CH2    0  -0.390   -9.2770   3.9109  3.8345
 TP9  N3    N  NH1    0  -0.623   -7.9786   3.3514  4.1655
 TP9  S1    S  S2     0  -0.252   -6.3982   1.7125  6.1168
 TP9  C5    C  C      0  -0.261   -6.6985   1.3412  4.4019
 TP9  C4    C  C      0   0.340   -7.5178   2.1480  3.6851
 TP9  CM4   C  CH3    0  -0.742   -7.9543   1.8054  2.2879
 TP9  C6    C  CH2    0  -0.508   -6.1341   0.0326  3.9315
 TP9  C7    C  CH2    0  -0.140   -6.9385  -1.1616  4.4184
 TP9  O7    O  O2     0  -0.599   -8.2571  -1.0686  3.9138
 TP9  PA    P  P      0   1.375   -9.3069  -2.2984  4.1591
 TP9  O1A   O  OP    -1  -0.793  -10.5550  -1.9447  3.4204
 TP9  O2A   O  O      0  -0.805   -8.6098  -3.6062  3.9415
 TP9  O3A   O  O2     0  -0.756   -9.5410  -2.1403  5.7841
 TP9  PB    P  P      0   1.357  -11.0002  -2.0850  6.5308
 TP9  O1B   O  OH1    0  -0.787  -10.4724  -2.1323  8.0788
 TP9  O2B   O  OP    -1  -0.786  -11.6533  -0.7534  6.2710
 TP9  O3B   O  O      0  -0.799  -11.7449  -3.3576  6.2961
 TP9  H1B   H  HOH1   0   0.463  -10.2138  -1.2650  8.4089
 TP9  H71   H  HCH2   0   0.196   -6.9424  -1.1722  5.5149
 TP9  H72   H  HCH2   0   0.211   -6.4571  -2.0860  4.0840
 TP9  H61   H  HCH2   0   0.239   -6.0576  -0.0066  2.8432
 TP9  H62   H  HCH2   0   0.239   -5.1124  -0.0884  4.3035
 TP9  HS1   H  HSH1   0   0.219   -5.1733   2.2537  6.0205
 TP9  HN3   H  HNH1   0   0.372   -7.6728   3.5609  5.1059
 TP9  H7'1  H  HCH2   0   0.267   -9.7014   3.3697  2.9880
 TP9  H7'2  H  HCH2   0   0.253   -9.1613   4.9461  3.4997
 TP9  H6'   H  HCR6   0   0.254  -10.3271   6.0177  5.1300
 TP9  H4'1  H  HNH2   0   0.431  -10.8537   0.6676  5.6288
 TP9  H4'2  H  HNH2   0   0.412   -9.6054   1.3180  4.6189
 TP9  HM21  H  HCH3   0   0.247  -13.9823   3.4192  7.7417
 TP9  HM22  H  HCH3   0   0.251  -12.7253   3.6413  8.9443
 TP9  HM23  H  HCH3   0   0.240  -13.4723   5.0553  8.1933
 TP9  HM41  H  HCH3   0   0.252   -7.9349   2.6897  1.6512
 TP9  HM42  H  HCH3   0   0.265   -7.3214   1.0497  1.8365
 TP9  HM43  H  HCH3   0   0.252   -8.9716   1.4102  2.2720

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
 TP9  N1'  C6'   aromatic  1.337  0.020  1.337
 TP9  N1'  C2'   aromatic  1.326  0.020  1.326
 TP9  C2'  N3'   aromatic  1.325  0.020  1.325
 TP9  C2'  CM2   single    1.498  0.020  1.498
 TP9  CM2  HM21  single    0.970  0.020  1.090
 TP9  CM2  HM22  single    0.970  0.020  1.090
 TP9  CM2  HM23  single    0.970  0.020  1.090
 TP9  N3'  C4'   aromatic  1.339  0.020  1.339
 TP9  C4'  C5'   aromatic  1.422  0.020  1.422
 TP9  C4'  N4'   single    1.335  0.020  1.335
 TP9  N4'  H4'1  single    0.860  0.020  1.020
 TP9  N4'  H4'2  single    0.860  0.020  1.020
 TP9  C5'  C7'   single    1.501  0.020  1.501
 TP9  C5'  C6'   aromatic  1.372  0.020  1.372
 TP9  C6'  H6'   single    0.930  0.020  1.080
 TP9  C7'  N3    single    1.452  0.020  1.452
 TP9  C7'  H7'1  single    0.970  0.020  1.090
 TP9  C7'  H7'2  single    0.970  0.020  1.090
 TP9  N3   C4    single    1.375  0.020  1.375
 TP9  N3   HN3   single    0.890  0.020  1.040
 TP9  S1   C5    single    1.780  0.020  1.780
 TP9  S1   HS1   single    1.200  0.020  1.300
 TP9  C5   C6    single    1.501  0.020  1.501
 TP9  C5   C4    double    1.355  0.020  1.355
 TP9  C4   CM4   single    1.503  0.020  1.503
 TP9  CM4  HM41  single    0.970  0.020  1.090
 TP9  CM4  HM42  single    0.970  0.020  1.090
 TP9  CM4  HM43  single    0.970  0.020  1.090
 TP9  C6   C7    single    1.520  0.020  1.520
 TP9  C6   H61   single    0.970  0.020  1.090
 TP9  C6   H62   single    0.970  0.020  1.090
 TP9  C7   O7    single    1.415  0.020  1.415
 TP9  C7   H71   single    0.970  0.020  1.090
 TP9  C7   H72   single    0.970  0.020  1.090
 TP9  O7   PA    single    1.635  0.020  1.635
 TP9  PA   O3A   single    1.649  0.020  1.649
 TP9  PA   O1A   single    1.493  0.020  1.493
 TP9  PA   O2A   double    1.498  0.020  1.498
 TP9  O3A  PB    single    1.640  0.020  1.640
 TP9  PB   O1B   single    1.636  0.020  1.636
 TP9  PB   O2B   single    1.506  0.020  1.506
 TP9  PB   O3B   double    1.493  0.020  1.493
 TP9  O1B  H1B   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
 TP9  C6'   N1'  C2'   115.21  3.000
 TP9  N3'   C2'  CM2   116.35  3.000
 TP9  CM2   C2'  N1'   117.70  3.000
 TP9  N3'   C2'  N1'   125.94  3.000
 TP9  HM23  CM2  HM22  108.37  3.000
 TP9  HM23  CM2  HM21  108.95  3.000
 TP9  HM22  CM2  HM21  107.02  3.000
 TP9  HM23  CM2  C2'   111.21  3.000
 TP9  HM22  CM2  C2'   110.48  3.000
 TP9  HM21  CM2  C2'   110.68  3.000
 TP9  C4'   N3'  C2'   118.85  3.000
 TP9  C5'   C4'  N4'   123.37  3.000
 TP9  N4'   C4'  N3'   116.84  3.000
 TP9  C5'   C4'  N3'   119.77  3.000
 TP9  H4'2  N4'  H4'1  116.73  3.000
 TP9  H4'2  N4'  C4'   122.08  3.000
 TP9  H4'1  N4'  C4'   119.73  3.000
 TP9  C7'   C5'  C6'   120.63  3.000
 TP9  C6'   C5'  C4'   115.37  3.000
 TP9  C7'   C5'  C4'   123.97  3.000
 TP9  H6'   C6'  C5'   119.04  3.000
 TP9  H6'   C6'  N1'   116.17  3.000
 TP9  C5'   C6'  N1'   124.79  3.000
 TP9  H7'2  C7'  H7'1  105.85  3.000
 TP9  H7'2  C7'  N3    109.87  3.000
 TP9  H7'1  C7'  N3    109.49  3.000
 TP9  H7'2  C7'  C5'   107.98  3.000
 TP9  H7'1  C7'  C5'   109.78  3.000
 TP9  N3    C7'  C5'   113.57  3.000
 TP9  HN3   N3   C4    113.89  3.000
 TP9  HN3   N3   C7'   113.75  3.000
 TP9  C4    N3   C7'   123.86  3.000
 TP9  HS1   S1   C5     99.72  3.000
 TP9  C6    C5   C4    125.50  3.000
 TP9  C4    C5   S1    119.17  3.000
 TP9  C6    C5   S1    114.86  3.000
 TP9  CM4   C4   C5    122.11  3.000
 TP9  CM4   C4   N3    115.26  3.000
 TP9  C5    C4   N3    122.60  3.000
 TP9  HM43  CM4  HM42  106.60  3.000
 TP9  HM43  CM4  HM41  107.58  3.000
 TP9  HM42  CM4  HM41  108.18  3.000
 TP9  HM43  CM4  C4    111.51  3.000
 TP9  HM42  CM4  C4    112.10  3.000
 TP9  HM41  CM4  C4    110.66  3.000
 TP9  H62   C6   H61   105.64  3.000
 TP9  H62   C6   C7    107.37  3.000
 TP9  H61   C6   C7    109.16  3.000
 TP9  H62   C6   C5    109.94  3.000
 TP9  H61   C6   C5    111.72  3.000
 TP9  C7    C6   C5    112.68  3.000
 TP9  H72   C7   H71   107.39  3.000
 TP9  H72   C7   O7    110.88  3.000
 TP9  H71   C7   O7    110.73  3.000
 TP9  H72   C7   C6    109.44  3.000
 TP9  H71   C7   C6    109.26  3.000
 TP9  O7    C7   C6    109.11  3.000
 TP9  PA    O7   C7    119.69  3.000
 TP9  O3A   PA   O2A   107.03  3.000
 TP9  O2A   PA   O1A   121.61  3.000
 TP9  O3A   PA   O1A   110.25  3.000
 TP9  O2A   PA   O7    109.63  3.000
 TP9  O1A   PA   O7    106.52  3.000
 TP9  O3A   PA   O7     99.60  3.000
 TP9  PB    O3A  PA    125.31  3.000
 TP9  O3B   PB   O2B   120.69  3.000
 TP9  O3B   PB   O1B   106.56  3.000
 TP9  O2B   PB   O1B   109.19  3.000
 TP9  O3B   PB   O3A   110.09  3.000
 TP9  O2B   PB   O3A   109.70  3.000
 TP9  O1B   PB   O3A    98.20  3.000
 TP9  H1B   O1B  PB    112.62  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
 TP9  CONST_01  C4'   C5'  C6'  N1'     0.00   0.0  0
 TP9  CONST_02  C4'   N3'  C2'  N1'     0.00   0.0  0
 TP9  CONST_03  C5'   C6'  N1'  C2'     0.00   0.0  0
 TP9  CONST_04  C5'   C4'  N3'  C2'     0.00   0.0  0
 TP9  CONST_05  C6'   N1'  C2'  N3'     0.00   0.0  0
 TP9  CONST_06  C6'   C5'  C4'  N3'     0.00   0.0  0
 TP9  CONST_07  C7'   C5'  C6'  N1'   180.00   0.0  0
 TP9  CONST_08  N4'   C4'  N3'  C2'   180.00   0.0  0
 TP9  CONST_09  C6'   N1'  C2'  CM2   180.00   0.0  0
 TP9  CONST_10  C4'   N3'  C2'  CM2   180.00   0.0  0
 TP9  CONST_11  C7'   C5'  C4'  N3'   180.00   0.0  0
 TP9  CONST_12  C6'   C5'  C4'  N4'   180.00   0.0  0
 TP9  CONST_13  H6'   C6'  N1'  C2'   180.00   0.0  0
 TP9  CONST_14  H4'1  N4'  C4'  N3'     0.00   0.0  0
 TP9  CONST_15  H4'2  N4'  C4'  N3'   180.00   0.0  0
 TP9  Var_01    N3    C7'  C5'  C4'   -66.68  30.0  2
 TP9  Var_02    HM21  CM2  C2'  N1'   129.84  30.0  2
 TP9  Var_03    C4    N3   C7'  C5'   109.50  30.0  3
 TP9  Var_04    S1    C5   C4   N3      9.65   0.0  2
 TP9  Var_05    C5    C4   N3   C7'  -147.58  30.0  2
 TP9  Var_06    C7    C6   C5   S1     74.94  30.0  3
 TP9  Var_07    O7    C7   C6   C5     61.03  30.0  3
 TP9  Var_08    O3A   PA   O7   C7     69.82  30.0  3
 TP9  Var_09    O1B   PB   O3A  PA    172.67  30.0  3
 TP9  Var_10    HM41  CM4  C4   N3     39.75  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
 TP9  plan-1  N1'   0.020
 TP9  plan-1  C2'   0.020
 TP9  plan-1  CM2   0.020
 TP9  plan-1  N3'   0.020
 TP9  plan-1  C4'   0.020
 TP9  plan-1  N4'   0.020
 TP9  plan-1  C5'   0.020
 TP9  plan-1  C6'   0.020
 TP9  plan-1  C7'   0.020
 TP9  plan-1  H6'   0.020
 TP9  plan-2  C4'   0.020
 TP9  plan-2  N4'   0.020
 TP9  plan-2  H4'1  0.020
 TP9  plan-2  H4'2  0.020
 TP9  plan-3  N3    0.020
 TP9  plan-3  S1    0.020
 TP9  plan-3  C5    0.020
 TP9  plan-3  C4    0.020
 TP9  plan-3  CM4   0.020
 TP9  plan-3  C6    0.020

