# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri May  8 06:54:32 2020
#   Inital geometry file: a 69 line input string
#   Ligand name: [(3~{R})-4-azanyl-2,2-dimethyl-3-oxidanyl-4-oxidanylidene-butyl] dihydrogen phosphate
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC(C)(CO[P](O)(O)=O)[C@@H](O)C(N)=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
 J8T  J8T  '[(3~{R})-4-azanyl-2,2-dimethyl-3-oxidanyl-4-oxidanylidene-butyl] dihydrogen phosphate'  ligand  28  14  .  2021-08-12  2021-08-12  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_J8T
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
 J8T  C4   C  CH2   0  -0.154   0.0099  -0.1617   0.3777
 J8T  C5   C  CT    0  -0.163  -1.0783  -0.9269  -0.3731
 J8T  C6   C  CH3   0  -0.670  -1.0024  -0.6207  -1.8701
 J8T  C7   C  CH3   0  -0.642  -0.9127  -2.4355  -0.1628
 J8T  O3   O  OH1   0  -0.742   2.5126   1.5289  -0.7626
 J8T  O4   O  O     0  -0.712   2.7858   0.7167   1.5968
 J8T  O5   O  O2    0  -0.588   1.2900  -0.6191  -0.0800
 J8T  P1   P  P     0   1.452   2.5863   0.2596   0.2088
 J8T  O6   O  OH1   0  -0.662  -2.6224  -0.8686   1.5379
 J8T  O7   O  O     0  -0.491  -2.4988   1.7372   0.9478
 J8T  C8   C  CH1   0  -0.032  -2.4725  -0.5253   0.1878
 J8T  C9   C  C     0   0.486  -2.7826   0.9667   0.0377
 J8T  N2   N  NH2   0  -0.788  -3.3709   1.3424  -1.0972
 J8T  H1   H  HCH2  0   0.244  -0.0867   0.9129   0.1995
 J8T  H2   H  HCH2  0   0.247  -0.0605  -0.3379   1.4535
 J8T  H3   H  HCH3  0   0.248  -0.0908  -1.0346  -2.3005
 J8T  H4   H  HCH3  0   0.235  -1.8429  -1.0714  -2.4028
 J8T  H5   H  HCH3  0   0.235  -1.0062   0.4497  -2.0795
 J8T  H6   H  HCH3  0   0.236  -0.8990  -2.7039   0.8933
 J8T  H7   H  HCH3  0   0.230  -1.7340  -2.9786  -0.6353
 J8T  H8   H  HCH3  0   0.239   0.0126  -2.7937  -0.6128
 J8T  H9   H  HOH1  0   0.493   2.4425   1.3332  -1.7064
 J8T  H11  H  HOH1  0   0.445  -2.3815  -0.0928   2.0612
 J8T  H12  H  HCH1  0   0.259  -3.2119  -1.0992  -0.3829
 J8T  H13  H  HNH2  0   0.409  -3.5690   2.3138  -1.2780
 J8T  H14  H  HNH2  0   0.414  -3.6191   0.6783  -1.8103
 J8T  O1   O  OH1   0  -0.731   3.6477  -0.7612  -0.4008
 J8T  H10  H  HOH1  0   0.504   4.5685  -0.5083  -0.2510

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
 J8T  O3  P1   single  1.600  0.020  1.600
 J8T  P1  O4   double  1.475  0.020  1.475
 J8T  P1  O5   single  1.592  0.020  1.592
 J8T  O5  C4   single  1.434  0.020  1.434
 J8T  C4  C5   single  1.528  0.020  1.528
 J8T  C7  C5   single  1.532  0.020  1.532
 J8T  C5  C8   single  1.556  0.020  1.556
 J8T  C5  C6   single  1.530  0.020  1.530
 J8T  C8  O6   single  1.401  0.020  1.401
 J8T  C8  C9   single  1.531  0.020  1.531
 J8T  O7  C9   double  1.226  0.020  1.226
 J8T  C9  N2   single  1.332  0.020  1.332
 J8T  C4  H1   single  0.970  0.020  1.090
 J8T  C4  H2   single  0.970  0.020  1.090
 J8T  C6  H3   single  0.970  0.020  1.090
 J8T  C6  H4   single  0.970  0.020  1.090
 J8T  C6  H5   single  0.970  0.020  1.090
 J8T  C7  H6   single  0.970  0.020  1.090
 J8T  C7  H7   single  0.970  0.020  1.090
 J8T  C7  H8   single  0.970  0.020  1.090
 J8T  O3  H9   single  0.850  0.020  0.980
 J8T  O6  H11  single  0.850  0.020  0.980
 J8T  C8  H12  single  0.970  0.020  1.090
 J8T  N2  H13  single  0.860  0.020  1.020
 J8T  N2  H14  single  0.860  0.020  1.020
 J8T  P1  O1   single  1.594  0.020  1.594
 J8T  O1  H10  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
 J8T  H2   C4  H1   108.26  3.000
 J8T  H2   C4  O5   108.68  3.000
 J8T  H1   C4  O5   109.88  3.000
 J8T  H2   C4  C5   110.94  3.000
 J8T  H1   C4  C5   110.44  3.000
 J8T  O5   C4  C5   108.61  3.000
 J8T  C8   C5  C7   107.55  3.000
 J8T  C8   C5  C6   110.22  3.000
 J8T  C7   C5  C6   109.03  3.000
 J8T  C6   C5  C4   110.20  3.000
 J8T  C8   C5  C4   109.39  3.000
 J8T  C7   C5  C4   110.41  3.000
 J8T  H5   C6  H4   107.97  3.000
 J8T  H5   C6  H3   107.46  3.000
 J8T  H4   C6  H3   107.12  3.000
 J8T  H5   C6  C5   112.59  3.000
 J8T  H4   C6  C5   110.88  3.000
 J8T  H3   C6  C5   110.61  3.000
 J8T  H8   C7  H7   107.25  3.000
 J8T  H8   C7  H6   107.98  3.000
 J8T  H7   C7  H6   107.83  3.000
 J8T  H8   C7  C5   111.02  3.000
 J8T  H7   C7  C5   110.42  3.000
 J8T  H6   C7  C5   112.14  3.000
 J8T  H9   O3  P1   115.82  3.000
 J8T  P1   O5  C4   119.51  3.000
 J8T  O1   P1  O5    96.85  3.000
 J8T  O1   P1  O4   117.93  3.000
 J8T  O5   P1  O4   116.86  3.000
 J8T  O1   P1  O3   107.85  3.000
 J8T  O5   P1  O3   106.87  3.000
 J8T  O4   P1  O3   109.37  3.000
 J8T  H11  O6  C8   107.37  3.000
 J8T  H12  C8  C9   108.81  3.000
 J8T  H12  C8  O6   107.53  3.000
 J8T  C9   C8  O6   108.15  3.000
 J8T  H12  C8  C5   106.36  3.000
 J8T  C9   C8  C5   113.43  3.000
 J8T  O6   C8  C5   112.34  3.000
 J8T  N2   C9  C8   116.59  3.000
 J8T  N2   C9  O7   123.88  3.000
 J8T  C8   C9  O7   119.52  3.000
 J8T  H14  N2  H13  117.45  3.000
 J8T  H14  N2  C9   121.79  3.000
 J8T  H13  N2  C9   120.75  3.000
 J8T  H10  O1  P1   114.05  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
 J8T  CONST_01  H13  N2  C9  O7    0.00   0.0  0
 J8T  CONST_02  H14  N2  C9  O7  180.00   0.0  0
 J8T  Var_01    O3   P1  O5  C4  -73.02  30.0  1
 J8T  Var_02    O5   C4  C5  C6  -63.06  30.0  1
 J8T  Var_03    H6   C7  C5  C4   55.37  30.0  3
 J8T  Var_04    H3   C6  C5  C4   67.72  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
 J8T  chir_01  C8  C5  O6  C9  negativ

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
 J8T  plan-1  O7   0.020
 J8T  plan-1  C8   0.020
 J8T  plan-1  C9   0.020
 J8T  plan-1  N2   0.020
 J8T  plan-1  H13  0.020
 J8T  plan-1  H14  0.020

