# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Mar 30 23:48:03 2020
#   Inital geometry file: a 73 line input string
#   Ligand name: dimethyl benzoylphosphoramidate
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CO[P](=O)(NC(=O)c1ccccc1)OC
#
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
 2NX  2NX  'dimethyl benzoylphosphoramidate'  ligand  27  15  .  2021-08-04  2021-08-04  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_2NX
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
 2NX  CAA  C  CH3   0  -0.422   2.3228   2.5215   0.0905
 2NX  OAK  O  O2    0  -0.572   2.4934   1.2093  -0.4573
 2NX  PAO  P  P     0   1.482   2.1242  -0.0581   0.4228
 2NX  OAL  O  O2    0  -0.571   2.5229  -1.1706  -0.6354
 2NX  CAB  C  CH3   0  -0.423   2.3240  -2.5522  -0.3161
 2NX  OAD  O  O     0  -0.695   2.7168  -0.1529   1.7715
 2NX  NAJ  N  NH1   0  -0.867   0.4376  -0.0804   0.5739
 2NX  CAM  C  C     0   0.556  -0.4530   0.0044  -0.4657
 2NX  OAC  O  O     0  -0.439  -0.0796   0.0484  -1.6196
 2NX  CAN  C  CR6   0  -0.029  -1.8976   0.0324  -0.1017
 2NX  CAH  C  CR16  0  -0.261  -2.8227  -0.3022  -1.0900
 2NX  CAF  C  CR16  0  -0.241  -4.1797  -0.2841  -0.8129
 2NX  CAE  C  CR16  0  -0.246  -4.6278   0.0847   0.4495
 2NX  CAG  C  CR16  0  -0.238  -3.7134   0.4339   1.4335
 2NX  CAI  C  CR16  0  -0.291  -2.3538   0.4049   1.1619
 2NX  H1   H  HCH3  0   0.261   2.5932   3.2232  -0.6930
 2NX  H2   H  HCH3  0   0.237   1.2868   2.6991   0.3818
 2NX  H3   H  HCH3  0   0.246   2.9717   2.6773   0.9516
 2NX  H4   H  HCH3  0   0.246   2.9530  -2.8575   0.5195
 2NX  H5   H  HCH3  0   0.239   1.2802  -2.7585  -0.0759
 2NX  H6   H  HCH3  0   0.261   2.6011  -3.1204  -1.1993
 2NX  H7   H  HNH1  0   0.435   0.0831  -0.2100   1.5110
 2NX  H8   H  HCR6  0   0.266  -2.4796  -0.5878  -2.0751
 2NX  H9   H  HCR6  0   0.267  -4.8889  -0.5561  -1.5833
 2NX  H10  H  HCR6  0   0.269  -5.6882   0.1035   0.6647
 2NX  H11  H  HCR6  0   0.270  -4.0565   0.7348   2.4141
 2NX  H12  H  HCR6  0   0.262  -1.6670   0.7012   1.9448

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
 2NX  CAA  OAK  single    1.432  0.020  1.432
 2NX  OAK  PAO  single    1.586  0.020  1.586
 2NX  OAD  PAO  double    1.476  0.020  1.476
 2NX  PAO  NAJ  single    1.694  0.020  1.694
 2NX  PAO  OAL  single    1.586  0.020  1.586
 2NX  NAJ  CAM  single    1.371  0.020  1.371
 2NX  OAL  CAB  single    1.432  0.020  1.432
 2NX  CAI  CAG  aromatic  1.387  0.020  1.387
 2NX  CAI  CAN  aromatic  1.394  0.020  1.394
 2NX  CAM  OAC  double    1.214  0.020  1.214
 2NX  CAM  CAN  single    1.490  0.020  1.490
 2NX  CAG  CAE  aromatic  1.388  0.020  1.388
 2NX  CAN  CAH  aromatic  1.394  0.020  1.394
 2NX  CAE  CAF  aromatic  1.389  0.020  1.389
 2NX  CAH  CAF  aromatic  1.385  0.020  1.385
 2NX  CAA  H1   single    0.970  0.020  1.090
 2NX  CAA  H2   single    0.970  0.020  1.090
 2NX  CAA  H3   single    0.970  0.020  1.090
 2NX  CAB  H4   single    0.970  0.020  1.090
 2NX  CAB  H5   single    0.970  0.020  1.090
 2NX  CAB  H6   single    0.970  0.020  1.090
 2NX  NAJ  H7   single    0.860  0.020  1.020
 2NX  CAH  H8   single    0.930  0.020  1.080
 2NX  CAF  H9   single    0.930  0.020  1.080
 2NX  CAE  H10  single    0.930  0.020  1.080
 2NX  CAG  H11  single    0.930  0.020  1.080
 2NX  CAI  H12  single    0.930  0.020  1.080

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
 2NX  H3   CAA  H2   109.35  3.000
 2NX  H3   CAA  H1   109.24  3.000
 2NX  H2   CAA  H1   108.90  3.000
 2NX  H3   CAA  OAK  111.25  3.000
 2NX  H2   CAA  OAK  111.37  3.000
 2NX  H1   CAA  OAK  106.64  3.000
 2NX  PAO  OAK  CAA  119.48  3.000
 2NX  NAJ  PAO  OAD  108.51  3.000
 2NX  NAJ  PAO  OAL  107.49  3.000
 2NX  OAD  PAO  OAL  117.62  3.000
 2NX  OAL  PAO  OAK   97.57  3.000
 2NX  NAJ  PAO  OAK  106.96  3.000
 2NX  OAD  PAO  OAK  117.69  3.000
 2NX  CAB  OAL  PAO  119.54  3.000
 2NX  H6   CAB  H5   108.93  3.000
 2NX  H6   CAB  H4   109.26  3.000
 2NX  H5   CAB  H4   109.30  3.000
 2NX  H6   CAB  OAL  106.74  3.000
 2NX  H5   CAB  OAL  111.38  3.000
 2NX  H4   CAB  OAL  111.17  3.000
 2NX  H7   NAJ  CAM  118.89  3.000
 2NX  H7   NAJ  PAO  115.72  3.000
 2NX  CAM  NAJ  PAO  125.33  3.000
 2NX  CAN  CAM  OAC  121.99  3.000
 2NX  CAN  CAM  NAJ  116.46  3.000
 2NX  OAC  CAM  NAJ  121.54  3.000
 2NX  CAI  CAN  CAH  119.30  3.000
 2NX  CAH  CAN  CAM  117.75  3.000
 2NX  CAI  CAN  CAM  122.93  3.000
 2NX  H8   CAH  CAF  119.77  3.000
 2NX  H8   CAH  CAN  119.89  3.000
 2NX  CAF  CAH  CAN  120.33  3.000
 2NX  H9   CAF  CAE  120.15  3.000
 2NX  H9   CAF  CAH  119.77  3.000
 2NX  CAE  CAF  CAH  120.08  3.000
 2NX  H10  CAE  CAG  120.01  3.000
 2NX  H10  CAE  CAF  120.09  3.000
 2NX  CAG  CAE  CAF  119.90  3.000
 2NX  H11  CAG  CAI  119.63  3.000
 2NX  H11  CAG  CAE  120.25  3.000
 2NX  CAI  CAG  CAE  120.11  3.000
 2NX  H12  CAI  CAG  118.32  3.000
 2NX  H12  CAI  CAN  121.40  3.000
 2NX  CAG  CAI  CAN  120.26  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
 2NX  CONST_01  CAE  CAG  CAI  CAN     0.00   0.0  0
 2NX  CONST_02  CAE  CAF  CAH  CAN     0.00   0.0  0
 2NX  CONST_03  CAG  CAI  CAN  CAH     0.00   0.0  0
 2NX  CONST_04  CAG  CAE  CAF  CAH     0.00   0.0  0
 2NX  CONST_05  CAI  CAG  CAE  CAF     0.00   0.0  0
 2NX  CONST_06  CAI  CAN  CAH  CAF     0.00   0.0  0
 2NX  CONST_07  CAG  CAI  CAN  CAM   180.00   0.0  0
 2NX  CONST_08  CAF  CAH  CAN  CAM   180.00   0.0  0
 2NX  CONST_09  H11  CAG  CAI  CAN   180.00   0.0  0
 2NX  CONST_10  H9   CAF  CAH  CAN   180.00   0.0  0
 2NX  CONST_11  H12  CAI  CAN  CAH   180.00   0.0  0
 2NX  CONST_12  H10  CAE  CAF  CAH   180.00   0.0  0
 2NX  CONST_13  H8   CAH  CAF  CAE   180.00   0.0  0
 2NX  CONST_14  CAN  CAM  NAJ  PAO   180.00   0.0  0
 2NX  CONST_15  H7   NAJ  CAM  CAN     0.00   0.0  0
 2NX  CONST_16  OAC  CAM  NAJ  PAO     0.00   0.0  0
 2NX  Var_01    CAI  CAN  CAM  NAJ    21.26  30.0  2
 2NX  Var_02    OAD  PAO  OAK  CAA   -52.29  30.0  3
 2NX  Var_03    CAM  NAJ  PAO  OAK    51.34  30.0  3
 2NX  Var_04    H1   CAA  OAK  PAO  -177.62  30.0  3
 2NX  Var_05    H4   CAB  OAL  PAO   -64.59  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
 2NX  plan-1  CAM  0.020
 2NX  plan-1  CAN  0.020
 2NX  plan-1  CAH  0.020
 2NX  plan-1  CAF  0.020
 2NX  plan-1  CAE  0.020
 2NX  plan-1  CAG  0.020
 2NX  plan-1  CAI  0.020
 2NX  plan-1  H8   0.020
 2NX  plan-1  H9   0.020
 2NX  plan-1  H10  0.020
 2NX  plan-1  H11  0.020
 2NX  plan-1  H12  0.020
 2NX  plan-2  PAO  0.020
 2NX  plan-2  NAJ  0.020
 2NX  plan-2  CAM  0.020
 2NX  plan-2  OAC  0.020
 2NX  plan-2  CAN  0.020
 2NX  plan-2  H7   0.020

