# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon May 18 04:26:13 2020
#   Inital geometry file: a 95 line input string
#   Ligand name: 2-{[(S)-hydroxy(4-nitrophenoxy)phosphoryl]oxy}-N,N,N-trimethylethanaminium
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[N+](C)(C)CCO[P@@](O)(=O)Oc1ccc(cc1)[N+]([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
 NCH  NCH  2-{[(S)-hydroxy(4-nitrophenoxy)phosphoryl]oxy}-N,N,N-trimethylethanaminium  ligand  38  20  .  2023-02-16  2023-02-16
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_NCH
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
 NCH  O4   O  O      0  -0.676  -0.3105   0.3900  -2.3176
 NCH  P1   P  P      0   1.466  -0.6153  -0.4246  -1.1325
 NCH  O1   O  OH1    0  -0.720  -0.2320  -1.9461  -1.3793
 NCH  O3   O  O2     0  -0.600   0.1069   0.0060   0.2457
 NCH  O2   O  O2     0  -0.575  -2.1039  -0.3765  -0.5718
 NCH  C1   C  CH2    0  -0.207  -3.2103  -0.2784  -1.4737
 NCH  C2   C  CH2    0  -0.352  -4.4991  -0.5528  -0.7427
 NCH  N1   N  NT     1  -0.386  -4.9979   0.4968   0.2135
 NCH  C3   C  CH3    0  -0.557  -5.1645   1.8105  -0.4663
 NCH  C5   C  CH3    0  -0.541  -4.1001   0.6620   1.3942
 NCH  C4   C  CH3    0  -0.547  -6.3321   0.0355   0.6984
 NCH  C1A  C  CR6    0   0.255   4.2008   0.1190   0.5827
 NCH  N1A  N  N      1   0.331   5.6480   0.1605   0.7155
 NCH  O1N  O  O     -1  -0.376   6.2362   1.0952   0.2251
 NCH  O2N  O  O      0  -0.376   6.1900  -0.7423   1.3082
 NCH  C2A  C  CR16   0  -0.260   3.5546   1.1430  -0.0952
 NCH  C3A  C  CR16   0  -0.304   2.1784   1.1015  -0.2241
 NCH  C4A  C  CR6    0   0.384   1.4763   0.0401   0.3292
 NCH  C5A  C  CR16   0  -0.315   2.1252  -0.9819   1.0063
 NCH  C6A  C  CR16   0  -0.260   3.5011  -0.9426   1.1385
 NCH  HO1  H  HOH1   0   0.506  -0.4692  -2.5768  -0.6845
 NCH  H11  H  HCH2   0   0.291  -3.1467  -1.0457  -2.2484
 NCH  H12  H  HCH2   0   0.281  -3.2078   0.6912  -1.9728
 NCH  H21  H  HCH2   0   0.322  -4.4308  -1.4856  -0.1835
 NCH  H22  H  HCH2   0   0.321  -5.2776  -0.6691  -1.4968
 NCH  H31  H  HCH3   0   0.299  -4.1964   2.2063  -0.7565
 NCH  H32  H  HCH3   0   0.299  -5.7938   1.6853  -1.3435
 NCH  H33  H  HCH3   0   0.302  -5.6372   2.5011   0.2269
 NCH  H51  H  HCH3   0   0.293  -4.5929   1.3183   2.1062
 NCH  H52  H  HCH3   0   0.296  -3.9266  -0.3085   1.8501
 NCH  H53  H  HCH3   0   0.297  -3.1594   1.1057   1.0892
 NCH  H41  H  HCH3   0   0.298  -7.0130  -0.0446  -0.1445
 NCH  H42  H  HCH3   0   0.298  -6.2214  -0.9348   1.1749
 NCH  H43  H  HCH3   0   0.298  -6.7171   0.7558   1.4142
 NCH  H2A  H  HCR6   0   0.308   4.1034   1.9689  -0.5226
 NCH  H3A  H  HCR6   0   0.300   1.6590   1.8979  -0.7384
 NCH  H5A  H  HCR6   0   0.298   1.5613  -1.7981   1.4369
 NCH  H6A  H  HCR6   0   0.308   4.0090  -1.7367   1.6651

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
 NCH  O4   P1   double    1.470  0.020  1.470
 NCH  P1   O1   single    1.588  0.020  1.588
 NCH  P1   O3   single    1.614  0.020  1.614
 NCH  P1   O2   single    1.591  0.020  1.591
 NCH  O1   HO1  single    0.850  0.020  0.980
 NCH  O3   C4A  single    1.372  0.020  1.372
 NCH  O2   C1   single    1.431  0.020  1.431
 NCH  C1   C2   single    1.507  0.020  1.507
 NCH  C1   H11  single    0.970  0.020  1.090
 NCH  C1   H12  single    0.970  0.020  1.090
 NCH  C2   N1   single    1.505  0.020  1.505
 NCH  C2   H21  single    0.970  0.020  1.090
 NCH  C2   H22  single    0.970  0.020  1.090
 NCH  N1   C3   single    1.488  0.020  1.488
 NCH  N1   C5   single    1.492  0.020  1.492
 NCH  N1   C4   single    1.493  0.020  1.493
 NCH  C3   H31  single    0.970  0.020  1.090
 NCH  C3   H32  single    0.970  0.020  1.090
 NCH  C3   H33  single    0.970  0.020  1.090
 NCH  C5   H51  single    0.970  0.020  1.090
 NCH  C5   H52  single    0.970  0.020  1.090
 NCH  C5   H53  single    0.970  0.020  1.090
 NCH  C4   H41  single    0.970  0.020  1.090
 NCH  C4   H42  single    0.970  0.020  1.090
 NCH  C4   H43  single    0.970  0.020  1.090
 NCH  C1A  N1A  single    1.454  0.020  1.454
 NCH  C1A  C2A  aromatic  1.388  0.020  1.388
 NCH  C1A  C6A  aromatic  1.388  0.020  1.388
 NCH  N1A  O1N  single    1.208  0.020  1.208
 NCH  N1A  O2N  double    1.208  0.020  1.208
 NCH  C2A  C3A  aromatic  1.383  0.020  1.383
 NCH  C2A  H2A  single    0.930  0.020  1.080
 NCH  C3A  C4A  aromatic  1.388  0.020  1.388
 NCH  C3A  H3A  single    0.930  0.020  1.080
 NCH  C4A  C5A  aromatic  1.387  0.020  1.387
 NCH  C5A  C6A  aromatic  1.383  0.020  1.383
 NCH  C5A  H5A  single    0.930  0.020  1.080
 NCH  C6A  H6A  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
 NCH  O2   P1   O3    96.29  3.000
 NCH  O2   P1   O1   108.02  3.000
 NCH  O3   P1   O1   106.27  3.000
 NCH  O2   P1   O4   117.47  3.000
 NCH  O3   P1   O4   116.59  3.000
 NCH  O1   P1   O4   110.83  3.000
 NCH  HO1  O1   P1   116.97  3.000
 NCH  C4A  O3   P1   120.33  3.000
 NCH  C1   O2   P1   120.22  3.000
 NCH  H12  C1   H11  107.45  3.000
 NCH  H12  C1   C2   112.70  3.000
 NCH  H11  C1   C2   105.43  3.000
 NCH  H12  C1   O2   110.35  3.000
 NCH  H11  C1   O2   110.73  3.000
 NCH  C2   C1   O2   110.06  3.000
 NCH  H22  C2   H21  107.97  3.000
 NCH  H22  C2   N1   106.10  3.000
 NCH  H21  C2   N1   106.97  3.000
 NCH  H22  C2   C1   107.13  3.000
 NCH  H21  C2   C1   110.56  3.000
 NCH  N1   C2   C1   117.69  3.000
 NCH  C4   N1   C5   108.35  3.000
 NCH  C4   N1   C3   108.73  3.000
 NCH  C5   N1   C3   109.33  3.000
 NCH  C4   N1   C2   106.68  3.000
 NCH  C5   N1   C2   112.36  3.000
 NCH  C3   N1   C2   111.26  3.000
 NCH  H33  C3   H32  109.65  3.000
 NCH  H33  C3   H31  109.07  3.000
 NCH  H32  C3   H31  110.04  3.000
 NCH  H33  C3   N1   108.56  3.000
 NCH  H32  C3   N1   109.37  3.000
 NCH  H31  C3   N1   110.12  3.000
 NCH  H53  C5   H52  110.20  3.000
 NCH  H53  C5   H51  109.31  3.000
 NCH  H52  C5   H51  109.70  3.000
 NCH  H53  C5   N1   110.17  3.000
 NCH  H52  C5   N1   109.22  3.000
 NCH  H51  C5   N1   108.21  3.000
 NCH  H43  C4   H42  109.83  3.000
 NCH  H43  C4   H41  109.76  3.000
 NCH  H42  C4   H41  109.77  3.000
 NCH  H43  C4   N1   109.03  3.000
 NCH  H42  C4   N1   109.11  3.000
 NCH  H41  C4   N1   109.32  3.000
 NCH  C6A  C1A  C2A  121.69  3.000
 NCH  C6A  C1A  N1A  119.16  3.000
 NCH  C2A  C1A  N1A  119.15  3.000
 NCH  O2N  N1A  O1N  123.96  3.000
 NCH  O2N  N1A  C1A  118.03  3.000
 NCH  O1N  N1A  C1A  118.01  3.000
 NCH  H2A  C2A  C3A  119.46  3.000
 NCH  H2A  C2A  C1A  121.40  3.000
 NCH  C3A  C2A  C1A  119.13  3.000
 NCH  H3A  C3A  C4A  120.67  3.000
 NCH  H3A  C3A  C2A  120.03  3.000
 NCH  C4A  C3A  C2A  119.29  3.000
 NCH  C5A  C4A  C3A  121.43  3.000
 NCH  C5A  C4A  O3   118.57  3.000
 NCH  C3A  C4A  O3   119.98  3.000
 NCH  H5A  C5A  C6A  120.15  3.000
 NCH  H5A  C5A  C4A  120.43  3.000
 NCH  C6A  C5A  C4A  119.42  3.000
 NCH  H6A  C6A  C5A  119.58  3.000
 NCH  H6A  C6A  C1A  121.39  3.000
 NCH  C5A  C6A  C1A  119.03  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
 NCH  CONST_01  C4A  C3A  C2A  C1A     0.00   0.0  0
 NCH  CONST_02  C4A  C5A  C6A  C1A     0.00   0.0  0
 NCH  CONST_03  C5A  C6A  C1A  C2A     0.00   0.0  0
 NCH  CONST_04  C5A  C4A  C3A  C2A     0.00   0.0  0
 NCH  CONST_05  C6A  C1A  C2A  C3A     0.00   0.0  0
 NCH  CONST_06  C6A  C5A  C4A  C3A     0.00   0.0  0
 NCH  CONST_07  C2A  C3A  C4A  O3    180.00   0.0  0
 NCH  CONST_08  C6A  C5A  C4A  O3    180.00   0.0  0
 NCH  CONST_09  C3A  C2A  C1A  N1A   180.00   0.0  0
 NCH  CONST_10  C5A  C6A  C1A  N1A   180.00   0.0  0
 NCH  CONST_11  H3A  C3A  C2A  C1A   180.00   0.0  0
 NCH  CONST_12  H5A  C5A  C6A  C1A   180.00   0.0  0
 NCH  CONST_13  H6A  C6A  C1A  C2A   180.00   0.0  0
 NCH  CONST_14  H2A  C2A  C3A  C4A   180.00   0.0  0
 NCH  CONST_15  C2A  C1A  N1A  O1N     0.00   0.0  0
 NCH  CONST_16  C6A  C1A  N1A  O1N   180.00   0.0  0
 NCH  CONST_17  C2A  C1A  N1A  O2N   180.00   0.0  0
 NCH  CONST_18  C6A  C1A  N1A  O2N     0.00   0.0  0
 NCH  Var_01    C3A  C4A  O3   P1     77.46  30.0  2
 NCH  Var_02    C2   C1   O2   P1    167.61  30.0  3
 NCH  Var_03    N1   C2   C1   O2     72.08  30.0  3
 NCH  Var_04    C3   N1   C2   C1     56.55  30.0  3
 NCH  Var_05    H31  C3   N1   C2    -67.43  30.0  3
 NCH  Var_06    H51  C5   N1   C2   -171.61  30.0  3
 NCH  Var_07    H41  C4   N1   C2    -61.48  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
 NCH  chir_01  P1  O1  O3  O2  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
 NCH  plan-1  O3   0.020
 NCH  plan-1  C1A  0.020
 NCH  plan-1  N1A  0.020
 NCH  plan-1  C2A  0.020
 NCH  plan-1  C3A  0.020
 NCH  plan-1  C4A  0.020
 NCH  plan-1  C5A  0.020
 NCH  plan-1  C6A  0.020
 NCH  plan-1  H2A  0.020
 NCH  plan-1  H3A  0.020
 NCH  plan-1  H5A  0.020
 NCH  plan-1  H6A  0.020
 NCH  plan-2  C1A  0.020
 NCH  plan-2  N1A  0.020
 NCH  plan-2  O1N  0.020
 NCH  plan-2  O2N  0.020

