# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu May  7 13:43:00 2020
#   Inital geometry file: a 80 line input string
#   Ligand name: (1R)-1-(phenoxymethyl)propyl (R)-methylphosphonochloridoate
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC[C@H](COc1ccccc1)O[P@](C)(Cl)=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
 INK  INK  '(1R)-1-(phenoxymethyl)propyl (R)-methylphosphonochloridoate'  ligand  32  16  .  2021-08-11  2021-08-11  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_INK
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
 INK  P     P   P     0   1.209  -1.0684   0.0562   1.7672
 INK  CL    CL  CL    0  -0.277  -1.0470   0.2314   3.8197
 INK  C1    C   CH3   0  -0.917  -2.1591   1.3771   1.2614
 INK  O1    O   O     0  -0.664  -1.4344  -1.3222   1.3824
 INK  O2    O   O2    0  -0.581   0.3776   0.5823   1.3576
 INK  C2    C   CH1   0  -0.015   1.4365  -0.2755   0.8819
 INK  C3    C   CH2   0  -0.439   2.7256   0.0857   1.5927
 INK  C4    C   CH3   0  -0.670   2.6638  -0.1163   3.1002
 INK  C5    C   CH2   0  -0.165   1.5353  -0.0674  -0.6148
 INK  O3    O   O2    0  -0.476   0.3049  -0.4681  -1.1757
 INK  C6    C   CR16  0  -0.241   0.5305   0.6711  -4.6555
 INK  C7    C   CR16  0  -0.281  -0.7640   0.4087  -5.0747
 INK  C8    C   CR16  0  -0.241  -1.6688  -0.1427  -4.1723
 INK  C9    C   CR16  0  -0.345  -1.2859  -0.4214  -2.8722
 INK  C10   C   CR6   0   0.389   0.0197  -0.1540  -2.4559
 INK  C11   C   CR16  0  -0.376   0.9331   0.3935  -3.3527
 INK  HC11  H   HCH3  0   0.294  -3.1527   1.2019   1.6694
 INK  HC12  H   HCH3  0   0.296  -1.7936   2.3432   1.6025
 INK  HC13  H   HCH3  0   0.289  -2.2206   1.3807   0.1730
 INK  HC2   H   HCH1  0   0.257   1.1844  -1.3207   1.0875
 INK  HC31  H   HCH2  0   0.238   2.9984   1.1190   1.3602
 INK  HC32  H   HCH2  0   0.243   3.5129  -0.5426   1.1688
 INK  HC41  H   HCH3  0   0.238   3.6570  -0.0164   3.5369
 INK  HC42  H   HCH3  0   0.229   2.0169   0.6163   3.5803
 INK  HC43  H   HCH3  0   0.224   2.2891  -1.1097   3.3521
 INK  HC51  H   HCH2  0   0.234   1.7441   0.9868  -0.8293
 INK  HC52  H   HCH2  0   0.239   2.3668  -0.6632  -1.0071
 INK  HC7   H   HCR6  0   0.253  -1.0658   0.6280  -6.0901
 INK  HC8   H   HCR6  0   0.258  -2.6844  -0.3546  -4.4812
 INK  HC9   H   HCR6  0   0.262  -1.9895  -0.8466  -2.1667
 INK  H11   H   HCR6  0   0.277   1.9536   0.6051  -3.0625
 INK  HC6   H   HCR6  0   0.259   1.2487   1.0955  -5.3456

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
 INK  P    CL    single    2.060  0.020  2.060
 INK  P    C1    single    1.786  0.020  1.786
 INK  P    O1    double    1.477  0.020  1.477
 INK  P    O2    single    1.592  0.020  1.592
 INK  C1   HC11  single    0.970  0.020  1.090
 INK  C1   HC12  single    0.970  0.020  1.090
 INK  C1   HC13  single    0.970  0.020  1.090
 INK  O2   C2    single    1.443  0.020  1.443
 INK  C2   C3    single    1.516  0.020  1.516
 INK  C2   C5    single    1.514  0.020  1.514
 INK  C2   HC2   single    0.970  0.020  1.090
 INK  C3   C4    single    1.522  0.020  1.522
 INK  C3   HC31  single    0.970  0.020  1.090
 INK  C3   HC32  single    0.970  0.020  1.090
 INK  C4   HC41  single    0.970  0.020  1.090
 INK  C4   HC42  single    0.970  0.020  1.090
 INK  C4   HC43  single    0.970  0.020  1.090
 INK  C5   O3    single    1.410  0.020  1.410
 INK  C5   HC51  single    0.970  0.020  1.090
 INK  C5   HC52  single    0.970  0.020  1.090
 INK  O3   C10   single    1.349  0.020  1.349
 INK  C6   C7    aromatic  1.386  0.020  1.386
 INK  C6   C11   aromatic  1.392  0.020  1.392
 INK  C6   HC6   single    0.930  0.020  1.080
 INK  C7   C8    aromatic  1.392  0.020  1.392
 INK  C7   HC7   single    0.930  0.020  1.080
 INK  C8   C9    aromatic  1.384  0.020  1.384
 INK  C8   HC8   single    0.930  0.020  1.080
 INK  C9   C10   aromatic  1.396  0.020  1.396
 INK  C9   HC9   single    0.930  0.020  1.080
 INK  C10  C11   aromatic  1.392  0.020  1.392
 INK  C11  H11   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
 INK  O2    P    O1    117.80  3.000
 INK  O2    P    C1    103.73  3.000
 INK  O1    P    C1    117.71  3.000
 INK  O2    P    CL    102.64  3.000
 INK  O1    P    CL    109.97  3.000
 INK  C1    P    CL    103.04  3.000
 INK  HC13  C1   HC12  109.21  3.000
 INK  HC13  C1   HC11  108.86  3.000
 INK  HC12  C1   HC11  109.41  3.000
 INK  HC13  C1   P     108.64  3.000
 INK  HC12  C1   P     111.28  3.000
 INK  HC11  C1   P     109.41  3.000
 INK  C2    O2   P     123.69  3.000
 INK  HC2   C2   C5    109.38  3.000
 INK  HC2   C2   C3    109.59  3.000
 INK  C5    C2   C3    112.04  3.000
 INK  HC2   C2   O2    109.67  3.000
 INK  C5    C2   O2    106.98  3.000
 INK  C3    C2   O2    109.14  3.000
 INK  HC32  C3   HC31  106.32  3.000
 INK  HC32  C3   C4    109.70  3.000
 INK  HC31  C3   C4    110.25  3.000
 INK  HC32  C3   C2    107.09  3.000
 INK  HC31  C3   C2    109.72  3.000
 INK  C4    C3   C2    113.47  3.000
 INK  HC43  C4   HC42  107.86  3.000
 INK  HC43  C4   HC41  107.70  3.000
 INK  HC42  C4   HC41  107.65  3.000
 INK  HC43  C4   C3    111.31  3.000
 INK  HC42  C4   C3    111.81  3.000
 INK  HC41  C4   C3    110.35  3.000
 INK  HC52  C5   HC51  107.97  3.000
 INK  HC52  C5   O3    111.42  3.000
 INK  HC51  C5   O3    111.20  3.000
 INK  HC52  C5   C2    109.19  3.000
 INK  HC51  C5   C2    109.76  3.000
 INK  O3    C5   C2    107.29  3.000
 INK  C10   O3   C5    119.73  3.000
 INK  HC6   C6   C11   118.88  3.000
 INK  HC6   C6   C7    120.07  3.000
 INK  C11   C6   C7    121.05  3.000
 INK  HC7   C7   C8    120.50  3.000
 INK  HC7   C7   C6    120.41  3.000
 INK  C8    C7   C6    119.09  3.000
 INK  HC8   C8   C9    119.23  3.000
 INK  HC8   C8   C7    120.16  3.000
 INK  C9    C8   C7    120.60  3.000
 INK  HC9   C9   C10   119.23  3.000
 INK  HC9   C9   C8    120.74  3.000
 INK  C10   C9   C8    120.03  3.000
 INK  C11   C10  C9    119.78  3.000
 INK  C11   C10  O3    124.35  3.000
 INK  C9    C10  O3    115.86  3.000
 INK  H11   C11  C10   121.53  3.000
 INK  H11   C11  C6    119.01  3.000
 INK  C10   C11  C6    119.45  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
 INK  CONST_01  C9    C8   C7   C6      0.00   0.0  0
 INK  CONST_02  C9    C10  C11  C6      0.00   0.0  0
 INK  CONST_03  C10   C11  C6   C7      0.00   0.0  0
 INK  CONST_04  C10   C9   C8   C7      0.00   0.0  0
 INK  CONST_05  C11   C6   C7   C8      0.00   0.0  0
 INK  CONST_06  C11   C10  C9   C8      0.00   0.0  0
 INK  CONST_07  C8    C9   C10  O3    180.00   0.0  0
 INK  CONST_08  C6    C11  C10  O3    180.00   0.0  0
 INK  CONST_09  HC8   C8   C7   C6    180.00   0.0  0
 INK  CONST_10  H11   C11  C6   C7    180.00   0.0  0
 INK  CONST_11  HC9   C9   C8   C7    180.00   0.0  0
 INK  CONST_12  HC6   C6   C7   C8    180.00   0.0  0
 INK  CONST_13  HC7   C7   C8   C9    180.00   0.0  0
 INK  Var_01    C9    C10  O3   C5   -171.33  30.0  2
 INK  Var_02    HC51  C5   O3   C10    47.31  30.0  1
 INK  Var_03    HC11  C1   P    CL    -62.43  30.0  3
 INK  Var_04    HC41  C4   C3   C2    169.86  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
 INK  chir_02  C2  O2  C3  C5  positiv
 INK  chir_03  P   C1  O1  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
 INK  plan-1  O3   0.020
 INK  plan-1  C6   0.020
 INK  plan-1  C7   0.020
 INK  plan-1  C8   0.020
 INK  plan-1  C9   0.020
 INK  plan-1  C10  0.020
 INK  plan-1  C11  0.020
 INK  plan-1  HC7  0.020
 INK  plan-1  HC8  0.020
 INK  plan-1  HC9  0.020
 INK  plan-1  H11  0.020
 INK  plan-1  HC6  0.020

