# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Jul 21 02:29:51 2021
#   Inital geometry file: a 87 line input string
#   Ligand name: [(1R)-3-[acetyl(hydroxy)amino]-1-(3,4-dichlorophenyl)propyl]phosphonic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC(=O)N(O)CC[C@H](c1ccc(Cl)c(Cl)c1)[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
 DCV  DCV  '[(1R)-3-[acetyl(hydroxy)amino]-1-(3,4-dichlorophenyl)propyl]phosphonic acid'  ligand  34  20  .  2022-11-17  2022-11-17
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_DCV
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
 DCV  C1    C   C     0   0.491  39.0180  -20.9625   9.3150
 DCV  N1    N   NT    0  -0.168  37.6915  -21.1161   9.1526
 DCV  O1    O   O     0  -0.513  39.7853  -21.3031   8.4174
 DCV  CL1   CL  CL    0  -0.096  35.6811  -14.2478   7.1669
 DCV  C2    C   CH2   0  -0.310  36.6387  -20.5107   9.9276
 DCV  O2    O   OH1   0  -0.563  37.2663  -21.5556   7.9174
 DCV  CL2   CL  CL    0  -0.096  32.5499  -13.9790   6.9924
 DCV  C3    C   CH2   0  -0.451  36.2478  -19.1344   9.3910
 DCV  C4    C   CH1   0  -0.632  35.0342  -18.5100  10.0929
 DCV  C5    C   CH3   0  -0.800  39.4835  -20.3912  10.6271
 DCV  PA1   P   P     0   1.395  35.3121  -17.8866  11.7825
 DCV  CAC   C   CR6   0   0.145  34.4280  -17.3723   9.3035
 DCV  CAD   C   CR16  0  -0.298  33.0454  -17.2383   9.2243
 DCV  CAE   C   CR16  0  -0.249  35.2276  -16.4322   8.6646
 DCV  CAF   C   CR16  0  -0.202  32.4706  -16.2000   8.5127
 DCV  CAG   C   CR6   0   0.020  34.6565  -15.3894   7.9513
 DCV  CAH   C   CR6   0  -0.019  33.2745  -15.2679   7.8744
 DCV  OP1   O   OH1   0  -0.744  36.6577  -17.0341  11.5818
 DCV  OP2   O   OH1   0  -0.744  35.7456  -19.1964  12.6088
 DCV  OP3   O   O     0  -0.703  34.1736  -17.1494  12.3830
 DCV  H2    H   HCH2  0   0.276  35.7793  -21.1843   9.9180
 DCV  H2A   H   HCH2  0   0.276  36.9784  -20.4663  10.9584
 DCV  HO2   H   HOH1  0   0.468  38.0810  -21.5814   7.3858
 DCV  H3    H   HCH2  0   0.256  37.1118  -18.4682   9.4320
 DCV  H3A   H   HCH2  0   0.273  35.9874  -19.2420   8.3363
 DCV  H4    H   HCH1  0   0.323  34.2611  -19.2789  10.2033
 DCV  H5    H   HCH3  0   0.280  40.5697  -20.3611  10.6330
 DCV  H5A   H   HCH3  0   0.267  39.1133  -19.3767  10.7832
 DCV  H5B   H   HCH3  0   0.277  39.1509  -20.9978  11.4696
 DCV  HAD   H   HCR6  0   0.272  32.4037  -17.9585   9.7152
 DCV  HAE   H   HCR6  0   0.285  36.3061  -16.5027   8.7037
 DCV  HAF   H   HCR6  0   0.290  31.3946  -16.1105   8.4522
 DCV  HOP1  H   HOH1  0   0.496  36.8502  -16.4173  12.3016
 DCV  HOP2  H   HOH1  0   0.497  35.4480  -19.1914  13.5288

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
 DCV  O1   C1    double    1.229  0.020  1.229
 DCV  C1   N1    single    1.345  0.020  1.345
 DCV  C1   C5    single    1.505  0.020  1.505
 DCV  O2   N1    single    1.378  0.020  1.378
 DCV  N1   C2    single    1.441  0.020  1.441
 DCV  CL1  CAG   single    1.723  0.020  1.723
 DCV  C3   C2    single    1.528  0.020  1.528
 DCV  C2   H2    single    0.970  0.020  1.090
 DCV  C2   H2A   single    0.970  0.020  1.090
 DCV  O2   HO2   single    0.850  0.020  0.980
 DCV  CL2  CAH   single    1.722  0.020  1.722
 DCV  C3   C4    single    1.535  0.020  1.535
 DCV  C3   H3    single    0.970  0.020  1.090
 DCV  C3   H3A   single    0.970  0.020  1.090
 DCV  CAC  C4    single    1.512  0.020  1.512
 DCV  C4   PA1   single    1.822  0.020  1.822
 DCV  C4   H4    single    0.970  0.020  1.090
 DCV  C5   H5    single    0.970  0.020  1.090
 DCV  C5   H5A   single    0.970  0.020  1.090
 DCV  C5   H5B   single    0.970  0.020  1.090
 DCV  PA1  OP3   double    1.483  0.020  1.483
 DCV  PA1  OP1   single    1.605  0.020  1.605
 DCV  PA1  OP2   single    1.608  0.020  1.608
 DCV  CAE  CAC   aromatic  1.390  0.020  1.390
 DCV  CAD  CAC   aromatic  1.391  0.020  1.391
 DCV  CAF  CAD   aromatic  1.384  0.020  1.384
 DCV  CAD  HAD   single    0.930  0.020  1.080
 DCV  CAG  CAE   aromatic  1.387  0.020  1.387
 DCV  CAE  HAE   single    0.930  0.020  1.080
 DCV  CAH  CAF   aromatic  1.387  0.020  1.387
 DCV  CAF  HAF   single    0.930  0.020  1.080
 DCV  CAH  CAG   aromatic  1.390  0.020  1.390
 DCV  OP1  HOP1  single    0.850  0.020  0.980
 DCV  OP2  HOP2  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
 DCV  C5    C1   O1   123.29  3.000
 DCV  C5    C1   N1   116.98  3.000
 DCV  O1    C1   N1   119.72  3.000
 DCV  O2    N1   C2   112.99  3.000
 DCV  C2    N1   C1   127.42  3.000
 DCV  O2    N1   C1   116.67  3.000
 DCV  H2A   C2   H2   106.24  3.000
 DCV  H2A   C2   C3   112.11  3.000
 DCV  H2    C2   C3   110.56  3.000
 DCV  H2A   C2   N1   107.41  3.000
 DCV  H2    C2   N1   108.14  3.000
 DCV  C3    C2   N1   112.12  3.000
 DCV  HO2   O2   N1   103.87  3.000
 DCV  H3A   C3   H3   106.57  3.000
 DCV  H3A   C3   C4   107.05  3.000
 DCV  H3    C3   C4   111.12  3.000
 DCV  H3A   C3   C2   108.15  3.000
 DCV  H3    C3   C2   109.51  3.000
 DCV  C4    C3   C2   114.09  3.000
 DCV  H4    C4   CAC  107.32  3.000
 DCV  H4    C4   PA1  104.73  3.000
 DCV  CAC   C4   PA1  106.73  3.000
 DCV  H4    C4   C3   108.57  3.000
 DCV  PA1   C4   C3   116.27  3.000
 DCV  CAC   C4   C3   112.61  3.000
 DCV  H5B   C5   H5A  107.66  3.000
 DCV  H5B   C5   H5   108.43  3.000
 DCV  H5A   C5   H5   108.22  3.000
 DCV  H5B   C5   C1   111.61  3.000
 DCV  H5A   C5   C1   111.88  3.000
 DCV  H5    C5   C1   108.93  3.000
 DCV  OP3   PA1  OP2  113.81  3.000
 DCV  OP2   PA1  OP1  105.72  3.000
 DCV  OP3   PA1  OP1  115.47  3.000
 DCV  OP2   PA1  C4   103.82  3.000
 DCV  OP1   PA1  C4   101.16  3.000
 DCV  OP3   PA1  C4   115.36  3.000
 DCV  CAE   CAC  CAD  118.71  3.000
 DCV  CAD   CAC  C4   120.05  3.000
 DCV  CAE   CAC  C4   121.23  3.000
 DCV  HAD   CAD  CAF  119.09  3.000
 DCV  HAD   CAD  CAC  119.95  3.000
 DCV  CAF   CAD  CAC  120.95  3.000
 DCV  HAE   CAE  CAG  118.58  3.000
 DCV  HAE   CAE  CAC  120.87  3.000
 DCV  CAG   CAE  CAC  120.55  3.000
 DCV  HAF   CAF  CAH  119.70  3.000
 DCV  HAF   CAF  CAD  120.28  3.000
 DCV  CAH   CAF  CAD  120.02  3.000
 DCV  CAH   CAG  CAE  120.26  3.000
 DCV  CAH   CAG  CL1  120.55  3.000
 DCV  CAE   CAG  CL1  119.18  3.000
 DCV  CAG   CAH  CAF  119.50  3.000
 DCV  CAG   CAH  CL2  120.82  3.000
 DCV  CAF   CAH  CL2  119.68  3.000
 DCV  HOP1  OP1  PA1  114.35  3.000
 DCV  HOP2  OP2  PA1  113.68  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
 DCV  CONST_01  CAH  CAG  CAE  CAC    0.00   0.0  0
 DCV  CONST_02  CAH  CAF  CAD  CAC    0.00   0.0  0
 DCV  CONST_03  CAG  CAE  CAC  CAD    0.00   0.0  0
 DCV  CONST_04  CAG  CAH  CAF  CAD    0.00   0.0  0
 DCV  CONST_05  CAF  CAD  CAC  CAE    0.00   0.0  0
 DCV  CONST_06  CAF  CAH  CAG  CAE    0.00   0.0  0
 DCV  CONST_07  CAC  CAE  CAG  CL1  180.00   0.0  0
 DCV  CONST_08  CAF  CAH  CAG  CL1  180.00   0.0  0
 DCV  CONST_09  CAD  CAF  CAH  CL2  180.00   0.0  0
 DCV  CONST_10  CAE  CAG  CAH  CL2  180.00   0.0  0
 DCV  CONST_11  CAG  CAE  CAC  C4   180.00   0.0  0
 DCV  CONST_12  CAF  CAD  CAC  C4   180.00   0.0  0
 DCV  CONST_13  HAF  CAF  CAD  CAC  180.00   0.0  0
 DCV  CONST_14  HAE  CAE  CAC  CAD  180.00   0.0  0
 DCV  CONST_15  HAD  CAD  CAC  CAE  180.00   0.0  0
 DCV  CONST_16  O2   N1   C1   O1     0.00   0.0  0
 DCV  CONST_19  C5   C1   N1   O2   180.00   0.0  0
 DCV  Var_01    C3   C2   N1   C1    87.12  30.0  3
 DCV  Var_02    C4   C3   C2   N1   174.06  30.0  2
 DCV  Var_03    H5   C5   C1   N1   177.77  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
 DCV  chir_01  C4  C3  CAC  PA1  positiv

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
 DCV  plan-1  CL1  0.020
 DCV  plan-1  CL2  0.020
 DCV  plan-1  C4   0.020
 DCV  plan-1  CAC  0.020
 DCV  plan-1  CAD  0.020
 DCV  plan-1  CAE  0.020
 DCV  plan-1  CAF  0.020
 DCV  plan-1  CAG  0.020
 DCV  plan-1  CAH  0.020
 DCV  plan-1  HAD  0.020
 DCV  plan-1  HAE  0.020
 DCV  plan-1  HAF  0.020
 DCV  plan-2  C1   0.020
 DCV  plan-2  N1   0.020
 DCV  plan-2  O1   0.020
 DCV  plan-2  C2   0.020
 DCV  plan-2  O2   0.020
 DCV  plan-2  C5   0.020

