# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Apr 27 00:50:51 2020
#   Inital geometry file: a 115 line input string
#   Ligand name: [(3~{R},4~{R},5~{S})-4-acetamido-5-azanyl-3-pentan-3-yloxy-cyclohexen-1-yl]-methoxy-phosphinic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCC(CC)O[C@@H]1C=C(C[C@H](N)[C@H]1NC(C)=O)[P](O)(=O)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
 EEW  EEW  '[(3~{R},4~{R},5~{S})-4-acetamido-5-azanyl-3-pentan-3-yloxy-cyclohexen-1-yl]-methoxy-phosphinic acid'  ligand  48  22  .  2021-08-08  2021-08-08  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_EEW
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
 EEW  C4   C  CH1    0  -0.084   0.2495  -2.3762  -0.2192
 EEW  C5   C  CH1    0  -0.100   1.1893  -1.2566   0.2257
 EEW  C6   C  CH1    0   0.052   0.7945   0.0536  -0.4528
 EEW  C11  C  CH3    0  -0.787   4.9542  -1.6637   0.1997
 EEW  C7   C  C1     0  -0.252  -0.6887   0.2904  -0.3730
 EEW  C9   C  CH2    0  -0.431   1.3888   3.4536   0.4532
 EEW  C3   C  CH2    0  -0.495  -1.1623  -2.0575   0.2533
 EEW  C91  C  CH3    0  -0.668  -0.0042   3.4504   1.0652
 EEW  C81  C  CH2    0  -0.410   3.0365   2.4487  -1.1541
 EEW  C82  C  CH3    0  -0.678   3.3689   1.4070  -2.2127
 EEW  O7   O  O2     0  -0.502   1.5249   1.0860   0.1711
 EEW  C2   C  C      0  -0.246  -1.5821  -0.6474  -0.0620
 EEW  P    P  P      0   1.260  -3.3745  -0.3787   0.0354
 EEW  OP1  O  O      0  -0.804  -3.8393  -0.7342   1.4232
 EEW  OP2  O  OP    -1  -0.800  -4.0357  -1.0443  -1.1432
 EEW  OP3  O  O2     0  -0.615  -3.4229   1.2564  -0.1618
 EEW  CP1  C  CH3    0  -0.397  -4.6697   1.9013   0.0000
 EEW  N4   N  NH2    0  -0.798   0.6764  -3.6432   0.3499
 EEW  N5   N  NH1    0  -0.636   2.5663  -1.5793  -0.0637
 EEW  O10  O  O      0  -0.501   3.4429  -1.1389   1.9781
 EEW  H1   H  HCH1   0   0.206   0.2413  -2.3891  -1.3226
 EEW  H2   H  HCH1   0   0.251   1.0964  -1.1393   1.3080
 EEW  H3   H  HCH1   0   0.215   1.0737  -0.0199  -1.5164
 EEW  H4   H  HCH3   0   0.266   5.3898  -0.6991  -0.0694
 EEW  H5   H  HCH3   0   0.263   5.6126  -2.1298   0.9299
 EEW  H6   H  HCH3   0   0.250   4.9306  -2.2794  -0.6985
 EEW  H7   H  H      0   0.252  -1.0182   1.2968  -0.6027
 EEW  H8   H  HCH1   0   0.201   0.9002   2.3728  -1.3330
 EEW  H9   H  HCH2   0   0.215   2.1421   3.4141   1.2472
 EEW  H10  H  HCH2   0   0.218   1.5513   4.3978  -0.0729
 EEW  H11  H  HCH2   0   0.247  -1.8623  -2.7666  -0.2003
 EEW  H12  H  HCH2   0   0.243  -1.2228  -2.2255   1.3342
 EEW  H13  H  HCH3   0   0.228  -0.1215   4.2805   1.7628
 EEW  H14  H  HCH3   0   0.216  -0.7773   3.5525   0.3009
 EEW  H15  H  HCH3   0   0.224  -0.1992   2.5277   1.6108
 EEW  H16  H  HCH2   0   0.214   3.1043   3.4452  -1.5999
 EEW  H17  H  HCH2   0   0.215   3.7872   2.4178  -0.3579
 EEW  H18  H  HCH3   0   0.233   4.3390   1.6136  -2.6663
 EEW  H19  H  HCH3   0   0.216   3.4185   0.4050  -1.7884
 EEW  H20  H  HCH3   0   0.218   2.6266   1.3952  -3.0134
 EEW  H22  H  HCH3   0   0.209  -5.0468   1.8140   1.0225
 EEW  H23  H  HCH3   0   0.227  -4.5346   2.9588  -0.2260
 EEW  H24  H  HCH3   0   0.205  -5.4318   1.5045  -0.6774
 EEW  H25  H  HNH2   0   0.347   0.0345  -4.3683   0.0521
 EEW  H26  H  HNH2   0   0.345   1.5758  -3.9036  -0.0352
 EEW  H28  H  HNH1   0   0.395   2.7926  -1.7960  -1.0225
 EEW  C8   C  CH1    0   0.053   1.6500   2.3156  -0.5288
 EEW  C10  C  C      0   0.518   3.5883  -1.4382   0.8021

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
 EEW  N4   C4   single  1.453  0.020  1.453
 EEW  C11  C10  single  1.510  0.020  1.510
 EEW  O10  C10  double  1.222  0.020  1.222
 EEW  C4   C3   single  1.523  0.020  1.523
 EEW  C4   C5   single  1.528  0.020  1.528
 EEW  C10  N5   single  1.347  0.020  1.347
 EEW  C3   C2   single  1.505  0.020  1.505
 EEW  N5   C5   single  1.444  0.020  1.444
 EEW  C5   C6   single  1.527  0.020  1.527
 EEW  OP1  P    deloc   1.506  0.020  1.506
 EEW  C2   P    single  1.815  0.020  1.815
 EEW  C2   C7   double  1.332  0.020  1.332
 EEW  CP1  OP3  single  1.413  0.020  1.413
 EEW  OP3  P    single  1.648  0.020  1.648
 EEW  P    OP2  deloc   1.506  0.020  1.506
 EEW  C6   C7   single  1.504  0.020  1.504
 EEW  C6   O7   single  1.410  0.020  1.410
 EEW  O7   C8   single  1.420  0.020  1.420
 EEW  C82  C81  single  1.522  0.020  1.522
 EEW  C8   C81  single  1.527  0.020  1.527
 EEW  C8   C9   single  1.526  0.020  1.526
 EEW  C9   C91  single  1.521  0.020  1.521
 EEW  C4   H1   single  0.970  0.020  1.090
 EEW  C5   H2   single  0.970  0.020  1.090
 EEW  C6   H3   single  0.970  0.020  1.090
 EEW  C11  H4   single  0.970  0.020  1.090
 EEW  C11  H5   single  0.970  0.020  1.090
 EEW  C11  H6   single  0.970  0.020  1.090
 EEW  C7   H7   single  0.930  0.020  1.080
 EEW  C8   H8   single  0.970  0.020  1.090
 EEW  C9   H9   single  0.970  0.020  1.090
 EEW  C9   H10  single  0.970  0.020  1.090
 EEW  C3   H11  single  0.970  0.020  1.090
 EEW  C3   H12  single  0.970  0.020  1.090
 EEW  C91  H13  single  0.970  0.020  1.090
 EEW  C91  H14  single  0.970  0.020  1.090
 EEW  C91  H15  single  0.970  0.020  1.090
 EEW  C81  H16  single  0.970  0.020  1.090
 EEW  C81  H17  single  0.970  0.020  1.090
 EEW  C82  H18  single  0.970  0.020  1.090
 EEW  C82  H19  single  0.970  0.020  1.090
 EEW  C82  H20  single  0.970  0.020  1.090
 EEW  CP1  H22  single  0.970  0.020  1.090
 EEW  CP1  H23  single  0.970  0.020  1.090
 EEW  CP1  H24  single  0.970  0.020  1.090
 EEW  N4   H25  single  0.890  0.020  1.040
 EEW  N4   H26  single  0.890  0.020  1.040
 EEW  N5   H28  single  0.860  0.020  1.020

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
 EEW  H1   C4   N4   112.55  3.000
 EEW  H1   C4   C3   107.81  3.000
 EEW  N4   C4   C3   109.48  3.000
 EEW  H1   C4   C5   107.72  3.000
 EEW  C3   C4   C5   109.06  3.000
 EEW  N4   C4   C5   110.13  3.000
 EEW  H2   C5   N5   107.68  3.000
 EEW  H2   C5   C6   109.02  3.000
 EEW  N5   C5   C6   110.44  3.000
 EEW  H2   C5   C4   108.35  3.000
 EEW  C6   C5   C4   109.89  3.000
 EEW  N5   C5   C4   111.38  3.000
 EEW  H3   C6   O7   110.16  3.000
 EEW  H3   C6   C7   108.15  3.000
 EEW  O7   C6   C7   111.84  3.000
 EEW  H3   C6   C5   107.82  3.000
 EEW  O7   C6   C5   107.32  3.000
 EEW  C7   C6   C5   111.49  3.000
 EEW  H6   C11  H5   108.92  3.000
 EEW  H6   C11  H4   107.74  3.000
 EEW  H5   C11  H4   107.60  3.000
 EEW  H6   C11  C10  113.20  3.000
 EEW  H5   C11  C10  110.10  3.000
 EEW  H4   C11  C10  109.10  3.000
 EEW  H7   C7   C2   119.96  3.000
 EEW  H7   C7   C6   115.77  3.000
 EEW  C2   C7   C6   124.26  3.000
 EEW  H10  C9   H9   106.13  3.000
 EEW  H10  C9   C91  109.37  3.000
 EEW  H9   C9   C91  109.76  3.000
 EEW  H10  C9   C8   108.00  3.000
 EEW  H9   C9   C8   108.78  3.000
 EEW  C91  C9   C8   114.46  3.000
 EEW  H12  C3   H11  105.91  3.000
 EEW  H12  C3   C2   109.57  3.000
 EEW  H11  C3   C2   109.99  3.000
 EEW  H12  C3   C4   108.98  3.000
 EEW  H11  C3   C4   109.19  3.000
 EEW  C2   C3   C4   112.94  3.000
 EEW  H15  C91  H14  107.64  3.000
 EEW  H15  C91  H13  107.76  3.000
 EEW  H14  C91  H13  107.48  3.000
 EEW  H15  C91  C9   111.54  3.000
 EEW  H14  C91  C9   111.50  3.000
 EEW  H13  C91  C9   110.74  3.000
 EEW  H17  C81  H16  106.24  3.000
 EEW  H17  C81  C82  109.68  3.000
 EEW  H16  C81  C82  109.06  3.000
 EEW  H17  C81  C8   108.81  3.000
 EEW  H16  C81  C8   107.62  3.000
 EEW  C82  C81  C8   115.06  3.000
 EEW  H20  C82  H19  107.85  3.000
 EEW  H20  C82  H18  107.56  3.000
 EEW  H19  C82  H18  107.20  3.000
 EEW  H20  C82  C81  111.65  3.000
 EEW  H19  C82  C81  111.63  3.000
 EEW  H18  C82  C81  110.73  3.000
 EEW  C8   O7   C6   117.48  3.000
 EEW  P    C2   C3   113.77  3.000
 EEW  P    C2   C7   124.79  3.000
 EEW  C3   C2   C7   121.44  3.000
 EEW  OP3  P    OP2  109.39  3.000
 EEW  OP2  P    OP1  118.76  3.000
 EEW  OP3  P    OP1  109.60  3.000
 EEW  OP2  P    C2   109.03  3.000
 EEW  OP3  P    C2    99.76  3.000
 EEW  OP1  P    C2   108.61  3.000
 EEW  CP1  OP3  P    117.72  3.000
 EEW  H24  CP1  H23  108.05  3.000
 EEW  H24  CP1  H22  108.04  3.000
 EEW  H23  CP1  H22  108.32  3.000
 EEW  H24  CP1  OP3  112.22  3.000
 EEW  H23  CP1  OP3  108.05  3.000
 EEW  H22  CP1  OP3  112.03  3.000
 EEW  H26  N4   H25  105.48  3.000
 EEW  H26  N4   C4   109.66  3.000
 EEW  H25  N4   C4   108.83  3.000
 EEW  H28  N5   C10  117.60  3.000
 EEW  H28  N5   C5   116.91  3.000
 EEW  C10  N5   C5   124.85  3.000
 EEW  H8   C8   O7   110.17  3.000
 EEW  H8   C8   C81  108.34  3.000
 EEW  O7   C8   C81  110.93  3.000
 EEW  H8   C8   C9   108.35  3.000
 EEW  C81  C8   C9   110.74  3.000
 EEW  O7   C8   C9   108.27  3.000
 EEW  O10  C10  N5   123.64  3.000
 EEW  N5   C10  C11  114.48  3.000
 EEW  O10  C10  C11  121.88  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
 EEW  CONST_01  C11  C10  N5   C5    180.00   0.0  0
 EEW  CONST_02  O10  C10  N5   C5      0.00   0.0  0
 EEW  CONST_03  H28  N5   C10  C11     0.00   0.0  0
 EEW  Var_01    C7   C2   C3   C4    -17.25  30.0  1
 EEW  Var_02    C3   C2   C7   C6      0.47  30.0  1
 EEW  Var_03    OP1  P    C2   C7   -121.46  30.0  3
 EEW  Var_04    C81  C8   O7   C6   -103.12  30.0  3
 EEW  Var_05    C82  C81  C8   C9   -176.58  30.0  3
 EEW  Var_06    O7   C8   C9   C91   -61.65  30.0  1
 EEW  Var_07    H18  C82  C81  C8    175.54  30.0  3
 EEW  Var_08    H13  C91  C9   C8    179.42  30.0  3
 EEW  Var_09    H22  CP1  OP3  P      64.33  30.0  3
 EEW  Var_10    H4   C11  C10  N5     96.76  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
 EEW  chir_01  C4  N4  C3  C5  negativ
 EEW  chir_02  C5  N5  C6  C4  negativ
 EEW  chir_03  C6  O7  C7  C5  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
 EEW  plan-1  C5   0.020
 EEW  plan-1  C11  0.020
 EEW  plan-1  N5   0.020
 EEW  plan-1  O10  0.020
 EEW  plan-1  H28  0.020
 EEW  plan-1  C10  0.020

