# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Apr 10 07:58:51 2020
#   Inital geometry file: a 113 line input string
#   Ligand name: [(2R)-2-{2-[hydroxy(methyl)amino]-2-oxoethyl}-5-(3-methoxyphenyl)pentyl]phosphonic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: COc1cccc(CCC[C@H](CC(=O)N(C)O)C[P](O)(O)=O)c1
#
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
 6JB  6JB  '[(2R)-2-{2-[hydroxy(methyl)amino]-2-oxoethyl}-5-(3-methoxyphenyl)pentyl]phosphonic acid'  ligand  45  23  .  2021-08-05  2023-02-02
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_6JB
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
 6JB  C1   C  CH2    0  -0.713  -1.4228  -1.5903   0.4980
 6JB  C2   C  CH1    0  -0.207  -1.6168  -0.1463   0.0288
 6JB  C3   C  CH2    0  -0.584  -3.0007   0.3458   0.4482
 6JB  C4   C  C      0   0.545  -3.4519   1.6047  -0.2490
 6JB  O7   O  OP    -1  -0.915  -1.9275  -4.2177   0.2212
 6JB  O8   O  O      0  -0.895  -3.8880  -2.6096  -0.1549
 6JB  C11  C  CH3    0  -0.514  -5.1636   3.3964  -0.2898
 6JB  C15  C  CH2    0  -0.504   1.8837   1.5409   0.6120
 6JB  C17  C  CR16   0  -0.410   4.1286   0.4430   0.8318
 6JB  C18  C  CR16   0  -0.337   3.7157   1.8034  -1.0982
 6JB  C19  C  CR6    0   0.397   5.4077   0.1411   0.3589
 6JB  C20  C  CR16   0  -0.226   4.9825   1.5044  -1.5679
 6JB  C21  C  CR16   0  -0.403   5.8404   0.6751  -0.8520
 6JB  P5   P  P      0   1.167  -2.3956  -2.8965  -0.4096
 6JB  O6   O  OP    -1  -0.911  -1.9927  -2.7398  -1.8831
 6JB  N9   N  NT     0  -0.211  -4.4825   2.2822   0.3222
 6JB  O10  O  OH1    0  -0.549  -5.2028   1.6629   1.3133
 6JB  O12  O  O      0  -0.501  -2.9398   2.0259  -1.2777
 6JB  C13  C  CH2    0  -0.400  -0.5401   0.7976   0.5771
 6JB  C16  C  CR6    0   0.153   3.2759   1.2700   0.1155
 6JB  C23  C  CH3    0  -0.435   7.4507  -1.0142   0.7098
 6JB  H1   H  HCH2   0   0.197  -0.3677  -1.8666   0.3953
 6JB  H2   H  HCH2   0   0.176  -1.6347  -1.6477   1.5745
 6JB  H3   H  HCH1   0   0.197  -1.5534  -0.1418  -1.0638
 6JB  H4   H  HCH2   0   0.294  -3.7284  -0.4472   0.2379
 6JB  H5   H  HCH2   0   0.228  -3.0199   0.4807   1.5337
 6JB  H7   H  HCH3   0   0.252  -4.5068   3.8654  -1.0148
 6JB  H8   H  HCH3   0   0.239  -6.0793   3.0820  -0.7960
 6JB  H9   H  HCH3   0   0.243  -5.4181   4.1340   0.4714
 6JB  H10  H  HCH2   0   0.214   0.8566   0.6406  -1.0551
 6JB  H11  H  HCH2   0   0.220   1.1922  -0.4622   0.2628
 6JB  H12  H  HCH2   0   0.234   1.5891   2.5605   0.3471
 6JB  H13  H  HCH2   0   0.233   1.8600   1.4831   1.7038
 6JB  H14  H  HCR6   0   0.249   3.8080   0.0201   1.7778
 6JB  H15  H  HCR6   0   0.241   3.0637   2.4541  -1.6680
 6JB  H16  H  HCR6   0   0.254   5.3207   1.9220  -2.5077
 6JB  H17  H  HCR6   0   0.274   6.8250   0.4647  -1.2470
 6JB  H19  H  HOH1   0   0.474  -4.9228   2.0697   2.1445
 6JB  H20  H  HCH2   0   0.213  -0.8131   1.8343   0.3539
 6JB  H21  H  HCH2   0   0.195  -0.5258   0.7164   1.6715
 6JB  H22  H  HCH3   0   0.227   7.4391  -1.5492  -0.2437
 6JB  H23  H  HCH3   0   0.226   8.0955  -0.1369   0.6117
 6JB  H24  H  HCH3   0   0.258   7.8658  -1.6693   1.4719
 6JB  C14  C  CH2    0  -0.413   0.8631   0.5556   0.0367
 6JB  O22  O  O2     0  -0.474   6.1500  -0.6700   1.1397

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
 6JB  C20  C21  aromatic  1.392  0.020  1.392
 6JB  C20  C18  aromatic  1.384  0.020  1.384
 6JB  C21  C19  aromatic  1.392  0.020  1.392
 6JB  C18  C16  aromatic  1.397  0.020  1.397
 6JB  C19  O22  single    1.349  0.020  1.349
 6JB  C19  C17  aromatic  1.397  0.020  1.397
 6JB  O22  C23  single    1.412  0.020  1.412
 6JB  C16  C17  aromatic  1.387  0.020  1.387
 6JB  C16  C15  single    1.503  0.020  1.503
 6JB  C15  C14  single    1.531  0.020  1.531
 6JB  C11  N9   single    1.442  0.020  1.442
 6JB  O10  N9   single    1.373  0.020  1.373
 6JB  C13  C14  single    1.523  0.020  1.523
 6JB  C13  C2   single    1.533  0.020  1.533
 6JB  N9   C4   single    1.359  0.020  1.359
 6JB  O8   P5   deloc     1.541  0.020  1.541
 6JB  C4   O12  double    1.224  0.020  1.224
 6JB  C4   C3   single    1.508  0.020  1.508
 6JB  C2   C3   single    1.527  0.020  1.527
 6JB  C2   C1   single    1.531  0.020  1.531
 6JB  C1   P5   single    1.864  0.020  1.864
 6JB  P5   O6   deloc     1.536  0.020  1.536
 6JB  P5   O7   deloc     1.537  0.020  1.537
 6JB  C1   H1   single    0.970  0.020  1.090
 6JB  C1   H2   single    0.970  0.020  1.090
 6JB  C2   H3   single    0.970  0.020  1.090
 6JB  C3   H4   single    0.970  0.020  1.090
 6JB  C3   H5   single    0.970  0.020  1.090
 6JB  C11  H7   single    0.970  0.020  1.090
 6JB  C11  H8   single    0.970  0.020  1.090
 6JB  C11  H9   single    0.970  0.020  1.090
 6JB  C14  H10  single    0.970  0.020  1.090
 6JB  C14  H11  single    0.970  0.020  1.090
 6JB  C15  H12  single    0.970  0.020  1.090
 6JB  C15  H13  single    0.970  0.020  1.090
 6JB  C17  H14  single    0.930  0.020  1.080
 6JB  C18  H15  single    0.930  0.020  1.080
 6JB  C20  H16  single    0.930  0.020  1.080
 6JB  C21  H17  single    0.930  0.020  1.080
 6JB  O10  H19  single    0.850  0.020  0.980
 6JB  C13  H20  single    0.970  0.020  1.090
 6JB  C13  H21  single    0.970  0.020  1.090
 6JB  C23  H22  single    0.970  0.020  1.090
 6JB  C23  H23  single    0.970  0.020  1.090
 6JB  C23  H24  single    0.970  0.020  1.090

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
 6JB  H2   C1   H1   105.34  3.000
 6JB  H2   C1   P5   109.86  3.000
 6JB  H1   C1   P5   106.27  3.000
 6JB  H2   C1   C2   108.97  3.000
 6JB  H1   C1   C2   109.35  3.000
 6JB  P5   C1   C2   116.46  3.000
 6JB  H3   C2   C13  108.29  3.000
 6JB  H3   C2   C3   108.98  3.000
 6JB  C13  C2   C3   109.86  3.000
 6JB  H3   C2   C1   107.61  3.000
 6JB  C3   C2   C1   109.55  3.000
 6JB  C13  C2   C1   112.47  3.000
 6JB  H5   C3   H4   105.53  3.000
 6JB  H5   C3   C4   110.52  3.000
 6JB  H4   C3   C4   108.44  3.000
 6JB  H5   C3   C2   109.15  3.000
 6JB  H4   C3   C2   108.40  3.000
 6JB  C4   C3   C2   114.40  3.000
 6JB  O12  C4   N9   119.93  3.000
 6JB  O12  C4   C3   123.41  3.000
 6JB  N9   C4   C3   116.66  3.000
 6JB  H9   C11  H8   108.82  3.000
 6JB  H9   C11  H7   108.39  3.000
 6JB  H8   C11  H7   108.80  3.000
 6JB  H9   C11  N9   109.67  3.000
 6JB  H8   C11  N9   111.71  3.000
 6JB  H7   C11  N9   109.37  3.000
 6JB  H13  C15  H12  106.57  3.000
 6JB  H13  C15  C16  109.90  3.000
 6JB  H12  C15  C16  109.73  3.000
 6JB  H13  C15  C14  109.07  3.000
 6JB  H12  C15  C14  109.24  3.000
 6JB  C16  C15  C14  112.18  3.000
 6JB  H14  C17  C16  120.07  3.000
 6JB  H14  C17  C19  118.79  3.000
 6JB  C16  C17  C19  121.13  3.000
 6JB  H15  C18  C16  119.80  3.000
 6JB  H15  C18  C20  120.15  3.000
 6JB  C16  C18  C20  120.05  3.000
 6JB  O22  C19  C21  124.27  3.000
 6JB  O22  C19  C17  115.98  3.000
 6JB  C21  C19  C17  119.74  3.000
 6JB  H16  C20  C21  118.94  3.000
 6JB  H16  C20  C18  119.83  3.000
 6JB  C21  C20  C18  121.23  3.000
 6JB  H17  C21  C20  119.30  3.000
 6JB  H17  C21  C19  121.73  3.000
 6JB  C20  C21  C19  118.97  3.000
 6JB  O6   P5   O8   113.18  3.000
 6JB  O6   P5   O7   113.68  3.000
 6JB  O8   P5   O7   112.77  3.000
 6JB  O7   P5   C1   104.10  3.000
 6JB  O6   P5   C1   105.00  3.000
 6JB  O8   P5   C1   107.13  3.000
 6JB  O10  N9   C11  114.02  3.000
 6JB  O10  N9   C4   118.45  3.000
 6JB  C11  N9   C4   124.39  3.000
 6JB  H19  O10  N9   106.20  3.000
 6JB  H21  C13  H20  106.05  3.000
 6JB  H21  C13  C14  109.28  3.000
 6JB  H20  C13  C14  107.93  3.000
 6JB  H21  C13  C2   108.67  3.000
 6JB  H20  C13  C2   109.56  3.000
 6JB  C14  C13  C2   114.98  3.000
 6JB  C18  C16  C17  118.86  3.000
 6JB  C17  C16  C15  120.43  3.000
 6JB  C18  C16  C15  120.66  3.000
 6JB  H24  C23  H23  108.73  3.000
 6JB  H24  C23  H22  108.69  3.000
 6JB  H23  C23  H22  108.70  3.000
 6JB  H24  C23  O22  106.57  3.000
 6JB  H23  C23  O22  112.02  3.000
 6JB  H22  C23  O22  112.02  3.000
 6JB  H11  C14  H10  106.27  3.000
 6JB  H11  C14  C13  110.60  3.000
 6JB  H10  C14  C13  109.63  3.000
 6JB  H11  C14  C15  108.71  3.000
 6JB  H10  C14  C15  109.19  3.000
 6JB  C13  C14  C15  112.25  3.000
 6JB  C23  O22  C19  118.51  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
 6JB  CONST_01  C20  C21  C19  C17     0.00   0.0  0
 6JB  CONST_02  C20  C18  C16  C17     0.00   0.0  0
 6JB  CONST_03  C19  C21  C20  C18     0.00   0.0  0
 6JB  CONST_04  C19  C17  C16  C18     0.00   0.0  0
 6JB  CONST_05  C16  C18  C20  C21     0.00   0.0  0
 6JB  CONST_06  C16  C17  C19  C21     0.00   0.0  0
 6JB  CONST_07  C20  C18  C16  C15   180.00   0.0  0
 6JB  CONST_08  C19  C17  C16  C15   180.00   0.0  0
 6JB  CONST_09  O22  C19  C21  C20   180.00   0.0  0
 6JB  CONST_10  O22  C19  C17  C16   180.00   0.0  0
 6JB  CONST_11  H17  C21  C19  C17   180.00   0.0  0
 6JB  CONST_12  H15  C18  C16  C17   180.00   0.0  0
 6JB  CONST_13  H14  C17  C16  C18   180.00   0.0  0
 6JB  CONST_14  H16  C20  C21  C19   180.00   0.0  0
 6JB  CONST_15  C11  N9   C4   C3    180.00   0.0  0
 6JB  CONST_16  O10  N9   C4   C3      0.00   0.0  0
 6JB  CONST_17  O12  C4   N9   C11     0.00   0.0  0
 6JB  CONST_18  O12  C4   N9   O10   180.00   0.0  0
 6JB  Var_01    C18  C16  C15  C14    85.44  30.0  1
 6JB  Var_02    C16  C15  C14  C13   177.96  30.0  2
 6JB  Var_03    H22  C23  O22  C19   -60.97  30.0  3
 6JB  Var_04    C15  C14  C13  C2    179.34  30.0  3
 6JB  Var_05    N9   C4   C3   C2   -162.83  30.0  1
 6JB  Var_06    O8   P5   C1   C2    -63.71  30.0  3
 6JB  Var_07    H7   C11  N9   C4    -23.89  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
 6JB  chir_01  C2  C13  C3  C1  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
 6JB  plan-1  C15  0.020
 6JB  plan-1  C17  0.020
 6JB  plan-1  C18  0.020
 6JB  plan-1  C19  0.020
 6JB  plan-1  C20  0.020
 6JB  plan-1  C21  0.020
 6JB  plan-1  C16  0.020
 6JB  plan-1  H14  0.020
 6JB  plan-1  H15  0.020
 6JB  plan-1  H16  0.020
 6JB  plan-1  H17  0.020
 6JB  plan-1  O22  0.020
 6JB  plan-2  C3   0.020
 6JB  plan-2  C4   0.020
 6JB  plan-2  C11  0.020
 6JB  plan-2  N9   0.020
 6JB  plan-2  O10  0.020
 6JB  plan-2  O12  0.020

