# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Apr 10 06:47:20 2020
#   Inital geometry file: a 113 line input string
#   Ligand name: [(2R)-2-{2-[hydroxy(methyl)amino]-2-oxoethyl}-5-(4-methoxyphenyl)pentyl]phosphonic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: COc1ccc(CCC[C@H](CC(=O)N(C)O)C[P](O)(O)=O)cc1
#
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
 6J8  6J8  '[(2R)-2-{2-[hydroxy(methyl)amino]-2-oxoethyl}-5-(4-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_6J8
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
 6J8  C1   C  CH2    0  -0.713   1.6953   1.5855   0.7921
 6J8  C2   C  CH1    0  -0.203   1.7201   0.1716   0.2056
 6J8  C3   C  CH2    0  -0.595   3.0979  -0.4524   0.4184
 6J8  C4   C  C      0   0.544   3.3656  -1.6680  -0.4339
 6J8  O6   O  OP    -1  -0.911   2.1147   2.8508  -1.5637
 6J8  O7   O  OP    -1  -0.913   2.3596   4.1864   0.6214
 6J8  C11  C  CH3    0  -0.515   4.8748  -3.6175  -0.7653
 6J8  C13  C  CH2    0  -0.402   0.6377  -0.7254   0.8168
 6J8  C14  C  CH2    0  -0.413  -0.7848  -0.3956   0.3825
 6J8  C15  C  CH2    0  -0.501  -1.8210  -1.2818   1.0769
 6J8  C16  C  C      0   0.119  -3.2258  -1.0057   0.6201
 6J8  C17  C  C1     0  -0.295  -3.7204  -1.5736  -0.5556
 6J8  C18  C  C1     0  -0.307  -4.0683  -0.1530   1.3205
 6J8  C23  C  CH3    0  -0.434  -7.9529   0.5989  -0.0939
 6J8  O12  O  O      0  -0.504   2.6738  -1.9842  -1.3940
 6J8  N9   N  NT     0  -0.206   4.4670  -2.3951  -0.1217
 6J8  O10  O  OH1    0  -0.549   5.1826  -2.0843   1.0047
 6J8  P5   P  P      0   1.166   2.6662   2.8820  -0.1307
 6J8  O8   O  O      0  -0.895   4.1503   2.4758  -0.0426
 6J8  C19  C  C1     0  -0.327  -4.9983  -1.3049  -1.0097
 6J8  C21  C  C      0   0.360  -5.8328  -0.4463  -0.2906
 6J8  O22  O  O2     0  -0.474  -7.0663  -0.2435  -0.8000
 6J8  C20  C  C1     0  -0.368  -5.3585   0.1323   0.8826
 6J8  H1   H  HCH2   0   0.195   0.6582   1.9363   0.8344
 6J8  H2   H  HCH2   0   0.177   2.0291   1.5418   1.8376
 6J8  H3   H  HCH1   0   0.195   1.5325   0.2565  -0.8692
 6J8  H4   H  HCH2   0   0.292   3.8595   0.3055   0.1963
 6J8  H5   H  HCH2   0   0.237   3.2271  -0.6937   1.4772
 6J8  H8   H  HCH3   0   0.241   5.8988  -3.5346  -1.1334
 6J8  H9   H  HCH3   0   0.243   4.8182  -4.4578  -0.0711
 6J8  H10  H  HCH3   0   0.254   4.2211  -3.8175  -1.6078
 6J8  H11  H  HCH2   0   0.212   0.8303  -1.7719   0.5601
 6J8  H12  H  HCH2   0   0.195   0.7087  -0.6640   1.9102
 6J8  H13  H  HCH2   0   0.218  -1.0180   0.6523   0.5908
 6J8  H14  H  HCH2   0   0.214  -0.8710  -0.5206  -0.7022
 6J8  H15  H  HCH2   0   0.230  -1.5754  -2.3318   0.8895
 6J8  H16  H  HCH2   0   0.232  -1.7467  -1.1361   2.1584
 6J8  H17  H  H      0   0.245  -3.0914  -2.2466  -1.1271
 6J8  H18  H  H      0   0.246  -3.7223   0.3054   2.2399
 6J8  H19  H  HCH3   0   0.226  -8.1597   0.2246   0.9125
 6J8  H20  H  HCH3   0   0.226  -7.5736   1.6215  -0.0168
 6J8  H21  H  HCH3   0   0.257  -8.8823   0.6148  -0.6584
 6J8  H22  H  HOH1   0   0.474   5.9163  -1.5230   0.7179
 6J8  H23  H  H      0   0.257  -5.3621  -1.7622  -1.9219
 6J8  H24  H  H      0   0.274  -5.9725   0.8011   1.4704

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
 6J8  C23  O22  single    1.412  0.020  1.412
 6J8  O22  C21  single    1.350  0.020  1.350
 6J8  C20  C21  aromatic  1.391  0.020  1.391
 6J8  C20  C18  aromatic  1.392  0.020  1.392
 6J8  C21  C19  aromatic  1.397  0.020  1.397
 6J8  C18  C16  aromatic  1.388  0.020  1.388
 6J8  C19  C17  aromatic  1.383  0.020  1.383
 6J8  C16  C17  aromatic  1.396  0.020  1.396
 6J8  C16  C15  single    1.503  0.020  1.503
 6J8  C15  C14  single    1.530  0.020  1.530
 6J8  C11  N9   single    1.440  0.020  1.440
 6J8  O10  N9   single    1.370  0.020  1.370
 6J8  N9   C4   single    1.356  0.020  1.356
 6J8  C13  C14  single    1.523  0.020  1.523
 6J8  C13  C2   single    1.533  0.020  1.533
 6J8  O8   P5   deloc     1.541  0.020  1.541
 6J8  C4   O12  double    1.225  0.020  1.225
 6J8  C4   C3   single    1.509  0.020  1.509
 6J8  C2   C3   single    1.528  0.020  1.528
 6J8  C2   C1   single    1.531  0.020  1.531
 6J8  P5   C1   single    1.864  0.020  1.864
 6J8  P5   O6   deloc     1.536  0.020  1.536
 6J8  P5   O7   deloc     1.537  0.020  1.537
 6J8  C1   H1   single    0.970  0.020  1.090
 6J8  C1   H2   single    0.970  0.020  1.090
 6J8  C2   H3   single    0.970  0.020  1.090
 6J8  C3   H4   single    0.970  0.020  1.090
 6J8  C3   H5   single    0.970  0.020  1.090
 6J8  C11  H8   single    0.970  0.020  1.090
 6J8  C11  H9   single    0.970  0.020  1.090
 6J8  C11  H10  single    0.970  0.020  1.090
 6J8  C13  H11  single    0.970  0.020  1.090
 6J8  C13  H12  single    0.970  0.020  1.090
 6J8  C14  H13  single    0.970  0.020  1.090
 6J8  C14  H14  single    0.970  0.020  1.090
 6J8  C15  H15  single    0.970  0.020  1.090
 6J8  C15  H16  single    0.970  0.020  1.090
 6J8  C17  H17  single    0.930  0.020  1.080
 6J8  C18  H18  single    0.930  0.020  1.080
 6J8  C23  H19  single    0.970  0.020  1.090
 6J8  C23  H20  single    0.970  0.020  1.090
 6J8  C23  H21  single    0.970  0.020  1.090
 6J8  O10  H22  single    0.850  0.020  0.980
 6J8  C19  H23  single    0.930  0.020  1.080
 6J8  C20  H24  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
 6J8  H2   C1   H1   105.29  3.000
 6J8  H2   C1   P5   109.92  3.000
 6J8  H1   C1   P5   106.82  3.000
 6J8  H2   C1   C2   108.84  3.000
 6J8  H1   C1   C2   109.01  3.000
 6J8  P5   C1   C2   116.38  3.000
 6J8  H3   C2   C13  108.42  3.000
 6J8  H3   C2   C3   108.85  3.000
 6J8  C13  C2   C3   110.02  3.000
 6J8  H3   C2   C1   107.57  3.000
 6J8  C3   C2   C1   109.78  3.000
 6J8  C13  C2   C1   112.10  3.000
 6J8  H5   C3   H4   105.46  3.000
 6J8  H5   C3   C4   110.38  3.000
 6J8  H4   C3   C4   108.61  3.000
 6J8  H5   C3   C2   109.37  3.000
 6J8  H4   C3   C2   108.40  3.000
 6J8  C4   C3   C2   114.23  3.000
 6J8  N9   C4   O12  120.05  3.000
 6J8  O12  C4   C3   123.42  3.000
 6J8  N9   C4   C3   116.49  3.000
 6J8  H10  C11  H9   108.71  3.000
 6J8  H10  C11  H8   108.51  3.000
 6J8  H9   C11  H8   108.76  3.000
 6J8  H10  C11  N9   109.45  3.000
 6J8  H9   C11  N9   110.76  3.000
 6J8  H8   C11  N9   110.60  3.000
 6J8  H12  C13  H11  106.01  3.000
 6J8  H12  C13  C14  109.40  3.000
 6J8  H11  C13  C14  107.72  3.000
 6J8  H12  C13  C2   108.59  3.000
 6J8  H11  C13  C2   109.99  3.000
 6J8  C14  C13  C2   114.77  3.000
 6J8  H14  C14  H13  106.33  3.000
 6J8  H14  C14  C15  109.27  3.000
 6J8  H13  C14  C15  108.91  3.000
 6J8  H14  C14  C13  109.33  3.000
 6J8  H13  C14  C13  110.63  3.000
 6J8  C15  C14  C13  112.19  3.000
 6J8  H16  C15  H15  106.36  3.000
 6J8  H16  C15  C16  109.85  3.000
 6J8  H15  C15  C16  109.51  3.000
 6J8  H16  C15  C14  109.00  3.000
 6J8  H15  C15  C14  109.02  3.000
 6J8  C16  C15  C14  112.88  3.000
 6J8  C18  C16  C17  117.37  3.000
 6J8  C17  C16  C15  120.82  3.000
 6J8  C18  C16  C15  121.79  3.000
 6J8  H17  C17  C19  118.94  3.000
 6J8  H17  C17  C16  119.40  3.000
 6J8  C19  C17  C16  121.66  3.000
 6J8  H18  C18  C20  118.42  3.000
 6J8  H18  C18  C16  119.60  3.000
 6J8  C20  C18  C16  121.98  3.000
 6J8  H21  C23  H20  108.62  3.000
 6J8  H21  C23  H19  108.74  3.000
 6J8  H20  C23  H19  108.71  3.000
 6J8  H21  C23  O22  106.60  3.000
 6J8  H20  C23  O22  112.04  3.000
 6J8  H19  C23  O22  112.01  3.000
 6J8  O10  N9   C11  114.33  3.000
 6J8  O10  N9   C4   119.46  3.000
 6J8  C11  N9   C4   125.59  3.000
 6J8  H22  O10  N9   106.50  3.000
 6J8  O8   P5   O7   112.82  3.000
 6J8  O7   P5   O6   113.73  3.000
 6J8  O8   P5   O6   113.19  3.000
 6J8  O7   P5   C1   104.13  3.000
 6J8  O6   P5   C1   105.11  3.000
 6J8  O8   P5   C1   106.85  3.000
 6J8  H23  C19  C21  119.50  3.000
 6J8  H23  C19  C17  120.32  3.000
 6J8  C21  C19  C17  120.18  3.000
 6J8  C20  C21  O22  124.55  3.000
 6J8  C20  C21  C19  119.09  3.000
 6J8  O22  C21  C19  116.36  3.000
 6J8  C21  O22  C23  118.34  3.000
 6J8  H24  C20  C21  121.46  3.000
 6J8  H24  C20  C18  118.81  3.000
 6J8  C21  C20  C18  119.73  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
 6J8  CONST_01  C21  C20  C18  C16     0.00   0.0  0
 6J8  CONST_02  C21  C19  C17  C16     0.00   0.0  0
 6J8  CONST_03  C20  C21  C19  C17     0.00   0.0  0
 6J8  CONST_04  C20  C18  C16  C17     0.00   0.0  0
 6J8  CONST_05  C19  C21  C20  C18     0.00   0.0  0
 6J8  CONST_06  C19  C17  C16  C18     0.00   0.0  0
 6J8  CONST_07  C20  C18  C16  C15   180.00   0.0  0
 6J8  CONST_08  C19  C17  C16  C15   180.00   0.0  0
 6J8  CONST_09  O22  C21  C19  C17   180.00   0.0  0
 6J8  CONST_10  O22  C21  C20  C18   180.00   0.0  0
 6J8  CONST_11  H24  C20  C18  C16   180.00   0.0  0
 6J8  CONST_12  H23  C19  C17  C16   180.00   0.0  0
 6J8  CONST_13  H18  C18  C16  C17   180.00   0.0  0
 6J8  CONST_14  H17  C17  C16  C18   180.00   0.0  0
 6J8  CONST_15  C11  N9   C4   C3    180.00   0.0  0
 6J8  CONST_16  O10  N9   C4   C3      0.00   0.0  0
 6J8  CONST_17  O12  C4   N9   C11     0.00   0.0  0
 6J8  CONST_18  O10  N9   C4   O12   180.00   0.0  0
 6J8  Var_01    C18  C16  C15  C14   -95.82  30.0  2
 6J8  Var_02    C20  C21  O22  C23    -0.85  30.0  2
 6J8  Var_03    C16  C15  C14  C13  -177.78  30.0  1
 6J8  Var_04    H19  C23  O22  C21   -60.34  30.0  3
 6J8  Var_05    C15  C14  C13  C2   -177.30  30.0  3
 6J8  Var_06    N9   C4   C3   C2   -168.80  30.0  1
 6J8  Var_07    O8   P5   C1   C2    -64.74  30.0  3
 6J8  Var_08    H8   C11  N9   C4    125.21  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
 6J8  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
 6J8  plan-1  C15  0.020
 6J8  plan-1  C16  0.020
 6J8  plan-1  C17  0.020
 6J8  plan-1  C18  0.020
 6J8  plan-1  C19  0.020
 6J8  plan-1  C21  0.020
 6J8  plan-1  O22  0.020
 6J8  plan-1  C20  0.020
 6J8  plan-1  H17  0.020
 6J8  plan-1  H18  0.020
 6J8  plan-1  H23  0.020
 6J8  plan-1  H24  0.020
 6J8  plan-2  C3   0.020
 6J8  plan-2  C4   0.020
 6J8  plan-2  C11  0.020
 6J8  plan-2  O12  0.020
 6J8  plan-2  N9   0.020
 6J8  plan-2  O10  0.020

