# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon May 25 22:52:37 2020
#   Inital geometry file: a 111 line input string
#   Ligand name: [(2R)-2-{2-[hydroxy(methyl)amino]-2-oxoethyl}-6-phenylhexyl]phosphonic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CN(O)C(=O)C[C@@H](CCCCc1ccccc1)C[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
 R77  R77  '[(2R)-2-{2-[hydroxy(methyl)amino]-2-oxoethyl}-6-phenylhexyl]phosphonic acid'  ligand  46  22  .  2021-08-23  2021-08-23  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_R77
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
 R77  O6   O  OH1   0  -0.754   0.3879   3.3463   0.4272
 R77  P4   P  P     0   1.385   1.5861   2.4728  -0.2100
 R77  O5   O  O     0  -0.717   1.3497   2.3479  -1.6695
 R77  O7   O  OH1   0  -0.748   2.9454   3.2348   0.2035
 R77  C1   C  CH2   0  -0.780   1.7421   0.9335   0.7373
 R77  C2   C  CH1   0  -0.220   1.4619  -0.3482  -0.0743
 R77  C3   C  CH2   0  -0.571   2.4624  -1.4382   0.2969
 R77  C8   C  C     0   0.549   3.8689  -1.1275  -0.1749
 R77  N9   N  NT    0  -0.207   4.8257  -2.0210   0.1652
 R77  O10  O  OH1   0  -0.546   4.5116  -3.0094   1.0609
 R77  C11  C  CH3   0  -0.516   6.2368  -1.8571  -0.0812
 R77  O12  O  O     0  -0.484   4.1367  -0.1476  -0.8556
 R77  C13  C  CH2   0  -0.411   0.0417  -0.8658   0.1569
 R77  C14  C  CH2   0  -0.436  -1.0672   0.1114  -0.2119
 R77  C15  C  CH2   0  -0.405  -2.4493  -0.5176  -0.0841
 R77  C16  C  CH2   0  -0.506  -3.5807   0.4840  -0.3207
 R77  C17  C  CR6   0   0.139  -4.9384  -0.1468  -0.1850
 R77  C19  C  CR16  0  -0.318  -5.6275  -0.6191  -1.2997
 R77  C21  C  CR16  0  -0.239  -6.8657  -1.2352  -1.1670
 R77  C22  C  CR16  0  -0.275  -7.4358  -1.3912   0.0895
 R77  C20  C  CR16  0  -0.240  -6.7588  -0.9248   1.2096
 R77  C18  C  CR16  0  -0.311  -5.5224  -0.3090   1.0706
 R77  H1   H  HOH1  0   0.486   0.4579   3.5122   1.3760
 R77  H2   H  HOH1  0   0.489   3.0649   4.0835  -0.2442
 R77  H3   H  HCH2  0   0.300   2.7560   0.9241   1.1378
 R77  H4   H  HCH2  0   0.287   1.0824   0.9780   1.6079
 R77  H5   H  HCH1  0   0.251   1.5702  -0.1359  -1.1399
 R77  H6   H  HCH2  0   0.270   2.4524  -1.6041   1.3776
 R77  H7   H  HCH2  0   0.276   2.1508  -2.3884  -0.1498
 R77  H8   H  HOH1  0   0.477   4.3757  -3.8139   0.5416
 R77  H9   H  HCH3  0   0.256   6.3835  -1.1009  -0.8455
 R77  H10  H  HCH3  0   0.245   6.7643  -1.5508   0.8243
 R77  H11  H  HCH3  0   0.248   6.6625  -2.7948  -0.4379
 R77  H12  H  HCH2  0   0.224  -0.0880  -1.7830  -0.4269
 R77  H13  H  HCH2  0   0.214  -0.0698  -1.1543   1.2089
 R77  H14  H  HCH2  0   0.215  -1.0244   0.9938   0.4343
 R77  H15  H  HCH2  0   0.218  -0.9170   0.4726  -1.2342
 R77  H16  H  HCH2  0   0.222  -2.5437  -1.3468  -0.7923
 R77  H17  H  HCH2  0   0.219  -2.5591  -0.9536   0.9144
 R77  H18  H  HCH2  0   0.236  -3.4852   1.3052   0.3956
 R77  H19  H  HCH2  0   0.236  -3.4736   0.9230  -1.3164
 R77  H20  H  HCR6  0   0.244  -5.1929  -0.4976  -2.2853
 R77  H21  H  HCR6  0   0.252  -7.3867  -1.5892  -2.0476
 R77  H22  H  HCR6  0   0.252  -8.4004  -1.8705   0.1962
 R77  H23  H  HCR6  0   0.252  -7.1960  -1.0382   2.1936
 R77  H24  H  HCR6  0   0.244  -5.0045   0.0548   1.9509

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
 R77  C21  C22  aromatic  1.389  0.020  1.389
 R77  C21  C19  aromatic  1.389  0.020  1.389
 R77  C22  C20  aromatic  1.389  0.020  1.389
 R77  C19  C17  aromatic  1.393  0.020  1.393
 R77  C20  C18  aromatic  1.388  0.020  1.388
 R77  C17  C18  aromatic  1.394  0.020  1.394
 R77  C17  C16  single    1.503  0.020  1.503
 R77  C16  C15  single    1.529  0.020  1.529
 R77  O10  N9   single    1.370  0.020  1.370
 R77  C11  N9   single    1.442  0.020  1.442
 R77  C15  C14  single    1.524  0.020  1.524
 R77  N9   C8   single    1.353  0.020  1.353
 R77  O5   P4   double    1.484  0.020  1.484
 R77  C14  C13  single    1.523  0.020  1.523
 R77  C8   O12  double    1.223  0.020  1.223
 R77  C8   C3   single    1.516  0.020  1.516
 R77  C2   C3   single    1.525  0.020  1.525
 R77  C2   C13  single    1.529  0.020  1.529
 R77  C2   C1   single    1.543  0.020  1.543
 R77  P4   O7   single    1.612  0.020  1.612
 R77  P4   C1   single    1.814  0.020  1.814
 R77  P4   O6   single    1.614  0.020  1.614
 R77  O6   H1   single    0.850  0.020  0.980
 R77  O7   H2   single    0.850  0.020  0.980
 R77  C1   H3   single    0.970  0.020  1.090
 R77  C1   H4   single    0.970  0.020  1.090
 R77  C2   H5   single    0.970  0.020  1.090
 R77  C3   H6   single    0.970  0.020  1.090
 R77  C3   H7   single    0.970  0.020  1.090
 R77  O10  H8   single    0.850  0.020  0.980
 R77  C11  H9   single    0.970  0.020  1.090
 R77  C11  H10  single    0.970  0.020  1.090
 R77  C11  H11  single    0.970  0.020  1.090
 R77  C13  H12  single    0.970  0.020  1.090
 R77  C13  H13  single    0.970  0.020  1.090
 R77  C14  H14  single    0.970  0.020  1.090
 R77  C14  H15  single    0.970  0.020  1.090
 R77  C15  H16  single    0.970  0.020  1.090
 R77  C15  H17  single    0.970  0.020  1.090
 R77  C16  H18  single    0.970  0.020  1.090
 R77  C16  H19  single    0.970  0.020  1.090
 R77  C19  H20  single    0.930  0.020  1.080
 R77  C21  H21  single    0.930  0.020  1.080
 R77  C22  H22  single    0.930  0.020  1.080
 R77  C20  H23  single    0.930  0.020  1.080
 R77  C18  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
 R77  H1   O6   P4   115.28  3.000
 R77  C1   P4   O7   101.22  3.000
 R77  C1   P4   O5   117.12  3.000
 R77  O7   P4   O5   115.24  3.000
 R77  C1   P4   O6   108.48  3.000
 R77  O7   P4   O6   105.60  3.000
 R77  O5   P4   O6   108.40  3.000
 R77  H2   O7   P4   113.59  3.000
 R77  H4   C1   H3   105.60  3.000
 R77  H4   C1   C2   110.07  3.000
 R77  H3   C1   C2   110.80  3.000
 R77  H4   C1   P4   109.23  3.000
 R77  H3   C1   P4   106.21  3.000
 R77  C2   C1   P4   114.50  3.000
 R77  H5   C2   C13  107.78  3.000
 R77  H5   C2   C3   108.14  3.000
 R77  C13  C2   C3   109.30  3.000
 R77  H5   C2   C1   109.50  3.000
 R77  C13  C2   C1   111.74  3.000
 R77  C3   C2   C1   110.28  3.000
 R77  H7   C3   H6   105.60  3.000
 R77  H7   C3   C8   108.35  3.000
 R77  H6   C3   C8   110.32  3.000
 R77  H7   C3   C2   109.52  3.000
 R77  H6   C3   C2   110.05  3.000
 R77  C8   C3   C2   112.73  3.000
 R77  O12  C8   N9   120.96  3.000
 R77  O12  C8   C3   122.74  3.000
 R77  N9   C8   C3   116.28  3.000
 R77  C11  N9   O10  114.71  3.000
 R77  C11  N9   C8   125.05  3.000
 R77  O10  N9   C8   118.60  3.000
 R77  H8   O10  N9   106.33  3.000
 R77  H11  C11  H10  108.90  3.000
 R77  H11  C11  H9   108.44  3.000
 R77  H10  C11  H9   108.87  3.000
 R77  H11  C11  N9   109.90  3.000
 R77  H10  C11  N9   111.29  3.000
 R77  H9   C11  N9   109.39  3.000
 R77  H13  C13  H12  106.21  3.000
 R77  H13  C13  C14  109.09  3.000
 R77  H12  C13  C14  108.79  3.000
 R77  H13  C13  C2   109.18  3.000
 R77  H12  C13  C2   108.24  3.000
 R77  C14  C13  C2   114.98  3.000
 R77  H15  C14  H14  106.26  3.000
 R77  H15  C14  C15  109.82  3.000
 R77  H14  C14  C15  108.58  3.000
 R77  H15  C14  C13  109.75  3.000
 R77  H14  C14  C13  110.23  3.000
 R77  C15  C14  C13  112.03  3.000
 R77  H17  C15  H16  106.24  3.000
 R77  H17  C15  C16  109.13  3.000
 R77  H16  C15  C16  109.41  3.000
 R77  H17  C15  C14  109.38  3.000
 R77  H16  C15  C14  109.67  3.000
 R77  C16  C15  C14  112.81  3.000
 R77  H19  C16  H18  106.64  3.000
 R77  H19  C16  C17  109.82  3.000
 R77  H18  C16  C17  109.56  3.000
 R77  H19  C16  C15  109.35  3.000
 R77  H18  C16  C15  109.01  3.000
 R77  C17  C16  C15  112.29  3.000
 R77  C18  C17  C19  118.29  3.000
 R77  C18  C17  C16  120.56  3.000
 R77  C19  C17  C16  121.12  3.000
 R77  H20  C19  C21  119.59  3.000
 R77  H20  C19  C17  119.43  3.000
 R77  C21  C19  C17  120.98  3.000
 R77  H21  C21  C22  120.11  3.000
 R77  H21  C21  C19  119.75  3.000
 R77  C22  C21  C19  120.14  3.000
 R77  H22  C22  C20  120.23  3.000
 R77  H22  C22  C21  120.32  3.000
 R77  C20  C22  C21  119.45  3.000
 R77  H23  C20  C18  119.81  3.000
 R77  H23  C20  C22  120.05  3.000
 R77  C18  C20  C22  120.14  3.000
 R77  H24  C18  C20  119.54  3.000
 R77  H24  C18  C17  119.48  3.000
 R77  C20  C18  C17  120.99  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
 R77  CONST_01  C22  C21  C19  C17     0.00   0.0  0
 R77  CONST_02  C22  C20  C18  C17     0.00   0.0  0
 R77  CONST_03  C20  C22  C21  C19     0.00   0.0  0
 R77  CONST_04  C20  C18  C17  C19     0.00   0.0  0
 R77  CONST_05  C18  C20  C22  C21     0.00   0.0  0
 R77  CONST_06  C18  C17  C19  C21     0.00   0.0  0
 R77  CONST_07  C21  C19  C17  C16   180.00   0.0  0
 R77  CONST_08  C20  C18  C17  C16   180.00   0.0  0
 R77  CONST_09  H21  C21  C19  C17   180.00   0.0  0
 R77  CONST_10  H23  C20  C18  C17   180.00   0.0  0
 R77  CONST_11  H22  C22  C21  C19   180.00   0.0  0
 R77  CONST_12  H24  C18  C17  C19   180.00   0.0  0
 R77  CONST_13  H20  C19  C21  C22   180.00   0.0  0
 R77  CONST_14  O10  N9   C8   C3      0.00   0.0  0
 R77  CONST_15  C11  N9   C8   C3    180.00   0.0  0
 R77  CONST_16  O12  C8   N9   O10   180.00   0.0  0
 R77  CONST_17  O12  C8   N9   C11     0.00   0.0  0
 R77  Var_01    C19  C17  C16  C15   -95.19  30.0  2
 R77  Var_02    C17  C16  C15  C14  -179.71  30.0  1
 R77  Var_03    C2   C1   P4   O6    116.94  30.0  3
 R77  Var_04    N9   C8   C3   C2    177.33  30.0  2
 R77  Var_05    C15  C14  C13  C2    174.45  30.0  1
 R77  Var_06    C16  C15  C14  C13   174.53  30.0  2
 R77  Var_07    H9   C11  N9   C8    -18.49  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
 R77  chir_01  C2  C3  C13  C1  negativ

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
 R77  plan-1  C16  0.020
 R77  plan-1  C17  0.020
 R77  plan-1  C19  0.020
 R77  plan-1  C21  0.020
 R77  plan-1  C22  0.020
 R77  plan-1  C20  0.020
 R77  plan-1  C18  0.020
 R77  plan-1  H20  0.020
 R77  plan-1  H21  0.020
 R77  plan-1  H22  0.020
 R77  plan-1  H23  0.020
 R77  plan-1  H24  0.020
 R77  plan-2  C3   0.020
 R77  plan-2  C8   0.020
 R77  plan-2  N9   0.020
 R77  plan-2  O10  0.020
 R77  plan-2  C11  0.020
 R77  plan-2  O12  0.020

