# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat May  2 00:01:03 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  44  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 PERFECT
;

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  OP    -1  -1.004   0.0056   1.5467   2.1564
 R77  P4   P  P      0   1.116   1.2875   1.9592   1.4157
 R77  O5   O  O      0  -0.741   1.0448   2.7192   0.1025
 R77  O7   O  OP    -1  -0.945   2.3055   2.6553   2.3365
 R77  C1   C  CH2    0  -0.719   2.1611   0.3873   0.9229
 R77  C2   C  CH1    0  -0.179   1.5398  -0.4706  -0.1803
 R77  C3   C  CH2    0  -0.553   2.3790  -1.7355  -0.4374
 R77  C8   C  C      0   0.544   3.7938  -1.4126  -0.8489
 R77  N9   N  NT     0  -0.193   4.8106  -1.8016  -0.0458
 R77  O10  O  OH1    0  -0.573   4.5409  -2.2231   1.2308
 R77  C11  C  CH3    0  -0.569   6.1941  -1.4549  -0.2663
 R77  O12  O  O      0  -0.460   4.0273  -0.8437  -1.9077
 R77  C13  C  CH2    0  -0.436   0.0909  -0.8921   0.1239
 R77  C14  C  CH2    0  -0.408  -0.9652  -0.0573  -0.5883
 R77  C15  C  CH2    0  -0.386  -2.3736  -0.4183  -0.1408
 R77  C16  C  CH2    0  -0.493  -3.4641   0.3451  -0.8946
 R77  C17  C  C      0   0.091  -4.8417  -0.0584  -0.4494
 R77  C19  C  C1     0  -0.253  -5.4937  -1.1392  -1.0417
 R77  C21  C  C1     0  -0.172  -6.7452  -1.5491  -0.6005
 R77  C22  C  C1     0  -0.271  -7.3687  -0.8817   0.4465
 R77  C20  C  C1     0  -0.295  -6.7301   0.1968   1.0458
 R77  C18  C  C1     0  -0.334  -5.4782   0.6019   0.6003
 R77  H3   H  HCH2   0   0.220   3.1740   0.6756   0.6151
 R77  H4   H  HCH2   0   0.163   2.2963  -0.2353   1.8169
 R77  H5   H  HCH1   0   0.184   1.5384   0.1209  -1.1019
 R77  H6   H  HCH2   0   0.233   2.3282  -2.3833   0.4362
 R77  H7   H  HCH2   0   0.285   1.9383  -2.2894  -1.2724
 R77  H8   H  HOH1   0   0.474   4.6431  -3.1848   1.2232
 R77  H9   H  HCH3   0   0.256   6.3524  -1.2353  -1.3168
 R77  H10  H  HCH3   0   0.240   6.4872  -0.5840   0.3242
 R77  H11  H  HCH3   0   0.257   6.8292  -2.2961   0.0090
 R77  H12  H  HCH2   0   0.197  -0.0589  -1.9432  -0.1497
 R77  H13  H  HCH2   0   0.242  -0.0772  -0.8250   1.2004
 R77  H14  H  HCH2   0   0.201  -0.7723   0.9993  -0.4000
 R77  H15  H  HCH2   0   0.212  -0.8754  -0.2100  -1.6710
 R77  H16  H  HCH2   0   0.218  -2.5375  -1.4941  -0.2689
 R77  H17  H  HCH2   0   0.168  -2.4670  -0.2152   0.9310
 R77  H18  H  HCH2   0   0.242  -3.3244   1.4190  -0.7422
 R77  H19  H  HCH2   0   0.235  -3.3541   0.1628  -1.9675
 R77  H20  H  H      0   0.259  -5.0161  -1.6665  -1.8603
 R77  H21  H  H      0   0.182  -7.2364  -2.3881  -1.0773
 R77  H22  H  H      0   0.250  -8.3458  -1.1965   0.7897
 R77  H23  H  H      0   0.269  -7.2096   0.7270   1.8591
 R77  H24  H  H      0   0.249  -4.9882   1.4458   1.0730

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  1.394  0.020  1.394
 R77  C20  C18  aromatic  1.389  0.020  1.389
 R77  C17  C18  aromatic  1.394  0.020  1.394
 R77  C17  C16  single    1.503  0.020  1.503
 R77  C16  C15  single    1.530  0.020  1.530
 R77  O10  N9   single    1.371  0.020  1.371
 R77  C11  N9   single    1.443  0.020  1.443
 R77  C15  C14  single    1.521  0.020  1.521
 R77  N9   C8   single    1.353  0.020  1.353
 R77  O5   P4   deloc     1.537  0.020  1.537
 R77  C14  C13  single    1.523  0.020  1.523
 R77  C8   O12  double    1.224  0.020  1.224
 R77  C8   C3   single    1.508  0.020  1.508
 R77  C2   C3   single    1.540  0.020  1.540
 R77  C2   C13  single    1.539  0.020  1.539
 R77  C2   C1   single    1.529  0.020  1.529
 R77  P4   O7   deloc     1.539  0.020  1.539
 R77  P4   C1   single    1.865  0.020  1.865
 R77  P4   O6   deloc     1.537  0.020  1.537
 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  C1   P4   O7   103.27  3.000
 R77  C1   P4   O5   105.37  3.000
 R77  O7   P4   O5   113.08  3.000
 R77  C1   P4   O6   106.97  3.000
 R77  O7   P4   O6   112.63  3.000
 R77  O5   P4   O6   114.39  3.000
 R77  H4   C1   H3   105.30  3.000
 R77  H4   C1   C2   108.62  3.000
 R77  H3   C1   C2   108.67  3.000
 R77  H4   C1   P4   108.70  3.000
 R77  H3   C1   P4   106.57  3.000
 R77  C2   C1   P4   118.24  3.000
 R77  H5   C2   C13  108.24  3.000
 R77  H5   C2   C3   107.69  3.000
 R77  C13  C2   C3   108.73  3.000
 R77  H5   C2   C1   107.73  3.000
 R77  C13  C2   C1   113.17  3.000
 R77  C3   C2   C1   111.09  3.000
 R77  H7   C3   H6   106.99  3.000
 R77  H7   C3   C8   106.13  3.000
 R77  H6   C3   C8   112.96  3.000
 R77  H7   C3   C2   108.88  3.000
 R77  H6   C3   C2   109.23  3.000
 R77  C8   C3   C2   112.39  3.000
 R77  O12  C8   N9   120.24  3.000
 R77  O12  C8   C3   120.94  3.000
 R77  N9   C8   C3   118.78  3.000
 R77  C11  N9   O10  113.87  3.000
 R77  C11  N9   C8   124.10  3.000
 R77  O10  N9   C8   119.56  3.000
 R77  H8   O10  N9   106.12  3.000
 R77  H11  C11  H10  108.83  3.000
 R77  H11  C11  H9   108.42  3.000
 R77  H10  C11  H9   108.84  3.000
 R77  H11  C11  N9   109.55  3.000
 R77  H10  C11  N9   111.48  3.000
 R77  H9   C11  N9   109.66  3.000
 R77  H13  C13  H12  106.50  3.000
 R77  H13  C13  C14  108.70  3.000
 R77  H12  C13  C14  108.30  3.000
 R77  H13  C13  C2   108.85  3.000
 R77  H12  C13  C2   109.99  3.000
 R77  C14  C13  C2   114.22  3.000
 R77  H15  C14  H14  106.91  3.000
 R77  H15  C14  C15  109.45  3.000
 R77  H14  C14  C15  110.05  3.000
 R77  H15  C14  C13  109.18  3.000
 R77  H14  C14  C13  109.13  3.000
 R77  C15  C14  C13  111.98  3.000
 R77  H17  C15  H16  106.49  3.000
 R77  H17  C15  C16  109.21  3.000
 R77  H16  C15  C16  109.01  3.000
 R77  H17  C15  C14  108.84  3.000
 R77  H16  C15  C14  109.70  3.000
 R77  C16  C15  C14  113.37  3.000
 R77  H19  C16  H18  106.71  3.000
 R77  H19  C16  C17  109.75  3.000
 R77  H18  C16  C17  109.84  3.000
 R77  H19  C16  C15  109.18  3.000
 R77  H18  C16  C15  109.29  3.000
 R77  C17  C16  C15  111.93  3.000
 R77  C18  C17  C19  118.27  3.000
 R77  C18  C17  C16  120.96  3.000
 R77  C19  C17  C16  120.72  3.000
 R77  H20  C19  C21  119.54  3.000
 R77  H20  C19  C17  119.45  3.000
 R77  C21  C19  C17  121.01  3.000
 R77  H21  C21  C22  120.02  3.000
 R77  H21  C21  C19  119.84  3.000
 R77  C22  C21  C19  120.14  3.000
 R77  H22  C22  C20  120.26  3.000
 R77  H22  C22  C21  120.29  3.000
 R77  C20  C22  C21  119.45  3.000
 R77  H23  C20  C18  119.81  3.000
 R77  H23  C20  C22  120.04  3.000
 R77  C18  C20  C22  120.15  3.000
 R77  H24  C18  C20  119.63  3.000
 R77  H24  C18  C17  119.38  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   -87.48  30.0  2
 R77  Var_02    C17  C16  C15  C14   178.71  30.0  1
 R77  Var_03    C2   C1   P4   O6     70.60  30.0  3
 R77  Var_04    N9   C8   C3   C2    116.64  30.0  1
 R77  Var_05    C15  C14  C13  C2   -173.96  30.0  1
 R77  Var_06    C16  C15  C14  C13  -176.69  30.0  1
 R77  Var_07    H9   C11  N9   C8    -24.05  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

