# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat May  2 04:42:36 2020
#   Inital geometry file: a 87 line input string
#   Ligand name: {(2R)-4-[hydroxy(methyl)amino]-4-oxo-2-phenylbutyl}phosphonic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CN(O)C(=O)C[C@@H](C[P](O)(O)=O)c1ccccc1
#
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
 RF7  RF7  '{(2R)-4-[hydroxy(methyl)amino]-4-oxo-2-phenylbutyl}phosphonic acid'  ligand  32  18  .  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_RF7
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
 RF7  O6   O  OP    -1  -0.889  -2.2540  -1.3090   1.1002
 RF7  P4   P  P      0   1.174  -0.9524  -2.0074   0.6982
 RF7  O5   O  OP    -1  -0.918  -0.4559  -3.0221   1.7412
 RF7  O7   O  O      0  -0.912  -0.9577  -2.5579  -0.7362
 RF7  C1   C  CH2    0  -0.723   0.3767  -0.6965   0.6896
 RF7  C2   C  CH1    0  -0.320   0.2249   0.3531  -0.4096
 RF7  C3   C  CH2    0  -0.526   1.4481   1.2927  -0.5238
 RF7  C8   C  C      0   0.509   2.6934   0.5221  -0.8928
 RF7  N9   N  NT     0  -0.191   3.5954   0.2629   0.0798
 RF7  O10  O  OH1    0  -0.547   3.3985   0.7442   1.3466
 RF7  C11  C  CH3    0  -0.512   4.8216  -0.4746  -0.0940
 RF7  O12  O  O      0  -0.503   2.8712   0.1182  -2.0359
 RF7  C13  C  CR6    0   0.235  -1.0048   1.2153  -0.2577
 RF7  C15  C  CR16   0  -0.308  -1.2668   1.8995   0.9272
 RF7  C16  C  CR16   0  -0.247  -2.3521   2.7553   1.0353
 RF7  C18  C  CR16   0  -0.283  -3.2063   2.9422  -0.0459
 RF7  C17  C  CR16   0  -0.245  -2.9556   2.2689  -1.2330
 RF7  C14  C  CR16   0  -0.333  -1.8619   1.4169  -1.3335
 RF7  H3   H  HCH2   0   0.190   0.4291  -0.2126   1.6724
 RF7  H4   H  HCH2   0   0.195   1.3327  -1.2176   0.5561
 RF7  H5   H  HCH1   0   0.229   0.1354  -0.1854  -1.3572
 RF7  H6   H  HCH2   0   0.260   1.2769   2.0053  -1.3344
 RF7  H7   H  HCH2   0   0.251   1.5606   1.8696   0.3930
 RF7  H8   H  HOH1   0   0.473   2.8952   0.0669   1.8213
 RF7  H9   H  HCH3   0   0.255   4.9085  -0.7896  -1.1282
 RF7  H10  H  HCH3   0   0.247   5.6814   0.1472   0.1581
 RF7  H11  H  HCH3   0   0.244   4.8288  -1.3612   0.5425
 RF7  H12  H  HCR6   0   0.233  -0.6130   1.7660   1.7810
 RF7  H13  H  HCR6   0   0.242  -2.5345   3.2788   1.9660
 RF7  H14  H  HCR6   0   0.244  -4.0549   3.6095   0.0367
 RF7  H15  H  HCR6   0   0.243  -3.6102   2.4083  -2.0846
 RF7  H16  H  HCR6   0   0.234  -1.6707   0.9002  -2.2672

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
 RF7  C11  N9   single    1.441  0.020  1.441
 RF7  O10  N9   single    1.369  0.020  1.369
 RF7  N9   C8   single    1.352  0.020  1.352
 RF7  C8   O12  double    1.225  0.020  1.225
 RF7  C8   C3   single    1.510  0.020  1.510
 RF7  O7   P4   deloc     1.536  0.020  1.536
 RF7  C1   P4   single    1.867  0.020  1.867
 RF7  C1   C2   single    1.527  0.020  1.527
 RF7  C3   C2   single    1.547  0.020  1.547
 RF7  P4   O5   deloc     1.538  0.020  1.538
 RF7  P4   O6   deloc     1.531  0.020  1.531
 RF7  C2   C13  single    1.510  0.020  1.510
 RF7  C15  C13  aromatic  1.393  0.020  1.393
 RF7  C15  C16  aromatic  1.386  0.020  1.386
 RF7  C13  C14  aromatic  1.390  0.020  1.390
 RF7  C16  C18  aromatic  1.391  0.020  1.391
 RF7  C14  C17  aromatic  1.390  0.020  1.390
 RF7  C18  C17  aromatic  1.388  0.020  1.388
 RF7  C1   H3   single    0.970  0.020  1.090
 RF7  C1   H4   single    0.970  0.020  1.090
 RF7  C2   H5   single    0.970  0.020  1.090
 RF7  C3   H6   single    0.970  0.020  1.090
 RF7  C3   H7   single    0.970  0.020  1.090
 RF7  O10  H8   single    0.850  0.020  0.980
 RF7  C11  H9   single    0.970  0.020  1.090
 RF7  C11  H10  single    0.970  0.020  1.090
 RF7  C11  H11  single    0.970  0.020  1.090
 RF7  C15  H12  single    0.930  0.020  1.080
 RF7  C16  H13  single    0.930  0.020  1.080
 RF7  C18  H14  single    0.930  0.020  1.080
 RF7  C17  H15  single    0.930  0.020  1.080
 RF7  C14  H16  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
 RF7  C1   P4   O7   104.46  3.000
 RF7  C1   P4   O5   103.69  3.000
 RF7  O7   P4   O5   113.45  3.000
 RF7  O5   P4   O6   113.43  3.000
 RF7  C1   P4   O6   106.63  3.000
 RF7  O7   P4   O6   113.94  3.000
 RF7  H4   C1   H3   106.08  3.000
 RF7  H4   C1   C2   108.99  3.000
 RF7  H3   C1   C2   110.27  3.000
 RF7  H4   C1   P4   106.71  3.000
 RF7  H3   C1   P4   109.86  3.000
 RF7  C2   C1   P4   114.53  3.000
 RF7  H5   C2   C13  107.56  3.000
 RF7  H5   C2   C3   107.45  3.000
 RF7  C13  C2   C3   107.74  3.000
 RF7  H5   C2   C1   107.06  3.000
 RF7  C13  C2   C1   113.65  3.000
 RF7  C3   C2   C1   113.08  3.000
 RF7  H7   C3   H6   107.17  3.000
 RF7  H7   C3   C8   113.00  3.000
 RF7  H6   C3   C8   106.30  3.000
 RF7  H7   C3   C2   109.96  3.000
 RF7  H6   C3   C2   109.09  3.000
 RF7  C8   C3   C2   111.11  3.000
 RF7  O12  C8   N9   120.75  3.000
 RF7  O12  C8   C3   121.05  3.000
 RF7  N9   C8   C3   118.18  3.000
 RF7  C11  N9   O10  114.44  3.000
 RF7  O10  N9   C8   120.16  3.000
 RF7  C11  N9   C8   125.39  3.000
 RF7  H8   O10  N9   106.40  3.000
 RF7  H11  C11  H10  108.85  3.000
 RF7  H11  C11  H9   108.64  3.000
 RF7  H10  C11  H9   108.83  3.000
 RF7  H11  C11  N9   110.54  3.000
 RF7  H10  C11  N9   110.55  3.000
 RF7  H9   C11  N9   109.37  3.000
 RF7  C14  C13  C15  118.10  3.000
 RF7  C14  C13  C2   120.48  3.000
 RF7  C15  C13  C2   121.28  3.000
 RF7  H12  C15  C16  119.14  3.000
 RF7  H12  C15  C13  119.75  3.000
 RF7  C16  C15  C13  121.11  3.000
 RF7  H13  C16  C18  119.97  3.000
 RF7  H13  C16  C15  119.81  3.000
 RF7  C18  C16  C15  120.21  3.000
 RF7  H14  C18  C17  120.39  3.000
 RF7  H14  C18  C16  120.34  3.000
 RF7  C17  C18  C16  119.27  3.000
 RF7  H15  C17  C14  119.84  3.000
 RF7  H15  C17  C18  120.07  3.000
 RF7  C14  C17  C18  120.09  3.000
 RF7  H16  C14  C17  119.54  3.000
 RF7  H16  C14  C13  119.25  3.000
 RF7  C17  C14  C13  121.20  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
 RF7  CONST_01  C18  C16  C15  C13     0.00   0.0  0
 RF7  CONST_02  C18  C17  C14  C13     0.00   0.0  0
 RF7  CONST_03  C17  C14  C13  C15     0.00   0.0  0
 RF7  CONST_04  C17  C18  C16  C15     0.00   0.0  0
 RF7  CONST_05  C14  C13  C15  C16     0.00   0.0  0
 RF7  CONST_06  C14  C17  C18  C16     0.00   0.0  0
 RF7  CONST_07  C16  C15  C13  C2    180.00   0.0  0
 RF7  CONST_08  C17  C14  C13  C2    180.00   0.0  0
 RF7  CONST_09  H13  C16  C15  C13   180.00   0.0  0
 RF7  CONST_10  H15  C17  C14  C13   180.00   0.0  0
 RF7  CONST_11  H16  C14  C13  C15   180.00   0.0  0
 RF7  CONST_12  H14  C18  C16  C15   180.00   0.0  0
 RF7  CONST_13  H12  C15  C16  C18   180.00   0.0  0
 RF7  CONST_14  C11  N9   C8   C3    180.00   0.0  0
 RF7  CONST_15  O10  N9   C8   C3      0.00   0.0  0
 RF7  CONST_16  O12  C8   N9   O10   180.00   0.0  0
 RF7  CONST_17  O12  C8   N9   C11     0.00   0.0  0
 RF7  Var_01    C2   C1   P4   O6    -67.91  30.0  3
 RF7  Var_02    N9   C8   C3   C2   -103.22  30.0  1
 RF7  Var_03    H9   C11  N9   C8      0.02  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
 RF7  chir_01  C2  C1  C3  C13  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
 RF7  plan-1  C2   0.020
 RF7  plan-1  C13  0.020
 RF7  plan-1  C15  0.020
 RF7  plan-1  C16  0.020
 RF7  plan-1  C18  0.020
 RF7  plan-1  C17  0.020
 RF7  plan-1  C14  0.020
 RF7  plan-1  H12  0.020
 RF7  plan-1  H13  0.020
 RF7  plan-1  H14  0.020
 RF7  plan-1  H15  0.020
 RF7  plan-1  H16  0.020
 RF7  plan-2  C3   0.020
 RF7  plan-2  C8   0.020
 RF7  plan-2  N9   0.020
 RF7  plan-2  O10  0.020
 RF7  plan-2  C11  0.020
 RF7  plan-2  O12  0.020

