# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed May 13 05:25:37 2020
#   Inital geometry file: a 111 line input string
#   Ligand name: [(2R)-2-{2-[hydroxy(methyl)amino]-2-oxoethyl}-5-(3-methylphenyl)pentyl]phosphonic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CN(O)C(=O)C[C@@H](CCCc1cccc(C)c1)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
 L56  L56  '[(2R)-2-{2-[hydroxy(methyl)amino]-2-oxoethyl}-5-(3-methylphenyl)pentyl]phosphonic acid'  ligand  44  22  .  2021-08-12  2021-08-12  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_L56
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
 L56  O8   O  O      0  -0.875   3.6990   1.1453  -0.8953
 L56  P5   P  P      0   1.175   2.2721   1.7198  -0.8890
 L56  O7   O  OP    -1  -0.904   1.8432   2.2904   0.4742
 L56  O6   O  OP    -1  -0.917   2.0129   2.6896  -2.0554
 L56  C1   C  CH2    0  -0.726   1.1479   0.2786  -1.2470
 L56  C2   C  CH1    0  -0.184   0.9991  -0.7971  -0.1595
 L56  C3   C  CH2    0  -0.581   2.3004  -1.0717   0.5940
 L56  C4   C  C      0   0.593   3.4361  -1.5098  -0.2935
 L56  N9   N  NT     0  -0.214   4.6930  -1.4993   0.2464
 L56  C11  C  CH3    0  -0.515   5.8675  -1.4892  -0.5915
 L56  O10  O  OH1    0  -0.552   4.8744  -0.7834   1.4096
 L56  O12  O  O      0  -0.513   3.2626  -2.0100  -1.3953
 L56  C13  C  CH2    0  -0.409  -0.0795  -0.4374   0.8679
 L56  C14  C  CH2    0  -0.416  -1.4913  -0.3616   0.2970
 L56  C15  C  CH2    0  -0.505  -2.5631  -0.2916   1.3866
 L56  C16  C  C      0   0.160  -3.9409  -0.1056   0.8153
 L56  C18  C  C1     0  -0.340  -4.5047   1.1625   0.7106
 L56  C20  C  C1     0  -0.225  -5.7597   1.3288   0.1391
 L56  C21  C  C1     0  -0.319  -6.4626   0.2328  -0.3384
 L56  C19  C  C      0   0.119  -5.9195  -1.0486  -0.2495
 L56  C17  C  C1     0  -0.367  -4.6639  -1.1958   0.3331
 L56  C22  C  CH3    0  -0.725  -6.6634  -2.2349  -0.7921
 L56  H3   H  HCH2   0   0.191   0.1566   0.6671  -1.5013
 L56  H4   H  HCH2   0   0.195   1.5148  -0.1899  -2.1636
 L56  H5   H  HCH1   0   0.186   0.6802  -1.7322  -0.6371
 L56  H6   H  HCH2   0   0.258   2.5800  -0.1877   1.1608
 L56  H7   H  HCH2   0   0.240   2.1321  -1.8710   1.3282
 L56  H8   H  HCH3   0   0.231   6.1122  -0.4729  -0.9095
 L56  H9   H  HCH3   0   0.232   6.7125  -1.9122  -0.0496
 L56  H10  H  HCH3   0   0.241   5.6910  -2.0987  -1.4720
 L56  H11  H  HOH1   0   0.466   5.0272  -1.4470   2.0933
 L56  H12  H  HCH2   0   0.194  -0.0705  -1.1863   1.6702
 L56  H13  H  HCH2   0   0.217   0.1860   0.5196   1.3242
 L56  H14  H  HCH2   0   0.219  -1.5928   0.5108  -0.3540
 L56  H15  H  HCH2   0   0.209  -1.6814  -1.2353  -0.3367
 L56  H16  H  HCH2   0   0.232  -2.5261  -1.2062   1.9856
 L56  H17  H  HCH2   0   0.232  -2.3361   0.5347   2.0662
 L56  H18  H  H      0   0.241  -3.9627   2.0243   1.0831
 L56  H19  H  H      0   0.248  -6.1927   2.3188   0.0680
 L56  H20  H  H      0   0.242  -7.4419   0.3737  -0.7811
 L56  H21  H  H      0   0.234  -4.2361  -2.1898   0.4205
 L56  H22  H  HCH3   0   0.246  -6.5632  -2.2942  -1.8780
 L56  H23  H  HCH3   0   0.242  -6.2853  -3.1696  -0.3796
 L56  H24  H  HCH3   0   0.242  -7.7296  -2.1753  -0.5727

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
 L56  C20  C21  aromatic  1.387  0.020  1.387
 L56  C20  C18  aromatic  1.389  0.020  1.389
 L56  C21  C19  aromatic  1.395  0.020  1.395
 L56  C18  C16  aromatic  1.392  0.020  1.392
 L56  C19  C22  single    1.502  0.020  1.502
 L56  C19  C17  aromatic  1.392  0.020  1.392
 L56  C16  C17  aromatic  1.394  0.020  1.394
 L56  C16  C15  single    1.503  0.020  1.503
 L56  C15  C14  single    1.530  0.020  1.530
 L56  C11  N9   single    1.443  0.020  1.443
 L56  O10  N9   single    1.378  0.020  1.378
 L56  C13  C14  single    1.525  0.020  1.525
 L56  C13  C2   single    1.532  0.020  1.532
 L56  N9   C4   single    1.368  0.020  1.368
 L56  O8   P5   deloc     1.538  0.020  1.538
 L56  C4   O12  double    1.222  0.020  1.222
 L56  C4   C3   single    1.506  0.020  1.506
 L56  C2   C3   single    1.529  0.020  1.529
 L56  C2   C1   single    1.537  0.020  1.537
 L56  C1   P5   single    1.862  0.020  1.862
 L56  P5   O6   deloc     1.539  0.020  1.539
 L56  P5   O7   deloc     1.539  0.020  1.539
 L56  C1   H3   single    0.970  0.020  1.090
 L56  C1   H4   single    0.970  0.020  1.090
 L56  C2   H5   single    0.970  0.020  1.090
 L56  C3   H6   single    0.970  0.020  1.090
 L56  C3   H7   single    0.970  0.020  1.090
 L56  C11  H8   single    0.970  0.020  1.090
 L56  C11  H9   single    0.970  0.020  1.090
 L56  C11  H10  single    0.970  0.020  1.090
 L56  O10  H11  single    0.850  0.020  0.980
 L56  C13  H12  single    0.970  0.020  1.090
 L56  C13  H13  single    0.970  0.020  1.090
 L56  C14  H14  single    0.970  0.020  1.090
 L56  C14  H15  single    0.970  0.020  1.090
 L56  C15  H16  single    0.970  0.020  1.090
 L56  C15  H17  single    0.970  0.020  1.090
 L56  C18  H18  single    0.930  0.020  1.080
 L56  C20  H19  single    0.930  0.020  1.080
 L56  C21  H20  single    0.930  0.020  1.080
 L56  C17  H21  single    0.930  0.020  1.080
 L56  C22  H22  single    0.970  0.020  1.090
 L56  C22  H23  single    0.970  0.020  1.090
 L56  C22  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
 L56  C1   P5   O6   103.91  3.000
 L56  O6   P5   O7   113.01  3.000
 L56  C1   P5   O7   106.80  3.000
 L56  O7   P5   O8   113.62  3.000
 L56  O6   P5   O8   112.86  3.000
 L56  C1   P5   O8   105.67  3.000
 L56  H4   C1   H3   105.15  3.000
 L56  H4   C1   C2   109.02  3.000
 L56  H3   C1   C2   108.97  3.000
 L56  H4   C1   P5   106.88  3.000
 L56  H3   C1   P5   108.46  3.000
 L56  C2   C1   P5   117.65  3.000
 L56  H5   C2   C13  106.69  3.000
 L56  H5   C2   C3   107.99  3.000
 L56  C13  C2   C3   108.11  3.000
 L56  H5   C2   C1   108.46  3.000
 L56  C3   C2   C1   113.08  3.000
 L56  C13  C2   C1   112.23  3.000
 L56  H7   C3   H6   106.42  3.000
 L56  H7   C3   C4   107.32  3.000
 L56  H6   C3   C4   110.48  3.000
 L56  H7   C3   C2   109.26  3.000
 L56  H6   C3   C2   109.27  3.000
 L56  C4   C3   C2   113.81  3.000
 L56  O12  C4   N9   119.29  3.000
 L56  O12  C4   C3   122.89  3.000
 L56  N9   C4   C3   117.25  3.000
 L56  O10  N9   C11  112.30  3.000
 L56  O10  N9   C4   117.27  3.000
 L56  C11  N9   C4   121.25  3.000
 L56  H10  C11  H9   108.16  3.000
 L56  H10  C11  H8   108.83  3.000
 L56  H9   C11  H8   109.41  3.000
 L56  H10  C11  N9   109.56  3.000
 L56  H9   C11  N9   109.87  3.000
 L56  H8   C11  N9   110.97  3.000
 L56  H11  O10  N9   105.17  3.000
 L56  H13  C13  H12  106.87  3.000
 L56  H13  C13  C14  109.74  3.000
 L56  H12  C13  C14  108.37  3.000
 L56  H13  C13  C2   108.33  3.000
 L56  H12  C13  C2   108.92  3.000
 L56  C14  C13  C2   114.35  3.000
 L56  H15  C14  H14  106.00  3.000
 L56  H15  C14  C15  109.08  3.000
 L56  H14  C14  C15  108.81  3.000
 L56  H15  C14  C13  109.72  3.000
 L56  H14  C14  C13  110.40  3.000
 L56  C15  C14  C13  112.60  3.000
 L56  H17  C15  H16  106.52  3.000
 L56  H17  C15  C16  109.45  3.000
 L56  H16  C15  C16  110.03  3.000
 L56  H17  C15  C14  109.37  3.000
 L56  H16  C15  C14  109.15  3.000
 L56  C16  C15  C14  112.16  3.000
 L56  C17  C16  C18  118.45  3.000
 L56  C17  C16  C15  120.67  3.000
 L56  C18  C16  C15  120.84  3.000
 L56  H18  C18  C20  119.86  3.000
 L56  H18  C18  C16  119.73  3.000
 L56  C20  C18  C16  120.40  3.000
 L56  H19  C20  C21  119.82  3.000
 L56  H19  C20  C18  119.85  3.000
 L56  C21  C20  C18  120.33  3.000
 L56  H20  C21  C19  119.83  3.000
 L56  H20  C21  C20  119.72  3.000
 L56  C19  C21  C20  120.45  3.000
 L56  C22  C19  C17  120.97  3.000
 L56  C17  C19  C21  118.37  3.000
 L56  C22  C19  C21  120.65  3.000
 L56  H21  C17  C19  119.07  3.000
 L56  H21  C17  C16  118.93  3.000
 L56  C19  C17  C16  121.99  3.000
 L56  H24  C22  H23  108.07  3.000
 L56  H24  C22  H22  107.03  3.000
 L56  H23  C22  H22  107.34  3.000
 L56  H24  C22  C19  111.63  3.000
 L56  H23  C22  C19  111.65  3.000
 L56  H22  C22  C19  110.90  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
 L56  CONST_01  C21  C20  C18  C16    0.00   0.0  0
 L56  CONST_02  C21  C19  C17  C16    0.00   0.0  0
 L56  CONST_03  C19  C21  C20  C18    0.00   0.0  0
 L56  CONST_04  C19  C17  C16  C18    0.00   0.0  0
 L56  CONST_05  C17  C19  C21  C20    0.00   0.0  0
 L56  CONST_06  C17  C16  C18  C20    0.00   0.0  0
 L56  CONST_07  C20  C18  C16  C15  180.00   0.0  0
 L56  CONST_08  C19  C17  C16  C15  180.00   0.0  0
 L56  CONST_09  C22  C19  C17  C16  180.00   0.0  0
 L56  CONST_10  C22  C19  C21  C20  180.00   0.0  0
 L56  CONST_11  H19  C20  C18  C16  180.00   0.0  0
 L56  CONST_12  H20  C21  C20  C18  180.00   0.0  0
 L56  CONST_13  H21  C17  C16  C18  180.00   0.0  0
 L56  CONST_14  H18  C18  C20  C21  180.00   0.0  0
 L56  CONST_18  O12  C4   N9   O10  180.00   0.0  0
 L56  Var_01    C18  C16  C15  C14  -95.67  30.0  2
 L56  Var_02    H22  C22  C19  C21   78.54  30.0  2
 L56  Var_03    C16  C15  C14  C13  175.39  30.0  1
 L56  Var_04    C2   C1   P5   O8    69.83  30.0  3
 L56  Var_05    C15  C14  C13  C2   168.04  30.0  3
 L56  Var_06    N9   C4   C3   C2   166.39  30.0  2
 L56  Var_07    H8   C11  N9   C4    83.71  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
 L56  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
 L56  plan-1  C15  0.020
 L56  plan-1  C16  0.020
 L56  plan-1  C18  0.020
 L56  plan-1  C20  0.020
 L56  plan-1  C21  0.020
 L56  plan-1  C19  0.020
 L56  plan-1  C17  0.020
 L56  plan-1  C22  0.020
 L56  plan-1  H18  0.020
 L56  plan-1  H19  0.020
 L56  plan-1  H20  0.020
 L56  plan-1  H21  0.020
 L56  plan-2  C3   0.020
 L56  plan-2  C4   0.020
 L56  plan-2  N9   0.020
 L56  plan-2  C11  0.020
 L56  plan-2  O10  0.020
 L56  plan-2  O12  0.020

