# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed May 13 17:03:23 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  46  22  .  2021-08-13  2021-08-13  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

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  -0.722   3.2349   1.5802   0.8108
 L56  P5   P  P     0   1.395   1.9988   1.7602  -0.0079
 L56  O7   O  OH1   0  -0.735   0.8445   2.3015   0.9681
 L56  O6   O  OH1   0  -0.735   2.1337   2.8193  -1.2033
 L56  C1   C  CH2   0  -0.787   1.3968   0.3212  -0.9100
 L56  C2   C  CH1   0  -0.238   1.0935  -0.9662  -0.1240
 L56  C3   C  CH2   0  -0.552   2.3163  -1.5604   0.5879
 L56  C4   C  C     0   0.514   3.4761  -1.7582  -0.3637
 L56  N9   N  NT    0  -0.196   4.6421  -1.1474  -0.0814
 L56  C11  C  CH3   0  -0.513   5.8352  -1.2458  -0.8841
 L56  O10  O  OH1   0  -0.586   4.8251  -0.4792   1.0996
 L56  O12  O  O     0  -0.509   3.3338  -2.4267  -1.3836
 L56  C13  C  CH2   0  -0.421  -0.0619  -0.8431   0.8701
 L56  C14  C  CH2   0  -0.423  -1.3945  -0.4593   0.2417
 L56  C15  C  CH2   0  -0.505  -2.5224  -0.3905   1.2730
 L56  C16  C  CR6   0   0.162  -3.8590  -0.1276   0.6364
 L56  C18  C  CR16  0  -0.331  -4.1905   1.1461   0.1769
 L56  C20  C  CR16  0  -0.225  -5.4117   1.3718  -0.4403
 L56  C21  C  CR16  0  -0.322  -6.3180   0.3318  -0.6044
 L56  C19  C  CR6   0   0.118  -6.0117  -0.9495  -0.1544
 L56  C17  C  CR16  0  -0.371  -4.7780  -1.1574   0.4606
 L56  C22  C  CH3   0  -0.722  -6.9741  -2.0874  -0.3410
 L56  H1   H  HOH1  0   0.492   0.0368   2.6096   0.5369
 L56  H2   H  HOH1  0   0.499   2.5509   3.6558  -0.9525
 L56  H3   H  HCH2  0   0.308   0.5055   0.6343  -1.4597
 L56  H4   H  HCH2  0   0.310   2.1452   0.1132  -1.6797
 L56  H5   H  HCH1  0   0.259   0.7877  -1.6840  -0.8905
 L56  H6   H  HCH2  0   0.255   2.5727  -0.9761   1.4678
 L56  H7   H  HCH2  0   0.278   2.0375  -2.5531   0.9520
 L56  H8   H  HCH3  0   0.244   6.1811  -0.2520  -1.1705
 L56  H9   H  HCH3  0   0.245   6.6295  -1.7479  -0.3296
 L56  H10  H  HCH3  0   0.253   5.6243  -1.8159  -1.7823
 L56  H11  H  HOH1  0   0.475   4.3261   0.3696   1.0027
 L56  H12  H  HCH2  0   0.236  -0.1783  -1.8153   1.3589
 L56  H13  H  HCH2  0   0.227   0.1921  -0.1394   1.6677
 L56  H14  H  HCH2  0   0.215  -1.3263   0.5077  -0.2656
 L56  H15  H  HCH2  0   0.231  -1.6529  -1.1888  -0.5321
 L56  H16  H  HCH2  0   0.239  -2.5594  -1.3284   1.8335
 L56  H17  H  HCH2  0   0.239  -2.2957   0.3961   1.9988
 L56  H18  H  HCR6  0   0.239  -3.4930   1.9657   0.3081
 L56  H19  H  HCR6  0   0.249  -5.6650   2.3650  -0.7895
 L56  H20  H  HCR6  0   0.243  -7.2729   0.5217  -1.0805
 L56  H21  H  HCR6  0   0.236  -4.5266  -2.1510   0.8183
 L56  H22  H  HCH3  0   0.247  -6.7642  -2.6325  -1.2637
 L56  H23  H  HCH3  0   0.242  -6.9090  -2.8031   0.4779
 L56  H24  H  HCH3  0   0.242  -8.0034  -1.7349  -0.4009

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  1.389  0.020  1.389
 L56  C20  C18  aromatic  1.387  0.020  1.387
 L56  C21  C19  aromatic  1.392  0.020  1.392
 L56  C18  C16  aromatic  1.394  0.020  1.394
 L56  C19  C22  single    1.502  0.020  1.502
 L56  C19  C17  aromatic  1.394  0.020  1.394
 L56  C16  C17  aromatic  1.391  0.020  1.391
 L56  C16  C15  single    1.504  0.020  1.504
 L56  C15  C14  single    1.530  0.020  1.530
 L56  C11  N9   single    1.441  0.020  1.441
 L56  O10  N9   single    1.369  0.020  1.369
 L56  C13  C14  single    1.522  0.020  1.522
 L56  C13  C2   single    1.529  0.020  1.529
 L56  N9   C4   single    1.346  0.020  1.346
 L56  O8   P5   double    1.493  0.020  1.493
 L56  C4   O12  double    1.228  0.020  1.228
 L56  C4   C3   single    1.513  0.020  1.513
 L56  C2   C3   single    1.535  0.020  1.535
 L56  C2   C1   single    1.539  0.020  1.539
 L56  C1   P5   single    1.802  0.020  1.802
 L56  P5   O6   single    1.603  0.020  1.603
 L56  P5   O7   single    1.606  0.020  1.606
 L56  O7   H1   single    0.850  0.020  0.980
 L56  O6   H2   single    0.850  0.020  0.980
 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   100.51  3.000
 L56  O6   P5   O7   106.92  3.000
 L56  C1   P5   O7   109.47  3.000
 L56  O7   P5   O8   107.60  3.000
 L56  O6   P5   O8   114.76  3.000
 L56  C1   P5   O8   117.05  3.000
 L56  H1   O7   P5   115.93  3.000
 L56  H2   O6   P5   114.46  3.000
 L56  H4   C1   H3   104.99  3.000
 L56  H4   C1   C2   109.59  3.000
 L56  H3   C1   C2   109.63  3.000
 L56  H4   C1   P5   106.00  3.000
 L56  H3   C1   P5   107.19  3.000
 L56  C2   C1   P5   118.58  3.000
 L56  H5   C2   C13  107.29  3.000
 L56  H5   C2   C3   107.08  3.000
 L56  C13  C2   C3   109.37  3.000
 L56  H5   C2   C1   104.25  3.000
 L56  C3   C2   C1   113.82  3.000
 L56  C13  C2   C1   114.43  3.000
 L56  H7   C3   H6   106.17  3.000
 L56  H7   C3   C4   106.63  3.000
 L56  H6   C3   C4   113.49  3.000
 L56  H7   C3   C2   107.63  3.000
 L56  H6   C3   C2   110.82  3.000
 L56  C4   C3   C2   111.69  3.000
 L56  O12  C4   N9   121.44  3.000
 L56  O12  C4   C3   120.31  3.000
 L56  N9   C4   C3   118.21  3.000
 L56  O10  N9   C11  113.77  3.000
 L56  O10  N9   C4   121.20  3.000
 L56  C11  N9   C4   124.70  3.000
 L56  H10  C11  H9   108.70  3.000
 L56  H10  C11  H8   108.85  3.000
 L56  H9   C11  H8   108.79  3.000
 L56  H10  C11  N9   109.64  3.000
 L56  H9   C11  N9   110.55  3.000
 L56  H8   C11  N9   110.28  3.000
 L56  H11  O10  N9   105.48  3.000
 L56  H13  C13  H12  105.69  3.000
 L56  H13  C13  C14  110.01  3.000
 L56  H12  C13  C14  108.37  3.000
 L56  H13  C13  C2   110.52  3.000
 L56  H12  C13  C2   107.41  3.000
 L56  C14  C13  C2   114.42  3.000
 L56  H15  C14  H14  106.02  3.000
 L56  H15  C14  C15  109.43  3.000
 L56  H14  C14  C15  108.59  3.000
 L56  H15  C14  C13  109.30  3.000
 L56  H14  C14  C13  111.07  3.000
 L56  C15  C14  C13  112.24  3.000
 L56  H17  C15  H16  106.48  3.000
 L56  H17  C15  C16  109.83  3.000
 L56  H16  C15  C16  109.69  3.000
 L56  H17  C15  C14  109.08  3.000
 L56  H16  C15  C14  109.39  3.000
 L56  C16  C15  C14  112.20  3.000
 L56  C17  C16  C18  118.53  3.000
 L56  C17  C16  C15  120.74  3.000
 L56  C18  C16  C15  120.71  3.000
 L56  H18  C18  C20  119.82  3.000
 L56  H18  C18  C16  119.86  3.000
 L56  C20  C18  C16  120.32  3.000
 L56  H19  C20  C21  119.73  3.000
 L56  H19  C20  C18  119.92  3.000
 L56  C21  C20  C18  120.34  3.000
 L56  H20  C21  C19  119.81  3.000
 L56  H20  C21  C20  119.70  3.000
 L56  C19  C21  C20  120.49  3.000
 L56  C22  C19  C17  120.59  3.000
 L56  C17  C19  C21  118.33  3.000
 L56  C22  C19  C21  121.08  3.000
 L56  H21  C17  C19  119.13  3.000
 L56  H21  C17  C16  118.87  3.000
 L56  C19  C17  C16  121.99  3.000
 L56  H24  C22  H23  108.07  3.000
 L56  H24  C22  H22  107.25  3.000
 L56  H23  C22  H22  107.20  3.000
 L56  H24  C22  C19  111.54  3.000
 L56  H23  C22  C19  111.47  3.000
 L56  H22  C22  C19  111.10  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_15  C11  N9   C4   C3    180.00   0.0  0
 L56  CONST_16  O10  N9   C4   C3      0.00   0.0  0
 L56  CONST_17  O12  C4   N9   C11     0.00   0.0  0
 L56  CONST_18  O12  C4   N9   O10   180.00   0.0  0
 L56  Var_01    C18  C16  C15  C14   -75.54  30.0  2
 L56  Var_02    H22  C22  C19  C21    93.07  30.0  2
 L56  Var_03    C16  C15  C14  C13  -175.10  30.0  1
 L56  Var_04    C2   C1   P5   O8     56.18  30.0  3
 L56  Var_05    C15  C14  C13  C2    178.31  30.0  3
 L56  Var_06    N9   C4   C3   C2    122.26  30.0  2
 L56  Var_07    H8   C11  N9   C4    124.40  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

