# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon May 25 13:48:54 2020
#   Inital geometry file: a 105 line input string
#   Ligand name: [(2R)-2-{2-[hydroxy(methyl)amino]-2-oxoethyl}-5-phenylpentyl]phosphonic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CN(O)C(=O)C[C@@H](CCCc1ccccc1)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
 RC5  RC5  '[(2R)-2-{2-[hydroxy(methyl)amino]-2-oxoethyl}-5-phenylpentyl]phosphonic acid'  ligand  43  21  .  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_RC5
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
 RC5  O12  O  O     0  -0.489  -1.7908   2.1469  -1.3552
 RC5  C4   C  C     0   0.557  -2.5279   1.8351  -0.4317
 RC5  N9   N  NT    0  -0.210  -3.5738   2.6231  -0.0852
 RC5  O10  O  OH1   0  -0.546  -4.5179   2.1074   0.7666
 RC5  C11  C  CH3   0  -0.516  -4.0207   3.7586  -0.8553
 RC5  C3   C  CH2   0  -0.567  -2.3378   0.5764   0.3879
 RC5  C2   C  CH1   0  -0.244  -0.9849  -0.0954   0.1570
 RC5  C1   C  CH2   0  -0.762  -0.9825  -1.5145   0.7480
 RC5  P5   P  P     0   1.370  -1.8049  -2.7562  -0.2697
 RC5  O7   O  OH1   0  -0.746  -1.4280  -4.0977   0.5354
 RC5  O6   O  OH1   0  -0.749  -3.4024  -2.5841  -0.1248
 RC5  O8   O  O     0  -0.716  -1.4531  -2.7404  -1.7106
 RC5  C13  C  CH2   0  -0.417   0.1450   0.7282   0.7850
 RC5  C14  C  CH2   0  -0.420   1.5367   0.3496   0.2937
 RC5  C15  C  CH2   0  -0.505   2.6326   1.1708   0.9754
 RC5  C16  C  CR6   0   0.139   4.0023   0.8229   0.4644
 RC5  C17  C  CR16  0  -0.312   4.5184   1.4508  -0.6681
 RC5  C19  C  CR16  0  -0.239   5.7656   1.1057  -1.1711
 RC5  C21  C  CR16  0  -0.275   6.5204   0.1206  -0.5466
 RC5  C20  C  CR16  0  -0.240   6.0170  -0.5138   0.5818
 RC5  C18  C  CR16  0  -0.316   4.7687  -0.1642   1.0805
 RC5  H1   H  HOH1  0   0.477  -4.3723   2.5349   1.6217
 RC5  H2   H  HCH3  0   0.243  -4.7884   3.4806  -1.5806
 RC5  H3   H  HCH3  0   0.249  -4.4272   4.5124  -0.1825
 RC5  H4   H  HCH3  0   0.255  -3.1783   4.1926  -1.3842
 RC5  H5   H  HCH2  0   0.261  -2.4606   0.7908   1.4530
 RC5  H6   H  HCH2  0   0.282  -3.1582  -0.1005   0.1357
 RC5  H7   H  HCH1  0   0.243  -0.7990  -0.1634  -0.9183
 RC5  H8   H  HCH2  0   0.295   0.0453  -1.8701   0.8582
 RC5  H9   H  HCH2  0   0.287  -1.4091  -1.5148   1.7552
 RC5  H10  H  HOH1  0   0.493  -1.7069  -4.9135   0.0964
 RC5  H11  H  HOH1  0   0.489  -3.7446  -2.6336   0.7773
 RC5  H12  H  HCH2  0   0.238  -0.0131   1.7873   0.5692
 RC5  H13  H  HCH2  0   0.218   0.0953   0.6273   1.8754
 RC5  H14  H  HCH2  0   0.225   1.7340  -0.7126   0.4649
 RC5  H15  H  HCH2  0   0.227   1.5923   0.5012  -0.7888
 RC5  H16  H  HCH2  0   0.238   2.4382   2.2347   0.8117
 RC5  H17  H  HCH2  0   0.239   2.5840   1.0061   2.0553
 RC5  H18  H  HCR6  0   0.244   3.9357   2.2215  -1.1599
 RC5  H19  H  HCR6  0   0.252   6.1499   1.6089  -2.0494
 RC5  H20  H  HCR6  0   0.252   7.4950  -0.1476  -0.9336
 RC5  H21  H  HCR6  0   0.252   6.5997  -1.2799   1.0775
 RC5  H22  H  HCR6  0   0.244   4.3867  -0.6633   1.9641

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
 RC5  C20  C21  aromatic  1.389  0.020  1.389
 RC5  C20  C18  aromatic  1.389  0.020  1.389
 RC5  C21  C19  aromatic  1.389  0.020  1.389
 RC5  C18  C16  aromatic  1.393  0.020  1.393
 RC5  C19  C17  aromatic  1.388  0.020  1.388
 RC5  C16  C17  aromatic  1.394  0.020  1.394
 RC5  C16  C15  single    1.503  0.020  1.503
 RC5  C15  C14  single    1.530  0.020  1.530
 RC5  O10  N9   single    1.372  0.020  1.372
 RC5  C11  N9   single    1.443  0.020  1.443
 RC5  C13  C14  single    1.524  0.020  1.524
 RC5  C13  C2   single    1.533  0.020  1.533
 RC5  N9   C4   single    1.355  0.020  1.355
 RC5  O8   P5   double    1.483  0.020  1.483
 RC5  C4   O12  double    1.222  0.020  1.222
 RC5  C4   C3   single    1.514  0.020  1.514
 RC5  C2   C3   single    1.528  0.020  1.528
 RC5  C2   C1   single    1.537  0.020  1.537
 RC5  C1   P5   single    1.804  0.020  1.804
 RC5  P5   O6   single    1.613  0.020  1.613
 RC5  P5   O7   single    1.609  0.020  1.609
 RC5  O10  H1   single    0.850  0.020  0.980
 RC5  C11  H2   single    0.970  0.020  1.090
 RC5  C11  H3   single    0.970  0.020  1.090
 RC5  C11  H4   single    0.970  0.020  1.090
 RC5  C3   H5   single    0.970  0.020  1.090
 RC5  C3   H6   single    0.970  0.020  1.090
 RC5  C2   H7   single    0.970  0.020  1.090
 RC5  C1   H8   single    0.970  0.020  1.090
 RC5  C1   H9   single    0.970  0.020  1.090
 RC5  O7   H10  single    0.850  0.020  0.980
 RC5  O6   H11  single    0.850  0.020  0.980
 RC5  C13  H12  single    0.970  0.020  1.090
 RC5  C13  H13  single    0.970  0.020  1.090
 RC5  C14  H14  single    0.970  0.020  1.090
 RC5  C14  H15  single    0.970  0.020  1.090
 RC5  C15  H16  single    0.970  0.020  1.090
 RC5  C15  H17  single    0.970  0.020  1.090
 RC5  C17  H18  single    0.930  0.020  1.080
 RC5  C19  H19  single    0.930  0.020  1.080
 RC5  C21  H20  single    0.930  0.020  1.080
 RC5  C20  H21  single    0.930  0.020  1.080
 RC5  C18  H22  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
 RC5  C3   C4   N9   116.24  3.000
 RC5  C3   C4   O12  123.05  3.000
 RC5  N9   C4   O12  120.71  3.000
 RC5  C11  N9   O10  114.45  3.000
 RC5  C11  N9   C4   124.08  3.000
 RC5  O10  N9   C4   118.13  3.000
 RC5  H1   O10  N9   106.21  3.000
 RC5  H4   C11  H3   108.30  3.000
 RC5  H4   C11  H2   108.89  3.000
 RC5  H3   C11  H2   108.91  3.000
 RC5  H4   C11  N9   109.53  3.000
 RC5  H3   C11  N9   109.30  3.000
 RC5  H2   C11  N9   111.83  3.000
 RC5  H6   C3   H5   105.17  3.000
 RC5  H6   C3   C2   110.94  3.000
 RC5  H5   C3   C2   109.44  3.000
 RC5  H6   C3   C4   107.20  3.000
 RC5  H5   C3   C4   110.50  3.000
 RC5  C2   C3   C4   113.26  3.000
 RC5  H7   C2   C13  108.12  3.000
 RC5  H7   C2   C1   108.69  3.000
 RC5  C13  C2   C1   109.72  3.000
 RC5  H7   C2   C3   109.05  3.000
 RC5  C1   C2   C3   110.44  3.000
 RC5  C13  C2   C3   110.76  3.000
 RC5  H9   C1   H8   105.89  3.000
 RC5  H9   C1   P5   109.97  3.000
 RC5  H8   C1   P5   105.17  3.000
 RC5  H9   C1   C2   110.71  3.000
 RC5  H8   C1   C2   109.91  3.000
 RC5  P5   C1   C2   114.70  3.000
 RC5  O8   P5   O6   108.72  3.000
 RC5  O6   P5   O7   106.01  3.000
 RC5  O8   P5   O7   116.06  3.000
 RC5  O7   P5   C1   100.65  3.000
 RC5  O6   P5   C1   109.11  3.000
 RC5  O8   P5   C1   115.63  3.000
 RC5  H10  O7   P5   114.11  3.000
 RC5  H11  O6   P5   115.41  3.000
 RC5  H13  C13  H12  106.20  3.000
 RC5  H13  C13  C14  109.83  3.000
 RC5  H12  C13  C14  108.03  3.000
 RC5  H13  C13  C2   108.95  3.000
 RC5  H12  C13  C2   109.47  3.000
 RC5  C14  C13  C2   114.06  3.000
 RC5  H15  C14  H14  106.27  3.000
 RC5  H15  C14  C15  109.27  3.000
 RC5  H14  C14  C15  108.81  3.000
 RC5  H15  C14  C13  109.32  3.000
 RC5  H14  C14  C13  110.83  3.000
 RC5  C15  C14  C13  112.17  3.000
 RC5  H17  C15  H16  106.64  3.000
 RC5  H17  C15  C16  109.96  3.000
 RC5  H16  C15  C16  109.65  3.000
 RC5  H17  C15  C14  109.11  3.000
 RC5  H16  C15  C14  109.16  3.000
 RC5  C16  C15  C14  112.16  3.000
 RC5  C18  C16  C17  118.34  3.000
 RC5  C17  C16  C15  120.63  3.000
 RC5  C18  C16  C15  121.00  3.000
 RC5  H18  C17  C19  119.68  3.000
 RC5  H18  C17  C16  119.32  3.000
 RC5  C19  C17  C16  120.99  3.000
 RC5  H19  C19  C21  120.09  3.000
 RC5  H19  C19  C17  119.81  3.000
 RC5  C21  C19  C17  120.10  3.000
 RC5  H20  C21  C20  120.24  3.000
 RC5  H20  C21  C19  120.27  3.000
 RC5  C20  C21  C19  119.48  3.000
 RC5  H21  C20  C18  119.83  3.000
 RC5  H21  C20  C21  120.01  3.000
 RC5  C18  C20  C21  120.16  3.000
 RC5  H22  C18  C20  119.56  3.000
 RC5  H22  C18  C16  119.51  3.000
 RC5  C20  C18  C16  120.92  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
 RC5  CONST_01  C21  C20  C18  C16     0.00   0.0  0
 RC5  CONST_02  C21  C19  C17  C16     0.00   0.0  0
 RC5  CONST_03  C20  C21  C19  C17     0.00   0.0  0
 RC5  CONST_04  C20  C18  C16  C17     0.00   0.0  0
 RC5  CONST_05  C18  C20  C21  C19     0.00   0.0  0
 RC5  CONST_06  C18  C16  C17  C19     0.00   0.0  0
 RC5  CONST_07  C20  C18  C16  C15   180.00   0.0  0
 RC5  CONST_08  C19  C17  C16  C15   180.00   0.0  0
 RC5  CONST_09  H21  C20  C18  C16   180.00   0.0  0
 RC5  CONST_10  H19  C19  C17  C16   180.00   0.0  0
 RC5  CONST_11  H20  C21  C19  C17   180.00   0.0  0
 RC5  CONST_12  H22  C18  C16  C17   180.00   0.0  0
 RC5  CONST_13  H18  C17  C19  C21   180.00   0.0  0
 RC5  CONST_14  O10  N9   C4   O12   180.00   0.0  0
 RC5  CONST_15  C11  N9   C4   O12     0.00   0.0  0
 RC5  CONST_16  C3   C4   N9   O10     0.00   0.0  0
 RC5  CONST_17  C3   C4   N9   C11   180.00   0.0  0
 RC5  Var_01    C18  C16  C15  C14   -91.20  30.0  2
 RC5  Var_02    C16  C15  C14  C13  -178.48  30.0  1
 RC5  Var_03    C2   C3   C4   O12    12.61  30.0  3
 RC5  Var_04    C15  C14  C13  C2   -178.44  30.0  3
 RC5  Var_05    O8   P5   C1   C2     46.52  30.0  3
 RC5  Var_06    H2   C11  N9   C4     91.22  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
 RC5  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
 RC5  plan-1  C15  0.020
 RC5  plan-1  C16  0.020
 RC5  plan-1  C17  0.020
 RC5  plan-1  C19  0.020
 RC5  plan-1  C21  0.020
 RC5  plan-1  C20  0.020
 RC5  plan-1  C18  0.020
 RC5  plan-1  H18  0.020
 RC5  plan-1  H19  0.020
 RC5  plan-1  H20  0.020
 RC5  plan-1  H21  0.020
 RC5  plan-1  H22  0.020
 RC5  plan-2  O12  0.020
 RC5  plan-2  C4   0.020
 RC5  plan-2  N9   0.020
 RC5  plan-2  O10  0.020
 RC5  plan-2  C11  0.020
 RC5  plan-2  C3   0.020

