# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri May  1 20:48:48 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  41  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 GRAND
;

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  -0.499  -1.9416   2.0482  -1.4698
 RC5  C4   C  C      0   0.546  -2.5908   1.7746  -0.4694
 RC5  N9   N  NT     0  -0.213  -3.5935   2.5992  -0.0639
 RC5  O10  O  OH1    0  -0.549  -4.4783   2.1296   0.8766
 RC5  C11  C  CH3    0  -0.514  -4.1030   3.6972  -0.8483
 RC5  C3   C  CH2    0  -0.585  -2.3421   0.5489   0.3715
 RC5  C2   C  CH1    0  -0.207  -0.9823  -0.1075   0.1417
 RC5  C1   C  CH2    0  -0.713  -0.9811  -1.5103   0.7564
 RC5  P5   P  P      0   1.167  -1.9893  -2.8041  -0.1295
 RC5  O7   O  OP    -1  -0.914  -1.6940  -4.1014   0.6394
 RC5  O6   O  OP    -1  -0.896  -3.4644  -2.3699  -0.0266
 RC5  O8   O  O      0  -0.910  -1.4597  -2.8059  -1.5709
 RC5  C13  C  CH2    0  -0.401   0.1365   0.7709   0.7135
 RC5  C14  C  CH2    0  -0.415   1.5359   0.3874   0.2488
 RC5  C15  C  CH2    0  -0.504   2.6260   1.2077   0.9417
 RC5  C16  C  C      0   0.141   4.0051   0.8398   0.4720
 RC5  C17  C  C1     0  -0.317   4.6119   1.5295  -0.5759
 RC5  C19  C  C1     0  -0.239   5.8698   1.1654  -1.0388
 RC5  C21  C  C1     0  -0.276   6.5439   0.0988  -0.4586
 RC5  C20  C  C1     0  -0.240   5.9498  -0.5985   0.5857
 RC5  C18  C  C1     0  -0.314   4.6922  -0.2296   1.0444
 RC5  H1   H  HOH1   0   0.475  -4.2556   2.5788   1.7029
 RC5  H2   H  HCH3   0   0.238  -4.9454   3.3943  -1.4749
 RC5  H3   H  HCH3   0   0.244  -4.4298   4.4961  -0.1834
 RC5  H4   H  HCH3   0   0.251  -3.3149   4.0858  -1.4852
 RC5  H5   H  HCH2   0   0.230  -2.4564   0.7811   1.4343
 RC5  H6   H  HCH2   0   0.291  -3.1211  -0.1901   0.1489
 RC5  H7   H  HCH1   0   0.198  -0.8196  -0.2166  -0.9350
 RC5  H8   H  HCH2   0   0.195   0.0481  -1.8833   0.7969
 RC5  H9   H  HCH2   0   0.178  -1.3035  -1.4373   1.8038
 RC5  H12  H  HCH2   0   0.214  -0.0318   1.8192   0.4475
 RC5  H13  H  HCH2   0   0.195   0.0913   0.7247   1.8088
 RC5  H14  H  HCH2   0   0.219   1.7193  -0.6745   0.4344
 RC5  H15  H  HCH2   0   0.216   1.6118   0.5272  -0.8345
 RC5  H16  H  HCH2   0   0.233   2.4482   2.2718   0.7618
 RC5  H17  H  HCH2   0   0.234   2.5496   1.0575   2.0226
 RC5  H18  H  H      0   0.243   4.0933   2.3651  -1.0324
 RC5  H19  H  H      0   0.251   6.3258   1.7187  -1.8502
 RC5  H20  H  H      0   0.252   7.5262  -0.1839  -0.8146
 RC5  H21  H  H      0   0.251   6.4694  -1.4287   1.0472
 RC5  H22  H  H      0   0.244   4.2388  -0.7788   1.8622

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  1.388  0.020  1.388
 RC5  C21  C19  aromatic  1.389  0.020  1.389
 RC5  C18  C16  aromatic  1.394  0.020  1.394
 RC5  C19  C17  aromatic  1.389  0.020  1.389
 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    1.374  0.020  1.374
 RC5  C11  N9   single    1.442  0.020  1.442
 RC5  C13  C14  single    1.524  0.020  1.524
 RC5  C13  C2   single    1.533  0.020  1.533
 RC5  N9   C4   single    1.360  0.020  1.360
 RC5  O8   P5   deloc     1.536  0.020  1.536
 RC5  C4   O12  double    1.224  0.020  1.224
 RC5  C4   C3   single    1.507  0.020  1.507
 RC5  C2   C3   single    1.527  0.020  1.527
 RC5  C2   C1   single    1.532  0.020  1.532
 RC5  C1   P5   single    1.864  0.020  1.864
 RC5  P5   O6   deloc     1.541  0.020  1.541
 RC5  P5   O7   deloc     1.537  0.020  1.537
 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  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   116.64  3.000
 RC5  C3   C4   O12  123.40  3.000
 RC5  N9   C4   O12  119.96  3.000
 RC5  C11  N9   O10  113.89  3.000
 RC5  C11  N9   C4   124.04  3.000
 RC5  O10  N9   C4   118.14  3.000
 RC5  H1   O10  N9   106.14  3.000
 RC5  H4   C11  H3   108.26  3.000
 RC5  H4   C11  H2   108.82  3.000
 RC5  H3   C11  H2   108.78  3.000
 RC5  H4   C11  N9   109.58  3.000
 RC5  H3   C11  N9   109.41  3.000
 RC5  H2   C11  N9   111.91  3.000
 RC5  H6   C3   H5   105.42  3.000
 RC5  H6   C3   C2   108.20  3.000
 RC5  H5   C3   C2   109.29  3.000
 RC5  H6   C3   C4   108.52  3.000
 RC5  H5   C3   C4   110.62  3.000
 RC5  C2   C3   C4   114.37  3.000
 RC5  H7   C2   C13  108.39  3.000
 RC5  H7   C2   C1   107.67  3.000
 RC5  C13  C2   C1   112.00  3.000
 RC5  H7   C2   C3   108.86  3.000
 RC5  C1   C2   C3   109.51  3.000
 RC5  C13  C2   C3   110.33  3.000
 RC5  H9   C1   H8   105.26  3.000
 RC5  H9   C1   P5   109.91  3.000
 RC5  H8   C1   P5   106.82  3.000
 RC5  H9   C1   C2   108.76  3.000
 RC5  H8   C1   C2   109.12  3.000
 RC5  P5   C1   C2   116.39  3.000
 RC5  O8   P5   O6   113.15  3.000
 RC5  O6   P5   O7   112.85  3.000
 RC5  O8   P5   O7   113.73  3.000
 RC5  O7   P5   C1   104.13  3.000
 RC5  O6   P5   C1   106.88  3.000
 RC5  O8   P5   C1   105.09  3.000
 RC5  H13  C13  H12  106.06  3.000
 RC5  H13  C13  C14  109.37  3.000
 RC5  H12  C13  C14  107.95  3.000
 RC5  H13  C13  C2   108.55  3.000
 RC5  H12  C13  C2   110.24  3.000
 RC5  C14  C13  C2   114.35  3.000
 RC5  H15  C14  H14  106.27  3.000
 RC5  H15  C14  C15  109.28  3.000
 RC5  H14  C14  C15  108.92  3.000
 RC5  H15  C14  C13  109.47  3.000
 RC5  H14  C14  C13  110.29  3.000
 RC5  C15  C14  C13  112.42  3.000
 RC5  H17  C15  H16  106.54  3.000
 RC5  H17  C15  C16  109.84  3.000
 RC5  H16  C15  C16  109.63  3.000
 RC5  H17  C15  C14  108.91  3.000
 RC5  H16  C15  C14  109.35  3.000
 RC5  C16  C15  C14  112.40  3.000
 RC5  C18  C16  C17  118.28  3.000
 RC5  C17  C16  C15  120.90  3.000
 RC5  C18  C16  C15  120.79  3.000
 RC5  H18  C17  C19  119.66  3.000
 RC5  H18  C17  C16  119.32  3.000
 RC5  C19  C17  C16  121.01  3.000
 RC5  H19  C19  C21  120.07  3.000
 RC5  H19  C19  C17  119.82  3.000
 RC5  C21  C19  C17  120.11  3.000
 RC5  H20  C21  C20  120.29  3.000
 RC5  H20  C21  C19  120.25  3.000
 RC5  C20  C21  C19  119.47  3.000
 RC5  H21  C20  C18  119.84  3.000
 RC5  H21  C20  C21  120.00  3.000
 RC5  C18  C20  C21  120.16  3.000
 RC5  H22  C18  C20  119.55  3.000
 RC5  H22  C18  C16  119.47  3.000
 RC5  C20  C18  C16  120.97  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   -85.00  30.0  2
 RC5  Var_02    C16  C15  C14  C13  -179.36  30.0  1
 RC5  Var_03    C2   C3   C4   O12    17.23  30.0  3
 RC5  Var_04    C15  C14  C13  C2   -174.81  30.0  3
 RC5  Var_05    O8   P5   C1   C2     55.40  30.0  3
 RC5  Var_06    H2   C11  N9   C4     91.52  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

