# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat May  2 08:38:16 2020
#   Inital geometry file: a 105 line input string
#   Ligand name: (2S)-2-[(ammonioacetyl)amino]-7-{[(1S)-1-(hydroxyphosphinato)ethyl]amino}-7-oxoheptanoate
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[C@@H](NC(=O)CCCC[C@H](NC(=O)C[NH3+])C([O-])=O)[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
 RE1  RE1  (2S)-2-[(ammonioacetyl)amino]-7-{[(1S)-1-(hydroxyphosphinato)ethyl]amino}-7-oxoheptanoate  ligand  42  22  .  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_RE1
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
 RE1  N2   N  NT3    1  -0.789  -0.3669   3.2816   2.4914
 RE1  C4   C  CH2    0  -0.442  -0.9681   3.8981   1.2955
 RE1  C5   C  C      0   0.571   0.0368   3.8794   0.1512
 RE1  N3   N  NH1    0  -0.614  -0.4278   4.3923  -0.9796
 RE1  C6   C  CH1    0  -0.194   0.3241   4.5070  -2.2132
 RE1  C7   C  CH2    0  -0.380   0.5040   3.1511  -2.9034
 RE1  C8   C  CH2    0  -0.445  -0.8028   2.4747  -3.3010
 RE1  C9   C  CH2    0  -0.402  -0.5899   1.0318  -3.7396
 RE1  C10  C  CH2    0  -0.586  -1.8975   0.3344  -4.1075
 RE1  C11  C  C      0   0.564  -1.6759  -1.1190  -4.4758
 RE1  N4   N  NH1    0  -0.636  -2.3702  -2.0010  -3.7555
 RE1  C12  C  CH1    0  -0.285  -2.3229  -3.4453  -3.8931
 RE1  P1   P  P      0   1.157  -2.6288  -4.1799  -2.1915
 RE1  O3   O  O      0  -0.530   1.1569   3.4168   0.3213
 RE1  C13  C  C      0   0.392  -0.3967   5.5123  -3.1395
 RE1  O4   O  O      0  -0.404   0.2243   5.8171  -4.1698
 RE1  O5   O  OC    -1  -0.774  -1.5232   5.9117  -2.7840
 RE1  O6   O  O      0  -0.608  -0.8869  -1.4346  -5.3657
 RE1  C14  C  CH3    0  -0.645  -3.3368  -3.9224  -4.9258
 RE1  O7   O  O      0  -0.797  -1.3785  -3.8479  -1.3725
 RE1  O8   O  OP    -1  -0.984  -3.8895  -3.4326  -1.7224
 RE1  H1   H  HNT3   0   0.472   0.4608   3.7868   2.8066
 RE1  H2   H  HNT3   0   0.475  -0.0818   2.3182   2.3193
 RE1  H3   H  HNT3   0   0.489  -1.0280   3.2691   3.2669
 RE1  H4   H  HCH2   0   0.372  -1.8653   3.3364   1.0428
 RE1  H5   H  HCH2   0   0.363  -1.2600   4.9147   1.5529
 RE1  H6   H  HNH1   0   0.393  -1.3498   4.8101  -1.0172
 RE1  H7   H  HCH1   0   0.207   1.3161   4.9092  -1.9835
 RE1  H8   H  HCH2   0   0.214   1.1327   3.2984  -3.7845
 RE1  H9   H  HCH2   0   0.205   1.0652   2.4898  -2.2376
 RE1  H10  H  HCH2   0   0.167  -1.4966   2.4921  -2.4547
 RE1  H11  H  HCH2   0   0.220  -1.2860   3.0337  -4.1090
 RE1  H12  H  HCH2   0   0.224  -0.1024   0.4808  -2.9286
 RE1  H13  H  HCH2   0   0.227   0.0935   0.9970  -4.5915
 RE1  H14  H  HCH2   0   0.277  -2.6062   0.4250  -3.2806
 RE1  H15  H  HCH2   0   0.269  -2.3510   0.8400  -4.9657
 RE1  H16  H  HNH1   0   0.368  -3.0068  -1.6632  -3.0489
 RE1  H17  H  HCH1   0   0.220  -1.3190  -3.7173  -4.2292
 RE1  H18  H  HCH3   0   0.193  -3.1646  -3.4700  -5.9054
 RE1  H19  H  HCH3   0   0.188  -4.3506  -3.6693  -4.6092
 RE1  H20  H  HCH3   0   0.209  -3.2850  -5.0050  -5.0371
 RE1  O9   O  OP    -1  -0.922  -2.8370  -5.6782  -2.4345

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
 RE1  N2   C4   single  1.474  0.020  1.474
 RE1  N2   H1   single  0.890  0.020  1.040
 RE1  N2   H2   single  0.890  0.020  1.040
 RE1  N2   H3   single  0.890  0.020  1.040
 RE1  C4   C5   single  1.523  0.020  1.523
 RE1  C4   H4   single  0.970  0.020  1.090
 RE1  C4   H5   single  0.970  0.020  1.090
 RE1  C5   N3   single  1.326  0.020  1.326
 RE1  C5   O3   double  1.224  0.020  1.224
 RE1  N3   C6   single  1.449  0.020  1.449
 RE1  N3   H6   single  0.860  0.020  1.020
 RE1  C6   C7   single  1.532  0.020  1.532
 RE1  C6   C13  single  1.545  0.020  1.545
 RE1  C6   H7   single  0.970  0.020  1.090
 RE1  C7   C8   single  1.524  0.020  1.524
 RE1  C7   H8   single  0.970  0.020  1.090
 RE1  C7   H9   single  0.970  0.020  1.090
 RE1  C8   C9   single  1.523  0.020  1.523
 RE1  C8   H10  single  0.970  0.020  1.090
 RE1  C8   H11  single  0.970  0.020  1.090
 RE1  C9   C10  single  1.527  0.020  1.527
 RE1  C9   H12  single  0.970  0.020  1.090
 RE1  C9   H13  single  0.970  0.020  1.090
 RE1  C10  C11  single  1.516  0.020  1.516
 RE1  C10  H14  single  0.970  0.020  1.090
 RE1  C10  H15  single  0.970  0.020  1.090
 RE1  C11  N4   single  1.334  0.020  1.334
 RE1  C11  O6   double  1.230  0.020  1.230
 RE1  N4   C12  single  1.452  0.020  1.452
 RE1  N4   H16  single  0.860  0.020  1.020
 RE1  C12  P1   single  1.878  0.020  1.878
 RE1  C12  C14  single  1.524  0.020  1.524
 RE1  C12  H17  single  0.970  0.020  1.090
 RE1  P1   O7   deloc   1.531  0.020  1.531
 RE1  P1   O8   deloc   1.539  0.020  1.539
 RE1  C13  O4   deloc   1.241  0.020  1.241
 RE1  C13  O5   deloc   1.247  0.020  1.247
 RE1  C14  H18  single  0.970  0.020  1.090
 RE1  C14  H19  single  0.970  0.020  1.090
 RE1  C14  H20  single  0.970  0.020  1.090
 RE1  P1   O9   deloc   1.532  0.020  1.532

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
 RE1  H3   N2   H2   107.36  3.000
 RE1  H3   N2   H1   107.30  3.000
 RE1  H2   N2   H1   107.06  3.000
 RE1  H3   N2   C4   110.98  3.000
 RE1  H2   N2   C4   111.87  3.000
 RE1  H1   N2   C4   112.01  3.000
 RE1  H5   C4   H4   108.42  3.000
 RE1  H5   C4   C5   111.48  3.000
 RE1  H4   C4   C5   111.30  3.000
 RE1  H5   C4   N2   107.95  3.000
 RE1  H4   C4   N2   107.98  3.000
 RE1  C5   C4   N2   109.60  3.000
 RE1  O3   C5   N3   125.84  3.000
 RE1  O3   C5   C4   120.27  3.000
 RE1  N3   C5   C4   113.88  3.000
 RE1  H6   N3   C6   114.08  3.000
 RE1  H6   N3   C5   120.68  3.000
 RE1  C6   N3   C5   125.09  3.000
 RE1  H7   C6   C13  108.02  3.000
 RE1  H7   C6   C7   108.26  3.000
 RE1  C13  C6   C7   111.13  3.000
 RE1  H7   C6   N3   108.70  3.000
 RE1  C13  C6   N3   108.64  3.000
 RE1  C7   C6   N3   111.98  3.000
 RE1  H9   C7   H8   106.10  3.000
 RE1  H9   C7   C8   109.30  3.000
 RE1  H8   C7   C8   110.05  3.000
 RE1  H9   C7   C6   108.73  3.000
 RE1  H8   C7   C6   108.16  3.000
 RE1  C8   C7   C6   114.18  3.000
 RE1  H11  C8   H10  106.43  3.000
 RE1  H11  C8   C9   109.44  3.000
 RE1  H10  C8   C9   109.05  3.000
 RE1  H11  C8   C7   110.14  3.000
 RE1  H10  C8   C7   109.55  3.000
 RE1  C9   C8   C7   112.07  3.000
 RE1  H13  C9   H12  106.43  3.000
 RE1  H13  C9   C10  109.47  3.000
 RE1  H12  C9   C10  109.26  3.000
 RE1  H13  C9   C8   110.00  3.000
 RE1  H12  C9   C8   109.01  3.000
 RE1  C10  C9   C8   112.48  3.000
 RE1  H15  C10  H14  106.64  3.000
 RE1  H15  C10  C11  108.24  3.000
 RE1  H14  C10  C11  110.99  3.000
 RE1  H15  C10  C9   109.44  3.000
 RE1  H14  C10  C9   109.58  3.000
 RE1  C11  C10  C9   111.80  3.000
 RE1  O6   C11  N4   123.70  3.000
 RE1  O6   C11  C10  121.02  3.000
 RE1  N4   C11  C10  115.27  3.000
 RE1  H16  N4   C12  114.83  3.000
 RE1  H16  N4   C11  119.02  3.000
 RE1  C12  N4   C11  126.14  3.000
 RE1  H17  C12  C14  108.95  3.000
 RE1  H17  C12  P1   109.32  3.000
 RE1  C14  C12  P1   112.53  3.000
 RE1  H17  C12  N4   107.86  3.000
 RE1  C14  C12  N4   110.74  3.000
 RE1  P1   C12  N4   107.33  3.000
 RE1  O9   P1   O8   114.33  3.000
 RE1  O9   P1   O7   114.07  3.000
 RE1  O8   P1   O7   113.62  3.000
 RE1  O9   P1   C12  105.12  3.000
 RE1  O8   P1   C12  102.69  3.000
 RE1  O7   P1   C12  105.47  3.000
 RE1  O5   C13  O4   127.59  3.000
 RE1  O5   C13  C6   117.32  3.000
 RE1  O4   C13  C6   115.09  3.000
 RE1  H20  C14  H19  107.71  3.000
 RE1  H20  C14  H18  108.20  3.000
 RE1  H19  C14  H18  108.08  3.000
 RE1  H20  C14  C12  110.41  3.000
 RE1  H19  C14  C12  110.41  3.000
 RE1  H18  C14  C12  111.90  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
 RE1  CONST_01  C6   N3   C5   C4    180.00   0.0  0
 RE1  CONST_02  O3   C5   N3   C6      0.00   0.0  0
 RE1  CONST_03  C12  N4   C11  C10   180.00   0.0  0
 RE1  CONST_04  O6   C11  N4   C12     0.00   0.0  0
 RE1  CONST_05  H6   N3   C5   C4      0.00   0.0  0
 RE1  CONST_06  H16  N4   C11  C10     0.00   0.0  0
 RE1  Var_01    N3   C5   C4   N2    178.73  30.0  3
 RE1  Var_02    C9   C8   C7   C6   -169.29  30.0  3
 RE1  Var_03    C10  C9   C8   C7    178.60  30.0  3
 RE1  Var_04    C11  C10  C9   C8   -177.19  30.0  3
 RE1  Var_05    N4   C11  C10  C9    123.15  30.0  3
 RE1  Var_06    H1   N2   C4   C5     61.03  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
 RE1  chir_01  C6   N3  C7  C13  negativ
 RE1  chir_02  C12  N4  P1  C14  negativ

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
 RE1  plan-1  C4   0.020
 RE1  plan-1  C5   0.020
 RE1  plan-1  N3   0.020
 RE1  plan-1  C6   0.020
 RE1  plan-1  O3   0.020
 RE1  plan-1  H6   0.020
 RE1  plan-2  C10  0.020
 RE1  plan-2  C11  0.020
 RE1  plan-2  N4   0.020
 RE1  plan-2  C12  0.020
 RE1  plan-2  O6   0.020
 RE1  plan-2  H16  0.020
 RE1  plan-3  C6   0.020
 RE1  plan-3  C13  0.020
 RE1  plan-3  O4   0.020
 RE1  plan-3  O5   0.020

