# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat May  2 13:41:16 2020
#   Inital geometry file: a 91 line input string
#   Ligand name: (2S)-3-[(S)-[(1R)-1-amino-2-phenylethyl](hydroxy)phosphoryl]-2-methylpropanoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[C@H](C[P](O)(=O)[C@@H](N)Cc1ccccc1)C(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
 RT1  RT1  '(2S)-3-[(S)-[(1R)-1-amino-2-phenylethyl](hydroxy)phosphoryl]-2-methylpropanoic acid'  peptide  34  18  .  2022-03-23  2022-09-22
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_RT1
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
 RT1  C1   C  CR16   0  -0.322  -3.6673  -0.1773   1.2127
 RT1  C2   C  CR16   0  -0.245  -4.4032  -1.3554   1.1899
 RT1  C3   C  CR16   0  -0.278  -4.4674  -2.1120   0.0271
 RT1  C4   C  CR16   0  -0.252  -3.7868  -1.6822  -1.1061
 RT1  C5   C  CR16   0  -0.272  -3.0443  -0.5111  -1.0719
 RT1  C6   C  CR6    0   0.148  -2.9791   0.2621   0.0845
 RT1  C7   C  CH2    0  -0.512  -2.2015   1.5465   0.1207
 RT1  C8   C  CH1    0  -0.321  -0.7801   1.4319   0.6845
 RT1  P1   P  P      0   1.189   0.2976   0.3649  -0.3996
 RT1  O1   O  OP    -1  -0.832   0.1954   0.9376  -1.8072
 RT1  O2   O  O      0  -0.814  -0.0242  -1.1005  -0.1747
 RT1  N    N  NH2    0  -0.804  -0.2563   2.7908   0.8480
 RT1  C9   C  CH2    0  -0.686   1.9774   0.6883   0.2959
 RT1  CA   C  CH1    0  -0.366   3.0283  -0.3290  -0.1407
 RT1  C11  C  CH3    0  -0.656   3.3146  -0.2456  -1.6405
 RT1  C    C  C      0   0.420   4.3519  -0.2326   0.6574
 RT1  O    O  O      0  -0.607   4.4350   0.6089   1.5743
 RT1  H1   H  HCR6   0   0.239  -3.6344   0.4149   2.1209
 RT1  H9   H  HCR6   0   0.246  -4.9345  -1.6770   2.0771
 RT1  H3   H  HCR6   0   0.246  -5.0472  -3.0260   0.0018
 RT1  H4   H  HCR6   0   0.244  -3.8329  -2.2651  -2.0177
 RT1  H5   H  HCR6   0   0.232  -2.5006  -0.1880  -1.9513
 RT1  H6   H  HCH2   0   0.231  -2.1397   1.9656  -0.8873
 RT1  H7   H  HCH2   0   0.232  -2.7389   2.2768   0.7325
 RT1  H8   H  HCH1   0   0.221  -0.8369   0.9768   1.6798
 RT1  HN2  H  HNH2   0   0.351   0.6384   2.7553   1.3209
 RT1  H11  H  HCH2   0   0.208   2.3066   1.6981   0.0319
 RT1  H12  H  HCH2   0   0.219   1.8939   0.6692   1.3870
 RT1  H13  H  HCH1   0   0.210   2.6254  -1.3302   0.0571
 RT1  H14  H  HCH3   0   0.211   4.0563  -0.9846  -1.9388
 RT1  H15  H  HCH3   0   0.220   2.4132  -0.4078  -2.2296
 RT1  H16  H  HCH3   0   0.198   3.7009   0.7422  -1.9074
 RT1  H2   H  HNH2   0   0.333  -0.0569   3.1761  -0.0696
 RT1  OXT  O  OC    -1  -0.629   5.2521  -1.0321   0.3192

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
 RT1  C1   C2   aromatic  1.389  0.020  1.389
 RT1  C1   C6   aromatic  1.393  0.020  1.393
 RT1  C1   H1   single    0.930  0.020  1.080
 RT1  C2   C3   aromatic  1.389  0.020  1.389
 RT1  C2   H9   single    0.930  0.020  1.080
 RT1  C3   C4   aromatic  1.390  0.020  1.390
 RT1  C3   H3   single    0.930  0.020  1.080
 RT1  C4   C5   aromatic  1.387  0.020  1.387
 RT1  C4   H4   single    0.930  0.020  1.080
 RT1  C5   C6   aromatic  1.393  0.020  1.393
 RT1  C5   H5   single    0.930  0.020  1.080
 RT1  C6   C7   single    1.502  0.020  1.502
 RT1  C7   C8   single    1.533  0.020  1.533
 RT1  C7   H6   single    0.970  0.020  1.090
 RT1  C7   H7   single    0.970  0.020  1.090
 RT1  C8   N    single    1.465  0.020  1.465
 RT1  C8   P1   single    1.864  0.020  1.864
 RT1  C8   H8   single    0.970  0.020  1.090
 RT1  P1   O1   deloc     1.523  0.020  1.523
 RT1  P1   O2   deloc     1.517  0.020  1.517
 RT1  P1   C9   single    1.847  0.020  1.847
 RT1  N    HN2  single    0.890  0.020  1.040
 RT1  C9   CA   single    1.526  0.020  1.526
 RT1  C9   H11  single    0.970  0.020  1.090
 RT1  C9   H12  single    0.970  0.020  1.090
 RT1  CA   C11  single    1.529  0.020  1.529
 RT1  CA   C    single    1.525  0.021  1.525
 RT1  CA   H13  single    0.970  0.020  1.090
 RT1  C11  H14  single    0.970  0.020  1.090
 RT1  C11  H15  single    0.970  0.020  1.090
 RT1  C11  H16  single    0.970  0.020  1.090
 RT1  C    O    deloc     1.231  0.020  1.231
 RT1  N    H2   single    0.890  0.020  1.040
 RT1  C    OXT  deloc     1.251  0.020  1.251

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
 RT1  H1   C1   C6   119.41  3.000
 RT1  H1   C1   C2   119.53  3.000
 RT1  C6   C1   C2   121.07  3.000
 RT1  H9   C2   C3   120.10  3.000
 RT1  H9   C2   C1   119.88  3.000
 RT1  C3   C2   C1   120.02  3.000
 RT1  H3   C3   C4   120.28  3.000
 RT1  H3   C3   C2   120.28  3.000
 RT1  C4   C3   C2   119.44  3.000
 RT1  H4   C4   C5   119.86  3.000
 RT1  H4   C4   C3   119.93  3.000
 RT1  C5   C4   C3   120.21  3.000
 RT1  H5   C5   C6   119.01  3.000
 RT1  H5   C5   C4   120.04  3.000
 RT1  C6   C5   C4   120.95  3.000
 RT1  C7   C6   C5   121.27  3.000
 RT1  C7   C6   C1   120.41  3.000
 RT1  C5   C6   C1   118.32  3.000
 RT1  H7   C7   H6   106.71  3.000
 RT1  H7   C7   C8   107.44  3.000
 RT1  H6   C7   C8   108.37  3.000
 RT1  H7   C7   C6   109.27  3.000
 RT1  H6   C7   C6   109.56  3.000
 RT1  C8   C7   C6   115.14  3.000
 RT1  H8   C8   N    107.60  3.000
 RT1  H8   C8   P1   108.69  3.000
 RT1  N    C8   P1   112.89  3.000
 RT1  H8   C8   C7   108.47  3.000
 RT1  P1   C8   C7   111.40  3.000
 RT1  N    C8   C7   107.64  3.000
 RT1  C9   P1   O2   107.83  3.000
 RT1  C9   P1   O1   110.08  3.000
 RT1  O2   P1   O1   119.08  3.000
 RT1  C9   P1   C8   101.92  3.000
 RT1  O2   P1   C8   110.12  3.000
 RT1  O1   P1   C8   106.47  3.000
 RT1  H2   N    HN2  105.18  3.000
 RT1  H2   N    C8   108.75  3.000
 RT1  HN2  N    C8   109.59  3.000
 RT1  H12  C9   H11  106.23  3.000
 RT1  H12  C9   CA   109.03  3.000
 RT1  H11  C9   CA   109.80  3.000
 RT1  H12  C9   P1   107.64  3.000
 RT1  H11  C9   P1   110.14  3.000
 RT1  CA   C9   P1   113.70  3.000
 RT1  H13  CA   C    106.13  3.000
 RT1  H13  CA   C11  107.17  3.000
 RT1  C    CA   C11  110.00  3.000
 RT1  H13  CA   C9   107.68  3.000
 RT1  C    CA   C9   113.55  3.000
 RT1  C11  CA   C9   111.90  3.000
 RT1  H16  C11  H15  107.15  3.000
 RT1  H16  C11  H14  107.80  3.000
 RT1  H15  C11  H14  108.34  3.000
 RT1  H16  C11  CA   110.77  3.000
 RT1  H15  C11  CA   111.56  3.000
 RT1  H14  C11  CA   111.05  3.000
 RT1  OXT  C    O    125.60  3.000
 RT1  OXT  C    CA   120.80  1.700
 RT1  O    C    CA   120.80  1.700

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
 RT1  CONST_01  C4  C3  C2  C1    0.00   0.0  0
 RT1  CONST_02  C4  C5  C6  C1    0.00   0.0  0
 RT1  CONST_03  C5  C6  C1  C2    0.00   0.0  0
 RT1  CONST_04  C5  C4  C3  C2    0.00   0.0  0
 RT1  CONST_05  C6  C1  C2  C3    0.00   0.0  0
 RT1  CONST_06  C6  C5  C4  C3    0.00   0.0  0
 RT1  CONST_07  C7  C6  C1  C2  180.00   0.0  0
 RT1  CONST_08  C7  C6  C5  C4  180.00   0.0  0
 RT1  CONST_09  H3  C3  C2  C1  180.00   0.0  0
 RT1  CONST_10  H5  C5  C6  C1  180.00   0.0  0
 RT1  CONST_11  H4  C4  C3  C2  180.00   0.0  0
 RT1  CONST_12  H1  C1  C2  C3  180.00   0.0  0
 RT1  CONST_13  H9  C2  C3  C4  180.00   0.0  0
 RT1  Var_01    C8  C7  C6  C1   84.24  30.0  2
 RT1  Var_02    CA  C9  P1  C8  164.36  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
 RT1  chir_01  C8  C7  N    P1  positiv
 RT1  chir_03  CA  C9  C11  C   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
 RT1  plan-1  C1   0.020
 RT1  plan-1  C2   0.020
 RT1  plan-1  C3   0.020
 RT1  plan-1  C4   0.020
 RT1  plan-1  C5   0.020
 RT1  plan-1  C6   0.020
 RT1  plan-1  C7   0.020
 RT1  plan-1  H1   0.020
 RT1  plan-1  H9   0.020
 RT1  plan-1  H3   0.020
 RT1  plan-1  H4   0.020
 RT1  plan-1  H5   0.020
 RT1  plan-2  CA   0.020
 RT1  plan-2  C    0.020
 RT1  plan-2  O    0.020
 RT1  plan-2  OXT  0.020

