# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun May  3 20:23:21 2020
#   Inital geometry file: a 79 line input string
#   Ligand name: (3R,4R)-3-hydroxy-2-[(1S)-1-hydroxy-2-methylpropyl]-4-methyl-5-oxo-D-proline
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC(C)[C@H](O)[C@]1(NC(=O)[C@H](C)[C@H]1O)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
 SLR  SLR  (3R,4R)-3-hydroxy-2-[(1S)-1-hydroxy-2-methylpropyl]-4-methyl-5-oxo-D-proline  D-peptide  32  16  .  2022-03-23  2022-03-23
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_SLR
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
 SLR  O7    O  O     -1  -0.578   1.1911  -2.5737  -0.0896
 SLR  C1    C  CH1    0   0.061   0.5018  -0.2214   1.2757
 SLR  C2    C  CH1    0  -0.419   1.6475   0.8009   1.2625
 SLR  C3    C  C      0   0.526   1.5881   1.4368  -0.1113
 SLR  N4    N  NH1    0  -0.623   0.6995   0.7539  -0.8453
 SLR  C5    C  CT     0  -0.051   0.1100  -0.4104  -0.2093
 SLR  C6    C  C      0   0.454   0.7489  -1.6912  -0.8431
 SLR  OXT   O  OC     0  -0.608   0.7476  -1.6982  -2.0893
 SLR  O8    O  OH1    0  -0.678  -0.6084   0.2353   2.0299
 SLR  C11   C  CH1    0   0.054  -1.4213  -0.4782  -0.4584
 SLR  O12   O  OH1    0  -0.675  -1.9637  -1.5045   0.3409
 SLR  C13   C  CH1    0  -0.259  -2.1625   0.8860  -0.3707
 SLR  C14   C  CH3    0  -0.662  -2.3614   1.4673  -1.7713
 SLR  C15   C  CH3    0  -0.648  -3.5179   0.7767   0.3225
 SLR  H1    H  HCH1   0   0.243   0.8441  -1.1800   1.6702
 SLR  H2    H  HCH1   0   0.276   1.4825   1.5682   2.0245
 SLR  HN4   H  HNH1   0   0.384   0.6451   0.8753  -1.8453
 SLR  HO8   H  HOH1   0   0.459  -0.3720   0.1800   2.9613
 SLR  H11   H  HCH1   0   0.225  -1.5508  -0.8335  -1.4862
 SLR  HO12  H  HOH1   0   0.445  -1.8603  -1.2254   1.2594
 SLR  H13   H  HCH1   0   0.225  -1.5595   1.5975   0.1966
 SLR  H14   H  HCH3   0   0.214  -2.9875   0.8095  -2.3793
 SLR  H14A  H  HCH3   0   0.225  -2.8502   2.4421  -1.7227
 SLR  H14B  H  HCH3   0   0.219  -1.4196   1.6063  -2.3034
 SLR  H15   H  HCH3   0   0.212  -4.1876   0.0884  -0.1970
 SLR  H15A  H  HCH3   0   0.220  -3.4350   0.4481   1.3580
 SLR  H15B  H  HCH3   0   0.218  -4.0027   1.7548   0.3356
 SLR  C9    C  CH3    0  -0.664   3.0212   0.1734   1.4894
 SLR  H9    H  HCH3   0   0.232   3.2250  -0.6116   0.7610
 SLR  H9A   H  HCH3   0   0.237   3.8128   0.9183   1.4192
 SLR  H9B   H  HCH3   0   0.240   3.0674  -0.2759   2.4814
 SLR  O10   O  O      0  -0.503   2.2630   2.3814  -0.4938

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
 SLR  O7   C6    deloc   1.242  0.020  1.242
 SLR  O8   C1    single  1.418  0.020  1.418
 SLR  C1   C5    single  1.547  0.020  1.547
 SLR  C1   C2    single  1.536  0.020  1.536
 SLR  C1   H1    single  0.970  0.020  1.090
 SLR  C9   C2    single  1.527  0.020  1.527
 SLR  C2   C3    single  1.515  0.020  1.515
 SLR  C2   H2    single  0.970  0.020  1.090
 SLR  N4   C3    single  1.340  0.020  1.340
 SLR  C3   O10   double  1.222  0.020  1.222
 SLR  C5   N4    single  1.452  0.020  1.452
 SLR  N4   HN4   single  0.860  0.020  1.020
 SLR  C6   C5    single  1.565  0.020  1.565
 SLR  C5   C11   single  1.553  0.020  1.553
 SLR  OXT  C6    deloc   1.246  0.020  1.246
 SLR  O8   HO8   single  0.850  0.020  0.980
 SLR  C9   H9    single  0.970  0.020  1.090
 SLR  C9   H9A   single  0.970  0.020  1.090
 SLR  C9   H9B   single  0.970  0.020  1.090
 SLR  C11  C13   single  1.555  0.020  1.555
 SLR  C11  O12   single  1.409  0.020  1.409
 SLR  C11  H11   single  0.970  0.020  1.090
 SLR  O12  HO12  single  0.850  0.020  0.980
 SLR  C14  C13   single  1.529  0.020  1.529
 SLR  C13  C15   single  1.526  0.020  1.526
 SLR  C13  H13   single  0.970  0.020  1.090
 SLR  C14  H14   single  0.970  0.020  1.090
 SLR  C14  H14A  single  0.970  0.020  1.090
 SLR  C14  H14B  single  0.970  0.020  1.090
 SLR  C15  H15   single  0.970  0.020  1.090
 SLR  C15  H15A  single  0.970  0.020  1.090
 SLR  C15  H15B  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
 SLR  H1    C1   O8    109.65  3.000
 SLR  H1    C1   C5    108.60  3.000
 SLR  O8    C1   C5    110.58  3.000
 SLR  H1    C1   C2    110.72  3.000
 SLR  C5    C1   C2    105.19  3.000
 SLR  O8    C1   C2    111.98  3.000
 SLR  H2    C2   C9    108.68  3.000
 SLR  H2    C2   C3    109.35  3.000
 SLR  C9    C2   C3    110.02  3.000
 SLR  H2    C2   C1    110.40  3.000
 SLR  C3    C2   C1    104.95  3.000
 SLR  C9    C2   C1    113.34  3.000
 SLR  O10   C3   N4    126.07  3.000
 SLR  O10   C3   C2    125.91  3.000
 SLR  N4    C3   C2    107.99  3.000
 SLR  HN4   N4   C5    120.59  3.000
 SLR  HN4   N4   C3    121.16  3.000
 SLR  C5    N4   C3    115.98  3.000
 SLR  C11   C5   C6    107.57  3.000
 SLR  C11   C5   N4    111.42  3.000
 SLR  C6    C5   N4    108.24  3.000
 SLR  C11   C5   C1    114.14  3.000
 SLR  C6    C5   C1    112.65  3.000
 SLR  N4    C5   C1    102.69  3.000
 SLR  OXT   C6   C5    114.15  3.000
 SLR  OXT   C6   O7    127.09  3.000
 SLR  C5    C6   O7    118.76  3.000
 SLR  HO8   O8   C1    107.69  3.000
 SLR  H11   C11  C13   106.34  3.000
 SLR  H11   C11  O12   104.50  3.000
 SLR  C13   C11  O12   115.05  3.000
 SLR  H11   C11  C5    106.34  3.000
 SLR  O12   C11  C5    108.68  3.000
 SLR  C13   C11  C5    115.00  3.000
 SLR  HO12  O12  C11   106.73  3.000
 SLR  H13   C13  C15   107.53  3.000
 SLR  H13   C13  C14   107.46  3.000
 SLR  C15   C13  C14   109.12  3.000
 SLR  H13   C13  C11   109.75  3.000
 SLR  C15   C13  C11   112.71  3.000
 SLR  C14   C13  C11   110.11  3.000
 SLR  H14B  C14  H14A  107.13  3.000
 SLR  H14B  C14  H14   107.45  3.000
 SLR  H14A  C14  H14   107.80  3.000
 SLR  H14B  C14  C13   112.52  3.000
 SLR  H14A  C14  C13   110.91  3.000
 SLR  H14   C14  C13   110.81  3.000
 SLR  H15B  C15  H15A  107.01  3.000
 SLR  H15B  C15  H15   107.35  3.000
 SLR  H15A  C15  H15   107.98  3.000
 SLR  H15B  C15  C13   109.61  3.000
 SLR  H15A  C15  C13   112.69  3.000
 SLR  H15   C15  C13   111.95  3.000
 SLR  H9B   C9   H9A   108.04  3.000
 SLR  H9B   C9   H9    107.66  3.000
 SLR  H9A   C9   H9    108.27  3.000
 SLR  H9B   C9   C2    110.04  3.000
 SLR  H9A   C9   C2    111.29  3.000
 SLR  H9    C9   C2    111.40  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
 SLR  CONST_01  C5   N4   C3   C2     0.00   0.0  0
 SLR  CONST_02  O10  C3   N4   C5   180.00   0.0  0
 SLR  CONST_03  HN4  N4   C3   C2   180.00   0.0  0
 SLR  Var_01    H14  C14  C13  C11   62.27  30.0  3
 SLR  Var_02    H15  C15  C13  C11  -59.69  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
 SLR  chir_01  C1   O8   C5  C2   negativ
 SLR  chir_02  C2   C1   C9  C3   negativ
 SLR  chir_03  C5   C1   N4  C11  positiv
 SLR  chir_04  C11  O12  C5  C13  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
 SLR  plan-1  C2   0.020
 SLR  plan-1  C3   0.020
 SLR  plan-1  N4   0.020
 SLR  plan-1  C5   0.020
 SLR  plan-1  HN4  0.020
 SLR  plan-1  O10  0.020
 SLR  plan-2  O7   0.020
 SLR  plan-2  C5   0.020
 SLR  plan-2  C6   0.020
 SLR  plan-2  OXT  0.020

