# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Jul 22 23:05:32 2021
#   Inital geometry file: a 66 line input string
#   Ligand name: (5~{R})-5-~{tert}-butyl-2-methyl-1-oxidanyl-pyrazolidin-3-one
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CN1N(O)[C@H](CC1=O)C(C)(C)C
#
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
 SVD  SVD  (5~{R})-5-~{tert}-butyl-2-methyl-1-oxidanyl-pyrazolidin-3-one  ligand  28  12  .  2022-07-22  2022-07-22
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_SVD
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
 SVD  N1   N  NT    0  -0.087  35.4151  129.3424  21.7497
 SVD  C4   C  CH1   0  -0.059  34.6343  128.1310  21.4022
 SVD  C5   C  CH2   0  -0.618  35.2349  127.0324  22.2790
 SVD  C6   C  C     0   0.537  36.6112  127.5610  22.5986
 SVD  N    N  NT    0  -0.299  36.6336  128.8503  22.1961
 SVD  O    O  O     0  -0.480  37.5485  126.9573  23.0876
 SVD  C1   C  CT    0  -0.097  34.6703  127.8668  19.8829
 SVD  C2   C  CH3   0  -0.636  34.1063  129.0911  19.1579
 SVD  C3   C  CH3   0  -0.662  36.0789  127.5712  19.3663
 SVD  O1   O  OH1   0  -0.571  34.7896  129.9649  22.8570
 SVD  H1   H  HCH1  0   0.271  33.5973  128.3339  21.6694
 SVD  H2   H  HCH2  0   0.298  34.6781  126.8910  23.2084
 SVD  H3   H  HCH2  0   0.284  35.3050  126.0575  21.7983
 SVD  H4   H  HCH3  0   0.255  38.6555  129.1879  22.4467
 SVD  H5   H  HCH3  0   0.251  37.8378  130.3082  21.3481
 SVD  H6   H  HCH3  0   0.246  37.6240  130.4658  23.1027
 SVD  H7   H  HCH3  0   0.227  32.7475  126.8400  19.9566
 SVD  H8   H  HCH3  0   0.233  33.7010  126.4991  18.5134
 SVD  H9   H  HCH3  0   0.230  34.1281  125.7449  20.0398
 SVD  H10  H  HCH3  0   0.221  33.0859  129.3053  19.4845
 SVD  H11  H  HCH3  0   0.231  34.7118  129.9786  19.3399
 SVD  H12  H  HCH3  0   0.225  34.0774  128.9180  18.0805
 SVD  H13  H  HCH3  0   0.228  36.5282  126.7072  19.8611
 SVD  H14  H  HCH3  0   0.234  36.0398  127.3402  18.3001
 SVD  H15  H  HCH3  0   0.234  36.7501  128.4221  19.4902
 SVD  H16  H  HOH1  0   0.466  34.6901  130.8813  22.5768
 SVD  C7   C  CH3   0  -0.517  37.7445  129.7568  22.2827
 SVD  C    C  CH3   0  -0.647  33.7623  126.6691  19.5896

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
 SVD  C3  C1   single  1.529  0.020  1.529
 SVD  C2  C1   single  1.531  0.020  1.531
 SVD  C1  C    single  1.531  0.020  1.531
 SVD  C1  C4   single  1.543  0.020  1.543
 SVD  O1  N1   single  1.416  0.020  1.416
 SVD  C4  N1   single  1.483  0.020  1.483
 SVD  C4  C5   single  1.529  0.020  1.529
 SVD  N1  N    single  1.388  0.020  1.388
 SVD  C5  C6   single  1.509  0.020  1.509
 SVD  N   C6   single  1.351  0.020  1.351
 SVD  N   C7   single  1.436  0.020  1.436
 SVD  C6  O    double  1.217  0.020  1.217
 SVD  C4  H1   single  0.970  0.020  1.090
 SVD  C5  H2   single  0.970  0.020  1.090
 SVD  C5  H3   single  0.970  0.020  1.090
 SVD  C7  H4   single  0.970  0.020  1.090
 SVD  C7  H5   single  0.970  0.020  1.090
 SVD  C7  H6   single  0.970  0.020  1.090
 SVD  C   H7   single  0.970  0.020  1.090
 SVD  C   H8   single  0.970  0.020  1.090
 SVD  C   H9   single  0.970  0.020  1.090
 SVD  C2  H10  single  0.970  0.020  1.090
 SVD  C2  H11  single  0.970  0.020  1.090
 SVD  C2  H12  single  0.970  0.020  1.090
 SVD  C3  H13  single  0.970  0.020  1.090
 SVD  C3  H14  single  0.970  0.020  1.090
 SVD  C3  H15  single  0.970  0.020  1.090
 SVD  O1  H16  single  0.850  0.020  0.980

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
 SVD  O1   N1  N    106.99  3.000
 SVD  N    N1  C4   104.36  3.000
 SVD  O1   N1  C4   108.05  3.000
 SVD  H1   C4  C1   107.19  3.000
 SVD  H1   C4  C5   111.53  3.000
 SVD  C1   C4  C5   115.64  3.000
 SVD  H1   C4  N1   106.95  3.000
 SVD  C5   C4  N1   104.23  3.000
 SVD  C1   C4  N1   111.01  3.000
 SVD  H3   C5  H2   107.00  3.000
 SVD  H3   C5  C6   110.39  3.000
 SVD  H2   C5  C6   109.28  3.000
 SVD  H3   C5  C4   114.54  3.000
 SVD  H2   C5  C4   112.38  3.000
 SVD  C6   C5  C4   103.19  3.000
 SVD  O    C6  N    125.47  3.000
 SVD  O    C6  C5   127.86  3.000
 SVD  N    C6  C5   106.64  3.000
 SVD  C7   N   C6   126.66  3.000
 SVD  C7   N   N1   118.34  3.000
 SVD  C6   N   N1   114.82  3.000
 SVD  C3   C1  C2   109.51  3.000
 SVD  C2   C1  C    108.45  3.000
 SVD  C3   C1  C    109.29  3.000
 SVD  C    C1  C4   107.98  3.000
 SVD  C2   C1  C4   108.72  3.000
 SVD  C3   C1  C4   112.79  3.000
 SVD  H12  C2  H11  107.98  3.000
 SVD  H12  C2  H10  107.55  3.000
 SVD  H11  C2  H10  108.02  3.000
 SVD  H12  C2  C1   110.51  3.000
 SVD  H11  C2  C1   111.57  3.000
 SVD  H10  C2  C1   111.06  3.000
 SVD  H15  C3  H14  107.35  3.000
 SVD  H15  C3  H13  108.21  3.000
 SVD  H14  C3  H13  106.84  3.000
 SVD  H15  C3  C1   112.19  3.000
 SVD  H14  C3  C1   109.74  3.000
 SVD  H13  C3  C1   112.25  3.000
 SVD  H16  O1  N1   103.67  3.000
 SVD  H6   C7  H5   108.99  3.000
 SVD  H6   C7  H4   108.63  3.000
 SVD  H5   C7  H4   108.83  3.000
 SVD  H6   C7  N    111.72  3.000
 SVD  H5   C7  N    109.52  3.000
 SVD  H4   C7  N    109.10  3.000
 SVD  H9   C   H8   107.09  3.000
 SVD  H9   C   H7   107.77  3.000
 SVD  H8   C   H7   107.66  3.000
 SVD  H9   C   C1   112.62  3.000
 SVD  H8   C   C1   110.12  3.000
 SVD  H7   C   C1   111.35  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
 SVD  CONST_01  C5   C6  N   N1     0.00   0.0  0
 SVD  CONST_02  O    C6  N   N1   180.00   0.0  0
 SVD  CONST_03  C7   N   C6  C5   180.00   0.0  0
 SVD  CONST_04  O    C6  N   C7     0.00   0.0  0
 SVD  Var_01    C6   N   N1  C4   -20.63  30.0  1
 SVD  Var_02    N    C6  C5  C4    10.99  30.0  1
 SVD  Var_03    H4   C7  N   N1  -168.51  30.0  3
 SVD  Var_04    H13  C3  C1  C4    58.35  30.0  3
 SVD  Var_05    H10  C2  C1  C4   -58.24  30.0  3
 SVD  Var_06    H7   C   C1  C4    56.29  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
 SVD  chir_01  C4  C1  N1  C5  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
 SVD  plan-1  N1  0.020
 SVD  plan-1  C5  0.020
 SVD  plan-1  C6  0.020
 SVD  plan-1  N   0.020
 SVD  plan-1  O   0.020
 SVD  plan-1  C7  0.020

