# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Mar  9 08:55:55 2022
#   Inital geometry file: a 76 line input string
#   Ligand name: (3S,4R)-3-ethyl-4-[(1-methyl-1H-imidazol-5-yl)methyl]dihydrofuran-2(3H)-one
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC[C@H]1[C@H](COC1=O)Cc2cncn2C
#
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
 9PL  9PL  (3S,4R)-3-ethyl-4-[(1-methyl-1H-imidazol-5-yl)methyl]dihydrofuran-2(3H)-one  ligand  31  15  .  2022-03-11  2022-03-11
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_9PL
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
 9PL  N1    N  NR5   0  -0.440  -2.8040  -0.6233  -0.1140
 9PL  C2    C  CR15  0   0.076  -3.9658   0.0657  -0.1169
 9PL  N3    N  N     0  -0.449  -3.8456   1.2363   0.4527
 9PL  C4    C  CR15  0  -0.266  -2.5400   1.3077   0.8448
 9PL  C5    C  CR5   0   0.319  -1.8671   0.1647   0.5055
 9PL  C6    C  CH3   0  -0.536  -2.6074  -1.9561  -0.6364
 9PL  C7    C  CH2   0  -0.556  -0.4437  -0.2260   0.6882
 9PL  C8    C  CR15  0  -0.311   0.4019  -0.0546  -0.5835
 9PL  C9    C  CH2   0  -0.166   0.5425   1.4055  -0.9961
 9PL  O10   O  O     0  -0.441   1.6759   1.8910  -0.2573
 9PL  C11   C  CR5   0   0.587   2.4594   0.8771   0.1164
 9PL  C12   C  CR15  0  -0.408   1.8766  -0.4269  -0.3811
 9PL  C13   C  CH2   0  -0.442   2.1939  -1.6490   0.4734
 9PL  C14   C  CH3   0  -0.666   3.6209  -2.1520   0.2995
 9PL  O15   O  O     0  -0.430   3.4613   1.0669   0.7525
 9PL  H2    H  HCR5  0   0.275  -4.8683  -0.3430  -0.5472
 9PL  H4    H  HCR5  0   0.252  -2.1397   2.1712   1.3561
 9PL  H6    H  HCH3  0   0.259  -1.9299  -1.9516  -1.4893
 9PL  H6A   H  HCH3  0   0.261  -2.2034  -2.6143   0.1310
 9PL  H6B   H  HCH3  0   0.274  -3.5650  -2.3549  -0.9598
 9PL  H7    H  HCH2  0   0.273  -0.0309   0.3745   1.5035
 9PL  H7A   H  HCH2  0   0.274  -0.3821  -1.2645   1.0230
 9PL  H8    H  HCR5  0   0.282  -0.0351  -0.6380  -1.3954
 9PL  H9    H  HCH2  0   0.258   0.7464   1.5058  -2.0643
 9PL  H9A   H  HCH2  0   0.257  -0.3162   2.0263  -0.7439
 9PL  H12   H  HCR5  0   0.304   2.3096  -0.5854  -1.3797
 9PL  H13   H  HCH2  0   0.235   1.9987  -1.4381   1.5274
 9PL  H13A  H  HCH2  0   0.241   1.5025  -2.4462   0.1883
 9PL  H14   H  HCH3  0   0.221   3.8183  -2.4086  -0.7427
 9PL  H14A  H  HCH3  0   0.232   4.3517  -1.4046   0.6032
 9PL  H14B  H  HCH3  0   0.232   3.7911  -3.0459   0.8996

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
 9PL  C5   N1    aromatic  1.372  0.020  1.372
 9PL  N1   C2    aromatic  1.351  0.020  1.351
 9PL  N1   C6    single    1.445  0.020  1.445
 9PL  N3   C2    aromatic  1.307  0.020  1.307
 9PL  C2   H2    single    0.930  0.020  1.080
 9PL  C4   N3    aromatic  1.365  0.020  1.365
 9PL  C4   C5    aromatic  1.369  0.020  1.369
 9PL  C4   H4    single    0.930  0.020  1.080
 9PL  C7   C5    single    1.487  0.020  1.487
 9PL  C6   H6    single    0.970  0.020  1.090
 9PL  C6   H6A   single    0.970  0.020  1.090
 9PL  C6   H6B   single    0.970  0.020  1.090
 9PL  C8   C7    single    1.537  0.020  1.537
 9PL  C7   H7    single    0.970  0.020  1.090
 9PL  C7   H7A   single    0.970  0.020  1.090
 9PL  C12  C8    single    1.534  0.020  1.534
 9PL  C9   C8    single    1.524  0.020  1.524
 9PL  C8   H8    single    0.970  0.020  1.090
 9PL  O10  C9    single    1.437  0.020  1.437
 9PL  C9   H9    single    0.970  0.020  1.090
 9PL  C9   H9A   single    0.970  0.020  1.090
 9PL  C11  O10   single    1.335  0.020  1.335
 9PL  O15  C11   double    1.202  0.020  1.202
 9PL  C11  C12   single    1.513  0.020  1.513
 9PL  C13  C12   single    1.525  0.020  1.525
 9PL  C12  H12   single    0.970  0.020  1.090
 9PL  C14  C13   single    1.523  0.020  1.523
 9PL  C13  H13   single    0.970  0.020  1.090
 9PL  C13  H13A  single    0.970  0.020  1.090
 9PL  C14  H14   single    0.970  0.020  1.090
 9PL  C14  H14A  single    0.970  0.020  1.090
 9PL  C14  H14B  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
 9PL  C6    N1   C5    126.87  3.000
 9PL  C6    N1   C2    125.93  3.000
 9PL  C5    N1   C2    107.18  3.000
 9PL  H2    C2   N3    126.10  3.000
 9PL  H2    C2   N1    121.77  3.000
 9PL  N3    C2   N1    112.13  3.000
 9PL  C4    N3   C2    105.06  3.000
 9PL  H4    C4   C5    127.05  3.000
 9PL  H4    C4   N3    122.15  3.000
 9PL  C5    C4   N3    110.81  3.000
 9PL  C7    C5   C4    131.24  3.000
 9PL  C7    C5   N1    123.93  3.000
 9PL  C4    C5   N1    104.82  3.000
 9PL  H6B   C6   H6A   108.36  3.000
 9PL  H6B   C6   H6    108.46  3.000
 9PL  H6A   C6   H6    108.88  3.000
 9PL  H6B   C6   N1    109.04  3.000
 9PL  H6A   C6   N1    110.69  3.000
 9PL  H6    C6   N1    111.35  3.000
 9PL  H7A   C7   H7    105.79  3.000
 9PL  H7A   C7   C8    109.18  3.000
 9PL  H7    C7   C8    110.37  3.000
 9PL  H7A   C7   C5    109.95  3.000
 9PL  H7    C7   C5    107.98  3.000
 9PL  C8    C7   C5    113.31  3.000
 9PL  H8    C8   C12   110.70  3.000
 9PL  H8    C8   C9    110.35  3.000
 9PL  C12   C8   C9    100.35  3.000
 9PL  H8    C8   C7    109.61  3.000
 9PL  C9    C8   C7    112.44  3.000
 9PL  C12   C8   C7    113.12  3.000
 9PL  H9A   C9   H9    108.75  3.000
 9PL  H9A   C9   O10   108.06  3.000
 9PL  H9    C9   O10   108.94  3.000
 9PL  H9A   C9   C8    114.25  3.000
 9PL  H9    C9   C8    111.72  3.000
 9PL  O10   C9   C8    104.90  3.000
 9PL  C11   O10  C9    110.50  3.000
 9PL  O15   C11  C12   129.15  3.000
 9PL  C12   C11  O10   109.67  3.000
 9PL  O15   C11  O10   121.17  3.000
 9PL  H12   C12  C13   108.15  3.000
 9PL  H12   C12  C11   105.73  3.000
 9PL  C13   C12  C11   115.25  3.000
 9PL  H12   C12  C8    107.07  3.000
 9PL  C13   C12  C8    117.93  3.000
 9PL  C11   C12  C8    101.80  3.000
 9PL  H13A  C13  H13   106.23  3.000
 9PL  H13A  C13  C14   108.78  3.000
 9PL  H13   C13  C14   109.96  3.000
 9PL  H13A  C13  C12   107.87  3.000
 9PL  H13   C13  C12   110.42  3.000
 9PL  C14   C13  C12   113.31  3.000
 9PL  H14B  C14  H14A  107.74  3.000
 9PL  H14B  C14  H14   107.74  3.000
 9PL  H14A  C14  H14   107.85  3.000
 9PL  H14B  C14  C13   110.75  3.000
 9PL  H14A  C14  C13   111.74  3.000
 9PL  H14   C14  C13   110.87  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
 9PL  CONST_01  N3   C4   C5   N1     0.00   0.0  0
 9PL  CONST_02  C4   N3   C2   N1     0.00   0.0  0
 9PL  CONST_03  C4   C5   N1   C2     0.00   0.0  0
 9PL  CONST_04  C5   C4   N3   C2     0.00   0.0  0
 9PL  CONST_05  C5   N1   C2   N3     0.00   0.0  0
 9PL  CONST_06  C7   C5   N1   C2   180.00   0.0  0
 9PL  CONST_07  C6   N1   C2   N3   180.00   0.0  0
 9PL  CONST_08  C7   C5   C4   N3   180.00   0.0  0
 9PL  CONST_09  C6   N1   C5   C4   180.00   0.0  0
 9PL  CONST_10  H4   C4   C5   N1   180.00   0.0  0
 9PL  CONST_11  H2   C2   N3   C4   180.00   0.0  0
 9PL  Var_01    C12  C11  O10  C9     0.36  30.0  1
 9PL  Var_02    C8   C7   C5   N1    78.29  30.0  2
 9PL  Var_03    H9   C9   O10  C11  -97.81  30.0  1
 9PL  Var_04    H6   C6   N1   C2   114.91  30.0  2
 9PL  Var_05    H14  C14  C13  C12  -58.37  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
 9PL  chir_01  C8   C7  C12  C9   positiv
 9PL  chir_02  C12  C8  C11  C13  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
 9PL  plan-1  N1   0.020
 9PL  plan-1  C2   0.020
 9PL  plan-1  N3   0.020
 9PL  plan-1  C4   0.020
 9PL  plan-1  C5   0.020
 9PL  plan-1  C6   0.020
 9PL  plan-1  C7   0.020
 9PL  plan-1  H2   0.020
 9PL  plan-1  H4   0.020
 9PL  plan-2  O10  0.020
 9PL  plan-2  C11  0.020
 9PL  plan-2  C12  0.020
 9PL  plan-2  O15  0.020

