# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Mar  8 14:31:27 2022
#   Inital geometry file: a 100 line input string
#   Ligand name: 3-oxo-N-[(3S)-2-oxotetrahydrofuran-3-yl]decanamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CCCCCCCC(=O)CC(=O)N[C@H]1CCOC1=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
 3M5  3M5  3-oxo-N-[(3S)-2-oxotetrahydrofuran-3-yl]decanamide  ligand  42  19  .  2022-03-10  2022-03-10
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_3M5
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
 3M5  CA   C  CH1   0  -0.264  -4.2798   0.4930   0.5019
 3M5  CB   C  CH2   0  -0.510  -5.2875   0.6648  -0.6240
 3M5  C    C  C     0   0.580  -4.1781  -1.0298   0.6135
 3M5  O    O  O     0  -0.418  -3.7168  -1.6747   1.5116
 3M5  OAC  O  O2    0  -0.437  -4.6643  -1.5962  -0.4890
 3M5  CAB  C  CH2   0  -0.183  -5.1066  -0.6113  -1.4376
 3M5  N    N  NH1   0  -0.621  -2.9809   1.0372   0.1880
 3M5  CAG  C  C     0   0.553  -2.1338   1.5124   1.1226
 3M5  OAL  O  O     0  -0.477  -2.4053   1.5666   2.3089
 3M5  CAH  C  CH2   0  -0.702  -0.7999   1.9733   0.5836
 3M5  CAI  C  C     0   0.413   0.2419   0.8736   0.6736
 3M5  OAM  O  O     0  -0.388  -0.0487  -0.2392   1.0421
 3M5  CAJ  C  CH2   0  -0.558   1.6330   1.2715   0.2648
 3M5  CAN  C  CH2   0  -0.417   2.6702   0.1640   0.3504
 3M5  CAO  C  CH2   0  -0.414   4.0465   0.6358  -0.1026
 3M5  CAP  C  CH2   0  -0.412   5.1062  -0.4555  -0.0217
 3M5  CAQ  C  CH2   0  -0.406   6.4794   0.0051  -0.4931
 3M5  CAR  C  CH2   0  -0.418   7.5429  -1.0830  -0.4100
 3M5  CAS  C  CH3   0  -0.663   8.9101  -0.6138  -0.8878
 3M5  H1   H  HCH1  0   0.312  -4.6181   0.9156   1.4465
 3M5  H2   H  HCH2  0   0.284  -6.2924   0.7044  -0.2033
 3M5  H3   H  HCH2  0   0.285  -5.1333   1.5667  -1.2136
 3M5  H4   H  HCH2  0   0.267  -6.0267  -0.9689  -1.8939
 3M5  H5   H  HCH2  0   0.254  -4.3467  -0.5101  -2.2145
 3M5  H6   H  HNH1  0   0.414  -2.6777   1.0189  -0.7737
 3M5  H7   H  HCH2  0   0.304  -0.8604   2.3059  -0.4567
 3M5  H8   H  HCH2  0   0.308  -0.4553   2.8359   1.1586
 3M5  H9   H  HCH2  0   0.270   1.5755   1.6729  -0.7537
 3M5  H10  H  HCH2  0   0.271   1.9284   2.1279   0.8820
 3M5  H11  H  HCH2  0   0.224   2.7321  -0.2049   1.3779
 3M5  H12  H  HCH2  0   0.224   2.3573  -0.6852  -0.2634
 3M5  H13  H  HCH2  0   0.211   3.9837   1.0056  -1.1317
 3M5  H14  H  HCH2  0   0.212   4.3596   1.4908   0.5068
 3M5  H15  H  HCH2  0   0.208   5.1785  -0.8141   1.0109
 3M5  H16  H  HCH2  0   0.208   4.7867  -1.3170  -0.6188
 3M5  H17  H  HCH2  0   0.206   6.4077   0.3622  -1.5264
 3M5  H18  H  HCH2  0   0.206   6.7977   0.8686   0.1021
 3M5  H19  H  HCH2  0   0.210   7.6182  -1.4364   0.6230
 3M5  H20  H  HCH2  0   0.210   7.2230  -1.9469  -1.0012
 3M5  H21  H  HCH3  0   0.216   9.2653   0.2312  -0.2947
 3M5  H22  H  HCH3  0   0.226   9.6557  -1.4060  -0.8122
 3M5  H23  H  HCH3  0   0.215   8.8752  -0.2907  -1.9299

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
 3M5  O    C    double  1.198  0.020  1.198
 3M5  C    OAC  single  1.331  0.020  1.331
 3M5  C    CA   single  1.530  0.020  1.530
 3M5  OAC  CAB  single  1.437  0.020  1.437
 3M5  CA   CB   single  1.521  0.020  1.521
 3M5  CA   N    single  1.443  0.020  1.443
 3M5  CB   CAB  single  1.524  0.020  1.524
 3M5  N    CAG  single  1.348  0.020  1.348
 3M5  OAL  CAG  double  1.218  0.020  1.218
 3M5  CAG  CAH  single  1.511  0.020  1.511
 3M5  OAM  CAI  double  1.208  0.020  1.208
 3M5  CAH  CAI  single  1.517  0.020  1.517
 3M5  CAI  CAJ  single  1.504  0.020  1.504
 3M5  CAJ  CAN  single  1.520  0.020  1.520
 3M5  CAN  CAO  single  1.524  0.020  1.524
 3M5  CAQ  CAR  single  1.524  0.020  1.524
 3M5  CAQ  CAP  single  1.523  0.020  1.523
 3M5  CAO  CAP  single  1.523  0.020  1.523
 3M5  CAS  CAR  single  1.522  0.020  1.522
 3M5  CA   H1   single  0.970  0.020  1.090
 3M5  CB   H2   single  0.970  0.020  1.090
 3M5  CB   H3   single  0.970  0.020  1.090
 3M5  CAB  H4   single  0.970  0.020  1.090
 3M5  CAB  H5   single  0.970  0.020  1.090
 3M5  N    H6   single  0.860  0.020  1.020
 3M5  CAH  H7   single  0.970  0.020  1.090
 3M5  CAH  H8   single  0.970  0.020  1.090
 3M5  CAJ  H9   single  0.970  0.020  1.090
 3M5  CAJ  H10  single  0.970  0.020  1.090
 3M5  CAN  H11  single  0.970  0.020  1.090
 3M5  CAN  H12  single  0.970  0.020  1.090
 3M5  CAO  H13  single  0.970  0.020  1.090
 3M5  CAO  H14  single  0.970  0.020  1.090
 3M5  CAP  H15  single  0.970  0.020  1.090
 3M5  CAP  H16  single  0.970  0.020  1.090
 3M5  CAQ  H17  single  0.970  0.020  1.090
 3M5  CAQ  H18  single  0.970  0.020  1.090
 3M5  CAR  H19  single  0.970  0.020  1.090
 3M5  CAR  H20  single  0.970  0.020  1.090
 3M5  CAS  H21  single  0.970  0.020  1.090
 3M5  CAS  H22  single  0.970  0.020  1.090
 3M5  CAS  H23  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
 3M5  H1   CA   N    108.79  3.000
 3M5  H1   CA   C    110.10  3.000
 3M5  N    CA   C    109.35  3.000
 3M5  H1   CA   CB   113.12  3.000
 3M5  N    CA   CB   113.13  3.000
 3M5  C    CA   CB   102.15  3.000
 3M5  H3   CB   H2   108.03  3.000
 3M5  H3   CB   CAB  112.81  3.000
 3M5  H2   CB   CAB  110.24  3.000
 3M5  H3   CB   CA   113.62  3.000
 3M5  H2   CB   CA   109.23  3.000
 3M5  CAB  CB   CA   102.82  3.000
 3M5  OAC  C    O    122.16  3.000
 3M5  OAC  C    CA   109.79  3.000
 3M5  O    C    CA   128.02  3.000
 3M5  CAB  OAC  C    111.56  3.000
 3M5  H5   CAB  H4   108.72  3.000
 3M5  H5   CAB  OAC  108.61  3.000
 3M5  H4   CAB  OAC  108.18  3.000
 3M5  H5   CAB  CB   112.64  3.000
 3M5  H4   CAB  CB   113.51  3.000
 3M5  OAC  CAB  CB   104.95  3.000
 3M5  H6   N    CAG  118.60  3.000
 3M5  H6   N    CA   118.11  3.000
 3M5  CAG  N    CA   123.22  3.000
 3M5  CAH  CAG  OAL  122.05  3.000
 3M5  CAH  CAG  N    114.53  3.000
 3M5  OAL  CAG  N    123.42  3.000
 3M5  H8   CAH  H7   106.13  3.000
 3M5  H8   CAH  CAI  108.93  3.000
 3M5  H7   CAH  CAI  108.35  3.000
 3M5  H8   CAH  CAG  109.37  3.000
 3M5  H7   CAH  CAG  112.53  3.000
 3M5  CAI  CAH  CAG  111.34  3.000
 3M5  CAJ  CAI  OAM  123.32  3.000
 3M5  CAJ  CAI  CAH  115.30  3.000
 3M5  OAM  CAI  CAH  121.38  3.000
 3M5  H10  CAJ  H9   104.55  3.000
 3M5  H10  CAJ  CAN  110.72  3.000
 3M5  H9   CAJ  CAN  110.79  3.000
 3M5  H10  CAJ  CAI  107.64  3.000
 3M5  H9   CAJ  CAI  107.51  3.000
 3M5  CAN  CAJ  CAI  115.04  3.000
 3M5  H12  CAN  H11  106.36  3.000
 3M5  H12  CAN  CAO  109.39  3.000
 3M5  H11  CAN  CAO  109.43  3.000
 3M5  H12  CAN  CAJ  109.82  3.000
 3M5  H11  CAN  CAJ  109.72  3.000
 3M5  CAO  CAN  CAJ  111.96  3.000
 3M5  H14  CAO  H13  105.99  3.000
 3M5  H14  CAO  CAP  109.31  3.000
 3M5  H13  CAO  CAP  109.37  3.000
 3M5  H14  CAO  CAN  109.54  3.000
 3M5  H13  CAO  CAN  109.40  3.000
 3M5  CAP  CAO  CAN  113.00  3.000
 3M5  H16  CAP  H15  106.00  3.000
 3M5  H16  CAP  CAQ  109.39  3.000
 3M5  H15  CAP  CAQ  109.34  3.000
 3M5  H16  CAP  CAO  109.36  3.000
 3M5  H15  CAP  CAO  109.30  3.000
 3M5  CAQ  CAP  CAO  113.21  3.000
 3M5  H18  CAQ  H17  105.93  3.000
 3M5  H18  CAQ  CAR  109.29  3.000
 3M5  H17  CAQ  CAR  109.26  3.000
 3M5  H18  CAQ  CAP  109.39  3.000
 3M5  H17  CAQ  CAP  109.35  3.000
 3M5  CAR  CAQ  CAP  113.36  3.000
 3M5  H20  CAR  H19  105.96  3.000
 3M5  H20  CAR  CAS  109.65  3.000
 3M5  H19  CAR  CAS  109.51  3.000
 3M5  H20  CAR  CAQ  109.28  3.000
 3M5  H19  CAR  CAQ  109.27  3.000
 3M5  CAS  CAR  CAQ  112.93  3.000
 3M5  H23  CAS  H22  107.64  3.000
 3M5  H23  CAS  H21  107.45  3.000
 3M5  H22  CAS  H21  107.59  3.000
 3M5  H23  CAS  CAR  111.23  3.000
 3M5  H22  CAS  CAR  111.61  3.000
 3M5  H21  CAS  CAR  111.11  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
 3M5  CONST_01  OAL  CAG  N    CA      0.00   0.0  0
 3M5  CONST_02  CAH  CAG  N    CA    180.00   0.0  0
 3M5  CONST_03  H6   N    CAG  OAL   180.00   0.0  0
 3M5  Var_01    CAI  CAH  CAG  N     -94.47  30.0  3
 3M5  Var_02    OAM  CAI  CAH  CAG     5.24  30.0  3
 3M5  Var_03    CAN  CAJ  CAI  CAH  -179.70  30.0  3
 3M5  Var_04    CAO  CAN  CAJ  CAI   178.97  30.0  3
 3M5  Var_05    CAP  CAO  CAN  CAJ   179.80  30.0  3
 3M5  Var_06    CAQ  CAP  CAO  CAN   179.14  30.0  3
 3M5  Var_07    CAR  CAQ  CAP  CAO   179.84  30.0  1
 3M5  Var_08    CAS  CAR  CAQ  CAP   179.80  30.0  3
 3M5  Var_09    H21  CAS  CAR  CAQ    59.48  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
 3M5  chir_01  CA  C  CB  N  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
 3M5  plan-1  CA   0.020
 3M5  plan-1  N    0.020
 3M5  plan-1  CAG  0.020
 3M5  plan-1  OAL  0.020
 3M5  plan-1  CAH  0.020
 3M5  plan-1  H6   0.020
 3M5  plan-2  CAH  0.020
 3M5  plan-2  CAI  0.020
 3M5  plan-2  OAM  0.020
 3M5  plan-2  CAJ  0.020
 3M5  plan-3  CA   0.020
 3M5  plan-3  C    0.020
 3M5  plan-3  O    0.020
 3M5  plan-3  OAC  0.020

