# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Apr 18 01:18:26 2020
#   Inital geometry file: a 89 line input string
#   Ligand name: (3~{S},7~{R},10~{R},11~{R},13~{S})-11-methyl-2-oxidanylidene-1,4-diazatricyclo[8.3.0.0^{3,7}]tridec-8-ene-13-carboxylic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[C@@H]1C[C@H](N2[C@H]1C=C[C@H]3CCN[C@@H]3C2=O)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
 8SN  8SN  '(3~{S},7~{R},10~{R},11~{R},13~{S})-11-methyl-2-oxidanylidene-1,4-diazatricyclo[8.3.0.0^{3,7}]tridec-8-ene-13-carboxylic acid'  ligand  35  18  .  2021-08-06  2021-08-06  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_8SN
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
 8SN  N2   N  NH1    0  -0.617   2.9117   0.8446  -1.0711
 8SN  C22  C  CH2    0  -0.278   4.1010   0.4301  -0.3106
 8SN  C23  C  CH2    0  -0.480   3.6658  -0.7496   0.5652
 8SN  C8   C  CH1    0  -0.293   2.1676  -0.5175   0.7491
 8SN  C21  C  CH1    0  -0.196   1.7912   0.0338  -0.6333
 8SN  C25  C  C      0   0.543   0.5009   0.8142  -0.5456
 8SN  O7   O  O      0  -0.514   0.4897   2.0417  -0.5986
 8SN  C7   C  C1     0  -0.202   1.3908  -1.7258   1.1493
 8SN  C6   C  C1     0  -0.217   0.1979  -2.0779   0.6816
 8SN  C5   C  CH1    0  -0.038  -0.7010  -1.3686  -0.2949
 8SN  C4   C  CH1    0  -0.287  -2.1806  -1.6055   0.0681
 8SN  C3   C  CH2    0  -0.453  -2.8786  -0.3747  -0.4905
 8SN  C2   C  CH1    0  -0.202  -1.8894   0.7507  -0.1998
 8SN  N1   N  NT     0  -0.466  -0.6069   0.0902  -0.3733
 8SN  C1   C  C      0   0.415  -2.0742   1.3308   1.2217
 8SN  O2   O  O      0  -0.586  -1.2489   1.0084   2.0910
 8SN  C47  C  CH3    0  -0.666  -2.7188  -2.9269  -0.4476
 8SN  O1   O  OC    -1  -0.623  -3.0763   2.0629   1.3573
 8SN  H1   H  HNH1   0   0.346   2.6999   1.8162  -0.8864
 8SN  H96  H  HCH2   0   0.216   4.9188   0.1445  -0.9769
 8SN  H97  H  HCH2   0   0.221   4.4687   1.2539   0.3060
 8SN  H23  H  HCH2   0   0.232   3.8282  -1.6978   0.0460
 8SN  H95  H  HCH2   0   0.248   4.2114  -0.7958   1.5082
 8SN  H8   H  HCH1   0   0.256   2.0241   0.2765   1.4948
 8SN  H21  H  HCH1   0   0.248   1.6538  -0.8177  -1.3153
 8SN  H7   H  H      0   0.242   1.8587  -2.3792   1.8798
 8SN  H6   H  H      0   0.242  -0.2120  -3.0223   1.0284
 8SN  H5   H  HCH1   0   0.251  -0.5237  -1.7908  -1.2955
 8SN  H41  H  HCH1   0   0.246  -2.2654  -1.5880   1.1599
 8SN  H32  H  HCH2   0   0.230  -3.0260  -0.4824  -1.5696
 8SN  H31  H  HCH2   0   0.246  -3.8558  -0.1951  -0.0426
 8SN  H22  H  HCH1   0   0.244  -1.9933   1.5581  -0.9276
 8SN  H47  H  HCH3   0   0.232  -2.1847  -3.7784  -0.0226
 8SN  H93  H  HCH3   0   0.237  -3.7718  -3.0440  -0.1889
 8SN  H94  H  HCH3   0   0.221  -2.6324  -2.9878  -1.5345

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
 8SN  C22  C23  single  1.532  0.020  1.532
 8SN  C22  N2   single  1.471  0.020  1.471
 8SN  C23  C8   single  1.527  0.020  1.527
 8SN  N2   C21  single  1.451  0.020  1.451
 8SN  C8   C21  single  1.535  0.020  1.535
 8SN  C8   C7   single  1.491  0.020  1.491
 8SN  C21  C25  single  1.511  0.020  1.511
 8SN  C7   C6   double  1.329  0.020  1.329
 8SN  O7   C25  double  1.229  0.020  1.229
 8SN  C25  N1   single  1.335  0.020  1.335
 8SN  C6   C5   single  1.505  0.020  1.505
 8SN  N1   C5   single  1.464  0.020  1.464
 8SN  N1   C2   single  1.453  0.020  1.453
 8SN  C5   C4   single  1.542  0.020  1.542
 8SN  O2   C1   deloc   1.241  0.020  1.241
 8SN  C2   C1   single  1.546  0.020  1.546
 8SN  C2   C3   single  1.526  0.020  1.526
 8SN  C1   O1   deloc   1.248  0.020  1.248
 8SN  C4   C3   single  1.521  0.020  1.521
 8SN  C4   C47  single  1.517  0.020  1.517
 8SN  N2   H1   single  0.890  0.020  1.040
 8SN  C22  H96  single  0.970  0.020  1.090
 8SN  C22  H97  single  0.970  0.020  1.090
 8SN  C23  H23  single  0.970  0.020  1.090
 8SN  C23  H95  single  0.970  0.020  1.090
 8SN  C8   H8   single  0.970  0.020  1.090
 8SN  C21  H21  single  0.970  0.020  1.090
 8SN  C7   H7   single  0.930  0.020  1.080
 8SN  C6   H6   single  0.930  0.020  1.080
 8SN  C5   H5   single  0.970  0.020  1.090
 8SN  C4   H41  single  0.970  0.020  1.090
 8SN  C3   H32  single  0.970  0.020  1.090
 8SN  C3   H31  single  0.970  0.020  1.090
 8SN  C2   H22  single  0.970  0.020  1.090
 8SN  C47  H47  single  0.970  0.020  1.090
 8SN  C47  H93  single  0.970  0.020  1.090
 8SN  C47  H94  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
 8SN  H1   N2   C21  108.66  3.000
 8SN  H1   N2   C22  110.21  3.000
 8SN  C21  N2   C22  108.11  3.000
 8SN  H97  C22  H96  106.81  3.000
 8SN  H97  C22  C23  110.70  3.000
 8SN  H96  C22  C23  111.09  3.000
 8SN  H97  C22  N2   110.57  3.000
 8SN  H96  C22  N2   111.31  3.000
 8SN  C23  C22  N2   106.42  3.000
 8SN  H95  C23  H23  107.44  3.000
 8SN  H95  C23  C8   113.15  3.000
 8SN  H23  C23  C8   109.56  3.000
 8SN  H95  C23  C22  112.63  3.000
 8SN  H23  C23  C22  110.74  3.000
 8SN  C8   C23  C22  103.32  3.000
 8SN  H8   C8   C7   109.59  3.000
 8SN  H8   C8   C21  108.64  3.000
 8SN  C7   C8   C21  113.89  3.000
 8SN  H8   C8   C23  108.64  3.000
 8SN  C7   C8   C23  114.84  3.000
 8SN  C21  C8   C23  100.76  3.000
 8SN  H21  C21  C25  109.23  3.000
 8SN  H21  C21  C8   108.12  3.000
 8SN  C25  C21  C8   110.04  3.000
 8SN  H21  C21  N2   110.01  3.000
 8SN  C25  C21  N2   112.86  3.000
 8SN  C8   C21  N2   106.45  3.000
 8SN  N1   C25  O7   122.68  3.000
 8SN  N1   C25  C21  115.87  3.000
 8SN  O7   C25  C21  121.43  3.000
 8SN  H7   C7   C6   117.66  3.000
 8SN  H7   C7   C8   116.34  3.000
 8SN  C6   C7   C8   126.00  3.000
 8SN  H6   C6   C5   113.05  3.000
 8SN  H6   C6   C7   117.17  3.000
 8SN  C5   C6   C7   129.78  3.000
 8SN  H5   C5   N1   108.86  3.000
 8SN  H5   C5   C4   108.04  3.000
 8SN  N1   C5   C4   103.15  3.000
 8SN  H5   C5   C6   108.23  3.000
 8SN  C4   C5   C6   110.37  3.000
 8SN  N1   C5   C6   117.78  3.000
 8SN  H41  C4   C47  108.99  3.000
 8SN  H41  C4   C3   108.52  3.000
 8SN  C47  C4   C3   114.65  3.000
 8SN  H41  C4   C5   107.85  3.000
 8SN  C47  C4   C5   113.22  3.000
 8SN  C3   C4   C5   103.27  3.000
 8SN  H31  C3   H32  107.50  3.000
 8SN  H31  C3   C2   112.42  3.000
 8SN  H32  C3   C2   110.35  3.000
 8SN  H31  C3   C4   113.19  3.000
 8SN  H32  C3   C4   110.13  3.000
 8SN  C2   C3   C4   103.26  3.000
 8SN  H22  C2   C1   108.90  3.000
 8SN  H22  C2   N1   109.90  3.000
 8SN  C1   C2   N1   112.69  3.000
 8SN  H22  C2   C3   110.89  3.000
 8SN  C1   C2   C3   111.98  3.000
 8SN  N1   C2   C3   102.37  3.000
 8SN  C2   N1   C5   112.94  3.000
 8SN  C2   N1   C25  120.10  3.000
 8SN  C5   N1   C25  126.93  3.000
 8SN  O1   C1   O2   127.58  3.000
 8SN  O1   C1   C2   114.56  3.000
 8SN  O2   C1   C2   117.84  3.000
 8SN  H94  C47  H93  107.85  3.000
 8SN  H94  C47  H47  107.78  3.000
 8SN  H93  C47  H47  107.24  3.000
 8SN  H94  C47  C4   111.02  3.000
 8SN  H93  C47  C4   110.82  3.000
 8SN  H47  C47  C4   111.93  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
 8SN  Var_01  C8   C23  C22  N2   -26.02  30.0  1
 8SN  Var_02  C21  N2   C22  C23    3.44  30.0  1

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
 8SN  chir_01  C8   C23  C21  C7   negativ
 8SN  chir_02  C21  N2   C8   C25  negativ
 8SN  chir_03  C5   N1   C4   C6   positiv
 8SN  chir_04  C4   C5   C3   C47  negativ
 8SN  chir_05  C2   N1   C1   C3   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
 8SN  plan-1  C21  0.020
 8SN  plan-1  C25  0.020
 8SN  plan-1  O7   0.020
 8SN  plan-1  C5   0.020
 8SN  plan-1  C2   0.020
 8SN  plan-1  N1   0.020
 8SN  plan-2  C2   0.020
 8SN  plan-2  C1   0.020
 8SN  plan-2  O2   0.020
 8SN  plan-2  O1   0.020

