# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Jul 21 18:49:27 2021
#   Inital geometry file: a 148 line input string
#   Ligand name: ~{N}-[2-methoxy-5-(2-oxa-6-azaspiro[3.3]heptan-6-ylsulfonyl)phenyl]-3-methyl-4-oxidanylidene-5,6,7,8-tetrahydro-2~{H}-cyclohepta[c]pyrrole-1-carboxamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: COc1ccc(cc1NC(=O)c2[nH]c(C)c3C(=O)CCCCc23)[S](=O)(=O)N4CC5(COC5)C4
#
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
 L2Z  L2Z  ~{N}-[2-methoxy-5-(2-oxa-6-azaspiro[3.3]heptan-6-ylsulfonyl)phenyl]-3-methyl-4-oxidanylidene-5,6,7,8-tetrahydro-2~{H}-cyclohepta[c]pyrrole-1-carboxamide  ligand  60  33  .  2022-07-25  2023-02-15
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_L2Z
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
 L2Z  C1   C  CH3   0  -0.726  13.3452  -10.4978  -10.0955
 L2Z  C2   C  CR5   0  -0.158  14.6425  -10.6749   -7.8216
 L2Z  C3   C  C     0   0.338  14.5469  -12.1146   -7.6086
 L2Z  C4   C  CH2   0  -0.589  15.5348  -12.7217   -6.6439
 L2Z  C5   C  CH2   0  -0.429  15.2368  -12.4228   -5.1701
 L2Z  C6   C  CH2   0  -0.456  14.9988  -10.9499   -4.8424
 L2Z  C7   C  CH2   0  -0.581  15.8711   -9.9737   -5.6379
 L2Z  C8   C  CR5   0   0.048  15.3259   -9.7206   -7.0132
 L2Z  C10  C  C     0   0.478  15.6572   -7.1448   -7.3866
 L2Z  C12  C  CR6   0   0.349  18.2271   -6.1089   -4.9552
 L2Z  C13  C  CH3   0  -0.438  19.3804   -7.7042   -3.6174
 L2Z  C15  C  CR16  0  -0.243  18.5347   -3.7330   -4.7291
 L2Z  N    N  NR15  0  -0.661  14.4807   -8.7225   -8.8139
 L2Z  C    C  CR5   0   0.363  14.1238  -10.0040   -8.9312
 L2Z  O    O  O     0  -0.425  13.7472  -12.8026   -8.2221
 L2Z  C11  C  CR6   0   0.307  17.2851   -5.9012   -5.9896
 L2Z  C14  C  CR16  0  -0.373  18.8397   -5.0288   -4.3385
 L2Z  C16  C  CR6   0  -0.232  17.6156   -3.5347   -5.7439
 L2Z  C17  C  C     0  -0.265  18.4425   -2.3759   -8.7511
 L2Z  C18  C  C     0  -0.198  19.9428   -2.0624   -8.7685
 L2Z  C19  C  C     0  -0.116  20.5395   -1.1661   -9.8516
 L2Z  C20  C  C     0  -0.126  21.0027   -3.0636   -9.2090
 L2Z  C21  C  C     0  -0.264  19.8011   -1.5720   -7.3246
 L2Z  C22  C  CR16  0  -0.305  16.9870   -4.6054   -6.3782
 L2Z  C9   C  CR5   0   0.173  15.2148   -8.5109   -7.6711
 L2Z  N1   N  NH1   0  -0.765  16.7190   -7.0474   -6.5419
 L2Z  N2   N  N     0  -0.570  18.3422   -1.5752   -7.5196
 L2Z  O1   O  O     0  -0.474  15.1093   -6.1825   -7.9059
 L2Z  O3   O  O     0  -0.510  21.4926   -2.1714  -10.2172
 L2Z  O4   O  OS    0  -0.655  17.6096   -0.9695   -5.2383
 L2Z  O5   O  OS    0  -0.654  15.9586   -1.8857   -6.9170
 L2Z  S    S  S     0   1.394  17.2791   -1.8966   -6.3088
 L2Z  H1   H  HCH3  0   0.259  13.8461  -11.3373  -10.5759
 L2Z  H2   H  HCH3  0   0.261  12.3591  -10.8446   -9.7890
 L2Z  H3   H  HCH3  0   0.252  13.2138   -9.7101  -10.8361
 L2Z  H4   H  HCH2  0   0.265  15.5579  -13.8016   -6.7953
 L2Z  H5   H  HCH2  0   0.255  16.5305  -12.3416   -6.8894
 L2Z  H6   H  HCH2  0   0.240  14.3731  -13.0076   -4.8469
 L2Z  H7   H  HCH2  0   0.242  16.0890  -12.7879   -4.5927
 L2Z  H8   H  HCH2  0   0.249  15.1838  -10.8005   -3.7773
 L2Z  H9   H  HCH2  0   0.235  13.9504  -10.6878   -5.0058
 L2Z  H10  H  HCH2  0   0.258  16.9020  -10.3434   -5.6831
 L2Z  H11  H  HCH2  0   0.253  15.9086   -9.0351   -5.0838
 L2Z  H12  H  HCH3  0   0.270  19.3924   -8.7875   -3.5413
 L2Z  H13  H  HCH3  0   0.241  20.3835   -7.3516   -3.8646
 L2Z  H14  H  HCH3  0   0.241  19.0752   -7.2820   -2.6581
 L2Z  H15  H  HCR6  0   0.291  19.0086   -2.9033   -4.2238
 L2Z  H16  H  HNR5  0   0.416  14.2608   -8.0008   -9.4848
 L2Z  H17  H  HCR6  0   0.300  19.5519   -5.1763   -3.5393
 L2Z  H18  H  H     0   0.275  17.8422   -1.9994   -9.5785
 L2Z  H19  H  H     0   0.256  18.2407   -3.4426   -8.6071
 L2Z  H20  H  H     0   0.225  21.0130   -0.2493   -9.4870
 L2Z  H21  H  H     0   0.226  19.8602   -0.9125  -10.6710
 L2Z  H22  H  H     0   0.227  20.6162   -4.0000   -9.6226
 L2Z  H23  H  H     0   0.226  21.7560   -3.2955   -8.4497
 L2Z  H24  H  H     0   0.254  20.1544   -2.3127   -6.5990
 L2Z  H25  H  H     0   0.275  20.2169   -0.5955   -7.0798
 L2Z  H26  H  HCR6  0   0.308  16.2636   -4.4345   -7.1585
 L2Z  H27  H  HNH1  0   0.437  17.1820   -7.9075   -6.2922
 L2Z  O2   O  O2    0  -0.473  18.4512   -7.3892   -4.6419

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
 L2Z  O3   C19  single    1.433  0.020  1.433
 L2Z  O3   C20  single    1.433  0.020  1.433
 L2Z  C19  C18  single    1.527  0.020  1.527
 L2Z  C1   C    single    1.485  0.020  1.485
 L2Z  C17  C18  single    1.533  0.020  1.533
 L2Z  C17  N2   single    1.472  0.020  1.472
 L2Z  C20  C18  single    1.523  0.020  1.523
 L2Z  C18  C21  single    1.532  0.020  1.532
 L2Z  C    N    aromatic  1.335  0.020  1.335
 L2Z  C    C2   aromatic  1.397  0.020  1.397
 L2Z  N    C9   aromatic  1.375  0.020  1.375
 L2Z  O1   C10  double    1.223  0.020  1.223
 L2Z  O    C3   double    1.220  0.020  1.220
 L2Z  C2   C3   single    1.458  0.020  1.458
 L2Z  C2   C8   aromatic  1.425  0.020  1.425
 L2Z  C9   C10  single    1.464  0.020  1.464
 L2Z  C9   C8   aromatic  1.382  0.020  1.382
 L2Z  C3   C4   single    1.508  0.020  1.508
 L2Z  N2   C21  single    1.472  0.020  1.472
 L2Z  N2   S    single    1.643  0.020  1.643
 L2Z  C10  N1   single    1.360  0.020  1.360
 L2Z  O5   S    double    1.454  0.020  1.454
 L2Z  C8   C7   single    1.501  0.020  1.501
 L2Z  C4   C5   single    1.533  0.020  1.533
 L2Z  S    C16  single    1.765  0.020  1.765
 L2Z  S    O4   double    1.454  0.020  1.454
 L2Z  N1   C11  single    1.393  0.020  1.393
 L2Z  C22  C11  aromatic  1.385  0.020  1.385
 L2Z  C22  C16  aromatic  1.394  0.020  1.394
 L2Z  C7   C6   single    1.532  0.020  1.532
 L2Z  C11  C12  aromatic  1.414  0.020  1.414
 L2Z  C16  C15  aromatic  1.383  0.020  1.383
 L2Z  C5   C6   single    1.528  0.020  1.528
 L2Z  C12  O2   single    1.337  0.020  1.337
 L2Z  C12  C14  aromatic  1.386  0.020  1.386
 L2Z  C15  C14  aromatic  1.387  0.020  1.387
 L2Z  O2   C13  single    1.419  0.020  1.419
 L2Z  C1   H1   single    0.970  0.020  1.090
 L2Z  C1   H2   single    0.970  0.020  1.090
 L2Z  C1   H3   single    0.970  0.020  1.090
 L2Z  C4   H4   single    0.970  0.020  1.090
 L2Z  C4   H5   single    0.970  0.020  1.090
 L2Z  C5   H6   single    0.970  0.020  1.090
 L2Z  C5   H7   single    0.970  0.020  1.090
 L2Z  C6   H8   single    0.970  0.020  1.090
 L2Z  C6   H9   single    0.970  0.020  1.090
 L2Z  C7   H10  single    0.970  0.020  1.090
 L2Z  C7   H11  single    0.970  0.020  1.090
 L2Z  C13  H12  single    0.970  0.020  1.090
 L2Z  C13  H13  single    0.970  0.020  1.090
 L2Z  C13  H14  single    0.970  0.020  1.090
 L2Z  C15  H15  single    0.930  0.020  1.080
 L2Z  N    H16  single    0.860  0.020  1.020
 L2Z  C14  H17  single    0.930  0.020  1.080
 L2Z  C17  H18  single    0.970  0.020  1.090
 L2Z  C17  H19  single    0.970  0.020  1.090
 L2Z  C19  H20  single    0.970  0.020  1.090
 L2Z  C19  H21  single    0.970  0.020  1.090
 L2Z  C20  H22  single    0.970  0.020  1.090
 L2Z  C20  H23  single    0.970  0.020  1.090
 L2Z  C21  H24  single    0.970  0.020  1.090
 L2Z  C21  H25  single    0.970  0.020  1.090
 L2Z  C22  H26  single    0.930  0.020  1.080
 L2Z  N1   H27  single    0.860  0.020  1.020

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
 L2Z  H3   C1   H2   108.20  3.000
 L2Z  H3   C1   H1   108.24  3.000
 L2Z  H2   C1   H1   107.15  3.000
 L2Z  H3   C1   C    110.85  3.000
 L2Z  H2   C1   C    111.09  3.000
 L2Z  H1   C1   C    111.16  3.000
 L2Z  C    C2   C8   107.88  3.000
 L2Z  C8   C2   C3   127.55  3.000
 L2Z  C    C2   C3   124.47  3.000
 L2Z  O    C3   C4   121.59  3.000
 L2Z  C4   C3   C2   116.60  3.000
 L2Z  O    C3   C2   121.74  3.000
 L2Z  H5   C4   H4   107.07  3.000
 L2Z  H5   C4   C5   108.96  3.000
 L2Z  H4   C4   C5   109.31  3.000
 L2Z  H5   C4   C3   108.23  3.000
 L2Z  H4   C4   C3   108.88  3.000
 L2Z  C5   C4   C3   114.15  3.000
 L2Z  H7   C5   H6   106.35  3.000
 L2Z  H7   C5   C6   109.30  3.000
 L2Z  H6   C5   C6   109.25  3.000
 L2Z  H7   C5   C4   106.94  3.000
 L2Z  H6   C5   C4   109.50  3.000
 L2Z  C6   C5   C4   115.12  3.000
 L2Z  H9   C6   H8   106.00  3.000
 L2Z  H9   C6   C7   108.40  3.000
 L2Z  H8   C6   C7   108.85  3.000
 L2Z  H9   C6   C5   110.40  3.000
 L2Z  H8   C6   C5   108.36  3.000
 L2Z  C7   C6   C5   114.48  3.000
 L2Z  H11  C7   H10  106.19  3.000
 L2Z  H11  C7   C8   109.45  3.000
 L2Z  H10  C7   C8   111.14  3.000
 L2Z  H11  C7   C6   107.71  3.000
 L2Z  H10  C7   C6   110.00  3.000
 L2Z  C8   C7   C6   112.11  3.000
 L2Z  C9   C8   C7   127.82  3.000
 L2Z  C7   C8   C2   125.53  3.000
 L2Z  C9   C8   C2   106.12  3.000
 L2Z  O1   C10  N1   123.85  3.000
 L2Z  N1   C10  C9   115.05  3.000
 L2Z  O1   C10  C9   121.09  3.000
 L2Z  O2   C12  C14  124.59  3.000
 L2Z  C14  C12  C11  120.34  3.000
 L2Z  O2   C12  C11  115.06  3.000
 L2Z  H14  C13  H13  109.33  3.000
 L2Z  H14  C13  H12  109.11  3.000
 L2Z  H13  C13  H12  109.14  3.000
 L2Z  H14  C13  O2   111.45  3.000
 L2Z  H13  C13  O2   111.51  3.000
 L2Z  H12  C13  O2   106.22  3.000
 L2Z  H15  C15  C16  121.62  3.000
 L2Z  H15  C15  C14  119.27  3.000
 L2Z  C16  C15  C14  119.11  3.000
 L2Z  H16  N    C9   123.97  3.000
 L2Z  H16  N    C    124.71  3.000
 L2Z  C9   N    C    111.31  3.000
 L2Z  N    C    C2   106.98  3.000
 L2Z  C2   C    C1   131.14  3.000
 L2Z  N    C    C1   121.87  3.000
 L2Z  N1   C11  C22  124.83  3.000
 L2Z  C22  C11  C12  119.07  3.000
 L2Z  N1   C11  C12  116.10  3.000
 L2Z  H17  C14  C15  118.72  3.000
 L2Z  H17  C14  C12  120.92  3.000
 L2Z  C15  C14  C12  120.35  3.000
 L2Z  S    C16  C22  118.76  3.000
 L2Z  C22  C16  C15  121.55  3.000
 L2Z  S    C16  C15  119.63  3.000
 L2Z  H19  C17  H18  109.57  3.000
 L2Z  H19  C17  N2   114.03  3.000
 L2Z  H18  C17  N2   114.19  3.000
 L2Z  H19  C17  C18  112.40  3.000
 L2Z  H18  C17  C18  117.39  3.000
 L2Z  N2   C17  C18   87.99  3.000
 L2Z  C21  C18  C20  123.19  3.000
 L2Z  C21  C18  C19  121.12  3.000
 L2Z  C20  C18  C19   84.77  3.000
 L2Z  C21  C18  C17   87.95  3.000
 L2Z  C20  C18  C17  123.37  3.000
 L2Z  C19  C18  C17  120.70  3.000
 L2Z  H21  C19  H20  108.90  3.000
 L2Z  H21  C19  O3   112.62  3.000
 L2Z  H20  C19  O3   112.64  3.000
 L2Z  H21  C19  C18  115.12  3.000
 L2Z  H20  C19  C18  115.11  3.000
 L2Z  O3   C19  C18   91.67  3.000
 L2Z  H23  C20  H22  108.91  3.000
 L2Z  H23  C20  O3   112.64  3.000
 L2Z  H22  C20  O3   112.81  3.000
 L2Z  H23  C20  C18  114.69  3.000
 L2Z  H22  C20  C18  115.21  3.000
 L2Z  O3   C20  C18   91.84  3.000
 L2Z  H25  C21  H24  109.52  3.000
 L2Z  H25  C21  N2   114.21  3.000
 L2Z  H24  C21  N2   113.96  3.000
 L2Z  H25  C21  C18  117.62  3.000
 L2Z  H24  C21  C18  112.22  3.000
 L2Z  N2   C21  C18   88.06  3.000
 L2Z  H26  C22  C16  120.68  3.000
 L2Z  H26  C22  C11  119.74  3.000
 L2Z  C16  C22  C11  119.58  3.000
 L2Z  N    C9   C10  117.81  3.000
 L2Z  C10  C9   C8   134.46  3.000
 L2Z  N    C9   C8   107.70  3.000
 L2Z  H27  N1   C11  114.66  3.000
 L2Z  H27  N1   C10  116.82  3.000
 L2Z  C11  N1   C10  128.49  3.000
 L2Z  S    N2   C21  122.97  3.000
 L2Z  S    N2   C17  123.65  3.000
 L2Z  C21  N2   C17   92.55  3.000
 L2Z  C20  O3   C19   91.72  3.000
 L2Z  O5   S    O4   120.64  3.000
 L2Z  O4   S    N2   105.71  3.000
 L2Z  O5   S    N2   106.14  3.000
 L2Z  O4   S    C16  108.22  3.000
 L2Z  O5   S    C16  108.30  3.000
 L2Z  N2   S    C16  107.10  3.000
 L2Z  C13  O2   C12  119.45  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
 L2Z  CONST_01  C9   N    C    C2      0.00   0.0  0
 L2Z  CONST_02  N    C9   C8   C2      0.00   0.0  0
 L2Z  CONST_03  N    C    C2   C8      0.00   0.0  0
 L2Z  CONST_04  C    N    C9   C8      0.00   0.0  0
 L2Z  CONST_05  C16  C22  C11  C12     0.00   0.0  0
 L2Z  CONST_06  C16  C15  C14  C12     0.00   0.0  0
 L2Z  CONST_07  C11  C22  C16  C15     0.00   0.0  0
 L2Z  CONST_08  C11  C12  C14  C15     0.00   0.0  0
 L2Z  CONST_09  C9   C8   C2   C       0.00   0.0  0
 L2Z  CONST_10  C22  C11  C12  C14     0.00   0.0  0
 L2Z  CONST_11  C22  C16  C15  C14     0.00   0.0  0
 L2Z  CONST_12  C9   N    C    C1    180.00   0.0  0
 L2Z  CONST_13  C3   C2   C    C1      0.00   0.0  0
 L2Z  CONST_14  C8   C2   C    C1    180.00   0.0  0
 L2Z  CONST_15  C10  C9   C8   C2    180.00   0.0  0
 L2Z  CONST_16  C10  C9   C8   C7      0.00   0.0  0
 L2Z  CONST_17  C    N    C9   C10   180.00   0.0  0
 L2Z  CONST_18  O2   C12  C14  C15   180.00   0.0  0
 L2Z  CONST_19  S    C16  C22  C11   180.00   0.0  0
 L2Z  CONST_20  N1   C11  C12  C14   180.00   0.0  0
 L2Z  CONST_21  S    C16  C15  C14   180.00   0.0  0
 L2Z  CONST_22  N1   C11  C22  C16   180.00   0.0  0
 L2Z  CONST_23  O2   C12  C11  C22   180.00   0.0  0
 L2Z  CONST_24  H16  N    C    C2    180.00   0.0  0
 L2Z  CONST_25  H26  C22  C11  C12   180.00   0.0  0
 L2Z  CONST_26  H15  C15  C14  C12   180.00   0.0  0
 L2Z  CONST_27  H17  C14  C12  C11   180.00   0.0  0
 L2Z  CONST_28  C9   C10  N1   C11   180.00   0.0  0
 L2Z  CONST_29  C22  C11  N1   C10     0.00   0.0  0
 L2Z  CONST_30  C12  C11  N1   C10   180.00   0.0  0
 L2Z  CONST_31  H27  N1   C11  C12     0.00   0.0  0
 L2Z  CONST_32  O1   C10  N1   C11     0.00   0.0  0
 L2Z  Var_01    C5   C4   C3   C2     74.18  30.0  1
 L2Z  Var_02    C6   C7   C8   C2    -34.16  30.0  1
 L2Z  Var_03    C6   C5   C4   C3    -50.40  30.0  1
 L2Z  Var_04    C    C2   C3   C4    159.69  30.0  1
 L2Z  Var_05    C7   C6   C5   C4    -36.60  30.0  1
 L2Z  Var_06    C8   C7   C6   C5     80.90  30.0  1
 L2Z  Var_07    O3   C19  C18  C17  -125.22  30.0  1
 L2Z  Var_08    O3   C20  C18  C17   122.82  30.0  1
 L2Z  Var_09    N2   C21  C18  C17   -13.71  30.0  3
 L2Z  Var_10    N2   C17  C18  C19  -111.76  30.0  3
 L2Z  Var_11    N2   S    C16  C15    89.54  30.0  1
 L2Z  Var_12    C17  N2   S    C16    58.74  30.0  2
 L2Z  Var_13    O1   C10  C9   C8   -157.69  30.0  2
 L2Z  Var_14    C11  C12  O2   C13   179.94  30.0  2
 L2Z  Var_15    H1   C1   C    C2    -52.45  30.0  2
 L2Z  Var_16    H12  C13  O2   C12   179.87  30.0  3

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
 L2Z  plan-1  C1   0.020
 L2Z  plan-1  C2   0.020
 L2Z  plan-1  C3   0.020
 L2Z  plan-1  C7   0.020
 L2Z  plan-1  C8   0.020
 L2Z  plan-1  C10  0.020
 L2Z  plan-1  N    0.020
 L2Z  plan-1  C    0.020
 L2Z  plan-1  C9   0.020
 L2Z  plan-1  H16  0.020
 L2Z  plan-2  C12  0.020
 L2Z  plan-2  C15  0.020
 L2Z  plan-2  C11  0.020
 L2Z  plan-2  C14  0.020
 L2Z  plan-2  C16  0.020
 L2Z  plan-2  C22  0.020
 L2Z  plan-2  N1   0.020
 L2Z  plan-2  S    0.020
 L2Z  plan-2  H15  0.020
 L2Z  plan-2  H17  0.020
 L2Z  plan-2  H26  0.020
 L2Z  plan-2  O2   0.020
 L2Z  plan-3  C2   0.020
 L2Z  plan-3  C3   0.020
 L2Z  plan-3  C4   0.020
 L2Z  plan-3  O    0.020
 L2Z  plan-4  C10  0.020
 L2Z  plan-4  C11  0.020
 L2Z  plan-4  C9   0.020
 L2Z  plan-4  N1   0.020
 L2Z  plan-4  O1   0.020
 L2Z  plan-4  H27  0.020

