# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Jul 24 19:59:46 2021
#   Inital geometry file: a 154 line input string
#   Ligand name: ~{N}-[2-methoxy-5-(4-methylpiperazin-1-yl)sulfonyl-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)N4CCN(C)CC4
#
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
 L2N  L2N  ~{N}-[2-methoxy-5-(4-methylpiperazin-1-yl)sulfonyl-phenyl]-3-methyl-4-oxidanylidene-5,6,7,8-tetrahydro-2~{H}-cyclohepta[c]pyrrole-1-carboxamide  ligand  63  33  .  2022-03-22  2022-07-25
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_L2N
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
 L2N  N1   N  NH1   0  -0.757   4.6073  -13.8419  -23.4842
 L2N  O2   O  O2    0  -0.470   4.8766  -14.4290  -26.0131
 L2N  O3   O  OS    0  -0.654   6.3835  -18.0673  -20.8988
 L2N  C4   C  CH2   0  -0.588   2.5616   -8.5352  -24.7735
 L2N  C5   C  CH2   0  -0.427   1.7218   -9.3834  -25.7351
 L2N  C6   C  CH2   0  -0.456   1.6585  -10.8727  -25.4002
 L2N  C7   C  CH2   0  -0.579   2.9567  -11.4554  -24.8319
 L2N  C8   C  CR5   0   0.045   3.1099  -11.1670  -23.3664
 L2N  C9   C  CR5   0   0.175   3.5108  -12.0356  -22.3695
 L2N  C10  C  C     0   0.470   4.0042  -13.4142  -22.3419
 L2N  C11  C  CR6   0   0.298   4.9804  -15.1464  -23.8067
 L2N  C12  C  CR6   0   0.354   5.1141  -15.4486  -25.1811
 L2N  C13  C  CH3   0  -0.439   5.0389  -14.6203  -27.4090
 L2N  C14  C  CR16  0  -0.375   5.4697  -16.7278  -25.5838
 L2N  C15  C  CR16  0  -0.239   5.6885  -17.7242  -24.6428
 L2N  N2   N  N     0  -0.568   4.2826  -19.1933  -21.6511
 L2N  N    N  NR15  0  -0.661   3.3077  -11.4084  -21.1630
 L2N  C    C  CR5   0   0.362   2.8066  -10.1820  -21.3306
 L2N  C1   C  CH3   0  -0.724   2.5162   -9.2910  -20.1784
 L2N  C16  C  CR6   0  -0.214   5.5733  -17.4178  -23.2997
 L2N  C17  C  CH2   0  -0.317   3.4565  -18.2551  -20.8906
 L2N  C18  C  CH2   0  -0.275   2.2930  -19.0091  -20.2765
 L2N  C2   C  CR5   0  -0.157   2.6724   -9.9819  -22.7060
 L2N  C20  C  CH2   0  -0.278   2.3528  -20.6167  -22.0246
 L2N  C21  C  CH2   0  -0.311   3.5210  -19.9034  -22.6787
 L2N  C22  C  CR16  0  -0.289   5.2367  -16.1346  -22.8722
 L2N  C3   C  C     0   0.337   2.2207   -8.7380  -23.3180
 L2N  N3   N  NT    0  -0.415   1.5206  -19.6834  -21.2971
 L2N  O1   O  O     0  -0.469   3.8852  -14.1033  -21.3391
 L2N  S    S  S     0   1.377   5.7956  -18.6769  -22.0812
 L2N  H1   H  HNH1  0   0.431   4.7551  -13.1589  -24.2105
 L2N  H2   H  HCH2  0   0.253   3.6195   -8.7738  -24.9151
 L2N  H3   H  HCH2  0   0.265   2.4359   -7.4799  -25.0202
 L2N  H4   H  HCH2  0   0.241   2.1480   -9.2516  -26.7319
 L2N  H5   H  HCH2  0   0.239   0.7070   -8.9831  -25.7813
 L2N  H6   H  HCH2  0   0.234   0.8547  -11.0654  -24.6855
 L2N  H7   H  HCH2  0   0.249   1.3920  -11.4193  -26.3065
 L2N  H8   H  HCH2  0   0.252   2.9316  -12.5341  -24.9876
 L2N  H9   H  HCH2  0   0.256   3.8169  -11.0855  -25.4019
 L2N  H10  H  HCH3  0   0.269   4.8162  -13.6647  -27.8749
 L2N  H11  H  HCH3  0   0.240   6.0620  -14.9096  -27.6562
 L2N  H12  H  HCH3  0   0.239   4.3479  -15.3731  -27.7930
 L2N  H13  H  HCR6  0   0.296   5.5741  -16.9703  -26.6321
 L2N  H14  H  HCR6  0   0.287   5.9578  -18.7170  -24.9739
 L2N  H15  H  HNR5  0   0.415   3.5235  -11.8241  -20.2690
 L2N  H16  H  HCH3  0   0.262   1.4435   -9.1383  -20.0616
 L2N  H17  H  HCH3  0   0.250   2.9005   -9.7174  -19.2529
 L2N  H18  H  HCH3  0   0.260   2.9667   -8.3093  -20.3153
 L2N  H19  H  HCH2  0   0.274   4.0463  -17.8071  -20.0940
 L2N  H20  H  HCH2  0   0.238   3.0747  -17.4511  -21.5325
 L2N  H21  H  HCH2  0   0.203   2.6791  -19.7078  -19.5153
 L2N  H22  H  HCH2  0   0.251   1.6561  -18.2881  -19.7595
 L2N  H23  H  HCH3  0   0.236  -0.2861  -19.5794  -20.2588
 L2N  H24  H  HCH3  0   0.236  -0.2381  -20.7781  -21.5498
 L2N  H25  H  HCH3  0   0.196   0.5771  -21.1051  -20.0124
 L2N  H26  H  HCH2  0   0.250   1.7618  -21.0890  -22.8121
 L2N  H27  H  HCH2  0   0.203   2.7371  -21.4235  -21.3778
 L2N  H28  H  HCH2  0   0.236   3.1461  -19.2104  -23.4420
 L2N  H29  H  HCH2  0   0.275   4.1557  -20.6408  -23.1653
 L2N  H30  H  HCR6  0   0.303   5.1762  -15.9045  -21.8210
 L2N  O    O  O     0  -0.424   1.6408   -7.8796  -22.6731
 L2N  C19  C  CH3   0  -0.520   0.3456  -20.3211  -20.7495
 L2N  O4   O  OS    0  -0.653   6.4636  -19.8042  -22.7112

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
 L2N  C13  O2   single    1.418  0.020  1.418
 L2N  O2   C12  single    1.337  0.020  1.337
 L2N  C6   C5   single    1.528  0.020  1.528
 L2N  C6   C7   single    1.532  0.020  1.532
 L2N  C14  C12  aromatic  1.387  0.020  1.387
 L2N  C14  C15  aromatic  1.388  0.020  1.388
 L2N  C5   C4   single    1.533  0.020  1.533
 L2N  C12  C11  aromatic  1.414  0.020  1.414
 L2N  C7   C8   single    1.501  0.020  1.501
 L2N  C15  C16  aromatic  1.382  0.020  1.382
 L2N  C4   C3   single    1.509  0.020  1.509
 L2N  C11  N1   single    1.395  0.020  1.395
 L2N  C11  C22  aromatic  1.384  0.020  1.384
 L2N  N1   C10  single    1.361  0.020  1.361
 L2N  C8   C2   aromatic  1.425  0.020  1.425
 L2N  C8   C9   aromatic  1.382  0.020  1.382
 L2N  C16  C22  aromatic  1.394  0.020  1.394
 L2N  C16  S    single    1.766  0.020  1.766
 L2N  C3   C2   single    1.458  0.020  1.458
 L2N  C3   O    double    1.220  0.020  1.220
 L2N  C2   C    aromatic  1.396  0.020  1.396
 L2N  C10  C9   single    1.465  0.020  1.465
 L2N  C10  O1   double    1.223  0.020  1.223
 L2N  C9   N    aromatic  1.375  0.020  1.375
 L2N  O4   S    double    1.454  0.020  1.454
 L2N  C21  N2   single    1.463  0.020  1.463
 L2N  C21  C20  single    1.517  0.020  1.517
 L2N  S    N2   single    1.656  0.020  1.656
 L2N  S    O3   double    1.454  0.020  1.454
 L2N  N2   C17  single    1.463  0.020  1.463
 L2N  C    N    aromatic  1.335  0.020  1.335
 L2N  C    C1   single    1.485  0.020  1.485
 L2N  C20  N3   single    1.447  0.020  1.447
 L2N  C17  C18  single    1.516  0.020  1.516
 L2N  N3   C18  single    1.447  0.020  1.447
 L2N  N3   C19  single    1.445  0.020  1.445
 L2N  N1   H1   single    0.860  0.020  1.020
 L2N  C4   H2   single    0.970  0.020  1.090
 L2N  C4   H3   single    0.970  0.020  1.090
 L2N  C5   H4   single    0.970  0.020  1.090
 L2N  C5   H5   single    0.970  0.020  1.090
 L2N  C6   H6   single    0.970  0.020  1.090
 L2N  C6   H7   single    0.970  0.020  1.090
 L2N  C7   H8   single    0.970  0.020  1.090
 L2N  C7   H9   single    0.970  0.020  1.090
 L2N  C13  H10  single    0.970  0.020  1.090
 L2N  C13  H11  single    0.970  0.020  1.090
 L2N  C13  H12  single    0.970  0.020  1.090
 L2N  C14  H13  single    0.930  0.020  1.080
 L2N  C15  H14  single    0.930  0.020  1.080
 L2N  N    H15  single    0.860  0.020  1.020
 L2N  C1   H16  single    0.970  0.020  1.090
 L2N  C1   H17  single    0.970  0.020  1.090
 L2N  C1   H18  single    0.970  0.020  1.090
 L2N  C17  H19  single    0.970  0.020  1.090
 L2N  C17  H20  single    0.970  0.020  1.090
 L2N  C18  H21  single    0.970  0.020  1.090
 L2N  C18  H22  single    0.970  0.020  1.090
 L2N  C19  H23  single    0.970  0.020  1.090
 L2N  C19  H24  single    0.970  0.020  1.090
 L2N  C19  H25  single    0.970  0.020  1.090
 L2N  C20  H26  single    0.970  0.020  1.090
 L2N  C20  H27  single    0.970  0.020  1.090
 L2N  C21  H28  single    0.970  0.020  1.090
 L2N  C21  H29  single    0.970  0.020  1.090
 L2N  C22  H30  single    0.930  0.020  1.080

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
 L2N  H1   N1   C11  115.34  3.000
 L2N  H1   N1   C10  117.19  3.000
 L2N  C11  N1   C10  127.35  3.000
 L2N  C13  O2   C12  119.29  3.000
 L2N  H3   C4   H2   107.05  3.000
 L2N  H3   C4   C3   108.80  3.000
 L2N  H2   C4   C3   108.32  3.000
 L2N  H3   C4   C5   109.28  3.000
 L2N  H2   C4   C5   109.15  3.000
 L2N  C3   C4   C5   114.02  3.000
 L2N  H5   C5   H4   106.25  3.000
 L2N  H5   C5   C6   109.16  3.000
 L2N  H4   C5   C6   109.50  3.000
 L2N  H5   C5   C4   109.45  3.000
 L2N  H4   C5   C4   106.98  3.000
 L2N  C6   C5   C4   115.12  3.000
 L2N  H7   C6   H6   105.97  3.000
 L2N  H7   C6   C7   108.93  3.000
 L2N  H6   C6   C7   108.27  3.000
 L2N  H7   C6   C5   108.44  3.000
 L2N  H6   C6   C5   110.23  3.000
 L2N  C7   C6   C5   114.64  3.000
 L2N  H9   C7   H8   106.12  3.000
 L2N  H9   C7   C8   111.26  3.000
 L2N  H8   C7   C8   109.38  3.000
 L2N  H9   C7   C6   110.10  3.000
 L2N  H8   C7   C6   107.69  3.000
 L2N  C8   C7   C6   112.05  3.000
 L2N  C2   C8   C9   106.11  3.000
 L2N  C9   C8   C7   127.81  3.000
 L2N  C2   C8   C7   125.49  3.000
 L2N  N    C9   C10  117.56  3.000
 L2N  N    C9   C8   107.67  3.000
 L2N  C10  C9   C8   134.68  3.000
 L2N  O1   C10  C9   120.88  3.000
 L2N  O1   C10  N1   123.68  3.000
 L2N  C9   C10  N1   115.43  3.000
 L2N  C22  C11  C12  119.10  3.000
 L2N  C22  C11  N1   124.14  3.000
 L2N  C12  C11  N1   116.75  3.000
 L2N  C14  C12  C11  120.24  3.000
 L2N  C11  C12  O2   115.16  3.000
 L2N  C14  C12  O2   124.60  3.000
 L2N  H12  C13  H11  109.32  3.000
 L2N  H12  C13  H10  109.03  3.000
 L2N  H11  C13  H10  109.16  3.000
 L2N  H12  C13  O2   111.52  3.000
 L2N  H11  C13  O2   111.46  3.000
 L2N  H10  C13  O2   106.26  3.000
 L2N  H13  C14  C15  118.76  3.000
 L2N  H13  C14  C12  120.87  3.000
 L2N  C15  C14  C12  120.36  3.000
 L2N  H14  C15  C16  121.48  3.000
 L2N  H14  C15  C14  119.41  3.000
 L2N  C16  C15  C14  119.11  3.000
 L2N  S    N2   C21  116.40  3.000
 L2N  S    N2   C17  116.81  3.000
 L2N  C21  N2   C17  112.48  3.000
 L2N  H15  N    C    124.73  3.000
 L2N  H15  N    C9   123.90  3.000
 L2N  C    N    C9   111.36  3.000
 L2N  C2   C    C1   131.25  3.000
 L2N  C1   C    N    121.80  3.000
 L2N  C2   C    N    106.93  3.000
 L2N  H18  C1   H17  108.30  3.000
 L2N  H18  C1   H16  107.12  3.000
 L2N  H17  C1   H16  108.12  3.000
 L2N  H18  C1   C    111.25  3.000
 L2N  H17  C1   C    110.82  3.000
 L2N  H16  C1   C    111.08  3.000
 L2N  S    C16  C22  118.37  3.000
 L2N  S    C16  C15  120.12  3.000
 L2N  C22  C16  C15  121.48  3.000
 L2N  H20  C17  H19  108.37  3.000
 L2N  H20  C17  C18  109.53  3.000
 L2N  H19  C17  C18  108.92  3.000
 L2N  H20  C17  N2   111.24  3.000
 L2N  H19  C17  N2   109.79  3.000
 L2N  C18  C17  N2   108.96  3.000
 L2N  H22  C18  H21  107.20  3.000
 L2N  H22  C18  N3   109.29  3.000
 L2N  H21  C18  N3   112.24  3.000
 L2N  H22  C18  C17  108.11  3.000
 L2N  H21  C18  C17  109.02  3.000
 L2N  N3   C18  C17  110.84  3.000
 L2N  C3   C2   C    124.43  3.000
 L2N  C    C2   C8   107.92  3.000
 L2N  C3   C2   C8   127.59  3.000
 L2N  H27  C20  H26  107.16  3.000
 L2N  H27  C20  N3   112.18  3.000
 L2N  H26  C20  N3   109.30  3.000
 L2N  H27  C20  C21  109.17  3.000
 L2N  H26  C20  C21  108.01  3.000
 L2N  N3   C20  C21  110.89  3.000
 L2N  H29  C21  H28  108.44  3.000
 L2N  H29  C21  C20  108.88  3.000
 L2N  H28  C21  C20  109.51  3.000
 L2N  H29  C21  N2   109.84  3.000
 L2N  H28  C21  N2   111.10  3.000
 L2N  C20  C21  N2   109.04  3.000
 L2N  H30  C22  C16  120.61  3.000
 L2N  H30  C22  C11  119.72  3.000
 L2N  C16  C22  C11  119.67  3.000
 L2N  C2   C3   O    121.71  3.000
 L2N  O    C3   C4   121.51  3.000
 L2N  C2   C3   C4   116.72  3.000
 L2N  C20  N3   C19  111.94  3.000
 L2N  C19  N3   C18  111.88  3.000
 L2N  C20  N3   C18  110.39  3.000
 L2N  O4   S    C16  108.16  3.000
 L2N  O4   S    N2   106.89  3.000
 L2N  C16  S    N2   106.65  3.000
 L2N  N2   S    O3   106.79  3.000
 L2N  O4   S    O3   119.44  3.000
 L2N  C16  S    O3   108.24  3.000
 L2N  H25  C19  H24  107.78  3.000
 L2N  H25  C19  H23  107.75  3.000
 L2N  H24  C19  H23  107.76  3.000
 L2N  H25  C19  N3   113.40  3.000
 L2N  H24  C19  N3   110.00  3.000
 L2N  H23  C19  N3   109.96  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
 L2N  CONST_01  C    N    C9   C8      0.00   0.0  0
 L2N  CONST_02  C2   C    N    C9      0.00   0.0  0
 L2N  CONST_03  C15  C14  C12  C11     0.00   0.0  0
 L2N  CONST_04  C15  C16  C22  C11     0.00   0.0  0
 L2N  CONST_05  C16  C15  C14  C12     0.00   0.0  0
 L2N  CONST_06  C16  C22  C11  C12     0.00   0.0  0
 L2N  CONST_07  C22  C11  C12  C14     0.00   0.0  0
 L2N  CONST_08  C22  C16  C15  C14     0.00   0.0  0
 L2N  CONST_09  C14  C12  C11  N1    180.00   0.0  0
 L2N  CONST_10  C16  C22  C11  N1    180.00   0.0  0
 L2N  CONST_11  C15  C14  C12  O2    180.00   0.0  0
 L2N  CONST_12  C22  C11  C12  O2    180.00   0.0  0
 L2N  CONST_13  C1   C    N    C9    180.00   0.0  0
 L2N  CONST_14  C    N    C9   C10   180.00   0.0  0
 L2N  CONST_15  S    C16  C22  C11   180.00   0.0  0
 L2N  CONST_16  S    C16  C15  C14   180.00   0.0  0
 L2N  CONST_17  H15  N    C9   C8    180.00   0.0  0
 L2N  CONST_18  H13  C14  C12  C11   180.00   0.0  0
 L2N  CONST_19  H14  C15  C14  C12   180.00   0.0  0
 L2N  CONST_20  H30  C22  C11  C12   180.00   0.0  0
 L2N  CONST_21  C11  N1   C10  C9    180.00   0.0  0
 L2N  CONST_25  O1   C10  N1   C11     0.00   0.0  0
 L2N  Var_01    N3   C20  C21  N2     56.83  30.0  1
 L2N  Var_02    N3   C18  C17  N2    -57.14  30.0  1
 L2N  Var_03    C20  C21  N2   C17   -56.49  30.0  1
 L2N  Var_04    C20  N3   C18  C17    59.23  30.0  1
 L2N  Var_05    C21  N2   C17  C18    56.64  30.0  1
 L2N  Var_06    C21  C20  N3   C18   -59.06  30.0  1
 L2N  Var_07    N2   S    C16  C15   -98.03  30.0  2
 L2N  Var_08    C8   C9   C10  N1     25.12  30.0  2
 L2N  Var_09    C14  C12  O2   C13    -2.50  30.0  2
 L2N  Var_10    H16  C1   C    N    -111.84  30.0  2
 L2N  Var_11    H23  C19  N3   C18    58.76  30.0  3
 L2N  Var_12    H10  C13  O2   C12  -178.75  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
 L2N  plan-1  N1   0.020
 L2N  plan-1  O2   0.020
 L2N  plan-1  C11  0.020
 L2N  plan-1  C12  0.020
 L2N  plan-1  C14  0.020
 L2N  plan-1  C15  0.020
 L2N  plan-1  C16  0.020
 L2N  plan-1  C22  0.020
 L2N  plan-1  S    0.020
 L2N  plan-1  H13  0.020
 L2N  plan-1  H14  0.020
 L2N  plan-1  H30  0.020
 L2N  plan-2  C7   0.020
 L2N  plan-2  C8   0.020
 L2N  plan-2  C9   0.020
 L2N  plan-2  C10  0.020
 L2N  plan-2  N    0.020
 L2N  plan-2  C    0.020
 L2N  plan-2  C1   0.020
 L2N  plan-2  C2   0.020
 L2N  plan-2  C3   0.020
 L2N  plan-2  H15  0.020
 L2N  plan-3  N1   0.020
 L2N  plan-3  C9   0.020
 L2N  plan-3  C10  0.020
 L2N  plan-3  C11  0.020
 L2N  plan-3  O1   0.020
 L2N  plan-3  H1   0.020
 L2N  plan-4  C4   0.020
 L2N  plan-4  C2   0.020
 L2N  plan-4  C3   0.020
 L2N  plan-4  O    0.020

