# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Mar 18 11:25:49 2022
#   Inital geometry file: a 157 line input string
#   Ligand name: (5R,8S,11S)-5-methyl-8-(propan-2-yl)-11-[(1E)-4-sulfanylbut-1-en-1-yl]-3-thia-7,10,14,17,21-pentaazatricyclo[14.3.1.1~2,5~]henicosa-1(20),2(21),16,18-tetraene-6,9,13-trione
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC(C)[C@@H]1NC(=O)[C@]2(C)CSC(=N2)c3ccnc(CNC(=O)C[C@H](NC1=O)/C=C/CCS)c3
#
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
 L7G  L7G  (5R,8S,11S)-5-methyl-8-(propan-2-yl)-11-[(1E)-4-sulfanylbut-1-en-1-yl]-3-thia-7,10,14,17,21-pentaazatricyclo[14.3.1.1~2,5~]henicosa-1(20),2(21),16,18-tetraene-6,9,13-trione  ligand  64  33  .  2022-03-22  2022-03-22
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_L7G
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
 L7G  C1   C  CH2   0  -0.543  -6.8120   0.3852  -1.0240
 L7G  C2   C  CH2   0  -0.485  -5.7697   1.4232  -1.4292
 L7G  C3   C  C1    0  -0.218  -4.6408   1.4381  -0.4479
 L7G  C4   C  C1    0  -0.183  -3.4078   1.0390  -0.7288
 L7G  C5   C  CH1   0  -0.094  -2.2661   1.1267   0.2397
 L7G  C6   C  C     0   0.546  -1.9001  -1.3490   0.0915
 L7G  C7   C  CH1   0  -0.179  -0.8490  -2.4536   0.2325
 L7G  C8   C  CH1   0  -0.240  -0.5987  -2.8583   1.7048
 L7G  C9   C  CH3   0  -0.692   0.0399  -1.7594   2.5481
 L7G  C10  C  CH3   0  -0.658  -1.8710  -3.3893   2.3552
 L7G  C11  C  C     0   0.576   1.2815  -2.9647  -0.8912
 L7G  C12  C  CR5   0  -0.048   2.5227  -2.3253  -1.5266
 L7G  C13  C  CH3   0  -0.629   2.4038  -2.4086  -3.0496
 L7G  C14  C  CH2   0  -0.582   3.7937  -3.0455  -1.0175
 L7G  C15  C  CR5   0   0.087   3.7442  -0.5421  -0.8037
 L7G  C16  C  CR6   0   0.200   3.9856   0.8275  -0.3198
 L7G  C17  C  CR16  0  -0.395   5.2394   1.2860   0.0559
 L7G  C18  C  CR16  0  -0.064   5.3319   2.5651   0.5886
 L7G  C19  C  CR6   0   0.252   3.0846   2.9202   0.4152
 L7G  C20  C  CR16  0  -0.349   2.8960   1.6766  -0.1596
 L7G  C21  C  CH2   0  -0.338   1.9322   3.8514   0.7144
 L7G  C22  C  C     0   0.545  -0.1631   2.5678   0.6414
 L7G  C23  C  CH2   0  -0.600  -1.4009   2.3141  -0.1958
 L7G  N1   N  NH1   0  -0.683  -1.4487  -0.0844   0.2575
 L7G  N2   N  NH1   0  -0.656   0.3773  -2.0846  -0.4443
 L7G  N3   N  N     0  -0.383   2.5906  -0.9323  -1.1390
 L7G  N4   N  N     0  -0.421   4.2883   3.3572   0.7807
 L7G  N5   N  NH1   0  -0.634   0.6834   3.4673   0.1112
 L7G  O1   O  O     0  -0.456  -3.0542  -1.6370  -0.1649
 L7G  O2   O  O     0  -0.483   1.1627  -4.1778  -0.8335
 L7G  O3   O  O     0  -0.485   0.0486   1.9995   1.7051
 L7G  S1   S  S2    0  -0.261  -8.1753   0.4005  -2.2369
 L7G  S2   S  S2    0   0.073   5.0432  -1.7344  -0.8555
 L7G  H1   H  HCH2  0   0.269  -6.3598  -0.6059  -0.9932
 L7G  H2   H  HCH2  0   0.268  -7.2090   0.6111  -0.0342
 L7G  H3   H  HCH2  0   0.248  -5.3928   1.2004  -2.4304
 L7G  H4   H  HCH2  0   0.247  -6.2425   2.4089  -1.4742
 L7G  H5   H  H     0   0.241  -4.8806   1.7639   0.5617
 L7G  H6   H  H     0   0.249  -3.1584   0.7185  -1.7371
 L7G  H7   H  HCH1  0   0.268  -2.6591   1.3191   1.2435
 L7G  H8   H  HCH1  0   0.285  -1.2722  -3.3226  -0.2761
 L7G  H9   H  HCH1  0   0.252   0.1119  -3.6881   1.6495
 L7G  H10  H  HCH3  0   0.224  -0.6551  -0.9459   2.7641
 L7G  H11  H  HCH3  0   0.253   0.3571  -2.1672   3.5080
 L7G  H12  H  HCH3  0   0.225   0.9288  -1.3390   2.0727
 L7G  H13  H  HCH3  0   0.233  -2.3230  -4.1815   1.7567
 L7G  H14  H  HCH3  0   0.236  -1.6451  -3.8046   3.3378
 L7G  H15  H  HCH3  0   0.224  -2.6191  -2.6074   2.4958
 L7G  H16  H  HCH3  0   0.249   2.2785  -3.4428  -3.3686
 L7G  H17  H  HCH3  0   0.252   1.5517  -1.8285  -3.4032
 L7G  H18  H  HCH3  0   0.250   3.3073  -2.0148  -3.5172
 L7G  H19  H  HCH2  0   0.308   3.6540  -3.5054  -0.0398
 L7G  H20  H  HCH2  0   0.305   4.1480  -3.8059  -1.7099
 L7G  H22  H  HCR6  0   0.274   6.1318   0.6817  -0.0413
 L7G  H23  H  HCR6  0   0.275   6.2988   2.9562   0.8834
 L7G  H24  H  HCR6  0   0.258   1.9166   1.3489  -0.4704
 L7G  H25  H  HCH2  0   0.277   1.8129   3.9182   1.7977
 L7G  H26  H  HCH2  0   0.286   2.1845   4.8530   0.3677
 L7G  H27  H  HCH2  0   0.281  -1.1111   2.1912  -1.2437
 L7G  H28  H  HCH2  0   0.303  -2.0222   3.2130  -0.1579
 L7G  H29  H  HNH1  0   0.402  -0.5807   0.0286   0.7610
 L7G  H30  H  HNH1  0   0.402   0.6075  -1.1139  -0.5971
 L7G  H33  H  HNH1  0   0.414   0.4617   3.8636  -0.7881
 L7G  H34  H  HSH1  0   0.223  -8.9542  -0.5103  -1.6437

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
 L7G  C21  N5   single    1.439  0.020  1.439
 L7G  C21  C19  single    1.511  0.020  1.511
 L7G  N4   C19  single    1.332  0.020  1.332
 L7G  N4   C18  aromatic  1.324  0.020  1.324
 L7G  N5   C22  single    1.344  0.020  1.344
 L7G  C19  C20  aromatic  1.383  0.020  1.383
 L7G  C18  C17  aromatic  1.389  0.020  1.389
 L7G  C22  O3   double    1.224  0.020  1.224
 L7G  C22  C23  single    1.516  0.020  1.516
 L7G  C20  C16  aromatic  1.391  0.020  1.391
 L7G  C17  C16  single    1.387  0.020  1.387
 L7G  C23  C5   single    1.532  0.020  1.532
 L7G  C16  C15  single    1.473  0.020  1.473
 L7G  C1   S1   single    1.825  0.020  1.825
 L7G  C1   C2   single    1.526  0.020  1.526
 L7G  C3   C2   single    1.496  0.020  1.496
 L7G  C3   C4   double    1.326  0.020  1.326
 L7G  C5   C4   single    1.500  0.020  1.500
 L7G  C5   N1   single    1.461  0.020  1.461
 L7G  C15  N3   double    1.263  0.020  1.263
 L7G  C15  S2   single    1.764  0.020  1.764
 L7G  N3   C12  single    1.447  0.020  1.447
 L7G  N1   C6   single    1.353  0.020  1.353
 L7G  S2   C14  single    1.818  0.020  1.818
 L7G  C12  C13  single    1.530  0.020  1.530
 L7G  C12  C14  single    1.547  0.020  1.547
 L7G  C12  C11  single    1.534  0.020  1.534
 L7G  C6   O1   double    1.217  0.020  1.217
 L7G  C6   C7   single    1.531  0.020  1.531
 L7G  N2   C11  single    1.339  0.020  1.339
 L7G  N2   C7   single    1.448  0.020  1.448
 L7G  C9   C8   single    1.525  0.020  1.525
 L7G  C11  O2   double    1.220  0.020  1.220
 L7G  C7   C8   single    1.547  0.020  1.547
 L7G  C8   C10  single    1.524  0.020  1.524
 L7G  C1   H1   single    0.970  0.020  1.090
 L7G  C1   H2   single    0.970  0.020  1.090
 L7G  C2   H3   single    0.970  0.020  1.090
 L7G  C2   H4   single    0.970  0.020  1.090
 L7G  C3   H5   single    0.930  0.020  1.080
 L7G  C4   H6   single    0.930  0.020  1.080
 L7G  C5   H7   single    0.970  0.020  1.090
 L7G  C7   H8   single    0.970  0.020  1.090
 L7G  C8   H9   single    0.970  0.020  1.090
 L7G  C9   H10  single    0.970  0.020  1.090
 L7G  C9   H11  single    0.970  0.020  1.090
 L7G  C9   H12  single    0.970  0.020  1.090
 L7G  C10  H13  single    0.970  0.020  1.090
 L7G  C10  H14  single    0.970  0.020  1.090
 L7G  C10  H15  single    0.970  0.020  1.090
 L7G  C13  H16  single    0.970  0.020  1.090
 L7G  C13  H17  single    0.970  0.020  1.090
 L7G  C13  H18  single    0.970  0.020  1.090
 L7G  C14  H19  single    0.970  0.020  1.090
 L7G  C14  H20  single    0.970  0.020  1.090
 L7G  C17  H22  single    0.930  0.020  1.080
 L7G  C18  H23  single    0.930  0.020  1.080
 L7G  C20  H24  single    0.930  0.020  1.080
 L7G  C21  H25  single    0.970  0.020  1.090
 L7G  C21  H26  single    0.970  0.020  1.090
 L7G  C23  H27  single    0.970  0.020  1.090
 L7G  C23  H28  single    0.970  0.020  1.090
 L7G  N1   H29  single    0.890  0.020  1.040
 L7G  N2   H30  single    0.860  0.020  1.020
 L7G  N5   H33  single    0.860  0.020  1.020
 L7G  S1   H34  single    1.200  0.020  1.300

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
 L7G  H2   C1   H1   108.29  3.000
 L7G  H2   C1   S1   109.25  3.000
 L7G  H1   C1   S1   109.66  3.000
 L7G  H2   C1   C2   110.42  3.000
 L7G  H1   C1   C2   110.04  3.000
 L7G  S1   C1   C2   109.15  3.000
 L7G  H4   C2   H3   107.16  3.000
 L7G  H4   C2   C3   110.13  3.000
 L7G  H3   C2   C3   110.05  3.000
 L7G  H4   C2   C1   109.18  3.000
 L7G  H3   C2   C1   109.89  3.000
 L7G  C3   C2   C1   110.37  3.000
 L7G  H5   C3   C4   119.46  3.000
 L7G  H5   C3   C2   116.46  3.000
 L7G  C4   C3   C2   124.04  3.000
 L7G  H6   C4   C5   116.20  3.000
 L7G  H6   C4   C3   119.91  3.000
 L7G  C5   C4   C3   123.61  3.000
 L7G  H7   C5   N1   109.59  3.000
 L7G  H7   C5   C23  109.08  3.000
 L7G  N1   C5   C23  109.26  3.000
 L7G  H7   C5   C4   109.21  3.000
 L7G  N1   C5   C4   112.66  3.000
 L7G  C23  C5   C4   106.96  3.000
 L7G  O1   C6   N1   124.30  3.000
 L7G  O1   C6   C7   119.99  3.000
 L7G  N1   C6   C7   115.71  3.000
 L7G  H8   C7   N2   108.25  3.000
 L7G  H8   C7   C8   107.32  3.000
 L7G  N2   C7   C8   111.98  3.000
 L7G  H8   C7   C6   105.37  3.000
 L7G  C8   C7   C6   112.79  3.000
 L7G  N2   C7   C6   110.76  3.000
 L7G  H9   C8   C10  107.43  3.000
 L7G  H9   C8   C9   107.61  3.000
 L7G  C10  C8   C9   111.38  3.000
 L7G  H9   C8   C7   104.80  3.000
 L7G  C10  C8   C7   111.23  3.000
 L7G  C9   C8   C7   113.91  3.000
 L7G  H12  C9   H11  106.88  3.000
 L7G  H12  C9   H10  108.51  3.000
 L7G  H11  C9   H10  106.84  3.000
 L7G  H12  C9   C8   112.18  3.000
 L7G  H11  C9   C8   109.82  3.000
 L7G  H10  C9   C8   112.32  3.000
 L7G  H15  C10  H14  107.39  3.000
 L7G  H15  C10  H13  107.88  3.000
 L7G  H14  C10  H13  107.68  3.000
 L7G  H15  C10  C8   112.18  3.000
 L7G  H14  C10  C8   110.14  3.000
 L7G  H13  C10  C8   111.39  3.000
 L7G  O2   C11  N2   124.89  3.000
 L7G  O2   C11  C12  120.85  3.000
 L7G  N2   C11  C12  114.25  3.000
 L7G  N3   C12  C14  108.75  3.000
 L7G  C14  C12  C13  111.47  3.000
 L7G  N3   C12  C13  108.82  3.000
 L7G  C14  C12  C11  109.54  3.000
 L7G  C13  C12  C11  109.07  3.000
 L7G  N3   C12  C11  109.16  3.000
 L7G  H18  C13  H17  108.44  3.000
 L7G  H18  C13  H16  108.20  3.000
 L7G  H17  C13  H16  108.68  3.000
 L7G  H18  C13  C12  110.04  3.000
 L7G  H17  C13  C12  110.79  3.000
 L7G  H16  C13  C12  110.62  3.000
 L7G  H20  C14  H19  108.54  3.000
 L7G  H20  C14  S2   109.69  3.000
 L7G  H19  C14  S2   108.21  3.000
 L7G  H20  C14  C12  112.56  3.000
 L7G  H19  C14  C12  112.73  3.000
 L7G  S2   C14  C12  104.96  3.000
 L7G  S2   C15  N3   117.13  3.000
 L7G  S2   C15  C16  121.17  3.000
 L7G  N3   C15  C16  121.62  3.000
 L7G  C20  C16  C17  118.38  3.000
 L7G  C17  C16  C15  123.00  3.000
 L7G  C20  C16  C15  118.51  3.000
 L7G  H22  C17  C18  119.60  3.000
 L7G  H22  C17  C16  122.45  3.000
 L7G  C18  C17  C16  117.94  3.000
 L7G  H23  C18  N4   116.60  3.000
 L7G  H23  C18  C17  119.74  3.000
 L7G  N4   C18  C17  123.65  3.000
 L7G  N4   C19  C21  115.63  3.000
 L7G  N4   C19  C20  122.17  3.000
 L7G  C21  C19  C20  122.16  3.000
 L7G  H24  C20  C19  121.12  3.000
 L7G  H24  C20  C16  119.53  3.000
 L7G  C19  C20  C16  119.35  3.000
 L7G  H26  C21  H25  106.54  3.000
 L7G  H26  C21  N5   108.23  3.000
 L7G  H25  C21  N5   109.71  3.000
 L7G  H26  C21  C19  109.08  3.000
 L7G  H25  C21  C19  108.51  3.000
 L7G  N5   C21  C19  114.47  3.000
 L7G  O3   C22  N5   122.98  3.000
 L7G  O3   C22  C23  122.91  3.000
 L7G  N5   C22  C23  114.11  3.000
 L7G  H28  C23  H27  106.03  3.000
 L7G  H28  C23  C22  107.90  3.000
 L7G  H27  C23  C22  109.36  3.000
 L7G  H28  C23  C5   107.84  3.000
 L7G  H27  C23  C5   109.55  3.000
 L7G  C22  C23  C5   115.71  3.000
 L7G  H29  N1   C6   116.91  3.000
 L7G  H29  N1   C5   113.22  3.000
 L7G  C6   N1   C5   125.91  3.000
 L7G  H30  N2   C11  115.33  3.000
 L7G  H30  N2   C7   120.59  3.000
 L7G  C11  N2   C7   124.08  3.000
 L7G  C15  N3   C12  114.28  3.000
 L7G  C19  N4   C18  118.44  3.000
 L7G  H33  N5   C22  118.47  3.000
 L7G  H33  N5   C21  117.40  3.000
 L7G  C22  N5   C21  124.04  3.000
 L7G  H34  S1   C1    97.73  3.000
 L7G  C15  S2   C14   89.08  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
 L7G  CONST_01  N4   C19  C20  C16     0.00   0.0  0
 L7G  CONST_02  N4   C18  C17  C16     0.00   0.0  0
 L7G  CONST_03  C19  N4   C18  C17     0.00   0.0  0
 L7G  CONST_04  C19  C20  C16  C17     0.00   0.0  0
 L7G  CONST_05  C20  C19  N4   C18     0.00   0.0  0
 L7G  CONST_06  C20  C16  C17  C18     0.00   0.0  0
 L7G  CONST_07  C7   C6   N1   C5    180.00   0.0  0
 L7G  CONST_08  C12  C11  N2   C7    180.00   0.0  0
 L7G  CONST_09  C23  C22  N5   C21   180.00   0.0  0
 L7G  CONST_10  O1   C6   N1   C5      0.00   0.0  0
 L7G  CONST_11  O2   C11  N2   C7      0.00   0.0  0
 L7G  CONST_12  O3   C22  N5   C21     0.00   0.0  0
 L7G  CONST_13  H24  C20  C16  C15     0.00   0.0  0
 L7G  CONST_14  H22  C17  C16  C15     0.00   0.0  0
 L7G  CONST_15  H23  C18  C17  C16   180.00   0.0  0
 L7G  CONST_17  H30  N2   C11  C12     0.00   0.0  0
 L7G  CONST_18  H33  N5   C22  C23     0.00   0.0  0
 L7G  Var_01    N5   C22  C23  C5    169.64  30.0  1
 L7G  Var_02    C16  C15  N3   C12  -177.06  30.0  1
 L7G  Var_03    C22  N5   C21  C19    83.46  30.0  1
 L7G  Var_04    N5   C21  C19  C20   -12.22  30.0  1
 L7G  Var_05    H19  C14  S2   C15  -100.28  30.0  1
 L7G  Var_06    C5   C4   C3   C2    176.59   0.0  2
 L7G  Var_07    H10  C9   C8   C7     71.84  30.0  3
 L7G  Var_08    H13  C10  C8   C7     52.26  30.0  3
 L7G  Var_09    C4   C3   C2   C1    112.07  30.0  2
 L7G  Var_10    S1   C1   C2   C3    179.73  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
 L7G  chir_01  C5   C23  C4   N1  negativ
 L7G  chir_02  C7   N2   C6   C8  positiv
 L7G  chir_03  C12  C11  C14  N3  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
 L7G  plan-1  C15  0.020
 L7G  plan-1  C16  0.020
 L7G  plan-1  C17  0.020
 L7G  plan-1  C18  0.020
 L7G  plan-1  C19  0.020
 L7G  plan-1  C20  0.020
 L7G  plan-1  C21  0.020
 L7G  plan-1  N4   0.020
 L7G  plan-1  H22  0.020
 L7G  plan-1  H23  0.020
 L7G  plan-1  H24  0.020
 L7G  plan-2  C7   0.020
 L7G  plan-2  C11  0.020
 L7G  plan-2  C12  0.020
 L7G  plan-2  N2   0.020
 L7G  plan-2  O2   0.020
 L7G  plan-2  H30  0.020
 L7G  plan-3  C21  0.020
 L7G  plan-3  C22  0.020
 L7G  plan-3  C23  0.020
 L7G  plan-3  N5   0.020
 L7G  plan-3  O3   0.020
 L7G  plan-3  H33  0.020
 L7G  plan-4  C5   0.020
 L7G  plan-4  C6   0.020
 L7G  plan-4  C7   0.020
 L7G  plan-4  N1   0.020
 L7G  plan-4  O1   0.020
 L7G  plan-4  H29  0.020
 L7G  plan-5  C2   0.020
 L7G  plan-5  C3   0.020
 L7G  plan-5  C4   0.020
 L7G  plan-5  C5   0.020
 L7G  plan-5  H5   0.020
 L7G  plan-5  H6   0.020

