# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Apr 17 17:20:06 2020
#   Inital geometry file: a 131 line input string
#   Ligand name: 7-(cyclopropylmethyl)-2-methyl-10-[(methylsulfonyl)methyl]-2,4,6,7-tetrahydro-3H-2,4,7-triazadibenzo[cd,f]azulen-3-one
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CN1C=C2c3cc(C[S](C)(=O)=O)ccc3N(CC4CC4)Cc5c[nH]c(C1=O)c25
#
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
 8O4  8O4  7-(cyclopropylmethyl)-2-methyl-10-[(methylsulfonyl)methyl]-2,4,6,7-tetrahydro-3H-2,4,7-triazadibenzo[cd,f]azulen-3-one  ligand  51  28  .  2022-09-16  2022-09-16
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_8O4
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
 8O4  C4    C  CR15  0  -0.063   3.6664   0.0560   2.3696
 8O4  C5    C  CR6   0   0.131  -0.1054  -0.2964  -0.0710
 8O4  C6    C  CR56  0   0.166   2.1695   0.4982   0.7748
 8O4  C7    C  CR5   0  -0.084   2.4595  -0.3627   1.8589
 8O4  C8    C  CR6   0   0.141  -2.4823  -0.5635  -0.5499
 8O4  C10   C  CR56  0   0.128   3.2162   1.4031   0.6745
 8O4  C13   C  CR6   0   0.522   3.3370   2.4026  -0.3367
 8O4  C15   C  CH2   0  -0.496   2.1240  -3.8573  -2.2225
 8O4  C17   C  CH1   0  -0.253   1.4335  -3.6415  -0.9103
 8O4  C20   C  CH2   0  -0.711  -3.7567   0.0121  -1.0765
 8O4  C1    C  CR16  0  -0.306  -2.4551  -1.8365   0.0077
 8O4  C2    C  CR16  0  -0.252  -1.2701  -2.3241   0.5264
 8O4  C3    C  CR16  0  -0.397  -1.3206   0.1927  -0.5589
 8O4  C9    C  CR6   0   0.218  -0.0923  -1.5831   0.4997
 8O4  C11   C  CR16  0  -0.035   1.2289   1.4908  -1.1408
 8O4  C12   C  CR6   0  -0.073   1.0939   0.5559  -0.1624
 8O4  C14   C  CH2   0  -0.417   1.6298  -1.5544   2.2162
 8O4  C16   C  CH2   0  -0.468   0.8275  -3.1088  -2.1717
 8O4  C19   C  CH3   0  -0.796  -6.0826   1.4932  -0.5045
 8O4  N22   N  NR15  0  -0.654   4.1089   1.1263   1.6627
 8O4  N23   N  NT    0  -0.522   1.0598  -2.2102   1.0500
 8O4  N24   N  NR6   0  -0.537   2.2838   2.3630  -1.2351
 8O4  O25   O  O     0  -0.513   4.2652   3.2038  -0.4283
 8O4  O26   O  OS    0  -0.680  -5.0405  -0.1886   1.2432
 8O4  O27   O  OS    0  -0.679  -3.8038   1.9351   0.7564
 8O4  S28   S  S     0   1.202  -4.6300   0.8283   0.2752
 8O4  H4    H  HCR5  0   0.289   4.2460  -0.3455   3.1858
 8O4  H152  H  HCH2  0   0.248   2.1266  -4.8567  -2.6386
 8O4  H17   H  HCH1  0   0.248   0.9493  -4.5089  -0.4728
 8O4  H1    H  HCR6  0   0.253  -3.3507  -2.4436   0.0340
 8O4  H2    H  HCR6  0   0.250  -1.2344  -3.3136   0.9629
 8O4  H3    H  HCR6  0   0.249  -1.3654   1.1986  -0.9572
 8O4  H11   H  HCR6  0   0.293   0.5002   1.5986  -1.9319
 8O4  H142  H  HCH2  0   0.249   2.2373  -2.2808   2.7633
 8O4  H141  H  HCH2  0   0.255   0.8060  -1.2826   2.8815
 8O4  H162  H  HCH2  0   0.241   0.8521  -2.0362  -2.3249
 8O4  H161  H  HCH2  0   0.244  -0.0644  -3.5888  -2.5530
 8O4  H22   H  HNR5  0   0.413   4.9732   1.6168   1.8251
 8O4  H7    H  HCH2  0   0.323  -3.5899   0.7669  -1.8460
 8O4  H8    H  HCH2  0   0.324  -4.4277  -0.7520  -1.4710
 8O4  H9    H  HCH3  0   0.295  -6.6602   0.6838  -0.9450
 8O4  H10   H  HCH3  0   0.313  -6.6674   1.9894   0.2688
 8O4  H12   H  HCH3  0   0.295  -5.7903   2.2110  -1.2672
 8O4  C21   C  CH2   0  -0.277   2.0402  -2.6936   0.0873
 8O4  C18   C  CH3   0  -0.546   2.2680   3.2959  -2.3551
 8O4  H151  H  HCH2  0   0.240   3.0297  -3.2953  -2.4194
 8O4  H211  H  HCH2  0   0.236   2.8161  -3.2115   0.6602
 8O4  H212  H  HCH2  0   0.202   2.5473  -1.8816  -0.4563
 8O4  H183  H  HCH3  0   0.272   3.1496   3.9242  -2.3184
 8O4  H181  H  HCH3  0   0.260   2.2634   2.7507  -3.2974
 8O4  H182  H  HCH3  0   0.260   1.3823   3.9268  -2.3053

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
 8O4  C4   C7    aromatic  1.376  0.020  1.376
 8O4  C4   N22   aromatic  1.357  0.020  1.357
 8O4  C5   C3    aromatic  1.398  0.020  1.398
 8O4  C5   C9    aromatic  1.408  0.020  1.408
 8O4  C5   C12   single    1.474  0.020  1.474
 8O4  C6   C7    aromatic  1.414  0.020  1.414
 8O4  C6   C10   aromatic  1.387  0.020  1.387
 8O4  C6   C12   single    1.428  0.020  1.428
 8O4  C7   C14   single    1.495  0.020  1.495
 8O4  C8   C20   single    1.494  0.020  1.494
 8O4  C8   C1    aromatic  1.390  0.020  1.390
 8O4  C8   C3    aromatic  1.386  0.020  1.386
 8O4  C10  C13   single    1.427  0.020  1.427
 8O4  C10  N22   aromatic  1.360  0.020  1.360
 8O4  C13  N24   single    1.385  0.020  1.385
 8O4  C13  O25   double    1.230  0.020  1.230
 8O4  C15  C17   single    1.498  0.020  1.498
 8O4  C15  C16   single    1.498  0.020  1.498
 8O4  C17  C21   single    1.504  0.020  1.504
 8O4  C17  C16   single    1.497  0.020  1.497
 8O4  C20  S28   single    1.804  0.020  1.804
 8O4  C21  N23   single    1.456  0.020  1.456
 8O4  C1   C2    aromatic  1.382  0.020  1.382
 8O4  C2   C9    aromatic  1.392  0.020  1.392
 8O4  C9   N23   single    1.422  0.020  1.422
 8O4  C11  C12   double    1.360  0.020  1.360
 8O4  C11  N24   single    1.372  0.020  1.372
 8O4  C14  N23   single    1.454  0.020  1.454
 8O4  C18  N24   single    1.458  0.020  1.458
 8O4  C19  S28   single    1.778  0.020  1.778
 8O4  O26  S28   double    1.463  0.020  1.463
 8O4  O27  S28   double    1.463  0.020  1.463
 8O4  C4   H4    single    0.930  0.020  1.080
 8O4  C15  H151  single    0.970  0.020  1.090
 8O4  C15  H152  single    0.970  0.020  1.090
 8O4  C17  H17   single    0.970  0.020  1.090
 8O4  C21  H211  single    0.970  0.020  1.090
 8O4  C21  H212  single    0.970  0.020  1.090
 8O4  C1   H1    single    0.930  0.020  1.080
 8O4  C2   H2    single    0.930  0.020  1.080
 8O4  C3   H3    single    0.930  0.020  1.080
 8O4  C11  H11   single    0.930  0.020  1.080
 8O4  C14  H142  single    0.970  0.020  1.090
 8O4  C14  H141  single    0.970  0.020  1.090
 8O4  C16  H162  single    0.970  0.020  1.090
 8O4  C16  H161  single    0.970  0.020  1.090
 8O4  C18  H183  single    0.970  0.020  1.090
 8O4  C18  H181  single    0.970  0.020  1.090
 8O4  C18  H182  single    0.970  0.020  1.090
 8O4  N22  H22   single    0.860  0.020  1.020
 8O4  C20  H7    single    0.970  0.020  1.090
 8O4  C20  H8    single    0.970  0.020  1.090
 8O4  C19  H9    single    0.970  0.020  1.090
 8O4  C19  H10   single    0.970  0.020  1.090
 8O4  C19  H12   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
 8O4  H4    C4   N22   120.84  3.000
 8O4  H4    C4   C7    129.72  3.000
 8O4  N22   C4   C7    109.44  3.000
 8O4  C12   C5   C9    123.10  3.000
 8O4  C12   C5   C3    118.90  3.000
 8O4  C9    C5   C3    118.00  3.000
 8O4  C12   C6   C10   119.64  3.000
 8O4  C12   C6   C7    133.01  3.000
 8O4  C10   C6   C7    107.33  3.000
 8O4  C14   C7   C6    123.67  3.000
 8O4  C14   C7   C4    129.84  3.000
 8O4  C6    C7   C4    106.21  3.000
 8O4  C3    C8   C1    119.06  3.000
 8O4  C3    C8   C20   120.16  3.000
 8O4  C1    C8   C20   120.72  3.000
 8O4  N22   C10  C13   127.00  3.000
 8O4  N22   C10  C6    108.05  3.000
 8O4  C13   C10  C6    124.89  3.000
 8O4  O25   C13  N24   122.98  3.000
 8O4  O25   C13  C10   124.97  3.000
 8O4  N24   C13  C10   112.04  3.000
 8O4  H152  C15  H151  114.00  3.000
 8O4  H152  C15  C16   118.45  3.000
 8O4  H151  C15  C16   118.05  3.000
 8O4  H152  C15  C17   118.08  3.000
 8O4  H151  C15  C17   118.00  3.000
 8O4  C16   C15  C17    59.97  3.000
 8O4  H17   C17  C16   116.31  3.000
 8O4  H17   C17  C21   114.60  3.000
 8O4  C16   C17  C21   119.86  3.000
 8O4  H17   C17  C15   116.32  3.000
 8O4  C16   C17  C15    60.00  3.000
 8O4  C21   C17  C15   119.07  3.000
 8O4  H8    C20  H7    108.89  3.000
 8O4  H8    C20  S28   106.86  3.000
 8O4  H7    C20  S28   106.83  3.000
 8O4  H8    C20  C8    112.48  3.000
 8O4  H7    C20  C8    112.63  3.000
 8O4  S28   C20  C8    108.85  3.000
 8O4  H1    C1   C2    120.16  3.000
 8O4  H1    C1   C8    120.48  3.000
 8O4  C2    C1   C8    119.36  3.000
 8O4  H2    C2   C9    117.82  3.000
 8O4  H2    C2   C1    120.14  3.000
 8O4  C9    C2   C1    122.04  3.000
 8O4  H3    C3   C8    118.32  3.000
 8O4  H3    C3   C5    119.30  3.000
 8O4  C8    C3   C5    122.38  3.000
 8O4  N23   C9   C2    116.32  3.000
 8O4  N23   C9   C5    124.57  3.000
 8O4  C2    C9   C5    119.11  3.000
 8O4  H11   C11  N24   113.87  3.000
 8O4  H11   C11  C12   121.88  3.000
 8O4  N24   C11  C12   124.25  3.000
 8O4  C11   C12  C6    115.17  3.000
 8O4  C11   C12  C5    121.52  3.000
 8O4  C6    C12  C5    123.28  3.000
 8O4  H141  C14  H142  106.21  3.000
 8O4  H141  C14  N23   107.75  3.000
 8O4  H142  C14  N23   108.63  3.000
 8O4  H141  C14  C7    111.43  3.000
 8O4  H142  C14  C7    109.91  3.000
 8O4  N23   C14  C7    112.66  3.000
 8O4  H161  C16  H162  114.07  3.000
 8O4  H161  C16  C17   118.20  3.000
 8O4  H162  C16  C17   117.51  3.000
 8O4  H161  C16  C15   118.67  3.000
 8O4  H162  C16  C15   118.04  3.000
 8O4  C17   C16  C15    60.03  3.000
 8O4  H12   C19  H10   109.97  3.000
 8O4  H12   C19  H9    110.49  3.000
 8O4  H10   C19  H9    109.97  3.000
 8O4  H12   C19  S28   109.56  3.000
 8O4  H10   C19  S28   107.32  3.000
 8O4  H9    C19  S28   109.47  3.000
 8O4  H22   N22  C10   125.54  3.000
 8O4  H22   N22  C4    125.47  3.000
 8O4  C10   N22  C4    108.96  3.000
 8O4  C14   N23  C9    115.39  3.000
 8O4  C14   N23  C21   114.57  3.000
 8O4  C9    N23  C21   115.84  3.000
 8O4  C18   N24  C11   116.83  3.000
 8O4  C18   N24  C13   119.23  3.000
 8O4  C11   N24  C13   123.94  3.000
 8O4  O27   S28  O26   117.83  3.000
 8O4  O27   S28  C19   108.84  3.000
 8O4  O26   S28  C19   108.72  3.000
 8O4  O27   S28  C20   108.38  3.000
 8O4  O26   S28  C20   108.49  3.000
 8O4  C19   S28  C20   103.66  3.000
 8O4  H212  C21  H211  106.31  3.000
 8O4  H212  C21  N23   113.06  3.000
 8O4  H211  C21  N23   106.75  3.000
 8O4  H212  C21  C17   108.85  3.000
 8O4  H211  C21  C17   109.56  3.000
 8O4  N23   C21  C17   112.09  3.000
 8O4  H182  C18  H181  109.05  3.000
 8O4  H182  C18  H183  108.93  3.000
 8O4  H181  C18  H183  108.86  3.000
 8O4  H182  C18  N24   110.16  3.000
 8O4  H181  C18  N24   110.15  3.000
 8O4  H183  C18  N24   109.66  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
 8O4  CONST_01  C10   C6   C7   C4      0.00   0.0  0
 8O4  CONST_02  C6    C10  N22  C4      0.00   0.0  0
 8O4  CONST_03  C1    C8   C3   C5      0.00   0.0  0
 8O4  CONST_04  C1    C2   C9   C5      0.00   0.0  0
 8O4  CONST_05  N22   C4   C7   C6      0.00   0.0  0
 8O4  CONST_06  C10   N22  C4   C7      0.00   0.0  0
 8O4  CONST_07  N22   C10  C6   C7      0.00   0.0  0
 8O4  CONST_08  C9    C2   C1   C8      0.00   0.0  0
 8O4  CONST_09  C9    C5   C3   C8      0.00   0.0  0
 8O4  CONST_10  C3    C8   C1   C2      0.00   0.0  0
 8O4  CONST_11  C3    C5   C9   C2      0.00   0.0  0
 8O4  CONST_12  C11   N24  C13  C10     0.00   0.0  0
 8O4  CONST_13  C20   C8   C3   C5    180.00   0.0  0
 8O4  CONST_14  C2    C1   C8   C20   180.00   0.0  0
 8O4  CONST_15  C18   N24  C13  C10   180.00   0.0  0
 8O4  CONST_16  O25   C13  N24  C11   180.00   0.0  0
 8O4  CONST_17  H2    C2   C9   C5    180.00   0.0  0
 8O4  CONST_18  H4    C4   C7   C6    180.00   0.0  0
 8O4  CONST_19  H22   N22  C10  C6    180.00   0.0  0
 8O4  CONST_20  H3    C3   C8   C1    180.00   0.0  0
 8O4  CONST_21  H1    C1   C8   C3    180.00   0.0  0
 8O4  CONST_22  O25   C13  N24  C18     0.00   0.0  0
 8O4  Var_01    N23   C14  C7   C4   -138.65  30.0  1
 8O4  Var_02    C14   N23  C9   C5     63.95  30.0  1
 8O4  Var_03    C3    C5   C12  C6    149.87  30.0  1
 8O4  Var_04    C9    N23  C14  C7    -78.97  30.0  1
 8O4  Var_05    N23   C21  C17  C15   158.60  30.0  3
 8O4  Var_06    C21   C17  C16  C15   108.38  30.0  1
 8O4  Var_07    S28   C20  C8   C1     87.06  30.0  2
 8O4  Var_08    H183  C18  N24  C13     0.31  30.0  3
 8O4  Var_09    C19   S28  C20  C8    178.49  30.0  3
 8O4  Var_10    H9    C19  S28  C20    59.74  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
 8O4  chir_01  C17  C15  C21  C16  both

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
 8O4  plan-1  C4   0.020
 8O4  plan-1  C5   0.020
 8O4  plan-1  C6   0.020
 8O4  plan-1  C7   0.020
 8O4  plan-1  C10  0.020
 8O4  plan-1  C13  0.020
 8O4  plan-1  C11  0.020
 8O4  plan-1  C12  0.020
 8O4  plan-1  C14  0.020
 8O4  plan-1  N22  0.020
 8O4  plan-1  N24  0.020
 8O4  plan-1  O25  0.020
 8O4  plan-1  H4   0.020
 8O4  plan-1  H11  0.020
 8O4  plan-1  H22  0.020
 8O4  plan-1  C18  0.020
 8O4  plan-2  C5   0.020
 8O4  plan-2  C8   0.020
 8O4  plan-2  C20  0.020
 8O4  plan-2  C1   0.020
 8O4  plan-2  C2   0.020
 8O4  plan-2  C3   0.020
 8O4  plan-2  C9   0.020
 8O4  plan-2  C12  0.020
 8O4  plan-2  N23  0.020
 8O4  plan-2  H1   0.020
 8O4  plan-2  H2   0.020
 8O4  plan-2  H3   0.020

