# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Mar  7 20:33:35 2022
#   Inital geometry file: a 106 line input string
#   Ligand name: 6-[(11-bromanyl-6-oxidanylidene-8-thia-3,5,13-triazatricyclo[7.4.0.0^{2,7}]trideca-1(9),2(7),3,10,12-pentaen-4-yl)methylamino]hexanoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC(=O)CCCCCNCC1=Nc2c(sc3cc(Br)cnc23)C(=O)N1
#
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
 06E  06E  '6-[(11-bromanyl-6-oxidanylidene-8-thia-3,5,13-triazatricyclo[7.4.0.0^{2,7}]trideca-1(9),2(7),3,10,12-pentaen-4-yl)methylamino]hexanoic acid'  ligand  41  25  .  2022-08-09  2022-08-09
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_06E
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
 06E  C27  C   C      0   0.401  61.9398  54.0025   7.5358
 06E  O1   O   O      0  -0.610  62.1132  52.8521   7.0826
 06E  C28  C   CH2    0  -0.567  62.8301  54.4391   8.7196
 06E  C29  C   CH2    0  -0.412  63.3371  53.3185   9.6174
 06E  C30  C   CH2    0  -0.425  62.2284  52.6549  10.4258
 06E  C31  C   CH2    0  -0.444  62.6731  51.4370  11.2318
 06E  C32  C   CH2    0  -0.255  63.7623  51.7409  12.2490
 06E  N17  N   NH1    0  -0.599  64.0420  50.5759  13.0739
 06E  C33  C   CH2    0  -0.350  65.0972  50.8337  14.0369
 06E  C34  C   CR6    0   0.458  65.3756  49.5995  14.8445
 06E  N19  N   N      0  -0.444  66.3381  48.8007  14.5159
 06E  C36  C   CR56   0   0.319  66.4932  47.7011  15.2966
 06E  C42  C   CR56   0   0.243  67.5104  46.6932  15.1245
 06E  N20  N   N      0  -0.395  68.4403  46.6852  14.1727
 06E  C41  C   CR16   0  -0.063  69.3042  45.6943  14.1676
 06E  C40  C   CR6    0  -0.184  69.2772  44.6609  15.1187
 06E  BR   BR  BR     0   0.001  70.5660  43.2987  15.0290
 06E  C39  C   CR16   0  -0.134  68.3197  44.6430  16.1098
 06E  C38  C   CR56   0  -0.218  67.4125  45.6956  16.1063
 06E  S    S   S2     0   0.279  66.1096  45.9624  17.2177
 06E  C37  C   CR56   0  -0.408  65.6966  47.4128  16.3757
 06E  C35  C   CR6    0   0.563  64.6251  48.2836  16.7596
 06E  O    O   O      0  -0.440  63.8696  48.1324  17.7002
 06E  N18  N   NR16   0  -0.686  64.5519  49.3721  15.9039
 06E  H2   H   HCH2   0   0.223  63.6906  54.9722   8.2966
 06E  H3   H   HCH2   0   0.198  62.2981  55.1839   9.3202
 06E  H4   H   HCH2   0   0.199  63.8465  52.5656   9.0099
 06E  H5   H   HCH2   0   0.207  64.0931  53.7249  10.2956
 06E  H6   H   HCH2   0   0.202  61.7813  53.3937  11.1005
 06E  H7   H   HCH2   0   0.221  61.4303  52.3429   9.7475
 06E  H8   H   HCH2   0   0.220  61.8046  51.0249  11.7565
 06E  H9   H   HCH2   0   0.215  63.0252  50.6535  10.5542
 06E  H10  H   HCH2   0   0.224  64.6874  52.0175  11.7358
 06E  H11  H   HCH2   0   0.192  63.4690  52.6175  12.8498
 06E  H12  H   HNH1   0   0.348  63.1925  50.3221  13.5663
 06E  H14  H   HCH2   0   0.267  66.0107  51.0890  13.4993
 06E  H15  H   HCH2   0   0.232  64.8779  51.6703  14.7183
 06E  H16  H   HCR6   0   0.289  70.0570  45.7005  13.3877
 06E  H17  H   HCR6   0   0.311  68.2736  43.8571  16.8524
 06E  H18  H   HNR6   0   0.439  63.8281  50.0537  16.1049
 06E  OXT  O   OC    -1  -0.620  61.1409  54.8576   7.0991

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
 06E  O1   C27  deloc     1.249  0.020  1.249
 06E  C27  C28  single    1.544  0.020  1.544
 06E  C28  C29  single    1.523  0.020  1.523
 06E  C29  C30  single    1.524  0.020  1.524
 06E  C30  C31  single    1.527  0.020  1.527
 06E  C31  C32  single    1.521  0.020  1.521
 06E  C32  N17  single    1.455  0.020  1.455
 06E  N17  C33  single    1.452  0.020  1.452
 06E  C33  C34  single    1.501  0.020  1.501
 06E  N20  C41  aromatic  1.315  0.020  1.315
 06E  N20  C42  aromatic  1.331  0.020  1.331
 06E  C41  C40  aromatic  1.405  0.020  1.405
 06E  N19  C34  double    1.293  0.020  1.293
 06E  N19  C36  single    1.357  0.020  1.357
 06E  C34  N18  single    1.361  0.020  1.361
 06E  BR   C40  single    1.878  0.020  1.878
 06E  C42  C36  aromatic  1.442  0.020  1.442
 06E  C42  C38  aromatic  1.403  0.020  1.403
 06E  C40  C39  aromatic  1.378  0.020  1.378
 06E  C36  C37  aromatic  1.372  0.020  1.372
 06E  N18  C35  single    1.387  0.020  1.387
 06E  C38  C39  aromatic  1.390  0.020  1.390
 06E  C38  S    aromatic  1.733  0.020  1.733
 06E  C37  C35  single    1.433  0.020  1.433
 06E  C37  S    aromatic  1.727  0.020  1.727
 06E  C35  O    double    1.216  0.020  1.216
 06E  C28  H2   single    0.970  0.020  1.090
 06E  C28  H3   single    0.970  0.020  1.090
 06E  C29  H4   single    0.970  0.020  1.090
 06E  C29  H5   single    0.970  0.020  1.090
 06E  C30  H6   single    0.970  0.020  1.090
 06E  C30  H7   single    0.970  0.020  1.090
 06E  C31  H8   single    0.970  0.020  1.090
 06E  C31  H9   single    0.970  0.020  1.090
 06E  C32  H10  single    0.970  0.020  1.090
 06E  C32  H11  single    0.970  0.020  1.090
 06E  N17  H12  single    0.890  0.020  1.040
 06E  C33  H14  single    0.970  0.020  1.090
 06E  C33  H15  single    0.970  0.020  1.090
 06E  C41  H16  single    0.930  0.020  1.080
 06E  C39  H17  single    0.930  0.020  1.080
 06E  N18  H18  single    0.860  0.020  1.020
 06E  C27  OXT  deloc     1.249  0.020  1.249

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
 06E  OXT  C27  C28  116.31  3.000
 06E  OXT  C27  O1   126.35  3.000
 06E  C28  C27  O1   117.31  3.000
 06E  H3   C28  H2   105.20  3.000
 06E  H3   C28  C29  109.82  3.000
 06E  H2   C28  C29  108.89  3.000
 06E  H3   C28  C27  109.44  3.000
 06E  H2   C28  C27  107.10  3.000
 06E  C29  C28  C27  115.84  3.000
 06E  H5   C29  H4   106.16  3.000
 06E  H5   C29  C30  109.61  3.000
 06E  H4   C29  C30  109.50  3.000
 06E  H5   C29  C28  108.79  3.000
 06E  H4   C29  C28  109.53  3.000
 06E  C30  C29  C28  113.01  3.000
 06E  H7   C30  H6   106.06  3.000
 06E  H7   C30  C31  108.22  3.000
 06E  H6   C30  C31  109.37  3.000
 06E  H7   C30  C29  109.04  3.000
 06E  H6   C30  C29  109.26  3.000
 06E  C31  C30  C29  114.55  3.000
 06E  H9   C31  H8   106.41  3.000
 06E  H9   C31  C32  109.08  3.000
 06E  H8   C31  C32  108.83  3.000
 06E  H9   C31  C30  109.76  3.000
 06E  H8   C31  C30  108.79  3.000
 06E  C32  C31  C30  113.72  3.000
 06E  H11  C32  H10  106.25  3.000
 06E  H11  C32  N17  112.26  3.000
 06E  H10  C32  N17  107.82  3.000
 06E  H11  C32  C31  109.44  3.000
 06E  H10  C32  C31  110.03  3.000
 06E  N17  C32  C31  110.91  3.000
 06E  H12  N17  C33  109.34  3.000
 06E  H12  N17  C32  108.35  3.000
 06E  C33  N17  C32  111.95  3.000
 06E  H15  C33  H14  107.10  3.000
 06E  H15  C33  C34  109.19  3.000
 06E  H14  C33  C34  107.60  3.000
 06E  H15  C33  N17  113.62  3.000
 06E  H14  C33  N17  108.88  3.000
 06E  C34  C33  N17  110.23  3.000
 06E  N18  C34  N19  123.03  3.000
 06E  N18  C34  C33  116.35  3.000
 06E  N19  C34  C33  120.61  3.000
 06E  C36  N19  C34  116.06  3.000
 06E  C37  C36  C42  110.89  3.000
 06E  C37  C36  N19  123.80  3.000
 06E  C42  C36  N19  125.31  3.000
 06E  C38  C42  N20  123.03  3.000
 06E  C38  C42  C36  111.35  3.000
 06E  N20  C42  C36  125.62  3.000
 06E  C41  N20  C42  117.81  3.000
 06E  H16  C41  C40  120.31  3.000
 06E  H16  C41  N20  117.05  3.000
 06E  C40  C41  N20  122.63  3.000
 06E  C39  C40  BR   120.12  3.000
 06E  C39  C40  C41  120.65  3.000
 06E  BR   C40  C41  119.22  3.000
 06E  H17  C39  C38  121.60  3.000
 06E  H17  C39  C40  122.18  3.000
 06E  C38  C39  C40  116.23  3.000
 06E  S    C38  C39  127.29  3.000
 06E  S    C38  C42  113.06  3.000
 06E  C39  C38  C42  119.65  3.000
 06E  C37  S    C38   89.80  3.000
 06E  C35  C37  S    123.95  3.000
 06E  S    C37  C36  114.90  3.000
 06E  C35  C37  C36  121.14  3.000
 06E  N18  C35  O    122.84  3.000
 06E  O    C35  C37  126.60  3.000
 06E  N18  C35  C37  110.56  3.000
 06E  H18  N18  C35  116.29  3.000
 06E  H18  N18  C34  118.29  3.000
 06E  C35  N18  C34  125.42  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
 06E  CONST_01  C41  N20  C42  C36   180.00   0.0  0
 06E  CONST_02  C39  C38  C42  C36   180.00   0.0  0
 06E  CONST_03  S    C38  C42  C36     0.00   0.0  0
 06E  CONST_04  C38  S    C37  C36     0.00   0.0  0
 06E  CONST_05  C40  C41  N20  C42     0.00   0.0  0
 06E  CONST_06  S    C37  C36  C42     0.00   0.0  0
 06E  CONST_07  C40  C39  C38  C42     0.00   0.0  0
 06E  CONST_08  C37  S    C38  C42     0.00   0.0  0
 06E  CONST_09  C39  C40  C41  N20     0.00   0.0  0
 06E  CONST_10  C37  C36  C42  N20   180.00   0.0  0
 06E  CONST_11  C39  C38  C42  N20     0.00   0.0  0
 06E  CONST_12  S    C38  C42  N20   180.00   0.0  0
 06E  CONST_13  C38  C42  N20  C41     0.00   0.0  0
 06E  CONST_14  C38  C39  C40  C41     0.00   0.0  0
 06E  CONST_15  S    C38  C39  C40   180.00   0.0  0
 06E  CONST_16  C37  S    C38  C39   180.00   0.0  0
 06E  CONST_17  C37  C36  C42  C38     0.00   0.0  0
 06E  CONST_18  C37  C35  N18  C34     0.00   0.0  0
 06E  CONST_19  C35  N18  C34  N19     0.00   0.0  0
 06E  CONST_20  N18  C34  N19  C36     0.00   0.0  0
 06E  CONST_21  BR   C40  C41  N20   180.00   0.0  0
 06E  CONST_22  C38  C39  C40  BR    180.00   0.0  0
 06E  CONST_23  C36  N19  C34  C33   180.00   0.0  0
 06E  CONST_24  C35  N18  C34  C33   180.00   0.0  0
 06E  CONST_25  O    C35  N18  C34   180.00   0.0  0
 06E  CONST_26  H16  C41  N20  C42   180.00   0.0  0
 06E  CONST_27  H17  C39  C38  C42   180.00   0.0  0
 06E  CONST_28  H18  N18  C34  N19   180.00   0.0  0
 06E  Var_01    N19  C34  C33  N17    96.17  30.0  3
 06E  Var_02    C34  C33  N17  C32  -178.70  30.0  3
 06E  Var_03    C30  C29  C28  C27   -68.31  30.0  3
 06E  Var_04    C29  C28  C27  O1    -27.37  30.0  3
 06E  Var_05    C31  C30  C29  C28   174.18  30.0  3
 06E  Var_06    C32  C31  C30  C29    59.69  30.0  3
 06E  Var_07    N17  C32  C31  C30   174.14  30.0  3
 06E  Var_08    C33  N17  C32  C31   178.91  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
 06E  plan-1  C33  0.020
 06E  plan-1  C34  0.020
 06E  plan-1  N19  0.020
 06E  plan-1  C36  0.020
 06E  plan-1  C42  0.020
 06E  plan-1  N20  0.020
 06E  plan-1  C41  0.020
 06E  plan-1  C40  0.020
 06E  plan-1  BR   0.020
 06E  plan-1  C39  0.020
 06E  plan-1  C38  0.020
 06E  plan-1  S    0.020
 06E  plan-1  C37  0.020
 06E  plan-1  C35  0.020
 06E  plan-1  O    0.020
 06E  plan-1  N18  0.020
 06E  plan-1  H16  0.020
 06E  plan-1  H17  0.020
 06E  plan-1  H18  0.020
 06E  plan-2  C27  0.020
 06E  plan-2  O1   0.020
 06E  plan-2  C28  0.020
 06E  plan-2  OXT  0.020

