# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Mar  9 10:30:46 2022
#   Inital geometry file: a 71 line input string
#   Ligand name: (5~{S},6~{R})-5-methyl-7-thia-2-azatricyclo[6.3.1.0^{4,12}]dodeca-1(12),3,8,10-tetraene-6-carboxylic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[C@@H]1[C@@H](Sc2cccc3[nH]cc1c23)C(O)=O
#
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
 9E0  9E0  '(5~{S},6~{R})-5-methyl-7-thia-2-azatricyclo[6.3.1.0^{4,12}]dodeca-1(12),3,8,10-tetraene-6-carboxylic acid'  ligand  26  16  .  2022-03-11  2022-03-11
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_9E0
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
 9E0  C01  C  C1     0  -0.271   -8.3204  -27.7444  -10.0646
 9E0  C02  C  C1     0  -0.334   -7.5785  -27.0342  -11.0264
 9E0  C03  C  C1     0  -0.327   -9.5297  -27.2885   -9.5689
 9E0  C04  C  CR5    0   0.365  -10.0036  -26.0767  -10.0772
 9E0  C05  C  C      0  -0.216   -8.0549  -25.8345  -11.5274
 9E0  C06  C  CR5    0   0.093   -9.2791  -25.3672  -11.0484
 9E0  C07  C  CR5    0   0.064  -10.0040  -24.1924  -11.3862
 9E0  C08  C  CR15   0  -0.107  -11.1324  -24.2199  -10.6172
 9E0  C09  C  CH1    0  -0.513   -7.9741  -23.2383  -12.4300
 9E0  C10  C  CH1    0  -0.322   -9.5135  -23.2346  -12.4272
 9E0  C11  C  C      0   0.458   -7.3729  -22.2470  -13.4552
 9E0  C12  C  CH3    0  -0.650  -10.1072  -23.5530  -13.7987
 9E0  N01  N  NR15   0  -0.694  -11.1328  -25.3510   -9.8342
 9E0  O01  O  O      0  -0.579   -6.5199  -22.6972  -14.2407
 9E0  O02  O  OC    -1  -0.591   -7.8035  -21.0835  -13.3789
 9E0  S01  S  S2     0  -0.002   -7.2303  -24.8821  -12.7582
 9E0  H1   H  H      0   0.245   -7.9212  -28.6796   -9.6928
 9E0  H2   H  H      0   0.246   -6.6303  -27.4337  -11.3650
 9E0  H3   H  H      0   0.252  -10.0775  -27.8516   -8.8244
 9E0  H5   H  HCR5   0   0.277  -11.9500  -23.5180  -10.5571
 9E0  H7   H  HCH1   0   0.281   -7.6418  -22.9376  -11.4306
 9E0  H8   H  HCH1   0   0.246   -9.8057  -22.2165  -12.1554
 9E0  H9   H  HCH3   0   0.229  -11.1964  -23.5360  -13.7542
 9E0  H10  H  HCH3   0   0.227   -9.7960  -22.8254  -14.5495
 9E0  H11  H  HCH3   0   0.218   -9.8053  -24.5441  -14.1408
 9E0  H12  H  HNR5   0   0.404  -11.8554  -25.5922   -9.1767

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
 9E0  O01  C11  deloc     1.244  0.020  1.244
 9E0  C12  C10  single    1.528  0.020  1.528
 9E0  C11  O02  deloc     1.243  0.020  1.243
 9E0  C11  C09  single    1.548  0.020  1.548
 9E0  S01  C09  single    1.834  0.020  1.834
 9E0  S01  C05  single    1.761  0.020  1.761
 9E0  C10  C09  single    1.539  0.020  1.539
 9E0  C10  C07  single    1.497  0.020  1.497
 9E0  C05  C02  aromatic  1.385  0.020  1.385
 9E0  C05  C06  aromatic  1.395  0.020  1.395
 9E0  C07  C06  aromatic  1.421  0.020  1.421
 9E0  C07  C08  aromatic  1.366  0.020  1.366
 9E0  C02  C01  aromatic  1.407  0.020  1.407
 9E0  C06  C04  aromatic  1.404  0.020  1.404
 9E0  C08  N01  aromatic  1.376  0.020  1.376
 9E0  C01  C03  aromatic  1.384  0.020  1.384
 9E0  C04  C03  aromatic  1.397  0.020  1.397
 9E0  C04  N01  aromatic  1.364  0.020  1.364
 9E0  C01  H1   single    0.930  0.020  1.080
 9E0  C02  H2   single    0.930  0.020  1.080
 9E0  C03  H3   single    0.930  0.020  1.080
 9E0  C08  H5   single    0.930  0.020  1.080
 9E0  C09  H7   single    0.970  0.020  1.090
 9E0  C10  H8   single    0.970  0.020  1.090
 9E0  C12  H9   single    0.970  0.020  1.090
 9E0  C12  H10  single    0.970  0.020  1.090
 9E0  C12  H11  single    0.970  0.020  1.090
 9E0  N01  H12  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
 9E0  H1   C01  C03  118.92  3.000
 9E0  H1   C01  C02  118.44  3.000
 9E0  C03  C01  C02  122.63  3.000
 9E0  H2   C02  C05  120.51  3.000
 9E0  H2   C02  C01  119.28  3.000
 9E0  C05  C02  C01  120.21  3.000
 9E0  H3   C03  C04  122.00  3.000
 9E0  H3   C03  C01  121.15  3.000
 9E0  C04  C03  C01  116.86  3.000
 9E0  N01  C04  C06  106.35  3.000
 9E0  N01  C04  C03  132.65  3.000
 9E0  C06  C04  C03  121.00  3.000
 9E0  S01  C05  C06  118.01  3.000
 9E0  C06  C05  C02  117.90  3.000
 9E0  S01  C05  C02  124.08  3.000
 9E0  C07  C06  C05  130.00  3.000
 9E0  C07  C06  C04  108.60  3.000
 9E0  C05  C06  C04  121.40  3.000
 9E0  C10  C07  C08  132.46  3.000
 9E0  C08  C07  C06  105.72  3.000
 9E0  C10  C07  C06  121.80  3.000
 9E0  H5   C08  N01  120.19  3.000
 9E0  H5   C08  C07  130.10  3.000
 9E0  N01  C08  C07  109.71  3.000
 9E0  H7   C09  S01  106.63  3.000
 9E0  H7   C09  C11  108.11  3.000
 9E0  S01  C09  C11  107.34  3.000
 9E0  H7   C09  C10  107.52  3.000
 9E0  S01  C09  C10  114.08  3.000
 9E0  C11  C09  C10  112.84  3.000
 9E0  H8   C10  C12  108.26  3.000
 9E0  H8   C10  C09  105.66  3.000
 9E0  C12  C10  C09  112.73  3.000
 9E0  H8   C10  C07  109.58  3.000
 9E0  C09  C10  C07  109.11  3.000
 9E0  C12  C10  C07  111.31  3.000
 9E0  O02  C11  O01  127.96  3.000
 9E0  O02  C11  C09  115.11  3.000
 9E0  O01  C11  C09  116.93  3.000
 9E0  H11  C12  H10  108.13  3.000
 9E0  H11  C12  H9   107.66  3.000
 9E0  H10  C12  H9   107.61  3.000
 9E0  H11  C12  C10  111.30  3.000
 9E0  H10  C12  C10  111.59  3.000
 9E0  H9   C12  C10  110.38  3.000
 9E0  H12  N01  C08  124.69  3.000
 9E0  H12  N01  C04  125.68  3.000
 9E0  C08  N01  C04  109.62  3.000
 9E0  C09  S01  C05   99.78  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
 9E0  CONST_01  C06  C05  C02  C01    0.00  0.0  0
 9E0  CONST_02  C06  C04  C03  C01    0.00  0.0  0
 9E0  CONST_03  N01  C04  C03  C01  180.00  0.0  0
 9E0  CONST_04  C07  C06  C05  C02  180.00  0.0  0
 9E0  CONST_05  C04  C06  C05  C02    0.00  0.0  0
 9E0  CONST_06  C04  C03  C01  C02    0.00  0.0  0
 9E0  CONST_07  C05  C02  C01  C03    0.00  0.0  0
 9E0  CONST_08  C05  C06  C04  C03    0.00  0.0  0
 9E0  CONST_09  C07  C06  C04  C03  180.00  0.0  0
 9E0  CONST_10  C08  N01  C04  C03  180.00  0.0  0
 9E0  CONST_11  C08  C07  C06  C04    0.00  0.0  0
 9E0  CONST_12  C07  C08  N01  C04    0.00  0.0  0
 9E0  CONST_13  C08  C07  C06  C05  180.00  0.0  0
 9E0  CONST_14  N01  C04  C06  C05  180.00  0.0  0
 9E0  CONST_15  N01  C08  C07  C06    0.00  0.0  0
 9E0  CONST_16  C08  N01  C04  C06    0.00  0.0  0
 9E0  CONST_17  N01  C04  C06  C07    0.00  0.0  0
 9E0  CONST_18  H3   C03  C01  C02  180.00  0.0  0
 9E0  CONST_19  H2   C02  C01  C03  180.00  0.0  0
 9E0  CONST_20  H12  N01  C04  C03    0.00  0.0  0
 9E0  CONST_21  H1   C01  C03  C04  180.00  0.0  0
 9E0  CONST_22  H5   C08  N01  C04  180.00  0.0  0

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
 9E0  chir_01  C09  C11  S01  C10  positiv
 9E0  chir_02  C10  C07  C09  C12  negativ

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
 9E0  plan-1  C09  0.020
 9E0  plan-1  C11  0.020
 9E0  plan-1  O01  0.020
 9E0  plan-1  O02  0.020
 9E0  plan-2  C01  0.020
 9E0  plan-2  C02  0.020
 9E0  plan-2  C03  0.020
 9E0  plan-2  C04  0.020
 9E0  plan-2  C05  0.020
 9E0  plan-2  C06  0.020
 9E0  plan-2  C07  0.020
 9E0  plan-2  C08  0.020
 9E0  plan-2  C10  0.020
 9E0  plan-2  N01  0.020
 9E0  plan-2  S01  0.020
 9E0  plan-2  H1   0.020
 9E0  plan-2  H2   0.020
 9E0  plan-2  H3   0.020
 9E0  plan-2  H5   0.020
 9E0  plan-2  H12  0.020

