# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Apr 27 14:04:33 2020
#   Inital geometry file: a 138 line input string
#   Ligand name: (2~{R})-2-azanyl-3-[[2-(4-methoxyphenyl)-2-tricyclo[9.4.0.0^{3,8}]pentadeca-1(11),3,5,7,12,14-hexaenyl]sulfanyl]propanoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: COc1ccc(cc1)[C@]2(SC[C@H](N)C(O)=O)c3ccccc3CCc4ccccc24
#
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
 5C5  5C5  '(2~{R})-2-azanyl-3-[[2-(4-methoxyphenyl)-2-tricyclo[9.4.0.0^{3,8}]pentadeca-1(11),3,5,7,12,14-hexaenyl]sulfanyl]propanoic acid'  ligand  55  30  .  2022-11-17  2022-11-17
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_5C5
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
 5C5  O2   O  O     0  -0.430  -5.6842   0.8861  -0.7525
 5C5  C    C  C     0   0.553  -4.9053   0.0591  -1.1490
 5C5  O    O  OH1   0  -0.590  -5.1332  -1.2469  -1.1123
 5C5  C1   C  CH1   0  -0.226  -3.5367   0.3722  -1.7279
 5C5  N    N  NH2   0  -0.773  -3.4704   1.7717  -2.0703
 5C5  C2   C  CH2   0  -0.551  -2.4654  -0.1129  -0.7303
 5C5  S    S  S2    0   0.034  -0.8439   0.0426  -1.5171
 5C5  C3   C  CT    0  -0.473   0.2639  -0.1477  -0.0355
 5C5  C18  C  CR6   0   0.141   1.7108   0.0959  -0.4793
 5C5  C24  C  CR16  0  -0.298   2.0760   0.7025  -1.6767
 5C5  C23  C  CR16  0  -0.327   3.4045   0.9520  -1.9804
 5C5  C21  C  CR6   0   0.370   4.4124   0.6051  -1.0842
 5C5  O1   O  O2    0  -0.471   5.6749   0.8877  -1.4566
 5C5  C22  C  CH3   0  -0.437   6.7289   0.5521  -0.5764
 5C5  C20  C  CR16  0  -0.369   4.0624  -0.0019   0.1215
 5C5  C19  C  CR16  0  -0.248   2.7281  -0.2489   0.4045
 5C5  C17  C  CR6   0   0.193  -0.0239   1.0080   0.9476
 5C5  C16  C  CR16  0  -0.246  -0.0668   2.2880   0.3778
 5C5  C15  C  CR16  0  -0.262  -0.1902   3.4364   1.1352
 5C5  C14  C  CR16  0  -0.254  -0.2682   3.3397   2.5172
 5C5  C13  C  CR16  0  -0.320  -0.2293   2.0867   3.0960
 5C5  C12  C  CR6   0   0.062  -0.1085   0.9152   2.3403
 5C5  C11  C  CH2   0  -0.539  -0.1437  -0.3826   3.0889
 5C5  C10  C  CH2   0  -0.533  -1.1851  -1.3403   2.5219
 5C5  C9   C  CR6   0   0.062  -0.6209  -2.1672   1.4062
 5C5  C4   C  CR6   0   0.164   0.1028  -1.6325   0.3378
 5C5  C8   C  CR16  0  -0.322  -0.7617  -3.5570   1.5066
 5C5  C7   C  CR16  0  -0.255  -0.2080  -4.4237   0.5866
 5C5  C6   C  CR16  0  -0.268   0.5252  -3.8972  -0.4697
 5C5  C5   C  CR16  0  -0.244   0.6666  -2.5294  -0.5823
 5C5  H1   H  HOH1  0   0.485  -5.9960  -1.4260  -0.7088
 5C5  H2   H  HCH1  0   0.288  -3.4381  -0.2126  -2.6485
 5C5  H3   H  HNH2  0   0.346  -3.5093   2.3395  -1.2321
 5C5  H4   H  HNH2  0   0.357  -2.5776   1.9694  -2.5038
 5C5  H6   H  HCH2  0   0.275  -2.4926   0.5210   0.1599
 5C5  H7   H  HCH2  0   0.284  -2.6315  -1.1486  -0.4314
 5C5  H8   H  HCR6  0   0.256   1.3293   1.0014  -2.4014
 5C5  H9   H  HCR6  0   0.263   3.6645   1.4224  -2.9204
 5C5  H10  H  HCH3  0   0.228   6.6470   1.0782   0.3785
 5C5  H11  H  HCH3  0   0.229   6.7745  -0.5231  -0.3835
 5C5  H12  H  HCH3  0   0.260   7.6499   0.8585  -1.0661
 5C5  H13  H  HCR6  0   0.280   4.8097  -0.2867   0.8497
 5C5  H14  H  HCR6  0   0.256   2.4859  -0.7266   1.3463
 5C5  H15  H  HCR6  0   0.248  -0.0011   2.3930  -0.6961
 5C5  H16  H  HCR6  0   0.252  -0.2229   4.4008   0.6450
 5C5  H17  H  HCR6  0   0.254  -0.3657   4.2239   3.1335
 5C5  H18  H  HCR6  0   0.249  -0.3037   1.9970   4.1731
 5C5  H19  H  HCH2  0   0.256   0.8360  -0.8696   3.0943
 5C5  H20  H  HCH2  0   0.263  -1.5280  -2.0111   3.3106
 5C5  H21  H  HCR6  0   0.249  -1.3146  -3.9583   2.3475
 5C5  H22  H  HCR6  0   0.253  -0.3360  -5.4927   0.6963
 5C5  H23  H  HCR6  0   0.252   0.9818  -4.5465  -1.2052
 5C5  H24  H  HCR6  0   0.256   1.2266  -2.1427  -1.4238
 5C5  H5   H  HCH2  0   0.264  -0.3756  -0.1719   4.1337
 5C5  H25  H  HCH2  0   0.254  -2.0690  -0.7785   2.2066

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
 5C5  C14  C13  aromatic  1.381  0.020  1.381
 5C5  C14  C15  aromatic  1.388  0.020  1.388
 5C5  C13  C12  aromatic  1.399  0.020  1.399
 5C5  C15  C16  aromatic  1.381  0.020  1.381
 5C5  C12  C11  single    1.499  0.020  1.499
 5C5  C12  C17  aromatic  1.398  0.020  1.398
 5C5  C11  C10  single    1.524  0.020  1.524
 5C5  C10  C9   single    1.499  0.020  1.499
 5C5  C16  C17  aromatic  1.402  0.020  1.402
 5C5  C17  C3   single    1.544  0.020  1.544
 5C5  C8   C9   aromatic  1.401  0.020  1.401
 5C5  C8   C7   aromatic  1.380  0.020  1.380
 5C5  C9   C4   aromatic  1.397  0.020  1.397
 5C5  C7   C6   aromatic  1.389  0.020  1.389
 5C5  C4   C3   single    1.540  0.020  1.540
 5C5  C4   C5   aromatic  1.403  0.020  1.403
 5C5  C3   C18  single    1.533  0.020  1.533
 5C5  C3   S    single    1.860  0.020  1.860
 5C5  C6   C5   aromatic  1.380  0.020  1.380
 5C5  C24  C18  aromatic  1.391  0.020  1.391
 5C5  C24  C23  aromatic  1.385  0.020  1.385
 5C5  C18  C19  aromatic  1.391  0.020  1.391
 5C5  C23  C21  aromatic  1.393  0.020  1.393
 5C5  S    C2   single    1.809  0.020  1.809
 5C5  O2   C    double    1.203  0.020  1.203
 5C5  C2   C1   single    1.542  0.020  1.542
 5C5  C19  C20  aromatic  1.386  0.020  1.386
 5C5  C21  C20  aromatic  1.394  0.020  1.394
 5C5  C21  O1   single    1.346  0.020  1.346
 5C5  C    C1   single    1.519  0.020  1.519
 5C5  C    O    single    1.326  0.020  1.326
 5C5  C1   N    single    1.442  0.020  1.442
 5C5  O1   C22  single    1.414  0.020  1.414
 5C5  O    H1   single    0.850  0.020  0.980
 5C5  C1   H2   single    0.970  0.020  1.090
 5C5  N    H3   single    0.890  0.020  1.040
 5C5  N    H4   single    0.890  0.020  1.040
 5C5  C2   H6   single    0.970  0.020  1.090
 5C5  C2   H7   single    0.970  0.020  1.090
 5C5  C24  H8   single    0.930  0.020  1.080
 5C5  C23  H9   single    0.930  0.020  1.080
 5C5  C22  H10  single    0.970  0.020  1.090
 5C5  C22  H11  single    0.970  0.020  1.090
 5C5  C22  H12  single    0.970  0.020  1.090
 5C5  C20  H13  single    0.930  0.020  1.080
 5C5  C19  H14  single    0.930  0.020  1.080
 5C5  C16  H15  single    0.930  0.020  1.080
 5C5  C15  H16  single    0.930  0.020  1.080
 5C5  C14  H17  single    0.930  0.020  1.080
 5C5  C13  H18  single    0.930  0.020  1.080
 5C5  C11  H19  single    0.970  0.020  1.090
 5C5  C10  H20  single    0.970  0.020  1.090
 5C5  C8   H21  single    0.930  0.020  1.080
 5C5  C7   H22  single    0.930  0.020  1.080
 5C5  C6   H23  single    0.930  0.020  1.080
 5C5  C5   H24  single    0.930  0.020  1.080
 5C5  C11  H5   single    0.970  0.020  1.090
 5C5  C10  H25  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
 5C5  C1   C    O    111.62  3.000
 5C5  O    C    O2   123.81  3.000
 5C5  C1   C    O2   124.56  3.000
 5C5  H1   O    C    110.27  3.000
 5C5  H2   C1   C2   108.25  3.000
 5C5  H2   C1   N    108.33  3.000
 5C5  C2   C1   N    115.27  3.000
 5C5  H2   C1   C    106.95  3.000
 5C5  N    C1   C    109.39  3.000
 5C5  C2   C1   C    108.34  3.000
 5C5  H4   N    H3   106.19  3.000
 5C5  H4   N    C1   109.38  3.000
 5C5  H3   N    C1   110.22  3.000
 5C5  H7   C2   H6   108.88  3.000
 5C5  H7   C2   S    109.71  3.000
 5C5  H6   C2   S    109.06  3.000
 5C5  H7   C2   C1   111.73  3.000
 5C5  H6   C2   C1   109.09  3.000
 5C5  S    C2   C1   108.32  3.000
 5C5  C3   S    C2   100.29  3.000
 5C5  C4   C3   C17  123.23  3.000
 5C5  C4   C3   C18  108.80  3.000
 5C5  C17  C3   C18  103.97  3.000
 5C5  C18  C3   S    108.38  3.000
 5C5  C4   C3   S    103.26  3.000
 5C5  C17  C3   S    108.64  3.000
 5C5  C19  C18  C24  117.58  3.000
 5C5  C19  C18  C3   117.84  3.000
 5C5  C24  C18  C3   124.49  3.000
 5C5  H8   C24  C23  117.70  3.000
 5C5  H8   C24  C18  121.03  3.000
 5C5  C23  C24  C18  121.26  3.000
 5C5  H9   C23  C21  119.54  3.000
 5C5  H9   C23  C24  119.92  3.000
 5C5  C21  C23  C24  120.54  3.000
 5C5  C20  C21  O1   124.47  3.000
 5C5  O1   C21  C23  116.64  3.000
 5C5  C20  C21  C23  118.89  3.000
 5C5  C22  O1   C21  118.50  3.000
 5C5  H12  C22  H11  108.74  3.000
 5C5  H12  C22  H10  108.74  3.000
 5C5  H11  C22  H10  108.80  3.000
 5C5  H12  C22  O1   106.52  3.000
 5C5  H11  C22  O1   111.99  3.000
 5C5  H10  C22  O1   111.95  3.000
 5C5  H13  C20  C19  118.73  3.000
 5C5  H13  C20  C21  121.55  3.000
 5C5  C19  C20  C21  119.72  3.000
 5C5  H14  C19  C20  118.12  3.000
 5C5  H14  C19  C18  119.87  3.000
 5C5  C20  C19  C18  122.01  3.000
 5C5  C12  C17  C16  117.62  3.000
 5C5  C16  C17  C3   115.49  3.000
 5C5  C12  C17  C3   126.55  3.000
 5C5  H15  C16  C15  118.00  3.000
 5C5  H15  C16  C17  119.38  3.000
 5C5  C15  C16  C17  122.62  3.000
 5C5  H16  C15  C14  120.77  3.000
 5C5  H16  C15  C16  119.68  3.000
 5C5  C14  C15  C16  119.56  3.000
 5C5  H17  C14  C13  120.35  3.000
 5C5  H17  C14  C15  121.02  3.000
 5C5  C13  C14  C15  118.63  3.000
 5C5  H18  C13  C12  118.26  3.000
 5C5  H18  C13  C14  119.33  3.000
 5C5  C12  C13  C14  122.40  3.000
 5C5  C11  C12  C13  116.95  3.000
 5C5  C11  C12  C17  123.81  3.000
 5C5  C13  C12  C17  119.17  3.000
 5C5  H5   C11  H19  105.76  3.000
 5C5  H5   C11  C10  109.41  3.000
 5C5  H19  C11  C10  109.51  3.000
 5C5  H5   C11  C12  108.43  3.000
 5C5  H19  C11  C12  111.52  3.000
 5C5  C10  C11  C12  111.98  3.000
 5C5  H25  C10  H20  105.68  3.000
 5C5  H25  C10  C9   111.90  3.000
 5C5  H20  C10  C9   108.50  3.000
 5C5  H25  C10  C11  109.68  3.000
 5C5  H20  C10  C11  109.40  3.000
 5C5  C9   C10  C11  111.49  3.000
 5C5  C8   C9   C4   119.12  3.000
 5C5  C4   C9   C10  123.59  3.000
 5C5  C8   C9   C10  117.15  3.000
 5C5  C5   C4   C9   117.72  3.000
 5C5  C5   C4   C3   114.55  3.000
 5C5  C9   C4   C3   127.50  3.000
 5C5  H21  C8   C7   119.32  3.000
 5C5  H21  C8   C9   118.32  3.000
 5C5  C7   C8   C9   122.36  3.000
 5C5  H22  C7   C6   120.91  3.000
 5C5  H22  C7   C8   120.36  3.000
 5C5  C6   C7   C8   118.73  3.000
 5C5  H23  C6   C5   119.74  3.000
 5C5  H23  C6   C7   120.80  3.000
 5C5  C5   C6   C7   119.46  3.000
 5C5  H24  C5   C6   118.08  3.000
 5C5  H24  C5   C4   119.30  3.000
 5C5  C6   C5   C4   122.61  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
 5C5  CONST_01  C21  C23  C24  C18    0.00   0.0  0
 5C5  CONST_02  C21  C20  C19  C18    0.00   0.0  0
 5C5  CONST_03  C20  C19  C18  C24    0.00   0.0  0
 5C5  CONST_04  C20  C21  C23  C24    0.00   0.0  0
 5C5  CONST_05  C19  C18  C24  C23    0.00   0.0  0
 5C5  CONST_06  C19  C20  C21  C23    0.00   0.0  0
 5C5  CONST_07  C14  C13  C12  C17    0.00   0.0  0
 5C5  CONST_08  C14  C15  C16  C17    0.00   0.0  0
 5C5  CONST_09  C13  C14  C15  C16    0.00   0.0  0
 5C5  CONST_10  C13  C12  C17  C16    0.00   0.0  0
 5C5  CONST_11  C12  C13  C14  C15    0.00   0.0  0
 5C5  CONST_12  C12  C17  C16  C15    0.00   0.0  0
 5C5  CONST_13  C6   C7   C8   C9     0.00   0.0  0
 5C5  CONST_14  C6   C5   C4   C9     0.00   0.0  0
 5C5  CONST_15  C7   C8   C9   C4     0.00   0.0  0
 5C5  CONST_16  C7   C6   C5   C4     0.00   0.0  0
 5C5  CONST_17  C5   C4   C9   C8     0.00   0.0  0
 5C5  CONST_18  C5   C6   C7   C8     0.00   0.0  0
 5C5  CONST_19  C23  C24  C18  C3   180.00   0.0  0
 5C5  CONST_20  C20  C19  C18  C3   180.00   0.0  0
 5C5  CONST_21  O1   C21  C23  C24  180.00   0.0  0
 5C5  CONST_22  C19  C20  C21  O1   180.00   0.0  0
 5C5  CONST_23  H15  C16  C17  C3     0.00   0.0  0
 5C5  CONST_24  H24  C5   C4   C3     0.00   0.0  0
 5C5  CONST_25  H8   C24  C18  C3     0.00   0.0  0
 5C5  CONST_26  H14  C19  C18  C3     0.00   0.0  0
 5C5  CONST_27  H9   C23  C24  C18  180.00   0.0  0
 5C5  CONST_28  H13  C20  C19  C18  180.00   0.0  0
 5C5  CONST_29  H18  C13  C12  C17  180.00   0.0  0
 5C5  CONST_30  H16  C15  C16  C17  180.00   0.0  0
 5C5  CONST_31  H17  C14  C15  C16  180.00   0.0  0
 5C5  CONST_32  H21  C8   C9   C10    0.00   0.0  0
 5C5  CONST_33  H22  C7   C8   C9   180.00   0.0  0
 5C5  CONST_34  H23  C6   C5   C4   180.00   0.0  0
 5C5  CONST_35  H1   O    C    O2     0.00   0.0  0
 5C5  Var_01    C10  C11  C12  C17  -49.95  30.0  1
 5C5  Var_02    C9   C10  C11  C12   87.34  30.0  1
 5C5  Var_03    C8   C9   C10  C11  127.01  30.0  1
 5C5  Var_04    C20  C21  O1   C22    0.01  30.0  2
 5C5  Var_05    H6   C2   S    C3    47.10  30.0  3
 5C5  Var_06    H10  C22  O1   C21  -61.48  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
 5C5  chir_01  C1  C2   C   N    negativ
 5C5  chir_02  C3  C17  C4  C18  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
 5C5  plan-1  C3   0.020
 5C5  plan-1  C18  0.020
 5C5  plan-1  C24  0.020
 5C5  plan-1  C23  0.020
 5C5  plan-1  C21  0.020
 5C5  plan-1  O1   0.020
 5C5  plan-1  C20  0.020
 5C5  plan-1  C19  0.020
 5C5  plan-1  H8   0.020
 5C5  plan-1  H9   0.020
 5C5  plan-1  H13  0.020
 5C5  plan-1  H14  0.020
 5C5  plan-2  C3   0.020
 5C5  plan-2  C17  0.020
 5C5  plan-2  C16  0.020
 5C5  plan-2  C15  0.020
 5C5  plan-2  C14  0.020
 5C5  plan-2  C13  0.020
 5C5  plan-2  C12  0.020
 5C5  plan-2  C11  0.020
 5C5  plan-2  H15  0.020
 5C5  plan-2  H16  0.020
 5C5  plan-2  H17  0.020
 5C5  plan-2  H18  0.020
 5C5  plan-3  C3   0.020
 5C5  plan-3  C10  0.020
 5C5  plan-3  C9   0.020
 5C5  plan-3  C4   0.020
 5C5  plan-3  C8   0.020
 5C5  plan-3  C7   0.020
 5C5  plan-3  C6   0.020
 5C5  plan-3  C5   0.020
 5C5  plan-3  H21  0.020
 5C5  plan-3  H22  0.020
 5C5  plan-3  H23  0.020
 5C5  plan-3  H24  0.020
 5C5  plan-4  O2   0.020
 5C5  plan-4  C    0.020
 5C5  plan-4  O    0.020
 5C5  plan-4  C1   0.020
 5C5  plan-4  H1   0.020

