# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun Apr  5 03:59:41 2020
#   Inital geometry file: a 117 line input string
#   Ligand name: 4-cyclopropyl-2-(2-hydroxyethoxy)-N-[(1R,2s,3S,5s,7s)-5-hydroxytricyclo[3.3.1.1~3,7~]dec-2-yl]-1,3-thiazole-5-carboxamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OCCOc1sc(C(=O)NC2[C@@H]3CC4C[C@H]2CC(O)(C4)C3)c(n1)C5CC5
#
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
 4YQ  4YQ  4-cyclopropyl-2-(2-hydroxyethoxy)-N-[(1R,2s,3S,5s,7s)-5-hydroxytricyclo[3.3.1.1~3,7~]dec-2-yl]-1,3-thiazole-5-carboxamide  ligand  52  26  .  2022-07-23  2022-07-26
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_4YQ
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
 4YQ  O14   O  O     0  -0.490  -0.5561  -2.2539  -0.7988
 4YQ  C13   C  C     0   0.553  -0.1530  -1.1276  -0.5329
 4YQ  C5    C  CR5   0  -0.452   1.2760  -0.8575  -0.2978
 4YQ  S6    S  S2    0   0.157   1.9446   0.7472  -0.4291
 4YQ  C7    C  CR5   0   0.334   3.4865   0.0909   0.0075
 4YQ  O9    O  O2    0  -0.411   4.5727   0.8181   0.1164
 4YQ  C10   C  CH2   0  -0.224   4.4814   2.2293  -0.1049
 4YQ  C11   C  CH2   0  -0.178   5.8291   2.8444   0.1536
 4YQ  O12   O  OH1   0  -0.666   6.7488   2.3649  -0.7945
 4YQ  C4    C  CR5   0   0.451   2.2702  -1.7383   0.0473
 4YQ  N8    N  N     0  -0.451   3.5050  -1.1815   0.2141
 4YQ  C3    C  CH1   0  -0.383   2.1282  -3.1832   0.2794
 4YQ  C2    C  CH2   0  -0.467   2.9941  -3.8467   1.3201
 4YQ  C1    C  CH2   0  -0.468   3.2523  -4.1059  -0.1217
 4YQ  N15   N  NH1   0  -0.680  -0.9793  -0.0652  -0.4499
 4YQ  C16   C  CH1   0  -0.027  -2.4119  -0.1739  -0.6525
 4YQ  C17   C  CH1   0  -0.276  -3.0080   1.1734  -1.0788
 4YQ  C18   C  CH2   0  -0.449  -2.9302   2.1957   0.0590
 4YQ  C21   C  CH1   0  -0.261  -3.1568  -0.6815   0.5940
 4YQ  C20   C  CH2   0  -0.435  -3.0671   0.3424   1.7265
 4YQ  C22   C  CH2   0  -0.448  -4.6241  -0.9050   0.2224
 4YQ  C23   C  CT    0   0.253  -5.2517   0.4098  -0.2347
 4YQ  C25   C  CH2   0  -0.461  -4.4764   0.9399  -1.4459
 4YQ  O26   O  OH1   0  -0.686  -6.5992   0.1367  -0.5702
 4YQ  C24   C  CH2   0  -0.456  -5.1546   1.4333   0.9000
 4YQ  C19   C  CH1   0  -0.249  -3.6888   1.6662   1.2762
 4YQ  H15   H  HNH1  0   0.390  -0.6267   0.8096  -0.0959
 4YQ  H101  H  HCH2  0   0.257   4.1560   2.4199  -1.1329
 4YQ  H102  H  HCH2  0   0.258   3.7531   2.6699   0.5827
 4YQ  H111  H  HCH2  0   0.219   5.6933   3.9311   0.0913
 4YQ  H112  H  HCH2  0   0.218   6.1376   2.6200   1.1821
 4YQ  H12   H  HOH1  0   0.461   7.6124   2.7322  -0.5862
 4YQ  H3    H  HCH1  0   0.280   1.1291  -3.5732   0.1632
 4YQ  H21C  H  HCH2  0   0.255   3.6964  -3.2212   1.8549
 4YQ  H22C  H  HCH2  0   0.261   2.5327  -4.6245   1.9148
 4YQ  H11C  H  HCH2  0   0.261   2.9691  -5.0641  -0.5378
 4YQ  H12C  H  HCH2  0   0.255   4.1314  -3.6596  -0.5672
 4YQ  H16   H  HCH1  0   0.254  -2.5649  -0.8889  -1.4653
 4YQ  H17   H  HCH1  0   0.248  -2.4672   1.5422  -1.9553
 4YQ  H21   H  HCH1  0   0.246  -2.7178  -1.6314   0.9086
 4YQ  H181  H  HCH2  0   0.230  -1.8938   2.4210   0.3328
 4YQ  H182  H  HCH2  0   0.241  -3.3608   3.1439  -0.2751
 4YQ  H251  H  HCH2  0   0.234  -4.9246   1.8796  -1.7886
 4YQ  H252  H  HCH2  0   0.237  -4.5523   0.2273  -2.2737
 4YQ  H19   H  HCH1  0   0.235  -3.6333   2.3949   2.0892
 4YQ  H201  H  HCH2  0   0.234  -3.5949  -0.0382   2.6058
 4YQ  H202  H  HCH2  0   0.230  -2.0283   0.4926   2.0358
 4YQ  H221  H  HCH2  0   0.235  -4.7069  -1.6528  -0.5738
 4YQ  H222  H  HCH2  0   0.235  -5.1716  -1.2964   1.0858
 4YQ  H26   H  HOH1  0   0.439  -7.0132   0.9626  -0.8439
 4YQ  H241  H  HCH2  0   0.227  -5.6162   2.3772   0.5848
 4YQ  H242  H  HCH2  0   0.231  -5.7176   1.0757   1.7689

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
 4YQ  O14  C13   double    1.226  0.020  1.226
 4YQ  C13  C5    single    1.473  0.020  1.473
 4YQ  C13  N15   single    1.348  0.020  1.348
 4YQ  C5   S6    aromatic  1.743  0.020  1.743
 4YQ  C5   C4    aromatic  1.372  0.020  1.372
 4YQ  S6   C7    aromatic  1.732  0.020  1.732
 4YQ  C7   O9    single    1.312  0.020  1.312
 4YQ  C7   N8    aromatic  1.289  0.020  1.289
 4YQ  O9   C10   single    1.431  0.020  1.431
 4YQ  C10  C11   single    1.504  0.020  1.504
 4YQ  C11  O12   single    1.405  0.020  1.405
 4YQ  C4   N8    aromatic  1.365  0.020  1.365
 4YQ  C4   C3    single    1.470  0.020  1.470
 4YQ  C3   C2    single    1.508  0.020  1.508
 4YQ  C3   C1    single    1.509  0.020  1.509
 4YQ  C2   C1    single    1.488  0.020  1.488
 4YQ  N15  C16   single    1.451  0.020  1.451
 4YQ  C16  C17   single    1.534  0.020  1.534
 4YQ  C16  C21   single    1.538  0.020  1.538
 4YQ  C17  C18   single    1.532  0.020  1.532
 4YQ  C17  C25   single    1.531  0.020  1.531
 4YQ  C18  C19   single    1.529  0.020  1.529
 4YQ  C21  C20   single    1.529  0.020  1.529
 4YQ  C21  C22   single    1.530  0.020  1.530
 4YQ  C20  C19   single    1.530  0.020  1.530
 4YQ  C22  C23   single    1.527  0.020  1.527
 4YQ  C23  C25   single    1.533  0.020  1.533
 4YQ  C23  O26   single    1.415  0.020  1.415
 4YQ  C23  C24   single    1.531  0.020  1.531
 4YQ  C24  C19   single    1.531  0.020  1.531
 4YQ  N15  H15   single    0.860  0.020  1.020
 4YQ  C10  H101  single    0.970  0.020  1.090
 4YQ  C10  H102  single    0.970  0.020  1.090
 4YQ  C11  H111  single    0.970  0.020  1.090
 4YQ  C11  H112  single    0.970  0.020  1.090
 4YQ  O12  H12   single    0.850  0.020  0.980
 4YQ  C3   H3    single    0.970  0.020  1.090
 4YQ  C2   H21C  single    0.970  0.020  1.090
 4YQ  C2   H22C  single    0.970  0.020  1.090
 4YQ  C1   H11C  single    0.970  0.020  1.090
 4YQ  C1   H12C  single    0.970  0.020  1.090
 4YQ  C16  H16   single    0.970  0.020  1.090
 4YQ  C17  H17   single    0.970  0.020  1.090
 4YQ  C21  H21   single    0.970  0.020  1.090
 4YQ  C18  H181  single    0.970  0.020  1.090
 4YQ  C18  H182  single    0.970  0.020  1.090
 4YQ  C25  H251  single    0.970  0.020  1.090
 4YQ  C25  H252  single    0.970  0.020  1.090
 4YQ  C19  H19   single    0.970  0.020  1.090
 4YQ  C20  H201  single    0.970  0.020  1.090
 4YQ  C20  H202  single    0.970  0.020  1.090
 4YQ  C22  H221  single    0.970  0.020  1.090
 4YQ  C22  H222  single    0.970  0.020  1.090
 4YQ  O26  H26   single    0.850  0.020  0.980
 4YQ  C24  H241  single    0.970  0.020  1.090
 4YQ  C24  H242  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
 4YQ  N15   C13  C5    116.11  3.000
 4YQ  N15   C13  O14   122.40  3.000
 4YQ  C5    C13  O14   121.48  3.000
 4YQ  C4    C5   S6    109.38  3.000
 4YQ  C4    C5   C13   128.70  3.000
 4YQ  S6    C5   C13   121.92  3.000
 4YQ  C7    S6   C5     88.49  3.000
 4YQ  N8    C7   O9    121.47  3.000
 4YQ  N8    C7   S6    115.29  3.000
 4YQ  O9    C7   S6    123.24  3.000
 4YQ  C10   O9   C7    118.75  3.000
 4YQ  H102  C10  H101  108.79  3.000
 4YQ  H102  C10  C11   108.89  3.000
 4YQ  H101  C10  C11   110.89  3.000
 4YQ  H102  C10  O9    110.02  3.000
 4YQ  H101  C10  O9    109.62  3.000
 4YQ  C11   C10  O9    108.64  3.000
 4YQ  H112  C11  H111  106.91  3.000
 4YQ  H112  C11  O12   112.26  3.000
 4YQ  H111  C11  O12   112.38  3.000
 4YQ  H112  C11  C10   109.24  3.000
 4YQ  H111  C11  C10   106.53  3.000
 4YQ  O12   C11  C10   109.32  3.000
 4YQ  H12   O12  C11   108.14  3.000
 4YQ  C3    C4   N8    117.97  3.000
 4YQ  C3    C4   C5    126.90  3.000
 4YQ  N8    C4   C5    115.11  3.000
 4YQ  C4    N8   C7    111.72  3.000
 4YQ  H3    C3   C1    116.13  3.000
 4YQ  H3    C3   C2    116.56  3.000
 4YQ  C1    C3   C2     59.10  3.000
 4YQ  H3    C3   C4    115.32  3.000
 4YQ  C1    C3   C4    119.15  3.000
 4YQ  C2    C3   C4    119.08  3.000
 4YQ  H22C  C2   H21C  114.87  3.000
 4YQ  H22C  C2   C1    118.77  3.000
 4YQ  H21C  C2   C1    117.85  3.000
 4YQ  H22C  C2   C3    116.79  3.000
 4YQ  H21C  C2   C3    117.36  3.000
 4YQ  C1    C2   C3     60.48  3.000
 4YQ  H12C  C1   H11C  114.81  3.000
 4YQ  H12C  C1   C2    117.92  3.000
 4YQ  H11C  C1   C2    118.78  3.000
 4YQ  H12C  C1   C3    117.56  3.000
 4YQ  H11C  C1   C3    116.66  3.000
 4YQ  C2    C1   C3     60.42  3.000
 4YQ  H15   N15  C16   117.37  3.000
 4YQ  H15   N15  C13   119.43  3.000
 4YQ  C16   N15  C13   122.51  3.000
 4YQ  H16   C16  C21   108.60  3.000
 4YQ  H16   C16  C17   108.27  3.000
 4YQ  C21   C16  C17   109.08  3.000
 4YQ  H16   C16  N15   106.92  3.000
 4YQ  C21   C16  N15   112.94  3.000
 4YQ  C17   C16  N15   110.90  3.000
 4YQ  H17   C17  C25   109.48  3.000
 4YQ  H17   C17  C18   110.18  3.000
 4YQ  C25   C17  C18   109.18  3.000
 4YQ  H17   C17  C16   109.07  3.000
 4YQ  C25   C17  C16   107.78  3.000
 4YQ  C18   C17  C16   111.11  3.000
 4YQ  H182  C18  H181  105.70  3.000
 4YQ  H182  C18  C19   110.37  3.000
 4YQ  H181  C18  C19   109.98  3.000
 4YQ  H182  C18  C17   109.37  3.000
 4YQ  H181  C18  C17   111.78  3.000
 4YQ  C19   C18  C17   109.57  3.000
 4YQ  H21   C21  C22   109.16  3.000
 4YQ  H21   C21  C20   110.20  3.000
 4YQ  C22   C21  C20   109.50  3.000
 4YQ  H21   C21  C16   109.01  3.000
 4YQ  C22   C21  C16   108.41  3.000
 4YQ  C20   C21  C16   110.53  3.000
 4YQ  H202  C20  H201  106.18  3.000
 4YQ  H202  C20  C19   110.50  3.000
 4YQ  H201  C20  C19   109.97  3.000
 4YQ  H202  C20  C21   110.91  3.000
 4YQ  H201  C20  C21   109.51  3.000
 4YQ  C19   C20  C21   109.72  3.000
 4YQ  H222  C22  H221  106.95  3.000
 4YQ  H222  C22  C23   109.78  3.000
 4YQ  H221  C22  C23   109.82  3.000
 4YQ  H222  C22  C21   109.89  3.000
 4YQ  H221  C22  C21   110.41  3.000
 4YQ  C23   C22  C21   109.94  3.000
 4YQ  C24   C23  O26   111.40  3.000
 4YQ  C24   C23  C25   108.80  3.000
 4YQ  O26   C23  C25   111.16  3.000
 4YQ  C24   C23  C22   109.13  3.000
 4YQ  O26   C23  C22   107.23  3.000
 4YQ  C25   C23  C22   109.06  3.000
 4YQ  H252  C25  H251  107.05  3.000
 4YQ  H252  C25  C23   109.71  3.000
 4YQ  H251  C25  C23   109.68  3.000
 4YQ  H252  C25  C17   110.30  3.000
 4YQ  H251  C25  C17   109.65  3.000
 4YQ  C23   C25  C17   110.39  3.000
 4YQ  H26   O26  C23   108.13  3.000
 4YQ  H242  C24  H241  107.02  3.000
 4YQ  H242  C24  C19   110.29  3.000
 4YQ  H241  C24  C19   110.03  3.000
 4YQ  H242  C24  C23   109.69  3.000
 4YQ  H241  C24  C23   109.61  3.000
 4YQ  C19   C24  C23   110.14  3.000
 4YQ  H19   C19  C24   109.43  3.000
 4YQ  H19   C19  C20   109.70  3.000
 4YQ  C24   C19  C20   109.25  3.000
 4YQ  H19   C19  C18   109.63  3.000
 4YQ  C24   C19  C18   109.40  3.000
 4YQ  C20   C19  C18   109.41  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
 4YQ  CONST_01  N8   C7   S6   C5      0.00   0.0  0
 4YQ  CONST_02  C7   N8   C4   C5      0.00   0.0  0
 4YQ  CONST_03  N8   C4   C5   S6      0.00   0.0  0
 4YQ  CONST_04  C4   N8   C7   S6      0.00   0.0  0
 4YQ  CONST_05  C4   C5   S6   C7      0.00   0.0  0
 4YQ  CONST_06  C3   C4   C5   S6    180.00   0.0  0
 4YQ  CONST_07  C3   C4   N8   C7    180.00   0.0  0
 4YQ  CONST_08  C7   S6   C5   C13   180.00   0.0  0
 4YQ  CONST_09  N8   C4   C5   C13   180.00   0.0  0
 4YQ  CONST_10  C3   C4   C5   C13     0.00   0.0  0
 4YQ  CONST_11  O9   C7   S6   C5    180.00   0.0  0
 4YQ  CONST_12  C4   N8   C7   O9    180.00   0.0  0
 4YQ  CONST_13  C16  N15  C13  C5    180.00   0.0  0
 4YQ  CONST_14  C16  N15  C13  O14     0.00   0.0  0
 4YQ  CONST_15  H15  N15  C13  C5      0.00   0.0  0
 4YQ  Var_01    C2   C3   C4   C5   -146.13  30.0  2
 4YQ  Var_02    C1   C2   C3   C4   -108.47  30.0  1
 4YQ  Var_03    S6   C5   C13  O14   159.88  30.0  2
 4YQ  Var_04    N8   C7   O9   C10  -179.01  30.0  2
 4YQ  Var_05    C11  C10  O9   C7    176.79  30.0  3
 4YQ  Var_06    O12  C11  C10  O9     64.88  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
 4YQ  chir_02  C16  N15  C17  C21  positiv
 4YQ  chir_03  C17  C25  C18  C16  negativ
 4YQ  chir_04  C21  C22  C20  C16  positiv
 4YQ  chir_05  C23  C22  C25  C24  positiv
 4YQ  chir_06  C19  C18  C20  C24  positiv
 4YQ  chir_07  C3   C4   C2   C1   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
 4YQ  plan-1  C13  0.020
 4YQ  plan-1  C5   0.020
 4YQ  plan-1  S6   0.020
 4YQ  plan-1  C7   0.020
 4YQ  plan-1  O9   0.020
 4YQ  plan-1  C4   0.020
 4YQ  plan-1  N8   0.020
 4YQ  plan-1  C3   0.020
 4YQ  plan-2  O14  0.020
 4YQ  plan-2  C13  0.020
 4YQ  plan-2  C5   0.020
 4YQ  plan-2  N15  0.020
 4YQ  plan-2  C16  0.020
 4YQ  plan-2  H15  0.020

