# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Apr 24 09:28:22 2020
#   Inital geometry file: a 119 line input string
#   Ligand name: 1-[(1R,2R)-2-(3-acetyl-2-hydroxy-6-methoxyphenyl)cyclopropyl]-3-(5-cyanopyridin-2-yl)thiourea
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: COc1ccc(C(C)=O)c(O)c1[C@H]2C[C@H]2NC(=S)Nc3ccc(cn3)C#N
#
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
 MSD  MSD  1-[(1R,2R)-2-(3-acetyl-2-hydroxy-6-methoxyphenyl)cyclopropyl]-3-(5-cyanopyridin-2-yl)thiourea  ligand  45  27  .  2022-07-25  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_MSD
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
 MSD  C2    C  CR6   0  -0.100   1.0328   0.5722  -5.1747
 MSD  C3    C  CR16  0  -0.031  -0.2497   0.1132  -4.8821
 MSD  N4    N  N     0  -0.401  -0.7376   0.0688  -3.6576
 MSD  C5    C  CR6   0   0.554   0.0349   0.4581  -2.6549
 MSD  C6    C  CR16  0  -0.381   1.3353   0.9435  -2.8406
 MSD  C7    C  CR16  0  -0.112   1.8370   1.0060  -4.1184
 MSD  N8    N  NH1   0  -0.737  -0.4765   0.4452  -1.3721
 MSD  C9    C  C     0   0.422  -1.3740  -0.4342  -0.8139
 MSD  S10   S  S1    0  -0.368  -1.7393  -1.9231  -1.4580
 MSD  N11   N  NH1   0  -0.616  -1.8886   0.0343   0.3273
 MSD  C12   C  CH1   0  -0.054  -2.6044  -0.7434   1.2803
 MSD  C13   C  CH2   0  -0.505  -3.2080  -0.0402   2.4426
 MSD  C14   C  CH1   0  -0.257  -2.0318  -0.9495   2.6643
 MSD  C15   C  CR6   0  -0.146  -0.6997  -0.3846   3.0057
 MSD  C16   C  CR6   0   0.380  -0.5292   0.5311   4.0508
 MSD  C18   C  CR16  0  -0.399   0.7268   1.0980   4.3163
 MSD  C19   C  CR16  0  -0.283   1.8083   0.7252   3.5541
 MSD  C20   C  CR6   0  -0.191   1.7009  -0.2232   2.5328
 MSD  C21   C  CR6   0   0.376   0.4277  -0.7948   2.2895
 MSD  O22   O  OH1   0  -0.610   0.2616  -1.7378   1.3714
 MSD  C23   C  C     0   0.421   2.8502  -0.6264   1.7284
 MSD  O24   O  O     0  -0.468   2.7325  -1.4666   0.8345
 MSD  C25   C  CH3   0  -0.794   4.1891  -0.0017   1.9920
 MSD  O41   O  O2    0  -0.445  -1.6182   0.8162   4.7664
 MSD  C42   C  CSP   0   0.048   1.4938   0.6046  -6.5192
 MSD  N43   N  NS    0  -0.249   1.8629   0.6288  -7.6108
 MSD  C44   C  CH3   0  -0.442  -1.5409   1.7779   5.8042
 MSD  HC3   H  HCR6  0   0.290  -0.9063  -0.2131  -5.6808
 MSD  HC6   H  HCR6  0   0.293   1.9377   1.2557  -1.9981
 MSD  HC7   H  HCR6  0   0.298   2.8380   1.3723  -4.2994
 MSD  HN8   H  HNH1  0   0.417  -0.0283   1.0865  -0.7330
 MSD  H11N  H  HNH1  0   0.409  -1.7122   0.9993   0.5691
 MSD  H12C  H  HCH1  0   0.282  -3.1382  -1.5707   0.8349
 MSD  H131  H  HCH2  0   0.269  -4.1825  -0.3624   2.7844
 MSD  H132  H  HCH2  0   0.263  -3.0447   1.0276   2.5261
 MSD  H14C  H  HCH1  0   0.283  -2.2595  -1.9180   3.1013
 MSD  H18C  H  HCR6  0   0.285   0.8643   1.8177   5.1097
 MSD  H19C  H  HCR6  0   0.274   2.7663   1.1802   3.7682
 MSD  H22O  H  HOH1  0   0.471   1.1338  -1.8685   0.9277
 MSD  H251  H  HCH3  0   0.274   4.9277  -0.3892   1.2946
 MSD  H252  H  HCH3  0   0.272   4.1420   1.0830   1.8888
 MSD  H253  H  HCH3  0   0.273   4.5217  -0.2134   3.0092
 MSD  H441  H  HCH3  0   0.265  -2.5428   1.8599   6.2167
 MSD  H442  H  HCH3  0   0.235  -0.8577   1.4667   6.5974
 MSD  H443  H  HCH3  0   0.235  -1.2315   2.7561   5.4300

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
 MSD  C2   C3    aromatic  1.393  0.020  1.393
 MSD  C2   C7    aromatic  1.397  0.020  1.397
 MSD  C2   C42   single    1.422  0.020  1.422
 MSD  C3   N4    aromatic  1.319  0.020  1.319
 MSD  C3   HC3   single    0.930  0.020  1.080
 MSD  N4   C5    aromatic  1.324  0.020  1.324
 MSD  C5   C6    aromatic  1.400  0.020  1.400
 MSD  C5   N8    single    1.381  0.020  1.381
 MSD  C6   C7    aromatic  1.374  0.020  1.374
 MSD  C6   HC6   single    0.930  0.020  1.080
 MSD  C7   HC7   single    0.930  0.020  1.080
 MSD  N8   C9    single    1.375  0.020  1.375
 MSD  N8   HN8   single    0.860  0.020  1.020
 MSD  C9   S10   double    1.663  0.020  1.663
 MSD  C9   N11   single    1.337  0.020  1.337
 MSD  N11  C12   single    1.423  0.020  1.423
 MSD  N11  H11N  single    0.860  0.020  1.020
 MSD  C12  C13   single    1.487  0.020  1.487
 MSD  C12  C14   single    1.512  0.020  1.512
 MSD  C12  H12C  single    0.970  0.020  1.090
 MSD  C13  C14   single    1.503  0.020  1.503
 MSD  C13  H131  single    0.970  0.020  1.090
 MSD  C13  H132  single    0.970  0.020  1.090
 MSD  C14  C15   single    1.487  0.020  1.487
 MSD  C14  H14C  single    0.970  0.020  1.090
 MSD  C15  C16   aromatic  1.400  0.020  1.400
 MSD  C15  C21   aromatic  1.397  0.020  1.397
 MSD  C16  C18   aromatic  1.403  0.020  1.403
 MSD  C16  O41   single    1.334  0.020  1.334
 MSD  C18  C19   aromatic  1.375  0.020  1.375
 MSD  C18  H18C  single    0.930  0.020  1.080
 MSD  C19  C20   aromatic  1.398  0.020  1.398
 MSD  C19  H19C  single    0.930  0.020  1.080
 MSD  C20  C21   aromatic  1.417  0.020  1.417
 MSD  C20  C23   single    1.460  0.020  1.460
 MSD  C21  O22   single    1.327  0.020  1.327
 MSD  O22  H22O  single    0.850  0.020  0.980
 MSD  C23  O24   double    1.232  0.020  1.232
 MSD  C23  C25   single    1.501  0.020  1.501
 MSD  C25  H251  single    0.970  0.020  1.090
 MSD  C25  H252  single    0.970  0.020  1.090
 MSD  C25  H253  single    0.970  0.020  1.090
 MSD  O41  C44   single    1.417  0.020  1.417
 MSD  C42  N43   triple    1.153  0.020  1.153
 MSD  C44  H441  single    0.970  0.020  1.090
 MSD  C44  H442  single    0.970  0.020  1.090
 MSD  C44  H443  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
 MSD  C42   C2   C7    121.43  3.000
 MSD  C42   C2   C3    120.31  3.000
 MSD  C7    C2   C3    118.26  3.000
 MSD  HC3   C3   N4    116.73  3.000
 MSD  HC3   C3   C2    120.12  3.000
 MSD  N4    C3   C2    123.14  3.000
 MSD  C5    N4   C3    118.51  3.000
 MSD  N8    C5   C6    118.05  3.000
 MSD  N8    C5   N4    118.99  3.000
 MSD  C6    C5   N4    122.89  3.000
 MSD  HC6   C6   C7    120.51  3.000
 MSD  HC6   C6   C5    120.92  3.000
 MSD  C7    C6   C5    118.56  3.000
 MSD  HC7   C7   C6    120.61  3.000
 MSD  HC7   C7   C2    120.77  3.000
 MSD  C6    C7   C2    118.62  3.000
 MSD  HN8   N8   C9    116.03  3.000
 MSD  HN8   N8   C5    114.67  3.000
 MSD  C9    N8   C5    128.66  3.000
 MSD  N11   C9   S10   124.05  3.000
 MSD  N11   C9   N8    111.95  3.000
 MSD  S10   C9   N8    123.97  3.000
 MSD  H11N  N11  C12   116.71  3.000
 MSD  H11N  N11  C9    118.15  3.000
 MSD  C12   N11  C9    125.02  3.000
 MSD  H12C  C12  C14   117.39  3.000
 MSD  H12C  C12  C13   118.94  3.000
 MSD  C14   C12  C13    60.17  3.000
 MSD  H12C  C12  N11   113.00  3.000
 MSD  C14   C12  N11   119.80  3.000
 MSD  C13   C12  N11   117.99  3.000
 MSD  H132  C13  H131  113.89  3.000
 MSD  H132  C13  C14   117.83  3.000
 MSD  H131  C13  C14   118.56  3.000
 MSD  H132  C13  C12   117.73  3.000
 MSD  H131  C13  C12   118.16  3.000
 MSD  C14   C13  C12    60.75  3.000
 MSD  H14C  C14  C15   115.73  3.000
 MSD  H14C  C14  C13   115.75  3.000
 MSD  C15   C14  C13   120.34  3.000
 MSD  H14C  C14  C12   114.22  3.000
 MSD  C15   C14  C12   119.85  3.000
 MSD  C13   C14  C12    59.08  3.000
 MSD  C21   C15  C16   118.45  3.000
 MSD  C21   C15  C14   119.58  3.000
 MSD  C16   C15  C14   121.95  3.000
 MSD  O41   C16  C18   122.88  3.000
 MSD  O41   C16  C15   116.16  3.000
 MSD  C18   C16  C15   120.96  3.000
 MSD  H18C  C18  C19   119.21  3.000
 MSD  H18C  C18  C16   121.47  3.000
 MSD  C19   C18  C16   119.32  3.000
 MSD  H19C  C19  C20   119.86  3.000
 MSD  H19C  C19  C18   118.22  3.000
 MSD  C20   C19  C18   121.91  3.000
 MSD  C23   C20  C21   120.11  3.000
 MSD  C23   C20  C19   121.97  3.000
 MSD  C21   C20  C19   117.92  3.000
 MSD  O22   C21  C20   121.21  3.000
 MSD  O22   C21  C15   117.54  3.000
 MSD  C20   C21  C15   121.24  3.000
 MSD  H22O  O22  C21   107.13  3.000
 MSD  C25   C23  O24   119.76  3.000
 MSD  C25   C23  C20   119.39  3.000
 MSD  O24   C23  C20   120.85  3.000
 MSD  H253  C25  H252  107.12  3.000
 MSD  H253  C25  H251  108.77  3.000
 MSD  H252  C25  H251  108.85  3.000
 MSD  H253  C25  C23   110.79  3.000
 MSD  H252  C25  C23   111.03  3.000
 MSD  H251  C25  C23   110.19  3.000
 MSD  C44   O41  C16   119.57  3.000
 MSD  N43   C42  C2    180.00  3.000
 MSD  H443  C44  H442  109.08  3.000
 MSD  H443  C44  H441  108.89  3.000
 MSD  H442  C44  H441  108.82  3.000
 MSD  H443  C44  O41   111.87  3.000
 MSD  H442  C44  O41   111.88  3.000
 MSD  H441  C44  O41   106.20  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
 MSD  CONST_01  C5    N4   C3   C2      0.00   0.0  0
 MSD  CONST_02  C5    C6   C7   C2      0.00   0.0  0
 MSD  CONST_03  C6    C7   C2   C3      0.00   0.0  0
 MSD  CONST_04  C6    C5   N4   C3      0.00   0.0  0
 MSD  CONST_05  C7    C2   C3   N4      0.00   0.0  0
 MSD  CONST_06  C7    C6   C5   N4      0.00   0.0  0
 MSD  CONST_07  C19   C18  C16  C15     0.00   0.0  0
 MSD  CONST_08  C19   C20  C21  C15     0.00   0.0  0
 MSD  CONST_09  C20   C21  C15  C16     0.00   0.0  0
 MSD  CONST_10  C20   C19  C18  C16     0.00   0.0  0
 MSD  CONST_11  C21   C15  C16  C18     0.00   0.0  0
 MSD  CONST_12  C21   C20  C19  C18     0.00   0.0  0
 MSD  CONST_13  C18   C16  C15  C14   180.00   0.0  0
 MSD  CONST_14  C20   C21  C15  C14   180.00   0.0  0
 MSD  CONST_15  N8    C5   N4   C3    180.00   0.0  0
 MSD  CONST_16  C42   C2   C3   N4    180.00   0.0  0
 MSD  CONST_17  C42   C2   C7   C6    180.00   0.0  0
 MSD  CONST_18  N8    C5   C6   C7    180.00   0.0  0
 MSD  CONST_19  O41   C16  C15  C14     0.00   0.0  0
 MSD  CONST_20  O22   C21  C15  C14     0.00   0.0  0
 MSD  CONST_21  C23   C20  C21  C15   180.00   0.0  0
 MSD  CONST_22  O22   C21  C15  C16   180.00   0.0  0
 MSD  CONST_23  C23   C20  C19  C18   180.00   0.0  0
 MSD  CONST_24  O41   C16  C18  C19   180.00   0.0  0
 MSD  CONST_25  O22   C21  C20  C19   180.00   0.0  0
 MSD  CONST_26  O41   C16  C15  C21   180.00   0.0  0
 MSD  CONST_27  HC6   C6   C7   C2    180.00   0.0  0
 MSD  CONST_28  HC7   C7   C2   C3    180.00   0.0  0
 MSD  CONST_29  HC3   C3   N4   C5    180.00   0.0  0
 MSD  CONST_30  H18C  C18  C16  C15   180.00   0.0  0
 MSD  CONST_31  H19C  C19  C18  C16   180.00   0.0  0
 MSD  CONST_37  C12   N11  C9   N8    180.00   0.0  0
 MSD  CONST_38  C12   N11  C9   S10     0.00   0.0  0
 MSD  CONST_39  H11N  N11  C9   N8      0.00   0.0  0
 MSD  Var_01    C15   C14  C13  C12   108.77  30.0  1
 MSD  Var_02    C16   C15  C14  C12   120.81  30.0  2
 MSD  Var_03    C14   C13  C12  N11  -110.12  30.0  1
 MSD  Var_04    C13   C12  N11  C9   -174.96  30.0  3
 MSD  Var_05    O24   C23  C20  C19   179.86  30.0  2
 MSD  Var_06    H441  C44  O41  C16   178.36  30.0  3
 MSD  Var_07    H251  C25  C23  C20  -178.54  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
 MSD  chir_01  C12  N11  C13  C14  both
 MSD  chir_02  C14  C12  C13  C15  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
 MSD  plan-1  C2    0.020
 MSD  plan-1  C3    0.020
 MSD  plan-1  N4    0.020
 MSD  plan-1  C5    0.020
 MSD  plan-1  C6    0.020
 MSD  plan-1  C7    0.020
 MSD  plan-1  N8    0.020
 MSD  plan-1  C42   0.020
 MSD  plan-1  N43   0.020
 MSD  plan-1  HC3   0.020
 MSD  plan-1  HC6   0.020
 MSD  plan-1  HC7   0.020
 MSD  plan-2  C14   0.020
 MSD  plan-2  C15   0.020
 MSD  plan-2  C16   0.020
 MSD  plan-2  C18   0.020
 MSD  plan-2  C19   0.020
 MSD  plan-2  C20   0.020
 MSD  plan-2  C21   0.020
 MSD  plan-2  O22   0.020
 MSD  plan-2  C23   0.020
 MSD  plan-2  O41   0.020
 MSD  plan-2  H18C  0.020
 MSD  plan-2  H19C  0.020
 MSD  plan-3  C5    0.020
 MSD  plan-3  N8    0.020
 MSD  plan-3  C9    0.020
 MSD  plan-3  S10   0.020
 MSD  plan-3  N11   0.020
 MSD  plan-3  C12   0.020
 MSD  plan-3  HN8   0.020
 MSD  plan-3  H11N  0.020
 MSD  plan-4  C20   0.020
 MSD  plan-4  C23   0.020
 MSD  plan-4  O24   0.020
 MSD  plan-4  C25   0.020

