# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Apr  4 22:02:10 2020
#   Inital geometry file: a 113 line input string
#   Ligand name: (2Z,6S)-6-{3-chloro-5-[5-(prop-1-yn-1-yl)pyridin-3-yl]thiophen-2-yl}-2-imino-3,6-dimethyltetrahydropyrimidin-4(1H)-one
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC#Cc1cncc(c1)c2sc(c(Cl)c2)[C@]3(C)CC(=O)N(C)C(=N)N3
#
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
 0V6  0V6  (2Z,6S)-6-{3-chloro-5-[5-(prop-1-yn-1-yl)pyridin-3-yl]thiophen-2-yl}-2-imino-3,6-dimethyltetrahydropyrimidin-4(1H)-one  ligand  42  25  .  2022-07-22  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_0V6
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
 0V6  C2   C   CR5   0  -0.081   1.4049   0.6253  -0.4983
 0V6  S1   S   S2    0   0.260   0.3438  -0.6423  -0.9786
 0V6  C3   C   CR5   0   0.004   0.7127   1.5271   0.2565
 0V6  C4   C   CR15  0  -0.168  -0.6488   1.2015   0.4701
 0V6  C5   C   CR5   0  -0.224  -1.0022   0.0365  -0.1445
 0V6  C6   C   CH2   0  -0.586   3.3300  -0.7290  -1.3730
 0V6  C7   C   C     0   0.560   3.3800  -1.6742  -0.2024
 0V6  N8   N   NT    0  -0.523   3.5921  -1.1046   1.0267
 0V6  C9   C   C     0   0.626   3.9203   0.2470   1.2057
 0V6  N10  N   NH1   0  -0.649   3.7462   1.0437   0.1104
 0V6  C11  C   CT    0  -0.025   2.8540   0.6567  -0.9610
 0V6  C12  C   CH3   0  -0.629   2.9986   1.6405  -2.1175
 0V6  CL   CL  CL    0  -0.117   1.3845   2.9715   0.9135
 0V6  C14  C   CR6   0   0.060  -2.3058  -0.6183  -0.1506
 0V6  C15  C   CR16  0  -0.247  -3.4741   0.1135   0.0382
 0V6  C16  C   CR6   0  -0.157  -4.7019  -0.5418   0.0391
 0V6  C17  C   CR16  0  -0.094  -4.7024  -1.9245  -0.1717
 0V6  N18  N   N     0  -0.384  -3.5971  -2.6265  -0.3544
 0V6  C19  C   CR16  0  -0.102  -2.4332  -1.9958  -0.3367
 0V6  O21  O   O     0  -0.452   3.2501  -2.8736  -0.3435
 0V6  C22  C   CH3   0  -0.519   3.6390  -1.9599   2.2029
 0V6  C23  C   CSP   0   0.204  -5.9221   0.1643   0.2348
 0V6  C24  C   CSP   0  -0.040  -6.9587   0.7554   0.4033
 0V6  C25  C   CH3   0  -0.823  -8.2047   1.4712   0.6112
 0V6  H1   H   HCR5  0   0.290  -1.3177   1.8016   1.0701
 0V6  H2   H   HCH2  0   0.319   4.3425  -0.6360  -1.7776
 0V6  H3   H   HCH2  0   0.294   2.7235  -1.1716  -2.1641
 0V6  H4   H   HNH1  0   0.397   3.8748   2.0303   0.2713
 0V6  H5   H   HCH3  0   0.248   2.6917   2.6438  -1.8219
 0V6  H6   H   HCH3  0   0.254   4.0351   1.6783  -2.4537
 0V6  H7   H   HCH3  0   0.251   2.3744   1.3298  -2.9543
 0V6  H11  H   HCR6  0   0.276  -3.4379   1.1872   0.1708
 0V6  H12  H   HCR6  0   0.272  -5.6403  -2.4678  -0.1922
 0V6  H13  H   HCR6  0   0.268  -1.5522  -2.6169  -0.4665
 0V6  H14  H   H     0   0.335   4.5297   1.6140   2.3599
 0V6  H15  H   HCH3  0   0.247   4.6652  -2.1942   2.4832
 0V6  H16  H   HCH3  0   0.254   3.1584  -1.4575   3.0363
 0V6  H17  H   HCH3  0   0.257   3.1116  -2.8832   1.9916
 0V6  H18  H   HCH3  0   0.273  -9.0574   0.7950   0.5535
 0V6  H19  H   HCH3  0   0.273  -8.2197   1.9499   1.5907
 0V6  H20  H   HCH3  0   0.273  -8.3395   2.2476  -0.1422
 0V6  N20  N   N     0  -0.674   4.3736   0.6129   2.3369

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
 0V6  C2   S1   aromatic  1.721  0.020  1.721
 0V6  C2   C11  single    1.521  0.020  1.521
 0V6  C3   C2   aromatic  1.365  0.020  1.365
 0V6  C4   C3   aromatic  1.416  0.020  1.416
 0V6  C4   C5   aromatic  1.364  0.020  1.364
 0V6  C4   H1   single    0.930  0.020  1.080
 0V6  C5   S1   aromatic  1.723  0.020  1.723
 0V6  C6   C7   single    1.505  0.020  1.505
 0V6  C6   H2   single    0.970  0.020  1.090
 0V6  C6   H3   single    0.970  0.020  1.090
 0V6  C7   O21  double    1.215  0.020  1.215
 0V6  C7   N8   single    1.371  0.020  1.371
 0V6  N8   C22  single    1.455  0.020  1.455
 0V6  C9   N8   single    1.402  0.020  1.402
 0V6  C9   N20  double    1.272  0.020  1.272
 0V6  N10  C9   single    1.366  0.020  1.366
 0V6  N10  H4   single    0.890  0.020  1.040
 0V6  C11  C6   single    1.522  0.020  1.522
 0V6  C11  N10  single    1.447  0.020  1.447
 0V6  C12  C11  single    1.525  0.020  1.525
 0V6  C12  H5   single    0.970  0.020  1.090
 0V6  C12  H6   single    0.970  0.020  1.090
 0V6  C12  H7   single    0.970  0.020  1.090
 0V6  CL   C3   single    1.723  0.020  1.723
 0V6  C14  C5   single    1.459  0.020  1.459
 0V6  C14  C15  aromatic  1.391  0.020  1.391
 0V6  C15  C16  aromatic  1.392  0.020  1.392
 0V6  C15  H11  single    0.930  0.020  1.080
 0V6  C16  C23  single    1.423  0.020  1.423
 0V6  C17  C16  aromatic  1.399  0.020  1.399
 0V6  C17  H12  single    0.930  0.020  1.080
 0V6  N18  C19  aromatic  1.324  0.020  1.324
 0V6  N18  C17  aromatic  1.322  0.020  1.322
 0V6  C19  C14  aromatic  1.396  0.020  1.396
 0V6  C19  H13  single    0.930  0.020  1.080
 0V6  N20  H14  single    0.890  0.020  1.040
 0V6  C22  H15  single    0.970  0.020  1.090
 0V6  C22  H16  single    0.970  0.020  1.090
 0V6  C22  H17  single    0.970  0.020  1.090
 0V6  C23  C24  triple    1.205  0.020  1.205
 0V6  C24  C25  single    1.452  0.020  1.452
 0V6  C25  H18  single    0.970  0.020  1.090
 0V6  C25  H19  single    0.970  0.020  1.090
 0V6  C25  H20  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
 0V6  C11  C2   C3   129.62  3.000
 0V6  C3   C2   S1   109.16  3.000
 0V6  C11  C2   S1   121.16  3.000
 0V6  C5   S1   C2    93.23  3.000
 0V6  CL   C3   C4   120.67  3.000
 0V6  CL   C3   C2   124.55  3.000
 0V6  C4   C3   C2   114.78  3.000
 0V6  H1   C4   C5   124.35  3.000
 0V6  H1   C4   C3   123.45  3.000
 0V6  C5   C4   C3   112.18  3.000
 0V6  C14  C5   C4   128.09  3.000
 0V6  C14  C5   S1   121.28  3.000
 0V6  C4   C5   S1   110.63  3.000
 0V6  H3   C6   H2   106.31  3.000
 0V6  H3   C6   C11  113.07  3.000
 0V6  H2   C6   C11  108.19  3.000
 0V6  C11  C6   C7   111.81  3.000
 0V6  H3   C6   C7   109.13  3.000
 0V6  H2   C6   C7   108.07  3.000
 0V6  O21  C7   N8   122.06  3.000
 0V6  N8   C7   C6   116.19  3.000
 0V6  O21  C7   C6   121.74  3.000
 0V6  C22  N8   C9   117.12  3.000
 0V6  C9   N8   C7   123.43  3.000
 0V6  C22  N8   C7   119.04  3.000
 0V6  N20  C9   N10  126.21  3.000
 0V6  N10  C9   N8   115.48  3.000
 0V6  N20  C9   N8   118.29  3.000
 0V6  H4   N10  C11  117.30  3.000
 0V6  C11  N10  C9   121.09  3.000
 0V6  H4   N10  C9   115.27  3.000
 0V6  C12  C11  N10  109.29  3.000
 0V6  C12  C11  C6   110.63  3.000
 0V6  N10  C11  C6   104.54  3.000
 0V6  C12  C11  C2   109.53  3.000
 0V6  N10  C11  C2   111.57  3.000
 0V6  C6   C11  C2   111.19  3.000
 0V6  H7   C12  H6   108.53  3.000
 0V6  H7   C12  H5   108.02  3.000
 0V6  H6   C12  H5   108.62  3.000
 0V6  H7   C12  C11  110.14  3.000
 0V6  H6   C12  C11  110.27  3.000
 0V6  H5   C12  C11  111.18  3.000
 0V6  C19  C14  C15  117.42  3.000
 0V6  C19  C14  C5   121.67  3.000
 0V6  C15  C14  C5   120.91  3.000
 0V6  H11  C15  C16  119.77  3.000
 0V6  H11  C15  C14  120.68  3.000
 0V6  C16  C15  C14  119.55  3.000
 0V6  C23  C16  C17  120.72  3.000
 0V6  C17  C16  C15  117.76  3.000
 0V6  C23  C16  C15  121.52  3.000
 0V6  H12  C17  N18  117.03  3.000
 0V6  N18  C17  C16  123.06  3.000
 0V6  H12  C17  C16  119.91  3.000
 0V6  C19  N18  C17  118.69  3.000
 0V6  H13  C19  N18  116.05  3.000
 0V6  H13  C19  C14  120.43  3.000
 0V6  N18  C19  C14  123.51  3.000
 0V6  H17  C22  H16  109.18  3.000
 0V6  H17  C22  H15  108.98  3.000
 0V6  H16  C22  H15  108.61  3.000
 0V6  H17  C22  N8   109.11  3.000
 0V6  H16  C22  N8   109.53  3.000
 0V6  H15  C22  N8   111.39  3.000
 0V6  C24  C23  C16  180.00  3.000
 0V6  C25  C24  C23  180.00  3.000
 0V6  H20  C25  H19  107.84  3.000
 0V6  H20  C25  H18  107.98  3.000
 0V6  H19  C25  H18  108.01  3.000
 0V6  H20  C25  C24  110.99  3.000
 0V6  H19  C25  C24  110.91  3.000
 0V6  H18  C25  C24  110.97  3.000
 0V6  H14  N20  C9   111.05  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
 0V6  CONST_01  C4   C5   S1   C2      0.00   0.0  0
 0V6  CONST_02  C14  C5   S1   C2    180.00   0.0  0
 0V6  CONST_03  C5   C4   C3   C2      0.00   0.0  0
 0V6  CONST_04  C4   C3   C2   S1      0.00   0.0  0
 0V6  CONST_05  C3   C4   C5   S1      0.00   0.0  0
 0V6  CONST_08  C5   S1   C2   C3      0.00   0.0  0
 0V6  CONST_09  C14  C5   C4   C3    180.00   0.0  0
 0V6  CONST_12  C16  C15  C14  C5    180.00   0.0  0
 0V6  CONST_13  N18  C19  C14  C5    180.00   0.0  0
 0V6  CONST_14  C17  C16  C15  C14     0.00   0.0  0
 0V6  CONST_15  C17  N18  C19  C14     0.00   0.0  0
 0V6  CONST_16  N18  C19  C14  C15     0.00   0.0  0
 0V6  CONST_17  N18  C17  C16  C15     0.00   0.0  0
 0V6  CONST_18  C19  C14  C15  C16     0.00   0.0  0
 0V6  CONST_19  C19  N18  C17  C16     0.00   0.0  0
 0V6  CONST_20  C11  C2   C3   C4    180.00   0.0  0
 0V6  CONST_21  C11  C2   S1   C5    180.00   0.0  0
 0V6  CONST_22  C9   N8   C7   C6      0.00   0.0  0
 0V6  CONST_23  N10  C9   N8   C7      0.00   0.0  0
 0V6  CONST_25  CL   C3   C2   S1    180.00   0.0  0
 0V6  CONST_26  CL   C3   C4   C5    180.00   0.0  0
 0V6  CONST_27  CL   C3   C2   C11     0.00   0.0  0
 0V6  CONST_28  C23  C16  C15  C14   180.00   0.0  0
 0V6  CONST_29  C23  C16  C17  N18   180.00   0.0  0
 0V6  CONST_30  C22  N8   C7   C6    180.00   0.0  0
 0V6  CONST_31  N20  C9   N8   C7    180.00   0.0  0
 0V6  CONST_32  O21  C7   N8   C9    180.00   0.0  0
 0V6  CONST_33  C22  N8   C9   N10   180.00   0.0  0
 0V6  CONST_35  H1   C4   C3   C2    180.00   0.0  0
 0V6  CONST_36  H11  C15  C14  C5      0.00   0.0  0
 0V6  CONST_37  H13  C19  C14  C5      0.00   0.0  0
 0V6  CONST_38  H12  C17  C16  C15   180.00   0.0  0
 0V6  CONST_39  H4   N10  C9   N8    180.00   0.0  0
 0V6  CONST_40  C22  N8   C9   N20     0.00   0.0  0
 0V6  CONST_41  C22  N8   C7   O21     0.00   0.0  0
 0V6  CONST_42  H14  N20  C9   N8    180.00   0.0  0
 0V6  Var_01    H2   C6   C7   N8     91.08  30.0  1
 0V6  Var_02    H15  C22  N8   C7     97.76  30.0  3
 0V6  Var_03    H18  C25  C24  C23  -140.11  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
 0V6  chir_01  C11  C6  N10  C2  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
 0V6  plan-1  C2   0.020
 0V6  plan-1  S1   0.020
 0V6  plan-1  C3   0.020
 0V6  plan-1  C4   0.020
 0V6  plan-1  C5   0.020
 0V6  plan-1  C11  0.020
 0V6  plan-1  CL   0.020
 0V6  plan-1  C14  0.020
 0V6  plan-1  H1   0.020
 0V6  plan-2  C5   0.020
 0V6  plan-2  C14  0.020
 0V6  plan-2  C15  0.020
 0V6  plan-2  C16  0.020
 0V6  plan-2  C17  0.020
 0V6  plan-2  N18  0.020
 0V6  plan-2  C19  0.020
 0V6  plan-2  C23  0.020
 0V6  plan-2  C24  0.020
 0V6  plan-2  H11  0.020
 0V6  plan-2  H12  0.020
 0V6  plan-2  H13  0.020
 0V6  plan-3  C6   0.020
 0V6  plan-3  C7   0.020
 0V6  plan-3  N8   0.020
 0V6  plan-3  C9   0.020
 0V6  plan-3  N10  0.020
 0V6  plan-3  C11  0.020
 0V6  plan-3  O21  0.020
 0V6  plan-3  C22  0.020
 0V6  plan-3  H4   0.020
 0V6  plan-3  H14  0.020
 0V6  plan-3  N20  0.020

