# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Jul 21 05:31:16 2021
#   Inital geometry file: a 90 line input string
#   Ligand name: 4-(2-{[methyl(prop-2-yn-1-yl)amino]methyl}-1,3-thiazol-4-yl)piperidin-4-ol
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CN(CC#C)Cc1scc(n1)C2(O)CCNCC2
#
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
 D8V  D8V  4-(2-{[methyl(prop-2-yn-1-yl)amino]methyl}-1,3-thiazol-4-yl)piperidin-4-ol  ligand  37  18  .  2022-03-18  2022-07-24
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_D8V
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
 D8V  C4   C  CH2   0  -0.350   0.6507  11.8467   9.6481
 D8V  C5   C  CR5   0   0.052   1.3087  10.5564  10.0117
 D8V  C6   C  CR5   0   0.382   1.7104   8.3960  10.1815
 D8V  N1   N  N     0  -0.394   0.8283   9.3779   9.8054
 D8V  C7   C  CR15  0  -0.592   2.8833   8.8594  10.6884
 D8V  C8   C  CT    0   0.127   1.2924   6.9544  10.0145
 D8V  N2   N  NH1   0  -0.600   1.8082   4.3767   8.7784
 D8V  C9   C  CH2   0  -0.431   1.0144   6.6650   8.5357
 D8V  C10  C  CH2   0  -0.294   0.7111   5.1936   8.2906
 D8V  C11  C  CH2   0  -0.287   2.0024   4.5417  10.2076
 D8V  C12  C  CH2   0  -0.462   2.3695   5.9861  10.5131
 D8V  O    O  OH1   0  -0.669   0.0709   6.7430  10.7008
 D8V  S    S  S2    0   0.227   2.8941  10.5761  10.6999
 D8V  N    N  NT    0  -0.427   1.1037  12.9045  10.5255
 D8V  C    C  CH3   0  -0.532   0.4456  12.8505  11.8179
 D8V  C1   C  CH2   0  -0.413   0.9744  14.2253   9.9334
 D8V  C2   C  CSP   0   0.275   1.8597  14.4040   8.7857
 D8V  C3   C  CSP1  0  -0.539   2.5824  14.5610   7.8384
 D8V  H1   H  HCH2  0   0.282   0.9347  12.0872   8.6192
 D8V  H2   H  HCH2  0   0.248  -0.4404  11.7109   9.6514
 D8V  H3   H  HCR5  0   0.298   3.7232   8.2969  11.0634
 D8V  H4   H  HNH1  0   0.351   1.6225   3.4039   8.5727
 D8V  H6   H  HCH2  0   0.230   1.8950   6.9516   7.9552
 D8V  H7   H  HCH2  0   0.239   0.1857   7.2852   8.1872
 D8V  H8   H  HCH2  0   0.194  -0.2516   4.9335   8.7552
 D8V  H9   H  HCH2  0   0.231   0.5969   5.0269   7.2173
 D8V  H10  H  HCH2  0   0.191   1.1161   4.2571  10.7953
 D8V  H11  H  HCH2  0   0.233   2.8156   3.8890  10.5314
 D8V  H12  H  HCH2  0   0.230   3.3201   6.2182  10.0263
 D8V  H13  H  HCH2  0   0.239   2.5227   6.1112  11.5899
 D8V  H14  H  HOH1  0   0.444   0.2372   6.8160  11.6470
 D8V  H16  H  HCH3  0   0.245   0.8836  13.5889  12.4897
 D8V  H17  H  HCH3  0   0.212  -0.6352  13.0402  11.7566
 D8V  H18  H  HCH3  0   0.245   0.5896  11.8692  12.2692
 D8V  H19  H  HCH2  0   0.282   1.2373  14.9658  10.6928
 D8V  H20  H  HCH2  0   0.250  -0.0584  14.4547   9.6286
 D8V  H21  H  H     0   0.281   3.2272  14.7001   7.0010

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
 D8V  C9   C10  single    1.522  0.020  1.522
 D8V  C9   C8   single    1.532  0.020  1.532
 D8V  S    C7   aromatic  1.717  0.020  1.717
 D8V  S    C5   aromatic  1.728  0.020  1.728
 D8V  C10  N2   single    1.452  0.020  1.452
 D8V  C7   C6   aromatic  1.359  0.020  1.359
 D8V  N2   C11  single    1.452  0.020  1.452
 D8V  C5   C4   single    1.493  0.020  1.493
 D8V  C5   N1   aromatic  1.289  0.020  1.289
 D8V  C4   N    single    1.447  0.020  1.447
 D8V  C6   N1   aromatic  1.373  0.020  1.373
 D8V  C6   C8   single    1.510  0.020  1.510
 D8V  C8   C12  single    1.532  0.020  1.532
 D8V  C8   O    single    1.417  0.020  1.417
 D8V  C1   C2   single    1.461  0.020  1.461
 D8V  C1   N    single    1.453  0.020  1.453
 D8V  C12  C11  single    1.521  0.020  1.521
 D8V  C2   C3   triple    1.202  0.020  1.202
 D8V  N    C    single    1.451  0.020  1.451
 D8V  C4   H1   single    0.939  0.020  1.096
 D8V  C4   H2   single    0.939  0.020  1.096
 D8V  C7   H3   single    0.929  0.020  1.085
 D8V  N2   H4   single    0.868  0.020  1.013
 D8V  C9   H6   single    0.939  0.020  1.096
 D8V  C9   H7   single    0.939  0.020  1.096
 D8V  C10  H8   single    0.939  0.020  1.096
 D8V  C10  H9   single    0.939  0.020  1.096
 D8V  C11  H10  single    0.939  0.020  1.096
 D8V  C11  H11  single    0.939  0.020  1.096
 D8V  C12  H12  single    0.939  0.020  1.096
 D8V  C12  H13  single    0.939  0.020  1.096
 D8V  O    H14  single    0.832  0.020  0.971
 D8V  C    H16  single    0.939  0.020  1.096
 D8V  C    H17  single    0.939  0.020  1.096
 D8V  C    H18  single    0.939  0.020  1.096
 D8V  C1   H19  single    0.939  0.020  1.096
 D8V  C1   H20  single    0.939  0.020  1.096
 D8V  C3   H21  single    0.913  0.020  1.066

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
 D8V  H2   C4   H1   106.71  3.000
 D8V  H2   C4   N    113.52  3.000
 D8V  H1   C4   N    109.16  3.000
 D8V  H2   C4   C5   109.26  3.000
 D8V  H1   C4   C5   107.73  3.000
 D8V  N    C4   C5   110.25  3.000
 D8V  S    C5   N1   114.58  3.000
 D8V  N1   C5   C4   125.92  3.000
 D8V  S    C5   C4   119.42  3.000
 D8V  C8   C6   C7   127.27  3.000
 D8V  C8   C6   N1   118.34  3.000
 D8V  C7   C6   N1   114.39  3.000
 D8V  C6   N1   C5   111.75  3.000
 D8V  H3   C7   S    120.96  3.000
 D8V  H3   C7   C6   128.61  3.000
 D8V  S    C7   C6   110.42  3.000
 D8V  O    C8   C12  110.74  3.000
 D8V  O    C8   C9   106.43  3.000
 D8V  C12  C8   C9   108.80  3.000
 D8V  O    C8   C6   109.12  3.000
 D8V  C12  C8   C6   111.89  3.000
 D8V  C9   C8   C6   109.71  3.000
 D8V  H4   N2   C11  109.52  3.000
 D8V  H4   N2   C10  109.51  3.000
 D8V  C11  N2   C10  111.58  3.000
 D8V  H7   C9   H6   107.03  3.000
 D8V  H7   C9   C10  110.26  3.000
 D8V  H6   C9   C10  109.17  3.000
 D8V  H7   C9   C8   109.78  3.000
 D8V  H6   C9   C8   108.48  3.000
 D8V  C10  C9   C8   111.97  3.000
 D8V  H9   C10  H8   106.70  3.000
 D8V  H9   C10  C9   109.06  3.000
 D8V  H8   C10  C9   109.56  3.000
 D8V  H9   C10  N2   108.87  3.000
 D8V  H8   C10  N2   112.72  3.000
 D8V  C9   C10  N2   109.82  3.000
 D8V  H11  C11  H10  106.66  3.000
 D8V  H11  C11  C12  109.17  3.000
 D8V  H10  C11  C12  109.42  3.000
 D8V  H11  C11  N2   108.88  3.000
 D8V  H10  C11  N2   112.86  3.000
 D8V  C12  C11  N2   109.75  3.000
 D8V  H13  C12  H12  106.98  3.000
 D8V  H13  C12  C11  109.87  3.000
 D8V  H12  C12  C11  108.79  3.000
 D8V  H13  C12  C8   110.26  3.000
 D8V  H12  C12  C8   109.41  3.000
 D8V  C11  C12  C8   111.42  3.000
 D8V  H14  O    C8   108.40  3.000
 D8V  C7   S    C5    88.87  3.000
 D8V  C1   N    C    110.87  3.000
 D8V  C    N    C4   111.76  3.000
 D8V  C1   N    C4   112.92  3.000
 D8V  H18  C    H17  107.97  3.000
 D8V  H18  C    H16  107.55  3.000
 D8V  H17  C    H16  108.21  3.000
 D8V  H18  C    N    110.03  3.000
 D8V  H17  C    N    112.95  3.000
 D8V  H16  C    N    109.96  3.000
 D8V  H20  C1   H19  106.07  3.000
 D8V  H20  C1   C2   109.00  3.000
 D8V  H19  C1   C2   108.50  3.000
 D8V  H20  C1   N    112.69  3.000
 D8V  H19  C1   N    108.14  3.000
 D8V  C2   C1   N    112.18  3.000
 D8V  C3   C2   C1   180.00  3.000
 D8V  H21  C3   C2   180.00  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
 D8V  CONST_01  C6   C7   S    C5     0.00   0.0  0
 D8V  CONST_02  C7   C6   N1   C5     0.00   0.0  0
 D8V  CONST_03  S    C5   N1   C6     0.00   0.0  0
 D8V  CONST_04  C7   S    C5   N1     0.00   0.0  0
 D8V  CONST_05  S    C7   C6   N1     0.00   0.0  0
 D8V  CONST_06  C8   C6   N1   C5   180.00   0.0  0
 D8V  CONST_07  S    C7   C6   C8   180.00   0.0  0
 D8V  CONST_08  C7   S    C5   C4   180.00   0.0  0
 D8V  CONST_09  C6   N1   C5   C4   180.00   0.0  0
 D8V  CONST_10  H3   C7   S    C5   180.00   0.0  0
 D8V  Var_01    N2   C10  C9   C8   -56.47  30.0  1
 D8V  Var_02    N2   C11  C12  C8    57.87  30.0  1
 D8V  Var_03    C11  N2   C10  C9    61.32  30.0  1
 D8V  Var_04    C12  C11  N2   C10  -62.17  30.0  1
 D8V  Var_05    N    C4   C5   N1   153.31  30.0  2
 D8V  Var_06    C1   N    C4   C5   155.92  30.0  3
 D8V  Var_07    C2   C1   N    C4   -66.19  30.0  2
 D8V  Var_08    H16  C    N    C4   173.90  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
 D8V  chir_01  C8  C6  C12  C9  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
 D8V  plan-1  C4  0.020
 D8V  plan-1  C5  0.020
 D8V  plan-1  C6  0.020
 D8V  plan-1  N1  0.020
 D8V  plan-1  C7  0.020
 D8V  plan-1  C8  0.020
 D8V  plan-1  S   0.020
 D8V  plan-1  H3  0.020

