# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Aug  3 04:46:46 2022
#   Inital geometry file: a 111 line input string
#   Ligand name: [2-(1,3-benzodioxol-5-ylamino)-1,3-thiazol-4-yl]-[(3~{R},5~{S})-3,5-dimethylpiperidin-1-yl]methanone
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[C@@H]1C[C@H](C)CN(C1)C(=O)c2csc(Nc3ccc4OCOc4c3)n2
#
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
 W99  W99  "[2-(1,3-benzodioxol-5-ylamino)-1,3-thiazol-4-yl]-[(3R,5S)-3,5-dimethylpiperidin-1-yl]methanone"  ligand  46  25  .  2022-08-11  2022-09-22
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_W99
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
 W99  N    N  NH1   0  -0.771  140.3751  124.9393  160.4165
 W99  C    C  CH2   0   0.066  145.9266  125.8108  162.0891
 W99  O    O  O     0  -0.485  145.1063  125.3973  163.1709
 W99  C1   C  CR56  0   0.281  143.8539  125.2809  162.6555
 W99  C10  C  C     0   0.509  141.0179  126.3712  155.8100
 W99  C11  C  CH2   0  -0.316  141.7900  128.4452  156.9567
 W99  C12  C  CH1   0  -0.219  143.2209  128.8697  157.3066
 W99  C13  C  CH2   0  -0.410  144.0605  129.0491  156.0291
 W99  C14  C  CH1   0  -0.302  143.1897  129.2067  154.7914
 W99  C15  C  CH2   0  -0.229  142.3623  127.9385  154.6048
 W99  C16  C  CH3   0  -0.653  144.0102  129.4741  153.5383
 W99  C17  C  CH3   0  -0.667  143.8976  127.8976  158.2618
 W99  C2   C  CR16  0  -0.331  142.6600  125.0745  163.2994
 W99  C3   C  CR16  0  -0.364  141.5151  124.9738  162.5064
 W99  C4   C  CR6   0   0.355  141.5766  125.0706  161.1163
 W99  C5   C  CR16  0  -0.419  142.8081  125.2665  160.4701
 W99  C6   C  CR56  0   0.326  143.9133  125.3704  161.2769
 W99  C7   C  CR5   0   0.301  140.1060  125.2402  159.1248
 W99  C8   C  CR5   0   0.248  140.3098  125.8902  157.0365
 W99  C9   C  CR15  0  -0.546  139.0078  125.5238  156.9781
 W99  N1   N  N     0  -0.463  140.9292  125.7259  158.2476
 W99  N2   N  NT    0  -0.462  141.7728  127.4831  155.8654
 W99  O1   O  O     0  -0.489  140.8610  125.7435  154.7687
 W99  O2   O  O     0  -0.484  145.2011  125.5479  160.8945
 W99  S    S  S2    0   0.205  138.4916  124.9546  158.5168
 W99  H1   H  HNH1  0   0.424  139.5906  124.6402  160.9752
 W99  H2   H  HCH2  0   0.245  146.8556  125.2412  162.0889
 W99  H3   H  HCH2  0   0.251  141.2060  129.3207  156.6576
 W99  H4   H  HCH2  0   0.273  141.2974  128.0281  157.8303
 W99  H5   H  HCH1  0   0.234  143.1324  129.8386  157.8068
 W99  H6   H  HCH2  0   0.216  144.7033  128.1729  155.8816
 W99  H7   H  HCH2  0   0.238  144.7332  129.9030  156.1378
 W99  H8   H  HCH1  0   0.234  142.5153  130.0578  154.9370
 W99  H9   H  HCH2  0   0.238  141.5783  128.1060  153.8596
 W99  H10  H  HCH2  0   0.231  143.0106  127.1492  154.2128
 W99  H11  H  HCH3  0   0.233  144.5582  130.4127  153.6264
 W99  H12  H  HCH3  0   0.218  144.7376  128.6772  153.3694
 W99  H13  H  HCH3  0   0.229  143.3774  129.5416  152.6517
 W99  H14  H  HCH3  0   0.227  143.3714  127.8323  159.2146
 W99  H15  H  HCH3  0   0.218  143.9367  126.8952  157.8303
 W99  H16  H  HCH3  0   0.228  144.9237  128.2077  158.4669
 W99  H17  H  HCR6  0   0.274  142.5938  124.9948  164.3759
 W99  H18  H  HCR6  0   0.271  140.5578  124.8203  162.9892
 W99  H19  H  HCR6  0   0.306  142.8833  125.3379  159.3973
 W99  H20  H  HCR5  0   0.307  138.3335  125.5608  156.1378
 W99  H21  H  HCH2  0   0.229  146.1344  126.8846  162.1655

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
 W99  C16  C14  single    1.521  0.020  1.521
 W99  C14  C15  single    1.526  0.020  1.526
 W99  C14  C13  single    1.521  0.020  1.521
 W99  C15  N2   single    1.464  0.020  1.464
 W99  O1   C10  double    1.226  0.020  1.226
 W99  C13  C12  single    1.539  0.020  1.539
 W99  C10  N2   single    1.345  0.020  1.345
 W99  C10  C8   single    1.496  0.020  1.496
 W99  N2   C11  single    1.455  0.020  1.455
 W99  C11  C12  single    1.533  0.020  1.533
 W99  C8   C9   aromatic  1.354  0.020  1.354
 W99  C8   N1   aromatic  1.370  0.020  1.370
 W99  C9   S    aromatic  1.720  0.020  1.720
 W99  C12  C17  single    1.522  0.020  1.522
 W99  N1   C7   aromatic  1.297  0.020  1.297
 W99  S    C7   aromatic  1.749  0.020  1.749
 W99  C7   N    single    1.353  0.020  1.353
 W99  N    C4   single    1.397  0.020  1.397
 W99  C5   C4   aromatic  1.404  0.020  1.404
 W99  C5   C6   aromatic  1.372  0.020  1.372
 W99  O2   C6   single    1.355  0.020  1.355
 W99  O2   C    single    1.422  0.020  1.422
 W99  C4   C3   aromatic  1.395  0.020  1.395
 W99  C6   C1   aromatic  1.383  0.020  1.383
 W99  C    O    single    1.419  0.020  1.419
 W99  C3   C2   aromatic  1.396  0.020  1.396
 W99  C1   O    single    1.359  0.020  1.359
 W99  C1   C2   aromatic  1.372  0.020  1.372
 W99  N    H1   single    0.860  0.020  1.020
 W99  C    H2   single    0.970  0.020  1.090
 W99  C11  H3   single    0.970  0.020  1.090
 W99  C11  H4   single    0.970  0.020  1.090
 W99  C12  H5   single    0.970  0.020  1.090
 W99  C13  H6   single    0.970  0.020  1.090
 W99  C13  H7   single    0.970  0.020  1.090
 W99  C14  H8   single    0.970  0.020  1.090
 W99  C15  H9   single    0.970  0.020  1.090
 W99  C15  H10  single    0.970  0.020  1.090
 W99  C16  H11  single    0.970  0.020  1.090
 W99  C16  H12  single    0.970  0.020  1.090
 W99  C16  H13  single    0.970  0.020  1.090
 W99  C17  H14  single    0.970  0.020  1.090
 W99  C17  H15  single    0.970  0.020  1.090
 W99  C17  H16  single    0.970  0.020  1.090
 W99  C2   H17  single    0.930  0.020  1.080
 W99  C3   H18  single    0.930  0.020  1.080
 W99  C5   H19  single    0.930  0.020  1.080
 W99  C9   H20  single    0.930  0.020  1.080
 W99  C    H21  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
 W99  H1   N    C7   116.11  3.000
 W99  H1   N    C4   114.80  3.000
 W99  C7   N    C4   128.94  3.000
 W99  H21  C    H2   110.52  3.000
 W99  H21  C    O2   109.65  3.000
 W99  H2   C    O2   109.77  3.000
 W99  H21  C    O    109.98  3.000
 W99  H2   C    O    109.91  3.000
 W99  O2   C    O    106.95  3.000
 W99  C1   O    C    105.58  3.000
 W99  C6   C1   C2   121.00  3.000
 W99  C2   C1   O    129.54  3.000
 W99  C6   C1   O    109.44  3.000
 W99  O1   C10  N2   122.01  3.000
 W99  N2   C10  C8   119.85  3.000
 W99  O1   C10  C8   118.12  3.000
 W99  H4   C11  H3   106.56  3.000
 W99  H4   C11  N2   110.12  3.000
 W99  H3   C11  N2   108.53  3.000
 W99  H4   C11  C12  110.24  3.000
 W99  H3   C11  C12  109.82  3.000
 W99  N2   C11  C12  111.43  3.000
 W99  H5   C12  C17  108.35  3.000
 W99  H5   C12  C13  108.68  3.000
 W99  C17  C12  C13  110.67  3.000
 W99  H5   C12  C11  105.90  3.000
 W99  C17  C12  C11  112.43  3.000
 W99  C13  C12  C11  110.61  3.000
 W99  H7   C13  H6   106.08  3.000
 W99  H7   C13  C14  110.64  3.000
 W99  H6   C13  C14  107.99  3.000
 W99  H7   C13  C12  110.15  3.000
 W99  H6   C13  C12  109.76  3.000
 W99  C14  C13  C12  112.03  3.000
 W99  H8   C14  C16  107.75  3.000
 W99  H8   C14  C15  109.16  3.000
 W99  C16  C14  C15  109.74  3.000
 W99  H8   C14  C13  108.94  3.000
 W99  C15  C14  C13  108.89  3.000
 W99  C16  C14  C13  112.31  3.000
 W99  H10  C15  H9   106.91  3.000
 W99  H10  C15  N2   108.82  3.000
 W99  H9   C15  N2   110.20  3.000
 W99  H10  C15  C14  108.80  3.000
 W99  H9   C15  C14  110.15  3.000
 W99  N2   C15  C14  111.81  3.000
 W99  H13  C16  H12  107.80  3.000
 W99  H13  C16  H11  107.69  3.000
 W99  H12  C16  H11  107.81  3.000
 W99  H13  C16  C14  111.55  3.000
 W99  H12  C16  C14  111.00  3.000
 W99  H11  C16  C14  110.83  3.000
 W99  H16  C17  H15  107.55  3.000
 W99  H16  C17  H14  107.85  3.000
 W99  H15  C17  H14  107.91  3.000
 W99  H16  C17  C12  110.77  3.000
 W99  H15  C17  C12  110.75  3.000
 W99  H14  C17  C12  111.85  3.000
 W99  H17  C2   C3   120.65  3.000
 W99  H17  C2   C1   122.11  3.000
 W99  C3   C2   C1   117.24  3.000
 W99  H18  C3   C4   119.54  3.000
 W99  H18  C3   C2   118.80  3.000
 W99  C4   C3   C2   121.66  3.000
 W99  C5   C4   C3   120.46  3.000
 W99  C3   C4   N    117.06  3.000
 W99  C5   C4   N    122.47  3.000
 W99  H19  C5   C6   121.59  3.000
 W99  H19  C5   C4   121.90  3.000
 W99  C6   C5   C4   116.50  3.000
 W99  O2   C6   C5   127.55  3.000
 W99  O2   C6   C1   109.31  3.000
 W99  C5   C6   C1   123.13  3.000
 W99  S    C7   N1   114.32  3.000
 W99  S    C7   N    118.63  3.000
 W99  N1   C7   N    127.04  3.000
 W99  N1   C8   C9   116.13  3.000
 W99  N1   C8   C10  123.32  3.000
 W99  C9   C8   C10  120.47  3.000
 W99  H20  C9   S    121.40  3.000
 W99  H20  C9   C8   128.74  3.000
 W99  S    C9   C8   109.86  3.000
 W99  C8   N1   C7   110.83  3.000
 W99  C15  N2   C11  115.80  3.000
 W99  C11  N2   C10  125.75  3.000
 W99  C15  N2   C10  116.59  3.000
 W99  C6   O2   C    105.79  3.000
 W99  C9   S    C7    88.85  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
 W99  CONST_01  C4   C5   C6   C1      0.00   0.0  0
 W99  CONST_02  C4   C3   C2   C1      0.00   0.0  0
 W99  CONST_03  C5   C4   C3   C2      0.00   0.0  0
 W99  CONST_04  C5   C6   C1   C2      0.00   0.0  0
 W99  CONST_05  C6   C5   C4   C3      0.00   0.0  0
 W99  CONST_06  C6   C1   C2   C3      0.00   0.0  0
 W99  CONST_07  C9   C8   N1   C7      0.00   0.0  0
 W99  CONST_08  C8   C9   S    C7      0.00   0.0  0
 W99  CONST_09  S    C7   N1   C8      0.00   0.0  0
 W99  CONST_10  N1   C7   S    C9      0.00   0.0  0
 W99  CONST_11  S    C9   C8   N1      0.00   0.0  0
 W99  CONST_12  C8   N1   C7   N     180.00   0.0  0
 W99  CONST_13  C9   S    C7   N     180.00   0.0  0
 W99  CONST_14  C6   C5   C4   N     180.00   0.0  0
 W99  CONST_15  C2   C3   C4   N     180.00   0.0  0
 W99  CONST_16  S    C9   C8   C10   180.00   0.0  0
 W99  CONST_17  C7   N1   C8   C10   180.00   0.0  0
 W99  CONST_18  C8   C10  N2   C11     0.00   0.0  0
 W99  CONST_19  C8   C10  N2   C15   180.00   0.0  0
 W99  CONST_20  H17  C2   C1   O       0.00   0.0  0
 W99  CONST_21  H19  C5   C6   C1    180.00   0.0  0
 W99  CONST_22  H18  C3   C2   C1    180.00   0.0  0
 W99  CONST_23  H19  C5   C4   C3    180.00   0.0  0
 W99  CONST_24  H17  C2   C3   C4    180.00   0.0  0
 W99  CONST_25  H18  C3   C4   C5    180.00   0.0  0
 W99  CONST_26  H17  C2   C1   C6    180.00   0.0  0
 W99  CONST_27  H20  C9   S    C7    180.00   0.0  0
 W99  CONST_28  H20  C9   C8   N1    180.00   0.0  0
 W99  CONST_29  H19  C5   C6   O2      0.00   0.0  0
 W99  CONST_30  O1   C10  N2   C11   180.00   0.0  0
 W99  CONST_31  O1   C10  N2   C15     0.00   0.0  0
 W99  Var_01    C5   C6   O2   C     170.70  30.0  1
 W99  Var_02    C1   C6   O2   C     -10.31  30.0  1
 W99  Var_03    C6   C1   O    C      10.54  30.0  1
 W99  Var_04    C2   C1   O    C    -170.93  30.0  1
 W99  Var_05    C6   O2   C    O      16.65  30.0  1
 W99  Var_06    O2   C    O    C1    -16.69  30.0  1
 W99  Var_07    C14  C15  N2   C11    14.40  30.0  1
 W99  Var_08    C15  N2   C11  C12   -59.57  30.0  1
 W99  Var_09    C14  C15  N2   C10   179.78  30.0  1
 W99  Var_10    C12  C11  N2   C10   136.57  30.0  1
 W99  Var_11    C7   N    C4   C3    165.96  30.0  3
 W99  Var_12    N1   C7   N    C4     -0.04  30.0  1
 W99  Var_13    S    C7   N    C4    179.57  30.0  1
 W99  Var_14    C7   N    C4   C5    -15.23  30.0  3
 W99  Var_15    N2   C10  C8   C9    133.32  30.0  2
 W99  Var_16    N2   C10  C8   N1    -50.15  30.0  2
 W99  Var_17    H2   C    O    C1   -135.79  30.0  1
 W99  Var_18    H21  C    O    C1    102.32  30.0  1
 W99  Var_19    H9   C15  N2   C11  -108.46  30.0  1
 W99  Var_20    H10  C15  N2   C11   134.60  30.0  1
 W99  Var_21    H3   C11  N2   C15    61.48  30.0  1
 W99  Var_22    H4   C11  N2   C15   177.77  30.0  1
 W99  Var_23    H2   C    O2   C6    135.85  30.0  1
 W99  Var_24    H21  C    O2   C6   -102.57  30.0  1
 W99  Var_25    O1   C10  C8   C9    -45.04  30.0  2
 W99  Var_26    O1   C10  C8   N1    131.50  30.0  2
 W99  Var_27    H9   C15  N2   C10    56.92  30.0  1
 W99  Var_28    H10  C15  N2   C10   -60.02  30.0  1
 W99  Var_29    H3   C11  N2   C10  -102.38  30.0  1
 W99  Var_30    H4   C11  N2   C10    13.91  30.0  1
 W99  Var_31    H1   N    C4   C3     -9.26  30.0  3
 W99  Var_32    H1   N    C4   C5    169.55  30.0  3
 W99  Var_33    H1   N    C7   N1    175.12  30.0  2
 W99  Var_34    H1   N    C7   S      -5.26  30.0  2

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
 W99  chir_01  C12  C13  C11  C17  negativ
 W99  chir_02  C14  C16  C15  C13  negativ

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
 W99  plan-1  N    0.020
 W99  plan-1  C10  0.020
 W99  plan-1  C7   0.020
 W99  plan-1  C8   0.020
 W99  plan-1  C9   0.020
 W99  plan-1  N1   0.020
 W99  plan-1  S    0.020
 W99  plan-1  H20  0.020
 W99  plan-2  N    0.020
 W99  plan-2  O    0.020
 W99  plan-2  C1   0.020
 W99  plan-2  C2   0.020
 W99  plan-2  C3   0.020
 W99  plan-2  C4   0.020
 W99  plan-2  C5   0.020
 W99  plan-2  C6   0.020
 W99  plan-2  O2   0.020
 W99  plan-2  H17  0.020
 W99  plan-2  H18  0.020
 W99  plan-2  H19  0.020
 W99  plan-3  C10  0.020
 W99  plan-3  C11  0.020
 W99  plan-3  C15  0.020
 W99  plan-3  C8   0.020
 W99  plan-3  N2   0.020
 W99  plan-3  O1   0.020

