# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Mar  9 18:56:08 2022
#   Inital geometry file: a 153 line input string
#   Ligand name: N-[(1R,2R)-2-{[(5-chloro-1H-indol-2-yl)carbonyl]amino}cyclohexyl]-5-methyl-4,5,6,7-tetrahydro[1,3]thiazolo[5,4-c]pyridine-2-carboxamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CN1CCc2nc(sc2C1)C(=O)N[C@@H]3CCCC[C@H]3NC(=O)c4[nH]c5ccc(Cl)cc5c4
#
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
 D93  D93  N-[(1R,2R)-2-{[(5-chloro-1H-indol-2-yl)carbonyl]amino}cyclohexyl]-5-methyl-4,5,6,7-tetrahydro[1,3]thiazolo[5,4-c]pyridine-2-carboxamide  ligand  58  32  .  2022-03-18  2022-03-18
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_D93
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
 D93  CL1   CL  CL    0  -0.140  -2.8220   6.3201   5.7886
 D93  C16   C   CR6   0  -0.049  -1.5626   6.1652   4.5991
 D93  C17   C   CR16  0  -0.237  -0.7306   7.2742   4.3664
 D93  C18   C   CR16  0  -0.306   0.2833   7.2032   3.4370
 D93  C12   C   CR56  0   0.363   0.4479   6.0018   2.7465
 D93  N11   N   NR15  0  -0.721   1.3487   5.6475   1.7950
 D93  C15   C   CR16  0  -0.302  -1.4161   4.9753   3.9265
 D93  C13   C   CR56  0   0.068  -0.3905   4.8875   2.9756
 D93  C14   C   CR15  0  -0.428   0.0540   3.8521   2.1078
 D93  C10   C   CR5   0   0.266   1.1156   4.3596   1.4033
 D93  C9    C   C     0   0.493   2.0019   3.7598   0.3839
 D93  O19   O   O     0  -0.486   3.0280   4.3336   0.0434
 D93  N7    N   NH1   0  -0.665   1.6002   2.5819  -0.1184
 D93  C1    C   CH1   0  -0.078   2.3494   1.8477  -1.1206
 D93  C6    C   CH2   0  -0.470   1.4063   0.9530  -1.9226
 D93  C5    C   CH2   0  -0.450   0.8420  -0.2029  -1.0975
 D93  C4    C   CH2   0  -0.457   1.9453  -1.0133  -0.4251
 D93  C3    C   CH2   0  -0.452   2.8836  -0.1183   0.3804
 D93  C2    C   CH1   0  -0.092   3.4694   1.0153  -0.4572
 D93  N8    N   NH1   0  -0.649   4.3523   0.4766  -1.4730
 D93  C20   C   C     0   0.536   5.3804   1.1446  -2.0073
 D93  O31   O   O     0  -0.474   5.7610   2.2573  -1.6745
 D93  C21   C   CR5   0  -0.090   6.0755   0.4132  -3.0941
 D93  S25   S   S2    0   0.283   7.4357   1.1331  -3.8589
 D93  C24   C   CR5   0  -0.286   7.5546  -0.2422  -4.8721
 D93  C26   C   CH2   0  -0.354   8.5766  -0.4850  -5.9466
 D93  N27   N   NT    0  -0.400   8.1230  -1.5003  -6.8748
 D93  C30   C   CH3   0  -0.523   7.1727  -0.9980  -7.8484
 D93  C28   C   CH2   0  -0.331   7.6477  -2.6787  -6.1681
 D93  C29   C   CH2   0  -0.537   6.4118  -2.4280  -5.2933
 D93  C23   C   CR5   0   0.353   6.5701  -1.1376  -4.5595
 D93  N22   N   N     0  -0.404   5.7387  -0.7489  -3.5549
 D93  H17   H   HCR6  0   0.277  -0.8883   8.1884   4.9221
 D93  H18   H   HCR6  0   0.276   0.9261   8.0544   3.2556
 D93  HN11  H   HNR5  0   0.413   2.0770   6.2324   1.4167
 D93  H15   H   HCR6  0   0.274  -2.0688   4.1349   4.1228
 D93  H14   H   HCR5  0   0.263  -0.3569   2.8567   2.0408
 D93  HN7   H   HNH1  0   0.406   0.6992   2.2235   0.1543
 D93  H1    H   HCH1  0   0.273   2.8135   2.5757  -1.7892
 D93  H61   H   HCH2  0   0.243   1.9575   0.5574  -2.7793
 D93  H62   H   HCH2  0   0.256   0.5979   1.5591  -2.3378
 D93  H51   H   HCH2  0   0.249   0.2373  -0.8461  -1.7392
 D93  H52   H   HCH2  0   0.217   0.1574   0.1745  -0.3302
 D93  H41   H   HCH2  0   0.249   1.5072  -1.7660   0.2330
 D93  H42   H   HCH2  0   0.219   2.5040  -1.5776  -1.1798
 D93  H31   H   HCH2  0   0.239   2.3347   0.3247   1.2156
 D93  H32   H   HCH2  0   0.254   3.6950  -0.7012   0.8210
 D93  H2    H   HCH1  0   0.274   4.0611   1.6742   0.1804
 D93  HN8   H   HNH1  0   0.406   4.1551  -0.4340  -1.8623
 D93  H261  H   HCH2  0   0.264   8.8016   0.4334  -6.4922
 D93  H262  H   HCH2  0   0.271   9.5154  -0.8098  -5.4853
 D93  H301  H   HCH3  0   0.238   7.6325  -0.1995  -8.4323
 D93  H302  H   HCH3  0   0.205   6.2403  -0.6025  -7.4227
 D93  H303  H   HCH3  0   0.236   6.9073  -1.7992  -8.5395
 D93  H281  H   HCH2  0   0.246   8.4647  -3.0441  -5.5393
 D93  H282  H   HCH2  0   0.251   7.4365  -3.4654  -6.8946
 D93  H291  H   HCH2  0   0.264   6.2852  -3.2535  -4.5891
 D93  H292  H   HCH2  0   0.254   5.4998  -2.3968  -5.8974

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
 D93  CL1  C16   single    1.739  0.020  1.739
 D93  C16  C15   aromatic  1.375  0.020  1.375
 D93  C16  C17   aromatic  1.406  0.020  1.406
 D93  C17  C18   aromatic  1.377  0.020  1.377
 D93  C17  H17   single    0.930  0.020  1.080
 D93  C18  C12   aromatic  1.395  0.020  1.395
 D93  C18  H18   single    0.930  0.020  1.080
 D93  C12  C13   aromatic  1.413  0.020  1.413
 D93  C12  N11   single    1.357  0.020  1.357
 D93  N11  C10   single    1.366  0.020  1.366
 D93  N11  HN11  single    0.860  0.020  1.020
 D93  C15  C13   aromatic  1.401  0.020  1.401
 D93  C15  H15   single    0.930  0.020  1.080
 D93  C13  C14   single    1.422  0.020  1.422
 D93  C14  C10   double    1.371  0.020  1.371
 D93  C14  H14   single    0.930  0.020  1.080
 D93  C10  C9    single    1.478  0.020  1.478
 D93  C9   O19   double    1.224  0.020  1.224
 D93  C9   N7    single    1.342  0.020  1.342
 D93  N7   C1    single    1.451  0.020  1.451
 D93  N7   HN7   single    0.860  0.020  1.020
 D93  C1   C2    single    1.545  0.020  1.545
 D93  C1   C6    single    1.527  0.020  1.527
 D93  C1   H1    single    0.970  0.020  1.090
 D93  C6   C5    single    1.528  0.020  1.528
 D93  C6   H61   single    0.970  0.020  1.090
 D93  C6   H62   single    0.970  0.020  1.090
 D93  C5   C4    single    1.525  0.020  1.525
 D93  C5   H51   single    0.970  0.020  1.090
 D93  C5   H52   single    0.970  0.020  1.090
 D93  C4   C3    single    1.527  0.020  1.527
 D93  C4   H41   single    0.970  0.020  1.090
 D93  C4   H42   single    0.970  0.020  1.090
 D93  C3   C2    single    1.526  0.020  1.526
 D93  C3   H31   single    0.970  0.020  1.090
 D93  C3   H32   single    0.970  0.020  1.090
 D93  C2   N8    single    1.450  0.020  1.450
 D93  C2   H2    single    0.970  0.020  1.090
 D93  N8   C20   single    1.337  0.020  1.337
 D93  N8   HN8   single    0.860  0.020  1.020
 D93  C20  C21   single    1.483  0.020  1.483
 D93  C20  O31   double    1.222  0.020  1.222
 D93  C21  N22   double    1.295  0.020  1.295
 D93  C21  S25   single    1.719  0.020  1.719
 D93  S25  C24   single    1.712  0.020  1.712
 D93  C24  C26   single    1.503  0.020  1.503
 D93  C24  C23   double    1.367  0.020  1.367
 D93  C26  N27   single    1.448  0.020  1.448
 D93  C26  H261  single    0.970  0.020  1.090
 D93  C26  H262  single    0.970  0.020  1.090
 D93  N27  C30   single    1.450  0.020  1.450
 D93  N27  C28   single    1.454  0.020  1.454
 D93  C30  H301  single    0.970  0.020  1.090
 D93  C30  H302  single    0.970  0.020  1.090
 D93  C30  H303  single    0.970  0.020  1.090
 D93  C28  C29   single    1.535  0.020  1.535
 D93  C28  H281  single    0.970  0.020  1.090
 D93  C28  H282  single    0.970  0.020  1.090
 D93  C29  C23   single    1.493  0.020  1.493
 D93  C29  H291  single    0.970  0.020  1.090
 D93  C29  H292  single    0.970  0.020  1.090
 D93  C23  N22   single    1.361  0.020  1.361

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
 D93  C15   C16  C17   122.60  3.000
 D93  C17   C16  CL1   118.13  3.000
 D93  C15   C16  CL1   119.27  3.000
 D93  H17   C17  C18   119.85  3.000
 D93  H17   C17  C16   119.71  3.000
 D93  C18   C17  C16   120.45  3.000
 D93  H18   C18  C12   121.62  3.000
 D93  H18   C18  C17   120.66  3.000
 D93  C12   C18  C17   117.72  3.000
 D93  C13   C12  N11   107.55  3.000
 D93  N11   C12  C18   130.53  3.000
 D93  C13   C12  C18   121.91  3.000
 D93  HN11  N11  C10   124.26  3.000
 D93  HN11  N11  C12   126.24  3.000
 D93  C10   N11  C12   109.50  3.000
 D93  H15   C15  C13   121.06  3.000
 D93  H15   C15  C16   121.28  3.000
 D93  C13   C15  C16   117.66  3.000
 D93  C14   C13  C15   133.50  3.000
 D93  C14   C13  C12   106.84  3.000
 D93  C15   C13  C12   119.66  3.000
 D93  H14   C14  C10   127.18  3.000
 D93  H14   C14  C13   126.19  3.000
 D93  C10   C14  C13   106.61  3.000
 D93  C9    C10  C14   131.93  3.000
 D93  C9    C10  N11   118.55  3.000
 D93  C14   C10  N11   109.49  3.000
 D93  N7    C9   O19   123.93  3.000
 D93  N7    C9   C10   115.78  3.000
 D93  O19   C9   C10   120.29  3.000
 D93  HN7   N7   C1    117.97  3.000
 D93  HN7   N7   C9    118.60  3.000
 D93  C1    N7   C9    123.24  3.000
 D93  H1    C1   C2    108.30  3.000
 D93  H1    C1   C6    109.35  3.000
 D93  C2    C1   C6    110.94  3.000
 D93  H1    C1   N7    107.77  3.000
 D93  C6    C1   N7    109.89  3.000
 D93  C2    C1   N7    110.51  3.000
 D93  H62   C6   H61   106.03  3.000
 D93  H62   C6   C5    110.58  3.000
 D93  H61   C6   C5    109.61  3.000
 D93  H62   C6   C1    109.36  3.000
 D93  H61   C6   C1    108.19  3.000
 D93  C5    C6   C1    112.80  3.000
 D93  H52   C5   H51   105.59  3.000
 D93  H52   C5   C4    109.05  3.000
 D93  H51   C5   C4    110.30  3.000
 D93  H52   C5   C6    110.38  3.000
 D93  H51   C5   C6    109.44  3.000
 D93  C4    C5   C6    111.89  3.000
 D93  H42   C4   H41   105.35  3.000
 D93  H42   C4   C3    110.61  3.000
 D93  H41   C4   C3    109.44  3.000
 D93  H42   C4   C5    109.81  3.000
 D93  H41   C4   C5    109.99  3.000
 D93  C3    C4   C5    111.46  3.000
 D93  H32   C3   H31   106.33  3.000
 D93  H32   C3   C2    109.44  3.000
 D93  H31   C3   C2    108.12  3.000
 D93  H32   C3   C4    110.90  3.000
 D93  H31   C3   C4    109.39  3.000
 D93  C2    C3   C4    112.44  3.000
 D93  H2    C2   N8    107.68  3.000
 D93  H2    C2   C3    109.62  3.000
 D93  N8    C2   C3    110.02  3.000
 D93  H2    C2   C1    108.58  3.000
 D93  N8    C2   C1    109.93  3.000
 D93  C3    C2   C1    110.95  3.000
 D93  HN8   N8   C20   116.52  3.000
 D93  HN8   N8   C2    119.10  3.000
 D93  C20   N8   C2    124.23  3.000
 D93  C21   C20  O31   120.17  3.000
 D93  O31   C20  N8    125.83  3.000
 D93  C21   C20  N8    114.00  3.000
 D93  N22   C21  S25   115.06  3.000
 D93  S25   C21  C20   119.37  3.000
 D93  N22   C21  C20   125.56  3.000
 D93  C24   S25  C21    88.95  3.000
 D93  C23   C24  C26   123.20  3.000
 D93  C23   C24  S25   109.92  3.000
 D93  C26   C24  S25   126.88  3.000
 D93  H262  C26  H261  106.46  3.000
 D93  H262  C26  N27   109.30  3.000
 D93  H261  C26  N27   109.51  3.000
 D93  H262  C26  C24   109.25  3.000
 D93  H261  C26  C24   111.20  3.000
 D93  N27   C26  C24   111.00  3.000
 D93  C28   N27  C30   113.13  3.000
 D93  C28   N27  C26   111.04  3.000
 D93  C30   N27  C26   113.12  3.000
 D93  H303  C30  H302  107.66  3.000
 D93  H303  C30  H301  107.52  3.000
 D93  H302  C30  H301  107.56  3.000
 D93  H303  C30  N27   109.29  3.000
 D93  H302  C30  N27   114.88  3.000
 D93  H301  C30  N27   109.68  3.000
 D93  H282  C28  H281  106.64  3.000
 D93  H282  C28  C29   109.96  3.000
 D93  H281  C28  C29   109.17  3.000
 D93  H282  C28  N27   108.90  3.000
 D93  H281  C28  N27   107.82  3.000
 D93  C29   C28  N27   114.07  3.000
 D93  H292  C29  H291  106.30  3.000
 D93  H292  C29  C23   109.58  3.000
 D93  H291  C29  C23   110.40  3.000
 D93  H292  C29  C28   111.17  3.000
 D93  H291  C29  C28   109.71  3.000
 D93  C23   C29  C28   109.63  3.000
 D93  N22   C23  C29   123.03  3.000
 D93  N22   C23  C24   114.94  3.000
 D93  C29   C23  C24   122.01  3.000
 D93  C23   N22  C21   111.11  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
 D93  CONST_01  C12   C13  C15  C16     0.00   0.0  0
 D93  CONST_02  C12   C18  C17  C16     0.00   0.0  0
 D93  CONST_03  C13   C15  C16  C17     0.00   0.0  0
 D93  CONST_04  C13   C12  C18  C17     0.00   0.0  0
 D93  CONST_05  C15   C16  C17  C18     0.00   0.0  0
 D93  CONST_06  C15   C13  C12  C18     0.00   0.0  0
 D93  CONST_07  C13   C15  C16  CL1   180.00   0.0  0
 D93  CONST_08  C18   C17  C16  CL1   180.00   0.0  0
 D93  CONST_09  H18   C18  C17  C16   180.00   0.0  0
 D93  CONST_10  H15   C15  C16  C17   180.00   0.0  0
 D93  CONST_11  H17   C17  C18  C12   180.00   0.0  0
 D93  CONST_12  C1    N7   C9   C10   180.00   0.0  0
 D93  CONST_13  C21   C20  N8   C2    180.00   0.0  0
 D93  CONST_14  C1    N7   C9   O19     0.00   0.0  0
 D93  CONST_15  O31   C20  N8   C2      0.00   0.0  0
 D93  CONST_16  HN7   N7   C9   C10     0.00   0.0  0
 D93  CONST_17  HN8   N8   C20  C21     0.00   0.0  0
 D93  Var_01    C4    C5   C6   C1    -53.28  30.0  1
 D93  Var_02    C3    C4   C5   C6     52.82  30.0  1
 D93  Var_03    C2    C3   C4   C5    -54.58  30.0  1
 D93  Var_04    N27   C26  C24  S25  -160.81  30.0  1
 D93  Var_05    C28   N27  C26  C24   -49.35  30.0  1
 D93  Var_06    C28   C29  C23  C24    11.92  30.0  1
 D93  Var_07    C29   C28  N27  C26    63.97  30.0  1
 D93  Var_08    C23   C29  C28  N27   -42.56  30.0  1
 D93  Var_09    O19   C9   C10  N11    10.27  30.0  2
 D93  Var_10    N22   C21  C20  N8      2.09  30.0  2
 D93  Var_11    H301  C30  N27  C26    59.91  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
 D93  chir_01  C1  N7  C2  C6  negativ
 D93  chir_02  C2  N8  C3  C1  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
 D93  plan-1  CL1   0.020
 D93  plan-1  C16   0.020
 D93  plan-1  C17   0.020
 D93  plan-1  C18   0.020
 D93  plan-1  C12   0.020
 D93  plan-1  N11   0.020
 D93  plan-1  C15   0.020
 D93  plan-1  C13   0.020
 D93  plan-1  C14   0.020
 D93  plan-1  C10   0.020
 D93  plan-1  C9    0.020
 D93  plan-1  H17   0.020
 D93  plan-1  H18   0.020
 D93  plan-1  HN11  0.020
 D93  plan-1  H15   0.020
 D93  plan-1  H14   0.020
 D93  plan-2  C20   0.020
 D93  plan-2  C21   0.020
 D93  plan-2  S25   0.020
 D93  plan-2  C24   0.020
 D93  plan-2  C26   0.020
 D93  plan-2  C29   0.020
 D93  plan-2  C23   0.020
 D93  plan-2  N22   0.020
 D93  plan-3  C10   0.020
 D93  plan-3  C9    0.020
 D93  plan-3  O19   0.020
 D93  plan-3  N7    0.020
 D93  plan-3  C1    0.020
 D93  plan-3  HN7   0.020
 D93  plan-4  C2    0.020
 D93  plan-4  N8    0.020
 D93  plan-4  C20   0.020
 D93  plan-4  O31   0.020
 D93  plan-4  C21   0.020
 D93  plan-4  HN8   0.020

