# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr  1 23:47:03 2020
#   Inital geometry file: a 134 line input string
#   Ligand name: 5-(4-chlorophenyl)-N-{(S)-[5-(hydroxymethyl)-4-methyl-1,3-thiazol-2-yl][(2R)-piperidin-2-yl]methyl}-1H-pyrrole-2-carboxamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cc1nc(sc1CO)[C@@H](NC(=O)c2[nH]c(cc2)c3ccc(Cl)cc3)[C@H]4CCCCN4
#
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
 3ZM  3ZM  5-(4-chlorophenyl)-N-{(S)-[5-(hydroxymethyl)-4-methyl-1,3-thiazol-2-yl][(2R)-piperidin-2-yl]methyl}-1H-pyrrole-2-carboxamide  ligand  55  30  .  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_3ZM
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
 3ZM  C15   C   CR6   0   0.070   4.1336   0.2439   0.2830
 3ZM  C17   C   CR16  0  -0.190   6.4720   0.1214  -0.3358
 3ZM  C20   C   CR16  0  -0.318   3.8526  -0.7311  -0.6761
 3ZM  C22   C   CR15  0  -0.377   3.1781   1.4261   2.3618
 3ZM  C28   C   CH2   0  -0.440  -2.6032   3.6691  -2.7832
 3ZM  C01   C   CR5   0   0.091  -2.9871  -0.4878   0.3090
 3ZM  N02   N   N     0  -0.428  -2.1966  -1.4952   0.1569
 3ZM  C03   C   CR5   0   0.332  -2.8827  -2.6650  -0.0644
 3ZM  C04   C   CH3   0  -0.732  -2.1080  -3.9224  -0.2730
 3ZM  C05   C   CR5   0  -0.291  -4.2363  -2.5292  -0.0792
 3ZM  S06   S   S2    0   0.236  -4.6600  -0.8778   0.1989
 3ZM  C07   C   CH2   0  -0.207  -5.3096  -3.5308  -0.3287
 3ZM  O08   O   OH1   0  -0.666  -6.3944  -3.2341   0.5190
 3ZM  C09   C   CH1   0  -0.161  -2.5173   0.9160   0.5723
 3ZM  N10   N   NH1   0  -0.677  -1.0802   0.8874   0.7238
 3ZM  C12   C   CR5   0   0.190   1.0233   1.4127   1.7344
 3ZM  N13   N   NR15  0  -0.707   1.7773   0.8090   0.7671
 3ZM  C14   C   CR5   0   0.354   3.0887   0.8166   1.1216
 3ZM  C16   C   CR16  0  -0.328   5.4583   0.6589   0.4377
 3ZM  C18   C   CR6   0  -0.056   6.1625  -0.8406  -1.2861
 3ZM  C19   C   CR16  0  -0.193   4.8571  -1.2707  -1.4630
 3ZM  CL21  CL  CL    0  -0.125   7.4241  -1.5129  -2.2635
 3ZM  C23   C   CR15  0  -0.322   1.8798   1.8029   2.7425
 3ZM  O24   O   O     0  -0.479  -0.9948   2.3485   2.4609
 3ZM  C25   C   CH1   0  -0.073  -2.9738   1.8519  -0.5599
 3ZM  N26   N   NH1   0  -0.577  -2.4585   1.3679  -1.8281
 3ZM  C27   C   CH2   0  -0.312  -2.9115   2.1832  -2.9467
 3ZM  C29   C   CH2   0  -0.442  -3.1437   4.1819  -1.4524
 3ZM  C30   C   CH2   0  -0.429  -2.6442   3.3203  -0.2946
 3ZM  H171  H   HCR6  0   0.284   7.4912   0.4580  -0.2045
 3ZM  H201  H   HCR6  0   0.261   2.8447  -1.1028  -0.8108
 3ZM  H221  H   HCR5  0   0.259   4.0819   1.5570   2.9356
 3ZM  H282  H   HCH2  0   0.214  -1.5183   3.8164  -2.8220
 3ZM  H281  H   HCH2  0   0.227  -3.0282   4.2337  -3.6171
 3ZM  H043  H   HCH3  0   0.251  -1.3497  -4.0383   0.5017
 3ZM  H042  H   HCH3  0   0.246  -2.7465  -4.8037  -0.2562
 3ZM  H041  H   HCH3  0   0.253  -1.5917  -3.9074  -1.2345
 3ZM  H072  H   HCH2  0   0.233  -5.6085  -3.4905  -1.3834
 3ZM  H071  H   HCH2  0   0.221  -4.9084  -4.5360  -0.1537
 3ZM  H081  H   HOH1  0   0.463  -7.1536  -3.7444   0.2218
 3ZM  H091  H   HCH1  0   0.292  -2.9653   1.2721   1.5045
 3ZM  H101  H   HNH1  0   0.400  -0.6321   0.0685   0.3364
 3ZM  H131  H   HNR5  0   0.415   1.4441   0.5438  -0.1464
 3ZM  H161  H   HCR6  0   0.265   5.7040   1.4228   1.1641
 3ZM  H191  H   HCR6  0   0.284   4.6211  -2.0274  -2.1986
 3ZM  H231  H   HCR5  0   0.261   1.5882   2.2857   3.6614
 3ZM  H251  H   HCH1  0   0.229  -4.0685   1.7688  -0.6077
 3ZM  H261  H   HNH1  0   0.335  -1.4438   1.3974  -1.8001
 3ZM  H272  H   HCH2  0   0.216  -3.9936   2.0456  -3.0491
 3ZM  H271  H   HCH2  0   0.235  -2.4601   1.7943  -3.8617
 3ZM  H291  H   HCH2  0   0.233  -2.8601   5.2250  -1.2970
 3ZM  H292  H   HCH2  0   0.214  -4.2387   4.1569  -1.4728
 3ZM  H301  H   HCH2  0   0.230  -3.0946   3.6436   0.6470
 3ZM  H302  H   HCH2  0   0.218  -1.5614   3.4439  -0.1908
 3ZM  C11   C   C     0   0.519  -0.4318   1.5918   1.6827

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
 3ZM  C19   C20   aromatic  1.385  0.020  1.385
 3ZM  C19   C18   aromatic  1.386  0.020  1.386
 3ZM  C20   C15   aromatic  1.396  0.020  1.396
 3ZM  O24   C11   double    1.223  0.020  1.223
 3ZM  CL21  C18   single    1.732  0.020  1.732
 3ZM  C04   C03   single    1.492  0.020  1.492
 3ZM  C18   C17   aromatic  1.387  0.020  1.387
 3ZM  N02   C03   aromatic  1.374  0.020  1.374
 3ZM  N02   C01   aromatic  1.290  0.020  1.290
 3ZM  N13   C12   aromatic  1.367  0.020  1.367
 3ZM  N13   C14   aromatic  1.358  0.020  1.358
 3ZM  C03   C05   aromatic  1.360  0.020  1.360
 3ZM  C11   C12   single    1.467  0.020  1.467
 3ZM  C11   N10   single    1.355  0.020  1.355
 3ZM  C01   C09   single    1.504  0.020  1.504
 3ZM  C01   S06   aromatic  1.721  0.020  1.721
 3ZM  C09   N10   single    1.445  0.020  1.445
 3ZM  C09   C25   single    1.538  0.020  1.538
 3ZM  C15   C14   single    1.457  0.020  1.457
 3ZM  C15   C16   aromatic  1.397  0.020  1.397
 3ZM  C12   C23   aromatic  1.379  0.020  1.379
 3ZM  C14   C22   aromatic  1.385  0.020  1.385
 3ZM  N26   C25   single    1.452  0.020  1.452
 3ZM  N26   C27   single    1.456  0.020  1.456
 3ZM  C05   S06   aromatic  1.727  0.020  1.727
 3ZM  C05   C07   single    1.489  0.020  1.489
 3ZM  C17   C16   aromatic  1.384  0.020  1.384
 3ZM  C30   C25   single    1.528  0.020  1.528
 3ZM  C30   C29   single    1.527  0.020  1.527
 3ZM  O08   C07   single    1.408  0.020  1.408
 3ZM  C28   C27   single    1.526  0.020  1.526
 3ZM  C28   C29   single    1.525  0.020  1.525
 3ZM  C23   C22   aromatic  1.404  0.020  1.404
 3ZM  C17   H171  single    0.930  0.020  1.080
 3ZM  C20   H201  single    0.930  0.020  1.080
 3ZM  C22   H221  single    0.930  0.020  1.080
 3ZM  C28   H282  single    0.970  0.020  1.090
 3ZM  C28   H281  single    0.970  0.020  1.090
 3ZM  C04   H043  single    0.970  0.020  1.090
 3ZM  C04   H042  single    0.970  0.020  1.090
 3ZM  C04   H041  single    0.970  0.020  1.090
 3ZM  C07   H072  single    0.970  0.020  1.090
 3ZM  C07   H071  single    0.970  0.020  1.090
 3ZM  O08   H081  single    0.850  0.020  0.980
 3ZM  C09   H091  single    0.970  0.020  1.090
 3ZM  N10   H101  single    0.890  0.020  1.040
 3ZM  N13   H131  single    0.860  0.020  1.020
 3ZM  C16   H161  single    0.930  0.020  1.080
 3ZM  C19   H191  single    0.930  0.020  1.080
 3ZM  C23   H231  single    0.930  0.020  1.080
 3ZM  C25   H251  single    0.970  0.020  1.090
 3ZM  N26   H261  single    0.890  0.020  1.040
 3ZM  C27   H272  single    0.970  0.020  1.090
 3ZM  C27   H271  single    0.970  0.020  1.090
 3ZM  C29   H291  single    0.970  0.020  1.090
 3ZM  C29   H292  single    0.970  0.020  1.090
 3ZM  C30   H301  single    0.970  0.020  1.090
 3ZM  C30   H302  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
 3ZM  C16   C15  C14   119.97  3.000
 3ZM  C16   C15  C20   118.32  3.000
 3ZM  C14   C15  C20   121.70  3.000
 3ZM  H171  C17  C18   120.62  3.000
 3ZM  H171  C17  C16   120.11  3.000
 3ZM  C18   C17  C16   119.27  3.000
 3ZM  H201  C20  C19   118.08  3.000
 3ZM  H201  C20  C15   120.83  3.000
 3ZM  C19   C20  C15   121.08  3.000
 3ZM  H221  C22  C23   126.72  3.000
 3ZM  H221  C22  C14   125.73  3.000
 3ZM  C23   C22  C14   107.53  3.000
 3ZM  H281  C28  H282  106.77  3.000
 3ZM  H281  C28  C29   110.75  3.000
 3ZM  H282  C28  C29   109.67  3.000
 3ZM  H281  C28  C27   110.03  3.000
 3ZM  H282  C28  C27   109.10  3.000
 3ZM  C29   C28  C27   110.44  3.000
 3ZM  C09   C01  S06   121.76  3.000
 3ZM  S06   C01  N02   114.28  3.000
 3ZM  C09   C01  N02   123.95  3.000
 3ZM  C03   N02  C01   112.21  3.000
 3ZM  C05   C03  C04   126.82  3.000
 3ZM  C05   C03  N02   114.43  3.000
 3ZM  C04   C03  N02   118.74  3.000
 3ZM  H041  C04  H042  107.59  3.000
 3ZM  H041  C04  H043  107.36  3.000
 3ZM  H042  C04  H043  108.12  3.000
 3ZM  H041  C04  C03   110.93  3.000
 3ZM  H042  C04  C03   112.07  3.000
 3ZM  H043  C04  C03   110.58  3.000
 3ZM  C07   C05  S06   119.55  3.000
 3ZM  C07   C05  C03   130.68  3.000
 3ZM  S06   C05  C03   109.74  3.000
 3ZM  C05   S06  C01    89.34  3.000
 3ZM  H071  C07  H072  106.67  3.000
 3ZM  H071  C07  O08   112.27  3.000
 3ZM  H072  C07  O08   111.16  3.000
 3ZM  H071  C07  C05   109.04  3.000
 3ZM  H072  C07  C05   109.44  3.000
 3ZM  O08   C07  C05   108.22  3.000
 3ZM  H081  O08  C07   108.07  3.000
 3ZM  H091  C09  C25   107.92  3.000
 3ZM  H091  C09  N10   108.93  3.000
 3ZM  C25   C09  N10   112.60  3.000
 3ZM  H091  C09  C01   108.98  3.000
 3ZM  C25   C09  C01   110.27  3.000
 3ZM  N10   C09  C01   108.09  3.000
 3ZM  H101  N10  C11   118.70  3.000
 3ZM  H101  N10  C09   114.63  3.000
 3ZM  C11   N10  C09   122.66  3.000
 3ZM  C23   C12  N13   107.44  3.000
 3ZM  C23   C12  C11   127.39  3.000
 3ZM  N13   C12  C11   125.17  3.000
 3ZM  H131  N13  C14   123.86  3.000
 3ZM  H131  N13  C12   125.11  3.000
 3ZM  C14   N13  C12   110.20  3.000
 3ZM  N13   C14  C22   107.37  3.000
 3ZM  C22   C14  C15   129.95  3.000
 3ZM  N13   C14  C15   122.67  3.000
 3ZM  H161  C16  C17   118.88  3.000
 3ZM  H161  C16  C15   119.95  3.000
 3ZM  C17   C16  C15   121.16  3.000
 3ZM  CL21  C18  C19   119.58  3.000
 3ZM  CL21  C18  C17   119.56  3.000
 3ZM  C19   C18  C17   120.86  3.000
 3ZM  H191  C19  C18   120.64  3.000
 3ZM  H191  C19  C20   120.04  3.000
 3ZM  C18   C19  C20   119.31  3.000
 3ZM  H231  C23  C12   125.57  3.000
 3ZM  H231  C23  C22   126.96  3.000
 3ZM  C12   C23  C22   107.46  3.000
 3ZM  H251  C25  C30   107.17  3.000
 3ZM  H251  C25  N26   106.88  3.000
 3ZM  C30   C25  N26   113.29  3.000
 3ZM  H251  C25  C09   106.36  3.000
 3ZM  C30   C25  C09   113.13  3.000
 3ZM  N26   C25  C09   109.55  3.000
 3ZM  H261  N26  C27   108.40  3.000
 3ZM  H261  N26  C25   108.72  3.000
 3ZM  C27   N26  C25   111.95  3.000
 3ZM  H271  C27  H272  106.58  3.000
 3ZM  H271  C27  N26   108.40  3.000
 3ZM  H272  C27  N26   107.98  3.000
 3ZM  H271  C27  C28   110.67  3.000
 3ZM  H272  C27  C28   109.38  3.000
 3ZM  N26   C27  C28   113.57  3.000
 3ZM  H292  C29  H291  106.50  3.000
 3ZM  H292  C29  C30   109.16  3.000
 3ZM  H291  C29  C30   110.25  3.000
 3ZM  H292  C29  C28   109.29  3.000
 3ZM  H291  C29  C28   110.69  3.000
 3ZM  C30   C29  C28   110.85  3.000
 3ZM  H302  C30  H301  107.02  3.000
 3ZM  H302  C30  C29   109.37  3.000
 3ZM  H301  C30  C29   110.58  3.000
 3ZM  H302  C30  C25   109.77  3.000
 3ZM  H301  C30  C25   110.18  3.000
 3ZM  C29   C30  C25   109.87  3.000
 3ZM  O24   C11  C12   120.65  3.000
 3ZM  C12   C11  N10   115.86  3.000
 3ZM  O24   C11  N10   123.49  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
 3ZM  CONST_01  C18   C19  C20  C15    0.00   0.0  0
 3ZM  CONST_02  C12   N13  C14  C15  180.00   0.0  0
 3ZM  CONST_03  C23   C22  C14  C15  180.00   0.0  0
 3ZM  CONST_04  C18   C17  C16  C15    0.00   0.0  0
 3ZM  CONST_05  C20   C19  C18  C17    0.00   0.0  0
 3ZM  CONST_06  C20   C15  C16  C17    0.00   0.0  0
 3ZM  CONST_07  C14   C15  C16  C17  180.00   0.0  0
 3ZM  CONST_10  C12   N13  C14  C22    0.00   0.0  0
 3ZM  CONST_12  N13   C12  C23  C22    0.00   0.0  0
 3ZM  CONST_13  C05   C03  N02  C01    0.00   0.0  0
 3ZM  CONST_14  C03   C05  S06  C01    0.00   0.0  0
 3ZM  CONST_15  S06   C05  C03  N02    0.00   0.0  0
 3ZM  CONST_16  C05   S06  C01  N02    0.00   0.0  0
 3ZM  CONST_17  S06   C01  N02  C03    0.00   0.0  0
 3ZM  CONST_18  C14   C22  C23  C12    0.00   0.0  0
 3ZM  CONST_20  C23   C22  C14  N13    0.00   0.0  0
 3ZM  CONST_21  C23   C12  N13  C14    0.00   0.0  0
 3ZM  CONST_22  C19   C20  C15  C14  180.00   0.0  0
 3ZM  CONST_23  C19   C20  C15  C16    0.00   0.0  0
 3ZM  CONST_24  C19   C18  C17  C16    0.00   0.0  0
 3ZM  CONST_25  CL21  C18  C19  C20  180.00   0.0  0
 3ZM  CONST_26  C11   C12  C23  C22  180.00   0.0  0
 3ZM  CONST_27  C04   C03  N02  C01  180.00   0.0  0
 3ZM  CONST_28  C07   C05  S06  C01  180.00   0.0  0
 3ZM  CONST_29  C07   C05  C03  N02  180.00   0.0  0
 3ZM  CONST_30  C09   C01  N02  C03  180.00   0.0  0
 3ZM  CONST_31  S06   C05  C03  C04  180.00   0.0  0
 3ZM  CONST_32  C09   C01  S06  C05  180.00   0.0  0
 3ZM  CONST_33  C14   N13  C12  C11  180.00   0.0  0
 3ZM  CONST_34  CL21  C18  C17  C16  180.00   0.0  0
 3ZM  CONST_35  H191  C19  C20  C15  180.00   0.0  0
 3ZM  CONST_36  H131  N13  C14  C15    0.00   0.0  0
 3ZM  CONST_37  H221  C22  C14  C15    0.00   0.0  0
 3ZM  CONST_38  H171  C17  C16  C15  180.00   0.0  0
 3ZM  CONST_39  H161  C16  C15  C20  180.00   0.0  0
 3ZM  CONST_40  H231  C23  C12  N13  180.00   0.0  0
 3ZM  CONST_41  H201  C20  C15  C14    0.00   0.0  0
 3ZM  CONST_42  C12   C11  N10  C09  180.00   0.0  0
 3ZM  CONST_44  O24   C11  N10  C09    0.00   0.0  0
 3ZM  Var_01    C25   N26  C27  C28   54.32  30.0  1
 3ZM  Var_02    C25   C30  C29  C28  -53.80  30.0  1
 3ZM  Var_03    C29   C28  C27  N26  -53.46  30.0  1
 3ZM  Var_04    C30   C29  C28  C27   53.06  30.0  1
 3ZM  Var_05    O08   C07  C05  C03  143.24  30.0  2
 3ZM  Var_06    N13   C12  C11  N10   12.68  30.0  2
 3ZM  Var_07    H043  C04  C03  N02   48.83  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
 3ZM  chir_01  C09  C01  N10  C25  negativ
 3ZM  chir_02  C25  N26  C30  C09  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
 3ZM  plan-1  C01   0.020
 3ZM  plan-1  N02   0.020
 3ZM  plan-1  C03   0.020
 3ZM  plan-1  C04   0.020
 3ZM  plan-1  C05   0.020
 3ZM  plan-1  S06   0.020
 3ZM  plan-1  C07   0.020
 3ZM  plan-1  C09   0.020
 3ZM  plan-2  C15   0.020
 3ZM  plan-2  C22   0.020
 3ZM  plan-2  C12   0.020
 3ZM  plan-2  N13   0.020
 3ZM  plan-2  C14   0.020
 3ZM  plan-2  C23   0.020
 3ZM  plan-2  H221  0.020
 3ZM  plan-2  H131  0.020
 3ZM  plan-2  H231  0.020
 3ZM  plan-2  C11   0.020
 3ZM  plan-3  C15   0.020
 3ZM  plan-3  C17   0.020
 3ZM  plan-3  C20   0.020
 3ZM  plan-3  C14   0.020
 3ZM  plan-3  C16   0.020
 3ZM  plan-3  C18   0.020
 3ZM  plan-3  C19   0.020
 3ZM  plan-3  CL21  0.020
 3ZM  plan-3  H171  0.020
 3ZM  plan-3  H201  0.020
 3ZM  plan-3  H161  0.020
 3ZM  plan-3  H191  0.020
 3ZM  plan-4  C09   0.020
 3ZM  plan-4  N10   0.020
 3ZM  plan-4  C12   0.020
 3ZM  plan-4  O24   0.020
 3ZM  plan-4  H101  0.020
 3ZM  plan-4  C11   0.020

