# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Apr 23 02:42:58 2020
#   Inital geometry file: a 140 line input string
#   Ligand name: {(2S,4S)-4-[4-(3-methyl-1-phenyl-1H-pyrazol-5-yl)piperazin-1-yl]pyrrolidin-2-yl}(1,3-thiazolidin-3-yl)methanone
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cc1cc(N2CCN(CC2)[C@@H]3CN[C@@H](C3)C(=O)N4CCSC4)n(n1)c5ccccc5
#
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
 M51  M51  {(2S,4S)-4-[4-(3-methyl-1-phenyl-1H-pyrazol-5-yl)piperazin-1-yl]pyrrolidin-2-yl}(1,3-thiazolidin-3-yl)methanone  ligand  60  30  .  2021-08-14  2021-08-14  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_M51
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
 M51  C1    C  CR15  0  -0.572  -4.5674  -2.4840   0.1449
 M51  C2    C  CR5   0   0.282  -5.8248  -2.1380   0.6807
 M51  N3    N  N     0  -0.317  -5.9075  -0.8444   0.8978
 M51  N4    N  NR5   0  -0.455  -4.7320  -0.3256   0.4899
 M51  C5    C  CR5   0   0.637  -3.8817  -1.2940   0.0437
 M51  C6    C  CR6   0   0.305  -4.5452   1.0704   0.5515
 M51  C7    C  CR16  0  -0.273  -3.8931   1.7481  -0.4744
 M51  C8    C  CR16  0  -0.252  -3.7269   3.1227  -0.3891
 M51  C9    C  CR16  0  -0.259  -4.2211   3.8288   0.6993
 M51  C10   C  CR16  0  -0.253  -4.8841   3.1473   1.7115
 M51  C11   C  CR16  0  -0.287  -5.0427   1.7712   1.6457
 M51  C12   C  CH3   0  -0.737  -6.9613  -3.0491   0.9907
 M51  N13   N  NT    0  -0.517  -2.6064  -1.0198  -0.4092
 M51  C14   C  CH2   0  -0.307  -1.9971  -2.0823  -1.1879
 M51  C15   C  CH2   0  -0.296  -0.7245  -1.5800  -1.8392
 M51  N16   N  NT    0  -0.436   0.2172  -1.0918  -0.8453
 M51  C17   C  CH2   0  -0.292  -0.4072  -0.0099  -0.1050
 M51  C18   C  CH2   0  -0.315  -1.6709  -0.4899   0.5789
 M51  C19   C  CH1   0  -0.062   1.4745  -0.7040  -1.4652
 M51  C20   C  CH2   0  -0.319   2.2385  -1.9198  -2.0637
 M51  N21   N  NH1   0  -0.578   3.5799  -1.9465  -1.4859
 M51  C22   C  CH1   0  -0.247   3.8281  -0.5902  -1.0342
 M51  C23   C  CH2   0  -0.481   2.4808  -0.1037  -0.4786
 M51  C24   C  C     0   0.573   4.9212  -0.5573   0.0183
 M51  N25   N  NT    0  -0.473   5.6398   0.5733   0.1349
 M51  C26   C  CH2   0  -0.244   6.6928   0.6642   1.1432
 M51  C27   C  CH2   0  -0.601   7.4573   1.9458   0.8623
 M51  S28   S  S2    0  -0.003   6.1982   3.1106   0.2755
 M51  C29   C  CH2   0  -0.406   5.4371   1.7683  -0.6696
 M51  O30   O  O     0  -0.494   5.1139  -1.5200   0.7498
 M51  H1    H  HCR5  0   0.267  -4.2074  -3.4682  -0.1060
 M51  H7    H  HCR6  0   0.274  -3.5061   1.2087  -1.3272
 M51  H8    H  HCR6  0   0.262  -3.2152   3.6429  -1.1882
 M51  H9    H  HCR6  0   0.259  -4.0913   4.9013   0.7583
 M51  H10   H  HCR6  0   0.262  -5.2743   3.6858   2.5652
 M51  H11   H  HCR6  0   0.268  -5.5493   1.2416   2.4409
 M51  H12   H  HCH3  0   0.246  -6.6412  -3.8765   1.6248
 M51  H12A  H  HCH3  0   0.246  -7.7595  -2.5159   1.5042
 M51  H12B  H  HCH3  0   0.247  -7.3764  -3.4842   0.0803
 M51  H14   H  HCH2  0   0.215  -1.7632  -2.9594  -0.5664
 M51  H14A  H  HCH2  0   0.255  -2.6911  -2.4025  -1.9661
 M51  H15   H  HCH2  0   0.251  -0.2834  -2.4083  -2.3954
 M51  H15A  H  HCH2  0   0.202  -0.9740  -0.7947  -2.5736
 M51  H17   H  HCH2  0   0.253   0.2683   0.3564   0.6686
 M51  H17A  H  HCH2  0   0.199  -0.6551   0.8468  -0.7558
 M51  H18   H  HCH2  0   0.259  -2.1191   0.3484   1.1104
 M51  H18A  H  HCH2  0   0.228  -1.4208  -1.2584   1.3238
 M51  H19   H  HCH1  0   0.215   1.2908   0.0342  -2.2647
 M51  H20   H  HCH2  0   0.241   1.7343  -2.8623  -1.8488
 M51  H20A  H  HCH2  0   0.228   2.3009  -1.8226  -3.1498
 M51  HN21  H  HNH1  0   0.346   3.5785  -2.5497  -0.6716
 M51  H22   H  HCH1  0   0.272   4.1111   0.0156  -1.9021
 M51  H23   H  HCH2  0   0.256   2.4029   0.9809  -0.3952
 M51  H23A  H  HCH2  0   0.245   2.3320  -0.5327   0.5170
 M51  H26   H  HCH2  0   0.256   6.2552   0.6867   2.1433
 M51  H26A  H  HCH2  0   0.265   7.3560  -0.1989   1.0823
 M51  H27   H  HCH2  0   0.301   7.9329   2.3402   1.7579
 M51  H27A  H  HCH2  0   0.284   8.2179   1.8008   0.0947
 M51  H29   H  HCH2  0   0.288   5.9116   1.6757  -1.6489
 M51  H29A  H  HCH2  0   0.294   4.3833   2.0015  -0.8083

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
 M51  C1   C2    aromatic  1.410  0.020  1.410
 M51  C1   C5    aromatic  1.377  0.020  1.377
 M51  C2   N3    aromatic  1.314  0.020  1.314
 M51  C2   C12   single    1.489  0.020  1.489
 M51  N3   N4    aromatic  1.348  0.020  1.348
 M51  N4   C5    aromatic  1.364  0.020  1.364
 M51  N4   C6    single    1.410  0.020  1.410
 M51  C5   N13   single    1.381  0.020  1.381
 M51  C6   C7    aromatic  1.392  0.020  1.392
 M51  C6   C11   aromatic  1.391  0.020  1.391
 M51  C7   C8    aromatic  1.387  0.020  1.387
 M51  C8   C9    aromatic  1.388  0.020  1.388
 M51  C9   C10   aromatic  1.389  0.020  1.389
 M51  C10  C11   aromatic  1.387  0.020  1.387
 M51  N13  C14   single    1.451  0.020  1.451
 M51  N13  C18   single    1.460  0.020  1.460
 M51  C14  C15   single    1.515  0.020  1.515
 M51  C15  N16   single    1.454  0.020  1.454
 M51  N16  C17   single    1.452  0.020  1.452
 M51  N16  C19   single    1.455  0.020  1.455
 M51  C17  C18   single    1.515  0.020  1.515
 M51  C19  C20   single    1.556  0.020  1.556
 M51  C19  C23   single    1.532  0.020  1.532
 M51  C20  N21   single    1.461  0.020  1.461
 M51  N21  C22   single    1.451  0.020  1.451
 M51  C22  C23   single    1.536  0.020  1.536
 M51  C22  C24   single    1.518  0.020  1.518
 M51  C24  N25   single    1.345  0.020  1.345
 M51  C24  O30   double    1.224  0.020  1.224
 M51  N25  C26   single    1.461  0.020  1.461
 M51  N25  C29   single    1.455  0.020  1.455
 M51  C26  C27   single    1.519  0.020  1.519
 M51  C27  S28   single    1.813  0.020  1.813
 M51  S28  C29   single    1.810  0.020  1.810
 M51  C1   H1    single    0.930  0.020  1.080
 M51  C7   H7    single    0.930  0.020  1.080
 M51  C8   H8    single    0.930  0.020  1.080
 M51  C9   H9    single    0.930  0.020  1.080
 M51  C10  H10   single    0.930  0.020  1.080
 M51  C11  H11   single    0.930  0.020  1.080
 M51  C12  H12   single    0.970  0.020  1.090
 M51  C12  H12A  single    0.970  0.020  1.090
 M51  C12  H12B  single    0.970  0.020  1.090
 M51  C14  H14   single    0.970  0.020  1.090
 M51  C14  H14A  single    0.970  0.020  1.090
 M51  C15  H15   single    0.970  0.020  1.090
 M51  C15  H15A  single    0.970  0.020  1.090
 M51  C17  H17   single    0.970  0.020  1.090
 M51  C17  H17A  single    0.970  0.020  1.090
 M51  C18  H18   single    0.970  0.020  1.090
 M51  C18  H18A  single    0.970  0.020  1.090
 M51  C19  H19   single    0.970  0.020  1.090
 M51  C20  H20   single    0.970  0.020  1.090
 M51  C20  H20A  single    0.970  0.020  1.090
 M51  N21  HN21  single    0.890  0.020  1.040
 M51  C22  H22   single    0.970  0.020  1.090
 M51  C23  H23   single    0.970  0.020  1.090
 M51  C23  H23A  single    0.970  0.020  1.090
 M51  C26  H26   single    0.970  0.020  1.090
 M51  C26  H26A  single    0.970  0.020  1.090
 M51  C27  H27   single    0.970  0.020  1.090
 M51  C27  H27A  single    0.970  0.020  1.090
 M51  C29  H29   single    0.970  0.020  1.090
 M51  C29  H29A  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
 M51  H1    C1   C5    127.28  3.000
 M51  H1    C1   C2    127.63  3.000
 M51  C5    C1   C2    105.07  3.000
 M51  C12   C2   N3    121.32  3.000
 M51  C12   C2   C1    127.55  3.000
 M51  N3    C2   C1    111.12  3.000
 M51  N4    N3   C2    105.90  3.000
 M51  C6    N4   C5    129.41  3.000
 M51  C6    N4   N3    118.91  3.000
 M51  C5    N4   N3    111.68  3.000
 M51  N13   C5   N4    122.83  3.000
 M51  N13   C5   C1    130.96  3.000
 M51  N4    C5   C1    106.21  3.000
 M51  C11   C6   C7    120.13  3.000
 M51  C11   C6   N4    119.06  3.000
 M51  C7    C6   N4    120.80  3.000
 M51  H7    C7   C8    120.01  3.000
 M51  H7    C7   C6    120.43  3.000
 M51  C8    C7   C6    119.55  3.000
 M51  H8    C8   C9    120.18  3.000
 M51  H8    C8   C7    119.18  3.000
 M51  C9    C8   C7    120.63  3.000
 M51  H9    C9   C10   120.27  3.000
 M51  H9    C9   C8    120.27  3.000
 M51  C10   C9   C8    119.46  3.000
 M51  H10   C10  C11   119.34  3.000
 M51  H10   C10  C9    120.20  3.000
 M51  C11   C10  C9    120.46  3.000
 M51  H11   C11  C10   120.31  3.000
 M51  H11   C11  C6    119.94  3.000
 M51  C10   C11  C6    119.75  3.000
 M51  H12B  C12  H12A  108.05  3.000
 M51  H12B  C12  H12   107.11  3.000
 M51  H12A  C12  H12   108.22  3.000
 M51  H12B  C12  C2    111.14  3.000
 M51  H12A  C12  C2    110.98  3.000
 M51  H12   C12  C2    111.18  3.000
 M51  C18   N13  C14   111.08  3.000
 M51  C18   N13  C5    116.22  3.000
 M51  C14   N13  C5    114.73  3.000
 M51  H14A  C14  H14   107.71  3.000
 M51  H14A  C14  C15   108.97  3.000
 M51  H14   C14  C15   109.18  3.000
 M51  H14A  C14  N13   109.30  3.000
 M51  H14   C14  N13   111.70  3.000
 M51  C15   C14  N13   109.91  3.000
 M51  H15A  C15  H15   107.00  3.000
 M51  H15A  C15  N16   111.25  3.000
 M51  H15   C15  N16   109.98  3.000
 M51  H15A  C15  C14   109.39  3.000
 M51  H15   C15  C14   107.88  3.000
 M51  N16   C15  C14   111.19  3.000
 M51  C19   N16  C17   112.98  3.000
 M51  C19   N16  C15   110.98  3.000
 M51  C17   N16  C15   108.68  3.000
 M51  H17A  C17  H17   107.26  3.000
 M51  H17A  C17  C18   108.95  3.000
 M51  H17   C17  C18   107.64  3.000
 M51  H17A  C17  N16   111.97  3.000
 M51  H17   C17  N16   110.22  3.000
 M51  C18   C17  N16   110.65  3.000
 M51  H18A  C18  H18   107.52  3.000
 M51  H18A  C18  C17   109.74  3.000
 M51  H18   C18  C17   108.64  3.000
 M51  H18A  C18  N13   110.53  3.000
 M51  H18   C18  N13   110.23  3.000
 M51  C17   C18  N13   110.12  3.000
 M51  H19   C19  C23   108.29  3.000
 M51  H19   C19  C20   109.02  3.000
 M51  C23   C19  C20   103.39  3.000
 M51  H19   C19  N16   110.07  3.000
 M51  C23   C19  N16   113.44  3.000
 M51  C20   C19  N16   112.34  3.000
 M51  H20A  C20  H20   107.42  3.000
 M51  H20A  C20  N21   110.02  3.000
 M51  H20   C20  N21   109.32  3.000
 M51  H20A  C20  C19   109.94  3.000
 M51  H20   C20  C19   111.88  3.000
 M51  N21   C20  C19   108.25  3.000
 M51  HN21  N21  C22   107.85  3.000
 M51  HN21  N21  C20   109.11  3.000
 M51  C22   N21  C20   105.25  3.000
 M51  H22   C22  C24   110.57  3.000
 M51  H22   C22  C23   109.75  3.000
 M51  C24   C22  C23   111.95  3.000
 M51  H22   C22  N21   108.33  3.000
 M51  C24   C22  N21   111.06  3.000
 M51  C23   C22  N21   104.99  3.000
 M51  H23A  C23  H23   108.09  3.000
 M51  H23A  C23  C22   108.91  3.000
 M51  H23   C23  C22   113.90  3.000
 M51  H23A  C23  C19   110.06  3.000
 M51  H23   C23  C19   113.09  3.000
 M51  C22   C23  C19   102.65  3.000
 M51  O30   C24  N25   121.68  3.000
 M51  O30   C24  C22   120.71  3.000
 M51  N25   C24  C22   117.59  3.000
 M51  C29   N25  C26   115.54  3.000
 M51  C29   N25  C24   124.62  3.000
 M51  C26   N25  C24   119.83  3.000
 M51  H26A  C26  H26   108.14  3.000
 M51  H26A  C26  C27   110.58  3.000
 M51  H26   C26  C27   110.72  3.000
 M51  H26A  C26  N25   110.53  3.000
 M51  H26   C26  N25   110.16  3.000
 M51  C27   C26  N25   106.72  3.000
 M51  H27A  C27  H27   108.83  3.000
 M51  H27A  C27  S28   110.00  3.000
 M51  H27   C27  S28   109.70  3.000
 M51  H27A  C27  C26   111.67  3.000
 M51  H27   C27  C26   111.95  3.000
 M51  S28   C27  C26   104.62  3.000
 M51  C29   S28  C27    89.11  3.000
 M51  H29A  C29  H29   108.94  3.000
 M51  H29A  C29  S28   108.36  3.000
 M51  H29   C29  S28   110.40  3.000
 M51  H29A  C29  N25   112.42  3.000
 M51  H29   C29  N25   111.45  3.000
 M51  S28   C29  N25   105.18  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
 M51  CONST_01  N4   N3   C2   C1      0.00   0.0  0
 M51  CONST_02  N3   N4   C5   C1      0.00   0.0  0
 M51  CONST_03  C6   N4   C5   C1    180.00   0.0  0
 M51  CONST_04  N4   C5   C1   C2      0.00   0.0  0
 M51  CONST_05  C5   N4   N3   C2      0.00   0.0  0
 M51  CONST_06  C6   N4   N3   C2    180.00   0.0  0
 M51  CONST_07  C5   C1   C2   N3      0.00   0.0  0
 M51  CONST_10  C8   C7   C6   N4    180.00   0.0  0
 M51  CONST_11  C10  C11  C6   N4    180.00   0.0  0
 M51  CONST_14  C9   C8   C7   C6      0.00   0.0  0
 M51  CONST_15  C9   C10  C11  C6      0.00   0.0  0
 M51  CONST_16  C10  C11  C6   C7      0.00   0.0  0
 M51  CONST_17  C10  C9   C8   C7      0.00   0.0  0
 M51  CONST_18  C11  C6   C7   C8      0.00   0.0  0
 M51  CONST_19  C11  C10  C9   C8      0.00   0.0  0
 M51  CONST_20  N13  C5   C1   C2    180.00   0.0  0
 M51  CONST_21  N13  C5   N4   N3    180.00   0.0  0
 M51  CONST_22  N13  C5   N4   C6      0.00   0.0  0
 M51  CONST_23  C12  C2   N3   N4    180.00   0.0  0
 M51  CONST_24  C12  C2   C1   C5    180.00   0.0  0
 M51  CONST_25  C26  N25  C24  C22   180.00   0.0  0
 M51  CONST_26  C29  N25  C24  C22     0.00   0.0  0
 M51  CONST_27  H1   C1   C2   N3    180.00   0.0  0
 M51  CONST_28  H7   C7   C6   N4      0.00   0.0  0
 M51  CONST_29  H11  C11  C6   N4      0.00   0.0  0
 M51  CONST_30  H8   C8   C7   C6    180.00   0.0  0
 M51  CONST_31  H10  C10  C11  C6    180.00   0.0  0
 M51  CONST_32  H9   C9   C8   C7    180.00   0.0  0
 M51  CONST_33  O30  C24  N25  C26     0.00   0.0  0
 M51  CONST_34  O30  C24  N25  C29   180.00   0.0  0
 M51  Var_01    C14  N13  C5   C1     16.30  30.0  2
 M51  Var_02    C15  C14  N13  C5    169.61  30.0  1
 M51  Var_03    C17  C18  N13  C5   -169.94  30.0  1
 M51  Var_04    N16  C15  C14  N13    58.05  30.0  1
 M51  Var_05    N16  C17  C18  N13   -58.34  30.0  1
 M51  Var_06    C17  N16  C15  C14   -59.44  30.0  1
 M51  Var_07    C18  C17  N16  C15    59.41  30.0  1
 M51  Var_08    C22  N21  C20  C19   -22.14  30.0  1
 M51  Var_09    S28  C27  C26  N25    35.25  30.0  1
 M51  Var_10    S28  C29  N25  C26   -19.12  30.0  1
 M51  Var_11    C29  N25  C26  C27   -10.57  30.0  1
 M51  Var_12    H12  C12  C2   C1     52.77  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
 M51  chir_01  C19  N16  C20  C23  positiv
 M51  chir_02  C22  N21  C24  C23  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
 M51  plan-1  C1   0.020
 M51  plan-1  C2   0.020
 M51  plan-1  N3   0.020
 M51  plan-1  N4   0.020
 M51  plan-1  C5   0.020
 M51  plan-1  C6   0.020
 M51  plan-1  C12  0.020
 M51  plan-1  N13  0.020
 M51  plan-1  H1   0.020
 M51  plan-2  C22  0.020
 M51  plan-2  C24  0.020
 M51  plan-2  N25  0.020
 M51  plan-2  C26  0.020
 M51  plan-2  C29  0.020
 M51  plan-2  O30  0.020
 M51  plan-3  N4   0.020
 M51  plan-3  C6   0.020
 M51  plan-3  C7   0.020
 M51  plan-3  C8   0.020
 M51  plan-3  C9   0.020
 M51  plan-3  C10  0.020
 M51  plan-3  C11  0.020
 M51  plan-3  H7   0.020
 M51  plan-3  H8   0.020
 M51  plan-3  H9   0.020
 M51  plan-3  H10  0.020
 M51  plan-3  H11  0.020

