# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Apr 23 04:52:49 2020
#   Inital geometry file: a 131 line input string
#   Ligand name: (3R,4R)-1-{6-[3-(methylsulfonyl)phenyl]pyrimidin-4-yl}-4-(2,4,5-trifluorophenyl)piperidin-3-amine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[S](=O)(=O)c1cccc(c1)c2cc(ncn2)N3CC[C@@H]([C@@H](N)C3)c4cc(F)c(F)cc4F
#
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
 MA9  MA9  (3R,4R)-1-{6-[3-(methylsulfonyl)phenyl]pyrimidin-4-yl}-4-(2,4,5-trifluorophenyl)piperidin-3-amine  ligand  53  32  .  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_MA9
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
 MA9  C5    C  CR6   0  -0.184   3.8592  -6.2450  -1.9244
 MA9  C6    C  CR16  0  -0.239   5.2178  -6.5246  -1.8833
 MA9  C7    C  CR16  0  -0.226   5.9640  -6.0207  -0.8293
 MA9  C8    C  CR16  0  -0.264   5.3587  -5.2577   0.1568
 MA9  C10   C  CR6   0   0.277   3.3711  -4.1564   1.1743
 MA9  C15   C  CH2   0  -0.414  -0.7371  -0.6663   0.4247
 MA9  C17   C  CR6   0   0.021  -1.6843   1.5414   1.2160
 MA9  C21   C  CR6   0   0.396  -2.2961   4.1996   0.5901
 MA9  C24   C  CR6   0   0.514  -2.8915   2.1249   1.5670
 MA9  C26   C  CH1   0  -0.066  -0.4137   0.0764   2.7998
 MA9  C28   C  CH2   0  -0.319  -0.0690  -1.3790   3.1366
 MA9  F25   F  F     0  -0.306  -3.8049   1.4001   2.2302
 MA9  C23   C  CR16  0  -0.559  -3.2208   3.4337   1.2659
 MA9  F22   F  F     0  -0.302  -2.5739   5.4678   0.2793
 MA9  C19   C  CR6   0   0.408  -1.0756   3.6588   0.2292
 MA9  F     F  F     0  -0.307  -0.1913   4.4201  -0.4259
 MA9  C18   C  CR16  0  -0.463  -0.7742   2.3499   0.5377
 MA9  C16   C  CH1   0  -0.368  -1.3495   0.1201   1.5840
 MA9  C14   C  CH2   0  -0.321  -0.4082  -2.0903   0.8489
 MA9  N27   N  NH2   0  -0.778  -1.0140   0.7757   3.9170
 MA9  N     N  NT    0  -0.496   0.4798  -2.0885   1.9960
 MA9  C12   C  CR6   0   0.595   1.6481  -2.7570   2.0583
 MA9  C11   C  CR16  0  -0.457   2.1829  -3.4895   0.9740
 MA9  N29   N  N     0  -0.479   2.3271  -2.7145   3.2135
 MA9  C30   C  CR16  0   0.059   3.4678  -3.3715   3.2796
 MA9  N31   N  N     0  -0.466   4.0354  -4.0993   2.3384
 MA9  C9    C  CR6   0   0.083   3.9939  -4.9720   0.1074
 MA9  C32   C  CR16  0  -0.307   3.2407  -5.4834  -0.9458
 MA9  S     S  S     0   1.217   2.8798  -6.8849  -3.2616
 MA9  O     O  OS    0  -0.666   3.5372  -8.0818  -3.7809
 MA9  O4    O  OS    0  -0.666   1.4943  -6.9826  -2.8073
 MA9  C     C  CH3   0  -0.790   2.9753  -5.6131  -4.4999
 MA9  H6    H  HCR6  0   0.289   5.6900  -7.1263  -2.6479
 MA9  H7    H  HCR6  0   0.277   7.0236  -6.2293  -0.7745
 MA9  H8    H  HCR6  0   0.271   5.9495  -4.8738   0.9769
 MA9  H151  H  HCH2  0   0.237   0.1773  -0.1851   0.0684
 MA9  H152  H  HCH2  0   0.259  -1.4338  -0.6980  -0.4150
 MA9  H26   H  HCH1  0   0.237   0.5154   0.5948   2.5356
 MA9  H281  H  HCH2  0   0.278   0.6412  -1.4077   3.9574
 MA9  H282  H  HCH2  0   0.232  -0.9825  -1.8912   3.4674
 MA9  H23   H  HCR6  0   0.311  -4.1766   3.8496   1.5568
 MA9  H18   H  HCR6  0   0.290   0.1928   1.9619   0.2422
 MA9  H16   H  HCH1  0   0.256  -2.2737  -0.3955   1.8686
 MA9  H141  H  HCH2  0   0.248  -1.3295  -2.6190   1.1190
 MA9  H142  H  HCH2  0   0.276   0.0291  -2.6253   0.0123
 MA9  H271  H  HNH2  0   0.352  -0.3722   0.7962   4.7000
 MA9  H272  H  HNH2  0   0.340  -1.8357   0.2747   4.2356
 MA9  H11   H  HCR6  0   0.280   1.6970  -3.5193   0.0117
 MA9  H30   H  HCR6  0   0.253   3.9963  -3.3093   4.2262
 MA9  H32   H  HCR6  0   0.282   2.1736  -5.3112  -0.9927
 MA9  H1    H  HCH3  0   0.297   4.0144  -5.4609  -4.7823
 MA9  H2    H  HCH3  0   0.312   2.4005  -5.9554  -5.3602
 MA9  H3    H  HCH3  0   0.297   2.5489  -4.6928  -4.1078

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
 MA9  C5   S     single    1.777  0.020  1.777
 MA9  C5   C32   aromatic  1.386  0.020  1.386
 MA9  C5   C6    aromatic  1.388  0.020  1.388
 MA9  C6   C7    aromatic  1.386  0.020  1.386
 MA9  C6   H6    single    0.930  0.020  1.080
 MA9  C7   C8    aromatic  1.386  0.020  1.386
 MA9  C7   H7    single    0.930  0.020  1.080
 MA9  C8   C9    aromatic  1.395  0.020  1.395
 MA9  C8   H8    single    0.930  0.020  1.080
 MA9  C10  N31   aromatic  1.342  0.020  1.342
 MA9  C10  C9    single    1.480  0.020  1.480
 MA9  C10  C11   aromatic  1.377  0.020  1.377
 MA9  C15  C14   single    1.522  0.020  1.522
 MA9  C15  C16   single    1.529  0.020  1.529
 MA9  C15  H151  single    0.970  0.020  1.090
 MA9  C15  H152  single    0.970  0.020  1.090
 MA9  C17  C16   single    1.506  0.020  1.506
 MA9  C17  C18   aromatic  1.393  0.020  1.393
 MA9  C17  C24   aromatic  1.386  0.020  1.386
 MA9  C21  C19   aromatic  1.383  0.020  1.383
 MA9  C21  C23   aromatic  1.378  0.020  1.378
 MA9  C21  F22   single    1.335  0.020  1.335
 MA9  C24  F25   single    1.341  0.020  1.341
 MA9  C24  C23   aromatic  1.383  0.020  1.383
 MA9  C26  C28   single    1.533  0.020  1.533
 MA9  C26  C16   single    1.535  0.020  1.535
 MA9  C26  N27   single    1.448  0.020  1.448
 MA9  C26  H26   single    0.970  0.020  1.090
 MA9  C28  N     single    1.451  0.020  1.451
 MA9  C28  H281  single    0.970  0.020  1.090
 MA9  C28  H282  single    0.970  0.020  1.090
 MA9  C23  H23   single    0.930  0.020  1.080
 MA9  C19  C18   aromatic  1.378  0.020  1.378
 MA9  C19  F     single    1.338  0.020  1.338
 MA9  C18  H18   single    0.930  0.020  1.080
 MA9  C16  H16   single    0.970  0.020  1.090
 MA9  C14  N     single    1.451  0.020  1.451
 MA9  C14  H141  single    0.970  0.020  1.090
 MA9  C14  H142  single    0.970  0.020  1.090
 MA9  N27  H271  single    0.890  0.020  1.040
 MA9  N27  H272  single    0.890  0.020  1.040
 MA9  N    C12   single    1.347  0.020  1.347
 MA9  C12  N29   aromatic  1.341  0.020  1.341
 MA9  C12  C11   aromatic  1.414  0.020  1.414
 MA9  C11  H11   single    0.930  0.020  1.080
 MA9  N29  C30   aromatic  1.318  0.020  1.318
 MA9  C30  N31   aromatic  1.318  0.020  1.318
 MA9  C30  H30   single    0.930  0.020  1.080
 MA9  C9   C32   aromatic  1.392  0.020  1.392
 MA9  C32  H32   single    0.930  0.020  1.080
 MA9  S    C     single    1.778  0.020  1.778
 MA9  S    O4    double    1.461  0.020  1.461
 MA9  S    O     double    1.461  0.020  1.461
 MA9  C    H1    single    0.970  0.020  1.090
 MA9  C    H2    single    0.970  0.020  1.090
 MA9  C    H3    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
 MA9  S     C5   C32   118.91  3.000
 MA9  C32   C5   C6    121.79  3.000
 MA9  S     C5   C6    119.30  3.000
 MA9  H6    C6   C7    120.31  3.000
 MA9  H6    C6   C5    121.24  3.000
 MA9  C7    C6   C5    118.45  3.000
 MA9  H7    C7   C8    119.87  3.000
 MA9  H7    C7   C6    119.73  3.000
 MA9  C8    C7   C6    120.40  3.000
 MA9  H8    C8   C9    119.25  3.000
 MA9  H8    C8   C7    119.77  3.000
 MA9  C9    C8   C7    120.98  3.000
 MA9  C9    C10  N31   116.14  3.000
 MA9  C9    C10  C11   121.67  3.000
 MA9  N31   C10  C11   122.19  3.000
 MA9  H152  C15  H151  107.22  3.000
 MA9  H152  C15  C14   108.97  3.000
 MA9  H151  C15  C14   108.78  3.000
 MA9  H152  C15  C16   110.04  3.000
 MA9  H151  C15  C16   110.85  3.000
 MA9  C14   C15  C16   110.88  3.000
 MA9  C16   C17  C18   121.42  3.000
 MA9  C18   C17  C24   116.60  3.000
 MA9  C16   C17  C24   121.94  3.000
 MA9  C19   C21  F22   119.64  3.000
 MA9  F22   C21  C23   120.17  3.000
 MA9  C19   C21  C23   120.19  3.000
 MA9  C23   C24  F25   117.19  3.000
 MA9  C23   C24  C17   123.42  3.000
 MA9  F25   C24  C17   119.40  3.000
 MA9  H26   C26  N27   107.99  3.000
 MA9  H26   C26  C16   108.20  3.000
 MA9  N27   C26  C16   110.16  3.000
 MA9  H26   C26  C28   108.14  3.000
 MA9  N27   C26  C28   112.46  3.000
 MA9  C16   C26  C28   109.76  3.000
 MA9  H282  C28  H281  107.70  3.000
 MA9  H282  C28  N     108.87  3.000
 MA9  H281  C28  N     109.51  3.000
 MA9  H282  C28  C26   108.77  3.000
 MA9  H281  C28  C26   109.77  3.000
 MA9  N     C28  C26   112.12  3.000
 MA9  H23   C23  C24   121.03  3.000
 MA9  H23   C23  C21   120.73  3.000
 MA9  C24   C23  C21   118.24  3.000
 MA9  C18   C19  F     120.36  3.000
 MA9  F     C19  C21   119.24  3.000
 MA9  C18   C19  C21   120.40  3.000
 MA9  H18   C18  C19   118.32  3.000
 MA9  H18   C18  C17   120.54  3.000
 MA9  C19   C18  C17   121.14  3.000
 MA9  H16   C16  C26   107.16  3.000
 MA9  H16   C16  C17   108.67  3.000
 MA9  C26   C16  C17   110.86  3.000
 MA9  H16   C16  C15   107.02  3.000
 MA9  C26   C16  C15   109.99  3.000
 MA9  C17   C16  C15   112.90  3.000
 MA9  H142  C14  H141  106.91  3.000
 MA9  H142  C14  N     111.32  3.000
 MA9  H141  C14  N     108.68  3.000
 MA9  H142  C14  C15   109.49  3.000
 MA9  H141  C14  C15   109.78  3.000
 MA9  N     C14  C15   110.58  3.000
 MA9  H272  N27  H271  106.30  3.000
 MA9  H272  N27  C26   109.87  3.000
 MA9  H271  N27  C26   110.10  3.000
 MA9  C12   N    C14   124.52  3.000
 MA9  C12   N    C28   122.29  3.000
 MA9  C14   N    C28   112.99  3.000
 MA9  N29   C12  C11   119.06  3.000
 MA9  C11   C12  N     123.34  3.000
 MA9  N29   C12  N     117.60  3.000
 MA9  H11   C11  C12   121.89  3.000
 MA9  H11   C11  C10   120.34  3.000
 MA9  C12   C11  C10   117.76  3.000
 MA9  C30   N29  C12   117.76  3.000
 MA9  H30   C30  N31   116.39  3.000
 MA9  H30   C30  N29   115.88  3.000
 MA9  N31   C30  N29   127.74  3.000
 MA9  C30   N31  C10   115.46  3.000
 MA9  C32   C9   C10   121.33  3.000
 MA9  C32   C9   C8    118.74  3.000
 MA9  C10   C9   C8    119.92  3.000
 MA9  H32   C32  C9    120.52  3.000
 MA9  H32   C32  C5    119.81  3.000
 MA9  C9    C32  C5    119.65  3.000
 MA9  C     S    O4    108.38  3.000
 MA9  O4    S    O     118.84  3.000
 MA9  C     S    O     108.32  3.000
 MA9  O     S    C5    108.33  3.000
 MA9  O4    S    C5    108.22  3.000
 MA9  C     S    C5    103.71  3.000
 MA9  H3    C    H2    110.10  3.000
 MA9  H3    C    H1    110.48  3.000
 MA9  H2    C    H1    110.06  3.000
 MA9  H3    C    S     109.46  3.000
 MA9  H2    C    S     107.27  3.000
 MA9  H1    C    S     109.41  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
 MA9  CONST_01  C8   C9   C32  C5     0.00   0.0  0
 MA9  CONST_02  C10  C9   C32  C5   180.00   0.0  0
 MA9  CONST_03  C8   C7   C6   C5     0.00   0.0  0
 MA9  CONST_04  C9   C32  C5   C6     0.00   0.0  0
 MA9  CONST_05  C9   C8   C7   C6     0.00   0.0  0
 MA9  CONST_06  C32  C5   C6   C7     0.00   0.0  0
 MA9  CONST_07  C10  C9   C8   C7   180.00   0.0  0
 MA9  CONST_08  C32  C9   C8   C7     0.00   0.0  0
 MA9  CONST_11  N29  C30  N31  C10    0.00   0.0  0
 MA9  CONST_12  N29  C12  C11  C10    0.00   0.0  0
 MA9  CONST_13  C21  C19  C18  C17    0.00   0.0  0
 MA9  CONST_14  C21  C23  C24  C17    0.00   0.0  0
 MA9  CONST_15  C19  C18  C17  C24    0.00   0.0  0
 MA9  CONST_16  C19  C21  C23  C24    0.00   0.0  0
 MA9  CONST_17  C18  C19  C21  C23    0.00   0.0  0
 MA9  CONST_18  C18  C17  C24  C23    0.00   0.0  0
 MA9  CONST_19  N31  C30  N29  C12    0.00   0.0  0
 MA9  CONST_20  N31  C10  C11  C12    0.00   0.0  0
 MA9  CONST_21  C9   C10  C11  C12  180.00   0.0  0
 MA9  CONST_22  C30  N31  C10  C11    0.00   0.0  0
 MA9  CONST_24  C30  N29  C12  C11    0.00   0.0  0
 MA9  CONST_25  C9   C10  N31  C30  180.00   0.0  0
 MA9  CONST_27  N    C12  C11  C10  180.00   0.0  0
 MA9  CONST_28  C16  C17  C24  C23  180.00   0.0  0
 MA9  CONST_29  C16  C17  C18  C19  180.00   0.0  0
 MA9  CONST_30  C30  N29  C12  N    180.00   0.0  0
 MA9  CONST_31  S    C5   C6   C7   180.00   0.0  0
 MA9  CONST_32  F    C19  C18  C17  180.00   0.0  0
 MA9  CONST_33  F25  C24  C23  C21  180.00   0.0  0
 MA9  CONST_34  F22  C21  C23  C24  180.00   0.0  0
 MA9  CONST_35  C16  C17  C24  F25    0.00   0.0  0
 MA9  CONST_36  C18  C17  C24  F25  180.00   0.0  0
 MA9  CONST_37  F    C19  C21  C23  180.00   0.0  0
 MA9  CONST_38  C18  C19  C21  F22  180.00   0.0  0
 MA9  CONST_39  S    C5   C32  C9   180.00   0.0  0
 MA9  CONST_40  H7   C7   C6   C5   180.00   0.0  0
 MA9  CONST_41  H32  C32  C5   C6   180.00   0.0  0
 MA9  CONST_42  H8   C8   C7   C6   180.00   0.0  0
 MA9  CONST_43  H6   C6   C7   C8   180.00   0.0  0
 MA9  CONST_44  H30  C30  N31  C10  180.00   0.0  0
 MA9  CONST_45  H23  C23  C24  C17  180.00   0.0  0
 MA9  CONST_46  H18  C18  C19  C21  180.00   0.0  0
 MA9  CONST_47  H11  C11  C12  N      0.00   0.0  0
 MA9  Var_01    C28  N    C14  C15   57.94  30.0  1
 MA9  Var_02    C14  N    C28  C26  -57.58  30.0  1
 MA9  Var_03    N29  C12  N    C28   -2.10  30.0  2
 MA9  Var_04    N    C14  C15  C16  -56.69  30.0  1
 MA9  Var_05    C    S    C5   C6   -89.74  30.0  2
 MA9  Var_06    H1   C    S    C5    59.83  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
 MA9  chir_01  C26  C28  C16  N27  negativ
 MA9  chir_02  C16  C26  C17  C15  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
 MA9  plan-1  C5   0.020
 MA9  plan-1  C6   0.020
 MA9  plan-1  C7   0.020
 MA9  plan-1  C8   0.020
 MA9  plan-1  C10  0.020
 MA9  plan-1  C9   0.020
 MA9  plan-1  C32  0.020
 MA9  plan-1  S    0.020
 MA9  plan-1  H6   0.020
 MA9  plan-1  H7   0.020
 MA9  plan-1  H8   0.020
 MA9  plan-1  H32  0.020
 MA9  plan-2  C10  0.020
 MA9  plan-2  N    0.020
 MA9  plan-2  C12  0.020
 MA9  plan-2  C11  0.020
 MA9  plan-2  N29  0.020
 MA9  plan-2  C30  0.020
 MA9  plan-2  N31  0.020
 MA9  plan-2  C9   0.020
 MA9  plan-2  H11  0.020
 MA9  plan-2  H30  0.020
 MA9  plan-3  C17  0.020
 MA9  plan-3  C21  0.020
 MA9  plan-3  C24  0.020
 MA9  plan-3  F25  0.020
 MA9  plan-3  C23  0.020
 MA9  plan-3  F22  0.020
 MA9  plan-3  C19  0.020
 MA9  plan-3  F    0.020
 MA9  plan-3  C18  0.020
 MA9  plan-3  C16  0.020
 MA9  plan-3  H23  0.020
 MA9  plan-3  H18  0.020

