# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr  1 19:25:03 2020
#   Inital geometry file: a 130 line input string
#   Ligand name: 6-{[(3R,4R)-4-(2-{[2,2-difluoro-2-(3-fluorophenyl)ethyl]amino}ethoxy)pyrrolidin-3-yl]methyl}-4-methylpyridin-2-amine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cc1cc(N)nc(C[C@@H]2CNC[C@@H]2OCCNCC(F)(F)c3cccc(F)c3)c1
#
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
 3XB  3XB  6-{[(3R,4R)-4-(2-{[2,2-difluoro-2-(3-fluorophenyl)ethyl]amino}ethoxy)pyrrolidin-3-yl]methyl}-4-methylpyridin-2-amine  ligand  56  29  .  2021-08-04  2021-08-04  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_3XB
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
 3XB  C1    C  CH2   0  -0.166  -0.1436  -3.0373  -1.2689
 3XB  O1    O  O2    0  -0.490  -1.0665  -2.0739  -0.8171
 3XB  C2    C  CH2   0  -0.299   1.1501  -2.3333  -1.6074
 3XB  N2    N  NH1   0  -0.613   1.7575  -1.7655  -0.4176
 3XB  C3    C  CH2   0  -0.363   2.9310  -0.9827  -0.7171
 3XB  C4    C  CT    0   0.777   3.7236  -0.6520   0.5325
 3XB  F5    F  F     0  -0.347   2.9079  -0.0245   1.4346
 3XB  F6    F  F     0  -0.340   4.1271  -1.7999   1.1474
 3XB  N1'   N  NH1   0  -0.613  -3.3991  -2.9469   1.6571
 3XB  C11   C  CR6   0  -0.080   4.9203   0.2149   0.2446
 3XB  C12   C  CR16  0  -0.455   4.8030   1.5985   0.3103
 3XB  C13   C  CR6   0   0.551   5.9017   2.3704  -0.0119
 3XB  F13   F  F     0  -0.312   5.7871   3.7054   0.0567
 3XB  C14   C  CR16  0  -0.409   7.1089   1.8219  -0.3971
 3XB  C15   C  CR16  0  -0.223   7.2079   0.4397  -0.4606
 3XB  C16   C  CR16  0  -0.299   6.1235  -0.3653  -0.1419
 3XB  N1A   N  N     0  -0.485  -5.1489   0.7212  -1.0976
 3XB  C2'   C  CH2   0  -0.313  -2.2005  -3.3527   0.9445
 3XB  C2A   C  CR6   0   0.281  -4.0187   0.9088  -0.4124
 3XB  C3'   C  CH1   0   0.071  -2.2989  -2.6061  -0.4022
 3XB  C3A   C  CR16  0  -0.433  -3.8521   1.9520   0.4811
 3XB  C4'   C  CH1   0  -0.291  -3.3255  -1.4769  -0.1362
 3XB  C4A   C  CR6   0   0.204  -4.9068   2.8493   0.6849
 3XB  C5'   C  CH2   0  -0.269  -3.5450  -1.5310   1.3751
 3XB  C5A   C  CR16  0  -0.448  -6.0743   2.6517  -0.0233
 3XB  C6A   C  CR6   0   0.439  -6.1553   1.5686  -0.9161
 3XB  N6A   N  NH2   0  -0.840  -7.2744   1.3739  -1.6743
 3XB  C7A   C  CH2   0  -0.491  -2.9261  -0.0960  -0.6489
 3XB  C8A   C  CH3   0  -0.725  -4.7568   3.9993   1.6336
 3XB  H1    H  HCH2  0   0.207   0.0454  -3.8009  -0.5026
 3XB  H1A   H  HCH2  0   0.212  -0.5250  -3.5551  -2.1597
 3XB  H2    H  HCH2  0   0.234   1.8344  -3.0675  -2.0406
 3XB  H2A   H  HCH2  0   0.203   0.9589  -1.5831  -2.3907
 3XB  HN2   H  HNH1  0   0.350   1.0724  -1.1814   0.0455
 3XB  H3    H  HCH2  0   0.259   3.5891  -1.5546  -1.3773
 3XB  H3A   H  HCH2  0   0.237   2.7161  -0.0410  -1.2442
 3XB  HN1'  H  HNH1  0   0.350  -3.3231  -3.1334   2.6482
 3XB  H12   H  HCR6  0   0.285   3.8792   2.0801   0.6027
 3XB  H14   H  HCR6  0   0.286   7.9494   2.4571  -0.6440
 3XB  H15   H  HCR6  0   0.276   8.1425  -0.0132  -0.7621
 3XB  H16   H  HCR6  0   0.269   6.2262  -1.4402  -0.2027
 3XB  H2'   H  HCH2  0   0.203  -1.2728  -3.0294   1.4425
 3XB  H2'A  H  HCH2  0   0.230  -2.1571  -4.4381   0.8354
 3XB  H3'   H  HCH1  0   0.214  -2.6837  -3.2739  -1.1842
 3XB  H3AA  H  HCR6  0   0.240  -2.9195   2.0649   1.0203
 3XB  H4'   H  HCH1  0   0.251  -4.2617  -1.7586  -0.6244
 3XB  H5'   H  HCH2  0   0.230  -4.5306  -1.1678   1.6715
 3XB  H5'A  H  HCH2  0   0.193  -2.7947  -0.9041   1.8852
 3XB  H5A   H  HCR6  0   0.253  -6.9203   3.3173   0.1015
 3XB  HN6A  H  HNH2  0   0.387  -8.1313   1.7969  -1.3599
 3XB  HN6B  H  HNH2  0   0.379  -7.3885   0.4553  -2.0702
 3XB  H7A   H  HCH2  0   0.246  -2.7182  -0.1441  -1.7209
 3XB  H7AA  H  HCH2  0   0.239  -2.0105   0.2392  -0.1596
 3XB  H8A   H  HCH3  0   0.254  -4.1212   4.7730   1.1984
 3XB  H8AA  H  HCH3  0   0.246  -5.7164   4.4549   1.8725
 3XB  H8AB  H  HCH3  0   0.248  -4.2836   3.6841   2.5637

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
 3XB  O1   C1    single    1.409  0.020  1.409
 3XB  C2   C1    single    1.511  0.020  1.511
 3XB  C1   H1    single    0.970  0.020  1.090
 3XB  C1   H1A   single    0.970  0.020  1.090
 3XB  C3'  O1    single    1.405  0.020  1.405
 3XB  C2   N2    single    1.452  0.020  1.452
 3XB  C2   H2    single    0.970  0.020  1.090
 3XB  C2   H2A   single    0.970  0.020  1.090
 3XB  N2   C3    single    1.442  0.020  1.442
 3XB  N2   HN2   single    0.890  0.020  1.040
 3XB  C3   C4    single    1.516  0.020  1.516
 3XB  C3   H3    single    0.970  0.020  1.090
 3XB  C3   H3A   single    0.970  0.020  1.090
 3XB  F6   C4    single    1.363  0.020  1.363
 3XB  C4   C11   single    1.506  0.020  1.506
 3XB  C4   F5    single    1.369  0.020  1.369
 3XB  N1'  C5'   single    1.451  0.020  1.451
 3XB  N1'  C2'   single    1.452  0.020  1.452
 3XB  N1'  HN1'  single    0.890  0.020  1.040
 3XB  C16  C11   aromatic  1.391  0.020  1.391
 3XB  C11  C12   aromatic  1.390  0.020  1.390
 3XB  C12  C13   aromatic  1.381  0.020  1.381
 3XB  C12  H12   single    0.930  0.020  1.080
 3XB  C14  C13   aromatic  1.381  0.020  1.381
 3XB  C13  F13   single    1.342  0.020  1.342
 3XB  C15  C14   aromatic  1.387  0.020  1.387
 3XB  C14  H14   single    0.930  0.020  1.080
 3XB  C16  C15   aromatic  1.388  0.020  1.388
 3XB  C15  H15   single    0.930  0.020  1.080
 3XB  C16  H16   single    0.930  0.020  1.080
 3XB  C6A  N1A   aromatic  1.328  0.020  1.328
 3XB  C2A  N1A   aromatic  1.335  0.020  1.335
 3XB  C2'  C3'   single    1.543  0.020  1.543
 3XB  C2'  H2'   single    0.970  0.020  1.090
 3XB  C2'  H2'A  single    0.970  0.020  1.090
 3XB  C3A  C2A   aromatic  1.384  0.020  1.384
 3XB  C2A  C7A   single    1.503  0.020  1.503
 3XB  C4'  C3'   single    1.549  0.020  1.549
 3XB  C3'  H3'   single    0.970  0.020  1.090
 3XB  C4A  C3A   aromatic  1.400  0.020  1.400
 3XB  C3A  H3AA  single    0.930  0.020  1.080
 3XB  C5'  C4'   single    1.528  0.020  1.528
 3XB  C4'  C7A   single    1.526  0.020  1.526
 3XB  C4'  H4'   single    0.970  0.020  1.090
 3XB  C8A  C4A   single    1.498  0.020  1.498
 3XB  C4A  C5A   aromatic  1.380  0.020  1.380
 3XB  C5'  H5'   single    0.970  0.020  1.090
 3XB  C5'  H5'A  single    0.970  0.020  1.090
 3XB  C5A  C6A   aromatic  1.406  0.020  1.406
 3XB  C5A  H5A   single    0.930  0.020  1.080
 3XB  C6A  N6A   single    1.366  0.020  1.366
 3XB  N6A  HN6A  single    0.890  0.020  1.040
 3XB  N6A  HN6B  single    0.890  0.020  1.040
 3XB  C7A  H7A   single    0.970  0.020  1.090
 3XB  C7A  H7AA  single    0.970  0.020  1.090
 3XB  C8A  H8A   single    0.970  0.020  1.090
 3XB  C8A  H8AA  single    0.970  0.020  1.090
 3XB  C8A  H8AB  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
 3XB  H1A   C1   H1    107.33  3.000
 3XB  H1A   C1   C2    109.58  3.000
 3XB  H1    C1   C2    109.44  3.000
 3XB  H1A   C1   O1    110.79  3.000
 3XB  H1    C1   O1    111.38  3.000
 3XB  C2    C1   O1    108.31  3.000
 3XB  C3'   O1   C1    114.22  3.000
 3XB  H2A   C2   H2    106.52  3.000
 3XB  H2A   C2   N2    112.90  3.000
 3XB  H2    C2   N2    109.00  3.000
 3XB  H2A   C2   C1    109.15  3.000
 3XB  H2    C2   C1    108.17  3.000
 3XB  N2    C2   C1    110.91  3.000
 3XB  HN2   N2   C3    109.42  3.000
 3XB  HN2   N2   C2    108.51  3.000
 3XB  C3    N2   C2    112.50  3.000
 3XB  H3A   C3   H3    106.01  3.000
 3XB  H3A   C3   C4    108.08  3.000
 3XB  H3    C3   C4    107.28  3.000
 3XB  H3A   C3   N2    113.89  3.000
 3XB  H3    C3   N2    109.34  3.000
 3XB  C4    C3   N2    111.88  3.000
 3XB  C11   C4   F6    109.62  3.000
 3XB  C11   C4   F5    109.62  3.000
 3XB  F6    C4   F5    105.38  3.000
 3XB  F5    C4   C3    109.37  3.000
 3XB  C11   C4   C3    112.55  3.000
 3XB  F6    C4   C3    110.05  3.000
 3XB  HN1'  N1'  C5'   112.21  3.000
 3XB  HN1'  N1'  C2'   111.56  3.000
 3XB  C5'   N1'  C2'   105.09  3.000
 3XB  C16   C11  C12   120.10  3.000
 3XB  C12   C11  C4    119.80  3.000
 3XB  C16   C11  C4    120.04  3.000
 3XB  H12   C12  C13   119.58  3.000
 3XB  H12   C12  C11   121.86  3.000
 3XB  C13   C12  C11   118.57  3.000
 3XB  C14   C13  F13   118.96  3.000
 3XB  F13   C13  C12   118.45  3.000
 3XB  C14   C13  C12   122.59  3.000
 3XB  H14   C14  C15   121.27  3.000
 3XB  H14   C14  C13   120.63  3.000
 3XB  C15   C14  C13   118.10  3.000
 3XB  H15   C15  C16   119.77  3.000
 3XB  H15   C15  C14   119.46  3.000
 3XB  C16   C15  C14   120.78  3.000
 3XB  H16   C16  C15   119.31  3.000
 3XB  H16   C16  C11   120.83  3.000
 3XB  C15   C16  C11   119.86  3.000
 3XB  C6A   N1A  C2A   118.80  3.000
 3XB  H2'A  C2'  H2'   107.66  3.000
 3XB  H2'A  C2'  C3'   113.36  3.000
 3XB  H2'   C2'  C3'   107.84  3.000
 3XB  H2'A  C2'  N1'   111.08  3.000
 3XB  H2'   C2'  N1'   113.03  3.000
 3XB  C3'   C2'  N1'   103.91  3.000
 3XB  C7A   C2A  C3A   121.21  3.000
 3XB  C7A   C2A  N1A   116.15  3.000
 3XB  C3A   C2A  N1A   122.64  3.000
 3XB  H3'   C3'  C4'   109.48  3.000
 3XB  H3'   C3'  C2'   110.46  3.000
 3XB  C4'   C3'  C2'   104.19  3.000
 3XB  H3'   C3'  O1    109.12  3.000
 3XB  C4'   C3'  O1    110.85  3.000
 3XB  C2'   C3'  O1    112.65  3.000
 3XB  H3AA  C3A  C4A   120.63  3.000
 3XB  H3AA  C3A  C2A   120.24  3.000
 3XB  C4A   C3A  C2A   119.12  3.000
 3XB  H4'   C4'  C7A   107.90  3.000
 3XB  H4'   C4'  C5'   108.03  3.000
 3XB  C7A   C4'  C5'   113.70  3.000
 3XB  H4'   C4'  C3'   107.65  3.000
 3XB  C7A   C4'  C3'   115.36  3.000
 3XB  C5'   C4'  C3'   103.84  3.000
 3XB  C8A   C4A  C5A   121.31  3.000
 3XB  C5A   C4A  C3A   118.10  3.000
 3XB  C8A   C4A  C3A   120.59  3.000
 3XB  H5'A  C5'  H5'   107.43  3.000
 3XB  H5'A  C5'  C4'   109.85  3.000
 3XB  H5'   C5'  C4'   112.74  3.000
 3XB  H5'A  C5'  N1'   113.35  3.000
 3XB  H5'   C5'  N1'   111.27  3.000
 3XB  C4'   C5'  N1'   102.26  3.000
 3XB  H5A   C5A  C6A   120.09  3.000
 3XB  H5A   C5A  C4A   120.90  3.000
 3XB  C6A   C5A  C4A   119.01  3.000
 3XB  N6A   C6A  C5A   120.64  3.000
 3XB  N6A   C6A  N1A   117.01  3.000
 3XB  C5A   C6A  N1A   122.32  3.000
 3XB  HN6B  N6A  HN6A  114.21  3.000
 3XB  HN6B  N6A  C6A   116.19  3.000
 3XB  HN6A  N6A  C6A   117.68  3.000
 3XB  H7AA  C7A  H7A   107.09  3.000
 3XB  H7AA  C7A  C4'   110.30  3.000
 3XB  H7A   C7A  C4'   109.85  3.000
 3XB  H7AA  C7A  C2A   109.51  3.000
 3XB  H7A   C7A  C2A   108.78  3.000
 3XB  C4'   C7A  C2A   111.21  3.000
 3XB  H8AB  C8A  H8AA  108.44  3.000
 3XB  H8AB  C8A  H8A   107.00  3.000
 3XB  H8AA  C8A  H8A   107.70  3.000
 3XB  H8AB  C8A  C4A   111.21  3.000
 3XB  H8AA  C8A  C4A   111.83  3.000
 3XB  H8A   C8A  C4A   110.48  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
 3XB  CONST_01  C14   C15  C16  C11     0.00   0.0  0
 3XB  CONST_02  C14   C13  C12  C11     0.00   0.0  0
 3XB  CONST_03  C15   C16  C11  C12     0.00   0.0  0
 3XB  CONST_04  C15   C14  C13  C12     0.00   0.0  0
 3XB  CONST_05  C16   C11  C12  C13     0.00   0.0  0
 3XB  CONST_06  C16   C15  C14  C13     0.00   0.0  0
 3XB  CONST_07  C4A   C5A  C6A  N1A     0.00   0.0  0
 3XB  CONST_08  C4A   C3A  C2A  N1A     0.00   0.0  0
 3XB  CONST_09  C5A   C6A  N1A  C2A     0.00   0.0  0
 3XB  CONST_10  C5A   C4A  C3A  C2A     0.00   0.0  0
 3XB  CONST_11  C6A   N1A  C2A  C3A     0.00   0.0  0
 3XB  CONST_12  C6A   C5A  C4A  C3A     0.00   0.0  0
 3XB  CONST_13  C15   C16  C11  C4    180.00   0.0  0
 3XB  CONST_14  C13   C12  C11  C4    180.00   0.0  0
 3XB  CONST_15  F13   C13  C12  C11   180.00   0.0  0
 3XB  CONST_16  C15   C14  C13  F13   180.00   0.0  0
 3XB  CONST_17  N6A   C6A  N1A  C2A   180.00   0.0  0
 3XB  CONST_18  C8A   C4A  C3A  C2A   180.00   0.0  0
 3XB  CONST_19  C7A   C2A  C3A  C4A   180.00   0.0  0
 3XB  CONST_20  N6A   C6A  C5A  C4A   180.00   0.0  0
 3XB  CONST_21  C7A   C2A  N1A  C6A   180.00   0.0  0
 3XB  CONST_22  C8A   C4A  C5A  C6A   180.00   0.0  0
 3XB  CONST_23  H15   C15  C16  C11   180.00   0.0  0
 3XB  CONST_24  H16   C16  C11  C12   180.00   0.0  0
 3XB  CONST_25  H14   C14  C13  C12   180.00   0.0  0
 3XB  CONST_26  H12   C12  C13  C14   180.00   0.0  0
 3XB  CONST_27  H5A   C5A  C6A  N1A   180.00   0.0  0
 3XB  CONST_28  H3AA  C3A  C2A  N1A   180.00   0.0  0
 3XB  Var_01    C4'   C5'  N1'  C2'    46.52  30.0  1
 3XB  Var_02    C5'   N1'  C2'  C3'   -40.67  30.0  1
 3XB  Var_03    C4'   C7A  C2A  N1A   -66.36  30.0  2
 3XB  Var_04    C16   C11  C4   C3    -85.71  30.0  2
 3XB  Var_05    H8A   C8A  C4A  C3A    74.14  30.0  2
 3XB  Var_06    C11   C4   C3   N2   -177.54  30.0  3
 3XB  Var_07    H1    C1   O1   C3'   -56.55  30.0  3
 3XB  Var_08    C3    N2   C2   C1   -174.76  30.0  3
 3XB  Var_09    N2    C2   C1   O1     65.46  30.0  2
 3XB  Var_10    C4    C3   N2   C2   -167.49  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
 3XB  chir_01  C3'  O1   C2'  C4'  negativ
 3XB  chir_02  C4'  C3'  C5'  C7A  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
 3XB  plan-1  C4    0.020
 3XB  plan-1  C11   0.020
 3XB  plan-1  C12   0.020
 3XB  plan-1  C13   0.020
 3XB  plan-1  F13   0.020
 3XB  plan-1  C14   0.020
 3XB  plan-1  C15   0.020
 3XB  plan-1  C16   0.020
 3XB  plan-1  H12   0.020
 3XB  plan-1  H14   0.020
 3XB  plan-1  H15   0.020
 3XB  plan-1  H16   0.020
 3XB  plan-2  N1A   0.020
 3XB  plan-2  C2A   0.020
 3XB  plan-2  C3A   0.020
 3XB  plan-2  C4A   0.020
 3XB  plan-2  C5A   0.020
 3XB  plan-2  C6A   0.020
 3XB  plan-2  N6A   0.020
 3XB  plan-2  C7A   0.020
 3XB  plan-2  C8A   0.020
 3XB  plan-2  H3AA  0.020
 3XB  plan-2  H5A   0.020
 3XB  plan-3  C6A   0.020
 3XB  plan-3  N6A   0.020
 3XB  plan-3  HN6A  0.020
 3XB  plan-3  HN6B  0.020

