# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr  1 17:01:53 2020
#   Inital geometry file: a 130 line input string
#   Ligand name: 6-{[(3R,4R)-4-(2-{[2,2-difluoro-2-(4-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)c3ccc(F)cc3)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
 3XC  3XC  6-{[(3R,4R)-4-(2-{[2,2-difluoro-2-(4-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_3XC
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
 3XC  C1    C  CH2   0  -0.154   0.2251   2.9645  -1.2619
 3XC  O1    O  O2    0  -0.487   1.1628   2.0098  -0.8220
 3XC  C2    C  CH2   0  -0.285  -1.0586   2.2472  -1.6098
 3XC  N2    N  NH1   0  -0.602  -1.6584   1.6559  -0.4281
 3XC  C3    C  CH2   0  -0.342  -2.8440   0.8932  -0.7313
 3XC  C4    C  CT    0   0.775  -3.6159   0.5231   0.5201
 3XC  F5    F  F     0  -0.347  -2.7924  -0.1633   1.3724
 3XC  F6    F  F     0  -0.339  -3.9745   1.6528   1.1959
 3XC  N1'   N  NH1   0  -0.598   3.4883   2.9387   1.6608
 3XC  C11   C  CR6   0  -0.104  -4.8387  -0.3020   0.2283
 3XC  C12   C  CR16  0  -0.255  -4.7675  -1.6909   0.2183
 3XC  C13   C  CR16  0  -0.375  -5.8826  -2.4533  -0.0953
 3XC  C14   C  CR6   0   0.536  -7.0633  -1.8049  -0.3994
 3XC  F14   F  F     0  -0.308  -8.1463  -2.5350  -0.7006
 3XC  C15   C  CR16  0  -0.376  -7.1642  -0.4272  -0.4039
 3XC  C16   C  CR16  0  -0.248  -6.0416   0.3219  -0.0866
 3XC  N1A   N  N     0  -0.484   5.2141  -0.7944  -1.1428
 3XC  C2'   C  CH2   0  -0.298   2.2473   3.2707   0.9858
 3XC  C2A   C  CR6   0   0.286   4.1421  -0.9329  -0.3595
 3XC  C3'   C  CH1   0   0.085   2.3757   2.5574  -0.3741
 3XC  C3A   C  CR16  0  -0.410   4.0554  -1.9045   0.6214
 3XC  C4'   C  CH1   0  -0.291   3.4289   1.4469  -0.1226
 3XC  C4A   C  CR6   0   0.219   5.1295  -2.7814   0.8085
 3XC  C5'   C  CH2   0  -0.261   3.6997   1.5308   1.3807
 3XC  C5A   C  CR16  0  -0.418   6.2389  -2.6314   0.0014
 3XC  C6A   C  CR6   0   0.462   6.2419  -1.6181  -0.9722
 3XC  N6A   N  NH2   0  -0.817   7.3389  -1.4133  -1.7624
 3XC  C7A   C  CH2   0  -0.481   3.0272   0.0489  -0.5865
 3XC  C8A   C  CH3   0  -0.708   5.0599  -3.8652   1.8407
 3XC  H1    H  HCH2  0   0.204   0.0237   3.7149  -0.4861
 3XC  H1A   H  HCH2  0   0.205   0.5988   3.5001  -2.1455
 3XC  H2    H  HCH2  0   0.222  -1.7520   2.9795  -2.0317
 3XC  H2A   H  HCH2  0   0.198  -0.8598   1.5113  -2.4047
 3XC  HN2   H  HNH1  0   0.341  -0.9741   1.0553   0.0143
 3XC  H3    H  HCH2  0   0.240  -3.5094   1.4931  -1.3588
 3XC  H3A   H  HCH2  0   0.224  -2.6484  -0.0314  -1.2956
 3XC  HN1'  H  HNH1  0   0.332   3.4347   3.1262   2.6531
 3XC  H12   H  HCR6  0   0.252  -3.8430  -2.2004   0.4537
 3XC  H13   H  HCR6  0   0.262  -5.8302  -3.5338  -0.0998
 3XC  H15   H  HCR6  0   0.263  -8.1010   0.0556  -0.6484
 3XC  H16   H  HCR6  0   0.251  -6.1218   1.4006  -0.0920
 3XC  H2'   H  HCH2  0   0.198   1.3566   2.8707   1.4969
 3XC  H2'A  H  HCH2  0   0.224   2.1233   4.3518   0.8994
 3XC  H3'   H  HCH1  0   0.206   2.7588   3.2550  -1.1307
 3XC  H3AA  H  HCR6  0   0.220   3.1669  -1.9810   1.2363
 3XC  H4'   H  HCH1  0   0.251   4.3430   1.7274  -0.6518
 3XC  H5'   H  HCH2  0   0.228   4.7116   1.2200   1.6454
 3XC  H5'A  H  HCH2  0   0.184   3.0003   0.8715   1.9216
 3XC  H5A   H  HCR6  0   0.216   7.0980  -3.2826   0.1100
 3XC  HN6A  H  HNH2  0   0.355   7.9654  -2.1903  -1.8928
 3XC  HN6B  H  HNH2  0   0.356   7.1788  -0.8779  -2.6001
 3XC  H7A   H  HCH2  0   0.243   2.7826   0.0649  -1.6511
 3XC  H7AA  H  HCH2  0   0.229   2.1334  -0.2820  -0.0550
 3XC  H8A   H  HCH3  0   0.244   4.4455  -4.6938   1.4827
 3XC  H8AA  H  HCH3  0   0.233   6.0454  -4.2636   2.0765
 3XC  H8AB  H  HCH3  0   0.240   4.6039  -3.5052   2.7628

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
 3XC  O1   C1    single    1.409  0.020  1.409
 3XC  C1   C2    single    1.511  0.020  1.511
 3XC  C1   H1    single    0.970  0.020  1.090
 3XC  C1   H1A   single    0.970  0.020  1.090
 3XC  C3'  O1    single    1.404  0.020  1.404
 3XC  N2   C2    single    1.451  0.020  1.451
 3XC  C2   H2    single    0.970  0.020  1.090
 3XC  C2   H2A   single    0.970  0.020  1.090
 3XC  N2   C3    single    1.442  0.020  1.442
 3XC  N2   HN2   single    0.890  0.020  1.040
 3XC  C4   C3    single    1.516  0.020  1.516
 3XC  C3   H3    single    0.970  0.020  1.090
 3XC  C3   H3A   single    0.970  0.020  1.090
 3XC  F6   C4    single    1.364  0.020  1.364
 3XC  C4   F5    single    1.370  0.020  1.370
 3XC  C4   C11   single    1.504  0.020  1.504
 3XC  N1'  C5'   single    1.451  0.020  1.451
 3XC  N1'  C2'   single    1.451  0.020  1.451
 3XC  N1'  HN1'  single    0.890  0.020  1.040
 3XC  C16  C11   aromatic  1.391  0.020  1.391
 3XC  C11  C12   aromatic  1.391  0.020  1.391
 3XC  C12  C13   aromatic  1.387  0.020  1.387
 3XC  C12  H12   single    0.930  0.020  1.080
 3XC  C14  C13   aromatic  1.381  0.020  1.381
 3XC  C13  H13   single    0.930  0.020  1.080
 3XC  C15  C14   aromatic  1.381  0.020  1.381
 3XC  C14  F14   single    1.340  0.020  1.340
 3XC  C16  C15   aromatic  1.386  0.020  1.386
 3XC  C15  H15   single    0.930  0.020  1.080
 3XC  C16  H16   single    0.930  0.020  1.080
 3XC  C6A  N1A   aromatic  1.328  0.020  1.328
 3XC  C2A  N1A   aromatic  1.335  0.020  1.335
 3XC  C2'  C3'   single    1.541  0.020  1.541
 3XC  C2'  H2'   single    0.970  0.020  1.090
 3XC  C2'  H2'A  single    0.970  0.020  1.090
 3XC  C3A  C2A   aromatic  1.383  0.020  1.383
 3XC  C2A  C7A   single    1.503  0.020  1.503
 3XC  C4'  C3'   single    1.551  0.020  1.551
 3XC  C3'  H3'   single    0.970  0.020  1.090
 3XC  C4A  C3A   aromatic  1.399  0.020  1.399
 3XC  C3A  H3AA  single    0.930  0.020  1.080
 3XC  C5'  C4'   single    1.530  0.020  1.530
 3XC  C4'  C7A   single    1.527  0.020  1.527
 3XC  C4'  H4'   single    0.970  0.020  1.090
 3XC  C8A  C4A   single    1.498  0.020  1.498
 3XC  C4A  C5A   aromatic  1.380  0.020  1.380
 3XC  C5'  H5'   single    0.970  0.020  1.090
 3XC  C5'  H5'A  single    0.970  0.020  1.090
 3XC  C5A  C6A   aromatic  1.405  0.020  1.405
 3XC  C5A  H5A   single    0.930  0.020  1.080
 3XC  C6A  N6A   single    1.367  0.020  1.367
 3XC  N6A  HN6A  single    0.890  0.020  1.040
 3XC  N6A  HN6B  single    0.890  0.020  1.040
 3XC  C7A  H7A   single    0.970  0.020  1.090
 3XC  C7A  H7AA  single    0.970  0.020  1.090
 3XC  C8A  H8A   single    0.970  0.020  1.090
 3XC  C8A  H8AA  single    0.970  0.020  1.090
 3XC  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
 3XC  H1A   C1   H1    107.31  3.000
 3XC  H1A   C1   C2    109.58  3.000
 3XC  H1    C1   C2    109.34  3.000
 3XC  H1A   C1   O1    110.80  3.000
 3XC  H1    C1   O1    111.39  3.000
 3XC  C2    C1   O1    108.40  3.000
 3XC  C3'   O1   C1    114.22  3.000
 3XC  H2A   C2   H2    106.48  3.000
 3XC  H2A   C2   N2    112.96  3.000
 3XC  H2    C2   N2    108.96  3.000
 3XC  H2A   C2   C1    109.27  3.000
 3XC  H2    C2   C1    108.04  3.000
 3XC  N2    C2   C1    110.92  3.000
 3XC  HN2   N2   C3    109.50  3.000
 3XC  HN2   N2   C2    108.55  3.000
 3XC  C3    N2   C2    112.59  3.000
 3XC  H3A   C3   H3    105.95  3.000
 3XC  H3A   C3   C4    107.97  3.000
 3XC  H3    C3   C4    107.32  3.000
 3XC  H3A   C3   N2    113.95  3.000
 3XC  H3    C3   N2    109.31  3.000
 3XC  C4    C3   N2    111.97  3.000
 3XC  C11   C4   F6    109.67  3.000
 3XC  C11   C4   F5    109.56  3.000
 3XC  F6    C4   F5    105.35  3.000
 3XC  C11   C4   C3    112.82  3.000
 3XC  F5    C4   C3    109.26  3.000
 3XC  F6    C4   C3    109.91  3.000
 3XC  HN1'  N1'  C5'   112.15  3.000
 3XC  HN1'  N1'  C2'   111.63  3.000
 3XC  C5'   N1'  C2'   104.88  3.000
 3XC  C16   C11  C12   119.37  3.000
 3XC  C12   C11  C4    120.51  3.000
 3XC  C16   C11  C4    120.07  3.000
 3XC  H12   C12  C13   118.52  3.000
 3XC  H12   C12  C11   120.85  3.000
 3XC  C13   C12  C11   120.63  3.000
 3XC  H13   C13  C14   120.63  3.000
 3XC  H13   C13  C12   120.74  3.000
 3XC  C14   C13  C12   118.63  3.000
 3XC  C15   C14  F14   118.91  3.000
 3XC  F14   C14  C13   118.99  3.000
 3XC  C15   C14  C13   122.10  3.000
 3XC  H15   C15  C16   120.78  3.000
 3XC  H15   C15  C14   120.60  3.000
 3XC  C16   C15  C14   118.62  3.000
 3XC  H16   C16  C15   118.54  3.000
 3XC  H16   C16  C11   120.82  3.000
 3XC  C15   C16  C11   120.64  3.000
 3XC  C6A   N1A  C2A   118.80  3.000
 3XC  H2'A  C2'  H2'   107.72  3.000
 3XC  H2'A  C2'  C3'   113.45  3.000
 3XC  H2'   C2'  C3'   107.97  3.000
 3XC  H2'A  C2'  N1'   111.13  3.000
 3XC  H2'   C2'  N1'   113.11  3.000
 3XC  C3'   C2'  N1'   103.49  3.000
 3XC  C7A   C2A  C3A   121.30  3.000
 3XC  C7A   C2A  N1A   116.06  3.000
 3XC  C3A   C2A  N1A   122.63  3.000
 3XC  H3'   C3'  C4'   109.25  3.000
 3XC  H3'   C3'  C2'   110.06  3.000
 3XC  C4'   C3'  C2'   104.17  3.000
 3XC  H3'   C3'  O1    109.23  3.000
 3XC  C4'   C3'  O1    111.04  3.000
 3XC  C2'   C3'  O1    112.96  3.000
 3XC  H3AA  C3A  C4A   120.63  3.000
 3XC  H3AA  C3A  C2A   120.23  3.000
 3XC  C4A   C3A  C2A   119.13  3.000
 3XC  H4'   C4'  C7A   107.94  3.000
 3XC  H4'   C4'  C5'   108.29  3.000
 3XC  C7A   C4'  C5'   113.29  3.000
 3XC  H4'   C4'  C3'   107.79  3.000
 3XC  C7A   C4'  C3'   115.31  3.000
 3XC  C5'   C4'  C3'   103.90  3.000
 3XC  C8A   C4A  C5A   121.26  3.000
 3XC  C5A   C4A  C3A   118.09  3.000
 3XC  C8A   C4A  C3A   120.65  3.000
 3XC  H5'A  C5'  H5'   107.39  3.000
 3XC  H5'A  C5'  C4'   109.69  3.000
 3XC  H5'   C5'  C4'   112.76  3.000
 3XC  H5'A  C5'  N1'   113.14  3.000
 3XC  H5'   C5'  N1'   111.38  3.000
 3XC  C4'   C5'  N1'   102.54  3.000
 3XC  H5A   C5A  C6A   120.08  3.000
 3XC  H5A   C5A  C4A   120.89  3.000
 3XC  C6A   C5A  C4A   119.03  3.000
 3XC  N6A   C6A  C5A   120.67  3.000
 3XC  N6A   C6A  N1A   116.99  3.000
 3XC  C5A   C6A  N1A   122.31  3.000
 3XC  HN6B  N6A  HN6A  113.68  3.000
 3XC  HN6B  N6A  C6A   115.64  3.000
 3XC  HN6A  N6A  C6A   117.30  3.000
 3XC  H7AA  C7A  H7A   107.21  3.000
 3XC  H7AA  C7A  C4'   110.19  3.000
 3XC  H7A   C7A  C4'   109.98  3.000
 3XC  H7AA  C7A  C2A   109.63  3.000
 3XC  H7A   C7A  C2A   108.84  3.000
 3XC  C4'   C7A  C2A   110.92  3.000
 3XC  H8AB  C8A  H8AA  108.44  3.000
 3XC  H8AB  C8A  H8A   107.02  3.000
 3XC  H8AA  C8A  H8A   107.62  3.000
 3XC  H8AB  C8A  C4A   111.31  3.000
 3XC  H8AA  C8A  C4A   111.82  3.000
 3XC  H8A   C8A  C4A   110.44  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
 3XC  CONST_01  C14   C15  C16  C11     0.00   0.0  0
 3XC  CONST_02  C14   C13  C12  C11     0.00   0.0  0
 3XC  CONST_03  C15   C16  C11  C12     0.00   0.0  0
 3XC  CONST_04  C15   C14  C13  C12     0.00   0.0  0
 3XC  CONST_05  C16   C11  C12  C13     0.00   0.0  0
 3XC  CONST_06  C16   C15  C14  C13     0.00   0.0  0
 3XC  CONST_07  C4A   C5A  C6A  N1A     0.00   0.0  0
 3XC  CONST_08  C4A   C3A  C2A  N1A     0.00   0.0  0
 3XC  CONST_09  C5A   C6A  N1A  C2A     0.00   0.0  0
 3XC  CONST_10  C5A   C4A  C3A  C2A     0.00   0.0  0
 3XC  CONST_11  C6A   N1A  C2A  C3A     0.00   0.0  0
 3XC  CONST_12  C6A   C5A  C4A  C3A     0.00   0.0  0
 3XC  CONST_13  C15   C16  C11  C4    180.00   0.0  0
 3XC  CONST_14  C13   C12  C11  C4    180.00   0.0  0
 3XC  CONST_15  F14   C14  C13  C12   180.00   0.0  0
 3XC  CONST_16  C16   C15  C14  F14   180.00   0.0  0
 3XC  CONST_17  N6A   C6A  N1A  C2A   180.00   0.0  0
 3XC  CONST_18  C8A   C4A  C3A  C2A   180.00   0.0  0
 3XC  CONST_19  C7A   C2A  C3A  C4A   180.00   0.0  0
 3XC  CONST_20  N6A   C6A  C5A  C4A   180.00   0.0  0
 3XC  CONST_21  C7A   C2A  N1A  C6A   180.00   0.0  0
 3XC  CONST_22  C8A   C4A  C5A  C6A   180.00   0.0  0
 3XC  CONST_23  H15   C15  C16  C11   180.00   0.0  0
 3XC  CONST_24  H13   C13  C12  C11   180.00   0.0  0
 3XC  CONST_25  H16   C16  C11  C12   180.00   0.0  0
 3XC  CONST_26  H12   C12  C13  C14   180.00   0.0  0
 3XC  CONST_27  H5A   C5A  C6A  N1A   180.00   0.0  0
 3XC  CONST_28  H3AA  C3A  C2A  N1A   180.00   0.0  0
 3XC  Var_01    C4'   C5'  N1'  C2'    46.31  30.0  1
 3XC  Var_02    C5'   N1'  C2'  C3'   -42.62  30.0  1
 3XC  Var_03    C4'   C7A  C2A  N1A   -70.15  30.0  2
 3XC  Var_04    C16   C11  C4   C3    -86.38  30.0  2
 3XC  Var_05    H8A   C8A  C4A  C3A    77.23  30.0  2
 3XC  Var_06    C11   C4   C3   N2   -178.59  30.0  1
 3XC  Var_07    H1    C1   O1   C3'   -55.33  30.0  3
 3XC  Var_08    C3    N2   C2   C1   -176.49  30.0  1
 3XC  Var_09    N2    C2   C1   O1     65.47  30.0  3
 3XC  Var_10    C4    C3   N2   C2   -168.26  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
 3XC  chir_01  C3'  O1   C2'  C4'  negativ
 3XC  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
 3XC  plan-1  C4    0.020
 3XC  plan-1  C11   0.020
 3XC  plan-1  C12   0.020
 3XC  plan-1  C13   0.020
 3XC  plan-1  C14   0.020
 3XC  plan-1  F14   0.020
 3XC  plan-1  C15   0.020
 3XC  plan-1  C16   0.020
 3XC  plan-1  H12   0.020
 3XC  plan-1  H13   0.020
 3XC  plan-1  H15   0.020
 3XC  plan-1  H16   0.020
 3XC  plan-2  N1A   0.020
 3XC  plan-2  C2A   0.020
 3XC  plan-2  C3A   0.020
 3XC  plan-2  C4A   0.020
 3XC  plan-2  C5A   0.020
 3XC  plan-2  C6A   0.020
 3XC  plan-2  N6A   0.020
 3XC  plan-2  C7A   0.020
 3XC  plan-2  C8A   0.020
 3XC  plan-2  H3AA  0.020
 3XC  plan-2  H5A   0.020
 3XC  plan-3  C6A   0.020
 3XC  plan-3  N6A   0.020
 3XC  plan-3  HN6A  0.020
 3XC  plan-3  HN6B  0.020

