# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat May  9 20:42:32 2020
#   Inital geometry file: a 109 line input string
#   Ligand name: 4-[(2S)-3-(tert-butylamino)-2-oxidanyl-propoxy]-7-methyl-1H-indole-2-carbonitrile
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Cc1ccc(OC[C@@H](O)CNC(C)(C)C)c2cc([nH]c12)C#N
#
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
 XTK  XTK  4-[(2S)-3-(tert-butylamino)-2-oxidanyl-propoxy]-7-methyl-1H-indole-2-carbonitrile  ligand  45  22  .  2021-08-24  2021-08-24  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_XTK
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
 XTK  N3    N  NS    0  -0.245   5.6685  -3.5019  -0.1350
 XTK  C16   C  CSP   0   0.011   5.0081  -2.5565  -0.1102
 XTK  C1    C  CR5   0   0.301   4.1917  -1.4062  -0.0809
 XTK  N1    N  NR15  0  -0.728   4.7202  -0.1404  -0.0392
 XTK  C8    C  CR56  0   0.360   3.7039   0.7605  -0.0179
 XTK  C7    C  CR6   0   0.040   3.7642   2.1639   0.0246
 XTK  C6    C  CR16  0  -0.320   2.5415   2.7950   0.0320
 XTK  C5    C  CR16  0  -0.410   1.3064   2.1107   0.0020
 XTK  C2    C  CR15  0  -0.346   2.8210  -1.3394  -0.0866
 XTK  C3    C  CR56  0  -0.043   2.4954   0.0384  -0.0464
 XTK  C4    C  CR6   0   0.315   1.2679   0.7331  -0.0356
 XTK  O1    O  O2    0  -0.463   0.1634  -0.0277  -0.0643
 XTK  C9    C  CH2   0  -0.178  -1.0963   0.6174  -0.0536
 XTK  C10   C  CH1   0  -0.017  -2.1805  -0.4464  -0.0341
 XTK  O2    O  OH1   0  -0.659  -2.0885  -1.2540   1.1145
 XTK  C11   C  CH2   0  -0.310  -3.5390   0.2327  -0.1829
 XTK  N2    N  NH1   0  -0.592  -4.6142  -0.7333  -0.1324
 XTK  C12   C  CT    0   0.074  -5.9816  -0.2016  -0.1614
 XTK  C15   C  CH3   0  -0.652  -6.2626   0.6656  -1.3957
 XTK  C14   C  CH3   0  -0.648  -6.9173  -1.4087  -0.1756
 XTK  C13   C  CH3   0  -0.646  -6.2451   0.6102   1.1072
 XTK  C17   C  CH3   0  -0.736   5.0720   2.8913   0.0621
 XTK  H1    H  HNR5  0   0.428   5.7046   0.0755  -0.0297
 XTK  H2    H  HCR5  0   0.275   2.1490  -2.1814  -0.1147
 XTK  H6    H  HCR6  0   0.253   2.5151   3.8778   0.0625
 XTK  H171  H  HCH3  0   0.245   5.6834   2.6739  -0.8167
 XTK  H172  H  HCH3  0   0.254   4.9158   3.9683   0.0964
 XTK  H173  H  HCH3  0   0.245   5.6618   2.6142   0.9387
 XTK  H5    H  HCR6  0   0.277   0.3999   2.6999   0.0095
 XTK  H91C  H  HCH2  0   0.224  -1.1895   1.2622   0.8289
 XTK  H92C  H  HCH2  0   0.226  -1.2060   1.2514  -0.9408
 XTK  H10   H  HCH1  0   0.229  -2.0257  -1.1120  -0.8922
 XTK  HA    H  HOH1  0   0.445  -2.5946  -0.8392   1.8206
 XTK  H111  H  HCH2  0   0.228  -3.6617   0.9458   0.6385
 XTK  H112  H  HCH2  0   0.212  -3.5174   0.8312  -1.1052
 XTK  HB    H  HNH1  0   0.334  -4.5066  -1.3770  -0.9094
 XTK  H151  H  HCH3  0   0.220  -6.0927   0.1021  -2.3162
 XTK  H152  H  HCH3  0   0.223  -7.2988   1.0086  -1.4061
 XTK  H153  H  HCH3  0   0.226  -5.6268   1.5523  -1.4237
 XTK  H141  H  HCH3  0   0.227  -6.7643  -2.0339   0.7056
 XTK  H142  H  HCH3  0   0.223  -7.9603  -1.0895  -0.1882
 XTK  H143  H  HCH3  0   0.223  -6.7512  -2.0293  -1.0600
 XTK  H131  H  HCH3  0   0.226  -5.6547   1.5271   1.1446
 XTK  H132  H  HCH3  0   0.226  -7.2948   0.9026   1.1566
 XTK  H133  H  HCH3  0   0.225  -6.0153   0.0224   1.9977

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
 XTK  N3   C16   triple    1.153  0.020  1.153
 XTK  C16  C1    single    1.411  0.020  1.411
 XTK  C1   N1    aromatic  1.372  0.020  1.372
 XTK  C1   C2    aromatic  1.372  0.020  1.372
 XTK  N1   C8    aromatic  1.358  0.020  1.358
 XTK  C8   C7    aromatic  1.405  0.020  1.405
 XTK  C8   C3    aromatic  1.408  0.020  1.408
 XTK  C7   C6    aromatic  1.376  0.020  1.376
 XTK  C7   C17   single    1.497  0.020  1.497
 XTK  C6   C5    aromatic  1.412  0.020  1.412
 XTK  C5   C4    aromatic  1.379  0.020  1.379
 XTK  C2   C3    aromatic  1.416  0.020  1.416
 XTK  C3   C4    aromatic  1.410  0.020  1.410
 XTK  C4   O1    single    1.341  0.020  1.341
 XTK  O1   C9    single    1.415  0.020  1.415
 XTK  C9   C10   single    1.519  0.020  1.519
 XTK  C10  O2    single    1.407  0.020  1.407
 XTK  C10  C11   single    1.526  0.020  1.526
 XTK  C11  N2    single    1.446  0.020  1.446
 XTK  N2   C12   single    1.467  0.020  1.467
 XTK  C12  C15   single    1.534  0.020  1.534
 XTK  C12  C14   single    1.527  0.020  1.527
 XTK  C12  C13   single    1.529  0.020  1.529
 XTK  N1   H1    single    0.860  0.020  1.020
 XTK  C2   H2    single    0.930  0.020  1.080
 XTK  C6   H6    single    0.930  0.020  1.080
 XTK  C17  H171  single    0.970  0.020  1.090
 XTK  C17  H172  single    0.970  0.020  1.090
 XTK  C17  H173  single    0.970  0.020  1.090
 XTK  C5   H5    single    0.930  0.020  1.080
 XTK  C9   H91C  single    0.970  0.020  1.090
 XTK  C9   H92C  single    0.970  0.020  1.090
 XTK  C10  H10   single    0.970  0.020  1.090
 XTK  O2   HA    single    0.850  0.020  0.980
 XTK  C11  H111  single    0.970  0.020  1.090
 XTK  C11  H112  single    0.970  0.020  1.090
 XTK  N2   HB    single    0.890  0.020  1.040
 XTK  C15  H151  single    0.970  0.020  1.090
 XTK  C15  H152  single    0.970  0.020  1.090
 XTK  C15  H153  single    0.970  0.020  1.090
 XTK  C14  H141  single    0.970  0.020  1.090
 XTK  C14  H142  single    0.970  0.020  1.090
 XTK  C14  H143  single    0.970  0.020  1.090
 XTK  C13  H131  single    0.970  0.020  1.090
 XTK  C13  H132  single    0.970  0.020  1.090
 XTK  C13  H133  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
 XTK  C1    C16  N3    180.00  3.000
 XTK  C2    C1   N1    109.87  3.000
 XTK  C2    C1   C16   128.13  3.000
 XTK  N1    C1   C16   121.99  3.000
 XTK  H1    N1   C8    126.06  3.000
 XTK  H1    N1   C1    125.03  3.000
 XTK  C8    N1   C1    108.91  3.000
 XTK  C3    C8   C7    123.34  3.000
 XTK  C3    C8   N1    107.56  3.000
 XTK  C7    C8   N1    129.10  3.000
 XTK  C17   C7   C6    123.59  3.000
 XTK  C17   C7   C8    121.57  3.000
 XTK  C6    C7   C8    114.84  3.000
 XTK  H6    C6   C5    117.62  3.000
 XTK  H6    C6   C7    118.69  3.000
 XTK  C5    C6   C7    123.69  3.000
 XTK  H5    C5   C4    121.42  3.000
 XTK  H5    C5   C6    117.97  3.000
 XTK  C4    C5   C6    120.61  3.000
 XTK  H2    C2   C3    128.13  3.000
 XTK  H2    C2   C1    125.80  3.000
 XTK  C3    C2   C1    106.07  3.000
 XTK  C4    C3   C2    132.80  3.000
 XTK  C4    C3   C8    119.61  3.000
 XTK  C2    C3   C8    107.59  3.000
 XTK  O1    C4   C3    115.91  3.000
 XTK  O1    C4   C5    126.18  3.000
 XTK  C3    C4   C5    117.91  3.000
 XTK  C9    O1   C4    118.31  3.000
 XTK  H92C  C9   H91C  107.61  3.000
 XTK  H92C  C9   C10   110.13  3.000
 XTK  H91C  C9   C10   109.92  3.000
 XTK  H92C  C9   O1    110.28  3.000
 XTK  H91C  C9   O1    110.46  3.000
 XTK  C10   C9   O1    108.43  3.000
 XTK  H10   C10  C11   108.63  3.000
 XTK  H10   C10  O2    106.32  3.000
 XTK  C11   C10  O2    113.15  3.000
 XTK  H10   C10  C9    108.31  3.000
 XTK  C11   C10  C9    108.81  3.000
 XTK  O2    C10  C9    111.45  3.000
 XTK  HA    O2   C10   108.48  3.000
 XTK  H112  C11  H111  106.08  3.000
 XTK  H112  C11  N2    114.04  3.000
 XTK  H111  C11  N2    109.01  3.000
 XTK  H112  C11  C10   107.84  3.000
 XTK  H111  C11  C10   108.45  3.000
 XTK  N2    C11  C10   111.17  3.000
 XTK  HB    N2   C12   108.27  3.000
 XTK  HB    N2   C11   108.55  3.000
 XTK  C12   N2   C11   116.74  3.000
 XTK  C13   C12  C14   108.77  3.000
 XTK  C13   C12  C15   109.62  3.000
 XTK  C14   C12  C15   109.09  3.000
 XTK  C13   C12  N2    109.67  3.000
 XTK  C14   C12  N2    106.54  3.000
 XTK  C15   C12  N2    113.04  3.000
 XTK  H153  C15  H152  107.31  3.000
 XTK  H153  C15  H151  107.87  3.000
 XTK  H152  C15  H151  107.56  3.000
 XTK  H153  C15  C12   111.90  3.000
 XTK  H152  C15  C12   111.05  3.000
 XTK  H151  C15  C12   110.96  3.000
 XTK  H143  C14  H142  107.58  3.000
 XTK  H143  C14  H141  107.87  3.000
 XTK  H142  C14  H141  108.12  3.000
 XTK  H143  C14  C12   111.29  3.000
 XTK  H142  C14  C12   110.77  3.000
 XTK  H141  C14  C12   111.06  3.000
 XTK  H133  C13  H132  108.06  3.000
 XTK  H133  C13  H131  108.10  3.000
 XTK  H132  C13  H131  107.09  3.000
 XTK  H133  C13  C12   110.78  3.000
 XTK  H132  C13  C12   110.22  3.000
 XTK  H131  C13  C12   112.42  3.000
 XTK  H173  C17  H172  107.64  3.000
 XTK  H173  C17  H171  107.03  3.000
 XTK  H172  C17  H171  107.61  3.000
 XTK  H173  C17  C7    111.63  3.000
 XTK  H172  C17  C7    110.86  3.000
 XTK  H171  C17  C7    111.85  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
 XTK  CONST_01  C7    C8   N1   C1    180.00   0.0  0
 XTK  CONST_02  C3    C8   N1   C1      0.00   0.0  0
 XTK  CONST_03  C8    C3   C2   C1      0.00   0.0  0
 XTK  CONST_04  C4    C3   C2   C1    180.00   0.0  0
 XTK  CONST_05  C3    C2   C1   N1      0.00   0.0  0
 XTK  CONST_06  C6    C7   C8   N1    180.00   0.0  0
 XTK  CONST_07  C2    C3   C8   N1      0.00   0.0  0
 XTK  CONST_08  C4    C3   C8   N1    180.00   0.0  0
 XTK  CONST_09  C2    C1   N1   C8      0.00   0.0  0
 XTK  CONST_10  C5    C6   C7   C8      0.00   0.0  0
 XTK  CONST_11  C5    C4   C3   C8      0.00   0.0  0
 XTK  CONST_12  C2    C3   C8   C7    180.00   0.0  0
 XTK  CONST_13  C4    C3   C8   C7      0.00   0.0  0
 XTK  CONST_14  C4    C5   C6   C7      0.00   0.0  0
 XTK  CONST_15  C3    C8   C7   C6      0.00   0.0  0
 XTK  CONST_16  C3    C4   C5   C6      0.00   0.0  0
 XTK  CONST_17  C2    C3   C4   C5    180.00   0.0  0
 XTK  CONST_18  C8    N1   C1   C16   180.00   0.0  0
 XTK  CONST_19  C3    C2   C1   C16   180.00   0.0  0
 XTK  CONST_20  C17   C7   C8   N1      0.00   0.0  0
 XTK  CONST_21  O1    C4   C3   C8    180.00   0.0  0
 XTK  CONST_22  O1    C4   C5   C6    180.00   0.0  0
 XTK  CONST_23  C17   C7   C6   C5    180.00   0.0  0
 XTK  CONST_24  O1    C4   C3   C2      0.00   0.0  0
 XTK  CONST_25  C17   C7   C8   C3    180.00   0.0  0
 XTK  CONST_26  H2    C2   C1   N1    180.00   0.0  0
 XTK  CONST_27  H6    C6   C7   C8    180.00   0.0  0
 XTK  CONST_28  H1    N1   C8   C7      0.00   0.0  0
 XTK  CONST_29  H5    C5   C6   C7    180.00   0.0  0
 XTK  Var_01    H171  C17  C7   C8     60.12  30.0  2
 XTK  Var_02    C10   C9   O1   C4   -177.74  30.0  3
 XTK  Var_03    C12   N2   C11  C10   175.50  30.0  3
 XTK  Var_04    C15   C12  N2   C11    57.17  30.0  3
 XTK  Var_05    H151  C15  C12  N2     58.02  30.0  3
 XTK  Var_06    H141  C14  C12  N2     59.31  30.0  3
 XTK  Var_07    H131  C13  C12  N2     67.82  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
 XTK  chir_01  C10  C9  O2  C11  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
 XTK  plan-1  N3   0.020
 XTK  plan-1  C16  0.020
 XTK  plan-1  C1   0.020
 XTK  plan-1  N1   0.020
 XTK  plan-1  C8   0.020
 XTK  plan-1  C7   0.020
 XTK  plan-1  C6   0.020
 XTK  plan-1  C5   0.020
 XTK  plan-1  C2   0.020
 XTK  plan-1  C3   0.020
 XTK  plan-1  C4   0.020
 XTK  plan-1  O1   0.020
 XTK  plan-1  C17  0.020
 XTK  plan-1  H1   0.020
 XTK  plan-1  H2   0.020
 XTK  plan-1  H6   0.020
 XTK  plan-1  H5   0.020

