# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun May  3 06:43:43 2020
#   Inital geometry file: a 138 line input string
#   Ligand name: 2-azanyl-N-[4-[2-azanyl-3-cyano-1-(phenylmethyl)indol-5-yl]oxyphenyl]ethanamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: NCC(=O)Nc1ccc(Oc2ccc3n(Cc4ccccc4)c(N)c(C#N)c3c2)cc1
#
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
 S6L  S6L  2-azanyl-N-[4-[2-azanyl-3-cyano-1-(phenylmethyl)indol-5-yl]oxyphenyl]ethanamide  ligand  52  31  .  2021-08-23  2021-08-23  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_S6L
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
 S6L  O1    O  O     0  -0.468   7.1684  -0.4878  -0.3303
 S6L  C22   C  C     0   0.519   6.7899   0.5211  -0.8939
 S6L  C23   C  CH2   0  -0.417   7.6814   1.3249  -1.8253
 S6L  N4    N  NH2   0  -0.790   8.8906   0.6024  -2.1450
 S6L  N3    N  NH1   0  -0.740   5.5571   1.0668  -0.7341
 S6L  C19   C  CR6   0   0.356   4.4901   0.6045   0.0467
 S6L  C18   C  CR16  0  -0.297   4.6340  -0.2562   1.1351
 S6L  C17   C  CR16  0  -0.327   3.5221  -0.6482   1.8646
 S6L  C20   C  CR16  0  -0.333   3.2131   1.0655  -0.2724
 S6L  C21   C  CR16  0  -0.319   2.1038   0.6871   0.4645
 S6L  C16   C  CR6   0   0.340   2.2568  -0.1814   1.5381
 S6L  O     O  O2    0  -0.519   1.2223  -0.5746   2.3371
 S6L  C10   C  CR6   0   0.327  -0.0455  -0.6308   1.8118
 S6L  C9    C  CR16  0  -0.355  -1.0337   0.1367   2.4240
 S6L  C8    C  CR16  0  -0.289  -2.3488   0.0732   1.9805
 S6L  C11   C  CR16  0  -0.446  -0.3246  -1.4703   0.7431
 S6L  C12   C  CR56  0   0.135  -1.6351  -1.5264   0.2869
 S6L  C7    C  CR56  0   0.368  -2.6303  -0.7581   0.9124
 S6L  C13   C  CR5   0  -0.155  -2.2909  -2.2625  -0.7551
 S6L  C15   C  CSP   0  -0.046  -1.7166  -3.1738  -1.6456
 S6L  N2    N  NS    0  -0.280  -1.2357  -3.9283  -2.3806
 S6L  C14   C  CR5   0   0.586  -3.6420  -1.9104  -0.7191
 S6L  N1    N  NH2   0  -0.850  -4.6214  -2.3030  -1.5543
 S6L  N     N  NR5   0  -0.582  -3.8398  -1.0179   0.2843
 S6L  C6    C  CH2   0  -0.444  -5.0704  -0.3264   0.6109
 S6L  C3    C  CR6   0   0.136  -5.0955   1.0869   0.0860
 S6L  C2    C  CR16  0  -0.286  -4.9304   1.3422  -1.2741
 S6L  C1    C  CR16  0  -0.239  -4.9559   2.6436  -1.7518
 S6L  C4    C  CR16  0  -0.314  -5.2901   2.1534   0.9551
 S6L  C5    C  CR16  0  -0.239  -5.3200   3.4584   0.4777
 S6L  C     C  CR16  0  -0.264  -5.1503   3.7063  -0.8764
 S6L  H231  H  HCH2  0   0.262   7.1343   1.5296  -2.7490
 S6L  H232  H  HCH2  0   0.246   7.8418   2.3046  -1.3502
 S6L  H3    H  HNH1  0   0.413   5.3485   1.8706  -1.3076
 S6L  H41N  H  HNH2  0   0.356   9.4209   1.1414  -2.8164
 S6L  H42N  H  HNH2  0   0.347   9.4752   0.5288  -1.3229
 S6L  H18   H  HCR6  0   0.277   5.6028  -0.6283   1.4258
 S6L  H20   H  HCR6  0   0.274   3.0785   1.7391  -1.1104
 S6L  H17   H  HCR6  0   0.270   3.6455  -1.3191   2.7054
 S6L  H21   H  HCR6  0   0.279   1.1312   1.0743   0.1905
 S6L  H9    H  HCR6  0   0.268  -0.7751   0.7790   3.2554
 S6L  H11   H  HCR6  0   0.267   0.4540  -2.0663   0.2821
 S6L  H8    H  HCR6  0   0.270  -3.1114   0.6688   2.4641
 S6L  H11N  H  HNH2  0   0.412  -4.4313  -3.1052  -2.1337
 S6L  H12N  H  HNH2  0   0.413  -5.5794  -2.2588  -1.2467
 S6L  H61C  H  HCH2  0   0.292  -5.9146  -0.8964   0.2229
 S6L  H62C  H  HCH2  0   0.298  -5.1855  -0.3335   1.6958
 S6L  H2    H  HCR6  0   0.254  -4.7887   0.5232  -1.9696
 S6L  H4    H  HCR6  0   0.258  -5.4200   1.9691   2.0152
 S6L  H1    H  HCR6  0   0.260  -4.8288   2.8288  -2.8105
 S6L  H     H  HCR6  0   0.259  -5.1696   4.7218  -1.2503
 S6L  H5    H  HCR6  0   0.259  -5.4709   4.2791   1.1668

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
 S6L  O1   C22   double    1.216  0.020  1.216
 S6L  C22  C23   single    1.519  0.020  1.519
 S6L  C22  N3    single    1.358  0.020  1.358
 S6L  C23  N4    single    1.444  0.020  1.444
 S6L  N3   C19   single    1.401  0.020  1.401
 S6L  C19  C18   aromatic  1.395  0.020  1.395
 S6L  C19  C20   aromatic  1.395  0.020  1.395
 S6L  C18  C17   aromatic  1.386  0.020  1.386
 S6L  C17  C16   aromatic  1.388  0.020  1.388
 S6L  C20  C21   aromatic  1.384  0.020  1.384
 S6L  C21  C16   aromatic  1.389  0.020  1.389
 S6L  C16  O     single    1.365  0.020  1.365
 S6L  O    C10   single    1.374  0.020  1.374
 S6L  C10  C9    aromatic  1.393  0.020  1.393
 S6L  C10  C11   aromatic  1.387  0.020  1.387
 S6L  C9   C8    aromatic  1.389  0.020  1.389
 S6L  C8   C7    aromatic  1.382  0.020  1.382
 S6L  C11  C12   aromatic  1.389  0.020  1.389
 S6L  C12  C7    aromatic  1.404  0.020  1.404
 S6L  C12  C13   aromatic  1.434  0.020  1.434
 S6L  C7   N     aromatic  1.387  0.020  1.387
 S6L  C13  C15   single    1.398  0.020  1.398
 S6L  C13  C14   aromatic  1.397  0.020  1.397
 S6L  C15  N2    triple    1.158  0.020  1.158
 S6L  C14  N1    single    1.346  0.020  1.346
 S6L  C14  N     aromatic  1.357  0.020  1.357
 S6L  N    C6    single    1.449  0.020  1.449
 S6L  C6   C3    single    1.508  0.020  1.508
 S6L  C3   C2    aromatic  1.394  0.020  1.394
 S6L  C3   C4    aromatic  1.389  0.020  1.389
 S6L  C2   C1    aromatic  1.387  0.020  1.387
 S6L  C1   C     aromatic  1.391  0.020  1.391
 S6L  C4   C5    aromatic  1.390  0.020  1.390
 S6L  C5   C     aromatic  1.387  0.020  1.387
 S6L  C23  H231  single    0.970  0.020  1.090
 S6L  C23  H232  single    0.970  0.020  1.090
 S6L  N3   H3    single    0.860  0.020  1.020
 S6L  N4   H41N  single    0.890  0.020  1.040
 S6L  N4   H42N  single    0.890  0.020  1.040
 S6L  C18  H18   single    0.930  0.020  1.080
 S6L  C20  H20   single    0.930  0.020  1.080
 S6L  C17  H17   single    0.930  0.020  1.080
 S6L  C21  H21   single    0.930  0.020  1.080
 S6L  C9   H9    single    0.930  0.020  1.080
 S6L  C11  H11   single    0.930  0.020  1.080
 S6L  C8   H8    single    0.930  0.020  1.080
 S6L  N1   H11N  single    0.890  0.020  1.040
 S6L  N1   H12N  single    0.890  0.020  1.040
 S6L  C6   H61C  single    0.970  0.020  1.090
 S6L  C6   H62C  single    0.970  0.020  1.090
 S6L  C2   H2    single    0.930  0.020  1.080
 S6L  C4   H4    single    0.930  0.020  1.080
 S6L  C1   H1    single    0.930  0.020  1.080
 S6L  C    H     single    0.930  0.020  1.080
 S6L  C5   H5    single    0.930  0.020  1.080

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
 S6L  N3    C22  C23   113.10  3.000
 S6L  N3    C22  O1    124.17  3.000
 S6L  C23   C22  O1    122.71  3.000
 S6L  H232  C23  H231  105.72  3.000
 S6L  H232  C23  N4    114.76  3.000
 S6L  H231  C23  N4    109.01  3.000
 S6L  H232  C23  C22   106.97  3.000
 S6L  H231  C23  C22   108.87  3.000
 S6L  N4    C23  C22   111.24  3.000
 S6L  H42N  N4   H41N  105.98  3.000
 S6L  H42N  N4   C23   109.90  3.000
 S6L  H41N  N4   C23   108.63  3.000
 S6L  H3    N3   C19   114.97  3.000
 S6L  H3    N3   C22   116.17  3.000
 S6L  C19   N3   C22   128.66  3.000
 S6L  C20   C19  C18   118.48  3.000
 S6L  C20   C19  N3    117.44  3.000
 S6L  C18   C19  N3    124.06  3.000
 S6L  H18   C18  C17   118.78  3.000
 S6L  H18   C18  C19   121.07  3.000
 S6L  C17   C18  C19   120.15  3.000
 S6L  H17   C17  C16   119.68  3.000
 S6L  H17   C17  C18   119.50  3.000
 S6L  C16   C17  C18   120.83  3.000
 S6L  H20   C20  C21   118.82  3.000
 S6L  H20   C20  C19   119.74  3.000
 S6L  C21   C20  C19   121.43  3.000
 S6L  H21   C21  C16   121.21  3.000
 S6L  H21   C21  C20   119.18  3.000
 S6L  C16   C21  C20   119.60  3.000
 S6L  O     C16  C21   123.30  3.000
 S6L  O     C16  C17   117.16  3.000
 S6L  C21   C16  C17   119.50  3.000
 S6L  C10   O    C16   119.18  3.000
 S6L  C11   C10  C9    121.96  3.000
 S6L  C11   C10  O     120.33  3.000
 S6L  C9    C10  O     117.66  3.000
 S6L  H9    C9   C8    119.91  3.000
 S6L  H9    C9   C10   119.69  3.000
 S6L  C8    C9   C10   120.40  3.000
 S6L  H8    C8   C7    122.20  3.000
 S6L  H8    C8   C9    119.96  3.000
 S6L  C7    C8   C9    117.83  3.000
 S6L  H11   C11  C12   121.07  3.000
 S6L  H11   C11  C10   121.07  3.000
 S6L  C12   C11  C10   117.86  3.000
 S6L  C13   C12  C7    106.28  3.000
 S6L  C13   C12  C11   133.69  3.000
 S6L  C7    C12  C11   120.02  3.000
 S6L  N     C7   C12   108.29  3.000
 S6L  N     C7   C8    129.78  3.000
 S6L  C12   C7   C8    121.92  3.000
 S6L  C14   C13  C15   125.33  3.000
 S6L  C14   C13  C12   107.11  3.000
 S6L  C15   C13  C12   127.56  3.000
 S6L  N2    C15  C13   180.00  3.000
 S6L  N     C14  N1    122.99  3.000
 S6L  N     C14  C13   109.01  3.000
 S6L  N1    C14  C13   127.92  3.000
 S6L  H12N  N1   H11N  112.95  3.000
 S6L  H12N  N1   C14   119.34  3.000
 S6L  H11N  N1   C14   116.86  3.000
 S6L  C6    N    C14   127.18  3.000
 S6L  C6    N    C7    123.30  3.000
 S6L  C14   N    C7    109.31  3.000
 S6L  H62C  C6   H61C  105.59  3.000
 S6L  H62C  C6   C3    110.52  3.000
 S6L  H61C  C6   C3    110.69  3.000
 S6L  H62C  C6   N     108.10  3.000
 S6L  H61C  C6   N     109.15  3.000
 S6L  C3    C6   N     112.52  3.000
 S6L  C4    C3   C2    119.10  3.000
 S6L  C4    C3   C6    120.27  3.000
 S6L  C2    C3   C6    120.63  3.000
 S6L  H2    C2   C1    119.38  3.000
 S6L  H2    C2   C3    120.22  3.000
 S6L  C1    C2   C3    120.40  3.000
 S6L  H1    C1   C     120.10  3.000
 S6L  H1    C1   C2    119.70  3.000
 S6L  C     C1   C2    120.20  3.000
 S6L  H4    C4   C5    119.54  3.000
 S6L  H4    C4   C3    119.87  3.000
 S6L  C5    C4   C3    120.59  3.000
 S6L  H5    C5   C     120.21  3.000
 S6L  H5    C5   C4    119.75  3.000
 S6L  C     C5   C4    120.03  3.000
 S6L  H     C    C5    120.19  3.000
 S6L  H     C    C1    120.13  3.000
 S6L  C5    C    C1    119.68  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
 S6L  CONST_01  C16   C17  C18  C19     0.00   0.0  0
 S6L  CONST_02  C16   C21  C20  C19     0.00   0.0  0
 S6L  CONST_03  C21   C20  C19  C18     0.00   0.0  0
 S6L  CONST_04  C21   C16  C17  C18     0.00   0.0  0
 S6L  CONST_05  C20   C19  C18  C17     0.00   0.0  0
 S6L  CONST_06  C20   C21  C16  C17     0.00   0.0  0
 S6L  CONST_07  C7    C8   C9   C10     0.00   0.0  0
 S6L  CONST_08  C7    C12  C11  C10     0.00   0.0  0
 S6L  CONST_09  C13   C12  C11  C10   180.00   0.0  0
 S6L  CONST_10  C12   C11  C10  C9      0.00   0.0  0
 S6L  CONST_11  C12   C7   C8   C9      0.00   0.0  0
 S6L  CONST_12  N     C7   C8   C9    180.00   0.0  0
 S6L  CONST_13  C11   C10  C9   C8      0.00   0.0  0
 S6L  CONST_14  C11   C12  C7   C8      0.00   0.0  0
 S6L  CONST_15  C13   C12  C7   C8    180.00   0.0  0
 S6L  CONST_16  C14   N    C7   C8    180.00   0.0  0
 S6L  CONST_17  N     C7   C12  C11   180.00   0.0  0
 S6L  CONST_18  C14   C13  C12  C11   180.00   0.0  0
 S6L  CONST_19  C14   N    C7   C12     0.00   0.0  0
 S6L  CONST_20  N     C14  C13  C12     0.00   0.0  0
 S6L  CONST_21  C14   C13  C12  C7      0.00   0.0  0
 S6L  CONST_22  C13   C14  N    C7      0.00   0.0  0
 S6L  CONST_23  N     C7   C12  C13     0.00   0.0  0
 S6L  CONST_24  C     C1   C2   C3      0.00   0.0  0
 S6L  CONST_25  C     C5   C4   C3      0.00   0.0  0
 S6L  CONST_26  C5    C4   C3   C2      0.00   0.0  0
 S6L  CONST_27  C5    C    C1   C2      0.00   0.0  0
 S6L  CONST_28  C4    C3   C2   C1      0.00   0.0  0
 S6L  CONST_29  C4    C5   C    C1      0.00   0.0  0
 S6L  CONST_30  C17   C18  C19  N3    180.00   0.0  0
 S6L  CONST_31  C21   C20  C19  N3    180.00   0.0  0
 S6L  CONST_32  O     C16  C17  C18   180.00   0.0  0
 S6L  CONST_33  O     C16  C21  C20   180.00   0.0  0
 S6L  CONST_34  C8    C9   C10  O     180.00   0.0  0
 S6L  CONST_35  C12   C11  C10  O     180.00   0.0  0
 S6L  CONST_36  C6    N    C7   C8      0.00   0.0  0
 S6L  CONST_37  C15   C13  C12  C11     0.00   0.0  0
 S6L  CONST_38  C6    N    C7   C12   180.00   0.0  0
 S6L  CONST_39  N1    C14  C13  C12   180.00   0.0  0
 S6L  CONST_40  C15   C13  C12  C7    180.00   0.0  0
 S6L  CONST_41  N1    C14  N    C7    180.00   0.0  0
 S6L  CONST_42  C6    N    C14  C13   180.00   0.0  0
 S6L  CONST_43  N     C14  C13  C15   180.00   0.0  0
 S6L  CONST_44  C1    C2   C3   C6    180.00   0.0  0
 S6L  CONST_45  C5    C4   C3   C6    180.00   0.0  0
 S6L  CONST_46  H17   C17  C18  C19   180.00   0.0  0
 S6L  CONST_47  H21   C21  C20  C19   180.00   0.0  0
 S6L  CONST_48  H20   C20  C19  C18   180.00   0.0  0
 S6L  CONST_49  H18   C18  C19  C20   180.00   0.0  0
 S6L  CONST_50  H8    C8   C9   C10   180.00   0.0  0
 S6L  CONST_51  H11   C11  C10  C9    180.00   0.0  0
 S6L  CONST_52  H9    C9   C10  C11   180.00   0.0  0
 S6L  CONST_53  H1    C1   C2   C3    180.00   0.0  0
 S6L  CONST_54  H5    C5   C4   C3    180.00   0.0  0
 S6L  CONST_55  H4    C4   C3   C2    180.00   0.0  0
 S6L  CONST_56  H     C    C1   C2    180.00   0.0  0
 S6L  CONST_57  H2    C2   C3   C4    180.00   0.0  0
 S6L  CONST_63  C19   N3   C22  O1      0.00   0.0  0
 S6L  CONST_64  C19   N3   C22  C23   180.00   0.0  0
 S6L  Var_01    C9    C10  O    C16  -122.00  30.0  2
 S6L  Var_02    C3    C6   N    C7     73.93  30.0  2
 S6L  Var_03    C2    C3   C6   N      57.39  30.0  2
 S6L  Var_04    N4    C23  C22  O1     11.42  30.0  3
 S6L  Var_05    H41N  N4   C23  C22   175.95  30.0  3

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
 S6L  plan-1  N3    0.020
 S6L  plan-1  C19   0.020
 S6L  plan-1  C18   0.020
 S6L  plan-1  C17   0.020
 S6L  plan-1  C20   0.020
 S6L  plan-1  C21   0.020
 S6L  plan-1  C16   0.020
 S6L  plan-1  O     0.020
 S6L  plan-1  H18   0.020
 S6L  plan-1  H20   0.020
 S6L  plan-1  H17   0.020
 S6L  plan-1  H21   0.020
 S6L  plan-2  C6    0.020
 S6L  plan-2  C3    0.020
 S6L  plan-2  C2    0.020
 S6L  plan-2  C1    0.020
 S6L  plan-2  C4    0.020
 S6L  plan-2  C5    0.020
 S6L  plan-2  C     0.020
 S6L  plan-2  H2    0.020
 S6L  plan-2  H4    0.020
 S6L  plan-2  H1    0.020
 S6L  plan-2  H     0.020
 S6L  plan-2  H5    0.020
 S6L  plan-3  O     0.020
 S6L  plan-3  C10   0.020
 S6L  plan-3  C9    0.020
 S6L  plan-3  C8    0.020
 S6L  plan-3  C11   0.020
 S6L  plan-3  C12   0.020
 S6L  plan-3  C7    0.020
 S6L  plan-3  C13   0.020
 S6L  plan-3  C15   0.020
 S6L  plan-3  N2    0.020
 S6L  plan-3  C14   0.020
 S6L  plan-3  N1    0.020
 S6L  plan-3  N     0.020
 S6L  plan-3  C6    0.020
 S6L  plan-3  H9    0.020
 S6L  plan-3  H11   0.020
 S6L  plan-3  H8    0.020
 S6L  plan-4  O1    0.020
 S6L  plan-4  C22   0.020
 S6L  plan-4  C23   0.020
 S6L  plan-4  N3    0.020
 S6L  plan-4  C19   0.020
 S6L  plan-4  H3    0.020
 S6L  plan-5  C14   0.020
 S6L  plan-5  N1    0.020
 S6L  plan-5  H11N  0.020
 S6L  plan-5  H12N  0.020

