# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Apr 16 00:45:17 2020
#   Inital geometry file: a 114 line input string
#   Ligand name: (2E)-3-(6-aminopyridin-3-yl)-N-methyl-N-[(1-methyl-1H-indol-2-yl)methyl]prop-2-enamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CN(Cc1cc2ccccc2n1C)C(=O)/C=C/c3ccc(N)nc3
#
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
 AYM  AYM  (2E)-3-(6-aminopyridin-3-yl)-N-methyl-N-[(1-methyl-1H-indol-2-yl)methyl]prop-2-enamide  ligand  44  24  .  2022-07-24  2022-07-26
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_AYM
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
 AYM  N01   N  NH2   0  -0.825  -2.1543  -0.8202  -6.5764
 AYM  C02   C  CR6   0   0.469  -1.3237  -0.4463  -5.5800
 AYM  N03   N  N     0  -0.452  -1.2410  -1.2564  -4.5188
 AYM  C04   C  CR16  0  -0.103  -0.4598  -0.9072  -3.5128
 AYM  C05   C  CR6   0   0.030   0.3002   0.2608  -3.4652
 AYM  C06   C  CR16  0  -0.184   0.1947   1.1040  -4.5827
 AYM  C07   C  CR16  0  -0.376  -0.6062   0.7643  -5.6426
 AYM  C08   C  C1    0  -0.242   1.1647   0.6249  -2.3588
 AYM  C09   C  C1    0  -0.426   1.4453  -0.1100  -1.2730
 AYM  C10   C  C     0   0.572   2.3699   0.4099  -0.2432
 AYM  O11   O  O     0  -0.503   3.0104   1.4403  -0.4313
 AYM  N12   N  NT    0  -0.458   2.5228  -0.3092   0.9029
 AYM  C13   C  CH3   0  -0.541   3.4311   0.1879   1.9165
 AYM  C14   C  CH2   0  -0.478   1.5824  -1.3264   1.3519
 AYM  C15   C  CR5   0   0.379   0.3865  -0.7576   2.0541
 AYM  C16   C  CR15  0  -0.442  -0.7393  -0.2443   1.4694
 AYM  C17   C  CR56  0   0.082  -1.5859   0.2218   2.5156
 AYM  C18   C  CR56  0   0.347  -0.9098  -0.0479   3.7249
 AYM  N19   N  NR5   0  -0.567   0.2895  -0.6325   3.4224
 AYM  C20   C  CH3   0  -0.544   1.1972  -1.1319   4.4279
 AYM  C21   C  CR16  0  -0.350  -2.8445   0.8331   2.5582
 AYM  C22   C  CR16  0  -0.273  -3.3921   1.1491   3.7858
 AYM  C23   C  CR16  0  -0.281  -2.7077   0.8627   4.9789
 AYM  C24   C  CR16  0  -0.319  -1.4634   0.2612   4.9673
 AYM  H011  H  HNH2  0   0.392  -2.5050  -1.7631  -6.5767
 AYM  H012  H  HNH2  0   0.401  -2.0889  -0.3708  -7.4733
 AYM  H04   H  HCR6  0   0.256  -0.4386  -1.6055  -2.6823
 AYM  H06   H  HCR6  0   0.268   0.7560   2.0304  -4.6108
 AYM  H07   H  HCR6  0   0.272  -0.6884   1.4070  -6.5090
 AYM  H08   H  H     0   0.258   1.6283   1.6036  -2.4423
 AYM  H09   H  H     0   0.264   1.0134  -1.0941  -1.1605
 AYM  H131  H  HCH3  0   0.266   4.2547   0.7281   1.4611
 AYM  H132  H  HCH3  0   0.239   2.9355   0.8570   2.6259
 AYM  H133  H  HCH3  0   0.245   3.8416  -0.6553   2.4703
 AYM  H141  H  HCH2  0   0.298   1.2385  -1.9220   0.5112
 AYM  H142  H  HCH2  0   0.295   2.1245  -2.0256   1.9888
 AYM  H16   H  HCR5  0   0.247  -0.9321  -0.1978   0.4088
 AYM  H201  H  HCH3  0   0.258   0.8187  -2.0467   4.8857
 AYM  H202  H  HCH3  0   0.261   2.1704  -1.3441   3.9984
 AYM  H203  H  HCH3  0   0.260   1.3377  -0.3839   5.2062
 AYM  H21   H  HCR6  0   0.245  -3.3802   1.0514   1.6425
 AYM  H22   H  HCR6  0   0.246  -4.3640   1.6234   3.8347
 AYM  H23   H  HCR6  0   0.249  -3.1645   1.1153   5.9269
 AYM  H24   H  HCR6  0   0.263  -0.9471   0.0429   5.8934

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
 AYM  N01  C02   single    1.350  0.020  1.350
 AYM  N01  H011  single    0.890  0.020  1.040
 AYM  N01  H012  single    0.890  0.020  1.040
 AYM  C02  N03   aromatic  1.338  0.020  1.338
 AYM  C02  C07   aromatic  1.409  0.020  1.409
 AYM  N03  C04   aromatic  1.321  0.020  1.321
 AYM  C04  C05   aromatic  1.394  0.020  1.394
 AYM  C04  H04   single    0.930  0.020  1.080
 AYM  C05  C06   aromatic  1.404  0.020  1.404
 AYM  C05  C08   single    1.451  0.020  1.451
 AYM  C06  C07   aromatic  1.371  0.020  1.371
 AYM  C06  H06   single    0.930  0.020  1.080
 AYM  C07  H07   single    0.930  0.020  1.080
 AYM  C08  C09   double    1.341  0.020  1.341
 AYM  C08  H08   single    0.930  0.020  1.080
 AYM  C09  C10   single    1.478  0.020  1.478
 AYM  C09  H09   single    0.930  0.020  1.080
 AYM  C10  O11   double    1.228  0.020  1.228
 AYM  C10  N12   single    1.362  0.020  1.362
 AYM  N12  C13   single    1.449  0.020  1.449
 AYM  N12  C14   single    1.456  0.020  1.456
 AYM  C13  H131  single    0.970  0.020  1.090
 AYM  C13  H132  single    0.970  0.020  1.090
 AYM  C13  H133  single    0.970  0.020  1.090
 AYM  C14  C15   single    1.499  0.020  1.499
 AYM  C14  H141  single    0.970  0.020  1.090
 AYM  C14  H142  single    0.970  0.020  1.090
 AYM  C15  C16   aromatic  1.368  0.020  1.368
 AYM  C15  N19   aromatic  1.377  0.020  1.377
 AYM  C16  C17   aromatic  1.424  0.020  1.424
 AYM  C16  H16   single    0.930  0.020  1.080
 AYM  C17  C18   aromatic  1.411  0.020  1.411
 AYM  C17  C21   aromatic  1.400  0.020  1.400
 AYM  C18  N19   aromatic  1.368  0.020  1.368
 AYM  C18  C24   aromatic  1.395  0.020  1.395
 AYM  N19  C20   single    1.444  0.020  1.444
 AYM  C20  H201  single    0.970  0.020  1.090
 AYM  C20  H202  single    0.970  0.020  1.090
 AYM  C20  H203  single    0.970  0.020  1.090
 AYM  C21  C22   aromatic  1.381  0.020  1.381
 AYM  C21  H21   single    0.930  0.020  1.080
 AYM  C22  C23   aromatic  1.405  0.020  1.405
 AYM  C22  H22   single    0.930  0.020  1.080
 AYM  C23  C24   aromatic  1.382  0.020  1.382
 AYM  C23  H23   single    0.930  0.020  1.080
 AYM  C24  H24   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
 AYM  H012  N01  H011  116.19  3.000
 AYM  H012  N01  C02   119.65  3.000
 AYM  H011  N01  C02   118.31  3.000
 AYM  C07   C02  N03   121.62  3.000
 AYM  C07   C02  N01   121.24  3.000
 AYM  N03   C02  N01   117.12  3.000
 AYM  C04   N03  C02   118.73  3.000
 AYM  H04   C04  C05   120.15  3.000
 AYM  H04   C04  N03   115.10  3.000
 AYM  C05   C04  N03   124.74  3.000
 AYM  C08   C05  C06   120.08  3.000
 AYM  C08   C05  C04   124.13  3.000
 AYM  C06   C05  C04   115.79  3.000
 AYM  H06   C06  C07   119.63  3.000
 AYM  H06   C06  C05   119.68  3.000
 AYM  C07   C06  C05   120.69  3.000
 AYM  H07   C07  C06   121.08  3.000
 AYM  H07   C07  C02   120.49  3.000
 AYM  C06   C07  C02   118.43  3.000
 AYM  H08   C08  C09   117.83  3.000
 AYM  H08   C08  C05   114.96  3.000
 AYM  C09   C08  C05   127.22  3.000
 AYM  H09   C09  C10   119.85  3.000
 AYM  H09   C09  C08   119.99  3.000
 AYM  C10   C09  C08   120.15  3.000
 AYM  N12   C10  O11   120.90  3.000
 AYM  N12   C10  C09   118.09  3.000
 AYM  O11   C10  C09   120.98  3.000
 AYM  C14   N12  C13   115.39  3.000
 AYM  C14   N12  C10   123.78  3.000
 AYM  C13   N12  C10   118.56  3.000
 AYM  H133  C13  H132  108.34  3.000
 AYM  H133  C13  H131  108.23  3.000
 AYM  H132  C13  H131  108.16  3.000
 AYM  H133  C13  N12   109.04  3.000
 AYM  H132  C13  N12   112.30  3.000
 AYM  H131  C13  N12   110.67  3.000
 AYM  H142  C14  H141  104.95  3.000
 AYM  H142  C14  C15   111.50  3.000
 AYM  H141  C14  C15   108.55  3.000
 AYM  H142  C14  N12   107.88  3.000
 AYM  H141  C14  N12   110.41  3.000
 AYM  C15   C14  N12   113.24  3.000
 AYM  N19   C15  C16   109.42  3.000
 AYM  N19   C15  C14   123.78  3.000
 AYM  C16   C15  C14   126.77  3.000
 AYM  H16   C16  C17   126.99  3.000
 AYM  H16   C16  C15   125.67  3.000
 AYM  C17   C16  C15   107.33  3.000
 AYM  C21   C17  C18   119.21  3.000
 AYM  C21   C17  C16   134.40  3.000
 AYM  C18   C17  C16   106.38  3.000
 AYM  C24   C18  N19   129.76  3.000
 AYM  C24   C18  C17   122.05  3.000
 AYM  N19   C18  C17   108.19  3.000
 AYM  C20   N19  C18   123.02  3.000
 AYM  C20   N19  C15   128.04  3.000
 AYM  C18   N19  C15   108.67  3.000
 AYM  H203  C20  H202  107.56  3.000
 AYM  H203  C20  H201  108.72  3.000
 AYM  H202  C20  H201  108.27  3.000
 AYM  H203  C20  N19   109.97  3.000
 AYM  H202  C20  N19   110.85  3.000
 AYM  H201  C20  N19   111.36  3.000
 AYM  H21   C21  C22   120.62  3.000
 AYM  H21   C21  C17   120.46  3.000
 AYM  C22   C21  C17   118.92  3.000
 AYM  H22   C22  C23   119.24  3.000
 AYM  H22   C22  C21   119.76  3.000
 AYM  C23   C22  C21   121.00  3.000
 AYM  H23   C23  C24   119.27  3.000
 AYM  H23   C23  C22   119.38  3.000
 AYM  C24   C23  C22   121.34  3.000
 AYM  H24   C24  C23   120.66  3.000
 AYM  H24   C24  C18   121.86  3.000
 AYM  C23   C24  C18   117.47  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
 AYM  CONST_01  C05   C04  N03  C02     0.00   0.0  0
 AYM  CONST_02  C05   C06  C07  C02     0.00   0.0  0
 AYM  CONST_03  C06   C07  C02  N03     0.00   0.0  0
 AYM  CONST_04  C06   C05  C04  N03     0.00   0.0  0
 AYM  CONST_05  C07   C02  N03  C04     0.00   0.0  0
 AYM  CONST_06  C07   C06  C05  C04     0.00   0.0  0
 AYM  CONST_07  C18   C17  C16  C15     0.00   0.0  0
 AYM  CONST_08  C21   C17  C16  C15   180.00   0.0  0
 AYM  CONST_09  C17   C18  N19  C15     0.00   0.0  0
 AYM  CONST_10  C24   C18  N19  C15   180.00   0.0  0
 AYM  CONST_11  C18   N19  C15  C16     0.00   0.0  0
 AYM  CONST_12  N19   C18  C17  C16     0.00   0.0  0
 AYM  CONST_13  C24   C18  C17  C16   180.00   0.0  0
 AYM  CONST_14  C22   C21  C17  C16   180.00   0.0  0
 AYM  CONST_15  N19   C15  C16  C17     0.00   0.0  0
 AYM  CONST_16  C23   C24  C18  C17     0.00   0.0  0
 AYM  CONST_17  C23   C22  C21  C17     0.00   0.0  0
 AYM  CONST_18  C22   C21  C17  C18     0.00   0.0  0
 AYM  CONST_19  C22   C23  C24  C18     0.00   0.0  0
 AYM  CONST_20  C21   C17  C18  N19   180.00   0.0  0
 AYM  CONST_21  C23   C24  C18  N19   180.00   0.0  0
 AYM  CONST_22  C24   C18  C17  C21     0.00   0.0  0
 AYM  CONST_23  C24   C23  C22  C21     0.00   0.0  0
 AYM  CONST_24  C04   N03  C02  N01   180.00   0.0  0
 AYM  CONST_25  C06   C07  C02  N01   180.00   0.0  0
 AYM  CONST_26  C08   C05  C04  N03   180.00   0.0  0
 AYM  CONST_27  C08   C05  C06  C07   180.00   0.0  0
 AYM  CONST_28  C17   C16  C15  C14   180.00   0.0  0
 AYM  CONST_29  C18   N19  C15  C14   180.00   0.0  0
 AYM  CONST_30  C20   N19  C15  C16   180.00   0.0  0
 AYM  CONST_31  C20   N19  C18  C17   180.00   0.0  0
 AYM  CONST_32  C24   C18  N19  C20     0.00   0.0  0
 AYM  CONST_33  H04   C04  N03  C02   180.00   0.0  0
 AYM  CONST_34  H06   C06  C07  C02   180.00   0.0  0
 AYM  CONST_35  H07   C07  C02  N03   180.00   0.0  0
 AYM  CONST_36  H21   C21  C17  C16     0.00   0.0  0
 AYM  CONST_37  H24   C24  C18  C17   180.00   0.0  0
 AYM  CONST_38  H22   C22  C21  C17   180.00   0.0  0
 AYM  CONST_39  H16   C16  C17  C18   180.00   0.0  0
 AYM  CONST_40  H23   C23  C24  C18   180.00   0.0  0
 AYM  CONST_41  H011  N01  C02  N03     0.00   0.0  0
 AYM  CONST_42  H012  N01  C02  N03   180.00   0.0  0
 AYM  CONST_43  C13   N12  C10  C09   180.00   0.0  0
 AYM  CONST_45  C13   N12  C10  O11     0.00   0.0  0
 AYM  Var_01    C09   C08  C05  C04     4.81  30.0  2
 AYM  Var_02    C16   C15  C14  N12    82.29  30.0  2
 AYM  Var_03    H201  C20  N19  C15  -101.06  30.0  2
 AYM  Var_04    C10   C09  C08  C05   179.09   0.0  2
 AYM  Var_05    C15   C14  N12  C10   -81.34  30.0  3
 AYM  Var_06    O11   C10  C09  C08    -8.44  30.0  2
 AYM  Var_07    H131  C13  N12  C10   -31.63  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
 AYM  plan-1  N01   0.020
 AYM  plan-1  C02   0.020
 AYM  plan-1  N03   0.020
 AYM  plan-1  C04   0.020
 AYM  plan-1  C05   0.020
 AYM  plan-1  C06   0.020
 AYM  plan-1  C07   0.020
 AYM  plan-1  C08   0.020
 AYM  plan-1  H04   0.020
 AYM  plan-1  H06   0.020
 AYM  plan-1  H07   0.020
 AYM  plan-2  C14   0.020
 AYM  plan-2  C15   0.020
 AYM  plan-2  C16   0.020
 AYM  plan-2  C17   0.020
 AYM  plan-2  C18   0.020
 AYM  plan-2  N19   0.020
 AYM  plan-2  C20   0.020
 AYM  plan-2  C21   0.020
 AYM  plan-2  C22   0.020
 AYM  plan-2  C23   0.020
 AYM  plan-2  C24   0.020
 AYM  plan-2  H16   0.020
 AYM  plan-2  H21   0.020
 AYM  plan-2  H22   0.020
 AYM  plan-2  H23   0.020
 AYM  plan-2  H24   0.020
 AYM  plan-3  C09   0.020
 AYM  plan-3  C10   0.020
 AYM  plan-3  O11   0.020
 AYM  plan-3  N12   0.020
 AYM  plan-3  C13   0.020
 AYM  plan-3  C14   0.020
 AYM  plan-4  N01   0.020
 AYM  plan-4  C02   0.020
 AYM  plan-4  H011  0.020
 AYM  plan-4  H012  0.020
 AYM  plan-5  C05   0.020
 AYM  plan-5  C08   0.020
 AYM  plan-5  C09   0.020
 AYM  plan-5  C10   0.020
 AYM  plan-5  H08   0.020
 AYM  plan-5  H09   0.020

