# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu May  7 13:44:15 2020
#   Inital geometry file: a 148 line input string
#   Ligand name: (2E)-N-{4-[1-(3-aminobenzene-1-carbonyl)piperidin-4-yl]butyl}-3-(pyridin-3-yl)prop-2-enamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: Nc1cccc(c1)C(=O)N2CCC(CCCCNC(=O)\C=C\c3cccnc3)CC2
#
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
 HVM  HVM  (2E)-N-{4-[1-(3-aminobenzene-1-carbonyl)piperidin-4-yl]butyl}-3-(pyridin-3-yl)prop-2-enamide  ligand  60  30  .  2021-08-11  2021-08-11  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_HVM
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
 HVM  C13   C  CH2   0  -0.474   -1.5244   1.0715   0.4085
 HVM  C15   C  CH2   0  -0.402    0.9018   1.7774   0.2903
 HVM  C17   C  CH2   0  -0.417    3.2332   2.7222   0.2348
 HVM  C20   C  CH2   0  -0.315    4.3779   0.1885   1.0622
 HVM  C21   C  CH2   0  -0.418    2.9247   0.2722   0.6092
 HVM  C22   C  C     0   0.506    6.0537   1.0378  -0.5634
 HVM  C24   C  CR16  0  -0.314    6.5289  -0.9265  -2.0146
 HVM  C26   C  CR16  0  -0.325    7.7632  -2.8263  -1.1798
 HVM  C28   C  CR16  0  -0.334    7.2665  -0.9862   0.2834
 HVM  C01   C  CR16  0  -0.313  -10.9015  -0.9946  -0.6608
 HVM  C02   C  CR16  0  -0.066  -10.9865   0.0401  -1.5786
 HVM  N03   N  N     0  -0.395   -9.9516   0.8132  -1.8978
 HVM  C04   C  CR16  0  -0.101   -8.7911   0.5770  -1.3095
 HVM  C05   C  CR6   0   0.053   -8.5837  -0.4375  -0.3696
 HVM  C06   C  CR16  0  -0.192   -9.6824  -1.2340  -0.0500
 HVM  C07   C  C1    0  -0.235   -7.2966  -0.6921   0.2696
 HVM  C08   C  C1    0  -0.419   -6.1623  -0.0133   0.0824
 HVM  C09   C  C     0   0.578   -4.9184  -0.3965   0.7938
 HVM  O10   O  O     0  -0.505   -4.8599  -1.3366   1.5800
 HVM  N11   N  NH1   0  -0.667   -3.8568   0.3687   0.4998
 HVM  C12   C  CH2   0  -0.233   -2.5410   0.1496   1.0623
 HVM  C14   C  CH2   0  -0.426   -0.1173   0.8548   0.9490
 HVM  C16   C  CH1   0  -0.242    2.3199   1.6567   0.8418
 HVM  C18   C  CH2   0  -0.321    4.6680   2.5688   0.7191
 HVM  N19   N  NT    0  -0.438    5.1743   1.2345   0.4395
 HVM  C23   C  CR6   0  -0.058    6.6033  -0.3429  -0.7539
 HVM  C25   C  CR16  0  -0.242    7.1006  -2.1767  -2.2076
 HVM  C27   C  CR6   0   0.321    7.8670  -2.2346   0.0854
 HVM  O29   O  O     0  -0.494    6.4493   1.9390  -1.2939
 HVM  N30   N  NH2   0  -0.861    8.5839  -2.8400   1.0933
 HVM  H131  H  HCH2  0   0.230   -1.5298   0.9031  -0.6733
 HVM  H132  H  HCH2  0   0.230   -1.8229   2.1132   0.5662
 HVM  H151  H  HCH2  0   0.211    0.9206   1.5874  -0.7893
 HVM  H152  H  HCH2  0   0.219    0.5685   2.8142   0.4108
 HVM  H171  H  HCH2  0   0.221    3.2086   2.6538  -0.8582
 HVM  H172  H  HCH2  0   0.236    2.8739   3.7203   0.4989
 HVM  H201  H  HCH2  0   0.239    4.4404   0.3057   2.1485
 HVM  H202  H  HCH2  0   0.272    4.7826  -0.7905   0.8224
 HVM  H212  H  HCH2  0   0.217    2.8681   0.0220  -0.4568
 HVM  H211  H  HCH2  0   0.243    2.3602  -0.4954   1.1429
 HVM  H241  H  HCR6  0   0.250    6.0210  -0.4233  -2.8264
 HVM  H261  H  HCR6  0   0.259    8.2090  -3.7982  -1.3553
 HVM  H281  H  HCR6  0   0.262    7.3258  -0.5193   1.2607
 HVM  H021  H  HCR6  0   0.271  -11.9241   0.2543  -2.0786
 HVM  H041  H  HCR6  0   0.259   -7.9743   1.2290  -1.6002
 HVM  H061  H  HCR6  0   0.277   -9.5798  -2.0341   0.6729
 HVM  H1    H  H     0   0.266   -7.2822  -1.5264   0.9643
 HVM  H2    H  H     0   0.270   -6.1104   0.8308  -0.5966
 HVM  H111  H  HNH1  0   0.404   -3.9743   1.1386  -0.1391
 HVM  H122  H  HCH2  0   0.233   -2.2489  -0.8932   0.9109
 HVM  H121  H  HCH2  0   0.232   -2.5579   0.3194   2.1434
 HVM  H142  H  HCH2  0   0.217   -0.1089   1.0188   2.0318
 HVM  H141  H  HCH2  0   0.223    0.1648  -0.1907   0.7946
 HVM  H161  H  HCH1  0   0.214    2.2818   1.8302   1.9265
 HVM  H181  H  HCH2  0   0.261    5.3204   3.3100   0.2653
 HVM  H182  H  HCH2  0   0.241    4.7080   2.7160   1.8034
 HVM  H251  H  HCR6  0   0.255    7.0346  -2.6535  -3.1774
 HVM  H301  H  HNH2  0   0.380    8.3536  -2.5518   2.0306
 HVM  H302  H  HNH2  0   0.380    8.6828  -3.8400   1.0221
 HVM  H011  H  HCR6  0   0.276  -11.7699  -1.5970  -0.4330

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
 HVM  N30  C27   single    1.377  0.020  1.377
 HVM  O29  C22   double    1.226  0.020  1.226
 HVM  C27  C28   aromatic  1.399  0.020  1.399
 HVM  C27  C26   aromatic  1.401  0.020  1.401
 HVM  C28  C23   aromatic  1.389  0.020  1.389
 HVM  C26  C25   aromatic  1.385  0.020  1.385
 HVM  C23  C22   single    1.498  0.020  1.498
 HVM  C23  C24   aromatic  1.391  0.020  1.391
 HVM  C22  N19   single    1.348  0.020  1.348
 HVM  C25  C24   aromatic  1.388  0.020  1.388
 HVM  N19  C18   single    1.454  0.020  1.454
 HVM  N19  C20   single    1.455  0.020  1.455
 HVM  C18  C17   single    1.522  0.020  1.522
 HVM  C20  C21   single    1.525  0.020  1.525
 HVM  C17  C16   single    1.529  0.020  1.529
 HVM  C21  C16   single    1.529  0.020  1.529
 HVM  C16  C15   single    1.526  0.020  1.526
 HVM  C15  C14   single    1.524  0.020  1.524
 HVM  C14  C13   single    1.523  0.020  1.523
 HVM  C12  C13   single    1.520  0.020  1.520
 HVM  C12  N11   single    1.448  0.020  1.448
 HVM  N11  C09   single    1.341  0.020  1.341
 HVM  O10  C09   double    1.227  0.020  1.227
 HVM  C09  C08   single    1.483  0.020  1.483
 HVM  C08  C07   double    1.335  0.020  1.335
 HVM  C07  C05   single    1.460  0.020  1.460
 HVM  C05  C04   aromatic  1.398  0.020  1.398
 HVM  C05  C06   aromatic  1.394  0.020  1.394
 HVM  C04  N03   aromatic  1.322  0.020  1.322
 HVM  C06  C01   aromatic  1.384  0.020  1.384
 HVM  N03  C02   aromatic  1.331  0.020  1.331
 HVM  C01  C02   aromatic  1.386  0.020  1.386
 HVM  C13  H131  single    0.970  0.020  1.090
 HVM  C13  H132  single    0.970  0.020  1.090
 HVM  C15  H151  single    0.970  0.020  1.090
 HVM  C15  H152  single    0.970  0.020  1.090
 HVM  C17  H171  single    0.970  0.020  1.090
 HVM  C17  H172  single    0.970  0.020  1.090
 HVM  C20  H201  single    0.970  0.020  1.090
 HVM  C20  H202  single    0.970  0.020  1.090
 HVM  C21  H212  single    0.970  0.020  1.090
 HVM  C21  H211  single    0.970  0.020  1.090
 HVM  C24  H241  single    0.930  0.020  1.080
 HVM  C26  H261  single    0.930  0.020  1.080
 HVM  C28  H281  single    0.930  0.020  1.080
 HVM  C01  H011  single    0.930  0.020  1.080
 HVM  C02  H021  single    0.930  0.020  1.080
 HVM  C04  H041  single    0.930  0.020  1.080
 HVM  C06  H061  single    0.930  0.020  1.080
 HVM  C07  H1    single    0.930  0.020  1.080
 HVM  C08  H2    single    0.930  0.020  1.080
 HVM  N11  H111  single    0.860  0.020  1.020
 HVM  C12  H122  single    0.970  0.020  1.090
 HVM  C12  H121  single    0.970  0.020  1.090
 HVM  C14  H142  single    0.970  0.020  1.090
 HVM  C14  H141  single    0.970  0.020  1.090
 HVM  C16  H161  single    0.970  0.020  1.090
 HVM  C18  H181  single    0.970  0.020  1.090
 HVM  C18  H182  single    0.970  0.020  1.090
 HVM  C25  H251  single    0.930  0.020  1.080
 HVM  N30  H301  single    0.890  0.020  1.040
 HVM  N30  H302  single    0.890  0.020  1.040

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
 HVM  H132  C13  H131  106.70  3.000
 HVM  H132  C13  C14   109.64  3.000
 HVM  H131  C13  C14   109.48  3.000
 HVM  H132  C13  C12   109.43  3.000
 HVM  H131  C13  C12   109.17  3.000
 HVM  C14   C13  C12   112.27  3.000
 HVM  H152  C15  H151  106.11  3.000
 HVM  H152  C15  C16   108.52  3.000
 HVM  H151  C15  C16   109.04  3.000
 HVM  H152  C15  C14   108.77  3.000
 HVM  H151  C15  C14   109.39  3.000
 HVM  C16   C15  C14   114.66  3.000
 HVM  H172  C17  H171  106.89  3.000
 HVM  H172  C17  C18   108.97  3.000
 HVM  H171  C17  C18   109.41  3.000
 HVM  H172  C17  C16   110.12  3.000
 HVM  H171  C17  C16   109.83  3.000
 HVM  C18   C17  C16   111.50  3.000
 HVM  H202  C20  H201  107.12  3.000
 HVM  H202  C20  N19   110.46  3.000
 HVM  H201  C20  N19   108.46  3.000
 HVM  H202  C20  C21   109.82  3.000
 HVM  H201  C20  C21   110.09  3.000
 HVM  N19   C20  C21   110.81  3.000
 HVM  H211  C21  H212  106.74  3.000
 HVM  H211  C21  C16   110.96  3.000
 HVM  H212  C21  C16   109.52  3.000
 HVM  H211  C21  C20   107.99  3.000
 HVM  H212  C21  C20   109.00  3.000
 HVM  C16   C21  C20   112.43  3.000
 HVM  O29   C22  C23   118.91  3.000
 HVM  C23   C22  N19   117.92  3.000
 HVM  O29   C22  N19   123.14  3.000
 HVM  H241  C24  C25   120.53  3.000
 HVM  H241  C24  C23   120.66  3.000
 HVM  C25   C24  C23   118.80  3.000
 HVM  H261  C26  C27   119.65  3.000
 HVM  H261  C26  C25   119.83  3.000
 HVM  C27   C26  C25   120.52  3.000
 HVM  H281  C28  C27   119.20  3.000
 HVM  H281  C28  C23   119.97  3.000
 HVM  C27   C28  C23   120.82  3.000
 HVM  H011  C01  C06   121.19  3.000
 HVM  H011  C01  C02   120.43  3.000
 HVM  C06   C01  C02   118.38  3.000
 HVM  H021  C02  N03   116.57  3.000
 HVM  H021  C02  C01   120.40  3.000
 HVM  N03   C02  C01   123.03  3.000
 HVM  C04   N03  C02   118.17  3.000
 HVM  H041  C04  C05   120.29  3.000
 HVM  H041  C04  N03   115.74  3.000
 HVM  C05   C04  N03   123.97  3.000
 HVM  C07   C05  C06   119.67  3.000
 HVM  C06   C05  C04   116.85  3.000
 HVM  C07   C05  C04   123.48  3.000
 HVM  H061  C06  C05   120.02  3.000
 HVM  H061  C06  C01   120.37  3.000
 HVM  C05   C06  C01   119.60  3.000
 HVM  H1    C07  C08   117.98  3.000
 HVM  H1    C07  C05   115.21  3.000
 HVM  C08   C07  C05   126.81  3.000
 HVM  H2    C08  C09   117.46  3.000
 HVM  H2    C08  C07   121.61  3.000
 HVM  C09   C08  C07   120.92  3.000
 HVM  N11   C09  O10   122.68  3.000
 HVM  O10   C09  C08   123.04  3.000
 HVM  N11   C09  C08   114.28  3.000
 HVM  H111  N11  C12   117.91  3.000
 HVM  H111  N11  C09   118.87  3.000
 HVM  C12   N11  C09   123.22  3.000
 HVM  H121  C12  H122  106.79  3.000
 HVM  H121  C12  N11   110.26  3.000
 HVM  H122  C12  N11   109.47  3.000
 HVM  H121  C12  C13   109.95  3.000
 HVM  H122  C12  C13   109.89  3.000
 HVM  N11   C12  C13   110.42  3.000
 HVM  H141  C14  H142  106.30  3.000
 HVM  H141  C14  C15   110.19  3.000
 HVM  H142  C14  C15   109.35  3.000
 HVM  H141  C14  C13   108.92  3.000
 HVM  H142  C14  C13   109.68  3.000
 HVM  C15   C14  C13   112.23  3.000
 HVM  H161  C16  C21   107.87  3.000
 HVM  H161  C16  C17   107.61  3.000
 HVM  C21   C16  C17   109.54  3.000
 HVM  H161  C16  C15   108.17  3.000
 HVM  C21   C16  C15   112.59  3.000
 HVM  C17   C16  C15   110.88  3.000
 HVM  H182  C18  H181  107.45  3.000
 HVM  H182  C18  N19   107.52  3.000
 HVM  H181  C18  N19   109.66  3.000
 HVM  H182  C18  C17   109.64  3.000
 HVM  H181  C18  C17   111.36  3.000
 HVM  N19   C18  C17   111.07  3.000
 HVM  C18   N19  C22   120.26  3.000
 HVM  C18   N19  C20   112.75  3.000
 HVM  C22   N19  C20   124.79  3.000
 HVM  C28   C23  C24   120.52  3.000
 HVM  C24   C23  C22   118.83  3.000
 HVM  C28   C23  C22   120.46  3.000
 HVM  H251  C25  C26   119.17  3.000
 HVM  H251  C25  C24   119.74  3.000
 HVM  C26   C25  C24   121.09  3.000
 HVM  N30   C27  C28   120.80  3.000
 HVM  C28   C27  C26   118.22  3.000
 HVM  N30   C27  C26   120.93  3.000
 HVM  H302  N30  H301  111.86  3.000
 HVM  H302  N30  C27   115.84  3.000
 HVM  H301  N30  C27   115.86  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
 HVM  CONST_01  C27   C28  C23  C24     0.00   0.0  0
 HVM  CONST_02  C27   C26  C25  C24     0.00   0.0  0
 HVM  CONST_03  C23   C28  C27  C26     0.00   0.0  0
 HVM  CONST_04  C23   C24  C25  C26     0.00   0.0  0
 HVM  CONST_05  C25   C26  C27  C28     0.00   0.0  0
 HVM  CONST_06  C25   C24  C23  C28     0.00   0.0  0
 HVM  CONST_07  C04   C05  C06  C01     0.00   0.0  0
 HVM  CONST_08  C04   N03  C02  C01     0.00   0.0  0
 HVM  CONST_09  C05   C04  N03  C02     0.00   0.0  0
 HVM  CONST_10  C05   C06  C01  C02     0.00   0.0  0
 HVM  CONST_11  C06   C05  C04  N03     0.00   0.0  0
 HVM  CONST_12  C06   C01  C02  N03     0.00   0.0  0
 HVM  CONST_13  C27   C28  C23  C22   180.00   0.0  0
 HVM  CONST_14  C25   C24  C23  C22   180.00   0.0  0
 HVM  CONST_15  C07   C05  C06  C01   180.00   0.0  0
 HVM  CONST_16  C07   C05  C04  N03   180.00   0.0  0
 HVM  CONST_17  N30   C27  C28  C23   180.00   0.0  0
 HVM  CONST_18  N30   C27  C26  C25   180.00   0.0  0
 HVM  CONST_20  C23   C22  N19  C18   180.00   0.0  0
 HVM  CONST_21  H281  C28  C23  C24   180.00   0.0  0
 HVM  CONST_22  H261  C26  C25  C24   180.00   0.0  0
 HVM  CONST_23  H241  C24  C25  C26   180.00   0.0  0
 HVM  CONST_24  H041  C04  N03  C02   180.00   0.0  0
 HVM  CONST_25  H061  C06  C01  C02   180.00   0.0  0
 HVM  CONST_26  H011  C01  C02  N03   180.00   0.0  0
 HVM  CONST_27  H021  C02  N03  C04   180.00   0.0  0
 HVM  CONST_28  H251  C25  C24  C23   180.00   0.0  0
 HVM  CONST_30  O29   C22  N19  C18     0.00   0.0  0
 HVM  CONST_33  C12   N11  C09  C08   180.00   0.0  0
 HVM  CONST_34  C12   N11  C09  O10     0.00   0.0  0
 HVM  CONST_35  H111  N11  C09  C08     0.00   0.0  0
 HVM  Var_01    C20   N19  C18  C17   -58.75  30.0  1
 HVM  Var_02    C18   N19  C20  C21    57.55  30.0  1
 HVM  Var_03    N19   C18  C17  C16    55.90  30.0  1
 HVM  Var_04    N19   C20  C21  C16   -54.23  30.0  1
 HVM  Var_05    N19   C22  C23  C24   127.81  30.0  2
 HVM  Var_06    C08   C07  C05  C04     1.03  30.0  2
 HVM  Var_07    C09   C08  C07  C05  -179.32   0.0  2
 HVM  Var_08    C16   C15  C14  C13   177.03  30.0  1
 HVM  Var_09    C09   N11  C12  C13   173.16  30.0  3
 HVM  Var_10    C12   C13  C14  C15   179.87  30.0  3
 HVM  Var_11    N11   C09  C08  C07   179.53  30.0  1
 HVM  Var_12    C14   C13  C12  N11  -178.77  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
 HVM  chir_01  C16  C17  C21  C15  positiv

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
 HVM  plan-1  C01   0.020
 HVM  plan-1  C02   0.020
 HVM  plan-1  N03   0.020
 HVM  plan-1  C04   0.020
 HVM  plan-1  C05   0.020
 HVM  plan-1  C06   0.020
 HVM  plan-1  C07   0.020
 HVM  plan-1  H021  0.020
 HVM  plan-1  H041  0.020
 HVM  plan-1  H061  0.020
 HVM  plan-1  H011  0.020
 HVM  plan-2  C05   0.020
 HVM  plan-2  C07   0.020
 HVM  plan-2  C08   0.020
 HVM  plan-2  C09   0.020
 HVM  plan-2  H1    0.020
 HVM  plan-2  H2    0.020
 HVM  plan-3  C22   0.020
 HVM  plan-3  C24   0.020
 HVM  plan-3  C26   0.020
 HVM  plan-3  C28   0.020
 HVM  plan-3  C23   0.020
 HVM  plan-3  C25   0.020
 HVM  plan-3  C27   0.020
 HVM  plan-3  N30   0.020
 HVM  plan-3  H241  0.020
 HVM  plan-3  H261  0.020
 HVM  plan-3  H281  0.020
 HVM  plan-3  H251  0.020
 HVM  plan-4  C08   0.020
 HVM  plan-4  C09   0.020
 HVM  plan-4  O10   0.020
 HVM  plan-4  N11   0.020
 HVM  plan-4  C12   0.020
 HVM  plan-4  H111  0.020
 HVM  plan-5  C27   0.020
 HVM  plan-5  N30   0.020
 HVM  plan-5  H301  0.020
 HVM  plan-5  H302  0.020
 HVM  plan-6  C20   0.020
 HVM  plan-6  C22   0.020
 HVM  plan-6  C18   0.020
 HVM  plan-6  N19   0.020
 HVM  plan-6  C23   0.020
 HVM  plan-6  O29   0.020

