# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Mar 25 13:53:33 2022
#   Inital geometry file: a 110 line input string
#   Ligand name: (2S)-N-(cyclopropylmethyl)-2-methyl-4-(1-methyl-1H-pyrrole-2-carbonyl)piperazine-1-carboxamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[C@@H]1CN(CCN1C(=O)NCC2CC2)C(=O)c3cccn3C
#
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
 Y3V  Y3V  (2S)-N-(cyclopropylmethyl)-2-methyl-4-(1-methyl-1H-pyrrole-2-carbonyl)piperazine-1-carboxamide  ligand  46  22  .  2022-08-11  2023-02-15
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_Y3V
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
 Y3V  N1   N  NR6   0  -0.465  -18.5308  13.7151  25.2097
 Y3V  N3   N  NR6   0  -0.508  -19.9425  15.4921  26.8840
 Y3V  C4   C  C     0   0.497  -17.5272  12.9334  24.7461
 Y3V  C5   C  CR5   0   0.200  -16.4161  13.6107  24.0515
 Y3V  C6   C  CR15  0  -0.357  -15.7360  14.7588  24.4098
 Y3V  C7   C  CR15  0  -0.352  -14.6285  14.8795  23.5497
 Y3V  C8   C  CR15  0  -0.055  -14.6749  13.8045  22.6923
 Y3V  C10  C  C     0  -0.315  -18.8980  15.0272  24.7227
 Y3V  C13  C  CH2   0  -0.293  -21.3211  18.5885  28.3381
 Y3V  C15  C  CH2   0  -0.480  -20.1546  18.4997  30.6693
 Y3V  C1   C  CH3   0  -0.662  -18.4283  14.0711  28.2340
 Y3V  C11  C  C     0  -0.321  -19.0506  16.0163  25.8649
 Y3V  C12  C  C     0   0.755  -20.6559  16.2974  27.7421
 Y3V  C14  C  CH1   0  -0.246  -20.4203  19.2062  29.3771
 Y3V  C16  C  CH2   0  -0.491  -21.0170  19.7271  30.6482
 Y3V  C2   C  CR16  0  -0.106  -19.6581  14.1286  27.3323
 Y3V  C3   C  C     0  -0.309  -19.5236  13.2007  26.1284
 Y3V  N2   N  NR5   0  -0.449  -15.7458  13.0357  23.0056
 Y3V  N4   N  NH1   0  -0.686  -20.6503  17.6308  27.4854
 Y3V  O1   O  O     0  -0.484  -17.4952  11.7230  24.9393
 Y3V  O2   O  O     0  -0.542  -21.3039  15.8194  28.6689
 Y3V  H7   H  HCR5  0   0.263  -15.9985  15.4192  25.2221
 Y3V  H8   H  HCR5  0   0.246  -13.8851  15.6604  23.5500
 Y3V  H9   H  HCR5  0   0.277  -14.0289  13.5386  21.8709
 Y3V  H14  H  H     0   0.281  -18.1681  15.4014  24.0113
 Y3V  H13  H  H     0   0.255  -19.8566  14.9439  24.1980
 Y3V  H19  H  HCH2  0   0.245  -21.7302  19.3739  27.6985
 Y3V  H18  H  HCH2  0   0.239  -22.1692  18.0998  28.8162
 Y3V  H21  H  HCH2  0   0.245  -19.1645  18.5784  31.1000
 Y3V  H2   H  HCH3  0   0.238  -18.5577  14.7140  29.1047
 Y3V  H3   H  HCH3  0   0.233  -18.2670  13.0541  28.5935
 Y3V  H1   H  HCH3  0   0.228  -17.5229  14.3873  27.7139
 Y3V  H16  H  H     0   0.247  -18.0665  16.2700  26.2762
 Y3V  H15  H  H     0   0.259  -19.4664  16.9202  25.4218
 Y3V  H20  H  HCH1  0   0.249  -19.5961  19.7835  28.9687
 Y3V  H24  H  HCH2  0   0.242  -22.0828  19.5987  30.7955
 Y3V  H23  H  HCH2  0   0.247  -20.6210  20.6443  31.0646
 Y3V  H4   H  HCR6  0   0.266  -20.5230  13.7813  27.8941
 Y3V  H6   H  H     0   0.269  -19.2421  12.2074  26.4685
 Y3V  H5   H  H     0   0.252  -20.4883  13.1192  25.6158
 Y3V  H17  H  HNH1  0   0.398  -19.9825  18.0210  26.8439
 Y3V  C9   C  CH3   0  -0.516  -16.1036  11.8237  22.2971
 Y3V  H22  H  HCH2  0   0.243  -20.6355  17.5438  30.8325
 Y3V  H10  H  HCH3  0   0.254  -17.1684  11.8055  22.0772
 Y3V  H12  H  HCH3  0   0.256  -15.5607  11.8040  21.3561
 Y3V  H11  H  HCH3  0   0.253  -15.8469  10.9365  22.8712

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
 Y3V  C1   C2   single    1.526  0.020  1.526
 Y3V  C2   C3   single    1.526  0.020  1.526
 Y3V  C3   N1   single    1.447  0.020  1.447
 Y3V  N1   C4   single    1.354  0.020  1.354
 Y3V  C4   O1   double    1.226  0.020  1.226
 Y3V  C4   C5   single    1.475  0.020  1.475
 Y3V  C5   C6   aromatic  1.382  0.020  1.382
 Y3V  C6   C7   aromatic  1.408  0.020  1.408
 Y3V  C7   C8   aromatic  1.376  0.020  1.376
 Y3V  C8   N2   aromatic  1.355  0.020  1.355
 Y3V  N2   C9   single    1.449  0.020  1.449
 Y3V  N1   C10  single    1.447  0.020  1.447
 Y3V  C10  C11  single    1.519  0.020  1.519
 Y3V  C11  N3   single    1.452  0.020  1.452
 Y3V  N3   C12  single    1.376  0.020  1.376
 Y3V  C12  O2   double    1.228  0.020  1.228
 Y3V  C12  N4   single    1.358  0.020  1.358
 Y3V  N4   C13  single    1.447  0.020  1.447
 Y3V  C13  C14  single    1.507  0.020  1.507
 Y3V  C14  C15  single    1.497  0.020  1.497
 Y3V  C15  C16  single    1.500  0.020  1.500
 Y3V  C2   N3   single    1.463  0.020  1.463
 Y3V  C14  C16  single    1.498  0.020  1.498
 Y3V  C5   N2   aromatic  1.369  0.020  1.369
 Y3V  C6   H7   single    0.930  0.020  1.080
 Y3V  C7   H8   single    0.930  0.020  1.080
 Y3V  C8   H9   single    0.930  0.020  1.080
 Y3V  C10  H14  single    0.970  0.020  1.090
 Y3V  C10  H13  single    0.970  0.020  1.090
 Y3V  C13  H19  single    0.970  0.020  1.090
 Y3V  C13  H18  single    0.970  0.020  1.090
 Y3V  C15  H22  single    0.970  0.020  1.090
 Y3V  C15  H21  single    0.970  0.020  1.090
 Y3V  C1   H2   single    0.970  0.020  1.090
 Y3V  C1   H3   single    0.970  0.020  1.090
 Y3V  C1   H1   single    0.970  0.020  1.090
 Y3V  C11  H16  single    0.970  0.020  1.090
 Y3V  C11  H15  single    0.970  0.020  1.090
 Y3V  C14  H20  single    0.970  0.020  1.090
 Y3V  C16  H24  single    0.970  0.020  1.090
 Y3V  C16  H23  single    0.970  0.020  1.090
 Y3V  C2   H4   single    0.970  0.020  1.090
 Y3V  C3   H6   single    0.970  0.020  1.090
 Y3V  C3   H5   single    0.970  0.020  1.090
 Y3V  C9   H10  single    0.970  0.020  1.090
 Y3V  C9   H12  single    0.970  0.020  1.090
 Y3V  C9   H11  single    0.970  0.020  1.090
 Y3V  N4   H17  single    0.860  0.020  1.020

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
 Y3V  C3   N1   C10  111.22  3.000
 Y3V  C10  N1   C4   126.61  3.000
 Y3V  C3   N1   C4   121.37  3.000
 Y3V  C2   N3   C12  117.06  3.000
 Y3V  C2   N3   C11  115.59  3.000
 Y3V  C12  N3   C11  123.01  3.000
 Y3V  O1   C4   C5   120.51  3.000
 Y3V  C5   C4   N1   117.03  3.000
 Y3V  O1   C4   N1   122.37  3.000
 Y3V  N2   C5   C6   107.83  3.000
 Y3V  N2   C5   C4   122.40  3.000
 Y3V  C6   C5   C4   129.07  3.000
 Y3V  H7   C6   C7   126.78  3.000
 Y3V  H7   C6   C5   125.73  3.000
 Y3V  C7   C6   C5   107.47  3.000
 Y3V  H8   C7   C8   126.11  3.000
 Y3V  H8   C7   C6   127.20  3.000
 Y3V  C8   C7   C6   106.69  3.000
 Y3V  H9   C8   N2   120.64  3.000
 Y3V  H9   C8   C7   130.33  3.000
 Y3V  N2   C8   C7   109.02  3.000
 Y3V  H13  C10  H14  107.49  3.000
 Y3V  H13  C10  C11  108.77  3.000
 Y3V  H14  C10  C11  109.62  3.000
 Y3V  H13  C10  N1   108.31  3.000
 Y3V  H14  C10  N1   111.25  3.000
 Y3V  C11  C10  N1   111.28  3.000
 Y3V  H18  C13  H19  106.73  3.000
 Y3V  H18  C13  N4   108.82  3.000
 Y3V  H19  C13  N4   107.72  3.000
 Y3V  H18  C13  C14  110.28  3.000
 Y3V  H19  C13  C14  109.43  3.000
 Y3V  N4   C13  C14  113.60  3.000
 Y3V  H21  C15  H22  114.24  3.000
 Y3V  H21  C15  C16  118.15  3.000
 Y3V  H22  C15  C16  117.99  3.000
 Y3V  H21  C15  C14  118.14  3.000
 Y3V  H22  C15  C14  117.92  3.000
 Y3V  C16  C15  C14   59.97  3.000
 Y3V  H1   C1   H3   107.74  3.000
 Y3V  H1   C1   H2   107.96  3.000
 Y3V  H3   C1   H2   107.71  3.000
 Y3V  H1   C1   C2   112.10  3.000
 Y3V  H3   C1   C2   110.43  3.000
 Y3V  H2   C1   C2   110.74  3.000
 Y3V  H15  C11  H16  107.65  3.000
 Y3V  H15  C11  C10  105.83  3.000
 Y3V  H16  C11  C10  110.04  3.000
 Y3V  H15  C11  N3   110.52  3.000
 Y3V  H16  C11  N3   111.82  3.000
 Y3V  C10  C11  N3   110.76  3.000
 Y3V  O2   C12  N4   121.82  3.000
 Y3V  N4   C12  N3   117.04  3.000
 Y3V  O2   C12  N3   121.10  3.000
 Y3V  H20  C14  C16  115.89  3.000
 Y3V  H20  C14  C15  116.16  3.000
 Y3V  C16  C14  C15   60.14  3.000
 Y3V  H20  C14  C13  114.34  3.000
 Y3V  C16  C14  C13  119.30  3.000
 Y3V  C15  C14  C13  120.51  3.000
 Y3V  H23  C16  H24  114.08  3.000
 Y3V  H23  C16  C14  118.39  3.000
 Y3V  H24  C16  C14  117.77  3.000
 Y3V  H23  C16  C15  118.53  3.000
 Y3V  H24  C16  C15  117.81  3.000
 Y3V  C14  C16  C15   59.89  3.000
 Y3V  H4   C2   C3   106.46  3.000
 Y3V  H4   C2   C1   108.87  3.000
 Y3V  C3   C2   C1   111.85  3.000
 Y3V  H4   C2   N3   107.52  3.000
 Y3V  C3   C2   N3   110.00  3.000
 Y3V  C1   C2   N3   111.89  3.000
 Y3V  H5   C3   H6   107.85  3.000
 Y3V  H5   C3   C2   109.68  3.000
 Y3V  H6   C3   C2   109.37  3.000
 Y3V  H5   C3   N1   109.48  3.000
 Y3V  H6   C3   N1   110.23  3.000
 Y3V  C2   C3   N1   110.19  3.000
 Y3V  C9   N2   C8   123.83  3.000
 Y3V  C9   N2   C5   127.17  3.000
 Y3V  C8   N2   C5   108.99  3.000
 Y3V  H17  N4   C12  120.32  3.000
 Y3V  H17  N4   C13  115.29  3.000
 Y3V  C12  N4   C13  122.45  3.000
 Y3V  H11  C9   H12  108.93  3.000
 Y3V  H11  C9   H10  108.92  3.000
 Y3V  H12  C9   H10  108.29  3.000
 Y3V  H11  C9   N2   111.47  3.000
 Y3V  H12  C9   N2   108.38  3.000
 Y3V  H10  C9   N2   110.78  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
 Y3V  CONST_01  C8   C7   C6   C5      0.00   0.0  0
 Y3V  CONST_02  C7   C8   N2   C5      0.00   0.0  0
 Y3V  CONST_03  C8   N2   C5   C6      0.00   0.0  0
 Y3V  CONST_04  N2   C8   C7   C6      0.00   0.0  0
 Y3V  CONST_05  N2   C5   C6   C7      0.00   0.0  0
 Y3V  CONST_06  C7   C6   C5   C4    180.00   0.0  0
 Y3V  CONST_07  C8   N2   C5   C4    180.00   0.0  0
 Y3V  CONST_08  C9   N2   C5   C6    180.00   0.0  0
 Y3V  CONST_09  C9   N2   C8   C7    180.00   0.0  0
 Y3V  CONST_10  C3   N1   C4   C5    180.00   0.0  0
 Y3V  CONST_12  H8   C7   C6   C5    180.00   0.0  0
 Y3V  CONST_13  H9   C8   N2   C5    180.00   0.0  0
 Y3V  CONST_14  H7   C6   C7   C8    180.00   0.0  0
 Y3V  CONST_16  O2   C12  N3   C11   180.00   0.0  0
 Y3V  CONST_18  O1   C4   N1   C3      0.00   0.0  0
 Y3V  CONST_19  N4   C12  N3   C11     0.00   0.0  0
 Y3V  CONST_21  C13  N4   C12  N3    180.00   0.0  0
 Y3V  CONST_22  H17  N4   C12  N3      0.00   0.0  0
 Y3V  CONST_23  O2   C12  N4   C13     0.00   0.0  0
 Y3V  Var_01    N3   C11  C10  N1    -52.01  30.0  1
 Y3V  Var_02    C2   C3   N1   C10   -60.32  30.0  1
 Y3V  Var_03    C2   N3   C11  C10    49.37  30.0  1
 Y3V  Var_04    C3   N1   C10  C11    59.09  30.0  1
 Y3V  Var_05    C6   C5   C4   N1     44.87  30.0  2
 Y3V  Var_06    C16  C15  C14  C13  -108.46  30.0  1
 Y3V  Var_07    N4   C13  C14  C15   -83.51  30.0  2
 Y3V  Var_08    H10  C9   N2   C5     44.40  30.0  2
 Y3V  Var_09    C14  C13  N4   C12    94.43  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
 Y3V  chir_02  C2   C1   C3   N3   positiv
 Y3V  chir_03  C14  C13  C15  C16  both

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
 Y3V  plan-1  C4   0.020
 Y3V  plan-1  C5   0.020
 Y3V  plan-1  C6   0.020
 Y3V  plan-1  C7   0.020
 Y3V  plan-1  C8   0.020
 Y3V  plan-1  N2   0.020
 Y3V  plan-1  H7   0.020
 Y3V  plan-1  H8   0.020
 Y3V  plan-1  H9   0.020
 Y3V  plan-1  C9   0.020
 Y3V  plan-2  N3   0.020
 Y3V  plan-2  C13  0.020
 Y3V  plan-2  C11  0.020
 Y3V  plan-2  C12  0.020
 Y3V  plan-2  C2   0.020
 Y3V  plan-2  N4   0.020
 Y3V  plan-2  O2   0.020
 Y3V  plan-2  H17  0.020
 Y3V  plan-3  N1   0.020
 Y3V  plan-3  C4   0.020
 Y3V  plan-3  C5   0.020
 Y3V  plan-3  C10  0.020
 Y3V  plan-3  C3   0.020
 Y3V  plan-3  O1   0.020

