# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat May  9 01:58:28 2020
#   Inital geometry file: a 85 line input string
#   Ligand name: [4-(cyclopropanecarbonyl)piperazin-1-yl](furan-2-yl)methanone
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: O=C(C1CC1)N2CCN(CC2)C(=O)c3occc3
#
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
 JMM  JMM  '[4-(cyclopropanecarbonyl)piperazin-1-yl](furan-2-yl)methanone'  ligand  34  18  .  2022-09-22  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_JMM
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
 JMM  C10   C  CH2   0  -0.321   1.1645   1.7192   0.3183
 JMM  C13   C  CH2   0  -0.322  -0.2433  -0.6600  -0.4182
 JMM  C17   C  CH2   0  -0.461   5.2003  -1.1863   0.3013
 JMM  C01   C  CR15  0  -0.335  -4.9620  -1.2658   0.4537
 JMM  C02   C  CR15  0  -0.317  -4.2471  -0.0875   0.8024
 JMM  C03   C  CR5   0   0.214  -3.1379  -0.0681   0.0167
 JMM  O04   O  O     0  -0.406  -3.1369  -1.1461  -0.7997
 JMM  C05   C  CR15  0   0.013  -4.2408  -1.8618  -0.5273
 JMM  C06   C  C     0   0.502  -2.0982   0.9754  -0.0737
 JMM  O07   O  O     0  -0.479  -2.4113   2.1168   0.2407
 JMM  N08   N  NT    0  -0.465  -0.8680   0.6489  -0.5361
 JMM  C09   C  CH2   0  -0.324   0.1053   1.7038  -0.7732
 JMM  N11   N  NT    0  -0.476   1.7971   0.4147   0.4195
 JMM  C12   C  CH2   0  -0.311   0.8316  -0.6387   0.6655
 JMM  C14   C  C     0   0.596   3.0964   0.2561   0.0655
 JMM  O15   O  O     0  -0.509   3.7738   1.2015  -0.3233
 JMM  C16   C  CH1   0  -0.430   3.7034  -1.1005   0.1754
 JMM  C18   C  CH2   0  -0.465   4.5564  -1.5671  -0.9807
 JMM  H101  H  HCH2  0   0.275   1.9109   2.4789   0.1068
 JMM  H102  H  HCH2  0   0.255   0.7018   1.9611   1.2801
 JMM  H131  H  HCH2  0   0.284  -0.9658  -1.4285  -0.1668
 JMM  H132  H  HCH2  0   0.256   0.2043  -0.9279  -1.3790
 JMM  H171  H  HCH2  0   0.257   5.7555  -0.2591   0.3402
 JMM  H172  H  HCH2  0   0.261   5.5841  -1.9731   0.9371
 JMM  H021  H  HCR5  0   0.273  -4.5176   0.6468   1.5432
 JMM  H051  H  HCR5  0   0.288  -4.3884  -2.7608  -1.1037
 JMM  H092  H  HCH2  0   0.274  -0.3959   2.6663  -0.8280
 JMM  H091  H  HCH2  0   0.261   0.5804   1.5153  -1.7402
 JMM  H122  H  HCH2  0   0.256   0.3591  -0.4689   1.6378
 JMM  H121  H  HCH2  0   0.277   1.3022  -1.6156   0.7026
 JMM  H161  H  HCH1  0   0.286   3.1564  -1.8754   0.6909
 JMM  H181  H  HCH2  0   0.257   4.6596  -0.8941  -1.8218
 JMM  H182  H  HCH2  0   0.262   4.4912  -2.6144  -1.2438
 JMM  H011  H  HCR5  0   0.273  -5.8889  -1.6206   0.8727

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
 JMM  C01  C02   aromatic  1.422  0.020  1.422
 JMM  C01  C05   aromatic  1.356  0.020  1.356
 JMM  C02  C03   aromatic  1.359  0.020  1.359
 JMM  C05  O04   aromatic  1.344  0.020  1.344
 JMM  O07  C06   double    1.225  0.020  1.225
 JMM  C03  C06   single    1.476  0.020  1.476
 JMM  C03  O04   aromatic  1.352  0.020  1.352
 JMM  C06  N08   single    1.354  0.020  1.354
 JMM  N08  C09   single    1.455  0.020  1.455
 JMM  N08  C13   single    1.455  0.020  1.455
 JMM  C09  C10   single    1.521  0.020  1.521
 JMM  C13  C12   single    1.526  0.020  1.526
 JMM  C10  N11   single    1.453  0.020  1.453
 JMM  C12  N11   single    1.450  0.020  1.450
 JMM  N11  C14   single    1.356  0.020  1.356
 JMM  C14  O15   double    1.226  0.020  1.226
 JMM  C14  C16   single    1.490  0.020  1.490
 JMM  C18  C16   single    1.511  0.020  1.511
 JMM  C18  C17   single    1.484  0.020  1.484
 JMM  C16  C17   single    1.505  0.020  1.505
 JMM  C10  H101  single    0.970  0.020  1.090
 JMM  C10  H102  single    0.970  0.020  1.090
 JMM  C13  H131  single    0.970  0.020  1.090
 JMM  C13  H132  single    0.970  0.020  1.090
 JMM  C17  H171  single    0.970  0.020  1.090
 JMM  C17  H172  single    0.970  0.020  1.090
 JMM  C01  H011  single    0.930  0.020  1.080
 JMM  C02  H021  single    0.930  0.020  1.080
 JMM  C05  H051  single    0.930  0.020  1.080
 JMM  C09  H092  single    0.970  0.020  1.090
 JMM  C09  H091  single    0.970  0.020  1.090
 JMM  C12  H122  single    0.970  0.020  1.090
 JMM  C12  H121  single    0.970  0.020  1.090
 JMM  C16  H161  single    0.970  0.020  1.090
 JMM  C18  H181  single    0.970  0.020  1.090
 JMM  C18  H182  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
 JMM  H102  C10  H101  107.89  3.000
 JMM  H102  C10  N11   108.74  3.000
 JMM  H101  C10  N11   110.02  3.000
 JMM  H102  C10  C09   109.79  3.000
 JMM  H101  C10  C09   110.24  3.000
 JMM  N11   C10  C09   110.12  3.000
 JMM  H132  C13  H131  107.63  3.000
 JMM  H132  C13  C12   109.82  3.000
 JMM  H131  C13  C12   108.33  3.000
 JMM  H132  C13  N08   108.97  3.000
 JMM  H131  C13  N08   111.73  3.000
 JMM  C12   C13  N08   110.32  3.000
 JMM  H172  C17  H171  114.85  3.000
 JMM  H172  C17  C18   118.35  3.000
 JMM  H171  C17  C18   118.28  3.000
 JMM  H172  C17  C16   116.33  3.000
 JMM  H171  C17  C16   117.71  3.000
 JMM  C18   C17  C16    60.71  3.000
 JMM  H011  C01  C05   126.47  3.000
 JMM  H011  C01  C02   127.61  3.000
 JMM  C05   C01  C02   105.92  3.000
 JMM  H021  C02  C03   126.34  3.000
 JMM  H021  C02  C01   127.38  3.000
 JMM  C03   C02  C01   106.28  3.000
 JMM  C06   C03  O04   121.75  3.000
 JMM  O04   C03  C02   109.77  3.000
 JMM  C06   C03  C02   128.34  3.000
 JMM  C05   O04  C03   107.56  3.000
 JMM  H051  C05  O04   116.64  3.000
 JMM  H051  C05  C01   132.90  3.000
 JMM  O04   C05  C01   110.46  3.000
 JMM  N08   C06  O07   123.00  3.000
 JMM  N08   C06  C03   119.37  3.000
 JMM  O07   C06  C03   117.59  3.000
 JMM  C09   N08  C06   119.25  3.000
 JMM  C09   N08  C13   112.22  3.000
 JMM  C06   N08  C13   125.40  3.000
 JMM  H091  C09  H092  107.97  3.000
 JMM  H091  C09  N08   108.04  3.000
 JMM  H092  C09  N08   109.99  3.000
 JMM  H091  C09  C10   109.49  3.000
 JMM  H092  C09  C10   110.39  3.000
 JMM  N08   C09  C10   110.87  3.000
 JMM  C14   N11  C12   126.68  3.000
 JMM  C14   N11  C10   120.26  3.000
 JMM  C12   N11  C10   111.97  3.000
 JMM  H121  C12  H122  107.25  3.000
 JMM  H121  C12  N11   111.78  3.000
 JMM  H122  C12  N11   109.00  3.000
 JMM  H121  C12  C13   108.49  3.000
 JMM  H122  C12  C13   109.21  3.000
 JMM  N11   C12  C13   111.02  3.000
 JMM  C16   C14  O15   120.01  3.000
 JMM  C16   C14  N11   118.52  3.000
 JMM  O15   C14  N11   121.46  3.000
 JMM  H161  C16  C18   115.46  3.000
 JMM  H161  C16  C14   118.83  3.000
 JMM  C18   C16  C14   117.05  3.000
 JMM  H161  C16  C17   115.04  3.000
 JMM  C18   C16  C17    58.98  3.000
 JMM  C14   C16  C17   117.60  3.000
 JMM  H182  C18  H181  114.76  3.000
 JMM  H182  C18  C16   116.81  3.000
 JMM  H181  C18  C16   117.17  3.000
 JMM  H182  C18  C17   118.99  3.000
 JMM  H181  C18  C17   118.06  3.000
 JMM  C16   C18  C17    60.31  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
 JMM  CONST_01  O04   C03  C02  C01     0.00   0.0  0
 JMM  CONST_02  C03   O04  C05  C01     0.00   0.0  0
 JMM  CONST_03  O04   C05  C01  C02     0.00   0.0  0
 JMM  CONST_04  C05   O04  C03  C02     0.00   0.0  0
 JMM  CONST_05  C05   C01  C02  C03     0.00   0.0  0
 JMM  CONST_06  C06   C03  C02  C01   180.00   0.0  0
 JMM  CONST_07  C06   C03  O04  C05   180.00   0.0  0
 JMM  CONST_08  C16   C14  N11  C10   180.00   0.0  0
 JMM  CONST_10  C09   N08  C06  C03   180.00   0.0  0
 JMM  CONST_11  C16   C14  N11  C12     0.00   0.0  0
 JMM  CONST_12  H051  C05  C01  C02   180.00   0.0  0
 JMM  CONST_13  H011  C01  C02  C03   180.00   0.0  0
 JMM  CONST_14  H021  C02  C03  O04   180.00   0.0  0
 JMM  CONST_15  O15   C14  N11  C10     0.00   0.0  0
 JMM  CONST_17  C09   N08  C06  O07     0.00   0.0  0
 JMM  CONST_18  O15   C14  N11  C12   180.00   0.0  0
 JMM  Var_01    C13   N08  C09  C10   -56.08  30.0  1
 JMM  Var_02    C13   C12  N11  C10    56.52  30.0  1
 JMM  Var_03    N11   C10  C09  N08    55.77  30.0  1
 JMM  Var_04    N11   C12  C13  N08   -54.70  30.0  1
 JMM  Var_05    C12   C13  N08  C09    55.09  30.0  1
 JMM  Var_06    C12   N11  C10  C09   -56.71  30.0  1
 JMM  Var_07    C14   C16  C18  C17   107.45  30.0  1
 JMM  Var_08    N11   C14  C16  C17  -157.02  30.0  2
 JMM  Var_09    N08   C06  C03  C02   157.38  30.0  2
 JMM  Var_10    H171  C17  C18  C16  -107.67  30.0  1

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
 JMM  chir_01  C16  C14  C18  C17  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
 JMM  plan-1  C01   0.020
 JMM  plan-1  C02   0.020
 JMM  plan-1  C03   0.020
 JMM  plan-1  O04   0.020
 JMM  plan-1  C05   0.020
 JMM  plan-1  C06   0.020
 JMM  plan-1  H021  0.020
 JMM  plan-1  H051  0.020
 JMM  plan-1  H011  0.020
 JMM  plan-2  C10   0.020
 JMM  plan-2  N11   0.020
 JMM  plan-2  C12   0.020
 JMM  plan-2  C14   0.020
 JMM  plan-2  O15   0.020
 JMM  plan-2  C16   0.020
 JMM  plan-3  C13   0.020
 JMM  plan-3  C03   0.020
 JMM  plan-3  C06   0.020
 JMM  plan-3  O07   0.020
 JMM  plan-3  N08   0.020
 JMM  plan-3  C09   0.020

