# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Mar 25 09:12:25 2022
#   Inital geometry file: a 95 line input string
#   Ligand name: N-(cyclopropylmethyl)-4-(furan-2-carbonyl)piperazine-1-carboxamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: O=C(NCC1CC1)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
 Y1J  Y1J  N-(cyclopropylmethyl)-4-(furan-2-carbonyl)piperazine-1-carboxamide  ligand  39  20  .  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_Y1J
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
 Y1J  N1   N  NT    0  -0.512  -17.4423  15.4205  26.2602
 Y1J  C4   C  CH2   0  -0.485  -16.3016  20.3044  25.2233
 Y1J  C5   C  CH2   0  -0.278  -18.4502  14.9311  27.1847
 Y1J  C6   C  CH2   0  -0.325  -18.7063  13.4534  26.9603
 Y1J  C8   C  CR5   0   0.210  -21.3193  12.3929  25.9348
 Y1J  C10  C  CR15  0  -0.336  -23.2721  11.7984  26.8224
 Y1J  C13  C  CH2   0  -0.309  -17.6854  15.1015  24.8664
 Y1J  N    N  NH1   0  -0.677  -15.9123  17.0890  25.7161
 Y1J  C    C  C     0   0.742  -16.5948  16.4146  26.6818
 Y1J  O    O  O     0  -0.539  -16.4262  16.6509  27.8738
 Y1J  C1   C  CH2   0  -0.304  -15.0463  18.1973  26.0620
 Y1J  C11  C  CR15  0   0.017  -22.8095  12.9184  27.4302
 Y1J  C12  C  CH2   0  -0.307  -17.9749  13.6172  24.6853
 Y1J  C2   C  CH1   0  -0.248  -15.7840  19.4775  26.3593
 Y1J  C3   C  CH2   0  -0.488  -15.1366  20.7875  26.0356
 Y1J  C9   C  CR15  0  -0.313  -22.3043  11.4609  25.8377
 Y1J  N2   N  NT    0  -0.471  -19.0457  13.2077  25.5702
 Y1J  O1   O  O     0  -0.475  -20.1722  12.1087  23.9454
 Y1J  O2   O  O     0  -0.405  -21.6306  13.2860  26.9012
 Y1J  H7   H  HCH2  0   0.242  -16.1063  19.9586  24.2146
 Y1J  H8   H  HCH2  0   0.267  -18.1077  15.0832  28.2044
 Y1J  H9   H  HCH2  0   0.232  -19.3885  15.4854  27.0581
 Y1J  H11  H  HCH2  0   0.254  -17.7956  12.8898  27.1891
 Y1J  H10  H  HCH2  0   0.280  -19.4764  13.1011  27.6372
 Y1J  H13  H  HCR5  0   0.271  -24.1904  11.2805  27.0455
 Y1J  H18  H  HCH2  0   0.260  -16.8044  15.3199  24.2654
 Y1J  H17  H  HCH2  0   0.241  -18.5219  15.6871  24.4660
 Y1J  H    H  HNH1  0   0.398  -16.2869  17.1197  24.7827
 Y1J  H1   H  HCH2  0   0.247  -14.4243  17.9102  26.9095
 Y1J  H2   H  HCH2  0   0.242  -14.3700  18.3532  25.2185
 Y1J  H14  H  HCR5  0   0.286  -23.1992  13.5404  28.2200
 Y1J  H15  H  HCH2  0   0.248  -17.0742  13.0369  24.9092
 Y1J  H16  H  HCH2  0   0.276  -18.2488  13.4279  23.6512
 Y1J  H3   H  HCH1  0   0.253  -16.3954  19.4541  27.2547
 Y1J  H4   H  HCH2  0   0.249  -15.2903  21.6172  26.7133
 Y1J  H5   H  HCH2  0   0.242  -14.1564  20.7681  25.5739
 Y1J  H12  H  HCR5  0   0.271  -22.3335  10.6302  25.1516
 Y1J  C7   C  C     0   0.498  -20.1248  12.5576  25.0840
 Y1J  H6   H  HCH2  0   0.247  -17.2541  20.8042  25.3430

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
 Y1J  O    C    double    1.227  0.020  1.227
 Y1J  N    C    single    1.361  0.020  1.361
 Y1J  C1   N    single    1.448  0.020  1.448
 Y1J  C2   C1   single    1.507  0.020  1.507
 Y1J  C2   C3   single    1.497  0.020  1.497
 Y1J  C3   C4   single    1.500  0.020  1.500
 Y1J  C4   C2   single    1.497  0.020  1.497
 Y1J  C    N1   single    1.373  0.020  1.373
 Y1J  N1   C5   single    1.453  0.020  1.453
 Y1J  C5   C6   single    1.516  0.020  1.516
 Y1J  C6   N2   single    1.452  0.020  1.452
 Y1J  N2   C7   single    1.350  0.020  1.350
 Y1J  C7   O1   double    1.225  0.020  1.225
 Y1J  C8   C7   single    1.476  0.020  1.476
 Y1J  C8   C9   aromatic  1.359  0.020  1.359
 Y1J  C9   C10  aromatic  1.421  0.020  1.421
 Y1J  C10  C11  aromatic  1.356  0.020  1.356
 Y1J  C11  O2   aromatic  1.343  0.020  1.343
 Y1J  O2   C8   aromatic  1.352  0.020  1.352
 Y1J  C12  N2   single    1.448  0.020  1.448
 Y1J  C13  C12  single    1.523  0.020  1.523
 Y1J  N1   C13  single    1.450  0.020  1.450
 Y1J  C4   H6   single    0.970  0.020  1.090
 Y1J  C4   H7   single    0.970  0.020  1.090
 Y1J  C5   H8   single    0.970  0.020  1.090
 Y1J  C5   H9   single    0.970  0.020  1.090
 Y1J  C6   H11  single    0.970  0.020  1.090
 Y1J  C6   H10  single    0.970  0.020  1.090
 Y1J  C10  H13  single    0.930  0.020  1.080
 Y1J  C13  H18  single    0.970  0.020  1.090
 Y1J  C13  H17  single    0.970  0.020  1.090
 Y1J  N    H    single    0.860  0.020  1.020
 Y1J  C1   H1   single    0.970  0.020  1.090
 Y1J  C1   H2   single    0.970  0.020  1.090
 Y1J  C11  H14  single    0.930  0.020  1.080
 Y1J  C12  H15  single    0.970  0.020  1.090
 Y1J  C12  H16  single    0.970  0.020  1.090
 Y1J  C2   H3   single    0.970  0.020  1.090
 Y1J  C3   H4   single    0.970  0.020  1.090
 Y1J  C3   H5   single    0.970  0.020  1.090
 Y1J  C9   H12  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
 Y1J  C    N1   C13  123.91  3.000
 Y1J  C13  N1   C5   114.91  3.000
 Y1J  C    N1   C5   118.49  3.000
 Y1J  H7   C4   H6   114.13  3.000
 Y1J  H7   C4   C3   117.82  3.000
 Y1J  H6   C4   C3   118.35  3.000
 Y1J  H7   C4   C2   117.88  3.000
 Y1J  H6   C4   C2   118.38  3.000
 Y1J  C3   C4   C2    59.91  3.000
 Y1J  H9   C5   H8   107.89  3.000
 Y1J  H9   C5   C6   109.32  3.000
 Y1J  H8   C5   C6   109.19  3.000
 Y1J  H9   C5   N1   110.47  3.000
 Y1J  H8   C5   N1   109.35  3.000
 Y1J  C6   C5   N1   110.57  3.000
 Y1J  H10  C6   H11  107.04  3.000
 Y1J  H10  C6   N2   112.14  3.000
 Y1J  H11  C6   N2   107.90  3.000
 Y1J  H10  C6   C5   110.13  3.000
 Y1J  H11  C6   C5   109.28  3.000
 Y1J  N2   C6   C5   110.25  3.000
 Y1J  O2   C8   C9   109.70  3.000
 Y1J  O2   C8   C7   121.64  3.000
 Y1J  C9   C8   C7   128.45  3.000
 Y1J  H13  C10  C9   127.56  3.000
 Y1J  H13  C10  C11  126.51  3.000
 Y1J  C9   C10  C11  105.93  3.000
 Y1J  H17  C13  H18  107.97  3.000
 Y1J  H17  C13  C12  109.39  3.000
 Y1J  H18  C13  C12  106.48  3.000
 Y1J  H17  C13  N1   111.18  3.000
 Y1J  H18  C13  N1   110.53  3.000
 Y1J  C12  C13  N1   111.13  3.000
 Y1J  H    N    C1   114.88  3.000
 Y1J  H    N    C    119.11  3.000
 Y1J  C1   N    C    120.62  3.000
 Y1J  O    C    N    121.67  3.000
 Y1J  N    C    N1   116.77  3.000
 Y1J  O    C    N1   121.51  3.000
 Y1J  H2   C1   H1   106.54  3.000
 Y1J  H2   C1   C2   109.52  3.000
 Y1J  H1   C1   C2   110.47  3.000
 Y1J  H2   C1   N    107.16  3.000
 Y1J  H1   C1   N    108.99  3.000
 Y1J  C2   C1   N    113.86  3.000
 Y1J  H14  C11  O2   116.60  3.000
 Y1J  H14  C11  C10  132.97  3.000
 Y1J  O2   C11  C10  110.43  3.000
 Y1J  H16  C12  H15  108.05  3.000
 Y1J  H16  C12  N2   110.24  3.000
 Y1J  H15  C12  N2   109.48  3.000
 Y1J  H16  C12  C13  109.32  3.000
 Y1J  H15  C12  C13  109.63  3.000
 Y1J  N2   C12  C13  110.08  3.000
 Y1J  H3   C2   C3   116.19  3.000
 Y1J  H3   C2   C1   114.87  3.000
 Y1J  C3   C2   C1   119.28  3.000
 Y1J  H3   C2   C4   116.32  3.000
 Y1J  C3   C2   C4    60.14  3.000
 Y1J  C1   C2   C4   119.25  3.000
 Y1J  H5   C3   H4   114.14  3.000
 Y1J  H5   C3   C2   117.88  3.000
 Y1J  H4   C3   C2   118.31  3.000
 Y1J  H5   C3   C4   117.77  3.000
 Y1J  H4   C3   C4   118.41  3.000
 Y1J  C2   C3   C4    59.96  3.000
 Y1J  H12  C9   C10  127.27  3.000
 Y1J  H12  C9   C8   126.40  3.000
 Y1J  C10  C9   C8   106.32  3.000
 Y1J  C12  N2   C7   120.46  3.000
 Y1J  C12  N2   C6   111.37  3.000
 Y1J  C7   N2   C6   127.81  3.000
 Y1J  C11  O2   C8   107.62  3.000
 Y1J  O1   C7   N2   122.83  3.000
 Y1J  O1   C7   C8   117.63  3.000
 Y1J  N2   C7   C8   119.54  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
 Y1J  CONST_01  C11  C10  C9   C8      0.00   0.0  0
 Y1J  CONST_02  C10  C11  O2   C8      0.00   0.0  0
 Y1J  CONST_03  O2   C8   C9   C10     0.00   0.0  0
 Y1J  CONST_04  C9   C8   O2   C11     0.00   0.0  0
 Y1J  CONST_05  O2   C11  C10  C9      0.00   0.0  0
 Y1J  CONST_06  C10  C9   C8   C7    180.00   0.0  0
 Y1J  CONST_07  C11  O2   C8   C7    180.00   0.0  0
 Y1J  CONST_09  C12  N2   C7   C8    180.00   0.0  0
 Y1J  CONST_10  H13  C10  C9   C8    180.00   0.0  0
 Y1J  CONST_11  H14  C11  O2   C8    180.00   0.0  0
 Y1J  CONST_12  H12  C9   C10  C11   180.00   0.0  0
 Y1J  CONST_15  O    C    N1   C13   180.00   0.0  0
 Y1J  CONST_16  O1   C7   N2   C12     0.00   0.0  0
 Y1J  CONST_18  N    C    N1   C13     0.00   0.0  0
 Y1J  CONST_19  C1   N    C    N1    180.00   0.0  0
 Y1J  CONST_21  C1   N    C    O       0.00   0.0  0
 Y1J  Var_01    N2   C6   C5   N1    -54.37  30.0  1
 Y1J  Var_02    N2   C12  C13  N1     53.19  30.0  1
 Y1J  Var_03    C12  C13  N1   C5    -50.65  30.0  1
 Y1J  Var_04    C12  N2   C6   C5     60.06  30.0  1
 Y1J  Var_05    C13  N1   C5   C6     51.14  30.0  1
 Y1J  Var_06    C13  C12  N2   C6    -59.17  30.0  1
 Y1J  Var_07    C1   C2   C3   C4    108.90  30.0  1
 Y1J  Var_08    N2   C7   C8   C9   -157.21  30.0  2
 Y1J  Var_09    H6   C4   C3   C2    108.15  30.0  1
 Y1J  Var_10    N    C1   C2   C4    -78.22  30.0  3
 Y1J  Var_11    C2   C1   N    C     -77.48  30.0  2

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
 Y1J  chir_01  C2  C1  C3  C4  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
 Y1J  plan-1  C8   0.020
 Y1J  plan-1  C10  0.020
 Y1J  plan-1  C11  0.020
 Y1J  plan-1  C9   0.020
 Y1J  plan-1  O2   0.020
 Y1J  plan-1  H13  0.020
 Y1J  plan-1  H14  0.020
 Y1J  plan-1  H12  0.020
 Y1J  plan-1  C7   0.020
 Y1J  plan-2  N1   0.020
 Y1J  plan-2  C5   0.020
 Y1J  plan-2  C13  0.020
 Y1J  plan-2  N    0.020
 Y1J  plan-2  C    0.020
 Y1J  plan-2  O    0.020
 Y1J  plan-2  C1   0.020
 Y1J  plan-2  H    0.020
 Y1J  plan-3  C6   0.020
 Y1J  plan-3  C8   0.020
 Y1J  plan-3  C12  0.020
 Y1J  plan-3  N2   0.020
 Y1J  plan-3  O1   0.020
 Y1J  plan-3  C7   0.020

