# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Jul 29 05:28:10 2022
#   Inital geometry file: a 104 line input string
#   Ligand name: 3,4-dimethyl-7-[[(3~{S})-piperidin-3-yl]methoxy]chromen-2-one
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC1=C(C)c2ccc(OC[C@H]3CCCNC3)cc2OC1=O
#
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
 5IH  5IH  "3,4-dimethyl-7-[[(3~{S})-piperidin-3-yl]methoxy]chromen-2-one"  ligand  42  21  .  2022-09-22  2022-09-22
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_5IH
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
 5IH  CAB  C  CH3   0  -0.761  52.1025  151.7117  25.8055
 5IH  CAW  C  CR6   0   0.213  52.6401  153.0793  26.1048
 5IH  CAV  C  CR6   0  -0.238  53.8571  153.4565  25.6295
 5IH  CAA  C  CH3   0  -0.718  54.7425  152.5947  24.7850
 5IH  CAX  C  CR6   0   0.533  54.3940  154.7685  25.9346
 5IH  OAC  O  O     0  -0.427  55.4698  155.1833  25.5751
 5IH  OAS  O  O     0  -0.464  53.6367  155.6042  26.6873
 5IH  CAY  C  CR66  0   0.397  52.4176  155.2695  27.1565
 5IH  CAK  C  CR16  0  -0.470  51.7654  156.2461  27.8975
 5IH  CAZ  C  CR66  0  -0.024  51.8716  154.0132  26.8996
 5IH  CAJ  C  CR16  0  -0.331  50.5970  153.7672  27.4382
 5IH  CAI  C  CR16  0  -0.337  49.9268  154.7116  28.1759
 5IH  CAU  C  CR6   0   0.394  50.5077  155.9675  28.4131
 5IH  OAR  O  O2    0  -0.463  49.7865  156.8286  29.1369
 5IH  CAO  C  CH2   0  -0.171  50.3101  158.1271  29.3835
 5IH  CBA  C  CH1   0  -0.284  49.3024  158.9212  30.1901
 5IH  CAQ  C  CH2   0  -0.269  49.8231  160.3477  30.3605
 5IH  CAM  C  CH2   0  -0.421  49.0305  158.3027  31.5618
 5IH  CAL  C  CH2   0  -0.433  48.1365  159.2078  32.4032
 5IH  CAN  C  CH2   0  -0.290  48.7063  160.6158  32.4730
 5IH  NBB  N  NH1   0  -0.595  48.8820  161.1383  31.1293
 5IH  H1   H  HCH3  0   0.266  51.1448  151.5106  26.2743
 5IH  H2   H  HCH3  0   0.268  51.9732  151.5752  24.7313
 5IH  H3   H  HCH3  0   0.268  52.7970  150.9436  26.1457
 5IH  H4   H  HCH3  0   0.254  54.2711  151.6514  24.5258
 5IH  H5   H  HCH3  0   0.250  55.0052  153.0987  23.8537
 5IH  H6   H  HCH3  0   0.250  55.6793  152.3676  25.2974
 5IH  H7   H  HCR6  0   0.300  52.2573  157.1967  28.0510
 5IH  H8   H  HCR6  0   0.268  50.1147  152.8147  27.2750
 5IH  H9   H  HCR6  0   0.270  48.9455  154.4956  28.5776
 5IH  H10  H  HCH2  0   0.225  51.2560  158.0540  29.9346
 5IH  H11  H  HCH2  0   0.238  50.5159  158.6317  28.4321
 5IH  H12  H  HCH1  0   0.233  48.3641  158.9729  29.6252
 5IH  H13  H  HCH2  0   0.185  50.8203  160.3025  30.8327
 5IH  H14  H  HCH2  0   0.233  49.9563  160.8148  29.3814
 5IH  H15  H  HCH2  0   0.237  48.5768  157.3153  31.4589
 5IH  H16  H  HCH2  0   0.209  49.9878  158.1570  32.0767
 5IH  H17  H  HCH2  0   0.214  47.1349  159.2479  31.9649
 5IH  H18  H  HCH2  0   0.228  48.0283  158.8008  33.4108
 5IH  H19  H  HCH2  0   0.229  48.0266  161.2733  33.0191
 5IH  H20  H  HCH2  0   0.184  49.6513  160.5899  33.0421
 5IH  H21  H  HNH1  0   0.350  49.2112  162.0934  31.1776

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
 5IH  OAC  CAX  double    1.208  0.020  1.208
 5IH  CAA  CAV  single    1.497  0.020  1.497
 5IH  CAX  CAV  single    1.450  0.020  1.450
 5IH  CAX  OAS  single    1.356  0.020  1.356
 5IH  CAV  CAW  double    1.360  0.020  1.360
 5IH  OAS  CAY  single    1.348  0.020  1.348
 5IH  CAW  CAB  single    1.500  0.020  1.500
 5IH  CAW  CAZ  single    1.447  0.020  1.447
 5IH  CAY  CAZ  aromatic  1.394  0.020  1.394
 5IH  CAY  CAK  aromatic  1.389  0.020  1.389
 5IH  CAZ  CAJ  aromatic  1.405  0.020  1.405
 5IH  CAK  CAU  aromatic  1.387  0.020  1.387
 5IH  CAJ  CAI  aromatic  1.373  0.020  1.373
 5IH  CAU  CAI  aromatic  1.404  0.020  1.404
 5IH  CAU  OAR  single    1.336  0.020  1.336
 5IH  OAR  CAO  single    1.422  0.020  1.422
 5IH  CAO  CBA  single    1.515  0.020  1.515
 5IH  CBA  CAM  single    1.529  0.020  1.529
 5IH  CBA  CAQ  single    1.528  0.020  1.528
 5IH  CAM  CAL  single    1.525  0.020  1.525
 5IH  CAL  CAN  single    1.521  0.020  1.521
 5IH  CAQ  NBB  single    1.450  0.020  1.450
 5IH  NBB  CAN  single    1.452  0.020  1.452
 5IH  CAB  H1   single    0.970  0.020  1.090
 5IH  CAB  H2   single    0.970  0.020  1.090
 5IH  CAB  H3   single    0.970  0.020  1.090
 5IH  CAA  H4   single    0.970  0.020  1.090
 5IH  CAA  H5   single    0.970  0.020  1.090
 5IH  CAA  H6   single    0.970  0.020  1.090
 5IH  CAK  H7   single    0.930  0.020  1.080
 5IH  CAJ  H8   single    0.930  0.020  1.080
 5IH  CAI  H9   single    0.930  0.020  1.080
 5IH  CAO  H10  single    0.970  0.020  1.090
 5IH  CAO  H11  single    0.970  0.020  1.090
 5IH  CBA  H12  single    0.970  0.020  1.090
 5IH  CAQ  H13  single    0.970  0.020  1.090
 5IH  CAQ  H14  single    0.970  0.020  1.090
 5IH  CAM  H15  single    0.970  0.020  1.090
 5IH  CAM  H16  single    0.970  0.020  1.090
 5IH  CAL  H17  single    0.970  0.020  1.090
 5IH  CAL  H18  single    0.970  0.020  1.090
 5IH  CAN  H19  single    0.970  0.020  1.090
 5IH  CAN  H20  single    0.970  0.020  1.090
 5IH  NBB  H21  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
 5IH  H3   CAB  H2   107.14  3.000
 5IH  H3   CAB  H1   107.28  3.000
 5IH  H2   CAB  H1   107.32  3.000
 5IH  H3   CAB  CAW  110.60  3.000
 5IH  H2   CAB  CAW  110.69  3.000
 5IH  H1   CAB  CAW  113.53  3.000
 5IH  CAZ  CAW  CAV  119.22  3.000
 5IH  CAZ  CAW  CAB  120.51  3.000
 5IH  CAV  CAW  CAB  120.27  3.000
 5IH  CAX  CAV  CAA  114.88  3.000
 5IH  CAX  CAV  CAW  120.58  3.000
 5IH  CAA  CAV  CAW  124.54  3.000
 5IH  H6   CAA  H5   106.87  3.000
 5IH  H6   CAA  H4   107.69  3.000
 5IH  H5   CAA  H4   107.58  3.000
 5IH  H6   CAA  CAV  111.26  3.000
 5IH  H5   CAA  CAV  110.98  3.000
 5IH  H4   CAA  CAV  112.21  3.000
 5IH  OAS  CAX  OAC  116.81  3.000
 5IH  OAS  CAX  CAV  117.88  3.000
 5IH  OAC  CAX  CAV  125.31  3.000
 5IH  CAY  OAS  CAX  123.04  3.000
 5IH  CAZ  CAY  CAK  123.25  3.000
 5IH  CAK  CAY  OAS  115.84  3.000
 5IH  CAZ  CAY  OAS  120.91  3.000
 5IH  H7   CAK  CAU  122.42  3.000
 5IH  H7   CAK  CAY  118.70  3.000
 5IH  CAU  CAK  CAY  118.87  3.000
 5IH  CAJ  CAZ  CAY  116.26  3.000
 5IH  CAJ  CAZ  CAW  125.39  3.000
 5IH  CAY  CAZ  CAW  118.35  3.000
 5IH  H8   CAJ  CAI  118.02  3.000
 5IH  H8   CAJ  CAZ  120.10  3.000
 5IH  CAI  CAJ  CAZ  121.88  3.000
 5IH  H9   CAI  CAU  119.41  3.000
 5IH  H9   CAI  CAJ  120.32  3.000
 5IH  CAU  CAI  CAJ  120.27  3.000
 5IH  OAR  CAU  CAI  116.40  3.000
 5IH  OAR  CAU  CAK  124.13  3.000
 5IH  CAI  CAU  CAK  119.47  3.000
 5IH  CAO  OAR  CAU  118.93  3.000
 5IH  H11  CAO  H10  107.74  3.000
 5IH  H11  CAO  CBA  110.21  3.000
 5IH  H10  CAO  CBA  109.93  3.000
 5IH  H11  CAO  OAR  109.82  3.000
 5IH  H10  CAO  OAR  110.11  3.000
 5IH  CBA  CAO  OAR  109.03  3.000
 5IH  H12  CBA  CAM  109.21  3.000
 5IH  H12  CBA  CAQ  107.76  3.000
 5IH  CAM  CBA  CAQ  109.76  3.000
 5IH  H12  CBA  CAO  108.64  3.000
 5IH  CAQ  CBA  CAO  108.78  3.000
 5IH  CAM  CBA  CAO  112.57  3.000
 5IH  H14  CAQ  H13  106.89  3.000
 5IH  H14  CAQ  NBB  108.73  3.000
 5IH  H13  CAQ  NBB  112.44  3.000
 5IH  H14  CAQ  CBA  109.92  3.000
 5IH  H13  CAQ  CBA  108.49  3.000
 5IH  NBB  CAQ  CBA  110.31  3.000
 5IH  H16  CAM  H15  106.67  3.000
 5IH  H16  CAM  CAL  109.36  3.000
 5IH  H15  CAM  CAL  110.19  3.000
 5IH  H16  CAM  CBA  108.65  3.000
 5IH  H15  CAM  CBA  110.81  3.000
 5IH  CAL  CAM  CBA  111.04  3.000
 5IH  H18  CAL  H17  107.01  3.000
 5IH  H18  CAL  CAN  109.87  3.000
 5IH  H17  CAL  CAN  109.12  3.000
 5IH  H18  CAL  CAM  110.24  3.000
 5IH  H17  CAL  CAM  109.71  3.000
 5IH  CAN  CAL  CAM  110.80  3.000
 5IH  H20  CAN  H19  106.82  3.000
 5IH  H20  CAN  NBB  112.46  3.000
 5IH  H19  CAN  NBB  108.75  3.000
 5IH  H20  CAN  CAL  108.84  3.000
 5IH  H19  CAN  CAL  110.32  3.000
 5IH  NBB  CAN  CAL  109.63  3.000
 5IH  H21  NBB  CAN  109.56  3.000
 5IH  H21  NBB  CAQ  109.21  3.000
 5IH  CAN  NBB  CAQ  111.90  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
 5IH  CONST_01  CAI  CAJ  CAZ  CAY     0.00   0.0  0
 5IH  CONST_02  CAI  CAU  CAK  CAY     0.00   0.0  0
 5IH  CONST_03  CAJ  CAZ  CAY  CAK     0.00   0.0  0
 5IH  CONST_04  CAJ  CAI  CAU  CAK     0.00   0.0  0
 5IH  CONST_05  CAU  CAK  CAY  CAZ     0.00   0.0  0
 5IH  CONST_06  CAU  CAI  CAJ  CAZ     0.00   0.0  0
 5IH  CONST_07  OAR  CAU  CAK  CAY   180.00   0.0  0
 5IH  CONST_08  OAR  CAU  CAI  CAJ   180.00   0.0  0
 5IH  CONST_09  H8   CAJ  CAZ  CAW     0.00   0.0  0
 5IH  CONST_10  H7   CAK  CAY  OAS     0.00   0.0  0
 5IH  CONST_11  H8   CAJ  CAZ  CAY   180.00   0.0  0
 5IH  CONST_12  H9   CAI  CAU  CAK   180.00   0.0  0
 5IH  CONST_13  H7   CAK  CAY  CAZ   180.00   0.0  0
 5IH  CONST_14  H9   CAI  CAJ  CAZ   180.00   0.0  0
 5IH  CONST_15  H7   CAK  CAU  CAI   180.00   0.0  0
 5IH  CONST_16  H8   CAJ  CAI  CAU   180.00   0.0  0
 5IH  Var_01    OAS  CAX  CAV  CAW    -0.95  30.0  1
 5IH  Var_02    CAY  OAS  CAX  CAV    -0.11  30.0  1
 5IH  Var_03    CAY  CAZ  CAW  CAV    -0.45  30.0  1
 5IH  Var_04    CAJ  CAZ  CAW  CAV   179.08  30.0  1
 5IH  Var_05    CAZ  CAW  CAV  CAX     1.20  30.0  1
 5IH  Var_06    CAZ  CAY  OAS  CAX     0.87  30.0  1
 5IH  Var_07    CAK  CAY  OAS  CAX  -179.21  30.0  1
 5IH  Var_08    CAN  CAL  CAM  CBA   -52.80  30.0  1
 5IH  Var_09    CAN  NBB  CAQ  CBA    62.39  30.0  1
 5IH  Var_10    CAL  CAN  NBB  CAQ   -61.92  30.0  1
 5IH  Var_11    NBB  CAN  CAL  CAM    56.41  30.0  1
 5IH  Var_12    CAX  CAV  CAW  CAB  -178.90  30.0  1
 5IH  Var_13    CAY  CAZ  CAW  CAB   179.65  30.0  1
 5IH  Var_14    CAJ  CAZ  CAW  CAB    -0.82  30.0  1
 5IH  Var_15    OAC  CAX  CAV  CAW   178.85  30.0  1
 5IH  Var_16    OAS  CAX  CAV  CAA   179.47  30.0  1
 5IH  Var_17    CAZ  CAW  CAV  CAA  -179.26  30.0  1
 5IH  Var_18    CAY  OAS  CAX  OAC  -179.92  30.0  1
 5IH  Var_19    H17  CAL  CAM  CBA    67.76  30.0  1
 5IH  Var_20    H18  CAL  CAM  CBA  -174.64  30.0  1
 5IH  Var_21    H21  NBB  CAQ  CBA  -176.13  30.0  1
 5IH  Var_22    H19  CAN  NBB  CAQ   177.40  30.0  1
 5IH  Var_23    H20  CAN  NBB  CAQ    59.31  30.0  1
 5IH  Var_24    H19  CAN  CAL  CAM   176.14  30.0  1
 5IH  Var_25    H20  CAN  CAL  CAM   -66.97  30.0  1
 5IH  Var_26    H21  NBB  CAN  CAL   176.80  30.0  1
 5IH  Var_27    H15  CAM  CAL  CAN  -175.97  30.0  1
 5IH  Var_28    H16  CAM  CAL  CAN    67.09  30.0  1
 5IH  Var_29    H13  CAQ  NBB  CAN   -58.86  30.0  1
 5IH  Var_30    H14  CAQ  NBB  CAN  -177.02  30.0  1
 5IH  Var_31    H17  CAL  CAN  NBB   -64.50  30.0  1
 5IH  Var_32    H18  CAL  CAN  NBB   178.46  30.0  1
 5IH  Var_33    CAA  CAV  CAW  CAB     0.64  30.0  1
 5IH  Var_34    OAC  CAX  CAV  CAA    -0.74  30.0  1
 5IH  Var_35    CAO  OAR  CAU  CAK     1.34  30.0  2
 5IH  Var_36    CAO  OAR  CAU  CAI  -178.56  30.0  2
 5IH  Var_37    CBA  CAO  OAR  CAU   178.64  30.0  3
 5IH  Var_38    H4   CAA  CAV  CAW     4.40  30.0  3
 5IH  Var_39    H5   CAA  CAV  CAW   124.80  30.0  3
 5IH  Var_40    H6   CAA  CAV  CAW  -116.33  30.0  3
 5IH  Var_41    H1   CAB  CAW  CAV   177.42  30.0  3
 5IH  Var_42    H2   CAB  CAW  CAV   -61.81  30.0  3
 5IH  Var_43    H3   CAB  CAW  CAV    56.77  30.0  3
 5IH  Var_44    H4   CAA  CAV  CAX  -176.04  30.0  3
 5IH  Var_45    H5   CAA  CAV  CAX   -55.63  30.0  3
 5IH  Var_46    H6   CAA  CAV  CAX    63.23  30.0  3
 5IH  Var_47    H1   CAB  CAW  CAZ    -2.68  30.0  3
 5IH  Var_48    H2   CAB  CAW  CAZ   118.09  30.0  3
 5IH  Var_49    H3   CAB  CAW  CAZ  -123.33  30.0  3
 5IH  Var_50    H10  CAO  OAR  CAU   -60.68  30.0  3
 5IH  Var_51    H11  CAO  OAR  CAU    57.80  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
 5IH  chir_01  CBA  CAO  CAM  CAQ  negativ

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
 5IH  plan-1  CAV  0.020
 5IH  plan-1  CAX  0.020
 5IH  plan-1  OAC  0.020
 5IH  plan-1  OAS  0.020
 5IH  plan-2  CAW  0.020
 5IH  plan-2  OAS  0.020
 5IH  plan-2  CAY  0.020
 5IH  plan-2  CAK  0.020
 5IH  plan-2  CAZ  0.020
 5IH  plan-2  CAJ  0.020
 5IH  plan-2  CAI  0.020
 5IH  plan-2  CAU  0.020
 5IH  plan-2  OAR  0.020
 5IH  plan-2  H7   0.020
 5IH  plan-2  H8   0.020
 5IH  plan-2  H9   0.020

