# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Mar 11 02:45:35 2022
#   Inital geometry file: a 114 line input string
#   Ligand name: 3-(4-carbamoyl-1H-imidazol-1-yl)-1,3,4-trideoxy-5-O-naphthalen-2-yl-D-erythro-pentitol
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[C@H](O)[C@@H](CCOc1ccc2ccccc2c1)n3cnc(c3)C(N)=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
 FRC  FRC  3-(4-carbamoyl-1H-imidazol-1-yl)-1,3,4-trideoxy-5-O-naphthalen-2-yl-D-erythro-pentitol  ligand  46  25  .  2022-03-18  2022-03-18
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_FRC
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
 FRC  C1    C  CR15  0  -0.068  50.6883  54.1090  21.2254
 FRC  N2    N  NR5   0  -0.405  50.7815  55.0340  22.2195
 FRC  C3    C  CR15  0   0.110  50.7337  54.3569  23.3931
 FRC  N4    N  N     0  -0.460  50.6093  53.0721  23.2129
 FRC  C5    C  CR5   0  -0.023  50.5778  52.9002  21.8577
 FRC  C8    C  C     0   0.450  50.4320  51.5876  21.2056
 FRC  O9    O  O     0  -0.486  50.3676  51.4832  19.9850
 FRC  N10   N  NH2   0  -0.808  50.3766  50.5464  22.0474
 FRC  C13   C  CH1   0  -0.143  50.9468  56.4767  22.0888
 FRC  C14   C  CH1   0   0.084  52.4149  56.8586  21.8644
 FRC  O15   O  OH1   0  -0.661  53.1173  56.3870  22.9920
 FRC  C18   C  CH2   0  -0.513  50.0115  57.0555  21.0338
 FRC  C2    C  CH2   0  -0.192  48.5487  56.9322  21.4446
 FRC  C9    C  CH3   0  -0.719  53.0147  56.3410  20.5672
 FRC  O1    O  O2    0  -0.479  47.6741  57.4364  20.4506
 FRC  C11   C  CR16  0  -0.265  46.7021  53.3503  15.6378
 FRC  C17   C  CR16  0  -0.306  46.3022  54.6466  15.8252
 FRC  C12   C  CR66  0   0.085  46.6513  55.3449  17.0028
 FRC  C4    C  CR66  0   0.149  47.4216  54.6915  17.9968
 FRC  C15   C  CR16  0  -0.331  47.8226  53.3527  17.7762
 FRC  C6    C  CR16  0  -0.257  47.4716  52.7001  16.6246
 FRC  C7    C  CR16  0  -0.292  46.2617  56.6872  17.2319
 FRC  C16   C  CR16  0  -0.341  46.6200  57.3413  18.3732
 FRC  C19   C  CR6   0   0.389  47.3933  56.6863  19.3659
 FRC  C10   C  CR16  0  -0.456  47.7796  55.3832  19.1787
 FRC  H1    H  HCR5  0   0.319  50.7090  54.3603  20.1783
 FRC  H3    H  HCR5  0   0.287  50.7839  54.8632  24.3453
 FRC  H101  H  HNH2  0   0.401  50.2777  49.6085  21.6964
 FRC  H102  H  HNH2  0   0.405  50.4404  50.6813  23.0424
 FRC  H13   H  HCH1  0   0.287  50.6622  56.8936  23.0599
 FRC  H14   H  HCH1  0   0.216  52.4288  57.9575  21.8322
 FRC  HO    H  HOH1  0   0.454  54.0531  56.5791  22.8731
 FRC  H181  H  HCH2  0   0.262  50.1845  56.5901  20.0608
 FRC  H182  H  HCH2  0   0.273  50.2548  58.1134  20.9126
 FRC  H21   H  HCH2  0   0.268  48.3651  57.5447  22.3282
 FRC  H22   H  HCH2  0   0.235  48.2871  55.9038  21.7126
 FRC  H91   H  HCH3  0   0.240  52.4585  56.6911  19.6974
 FRC  H92   H  HCH3  0   0.249  54.0369  56.7087  20.4586
 FRC  H93   H  HCH3  0   0.237  53.0508  55.2516  20.5392
 FRC  H17   H  HCR6  0   0.252  45.7125  55.1539  15.0706
 FRC  H15   H  HCR6  0   0.252  48.4210  52.8514  18.5284
 FRC  H6    H  HCR6  0   0.254  47.7882  51.6770  16.4666
 FRC  H7    H  HCR6  0   0.257  45.6704  57.1994  16.4823
 FRC  H16   H  HCR6  0   0.264  46.3184  58.3684  18.5373
 FRC  H10   H  HCR6  0   0.275  48.3608  54.8472  19.9174
 FRC  H11   H  HCR6  0   0.253  46.4319  52.8222  14.7327

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
 FRC  C1   N2    aromatic  1.361  0.020  1.361
 FRC  C1   C5    aromatic  1.369  0.020  1.369
 FRC  C1   H1    single    0.930  0.020  1.080
 FRC  N2   C3    aromatic  1.356  0.020  1.356
 FRC  N2   C13   single    1.458  0.020  1.458
 FRC  C3   N4    aromatic  1.303  0.020  1.303
 FRC  C3   H3    single    0.930  0.020  1.080
 FRC  N4   C5    aromatic  1.366  0.020  1.366
 FRC  C5   C8    single    1.473  0.020  1.473
 FRC  C8   O9    double    1.227  0.020  1.227
 FRC  C8   N10   single    1.340  0.020  1.340
 FRC  N10  H101  single    0.860  0.020  1.020
 FRC  N10  H102  single    0.860  0.020  1.020
 FRC  C13  C14   single    1.534  0.020  1.534
 FRC  C13  C18   single    1.524  0.020  1.524
 FRC  C13  H13   single    0.970  0.020  1.090
 FRC  C14  O15   single    1.410  0.020  1.410
 FRC  C14  C9    single    1.520  0.020  1.520
 FRC  C14  H14   single    0.970  0.020  1.090
 FRC  O15  HO    single    0.850  0.020  0.980
 FRC  C18  C2    single    1.524  0.020  1.524
 FRC  C18  H181  single    0.970  0.020  1.090
 FRC  C18  H182  single    0.970  0.020  1.090
 FRC  C2   O1    single    1.417  0.020  1.417
 FRC  C2   H21   single    0.970  0.020  1.090
 FRC  C2   H22   single    0.970  0.020  1.090
 FRC  C9   H91   single    0.970  0.020  1.090
 FRC  C9   H92   single    0.970  0.020  1.090
 FRC  C9   H93   single    0.970  0.020  1.090
 FRC  O1   C19   single    1.348  0.020  1.348
 FRC  C11  C17   aromatic  1.370  0.020  1.370
 FRC  C11  C6    aromatic  1.410  0.020  1.410
 FRC  C11  H11   single    0.930  0.020  1.080
 FRC  C17  C12   aromatic  1.413  0.020  1.413
 FRC  C17  H17   single    0.930  0.020  1.080
 FRC  C12  C4    aromatic  1.417  0.020  1.417
 FRC  C12  C7    aromatic  1.416  0.020  1.416
 FRC  C4   C15   aromatic  1.415  0.020  1.415
 FRC  C4   C10   aromatic  1.415  0.020  1.415
 FRC  C15  C6    aromatic  1.369  0.020  1.369
 FRC  C15  H15   single    0.930  0.020  1.080
 FRC  C6   H6    single    0.930  0.020  1.080
 FRC  C7   C16   aromatic  1.363  0.020  1.363
 FRC  C7   H7    single    0.930  0.020  1.080
 FRC  C16  C19   aromatic  1.419  0.020  1.419
 FRC  C16  H16   single    0.930  0.020  1.080
 FRC  C19  C10   aromatic  1.372  0.020  1.372
 FRC  C10  H10   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
 FRC  H1    C1   C5    131.05  3.000
 FRC  H1    C1   N2    123.38  3.000
 FRC  C5    C1   N2    105.57  3.000
 FRC  C13   N2   C3    125.15  3.000
 FRC  C13   N2   C1    127.94  3.000
 FRC  C3    N2   C1    106.89  3.000
 FRC  H3    C3   N4    126.07  3.000
 FRC  H3    C3   N2    121.85  3.000
 FRC  N4    C3   N2    112.08  3.000
 FRC  C5    N4   C3    105.27  3.000
 FRC  C8    C5   N4    123.61  3.000
 FRC  C8    C5   C1    126.20  3.000
 FRC  N4    C5   C1    110.19  3.000
 FRC  N10   C8   O9    123.84  3.000
 FRC  N10   C8   C5    114.73  3.000
 FRC  O9    C8   C5    121.43  3.000
 FRC  H102  N10  H101  118.44  3.000
 FRC  H102  N10  C8    120.96  3.000
 FRC  H101  N10  C8    120.60  3.000
 FRC  H13   C13  C18   108.06  3.000
 FRC  H13   C13  C14   106.50  3.000
 FRC  C18   C13  C14   113.06  3.000
 FRC  H13   C13  N2    105.54  3.000
 FRC  C18   C13  N2    111.61  3.000
 FRC  C14   C13  N2    111.60  3.000
 FRC  H14   C14  C9    108.08  3.000
 FRC  H14   C14  O15   110.58  3.000
 FRC  C9    C14  O15   111.85  3.000
 FRC  H14   C14  C13   105.38  3.000
 FRC  C9    C14  C13   114.70  3.000
 FRC  O15   C14  C13   106.06  3.000
 FRC  HO    O15  C14   108.59  3.000
 FRC  H182  C18  H181  106.17  3.000
 FRC  H182  C18  C2    108.79  3.000
 FRC  H181  C18  C2    110.95  3.000
 FRC  H182  C18  C13   107.93  3.000
 FRC  H181  C18  C13   110.95  3.000
 FRC  C2    C18  C13   111.82  3.000
 FRC  H22   C2   H21   106.80  3.000
 FRC  H22   C2   O1    111.02  3.000
 FRC  H21   C2   O1    105.34  3.000
 FRC  H22   C2   C18   111.80  3.000
 FRC  H21   C2   C18   109.54  3.000
 FRC  O1    C2   C18   111.99  3.000
 FRC  H93   C9   H92   107.63  3.000
 FRC  H93   C9   H91   108.50  3.000
 FRC  H92   C9   H91   106.87  3.000
 FRC  H93   C9   C14   112.03  3.000
 FRC  H92   C9   C14   109.86  3.000
 FRC  H91   C9   C14   111.73  3.000
 FRC  C19   O1   C2    119.67  3.000
 FRC  H11   C11  C6    119.77  3.000
 FRC  H11   C11  C17   120.23  3.000
 FRC  C6    C11  C17   120.00  3.000
 FRC  H17   C17  C12   118.91  3.000
 FRC  H17   C17  C11   120.44  3.000
 FRC  C12   C17  C11   120.65  3.000
 FRC  C7    C12  C4    118.23  3.000
 FRC  C7    C12  C17   122.36  3.000
 FRC  C4    C12  C17   119.41  3.000
 FRC  C10   C4   C15   121.39  3.000
 FRC  C10   C4   C12   119.86  3.000
 FRC  C15   C4   C12   118.75  3.000
 FRC  H15   C15  C6    120.30  3.000
 FRC  H15   C15  C4    119.07  3.000
 FRC  C6    C15  C4    120.62  3.000
 FRC  H6    C6   C15   119.87  3.000
 FRC  H6    C6   C11   119.55  3.000
 FRC  C15   C6   C11   120.57  3.000
 FRC  H7    C7   C16   119.72  3.000
 FRC  H7    C7   C12   119.09  3.000
 FRC  C16   C7   C12   121.18  3.000
 FRC  H16   C16  C19   118.93  3.000
 FRC  H16   C16  C7    120.57  3.000
 FRC  C19   C16  C7    120.50  3.000
 FRC  C10   C19  C16   119.78  3.000
 FRC  C10   C19  O1    125.41  3.000
 FRC  C16   C19  O1    114.81  3.000
 FRC  H10   C10  C19   121.92  3.000
 FRC  H10   C10  C4    117.63  3.000
 FRC  C19   C10  C4    120.45  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
 FRC  CONST_01  N4    C3   N2   C1      0.00   0.0  0
 FRC  CONST_02  C3    N4   C5   C1      0.00   0.0  0
 FRC  CONST_03  N4    C5   C1   N2      0.00   0.0  0
 FRC  CONST_04  C5    N4   C3   N2      0.00   0.0  0
 FRC  CONST_05  C5    C1   N2   C3      0.00   0.0  0
 FRC  CONST_06  C4    C12  C17  C11     0.00   0.0  0
 FRC  CONST_07  C7    C12  C17  C11   180.00   0.0  0
 FRC  CONST_08  C4    C15  C6   C11     0.00   0.0  0
 FRC  CONST_09  C15   C6   C11  C17     0.00   0.0  0
 FRC  CONST_10  C15   C4   C12  C17     0.00   0.0  0
 FRC  CONST_11  C10   C4   C12  C17   180.00   0.0  0
 FRC  CONST_12  C16   C7   C12  C17   180.00   0.0  0
 FRC  CONST_13  C6    C11  C17  C12     0.00   0.0  0
 FRC  CONST_14  C6    C15  C4   C12     0.00   0.0  0
 FRC  CONST_15  C19   C10  C4   C12     0.00   0.0  0
 FRC  CONST_16  C19   C16  C7   C12     0.00   0.0  0
 FRC  CONST_17  C16   C7   C12  C4      0.00   0.0  0
 FRC  CONST_18  C16   C19  C10  C4      0.00   0.0  0
 FRC  CONST_19  C7    C12  C4   C15   180.00   0.0  0
 FRC  CONST_20  C19   C10  C4   C15   180.00   0.0  0
 FRC  CONST_21  C10   C4   C15  C6    180.00   0.0  0
 FRC  CONST_22  C10   C4   C12  C7      0.00   0.0  0
 FRC  CONST_23  C10   C19  C16  C7      0.00   0.0  0
 FRC  CONST_24  C8    C5   C1   N2    180.00   0.0  0
 FRC  CONST_25  C8    C5   N4   C3    180.00   0.0  0
 FRC  CONST_26  C13   N2   C3   N4    180.00   0.0  0
 FRC  CONST_27  C13   N2   C1   C5    180.00   0.0  0
 FRC  CONST_28  C7    C16  C19  O1    180.00   0.0  0
 FRC  CONST_29  C4    C10  C19  O1    180.00   0.0  0
 FRC  CONST_30  H3    C3   N2   C1    180.00   0.0  0
 FRC  CONST_31  H1    C1   N2   C3    180.00   0.0  0
 FRC  CONST_32  H15   C15  C6   C11   180.00   0.0  0
 FRC  CONST_33  H6    C6   C11  C17   180.00   0.0  0
 FRC  CONST_34  H7    C7   C12  C17     0.00   0.0  0
 FRC  CONST_35  H11   C11  C17  C12   180.00   0.0  0
 FRC  CONST_36  H10   C10  C4   C12   180.00   0.0  0
 FRC  CONST_37  H16   C16  C7   C12   180.00   0.0  0
 FRC  CONST_38  H17   C17  C12  C4    180.00   0.0  0
 FRC  CONST_39  H101  N10  C8   C5    180.00   0.0  0
 FRC  CONST_40  H102  N10  C8   C5      0.00   0.0  0
 FRC  Var_01    O9    C8   C5   C1     -1.66  30.0  2
 FRC  Var_02    C16   C19  O1   C2   -173.80  30.0  2
 FRC  Var_03    H21   C2   O1   C19  -162.26  30.0  1
 FRC  Var_04    O1    C2   C18  C13  -178.41  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
 FRC  chir_01  C13  N2   C14  C18  negativ
 FRC  chir_02  C14  O15  C13  C9   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
 FRC  plan-1  C1    0.020
 FRC  plan-1  N2    0.020
 FRC  plan-1  C3    0.020
 FRC  plan-1  N4    0.020
 FRC  plan-1  C5    0.020
 FRC  plan-1  C8    0.020
 FRC  plan-1  C13   0.020
 FRC  plan-1  H1    0.020
 FRC  plan-1  H3    0.020
 FRC  plan-2  O1    0.020
 FRC  plan-2  C11   0.020
 FRC  plan-2  C17   0.020
 FRC  plan-2  C12   0.020
 FRC  plan-2  C4    0.020
 FRC  plan-2  C15   0.020
 FRC  plan-2  C6    0.020
 FRC  plan-2  C7    0.020
 FRC  plan-2  C16   0.020
 FRC  plan-2  C19   0.020
 FRC  plan-2  C10   0.020
 FRC  plan-2  H17   0.020
 FRC  plan-2  H15   0.020
 FRC  plan-2  H6    0.020
 FRC  plan-2  H7    0.020
 FRC  plan-2  H16   0.020
 FRC  plan-2  H10   0.020
 FRC  plan-2  H11   0.020
 FRC  plan-3  C5    0.020
 FRC  plan-3  C8    0.020
 FRC  plan-3  O9    0.020
 FRC  plan-3  N10   0.020
 FRC  plan-3  H101  0.020
 FRC  plan-3  H102  0.020

