# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version 1.18.1-3865-
#   - file written: Sat May 30 12:19:00 2020
#   Inital geometry file: a 112 line input string
#   Ligand name: 4-O-[2-(acetylamino)-2-deoxy-alpha-D-glucopyranosyl]-beta-D-galactopyranose
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC(=O)N[C@@H]1[C@@H](O)[C@H](O)[C@@H](CO)O[C@@H]1O[C@@H]2[C@H](O)[C@@H](O)[C@H](O)O[C@@H]2CO
#
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
 4A4  4A4  4-O-[2-(acetylamino)-2-deoxy-alpha-D-glucopyranosyl]-beta-D-galactopyranose  ligand  51  26  .  2021-08-04  2021-08-04  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_4A4
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
 4A4  CAN   C  CH3   0  -0.780   1.0527   4.1842   1.2068
 4A4  CAM   C  C     0   0.522  -0.2080   3.6088   0.6108
 4A4  OAO   O  O     0  -0.500  -1.1225   4.3224   0.2254
 4A4  N2    N  NH1   0  -0.627  -0.2376   2.2639   0.5480
 4A4  C2    C  CH1   0  -0.166  -1.3538   1.4905   0.0696
 4A4  C3    C  CH1   0   0.052  -2.1012   0.8008   1.2060
 4A4  O3    O  OH1   0  -0.664  -2.6125   1.7935   2.0568
 4A4  C4    C  CH1   0  -0.010  -3.2078  -0.0743   0.6290
 4A4  O4    O  OH1   0  -0.675  -3.8095  -0.7541   1.7108
 4A4  C5    C  CH1   0  -0.023  -2.6362  -1.0562  -0.3996
 4A4  C6    C  CH2   0  -0.167  -3.7420  -1.8111  -1.1044
 4A4  O6    O  OH1   0  -0.665  -3.1822  -2.7556  -1.9831
 4A4  O5    O  O2    0  -0.496  -1.9150  -0.3462  -1.3987
 4A4  C1    C  CH1   0   0.294  -0.8705   0.4516  -0.9456
 4A4  O1    O  O2    0  -0.509   0.1321  -0.2747  -0.3055
 4A4  CAS   C  CH1   0  -0.018   1.0604  -0.9909  -1.0906
 4A4  CAR   C  CH1   0   0.035   1.4032  -2.2797  -0.3520
 4A4  OAX   O  OH1   0  -0.654   0.2420  -3.0423  -0.1731
 4A4  CAQ   C  CH1   0  -0.038   2.0914  -1.9535   0.9703
 4A4  OAW   O  OH1   0  -0.673   2.4872  -3.1765   1.5452
 4A4  CAP   C  CH1   0   0.268   3.2968  -1.0517   0.7113
 4A4  OAV   O  OH1   0  -0.660   3.8212  -0.6653   1.9270
 4A4  OAY   O  O2    0  -0.490   2.9078   0.1011   0.0019
 4A4  CAT   C  CH1   0  -0.000   2.3601  -0.1978  -1.2639
 4A4  CAU   C  CH2   0  -0.164   2.2032   1.0924  -2.0393
 4A4  OAZ   O  OH1   0  -0.668   3.4856   1.6035  -2.3111
 4A4  HAN1  H  HCH3  0   0.264   1.3819   5.0369   0.6158
 4A4  HAN2  H  HCH3  0   0.272   0.8402   4.5473   2.2135
 4A4  HAN3  H  HCH3  0   0.243   1.8698   3.4675   1.2728
 4A4  H2    H  HNH1  0   0.392   0.5527   1.7482   0.9043
 4A4  HA    H  HCH1  0   0.277  -2.0379   2.1691  -0.4444
 4A4  H3    H  HCH1  0   0.213  -1.3981   0.1494   1.7475
 4A4  H1    H  HCH1  0   0.244  -0.4933   0.9611  -1.8400
 4A4  HB    H  HOH1  0   0.450  -3.0907   1.3513   2.7664
 4A4  H4    H  HCH1  0   0.223  -3.9344   0.5813   0.1257
 4A4  HC    H  HOH1  0   0.462  -4.7477  -0.8633   1.5345
 4A4  H5    H  HCH1  0   0.244  -1.9755  -1.7693   0.1073
 4A4  H61C  H  HCH2  0   0.201  -4.3652  -2.2959  -0.3433
 4A4  H62C  H  HCH2  0   0.194  -4.3829  -1.0906  -1.6322
 4A4  H6    H  HOH1  0   0.454  -3.9049  -3.2395  -2.3924
 4A4  HAS   H  HCH1  0   0.259   0.6459  -1.2400  -2.0752
 4A4  HAR   H  HCH1  0   0.214   2.1278  -2.8223  -0.9818
 4A4  HAT   H  HCH1  0   0.224   3.0501  -0.8399  -1.8374
 4A4  HAX   H  HOH1  0   0.449   0.4714  -3.8076   0.3648
 4A4  HAQ   H  HCH1  0   0.231   1.3872  -1.4171   1.6212
 4A4  HAW   H  HOH1  0   0.458   2.7376  -3.0186   2.4606
 4A4  HAP   H  HCH1  0   0.186   4.0357  -1.6134   0.1115
 4A4  HAV   H  HOH1  0   0.466   4.7343  -0.3826   1.8099
 4A4  HAU1  H  HCH2  0   0.206   1.6525   0.8695  -2.9629
 4A4  HAU2  H  HCH2  0   0.198   1.6022   1.8071  -1.4651
 4A4  HAZ   H  HOH1  0   0.457   3.3814   2.4518  -2.7510

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
 4A4  CAN  CAM   single  1.509  0.020  1.509
 4A4  CAM  OAO   double  1.222  0.020  1.222
 4A4  CAM  N2    single  1.347  0.020  1.347
 4A4  N2   C2    single  1.440  0.020  1.440
 4A4  C2   C3    single  1.525  0.020  1.525
 4A4  C2   C1    single  1.531  0.020  1.531
 4A4  C3   O3    single  1.404  0.020  1.404
 4A4  C3   C4    single  1.524  0.020  1.524
 4A4  C4   O4    single  1.412  0.020  1.412
 4A4  C4   C5    single  1.533  0.020  1.533
 4A4  C5   C6    single  1.513  0.020  1.513
 4A4  C5   O5    single  1.422  0.020  1.422
 4A4  C6   O6    single  1.406  0.020  1.406
 4A4  O5   C1    single  1.390  0.020  1.390
 4A4  C1   O1    single  1.394  0.020  1.394
 4A4  O1   CAS   single  1.411  0.020  1.411
 4A4  CAS  CAR   single  1.524  0.020  1.524
 4A4  CAS  CAT   single  1.532  0.020  1.532
 4A4  CAR  OAX   single  1.401  0.020  1.401
 4A4  CAR  CAQ   single  1.526  0.020  1.526
 4A4  CAQ  OAW   single  1.408  0.020  1.408
 4A4  CAQ  CAP   single  1.528  0.020  1.528
 4A4  CAP  OAV   single  1.379  0.020  1.379
 4A4  CAP  OAY   single  1.408  0.020  1.408
 4A4  OAY  CAT   single  1.411  0.020  1.411
 4A4  CAT  CAU   single  1.513  0.020  1.513
 4A4  CAU  OAZ   single  1.407  0.020  1.407
 4A4  CAN  HAN1  single  0.970  0.020  1.090
 4A4  CAN  HAN2  single  0.970  0.020  1.090
 4A4  CAN  HAN3  single  0.970  0.020  1.090
 4A4  N2   H2    single  0.860  0.020  1.020
 4A4  C2   HA    single  0.970  0.020  1.090
 4A4  C3   H3    single  0.970  0.020  1.090
 4A4  C1   H1    single  0.970  0.020  1.090
 4A4  O3   HB    single  0.850  0.020  0.980
 4A4  C4   H4    single  0.970  0.020  1.090
 4A4  O4   HC    single  0.850  0.020  0.980
 4A4  C5   H5    single  0.970  0.020  1.090
 4A4  C6   H61C  single  0.970  0.020  1.090
 4A4  C6   H62C  single  0.970  0.020  1.090
 4A4  O6   H6    single  0.850  0.020  0.980
 4A4  CAS  HAS   single  0.970  0.020  1.090
 4A4  CAR  HAR   single  0.970  0.020  1.090
 4A4  CAT  HAT   single  0.970  0.020  1.090
 4A4  OAX  HAX   single  0.850  0.020  0.980
 4A4  CAQ  HAQ   single  0.970  0.020  1.090
 4A4  OAW  HAW   single  0.850  0.020  0.980
 4A4  CAP  HAP   single  0.970  0.020  1.090
 4A4  OAV  HAV   single  0.850  0.020  0.980
 4A4  CAU  HAU1  single  0.970  0.020  1.090
 4A4  CAU  HAU2  single  0.970  0.020  1.090
 4A4  OAZ  HAZ   single  0.850  0.020  0.980

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
 4A4  HAN3  CAN  HAN2  108.02  3.000
 4A4  HAN3  CAN  HAN1  108.75  3.000
 4A4  HAN2  CAN  HAN1  107.41  3.000
 4A4  HAN3  CAN  CAM   113.58  3.000
 4A4  HAN2  CAN  CAM   109.19  3.000
 4A4  HAN1  CAN  CAM   109.70  3.000
 4A4  N2    CAM  OAO   123.50  3.000
 4A4  N2    CAM  CAN   114.69  3.000
 4A4  OAO   CAM  CAN   121.81  3.000
 4A4  H2    N2   C2    116.75  3.000
 4A4  H2    N2   CAM   118.49  3.000
 4A4  C2    N2   CAM   124.68  3.000
 4A4  HA    C2   C1    107.90  3.000
 4A4  HA    C2   C3    108.95  3.000
 4A4  C1    C2   C3    110.00  3.000
 4A4  HA    C2   N2    107.95  3.000
 4A4  C1    C2   N2    109.88  3.000
 4A4  C3    C2   N2    112.04  3.000
 4A4  H3    C3   C4    108.07  3.000
 4A4  H3    C3   O3    110.67  3.000
 4A4  C4    C3   O3    111.77  3.000
 4A4  H3    C3   C2    108.73  3.000
 4A4  C4    C3   C2    109.47  3.000
 4A4  O3    C3   C2    108.08  3.000
 4A4  HB    O3   C3    107.62  3.000
 4A4  H4    C4   C5    108.72  3.000
 4A4  H4    C4   O4    110.84  3.000
 4A4  C5    C4   O4    111.38  3.000
 4A4  H4    C4   C3    108.09  3.000
 4A4  C5    C4   C3    110.56  3.000
 4A4  O4    C4   C3    107.20  3.000
 4A4  HC    O4   C4    109.28  3.000
 4A4  H5    C5   O5    110.11  3.000
 4A4  H5    C5   C6    109.35  3.000
 4A4  O5    C5   C6    107.01  3.000
 4A4  H5    C5   C4    109.34  3.000
 4A4  O5    C5   C4    109.92  3.000
 4A4  C6    C5   C4    111.08  3.000
 4A4  H62C  C6   H61C  106.95  3.000
 4A4  H62C  C6   O6    111.85  3.000
 4A4  H61C  C6   O6    111.28  3.000
 4A4  H62C  C6   C5    108.83  3.000
 4A4  H61C  C6   C5    108.22  3.000
 4A4  O6    C6   C5    109.59  3.000
 4A4  H6    O6   C6    107.75  3.000
 4A4  C1    O5   C5    116.01  3.000
 4A4  H1    C1   O1    111.68  3.000
 4A4  H1    C1   O5    105.03  3.000
 4A4  O1    C1   O5    113.02  3.000
 4A4  H1    C1   C2    109.53  3.000
 4A4  O1    C1   C2    106.03  3.000
 4A4  O5    C1   C2    111.62  3.000
 4A4  CAS   O1   C1    118.83  3.000
 4A4  HAS   CAS  CAT   109.66  3.000
 4A4  HAS   CAS  CAR   109.14  3.000
 4A4  CAT   CAS  CAR   107.55  3.000
 4A4  HAS   CAS  O1    111.48  3.000
 4A4  CAT   CAS  O1    110.99  3.000
 4A4  CAR   CAS  O1    107.91  3.000
 4A4  HAR   CAR  CAQ   107.68  3.000
 4A4  HAR   CAR  OAX   110.47  3.000
 4A4  CAQ   CAR  OAX   112.31  3.000
 4A4  HAR   CAR  CAS   106.68  3.000
 4A4  CAQ   CAR  CAS   109.91  3.000
 4A4  OAX   CAR  CAS   109.61  3.000
 4A4  HAX   OAX  CAR   107.85  3.000
 4A4  HAQ   CAQ  CAP   108.54  3.000
 4A4  HAQ   CAQ  OAW   111.24  3.000
 4A4  CAP   CAQ  OAW   111.11  3.000
 4A4  HAQ   CAQ  CAR   109.19  3.000
 4A4  CAP   CAQ  CAR   109.58  3.000
 4A4  OAW   CAQ  CAR   107.15  3.000
 4A4  HAW   OAW  CAQ   108.61  3.000
 4A4  HAP   CAP  OAY   109.11  3.000
 4A4  HAP   CAP  OAV   111.51  3.000
 4A4  OAY   CAP  OAV   108.64  3.000
 4A4  HAP   CAP  CAQ   108.64  3.000
 4A4  OAY   CAP  CAQ   110.53  3.000
 4A4  OAV   CAP  CAQ   108.42  3.000
 4A4  HAV   OAV  CAP   109.61  3.000
 4A4  CAT   OAY  CAP   112.68  3.000
 4A4  HAT   CAT  CAU   107.14  3.000
 4A4  HAT   CAT  OAY   110.29  3.000
 4A4  CAU   CAT  OAY   108.62  3.000
 4A4  HAT   CAT  CAS   106.74  3.000
 4A4  CAU   CAT  CAS   114.28  3.000
 4A4  OAY   CAT  CAS   109.71  3.000
 4A4  HAU2  CAU  HAU1  107.33  3.000
 4A4  HAU2  CAU  OAZ   111.35  3.000
 4A4  HAU1  CAU  OAZ   111.61  3.000
 4A4  HAU2  CAU  CAT   110.14  3.000
 4A4  HAU1  CAU  CAT   108.06  3.000
 4A4  OAZ   CAU  CAT   108.31  3.000
 4A4  HAZ   OAZ  CAU   108.07  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
 4A4  CONST_01  C2    N2   CAM  CAN  180.00   0.0  0
 4A4  CONST_02  C2    N2   CAM  OAO    0.00   0.0  0
 4A4  CONST_03  H2    N2   CAM  CAN    0.00   0.0  0
 4A4  Var_01    HAN1  CAN  CAM  OAO  -43.54  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
 4A4  chir_01  C2   N2   C3   C1   positiv
 4A4  chir_02  C3   O3   C2   C4   positiv
 4A4  chir_03  C4   O4   C5   C3   positiv
 4A4  chir_04  C5   O5   C4   C6   negativ
 4A4  chir_05  C1   O5   O1   C2   positiv
 4A4  chir_06  CAS  O1   CAR  CAT  positiv
 4A4  chir_07  CAR  OAX  CAQ  CAS  positiv
 4A4  chir_08  CAQ  OAW  CAP  CAR  negativ
 4A4  chir_09  CAP  OAV  OAY  CAQ  positiv
 4A4  chir_10  CAT  OAY  CAS  CAU  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
 4A4  plan-1  CAN  0.020
 4A4  plan-1  CAM  0.020
 4A4  plan-1  OAO  0.020
 4A4  plan-1  N2   0.020
 4A4  plan-1  C2   0.020
 4A4  plan-1  H2   0.020

