# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Apr  7 22:46:25 2020
#   Inital geometry file: a 113 line input string
#   Ligand name: N-{6-[(methoxycarbonyl)amino]hexanoyl}-beta-D-galactopyranosylamine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: COC(=O)NCCCCCC(=O)N[C@@H]1O[C@H](CO)[C@H](O)[C@H](O)[C@H]1O
#
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
 233  233  N-{6-[(methoxycarbonyl)amino]hexanoyl}-beta-D-galactopyranosylamine  ligand  50  24  .  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_233
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
 233  C1   C  CH1   0   0.210   0.3149   0.3376  -3.1602
 233  C2   C  CH1   0  -0.027   1.4145  -0.1051  -4.1308
 233  C3   C  CH1   0   0.009   1.0574   0.3572  -5.5369
 233  C4   C  CH1   0  -0.002  -0.3356  -0.1315  -5.9218
 233  C5   C  CH1   0  -0.014  -1.3228   0.3094  -4.8481
 233  C6   C  CH2   0  -0.156  -2.7316  -0.1679  -5.1293
 233  O2   O  OH1   0  -0.666   2.6504   0.4774  -3.7960
 233  O3   O  OH1   0  -0.673   1.9655  -0.1173  -6.4992
 233  O4   O  OH1   0  -0.671  -0.3846  -1.5315  -6.0434
 233  O5   O  O2    0  -0.488  -0.9361  -0.1613  -3.5730
 233  O6   O  OH1   0  -0.671  -3.6074   0.4575  -4.2214
 233  N1   N  NH1   0  -0.691   0.5876  -0.1393  -1.8463
 233  O7   O  O     0  -0.482  -0.0348   1.7279  -0.7311
 233  C7   C  C     0   0.574   0.3934   0.5871  -0.7168
 233  C8   C  CH2   0  -0.592   0.8030  -0.1207   0.5553
 233  C9   C  CH2   0  -0.415   0.1061   0.4085   1.7993
 233  C10  C  CH2   0  -0.421   0.5949  -0.2872   3.0631
 233  C11  C  CH2   0  -0.475  -0.0955   0.2337   4.3161
 233  C12  C  CH2   0  -0.230   0.4143  -0.4511   5.5734
 233  N13  N  NH1   0  -0.669  -0.2644   0.0710   6.7408
 233  C14  C  C     0   0.749   0.0319  -0.3402   7.9823
 233  O15  O  O     0  -0.527   0.8829  -1.1637   8.2578
 233  O16  O  O2    0  -0.483  -0.7321   0.2762   8.8923
 233  C17  C  CH3   0  -0.415  -0.5228  -0.0777  10.2537
 233  H1   H  HCH1  0   0.226   0.2948   1.4348  -3.1281
 233  H2   H  HCH1  0   0.229   1.4737  -1.2029  -4.1192
 233  H3   H  HCH1  0   0.214   1.0300   1.4591  -5.5328
 233  H4   H  HCH1  0   0.235  -0.6254   0.3600  -6.8626
 233  H5   H  HCH1  0   0.227  -1.3270   1.4119  -4.8563
 233  H9   H  HCH2  0   0.203  -2.9722   0.0906  -6.1688
 233  H10  H  HCH2  0   0.207  -2.7771  -1.2600  -5.0492
 233  H6   H  HOH1  0   0.457   3.0231   0.0092  -3.0428
 233  H7   H  HOH1  0   0.456   2.8584   0.1058  -6.2148
 233  H8   H  HOH1  0   0.453   0.3043  -1.7996  -6.6608
 233  H11  H  HOH1  0   0.457  -4.4949   0.1302  -4.3917
 233  H12  H  HNH1  0   0.403   0.8619  -1.1056  -1.7459
 233  H13  H  HCH2  0   0.276   1.8871   0.0050   0.6564
 233  H14  H  HCH2  0   0.257   0.6379  -1.1970   0.4560
 233  H15  H  HCH2  0   0.227  -0.9748   0.2719   1.7030
 233  H16  H  HCH2  0   0.227   0.2763   1.4836   1.8890
 233  H17  H  HCH2  0   0.220   1.6772  -0.1493   3.1579
 233  H18  H  HCH2  0   0.221   0.4304  -1.3662   2.9774
 233  H19  H  HCH2  0   0.231  -1.1757   0.0793   4.2287
 233  H20  H  HCH2  0   0.232   0.0628   1.3136   4.3995
 233  H21  H  HCH2  0   0.230   1.4926  -0.2941   5.6649
 233  H22  H  HCH2  0   0.228   0.2554  -1.5307   5.4931
 233  H23  H  HNH1  0   0.400  -0.9982   0.7491   6.6122
 233  H24  H  HCH3  0   0.246  -1.2318   0.5134  10.8270
 233  H25  H  HCH3  0   0.232  -0.7170  -1.1354  10.4325
 233  H26  H  HCH3  0   0.232   0.4881   0.1604  10.5848

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
 233  C1   C2   single  1.532  0.020  1.532
 233  C1   O5   single  1.409  0.020  1.409
 233  C1   N1   single  1.424  0.020  1.424
 233  C1   H1   single  0.970  0.020  1.090
 233  C2   C3   single  1.523  0.020  1.523
 233  C2   O2   single  1.407  0.020  1.407
 233  C2   H2   single  0.970  0.020  1.090
 233  C3   C4   single  1.526  0.020  1.526
 233  C3   O3   single  1.406  0.020  1.406
 233  C3   H3   single  0.970  0.020  1.090
 233  C4   C5   single  1.524  0.020  1.524
 233  C4   O4   single  1.406  0.020  1.406
 233  C4   H4   single  0.970  0.020  1.090
 233  C5   C6   single  1.514  0.020  1.514
 233  C5   O5   single  1.413  0.020  1.413
 233  C5   H5   single  0.970  0.020  1.090
 233  C6   O6   single  1.408  0.020  1.408
 233  C6   H9   single  0.970  0.020  1.090
 233  C6   H10  single  0.970  0.020  1.090
 233  O2   H6   single  0.850  0.020  0.980
 233  O3   H7   single  0.850  0.020  0.980
 233  O4   H8   single  0.850  0.020  0.980
 233  O6   H11  single  0.850  0.020  0.980
 233  N1   C7   single  1.357  0.020  1.357
 233  N1   H12  single  0.860  0.020  1.020
 233  O7   C7   double  1.219  0.020  1.219
 233  C7   C8   single  1.512  0.020  1.512
 233  C8   C9   single  1.521  0.020  1.521
 233  C8   H13  single  0.970  0.020  1.090
 233  C8   H14  single  0.970  0.020  1.090
 233  C9   C10  single  1.523  0.020  1.523
 233  C9   H15  single  0.970  0.020  1.090
 233  C9   H16  single  0.970  0.020  1.090
 233  C10  C11  single  1.522  0.020  1.522
 233  C10  H17  single  0.970  0.020  1.090
 233  C10  H18  single  0.970  0.020  1.090
 233  C11  C12  single  1.520  0.020  1.520
 233  C11  H19  single  0.970  0.020  1.090
 233  C11  H20  single  0.970  0.020  1.090
 233  C12  N13  single  1.448  0.020  1.448
 233  C12  H21  single  0.970  0.020  1.090
 233  C12  H22  single  0.970  0.020  1.090
 233  N13  C14  single  1.341  0.020  1.341
 233  N13  H23  single  0.860  0.020  1.020
 233  C14  O15  double  1.216  0.020  1.216
 233  C14  O16  single  1.339  0.020  1.339
 233  O16  C17  single  1.422  0.020  1.422
 233  C17  H24  single  0.970  0.020  1.090
 233  C17  H25  single  0.970  0.020  1.090
 233  C17  H26  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
 233  H1   C1   N1   108.13  3.000
 233  H1   C1   O5   110.26  3.000
 233  N1   C1   O5   108.77  3.000
 233  H1   C1   C2   108.69  3.000
 233  N1   C1   C2   110.50  3.000
 233  O5   C1   C2   110.45  3.000
 233  H2   C2   O2   111.32  3.000
 233  H2   C2   C3   109.00  3.000
 233  O2   C2   C3   107.46  3.000
 233  H2   C2   C1   108.70  3.000
 233  O2   C2   C1   111.11  3.000
 233  C3   C2   C1   109.21  3.000
 233  H3   C3   O3   110.86  3.000
 233  H3   C3   C4   107.37  3.000
 233  O3   C3   C4   108.00  3.000
 233  H3   C3   C2   107.82  3.000
 233  O3   C3   C2   112.22  3.000
 233  C4   C3   C2   110.48  3.000
 233  H4   C4   O4   111.20  3.000
 233  H4   C4   C5   107.61  3.000
 233  O4   C4   C5   109.06  3.000
 233  H4   C4   C3   108.24  3.000
 233  O4   C4   C3   111.87  3.000
 233  C5   C4   C3   108.73  3.000
 233  H5   C5   O5   109.93  3.000
 233  H5   C5   C6   108.08  3.000
 233  O5   C5   C6   108.49  3.000
 233  H5   C5   C4   106.66  3.000
 233  O5   C5   C4   111.23  3.000
 233  C6   C5   C4   112.38  3.000
 233  H10  C6   H9   107.15  3.000
 233  H10  C6   O6   111.70  3.000
 233  H9   C6   O6   111.70  3.000
 233  H10  C6   C5   109.83  3.000
 233  H9   C6   C5   107.79  3.000
 233  O6   C6   C5   108.60  3.000
 233  H6   O2   C2   108.97  3.000
 233  H7   O3   C3   108.57  3.000
 233  H8   O4   C4   107.92  3.000
 233  C5   O5   C1   112.92  3.000
 233  H11  O6   C6   107.99  3.000
 233  H12  N1   C7   117.95  3.000
 233  H12  N1   C1   117.66  3.000
 233  C7   N1   C1   124.14  3.000
 233  C8   C7   O7   122.90  3.000
 233  C8   C7   N1   114.26  3.000
 233  O7   C7   N1   122.80  3.000
 233  H14  C8   H13  105.70  3.000
 233  H14  C8   C9   110.35  3.000
 233  H13  C8   C9   109.75  3.000
 233  H14  C8   C7   110.09  3.000
 233  H13  C8   C7   106.96  3.000
 233  C9   C8   C7   113.65  3.000
 233  H16  C9   H15  106.51  3.000
 233  H16  C9   C10  109.36  3.000
 233  H15  C9   C10  109.46  3.000
 233  H16  C9   C8   109.77  3.000
 233  H15  C9   C8   109.72  3.000
 233  C10  C9   C8   111.88  3.000
 233  H18  C10  H17  106.22  3.000
 233  H18  C10  C11  109.48  3.000
 233  H17  C10  C11  109.51  3.000
 233  H18  C10  C9   109.69  3.000
 233  H17  C10  C9   109.36  3.000
 233  C11  C10  C9   112.40  3.000
 233  H20  C11  H19  106.73  3.000
 233  H20  C11  C12  109.45  3.000
 233  H19  C11  C12  109.48  3.000
 233  H20  C11  C10  109.56  3.000
 233  H19  C11  C10  109.48  3.000
 233  C12  C11  C10  112.00  3.000
 233  H22  C12  H21  106.91  3.000
 233  H22  C12  N13  110.30  3.000
 233  H21  C12  N13  110.06  3.000
 233  H22  C12  C11  109.58  3.000
 233  H21  C12  C11  109.59  3.000
 233  N13  C12  C11  110.33  3.000
 233  H23  N13  C14  119.04  3.000
 233  H23  N13  C12  118.77  3.000
 233  C14  N13  C12  122.17  3.000
 233  O16  C14  O15  123.87  3.000
 233  O16  C14  N13  111.23  3.000
 233  O15  C14  N13  124.90  3.000
 233  C17  O16  C14  116.88  3.000
 233  H26  C17  H25  109.10  3.000
 233  H26  C17  H24  109.03  3.000
 233  H25  C17  H24  108.97  3.000
 233  H26  C17  O16  111.89  3.000
 233  H25  C17  O16  111.85  3.000
 233  H24  C17  O16  105.88  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
 233  CONST_01  O7   C7   N1   C1      0.00   0.0  0
 233  CONST_02  C8   C7   N1   C1    180.00   0.0  0
 233  CONST_03  H12  N1   C7   O7    180.00   0.0  0
 233  Var_01    C9   C8   C7   N1   -156.85  30.0  3
 233  Var_02    C10  C9   C8   C7   -177.35  30.0  3
 233  Var_03    C11  C10  C9   C8   -179.99  30.0  3
 233  Var_04    C12  C11  C10  C9   -179.11  30.0  3
 233  Var_05    N13  C12  C11  C10   179.96  30.0  3
 233  Var_06    C14  N13  C12  C11  -177.99  30.0  3
 233  Var_07    O15  C14  N13  C12     0.55  30.0  2
 233  Var_08    H24  C17  O16  C14  -179.52  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
 233  chir_01  C1  C2  O5  N1  negativ
 233  chir_02  C2  O2  C1  C3  negativ
 233  chir_03  C3  O3  C2  C4  positiv
 233  chir_04  C4  O4  C5  C3  negativ
 233  chir_05  C5  O5  C4  C6  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
 233  plan-1  C1   0.020
 233  plan-1  N1   0.020
 233  plan-1  O7   0.020
 233  plan-1  C7   0.020
 233  plan-1  C8   0.020
 233  plan-1  H12  0.020
 233  plan-2  N13  0.020
 233  plan-2  C14  0.020
 233  plan-2  O15  0.020
 233  plan-2  O16  0.020

