# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Apr 11 00:58:56 2020
#   Inital geometry file: a 138 line input string
#   Ligand name: 5-(acetylamino)-2,6-anhydro-4-carbamimidamido-3,4,5-trideoxy-7-O-[(2-methoxyethyl)carbamoyl]-D-glycero-D-galacto-non-2-enonic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: COCCNC(=O)O[C@H]([C@H](O)CO)[C@@H]1OC(=C[C@H](NC(N)=N)[C@H]1NC(C)=O)C(O)=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
 6PY  6PY  '5-(acetylamino)-2,6-anhydro-4-carbamimidamido-3,4,5-trideoxy-7-O-[(2-methoxyethyl)carbamoyl]-D-glycero-D-galacto-non-2-enonic acid'  D-saccharide  56  30  .  2023-02-15  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_6PY
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
 6PY  N12  N  NH1    0  -0.647  -2.6588  -2.1321   0.0277
 6PY  C17  C  CH3    0  -0.394   4.9125  -2.5371   3.4755
 6PY  C20  C  CH2    0  -0.298   4.1234  -1.5852   0.0340
 6PY  C21  C  C      0   0.770   2.4732   0.0708  -0.6301
 6PY  C28  C  CH3    0  -0.777   0.6511  -2.5943  -3.1825
 6PY  C01  C  CH1    0   0.060  -0.8270   1.0758  -0.5917
 6PY  C02  C  CH1    0  -0.150  -1.0212  -0.4445  -0.5577
 6PY  C03  C  CH1    0  -0.062  -2.4969  -0.7289  -0.2770
 6PY  C04  C  C1     0  -0.376  -2.9611   0.1757   0.8328
 6PY  C05  C  C      0   0.174  -2.2636   1.2300   1.2593
 6PY  O06  O  O2     0  -0.472  -1.1104   1.6309   0.6762
 6PY  C07  C  CH1    0  -0.059   0.5839   1.4867  -0.9850
 6PY  C08  C  CH1    0   0.001   0.8058   3.0059  -0.9145
 6PY  C09  C  CH2    0  -0.167   2.1984   3.3856  -1.3971
 6PY  O10  O  OH1    0  -0.668   2.3396   4.7810  -1.2787
 6PY  O11  O  O2     0  -0.504   1.4931   0.8317  -0.1067
 6PY  O13  O  OH1    0  -0.656  -0.1964   3.6715  -1.6454
 6PY  C14  C  C      0   0.541  -3.8187  -2.8460  -0.0918
 6PY  N15  N  NH2    0  -0.824  -4.8752  -2.1729  -0.6633
 6PY  N16  N  N      0  -0.727  -3.9558  -4.0849   0.2193
 6PY  O18  O  O2     0  -0.488   4.1918  -2.3355   2.2861
 6PY  C19  C  CH2    0  -0.166   4.9964  -1.8590   1.2363
 6PY  N22  N  NH1    0  -0.657   3.1413  -0.5690   0.3418
 6PY  O23  O  O      0  -0.512   2.7300   0.0131  -1.8141
 6PY  N25  N  NH1    0  -0.635  -0.5709  -1.0670  -1.7718
 6PY  O26  O  O      0  -0.496   0.7136  -2.6518  -0.7957
 6PY  C27  C  C      0   0.540   0.2693  -2.1229  -1.8040
 6PY  C29  C  C      0   0.374  -2.6724   2.0851   2.4557
 6PY  O30  O  OC    -1  -0.591  -1.8796   2.9832   2.7795
 6PY  O31  O  O      0  -0.589  -3.7572   1.7926   2.9900
 6PY  H1   H  HNH1   0   0.384  -1.9535  -2.5428   0.6186
 6PY  H2   H  HCH3   0   0.206   5.3666  -1.6093   3.8427
 6PY  H3   H  HCH3   0   0.235   4.2194  -2.9048   4.2311
 6PY  H4   H  HCH3   0   0.206   5.7122  -3.2760   3.3494
 6PY  H5   H  HCH2   0   0.250   4.7634  -1.2378  -0.7764
 6PY  H6   H  HCH2   0   0.240   3.6395  -2.5076  -0.3024
 6PY  H7   H  HCH3   0   0.268   1.7132  -2.3996  -3.3329
 6PY  H8   H  HCH3   0   0.262   0.4995  -3.6700  -3.2586
 6PY  H9   H  HCH3   0   0.247   0.0968  -2.1057  -3.9816
 6PY  H10  H  HCH1   0   0.246  -1.5181   1.5000  -1.3337
 6PY  H11  H  HCH1   0   0.281  -0.4239  -0.8519   0.2615
 6PY  H12  H  HCH1   0   0.262  -3.0571  -0.5233  -1.1965
 6PY  H13  H  H      0   0.251  -3.8831  -0.0625   1.3457
 6PY  H14  H  HCH1   0   0.263   0.7503   1.1537  -2.0138
 6PY  H15  H  HCH1   0   0.247   0.6922   3.3370   0.1218
 6PY  H16  H  HCH2   0   0.208   2.9525   2.8610  -0.8006
 6PY  H17  H  HCH2   0   0.194   2.3238   3.0506  -2.4376
 6PY  H18  H  HOH1   0   0.456   3.2314   5.0133  -1.5517
 6PY  H19  H  HOH1   0   0.447  -0.0750   3.4856  -2.5835
 6PY  H20  H  HNH2   0   0.391  -5.0148  -1.2088  -0.4046
 6PY  H21  H  HNH2   0   0.382  -5.7354  -2.6962  -0.6249
 6PY  H22  H  H      0   0.310  -3.0714  -4.4824   0.5156
 6PY  H23  H  HCH2   0   0.218   5.7636  -2.5944   0.9585
 6PY  H24  H  HCH2   0   0.208   5.5211  -0.9396   1.5324
 6PY  H25  H  HNH1   0   0.395   2.7248  -0.5973   1.2600
 6PY  H26  H  HNH1   0   0.400  -0.9313  -0.7161  -2.6453

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
 6PY  N16  C14  double  1.285  0.020  1.285
 6PY  C28  C27  single  1.506  0.020  1.506
 6PY  O13  C08  single  1.408  0.020  1.408
 6PY  N25  C27  single  1.350  0.020  1.350
 6PY  N25  C02  single  1.437  0.020  1.437
 6PY  C14  N15  single  1.377  0.020  1.377
 6PY  C14  N12  single  1.367  0.020  1.367
 6PY  C27  O26  double  1.222  0.020  1.222
 6PY  O10  C09  single  1.407  0.020  1.407
 6PY  C03  C02  single  1.529  0.020  1.529
 6PY  C03  N12  single  1.445  0.020  1.445
 6PY  C03  C04  single  1.505  0.020  1.505
 6PY  C02  C01  single  1.533  0.020  1.533
 6PY  C01  C07  single  1.521  0.020  1.521
 6PY  C01  O06  single  1.413  0.020  1.413
 6PY  C08  C07  single  1.537  0.020  1.537
 6PY  C08  C09  single  1.522  0.020  1.522
 6PY  C07  O11  single  1.424  0.020  1.424
 6PY  O23  C21  double  1.213  0.020  1.213
 6PY  C04  C05  double  1.334  0.020  1.334
 6PY  O06  C05  single  1.353  0.020  1.353
 6PY  C05  C29  single  1.526  0.020  1.526
 6PY  O11  C21  single  1.347  0.020  1.347
 6PY  C21  N22  single  1.342  0.020  1.342
 6PY  C29  O31  deloc   1.244  0.020  1.244
 6PY  C29  O30  deloc   1.241  0.020  1.241
 6PY  N22  C20  single  1.446  0.020  1.446
 6PY  C20  C19  single  1.511  0.020  1.511
 6PY  C19  O18  single  1.406  0.020  1.406
 6PY  O18  C17  single  1.405  0.020  1.405
 6PY  N12  H1   single  0.860  0.020  1.020
 6PY  C17  H2   single  0.970  0.020  1.090
 6PY  C17  H3   single  0.970  0.020  1.090
 6PY  C17  H4   single  0.970  0.020  1.090
 6PY  C20  H5   single  0.970  0.020  1.090
 6PY  C20  H6   single  0.970  0.020  1.090
 6PY  C28  H7   single  0.970  0.020  1.090
 6PY  C28  H8   single  0.970  0.020  1.090
 6PY  C28  H9   single  0.970  0.020  1.090
 6PY  C01  H10  single  0.970  0.020  1.090
 6PY  C02  H11  single  0.970  0.020  1.090
 6PY  C03  H12  single  0.970  0.020  1.090
 6PY  C04  H13  single  0.930  0.020  1.080
 6PY  C07  H14  single  0.970  0.020  1.090
 6PY  C08  H15  single  0.970  0.020  1.090
 6PY  C09  H16  single  0.970  0.020  1.090
 6PY  C09  H17  single  0.970  0.020  1.090
 6PY  O10  H18  single  0.850  0.020  0.980
 6PY  O13  H19  single  0.850  0.020  0.980
 6PY  N15  H20  single  0.890  0.020  1.040
 6PY  N15  H21  single  0.890  0.020  1.040
 6PY  N16  H22  single  0.890  0.020  1.040
 6PY  C19  H23  single  0.970  0.020  1.090
 6PY  C19  H24  single  0.970  0.020  1.090
 6PY  N22  H25  single  0.890  0.020  1.040
 6PY  N25  H26  single  0.860  0.020  1.020

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
 6PY  H1   N12  C14  115.61  3.000
 6PY  H1   N12  C03  116.17  3.000
 6PY  C14  N12  C03  125.71  3.000
 6PY  H4   C17  H3   108.45  3.000
 6PY  H4   C17  H2   107.87  3.000
 6PY  H3   C17  H2   108.48  3.000
 6PY  H4   C17  O18  111.93  3.000
 6PY  H3   C17  O18  108.01  3.000
 6PY  H2   C17  O18  112.00  3.000
 6PY  H6   C20  H5   107.45  3.000
 6PY  H6   C20  N22  110.94  3.000
 6PY  H5   C20  N22  109.46  3.000
 6PY  H6   C20  C19  110.32  3.000
 6PY  H5   C20  C19  108.08  3.000
 6PY  N22  C20  C19  110.50  3.000
 6PY  O23  C21  N22  125.38  3.000
 6PY  N22  C21  O11  110.51  3.000
 6PY  O23  C21  O11  124.08  3.000
 6PY  H9   C28  H8   108.74  3.000
 6PY  H9   C28  H7   108.35  3.000
 6PY  H8   C28  H7   107.60  3.000
 6PY  H9   C28  C27  113.72  3.000
 6PY  H8   C28  C27  109.75  3.000
 6PY  H7   C28  C27  108.50  3.000
 6PY  H10  C01  C07  107.72  3.000
 6PY  H10  C01  O06  109.15  3.000
 6PY  C07  C01  O06  108.17  3.000
 6PY  H10  C01  C02  108.55  3.000
 6PY  O06  C01  C02  110.14  3.000
 6PY  C07  C01  C02  113.02  3.000
 6PY  H11  C02  N25  107.50  3.000
 6PY  H11  C02  C03  108.70  3.000
 6PY  N25  C02  C03  112.15  3.000
 6PY  H11  C02  C01  108.49  3.000
 6PY  C03  C02  C01  108.11  3.000
 6PY  N25  C02  C01  111.79  3.000
 6PY  H12  C03  C04  110.38  3.000
 6PY  H12  C03  C02  107.72  3.000
 6PY  C04  C03  C02  108.73  3.000
 6PY  H12  C03  N12  107.56  3.000
 6PY  C04  C03  N12  113.18  3.000
 6PY  C02  C03  N12  109.12  3.000
 6PY  H13  C04  C05  117.91  3.000
 6PY  H13  C04  C03  118.69  3.000
 6PY  C05  C04  C03  123.33  3.000
 6PY  C29  C05  O06  113.58  3.000
 6PY  C29  C05  C04  123.59  3.000
 6PY  O06  C05  C04  122.82  3.000
 6PY  C05  O06  C01  116.19  3.000
 6PY  H14  C07  O11  110.05  3.000
 6PY  H14  C07  C08  108.79  3.000
 6PY  O11  C07  C08  109.53  3.000
 6PY  H14  C07  C01  107.57  3.000
 6PY  O11  C07  C01  107.97  3.000
 6PY  C08  C07  C01  112.89  3.000
 6PY  H15  C08  O13  105.95  3.000
 6PY  H15  C08  C09  108.66  3.000
 6PY  O13  C08  C09  111.64  3.000
 6PY  H15  C08  C07  109.13  3.000
 6PY  C09  C08  C07  111.35  3.000
 6PY  O13  C08  C07  109.93  3.000
 6PY  H17  C09  H16  106.90  3.000
 6PY  H17  C09  O10  111.71  3.000
 6PY  H16  C09  O10  111.10  3.000
 6PY  H17  C09  C08  109.16  3.000
 6PY  H16  C09  C08  109.74  3.000
 6PY  O10  C09  C08  108.20  3.000
 6PY  H18  O10  C09  107.99  3.000
 6PY  C07  O11  C21  119.01  3.000
 6PY  H19  O13  C08  108.93  3.000
 6PY  N16  C14  N15  119.34  3.000
 6PY  N15  C14  N12  115.59  3.000
 6PY  N16  C14  N12  124.95  3.000
 6PY  H21  N15  H20  111.64  3.000
 6PY  H21  N15  C14  112.66  3.000
 6PY  H20  N15  C14  117.86  3.000
 6PY  H22  N16  C14  110.84  3.000
 6PY  C19  O18  C17  112.78  3.000
 6PY  H24  C19  H23  107.14  3.000
 6PY  H24  C19  O18  110.83  3.000
 6PY  H23  C19  O18  111.20  3.000
 6PY  H24  C19  C20  109.79  3.000
 6PY  H23  C19  C20  108.88  3.000
 6PY  O18  C19  C20  108.97  3.000
 6PY  H25  N22  C21  117.85  3.000
 6PY  H25  N22  C20  117.03  3.000
 6PY  C21  N22  C20  121.26  3.000
 6PY  H26  N25  C27  118.31  3.000
 6PY  H26  N25  C02  118.00  3.000
 6PY  C27  N25  C02  123.65  3.000
 6PY  O26  C27  N25  123.03  3.000
 6PY  O26  C27  C28  121.84  3.000
 6PY  N25  C27  C28  115.12  3.000
 6PY  O31  C29  O30  127.97  3.000
 6PY  O30  C29  C05  116.03  3.000
 6PY  O31  C29  C05  116.00  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
 6PY  CONST_01  C02  N25  C27  C28   180.00   0.0  0
 6PY  CONST_02  O26  C27  N25  C02     0.00   0.0  0
 6PY  CONST_03  N16  C14  N12  C03   180.00   0.0  0
 6PY  CONST_04  N15  C14  N12  C03     0.00   0.0  0
 6PY  CONST_05  H26  N25  C27  C28     0.00   0.0  0
 6PY  CONST_06  H22  N16  C14  N12     0.00   0.0  0
 6PY  CONST_08  H21  N15  C14  N12   180.00   0.0  0
 6PY  CONST_09  H1   N12  C14  N15   180.00   0.0  0
 6PY  Var_01    C04  C05  O06  C01    14.00  30.0  1
 6PY  Var_02    O06  C05  C04  C03     4.17  30.0  1
 6PY  Var_03    O31  C29  C05  C04    -3.89  30.0  2
 6PY  Var_04    C20  C19  O18  C17  -176.23  30.0  1
 6PY  Var_05    O23  C21  N22  C20   -10.43  30.0  1
 6PY  Var_06    C19  C20  N22  C21   163.78  30.0  3
 6PY  Var_07    N22  C20  C19  O18    61.46  30.0  1
 6PY  Var_08    H2   C17  O18  C19    60.67  30.0  3
 6PY  Var_09    H7   C28  C27  N25   112.99  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
 6PY  chir_01  C01  C02  C07  O06  positiv
 6PY  chir_02  C02  N25  C03  C01  positiv
 6PY  chir_03  C03  N12  C04  C02  negativ
 6PY  chir_04  C07  O11  C08  C01  positiv
 6PY  chir_05  C08  O13  C07  C09  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
 6PY  plan-1  C28  0.020
 6PY  plan-1  C02  0.020
 6PY  plan-1  N25  0.020
 6PY  plan-1  O26  0.020
 6PY  plan-1  C27  0.020
 6PY  plan-1  H26  0.020
 6PY  plan-2  N12  0.020
 6PY  plan-2  C03  0.020
 6PY  plan-2  C14  0.020
 6PY  plan-2  N15  0.020
 6PY  plan-2  N16  0.020
 6PY  plan-2  H1   0.020
 6PY  plan-2  H20  0.020
 6PY  plan-2  H21  0.020
 6PY  plan-2  H22  0.020
 6PY  plan-3  C05  0.020
 6PY  plan-3  C29  0.020
 6PY  plan-3  O30  0.020
 6PY  plan-3  O31  0.020
 6PY  plan-4  C21  0.020
 6PY  plan-4  O11  0.020
 6PY  plan-4  N22  0.020
 6PY  plan-4  O23  0.020

