# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Apr 28 04:08:14 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  57  30  .  2023-02-15  2023-02-16
;
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  -0.640  -2.6617  -2.1402   0.0041
 6PY  C17  C  CH3   0  -0.394   4.9123  -2.5879   3.4520
 6PY  C20  C  CH2   0  -0.299   4.1363  -1.5843   0.0222
 6PY  C21  C  C     0   0.771   2.4752   0.0640  -0.6300
 6PY  C28  C  CH3   0  -0.778   0.6581  -2.5109  -3.2823
 6PY  C01  C  CH1   0   0.051  -0.8294   1.0704  -0.6222
 6PY  C02  C  CH1   0  -0.147  -1.0338  -0.4497  -0.6061
 6PY  C03  C  CH1   0  -0.077  -2.5121  -0.7389  -0.3333
 6PY  C04  C  C1    0  -0.309  -3.0144   0.1736   0.7496
 6PY  C05  C  C     0   0.231  -2.3103   1.2200   1.1784
 6PY  O06  O  O2    0  -0.476  -1.1321   1.6088   0.6550
 6PY  C07  C  CH1   0  -0.060   0.5886   1.4792  -0.9866
 6PY  C08  C  CH1   0   0.000   0.8161   2.9971  -0.8953
 6PY  C09  C  CH2   0  -0.169   2.2122   3.3761  -1.3686
 6PY  O10  O  OH1   0  -0.668   2.3575   4.7694  -1.2346
 6PY  O11  O  O2    0  -0.504   1.4797   0.8062  -0.1055
 6PY  O13  O  OH1   0  -0.655  -0.1815   3.6752  -1.6198
 6PY  C14  C  C     0   0.523  -3.8868  -2.7631   0.1154
 6PY  N15  N  NH2   0  -0.812  -4.8878  -2.2217  -0.6550
 6PY  N16  N  N     0  -0.704  -4.1344  -3.7698   0.8674
 6PY  O18  O  O2    0  -0.488   4.1976  -2.3742   2.2611
 6PY  C19  C  CH2   0  -0.166   5.0033  -1.8659   1.2269
 6PY  N22  N  NH1   0  -0.657   3.1364  -0.5877   0.3375
 6PY  O23  O  O     0  -0.511   2.7463   0.0328  -1.8118
 6PY  N25  N  NH1   0  -0.634  -0.5915  -1.0527  -1.8311
 6PY  O26  O  O     0  -0.490   0.7315  -2.6285  -0.8933
 6PY  C27  C  C     0   0.535   0.2697  -2.0929  -1.8887
 6PY  C29  C  C     0   0.501  -2.7941   2.0682   2.3019
 6PY  O30  O  OH1   0  -0.583  -1.9786   3.0741   2.5588
 6PY  O31  O  O     0  -0.430  -3.8171   1.8512   2.9034
 6PY  H1   H  HNH1  0   0.383  -1.9863  -2.4645   0.6816
 6PY  H2   H  HCH3  0   0.206   5.3519  -1.6613   3.8391
 6PY  H3   H  HCH3  0   0.235   4.2184  -2.9779   4.1957
 6PY  H4   H  HCH3  0   0.206   5.7222  -3.3144   3.3188
 6PY  H5   H  HCH2  0   0.252   4.7775  -1.2135  -0.7767
 6PY  H6   H  HCH2  0   0.240   3.6690  -2.5078  -0.3338
 6PY  H7   H  HCH3  0   0.271   1.6164  -2.0488  -3.5243
 6PY  H8   H  HCH3  0   0.261   0.7865  -3.5902  -3.3284
 6PY  H9   H  HCH3  0   0.249  -0.0632  -2.2072  -4.0394
 6PY  H10  H  HCH1  0   0.262  -1.5102   1.5118  -1.3621
 6PY  H11  H  HCH1  0   0.289  -0.4359  -0.8717   0.2053
 6PY  H12  H  HCH1  0   0.272  -3.0629  -0.5325  -1.2557
 6PY  H13  H  H     0   0.281  -3.9711  -0.0444   1.2039
 6PY  H14  H  HCH1  0   0.268   0.7633   1.1574  -2.0176
 6PY  H15  H  HCH1  0   0.248   0.7029   3.3157   0.1451
 6PY  H16  H  HCH2  0   0.209   2.9616   2.8425  -0.7743
 6PY  H17  H  HCH2  0   0.196   2.3403   3.0514  -2.4120
 6PY  H18  H  HOH1  0   0.457   3.2520   5.0011  -1.4994
 6PY  H19  H  HOH1  0   0.448  -0.0452   3.5198  -2.5615
 6PY  H20  H  HNH2  0   0.387  -4.6327  -1.8853  -1.5704
 6PY  H21  H  HNH2  0   0.384  -5.7135  -2.7987  -0.6861
 6PY  H22  H  H     0   0.317  -3.3434  -3.9818   1.4645
 6PY  H23  H  HCH2  0   0.219   5.7840  -2.5841   0.9421
 6PY  H24  H  HCH2  0   0.208   5.5108  -0.9440   1.5441
 6PY  H25  H  HNH1  0   0.396   2.7125  -0.6344   1.2515
 6PY  H26  H  HNH1  0   0.403  -0.9629  -0.6911  -2.6959
 6PY  H27  H  HOH1  0   0.490  -2.3292   3.5989   3.2944

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  1.281  0.020  1.281
 6PY  C28  C27  single  1.506  0.020  1.506
 6PY  O13  C08  single  1.407  0.020  1.407
 6PY  N25  C27  single  1.352  0.020  1.352
 6PY  N25  C02  single  1.435  0.020  1.435
 6PY  C14  N15  single  1.374  0.020  1.374
 6PY  C14  N12  single  1.379  0.020  1.379
 6PY  C27  O26  double  1.221  0.020  1.221
 6PY  O10  C09  single  1.407  0.020  1.407
 6PY  C03  C02  single  1.531  0.020  1.531
 6PY  C03  N12  single  1.449  0.020  1.449
 6PY  C03  C04  single  1.503  0.020  1.503
 6PY  C02  C01  single  1.534  0.020  1.534
 6PY  C01  C07  single  1.520  0.020  1.520
 6PY  C01  O06  single  1.419  0.020  1.419
 6PY  C08  C07  single  1.538  0.020  1.538
 6PY  C08  C09  single  1.522  0.020  1.522
 6PY  C07  O11  single  1.422  0.020  1.422
 6PY  O23  C21  double  1.213  0.020  1.213
 6PY  C04  C05  double  1.332  0.020  1.332
 6PY  O06  C05  single  1.347  0.020  1.347
 6PY  C05  C29  single  1.489  0.020  1.489
 6PY  O11  C21  single  1.348  0.020  1.348
 6PY  C21  N22  single  1.341  0.020  1.341
 6PY  C29  O31  double  1.206  0.020  1.206
 6PY  C29  O30  single  1.320  0.020  1.320
 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  0.890  0.020  1.040
 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
 6PY  O30  H27  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
 6PY  H1   N12  C14  113.26  3.000
 6PY  H1   N12  C03  113.43  3.000
 6PY  C14  N12  C03  123.18  3.000
 6PY  H4   C17  H3   108.44  3.000
 6PY  H4   C17  H2   107.87  3.000
 6PY  H3   C17  H2   108.48  3.000
 6PY  H4   C17  O18  111.94  3.000
 6PY  H3   C17  O18  108.00  3.000
 6PY  H2   C17  O18  112.00  3.000
 6PY  H6   C20  H5   107.45  3.000
 6PY  H6   C20  N22  110.92  3.000
 6PY  H5   C20  N22  109.40  3.000
 6PY  H6   C20  C19  110.31  3.000
 6PY  H5   C20  C19  108.09  3.000
 6PY  N22  C20  C19  110.57  3.000
 6PY  O23  C21  N22  125.47  3.000
 6PY  N22  C21  O11  110.55  3.000
 6PY  O23  C21  O11  123.94  3.000
 6PY  H9   C28  H8   108.99  3.000
 6PY  H9   C28  H7   108.03  3.000
 6PY  H8   C28  H7   107.89  3.000
 6PY  H9   C28  C27  113.27  3.000
 6PY  H8   C28  C27  110.18  3.000
 6PY  H7   C28  C27  108.31  3.000
 6PY  H10  C01  C07  107.98  3.000
 6PY  H10  C01  O06  108.77  3.000
 6PY  C07  C01  O06  108.22  3.000
 6PY  H10  C01  C02  108.84  3.000
 6PY  O06  C01  C02  109.77  3.000
 6PY  C07  C01  C02  113.16  3.000
 6PY  H11  C02  N25  107.63  3.000
 6PY  H11  C02  C03  108.86  3.000
 6PY  N25  C02  C03  111.73  3.000
 6PY  H11  C02  C01  108.52  3.000
 6PY  C03  C02  C01  108.53  3.000
 6PY  N25  C02  C01  111.49  3.000
 6PY  H12  C03  C04  108.95  3.000
 6PY  H12  C03  C02  107.48  3.000
 6PY  C04  C03  C02  109.66  3.000
 6PY  H12  C03  N12  109.08  3.000
 6PY  C04  C03  N12  112.64  3.000
 6PY  C02  C03  N12  108.89  3.000
 6PY  H13  C04  C05  119.39  3.000
 6PY  H13  C04  C03  118.44  3.000
 6PY  C05  C04  C03  122.17  3.000
 6PY  C29  C05  O06  114.41  3.000
 6PY  C29  C05  C04  121.25  3.000
 6PY  O06  C05  C04  124.34  3.000
 6PY  C05  O06  C01  115.28  3.000
 6PY  H14  C07  O11  110.15  3.000
 6PY  H14  C07  C08  108.82  3.000
 6PY  O11  C07  C08  109.73  3.000
 6PY  H14  C07  C01  107.20  3.000
 6PY  O11  C07  C01  107.98  3.000
 6PY  C08  C07  C01  112.91  3.000
 6PY  H15  C08  O13  106.02  3.000
 6PY  H15  C08  C09  108.55  3.000
 6PY  O13  C08  C09  111.73  3.000
 6PY  H15  C08  C07  109.19  3.000
 6PY  C09  C08  C07  111.29  3.000
 6PY  O13  C08  C07  109.89  3.000
 6PY  H17  C09  H16  106.93  3.000
 6PY  H17  C09  O10  111.75  3.000
 6PY  H16  C09  O10  111.10  3.000
 6PY  H17  C09  C08  109.16  3.000
 6PY  H16  C09  C08  109.73  3.000
 6PY  O10  C09  C08  108.16  3.000
 6PY  H18  O10  C09  107.97  3.000
 6PY  C07  O11  C21  118.83  3.000
 6PY  H19  O13  C08  108.97  3.000
 6PY  N16  C14  N15  119.87  3.000
 6PY  N15  C14  N12  115.08  3.000
 6PY  N16  C14  N12  125.05  3.000
 6PY  H21  N15  H20  111.74  3.000
 6PY  H21  N15  C14  112.86  3.000
 6PY  H20  N15  C14  117.14  3.000
 6PY  H22  N16  C14  111.07  3.000
 6PY  C19  O18  C17  112.76  3.000
 6PY  H24  C19  H23  107.16  3.000
 6PY  H24  C19  O18  110.83  3.000
 6PY  H23  C19  O18  111.20  3.000
 6PY  H24  C19  C20  109.80  3.000
 6PY  H23  C19  C20  108.84  3.000
 6PY  O18  C19  C20  108.97  3.000
 6PY  H25  N22  C21  117.98  3.000
 6PY  H25  N22  C20  117.14  3.000
 6PY  C21  N22  C20  121.23  3.000
 6PY  H26  N25  C27  118.30  3.000
 6PY  H26  N25  C02  117.90  3.000
 6PY  C27  N25  C02  123.78  3.000
 6PY  O26  C27  N25  122.94  3.000
 6PY  O26  C27  C28  122.35  3.000
 6PY  N25  C27  C28  114.67  3.000
 6PY  O31  C29  O30  124.32  3.000
 6PY  O30  C29  C05  112.35  3.000
 6PY  O31  C29  C05  123.33  3.000
 6PY  H27  O30  C29  109.68  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_05  H27  O30  C29  C05   180.00   0.0  0
 6PY  CONST_06  H26  N25  C27  C28     0.00   0.0  0
 6PY  CONST_07  H22  N16  C14  N12     0.00   0.0  0
 6PY  CONST_09  H21  N15  C14  N12   180.00   0.0  0
 6PY  CONST_10  H1   N12  C14  N15   180.00   0.0  0
 6PY  Var_01    C04  C05  O06  C01    16.45  30.0  1
 6PY  Var_02    O06  C05  C04  C03     3.58  30.0  1
 6PY  Var_03    O31  C29  C05  C04     1.67  30.0  2
 6PY  Var_04    C20  C19  O18  C17  -176.33  30.0  2
 6PY  Var_05    O23  C21  N22  C20   -10.16  30.0  1
 6PY  Var_06    C19  C20  N22  C21   163.30  30.0  3
 6PY  Var_07    N22  C20  C19  O18    61.57  30.0  1
 6PY  Var_08    H2   C17  O18  C19    60.53  30.0  3
 6PY  Var_09    H7   C28  C27  N25    97.45  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-3  H27  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

