# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri May  8 10:24:40 2020
#   Inital geometry file: a 116 line input string
#   Ligand name: 4-{2-[4-(hydroxymethyl)-1H-1,2,3-triazol-1-yl]ethyl}phenyl alpha-D-mannopyranoside
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC[C@H]1O[C@H](Oc2ccc(CCn3cc(CO)nn3)cc2)[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
 J73  J73  '4-{2-[4-(hydroxymethyl)-1H-1,2,3-triazol-1-yl]ethyl}phenyl alpha-D-mannopyranoside'  ligand  50  27  .  2022-07-25  2022-07-26
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_J73
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
 J73  O42   O  OH1   0  -0.666   8.5982  -0.0763  -1.9803
 J73  C41   C  CH2   0  -0.203   8.6469   0.1778  -0.5997
 J73  C39   C  CR5   0   0.111   7.2473   0.3447  -0.1183
 J73  N38   N  N     0  -0.325   6.9431   0.6417   1.1621
 J73  N37   N  N     0  -0.107   5.6610   0.7232   1.2850
 J73  C40   C  CR15  0  -0.078   6.0728   0.2415  -0.8171
 J73  N36   N  NR5   0  -0.251   5.1240   0.4919   0.1043
 J73  C35   C  CH2   0  -0.292   3.6843   0.4400  -0.0547
 J73  C34   C  CH2   0  -0.527   3.1184  -0.9305   0.3160
 J73  C16   C  CR6   0   0.102   1.6303  -0.9616   0.1104
 J73  C17   C  CR16  0  -0.285   1.0894  -1.1830  -1.1553
 J73  C18   C  CR16  0  -0.335  -0.2779  -1.1745  -1.3624
 J73  C13   C  CR6   0   0.365  -1.1471  -0.9362  -0.2990
 J73  C14   C  CR16  0  -0.338  -0.6278  -0.7048   0.9704
 J73  C15   C  CR16  0  -0.297   0.7498  -0.7253   1.1580
 J73  O1    O  O2    0  -0.506  -2.4684  -0.9430  -0.6079
 J73  C1    C  CH1   0   0.206  -3.4404  -1.0356   0.4051
 J73  C2    C  CH1   0  -0.022  -4.7614  -1.3717  -0.2975
 J73  O2    O  OH1   0  -0.665  -5.7482  -1.6689   0.6545
 J73  C3    C  CH1   0   0.002  -5.2163  -0.1592  -1.1084
 J73  O3    O  OH1   0  -0.672  -6.4876  -0.3421  -1.6829
 J73  C4    C  CH1   0   0.031  -5.2818   1.0840  -0.2270
 J73  O4    O  OH1   0  -0.675  -5.5558   2.2338  -0.9911
 J73  C5    C  CH1   0  -0.015  -3.9306   1.2952   0.4576
 J73  O5    O  O2    0  -0.489  -3.5483   0.1229   1.1602
 J73  C6    C  CH2   0  -0.160  -3.9812   2.4211   1.4682
 J73  O6    O  OH1   0  -0.666  -2.6974   2.5997   2.0163
 J73  H42   H  HOH1  0   0.464   9.4948  -0.2320  -2.2897
 J73  H411  H  HCH2  0   0.223   9.1235  -0.6415  -0.0464
 J73  H412  H  HCH2  0   0.222   9.2224   1.0830  -0.3666
 J73  H40   H  HCR5  0   0.305   5.8424   0.0271  -1.8461
 J73  H351  H  HCH2  0   0.283   3.2500   1.2204   0.5690
 J73  H352  H  HCH2  0   0.277   3.4596   0.6818  -1.0927
 J73  H341  H  HCH2  0   0.262   3.6020  -1.6948  -0.2970
 J73  H342  H  HCH2  0   0.263   3.3625  -1.1505   1.3571
 J73  H17   H  HCR6  0   0.253   1.7463  -1.3726  -1.9966
 J73  H15   H  HCR6  0   0.253   1.1389  -0.5416   2.1528
 J73  H18   H  HCR6  0   0.263  -0.6814  -1.3600  -2.3501
 J73  H14   H  HCR6  0   0.280  -1.2659  -0.4902   1.8149
 J73  H1    H  HCH1  0   0.262  -3.1697  -1.8287   1.1139
 J73  H2    H  HCH1  0   0.239  -4.5918  -2.2189  -0.9762
 J73  HA    H  HOH1  0   0.458  -5.5543  -2.5293   1.0392
 J73  H3    H  HCH1  0   0.230  -4.4634   0.0238  -1.8862
 J73  HB    H  HOH1  0   0.458  -6.3961  -0.8839  -2.4726
 J73  H4    H  HCH1  0   0.215  -6.0491   0.9349   0.5476
 J73  HC    H  HOH1  0   0.453  -6.3808   2.0823  -1.4641
 J73  H5    H  HCH1  0   0.231  -3.1836   1.5403  -0.3107
 J73  H61C  H  HCH2  0   0.213  -4.3344   3.3233   0.9582
 J73  H62C  H  HCH2  0   0.195  -4.7248   2.1738   2.2391
 J73  H6    H  HOH1  0   0.456  -2.7264   3.3722   2.5877

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
 J73  O42  C41   single    1.405  0.020  1.405
 J73  C41  C39   single    1.489  0.020  1.489
 J73  C39  N38   aromatic  1.349  0.020  1.349
 J73  C39  C40   aromatic  1.371  0.020  1.371
 J73  N38  N37   aromatic  1.291  0.020  1.291
 J73  N37  N36   aromatic  1.318  0.020  1.318
 J73  C40  N36   aromatic  1.346  0.020  1.346
 J73  N36  C35   single    1.449  0.020  1.449
 J73  C35  C34   single    1.528  0.020  1.528
 J73  C34  C16   single    1.502  0.020  1.502
 J73  C16  C17   aromatic  1.394  0.020  1.394
 J73  C16  C15   aromatic  1.389  0.020  1.389
 J73  C17  C18   aromatic  1.383  0.020  1.383
 J73  C18  C13   aromatic  1.394  0.020  1.394
 J73  C13  C14   aromatic  1.391  0.020  1.391
 J73  C13  O1    single    1.357  0.020  1.357
 J73  C14  C15   aromatic  1.390  0.020  1.390
 J73  O1   C1    single    1.407  0.020  1.407
 J73  C1   C2    single    1.533  0.020  1.533
 J73  C1   O5    single    1.387  0.020  1.387
 J73  C2   O2    single    1.403  0.020  1.403
 J73  C2   C3    single    1.528  0.020  1.528
 J73  C3   O3    single    1.407  0.020  1.407
 J73  C3   C4    single    1.525  0.020  1.525
 J73  C4   O4    single    1.407  0.020  1.407
 J73  C4   C5    single    1.529  0.020  1.529
 J73  C5   O5    single    1.419  0.020  1.419
 J73  C5   C6    single    1.514  0.020  1.514
 J73  C6   O6    single    1.407  0.020  1.407
 J73  O42  H42   single    0.850  0.020  0.980
 J73  C41  H411  single    0.970  0.020  1.090
 J73  C41  H412  single    0.970  0.020  1.090
 J73  C40  H40   single    0.930  0.020  1.080
 J73  C35  H351  single    0.970  0.020  1.090
 J73  C35  H352  single    0.970  0.020  1.090
 J73  C34  H341  single    0.970  0.020  1.090
 J73  C34  H342  single    0.970  0.020  1.090
 J73  C17  H17   single    0.930  0.020  1.080
 J73  C15  H15   single    0.930  0.020  1.080
 J73  C18  H18   single    0.930  0.020  1.080
 J73  C14  H14   single    0.930  0.020  1.080
 J73  C1   H1    single    0.970  0.020  1.090
 J73  C2   H2    single    0.970  0.020  1.090
 J73  O2   HA    single    0.850  0.020  0.980
 J73  C3   H3    single    0.970  0.020  1.090
 J73  O3   HB    single    0.850  0.020  0.980
 J73  C4   H4    single    0.970  0.020  1.090
 J73  O4   HC    single    0.850  0.020  0.980
 J73  C5   H5    single    0.970  0.020  1.090
 J73  C6   H61C  single    0.970  0.020  1.090
 J73  C6   H62C  single    0.970  0.020  1.090
 J73  O6   H6    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
 J73  H42   O42  C41   108.26  3.000
 J73  H412  C41  H411  106.31  3.000
 J73  H412  C41  C39   109.37  3.000
 J73  H411  C41  C39   109.19  3.000
 J73  H412  C41  O42   112.09  3.000
 J73  H411  C41  O42   112.06  3.000
 J73  C39   C41  O42   107.78  3.000
 J73  C40   C39  N38   107.89  3.000
 J73  C40   C39  C41   129.20  3.000
 J73  N38   C39  C41   122.91  3.000
 J73  N37   N38  C39   109.17  3.000
 J73  N36   N37  N38   107.97  3.000
 J73  H40   C40  N36   122.73  3.000
 J73  H40   C40  C39   133.32  3.000
 J73  N36   C40  C39   103.95  3.000
 J73  C35   N36  C40   128.20  3.000
 J73  C35   N36  N37   120.63  3.000
 J73  C40   N36  N37   111.03  3.000
 J73  H352  C35  H351  107.72  3.000
 J73  H352  C35  C34   110.73  3.000
 J73  H351  C35  C34   110.85  3.000
 J73  H352  C35  N36   107.55  3.000
 J73  H351  C35  N36   107.91  3.000
 J73  C34   C35  N36   111.92  3.000
 J73  H342  C34  H341  107.17  3.000
 J73  H342  C34  C16   110.35  3.000
 J73  H341  C34  C16   110.31  3.000
 J73  H342  C34  C35   109.22  3.000
 J73  H341  C34  C35   109.10  3.000
 J73  C16   C34  C35   110.61  3.000
 J73  C15   C16  C17   117.76  3.000
 J73  C15   C16  C34   121.41  3.000
 J73  C17   C16  C34   120.78  3.000
 J73  H17   C17  C18   118.94  3.000
 J73  H17   C17  C16   119.82  3.000
 J73  C18   C17  C16   121.24  3.000
 J73  H18   C18  C13   119.52  3.000
 J73  H18   C18  C17   120.26  3.000
 J73  C13   C18  C17   120.22  3.000
 J73  O1    C13  C14   124.90  3.000
 J73  O1    C13  C18   115.64  3.000
 J73  C14   C13  C18   119.46  3.000
 J73  H14   C14  C15   118.87  3.000
 J73  H14   C14  C13   121.74  3.000
 J73  C15   C14  C13   119.38  3.000
 J73  H15   C15  C14   118.49  3.000
 J73  H15   C15  C16   119.57  3.000
 J73  C14   C15  C16   121.93  3.000
 J73  C1    O1   C13   120.61  3.000
 J73  H1    C1   O5    105.73  3.000
 J73  H1    C1   C2    110.48  3.000
 J73  O5    C1   C2    111.44  3.000
 J73  H1    C1   O1    110.01  3.000
 J73  O5    C1   O1    113.00  3.000
 J73  C2    C1   O1    106.24  3.000
 J73  H2    C2   C3    109.27  3.000
 J73  H2    C2   O2    111.37  3.000
 J73  C3    C2   O2    108.59  3.000
 J73  H2    C2   C1    108.61  3.000
 J73  C3    C2   C1    109.01  3.000
 J73  O2    C2   C1    109.96  3.000
 J73  HA    O2   C2    108.60  3.000
 J73  H3    C3   C4    107.63  3.000
 J73  H3    C3   O3    110.62  3.000
 J73  C4    C3   O3    107.64  3.000
 J73  H3    C3   C2    107.71  3.000
 J73  C4    C3   C2    110.66  3.000
 J73  O3    C3   C2    112.49  3.000
 J73  HB    O3   C3    108.81  3.000
 J73  H4    C4   C5    108.64  3.000
 J73  H4    C4   O4    110.92  3.000
 J73  C5    C4   O4    107.59  3.000
 J73  H4    C4   C3    109.04  3.000
 J73  C5    C4   C3    109.47  3.000
 J73  O4    C4   C3    111.13  3.000
 J73  HC    O4   C4    107.76  3.000
 J73  H5    C5   C6    108.88  3.000
 J73  H5    C5   O5    110.31  3.000
 J73  C6    C5   O5    107.03  3.000
 J73  H5    C5   C4    108.56  3.000
 J73  C6    C5   C4    111.84  3.000
 J73  O5    C5   C4    110.22  3.000
 J73  C5    O5   C1    116.19  3.000
 J73  H62C  C6   H61C  107.08  3.000
 J73  H62C  C6   O6    111.87  3.000
 J73  H61C  C6   O6    111.78  3.000
 J73  H62C  C6   C5    108.88  3.000
 J73  H61C  C6   C5    108.22  3.000
 J73  O6    C6   C5    108.90  3.000
 J73  H6    O6   C6    107.82  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
 J73  CONST_01  N36  N37  N38  C39     0.00   0.0  0
 J73  CONST_02  N37  N36  C40  C39     0.00   0.0  0
 J73  CONST_03  N36  C40  C39  N38     0.00   0.0  0
 J73  CONST_04  C40  N36  N37  N38     0.00   0.0  0
 J73  CONST_05  C40  C39  N38  N37     0.00   0.0  0
 J73  CONST_06  C13  C18  C17  C16     0.00   0.0  0
 J73  CONST_07  C13  C14  C15  C16     0.00   0.0  0
 J73  CONST_08  C14  C15  C16  C17     0.00   0.0  0
 J73  CONST_09  C14  C13  C18  C17     0.00   0.0  0
 J73  CONST_10  C15  C16  C17  C18     0.00   0.0  0
 J73  CONST_11  C15  C14  C13  C18     0.00   0.0  0
 J73  CONST_12  N37  N38  C39  C41   180.00   0.0  0
 J73  CONST_13  N36  C40  C39  C41   180.00   0.0  0
 J73  CONST_14  C35  N36  C40  C39   180.00   0.0  0
 J73  CONST_15  C35  N36  N37  N38   180.00   0.0  0
 J73  CONST_16  C18  C17  C16  C34   180.00   0.0  0
 J73  CONST_17  C14  C15  C16  C34   180.00   0.0  0
 J73  CONST_18  O1   C13  C18  C17   180.00   0.0  0
 J73  CONST_19  O1   C13  C14  C15   180.00   0.0  0
 J73  CONST_20  H40  C40  C39  N38   180.00   0.0  0
 J73  CONST_21  H18  C18  C17  C16   180.00   0.0  0
 J73  CONST_22  H14  C14  C15  C16   180.00   0.0  0
 J73  CONST_23  H15  C15  C16  C17   180.00   0.0  0
 J73  CONST_24  H17  C17  C18  C13   180.00   0.0  0
 J73  Var_01    N38  C39  C41  O42  -177.91  30.0  2
 J73  Var_02    C34  C35  N36  N37   -82.86  30.0  2
 J73  Var_03    C16  C34  C35  N36  -178.69  30.0  3
 J73  Var_04    C17  C16  C34  C35    81.82  30.0  2

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
 J73  chir_01  C1  O1  C2  O5  positiv
 J73  chir_02  C2  O2  C1  C3  positiv
 J73  chir_03  C3  O3  C2  C4  positiv
 J73  chir_04  C4  O4  C5  C3  positiv
 J73  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
 J73  plan-1  C41  0.020
 J73  plan-1  C39  0.020
 J73  plan-1  N38  0.020
 J73  plan-1  N37  0.020
 J73  plan-1  C40  0.020
 J73  plan-1  N36  0.020
 J73  plan-1  C35  0.020
 J73  plan-1  H40  0.020
 J73  plan-2  C34  0.020
 J73  plan-2  C16  0.020
 J73  plan-2  C17  0.020
 J73  plan-2  C18  0.020
 J73  plan-2  C13  0.020
 J73  plan-2  C14  0.020
 J73  plan-2  C15  0.020
 J73  plan-2  O1   0.020
 J73  plan-2  H17  0.020
 J73  plan-2  H15  0.020
 J73  plan-2  H18  0.020
 J73  plan-2  H14  0.020

