# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Mar 10 22:39:59 2022
#   Inital geometry file: a 143 line input string
#   Ligand name: (1S,2S,3R,4S,6R)-4,6-diamino-3-{[(2S,3R)-3-amino-6-(fluoromethyl)-3,4-dihydro-2H-pyran-2-yl]oxy}-2-hydroxycyclohexyl 3-deoxy-4-C-methyl-3-(methylamino)-beta-L-arabinopyranoside
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CN[C@@H]1[C@@H](O)[C@H](OC[C@]1(C)O)O[C@H]2[C@H](N)C[C@H](N)[C@@H](O[C@H]3OC(=CC[C@H]3N)CF)[C@@H]2O
#
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
 FSJ  FSJ  '(1S,2S,3R,4S,6R)-4,6-diamino-3-{[(2S,3R)-3-amino-6-(fluoromethyl)-3,4-dihydro-2H-pyran-2-yl]oxy}-2-hydroxycyclohexyl 3-deoxy-4-C-methyl-3-(methylamino)-beta-L-arabinopyranoside'  ligand  66  31  .  2022-03-18  2022-03-18
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK
;

data_comp_FSJ
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
 FSJ  C11  C  CR16  0   0.325  -3.7154  -0.4323  -0.2694
 FSJ  C12  C  CH1   0  -0.107   0.8682   2.2659  -0.4535
 FSJ  C13  C  CH1   0   0.217   2.3847  -0.6808   0.8827
 FSJ  C21  C  CR16  0  -0.205  -4.2177  -1.6813  -0.9814
 FSJ  C22  C  CH2   0  -0.465  -0.4388   3.0472  -0.3543
 FSJ  C23  C  CH1   0   0.043   3.7915  -0.1761   1.2163
 FSJ  C31  C  C     0  -0.463  -5.1281  -2.4243   0.0042
 FSJ  C32  C  CH1   0  -0.098  -1.6175   2.3419  -1.0170
 FSJ  C33  C  CH1   0  -0.095   4.7606  -0.4261   0.0511
 FSJ  C41  C  CR16  0  -0.373  -6.0666  -1.4647   0.6668
 FSJ  C42  C  CH1   0   0.031  -1.7861   0.9589  -0.3983
 FSJ  C43  C  CT    0   0.149   4.6804  -1.9029  -0.3904
 FSJ  C51  C  CR6   0   0.299  -5.8742  -0.1458   0.6260
 FSJ  C52  C  CH1   0   0.035  -0.5060   0.1475  -0.5499
 FSJ  C53  C  CH2   0  -0.183   3.2199  -2.2791  -0.6373
 FSJ  C61  C  CH2   0  -0.073  -6.8295   0.8434   1.1918
 FSJ  C62  C  CH1   0   0.047   0.6744   0.8604   0.1063
 FSJ  C83  C  CH3   0  -0.684   5.4751  -2.1625  -1.6651
 FSJ  N12  N  NH2   0  -0.803   1.9876   2.9128   0.2236
 FSJ  N21  N  NH2   0  -0.789  -4.8407  -1.3308  -2.2463
 FSJ  N33  N  NH1   0  -0.601   6.0948   0.0052   0.4202
 FSJ  F61  F  F     0  -0.381  -6.2337   1.5440   2.2418
 FSJ  O11  O  O2    0  -0.508  -2.8451   0.2819  -1.0568
 FSJ  O23  O  OH1   0  -0.707   3.7486   1.1650   1.6096
 FSJ  O43  O  OH1   0  -0.679   5.2053  -2.6597   0.6889
 FSJ  O51  O  O     0  -0.493  -4.8059   0.4390   0.0301
 FSJ  O52  O  OH1   0  -0.668  -0.7225  -1.1185   0.0259
 FSJ  O53  O  O2    0  -0.493   2.3887  -2.0166   0.4779
 FSJ  O62  O  O2    0  -0.522   1.8550   0.1268  -0.1318
 FSJ  H1   H  HCR6  0   0.221  -3.2520  -0.7293   0.6816
 FSJ  H2   H  HCH1  0   0.241   1.1442   2.1670  -1.5089
 FSJ  H3   H  HCH1  0   0.241   1.7515  -0.6404   1.7768
 FSJ  H4   H  HCR6  0   0.257  -3.3438  -2.3008  -1.1971
 FSJ  H5   H  HCH2  0   0.225  -0.6817   3.2167   0.7013
 FSJ  H6   H  HCH2  0   0.251  -0.3019   4.0339  -0.8055
 FSJ  H7   H  HCH1  0   0.215   4.1461  -0.7455   2.0825
 FSJ  H8   H  H     0   0.253  -5.6861  -3.2007  -0.5261
 FSJ  H9   H  H     0   0.248  -4.5310  -2.9505   0.7563
 FSJ  H10  H  HCH1  0   0.209  -1.3783   2.2011  -2.0846
 FSJ  H11  H  HCH1  0   0.230   4.4247   0.1811  -0.7984
 FSJ  H12  H  HCR6  0   0.254  -6.9415  -1.8424   1.1797
 FSJ  H13  H  HCH1  0   0.229  -2.0197   1.0882   0.6683
 FSJ  H14  H  HCH1  0   0.210  -0.2921   0.0534  -1.6265
 FSJ  H15  H  HCH2  0   0.214   2.8527  -1.7633  -1.5315
 FSJ  H16  H  HCH2  0   0.240   3.1402  -3.3519  -0.8323
 FSJ  H17  H  HCH2  0   0.221  -7.1326   1.5737   0.4390
 FSJ  H18  H  HCH2  0   0.226  -7.7158   0.3353   1.5699
 FSJ  H19  H  HCH1  0   0.223   0.4822   0.9336   1.1881
 FSJ  H20  H  HCH3  0   0.244   6.5302  -1.9257  -1.5288
 FSJ  H21  H  HCH3  0   0.237   5.4059  -3.2139  -1.9569
 FSJ  H22  H  HCH3  0   0.232   5.1010  -1.5681  -2.4992
 FSJ  H23  H  HCH3  0   0.192   6.9866   0.3127  -1.5234
 FSJ  H24  H  HCH3  0   0.221   6.2645   1.7239  -0.7515
 FSJ  H25  H  HCH3  0   0.227   7.7812   1.0783  -0.1490
 FSJ  H26  H  HNH2  0   0.367   2.3343   3.6798  -0.3387
 FSJ  H27  H  HNH2  0   0.357   1.6687   3.3289   1.0926
 FSJ  H29  H  HNH2  0   0.352  -5.0654  -2.1835  -2.7434
 FSJ  H30  H  HNH2  0   0.344  -5.7296  -0.8718  -2.0854
 FSJ  H35  H  HNH1  0   0.342   6.6516  -0.7818   0.7239
 FSJ  H37  H  HOH1  0   0.459   3.2409   1.7028   0.9593
 FSJ  H38  H  HOH1  0   0.449   5.2781  -3.5796   0.4132
 FSJ  H39  H  HOH1  0   0.451   0.0168  -1.6931  -0.2006
 FSJ  N32  N  NH2   0  -0.802  -2.8240   3.1241  -0.8106
 FSJ  C93  C  CH3   0  -0.524   6.8082   0.7983  -0.5550
 FSJ  H32  H  HNH2  0   0.345  -2.7461   3.9933  -1.3244
 FSJ  H33  H  HNH2  0   0.346  -3.6184   2.6397  -1.2086

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
 FSJ  C93  N33  single  1.445  0.020  1.445
 FSJ  N33  C33  single  1.450  0.020  1.450
 FSJ  O23  C23  single  1.398  0.020  1.398
 FSJ  C33  C23  single  1.536  0.020  1.536
 FSJ  C33  C43  single  1.543  0.020  1.543
 FSJ  C23  C13  single  1.531  0.020  1.531
 FSJ  C83  C43  single  1.524  0.020  1.524
 FSJ  O43  C43  single  1.419  0.020  1.419
 FSJ  C43  C53  single  1.528  0.020  1.528
 FSJ  N12  C12  single  1.459  0.020  1.459
 FSJ  O62  C13  single  1.401  0.020  1.401
 FSJ  O62  C62  single  1.410  0.020  1.410
 FSJ  C13  O53  single  1.396  0.020  1.396
 FSJ  C12  C62  single  1.525  0.020  1.525
 FSJ  C12  C22  single  1.526  0.020  1.526
 FSJ  C53  O53  single  1.415  0.020  1.415
 FSJ  C62  C52  single  1.527  0.020  1.527
 FSJ  C22  C32  single  1.525  0.020  1.525
 FSJ  C52  O52  single  1.408  0.020  1.408
 FSJ  C52  C42  single  1.523  0.020  1.523
 FSJ  C32  C42  single  1.524  0.020  1.524
 FSJ  C32  N32  single  1.453  0.020  1.453
 FSJ  C42  O11  single  1.419  0.020  1.419
 FSJ  N21  C21  single  1.453  0.020  1.453
 FSJ  O11  C11  single  1.374  0.020  1.374
 FSJ  C21  C31  single  1.534  0.020  1.534
 FSJ  C21  C11  single  1.523  0.020  1.523
 FSJ  C31  C41  single  1.497  0.020  1.497
 FSJ  C11  O51  single  1.428  0.020  1.428
 FSJ  C41  C51  double  1.333  0.020  1.333
 FSJ  O51  C51  single  1.356  0.020  1.356
 FSJ  C51  C61  single  1.487  0.020  1.487
 FSJ  C61  F61  single  1.396  0.020  1.396
 FSJ  C11  H1   single  0.970  0.020  1.090
 FSJ  C12  H2   single  0.970  0.020  1.090
 FSJ  C13  H3   single  0.970  0.020  1.090
 FSJ  C21  H4   single  0.970  0.020  1.090
 FSJ  C22  H5   single  0.970  0.020  1.090
 FSJ  C22  H6   single  0.970  0.020  1.090
 FSJ  C23  H7   single  0.970  0.020  1.090
 FSJ  C31  H8   single  0.970  0.020  1.090
 FSJ  C31  H9   single  0.970  0.020  1.090
 FSJ  C32  H10  single  0.970  0.020  1.090
 FSJ  C33  H11  single  0.970  0.020  1.090
 FSJ  C41  H12  single  0.930  0.020  1.080
 FSJ  C42  H13  single  0.970  0.020  1.090
 FSJ  C52  H14  single  0.970  0.020  1.090
 FSJ  C53  H15  single  0.970  0.020  1.090
 FSJ  C53  H16  single  0.970  0.020  1.090
 FSJ  C61  H17  single  0.970  0.020  1.090
 FSJ  C61  H18  single  0.970  0.020  1.090
 FSJ  C62  H19  single  0.970  0.020  1.090
 FSJ  C83  H20  single  0.970  0.020  1.090
 FSJ  C83  H21  single  0.970  0.020  1.090
 FSJ  C83  H22  single  0.970  0.020  1.090
 FSJ  C93  H23  single  0.970  0.020  1.090
 FSJ  C93  H24  single  0.970  0.020  1.090
 FSJ  C93  H25  single  0.970  0.020  1.090
 FSJ  N12  H26  single  0.890  0.020  1.040
 FSJ  N12  H27  single  0.890  0.020  1.040
 FSJ  N21  H29  single  0.890  0.020  1.040
 FSJ  N21  H30  single  0.890  0.020  1.040
 FSJ  N32  H32  single  0.890  0.020  1.040
 FSJ  N32  H33  single  0.890  0.020  1.040
 FSJ  N33  H35  single  0.890  0.020  1.040
 FSJ  O23  H37  single  0.850  0.020  0.980
 FSJ  O43  H38  single  0.850  0.020  0.980
 FSJ  O52  H39  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
 FSJ  H1   C11  O51  107.79  3.000
 FSJ  H1   C11  O11  111.68  3.000
 FSJ  O51  C11  O11  106.67  3.000
 FSJ  H1   C11  C21  108.78  3.000
 FSJ  O51  C11  C21  110.29  3.000
 FSJ  O11  C11  C21  111.55  3.000
 FSJ  H2   C12  N12  107.09  3.000
 FSJ  H2   C12  C62  107.61  3.000
 FSJ  N12  C12  C62  109.61  3.000
 FSJ  H2   C12  C22  108.95  3.000
 FSJ  C62  C12  C22  109.82  3.000
 FSJ  N12  C12  C22  113.56  3.000
 FSJ  H3   C13  O62  110.55  3.000
 FSJ  H3   C13  O53  105.87  3.000
 FSJ  O62  C13  O53  110.05  3.000
 FSJ  H3   C13  C23  109.92  3.000
 FSJ  O53  C13  C23  112.08  3.000
 FSJ  O62  C13  C23  108.37  3.000
 FSJ  H4   C21  N21  107.93  3.000
 FSJ  H4   C21  C31  109.08  3.000
 FSJ  N21  C21  C31  114.95  3.000
 FSJ  H4   C21  C11  107.07  3.000
 FSJ  C31  C21  C11  107.02  3.000
 FSJ  N21  C21  C11  110.52  3.000
 FSJ  H6   C22  H5   106.59  3.000
 FSJ  H6   C22  C32  109.56  3.000
 FSJ  H5   C22  C32  108.58  3.000
 FSJ  H6   C22  C12  109.14  3.000
 FSJ  H5   C22  C12  109.36  3.000
 FSJ  C32  C22  C12  113.38  3.000
 FSJ  H7   C23  O23  106.62  3.000
 FSJ  H7   C23  C33  108.12  3.000
 FSJ  O23  C23  C33  112.88  3.000
 FSJ  H7   C23  C13  107.35  3.000
 FSJ  C33  C23  C13  111.14  3.000
 FSJ  O23  C23  C13  110.44  3.000
 FSJ  H9   C31  H8   105.68  3.000
 FSJ  H9   C31  C41  110.23  3.000
 FSJ  H8   C31  C41  110.48  3.000
 FSJ  H9   C31  C21  110.52  3.000
 FSJ  H8   C31  C21  109.59  3.000
 FSJ  C41  C31  C21  110.24  3.000
 FSJ  H10  C32  N32  112.73  3.000
 FSJ  H10  C32  C42  107.52  3.000
 FSJ  N32  C32  C42  109.82  3.000
 FSJ  H10  C32  C22  108.18  3.000
 FSJ  N32  C32  C22  109.33  3.000
 FSJ  C42  C32  C22  109.19  3.000
 FSJ  H11  C33  N33  108.32  3.000
 FSJ  H11  C33  C43  106.99  3.000
 FSJ  N33  C33  C43  113.91  3.000
 FSJ  H11  C33  C23  107.71  3.000
 FSJ  C43  C33  C23  109.87  3.000
 FSJ  N33  C33  C23  109.82  3.000
 FSJ  H12  C41  C51  118.44  3.000
 FSJ  H12  C41  C31  119.53  3.000
 FSJ  C51  C41  C31  122.01  3.000
 FSJ  H13  C42  O11  110.35  3.000
 FSJ  H13  C42  C52  109.74  3.000
 FSJ  O11  C42  C52  109.08  3.000
 FSJ  H13  C42  C32  108.09  3.000
 FSJ  O11  C42  C32  109.09  3.000
 FSJ  C52  C42  C32  110.48  3.000
 FSJ  O43  C43  C83  110.63  3.000
 FSJ  O43  C43  C53  110.19  3.000
 FSJ  C83  C43  C53  108.73  3.000
 FSJ  C53  C43  C33  109.36  3.000
 FSJ  O43  C43  C33  105.88  3.000
 FSJ  C83  C43  C33  112.02  3.000
 FSJ  O51  C51  C61  112.73  3.000
 FSJ  C61  C51  C41  123.62  3.000
 FSJ  O51  C51  C41  123.62  3.000
 FSJ  H14  C52  O52  110.66  3.000
 FSJ  H14  C52  C62  108.04  3.000
 FSJ  O52  C52  C62  111.29  3.000
 FSJ  H14  C52  C42  107.81  3.000
 FSJ  O52  C52  C42  108.01  3.000
 FSJ  C62  C52  C42  110.99  3.000
 FSJ  H16  C53  H15  106.97  3.000
 FSJ  H16  C53  O53  106.24  3.000
 FSJ  H15  C53  O53  111.03  3.000
 FSJ  H16  C53  C43  109.88  3.000
 FSJ  H15  C53  C43  109.65  3.000
 FSJ  O53  C53  C43  112.84  3.000
 FSJ  H18  C61  H17  108.99  3.000
 FSJ  H18  C61  F61  108.68  3.000
 FSJ  H17  C61  F61  107.55  3.000
 FSJ  H18  C61  C51  110.15  3.000
 FSJ  H17  C61  C51  111.16  3.000
 FSJ  F61  C61  C51  110.24  3.000
 FSJ  H19  C62  O62  110.28  3.000
 FSJ  H19  C62  C52  108.55  3.000
 FSJ  O62  C62  C52  109.37  3.000
 FSJ  H19  C62  C12  108.76  3.000
 FSJ  C52  C62  C12  111.76  3.000
 FSJ  O62  C62  C12  108.12  3.000
 FSJ  H22  C83  H21  107.36  3.000
 FSJ  H22  C83  H20  108.02  3.000
 FSJ  H21  C83  H20  107.67  3.000
 FSJ  H22  C83  C43  111.59  3.000
 FSJ  H21  C83  C43  110.72  3.000
 FSJ  H20  C83  C43  111.29  3.000
 FSJ  H27  N12  H26  105.82  3.000
 FSJ  H27  N12  C12  109.76  3.000
 FSJ  H26  N12  C12  109.93  3.000
 FSJ  H30  N21  H29  105.36  3.000
 FSJ  H30  N21  C21  110.31  3.000
 FSJ  H29  N21  C21  108.63  3.000
 FSJ  H35  N33  C93  110.98  3.000
 FSJ  H35  N33  C33  110.59  3.000
 FSJ  C93  N33  C33  116.46  3.000
 FSJ  C42  O11  C11  117.06  3.000
 FSJ  H37  O23  C23  110.72  3.000
 FSJ  H38  O43  C43  108.64  3.000
 FSJ  C51  O51  C11  115.52  3.000
 FSJ  H39  O52  C52  108.80  3.000
 FSJ  C53  O53  C13  114.06  3.000
 FSJ  C62  O62  C13  119.62  3.000
 FSJ  H33  N32  H32  105.77  3.000
 FSJ  H33  N32  C32  109.77  3.000
 FSJ  H32  N32  C32  109.04  3.000
 FSJ  H25  C93  H24  107.08  3.000
 FSJ  H25  C93  H23  107.27  3.000
 FSJ  H24  C93  H23  107.30  3.000
 FSJ  H25  C93  N33  109.26  3.000
 FSJ  H24  C93  N33  109.94  3.000
 FSJ  H23  C93  N33  115.64  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
 FSJ  Var_01  C41  C51  O51  C11  -15.07  30.0  1
 FSJ  Var_02  C43  C53  O53  C13   58.64  30.0  1
 FSJ  Var_03  C51  C41  C31  C21  -15.16  30.0  1
 FSJ  Var_04  O51  C51  C41  C31   -2.28  30.0  1
 FSJ  Var_05  F61  C61  C51  C41  116.08  30.0  3
 FSJ  Var_06  H23  C93  N33  C33  -60.34  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
 FSJ  chir_01  C11  O11  C21  O51  positiv
 FSJ  chir_02  C12  N12  C62  C22  negativ
 FSJ  chir_03  C13  O62  O53  C23  negativ
 FSJ  chir_04  C21  N21  C31  C11  positiv
 FSJ  chir_05  C23  O23  C33  C13  positiv
 FSJ  chir_06  C32  C22  C42  N32  negativ
 FSJ  chir_07  C33  N33  C23  C43  positiv
 FSJ  chir_08  C42  O11  C52  C32  negativ
 FSJ  chir_09  C43  C33  O43  C53  negativ
 FSJ  chir_10  C52  O52  C62  C42  positiv
 FSJ  chir_11  C62  O62  C12  C52  negativ

