# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed Apr  1 17:06:58 2020
#   Inital geometry file: a 98 line input string
#   Ligand name: (3R,6R,7S)-7-[(2R,3aR)-hexahydropyrazolo[1,5-c][1,3]thiazin-2-yl]-6-(hydroxymethyl)-1,4-thiazepane-3-carboxylic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC[C@H]1CN[C@@H](CS[C@@H]1[C@H]2C[C@@H]3CCSCN3N2)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
 33V  33V  '(3R,6R,7S)-7-[(2R,3aR)-hexahydropyrazolo[1,5-c][1,3]thiazin-2-yl]-6-(hydroxymethyl)-1,4-thiazepane-3-carboxylic acid'  ligand  43  21  .  2022-07-22  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_33V
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
 33V  S1   S  S2     0  -0.005  -0.6627  -0.9249  -0.8371
 33V  C2   C  CH2    0  -0.606  -1.7959  -1.0215   0.5790
 33V  C3   C  CH1    0  -0.157  -3.2814  -0.7865   0.2663
 33V  N4   N  NH1    0  -0.592  -3.6730   0.5680  -0.0367
 33V  C5   C  CH2    0  -0.295  -2.8734   1.3142  -0.9795
 33V  C6   C  CH1    0  -0.259  -1.4567   1.7432  -0.5177
 33V  C7   C  CH2    0  -0.147  -1.2130   3.2156  -0.8471
 33V  O8   O  OH1    0  -0.672  -2.1848   3.9933  -0.1823
 33V  C31  C  C      0   0.397  -4.0893  -1.3109   1.4830
 33V  O32  O  O      0  -0.599  -4.5235  -0.4627   2.2864
 33V  O33  O  OC    -1  -0.613  -4.1935  -2.5492   1.5756
 33V  C61  C  CH1    0  -0.382  -0.3717   0.8596  -1.1415
 33V  C62  C  CH1    0  -0.055   1.0656   1.2246  -0.7621
 33V  N63  N  NH1    0  -0.480   2.0079   0.3765  -1.5104
 33V  N64  N  NT     0  -0.322   3.1266   0.1817  -0.6194
 33V  C65  C  CH1    0  -0.035   2.4855  -0.0770   0.6631
 33V  C66  C  CH2    0  -0.484   1.4279   1.0129   0.7163
 33V  C67  C  CH2    0  -0.409   3.9041  -0.9521  -1.0580
 33V  S68  S  S2     0  -0.029   5.3566  -1.1343   0.0095
 33V  C69  C  CH2    0  -0.573   4.4918  -1.2371   1.6052
 33V  C70  C  CH2    0  -0.414   3.5039  -0.0924   1.7853
 33V  H2   H  HCH2   0   0.276  -1.6715  -2.0534   0.9150
 33V  H1   H  HCH2   0   0.261  -1.4495  -0.3869   1.3976
 33V  H3   H  HCH1   0   0.207  -3.5194  -1.4221  -0.5947
 33V  H41  H  HNH1   0   0.329  -3.7770   1.0775   0.8314
 33V  H7   H  HCH2   0   0.219  -2.7949   0.7365  -1.9058
 33V  H6   H  HCH2   0   0.235  -3.4410   2.2100  -1.2386
 33V  H8   H  HCH1   0   0.239  -1.4067   1.6503   0.5733
 33V  H9   H  HCH2   0   0.208  -0.2096   3.5179  -0.5292
 33V  H72  H  HCH2   0   0.194  -1.2598   3.3521  -1.9374
 33V  H81  H  HOH1   0   0.455  -2.0450   4.9131  -0.4239
 33V  H13  H  HCH1   0   0.268  -0.4542   0.9625  -2.2300
 33V  H14  H  HCH1   0   0.247   1.2287   2.2728  -1.0301
 33V  H15  H  HNH1   0   0.358   2.3695   0.9131  -2.2918
 33V  H16  H  HCH1   0   0.211   1.9712  -1.0527   0.6351
 33V  H17  H  HCH2   0   0.242   1.8332   1.9298   1.1488
 33V  H18  H  HCH2   0   0.247   0.5747   0.7117   1.3242
 33V  H20  H  HCH2   0   0.237   3.3202  -1.8834  -1.0648
 33V  H19  H  HCH2   0   0.279   4.2900  -0.7815  -2.0646
 33V  H21  H  HCH2   0   0.262   3.9789  -2.1992   1.6720
 33V  H22  H  HCH2   0   0.284   5.2657  -1.2207   2.3727
 33V  H23  H  HCH2   0   0.230   4.0332   0.8630   1.8198
 33V  H24  H  HCH2   0   0.245   2.9868  -0.2169   2.7406

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
 33V  O32  C31  deloc   1.246  0.020  1.246
 33V  C5   N4   single  1.444  0.020  1.444
 33V  C5   C6   single  1.551  0.020  1.551
 33V  N4   C3   single  1.442  0.020  1.442
 33V  C7   C6   single  1.528  0.020  1.528
 33V  C7   O8   single  1.411  0.020  1.411
 33V  C6   C61  single  1.532  0.020  1.532
 33V  C31  C3   single  1.552  0.020  1.552
 33V  C31  O33  deloc   1.246  0.020  1.246
 33V  C3   C2   single  1.536  0.020  1.536
 33V  C67  N64  single  1.443  0.020  1.443
 33V  C67  S68  single  1.812  0.020  1.812
 33V  N63  N64  single  1.443  0.020  1.443
 33V  N63  C62  single  1.472  0.020  1.472
 33V  N64  C65  single  1.457  0.020  1.457
 33V  S68  C69  single  1.818  0.020  1.818
 33V  C61  C62  single  1.531  0.020  1.531
 33V  C61  S1   single  1.834  0.020  1.834
 33V  C62  C66  single  1.537  0.020  1.537
 33V  C2   S1   single  1.816  0.020  1.816
 33V  C65  C66  single  1.520  0.020  1.520
 33V  C65  C70  single  1.516  0.020  1.516
 33V  C69  C70  single  1.523  0.020  1.523
 33V  C2   H2   single  0.970  0.020  1.090
 33V  C2   H1   single  0.970  0.020  1.090
 33V  C3   H3   single  0.970  0.020  1.090
 33V  N4   H41  single  0.890  0.020  1.040
 33V  C5   H7   single  0.970  0.020  1.090
 33V  C5   H6   single  0.970  0.020  1.090
 33V  C6   H8   single  0.970  0.020  1.090
 33V  C7   H9   single  0.970  0.020  1.090
 33V  C7   H72  single  0.970  0.020  1.090
 33V  O8   H81  single  0.850  0.020  0.980
 33V  C61  H13  single  0.970  0.020  1.090
 33V  C62  H14  single  0.970  0.020  1.090
 33V  N63  H15  single  0.890  0.020  1.040
 33V  C65  H16  single  0.970  0.020  1.090
 33V  C66  H17  single  0.970  0.020  1.090
 33V  C66  H18  single  0.970  0.020  1.090
 33V  C67  H20  single  0.970  0.020  1.090
 33V  C67  H19  single  0.970  0.020  1.090
 33V  C69  H21  single  0.970  0.020  1.090
 33V  C69  H22  single  0.970  0.020  1.090
 33V  C70  H23  single  0.970  0.020  1.090
 33V  C70  H24  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
 33V  C61  S1   C2   106.27  3.000
 33V  H1   C2   H2   106.39  3.000
 33V  H1   C2   C3   111.74  3.000
 33V  H2   C2   C3   108.50  3.000
 33V  H1   C2   S1   110.83  3.000
 33V  H2   C2   S1   102.65  3.000
 33V  C3   C2   S1   115.88  3.000
 33V  H3   C3   C31  107.87  3.000
 33V  H3   C3   N4   108.70  3.000
 33V  C31  C3   N4   109.92  3.000
 33V  H3   C3   C2   106.33  3.000
 33V  C31  C3   C2   106.99  3.000
 33V  N4   C3   C2   116.68  3.000
 33V  H41  N4   C5   110.91  3.000
 33V  H41  N4   C3   108.70  3.000
 33V  C5   N4   C3   118.17  3.000
 33V  H6   C5   H7   105.64  3.000
 33V  H6   C5   C6   108.58  3.000
 33V  H7   C5   C6   109.43  3.000
 33V  H6   C5   N4   106.92  3.000
 33V  H7   C5   N4   108.64  3.000
 33V  C6   C5   N4   117.03  3.000
 33V  H8   C6   C61  108.91  3.000
 33V  H8   C6   C7   106.79  3.000
 33V  C61  C6   C7   110.79  3.000
 33V  H8   C6   C5   108.34  3.000
 33V  C61  C6   C5   111.48  3.000
 33V  C7   C6   C5   110.37  3.000
 33V  H72  C7   H9   107.00  3.000
 33V  H72  C7   O8   111.68  3.000
 33V  H9   C7   O8   110.01  3.000
 33V  H72  C7   C6   109.05  3.000
 33V  H9   C7   C6   110.46  3.000
 33V  O8   C7   C6   108.64  3.000
 33V  H81  O8   C7   107.99  3.000
 33V  O33  C31  O32  126.82  3.000
 33V  O33  C31  C3   115.95  3.000
 33V  O32  C31  C3   117.18  3.000
 33V  H13  C61  C62  107.12  3.000
 33V  H13  C61  C6   107.26  3.000
 33V  C62  C61  C6   115.25  3.000
 33V  H13  C61  S1   104.14  3.000
 33V  C62  C61  S1   109.87  3.000
 33V  C6   C61  S1   112.42  3.000
 33V  H14  C62  C66  109.42  3.000
 33V  H14  C62  N63  109.39  3.000
 33V  C66  C62  N63  104.99  3.000
 33V  H14  C62  C61  107.92  3.000
 33V  C66  C62  C61  115.28  3.000
 33V  N63  C62  C61  109.73  3.000
 33V  H15  N63  N64  105.69  3.000
 33V  H15  N63  C62  108.36  3.000
 33V  N64  N63  C62  105.08  3.000
 33V  C67  N64  C65  111.41  3.000
 33V  C65  N64  N63  103.08  3.000
 33V  C67  N64  N63  109.63  3.000
 33V  H16  C65  C70  108.85  3.000
 33V  H16  C65  C66  108.10  3.000
 33V  C70  C65  C66  116.68  3.000
 33V  H16  C65  N64  109.87  3.000
 33V  C70  C65  N64  110.98  3.000
 33V  C66  C65  N64  102.10  3.000
 33V  H18  C66  H17  107.55  3.000
 33V  H18  C66  C65  111.48  3.000
 33V  H17  C66  C65  110.97  3.000
 33V  H18  C66  C62  112.96  3.000
 33V  H17  C66  C62  110.67  3.000
 33V  C65  C66  C62  103.25  3.000
 33V  H19  C67  H20  108.34  3.000
 33V  H19  C67  S68  106.00  3.000
 33V  H20  C67  S68  110.14  3.000
 33V  H19  C67  N64  110.36  3.000
 33V  H20  C67  N64  112.42  3.000
 33V  S68  C67  N64  109.38  3.000
 33V  C69  S68  C67   98.13  3.000
 33V  H22  C69  H21  107.67  3.000
 33V  H22  C69  C70  111.47  3.000
 33V  H21  C69  C70  110.50  3.000
 33V  H22  C69  S68  106.23  3.000
 33V  H21  C69  S68  109.08  3.000
 33V  C70  C69  S68  111.71  3.000
 33V  H24  C70  H23  107.52  3.000
 33V  H24  C70  C69  108.94  3.000
 33V  H23  C70  C69  110.29  3.000
 33V  H24  C70  C65  109.29  3.000
 33V  H23  C70  C65  109.87  3.000
 33V  C69  C70  C65  110.86  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
 33V  Var_01  C67  N64  N63  C62  161.93  30.0  1
 33V  Var_02  S68  C67  N64  N63  176.87  30.0  1
 33V  Var_03  S68  C69  C70  C65   57.80  30.0  1
 33V  Var_04  C70  C69  S68  C67  -51.03  30.0  1

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
 33V  chir_01  C3   N4   C31  C2   positiv
 33V  chir_02  C6   C61  C7   C5   negativ
 33V  chir_03  C61  S1   C62  C6   positiv
 33V  chir_04  C62  N63  C66  C61  positiv
 33V  chir_05  C65  N64  C70  C66  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
 33V  plan-1  C3   0.020
 33V  plan-1  C31  0.020
 33V  plan-1  O32  0.020
 33V  plan-1  O33  0.020

