# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Jul 20 23:00:21 2021
#   Inital geometry file: a 97 line input string
#   Ligand name: (1S,2S,3S,4R,5R)-2-[(cyclopropylmethyl)amino]-4-(phenylsulfanyl)-6,8-dioxabicyclo[3.2.1]octan-3-ol (non-preferred name)
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: O[C@H]1[C@H](NCC2CC2)[C@H]3CO[C@H](O3)[C@@H]1Sc4ccccc4
#
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
 DDV  DDV  '(1S,2S,3S,4R,5R)-2-[(cyclopropylmethyl)amino]-4-(phenylsulfanyl)-6,8-dioxabicyclo[3.2.1]octan-3-ol (non-preferred name)'  ligand  42  21  .  2022-07-24  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_DDV
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
 DDV  C4   C  CR16  0  -0.268  -3.3033   9.8430   6.4822
 DDV  C5   C  CR16  0  -0.241  -2.5368  10.9371   6.8487
 DDV  C6   C  CH1   0  -0.490  -3.2387   5.7632   7.0203
 DDV  C7   C  CH1   0   0.099  -3.9693   4.5589   6.4294
 DDV  C8   C  CH1   0  -0.122  -3.7543   3.3217   7.3096
 DDV  C9   C  CR15  0  -0.105  -4.0122   3.6879   8.7919
 DDV  C10  C  CH2   0  -0.166  -2.7244   3.9047   9.5748
 DDV  C11  C  CR15  0   0.291  -3.4806   5.8010   8.5510
 DDV  C13  C  CH1   0  -0.262  -5.0204  -0.1167   6.5024
 DDV  C14  C  CH2   0  -0.493  -5.2792  -1.4369   7.1558
 DDV  C15  C  CH2   0  -0.490  -6.3900  -0.4387   7.0239
 DDV  O2   O  OH1   0  -0.665  -3.5178   4.3239   5.1240
 DDV  N    N  NH1   0  -0.617  -4.5553   2.2516   6.7563
 DDV  O1   O  O     0  -0.478  -4.5753   4.9978   8.8711
 DDV  O    O  O     0  -0.503  -2.3805   5.2426   9.2330
 DDV  S    S  S2    0   0.065  -3.8919   7.2345   6.1865
 DDV  C3   C  CR6   0  -0.100  -2.8511   8.5469   6.7407
 DDV  C2   C  CR16  0  -0.259  -1.6252   8.3687   7.3779
 DDV  C1   C  CR16  0  -0.236  -0.8695   9.4736   7.7513
 DDV  C    C  CR16  0  -0.270  -1.3151  10.7599   7.4875
 DDV  H1   H  HCR6  0   0.265  -4.2584   9.9983   5.9948
 DDV  H2   H  HCR6  0   0.262  -2.9027  11.9339   6.6396
 DDV  H3   H  HCH1  0   0.308  -2.1713   5.6685   6.8056
 DDV  H4   H  HCH1  0   0.222  -5.0488   4.7750   6.4268
 DDV  H5   H  HCH1  0   0.255  -2.7071   3.0169   7.1956
 DDV  H6   H  HCR5  0   0.276  -4.6947   2.9861   9.2736
 DDV  H7   H  HCH2  0   0.237  -2.8876   3.8153  10.6527
 DDV  H8   H  HCH2  0   0.238  -1.9238   3.2214   9.2869
 DDV  H9   H  HCR5  0   0.264  -3.6638   6.8158   8.9122
 DDV  H10  H  HCH2  0   0.201  -4.2977   0.7880   8.2955
 DDV  H11  H  HCH2  0   0.236  -3.1305   0.7665   6.9810
 DDV  H12  H  HCH1  0   0.254  -4.9026  -0.1294   5.4235
 DDV  H13  H  HCH2  0   0.244  -4.8668  -1.6068   8.1433
 DDV  H14  H  HCH2  0   0.251  -5.3039  -2.3190   6.5290
 DDV  H15  H  HCH2  0   0.243  -6.7165   0.0687   7.9243
 DDV  H16  H  HCH2  0   0.250  -7.1820  -0.6352   6.3126
 DDV  H17  H  HOH1  0   0.445  -3.8684   3.4549   4.8838
 DDV  H18  H  HNH1  0   0.351  -5.5393   2.4144   6.9453
 DDV  H20  H  HCR6  0   0.262  -1.2380   7.3819   7.5906
 DDV  H21  H  HCR6  0   0.262   0.0780   9.3173   8.2507
 DDV  H22  H  HCR6  0   0.258  -0.7201  11.6159   7.7769
 DDV  C12  C  CH2   0  -0.273  -4.1901   0.9187   7.2066

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
 DDV  O2   C7   single    1.401  0.020  1.401
 DDV  S    C3   single    1.764  0.020  1.764
 DDV  S    C6   single    1.813  0.020  1.813
 DDV  C7   C6   single    1.527  0.020  1.527
 DDV  C7   C8   single    1.534  0.020  1.534
 DDV  C15  C13  single    1.500  0.020  1.500
 DDV  C15  C14  single    1.499  0.020  1.499
 DDV  C3   C4   aromatic  1.397  0.020  1.397
 DDV  C3   C2   aromatic  1.393  0.020  1.393
 DDV  C4   C5   aromatic  1.385  0.020  1.385
 DDV  C13  C14  single    1.496  0.020  1.496
 DDV  C13  C12  single    1.503  0.020  1.503
 DDV  C6   C11  single    1.550  0.020  1.550
 DDV  C2   C1   aromatic  1.390  0.020  1.390
 DDV  N    C8   single    1.447  0.020  1.447
 DDV  N    C12  single    1.454  0.020  1.454
 DDV  C5   C    aromatic  1.390  0.020  1.390
 DDV  C8   C9   single    1.548  0.020  1.548
 DDV  C1   C    aromatic  1.387  0.020  1.387
 DDV  C11  O1   single    1.395  0.020  1.395
 DDV  C11  O    single    1.410  0.020  1.410
 DDV  C9   O1   single    1.428  0.020  1.428
 DDV  C9   C10  single    1.523  0.020  1.523
 DDV  O    C10  single    1.423  0.020  1.423
 DDV  C4   H1   single    0.930  0.020  1.080
 DDV  C5   H2   single    0.930  0.020  1.080
 DDV  C6   H3   single    0.970  0.020  1.090
 DDV  C7   H4   single    0.970  0.020  1.090
 DDV  C8   H5   single    0.970  0.020  1.090
 DDV  C9   H6   single    0.970  0.020  1.090
 DDV  C10  H7   single    0.970  0.020  1.090
 DDV  C10  H8   single    0.970  0.020  1.090
 DDV  C11  H9   single    0.970  0.020  1.090
 DDV  C12  H10  single    0.970  0.020  1.090
 DDV  C12  H11  single    0.970  0.020  1.090
 DDV  C13  H12  single    0.970  0.020  1.090
 DDV  C14  H13  single    0.970  0.020  1.090
 DDV  C14  H14  single    0.970  0.020  1.090
 DDV  C15  H15  single    0.970  0.020  1.090
 DDV  C15  H16  single    0.970  0.020  1.090
 DDV  O2   H17  single    0.850  0.020  0.980
 DDV  N    H18  single    0.890  0.020  1.040
 DDV  C2   H20  single    0.930  0.020  1.080
 DDV  C1   H21  single    0.930  0.020  1.080
 DDV  C    H22  single    0.930  0.020  1.080

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
 DDV  H1   C4   C3   120.11  3.000
 DDV  H1   C4   C5   119.57  3.000
 DDV  C3   C4   C5   120.32  3.000
 DDV  H2   C5   C    120.22  3.000
 DDV  H2   C5   C4   119.30  3.000
 DDV  C    C5   C4   120.48  3.000
 DDV  H3   C6   S    109.38  3.000
 DDV  H3   C6   C11  110.40  3.000
 DDV  S    C6   C11  112.22  3.000
 DDV  H3   C6   C7   108.83  3.000
 DDV  C11  C6   C7   109.06  3.000
 DDV  S    C6   C7   106.84  3.000
 DDV  H4   C7   O2   110.28  3.000
 DDV  H4   C7   C8   107.29  3.000
 DDV  O2   C7   C8   110.75  3.000
 DDV  H4   C7   C6   108.37  3.000
 DDV  C8   C7   C6   110.31  3.000
 DDV  O2   C7   C6   109.79  3.000
 DDV  H5   C8   N    106.46  3.000
 DDV  H5   C8   C9   108.93  3.000
 DDV  N    C8   C9   116.67  3.000
 DDV  H5   C8   C7   107.36  3.000
 DDV  C9   C8   C7   109.59  3.000
 DDV  N    C8   C7   107.43  3.000
 DDV  H6   C9   O1   108.60  3.000
 DDV  H6   C9   C10  113.18  3.000
 DDV  O1   C9   C10  100.04  3.000
 DDV  H6   C9   C8   112.01  3.000
 DDV  C10  C9   C8   112.64  3.000
 DDV  O1   C9   C8   109.62  3.000
 DDV  H8   C10  H7   108.56  3.000
 DDV  H8   C10  O    110.37  3.000
 DDV  H7   C10  O    110.46  3.000
 DDV  H8   C10  C9   113.31  3.000
 DDV  H7   C10  C9   111.65  3.000
 DDV  O    C10  C9   102.40  3.000
 DDV  H9   C11  O    109.81  3.000
 DDV  H9   C11  O1   109.10  3.000
 DDV  O    C11  O1   105.86  3.000
 DDV  H9   C11  C6   112.04  3.000
 DDV  O    C11  C6   110.26  3.000
 DDV  O1   C11  C6   109.57  3.000
 DDV  H12  C13  C15  116.24  3.000
 DDV  H12  C13  C14  116.28  3.000
 DDV  C15  C13  C14   60.05  3.000
 DDV  H12  C13  C12  114.45  3.000
 DDV  C14  C13  C12  119.94  3.000
 DDV  C15  C13  C12  119.30  3.000
 DDV  H14  C14  H13  114.12  3.000
 DDV  H14  C14  C15  118.34  3.000
 DDV  H13  C14  C15  117.81  3.000
 DDV  H14  C14  C13  118.05  3.000
 DDV  H13  C14  C13  118.08  3.000
 DDV  C15  C14  C13   60.13  3.000
 DDV  H16  C15  H15  114.23  3.000
 DDV  H16  C15  C14  118.62  3.000
 DDV  H15  C15  C14  117.50  3.000
 DDV  H16  C15  C13  118.58  3.000
 DDV  H15  C15  C13  117.60  3.000
 DDV  C14  C15  C13   59.81  3.000
 DDV  H17  O2   C7   105.38  3.000
 DDV  H18  N    C12  109.45  3.000
 DDV  H18  N    C8   110.30  3.000
 DDV  C12  N    C8   114.88  3.000
 DDV  C11  O1   C9   101.89  3.000
 DDV  C11  O    C10  107.46  3.000
 DDV  C3   S    C6   104.28  3.000
 DDV  C2   C3   S    124.59  3.000
 DDV  C2   C3   C4   119.22  3.000
 DDV  S    C3   C4   116.17  3.000
 DDV  H20  C2   C1   118.56  3.000
 DDV  H20  C2   C3   121.46  3.000
 DDV  C1   C2   C3   119.98  3.000
 DDV  H21  C1   C    120.20  3.000
 DDV  H21  C1   C2   119.03  3.000
 DDV  C    C1   C2   120.78  3.000
 DDV  H22  C    C1   120.42  3.000
 DDV  H22  C    C5   120.36  3.000
 DDV  C1   C    C5   119.22  3.000
 DDV  H11  C12  H10  106.37  3.000
 DDV  H11  C12  N    107.88  3.000
 DDV  H10  C12  N    112.97  3.000
 DDV  H11  C12  C13  110.05  3.000
 DDV  H10  C12  C13  109.12  3.000
 DDV  N    C12  C13  110.36  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
 DDV  CONST_01  C1   C2   C3   C4      0.00   0.0  0
 DDV  CONST_02  C1   C    C5   C4      0.00   0.0  0
 DDV  CONST_03  C2   C3   C4   C5      0.00   0.0  0
 DDV  CONST_04  C2   C1   C    C5      0.00   0.0  0
 DDV  CONST_05  C    C5   C4   C3      0.00   0.0  0
 DDV  CONST_06  C    C1   C2   C3      0.00   0.0  0
 DDV  CONST_07  S    C3   C4   C5    180.00   0.0  0
 DDV  CONST_08  C1   C2   C3   S     180.00   0.0  0
 DDV  CONST_09  H20  C2   C3   C4    180.00   0.0  0
 DDV  CONST_10  H22  C    C5   C4    180.00   0.0  0
 DDV  CONST_11  H21  C1   C    C5    180.00   0.0  0
 DDV  CONST_12  H2   C5   C4   C3    180.00   0.0  0
 DDV  CONST_13  H1   C4   C3   C2    180.00   0.0  0
 DDV  Var_01    C2   C3   S    C6     14.81  30.0  2
 DDV  Var_02    C14  C15  C13  C12  -109.71  30.0  1
 DDV  Var_03    H7   C10  O    C11  -108.79  30.0  3
 DDV  Var_04    H13  C14  C15  C13   108.11  30.0  1
 DDV  Var_05    C13  C12  N    C8   -176.18  30.0  3
 DDV  Var_06    N    C12  C13  C14  -153.60  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
 DDV  chir_01  C6   S    C7   C11  positiv
 DDV  chir_02  C7   O2   C6   C8   positiv
 DDV  chir_03  C8   N    C9   C7   positiv
 DDV  chir_04  C9   O1   C8   C10  negativ
 DDV  chir_05  C11  O    O1   C6   positiv
 DDV  chir_06  C13  C15  C14  C12  both

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
 DDV  plan-1  C4   0.020
 DDV  plan-1  C5   0.020
 DDV  plan-1  S    0.020
 DDV  plan-1  C3   0.020
 DDV  plan-1  C2   0.020
 DDV  plan-1  C1   0.020
 DDV  plan-1  C    0.020
 DDV  plan-1  H1   0.020
 DDV  plan-1  H2   0.020
 DDV  plan-1  H20  0.020
 DDV  plan-1  H21  0.020
 DDV  plan-1  H22  0.020

