# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Apr 18 08:42:10 2020
#   Inital geometry file: a 106 line input string
#   Ligand name: (2~{S})-3-[2-[(2~{R})-2-azanyl-3-oxidanyl-3-oxidanylidene-propyl]sulfinyl-1~{H}-imidazol-4-yl]-2-(trimethyl-$l^{4}-azanyl)propanoic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[N](C)(C)[C@@H](Cc1c[nH]c(n1)[S@](=O)C[C@H](N)C(O)=O)C(O)=O
#
data_comp_list
loop_
_chem_comp.id
_chem_comp.three_letter_code
_chem_comp.name
_chem_comp.group
_chem_comp.number_atoms_all
_chem_comp.number_atoms_nh
_chem_comp.desc_level
_chem_comp.initial_date
_chem_comp.modified_date
_chem_comp.source
 8VV  8VV  '(2~{S})-3-[2-[(2~{R})-2-azanyl-3-oxidanyl-3-oxidanylidene-propyl]sulfinyl-1~{H}-imidazol-4-yl]-2-(trimethyl-$l^{4}-azanyl)propanoic acid'  ligand  41  22  .  2022-07-24  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_8VV
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
 8VV  C1   C  CH1    0  -0.235  1.0907   -7.6388  50.5118
 8VV  C2   C  CH2    0  -0.580  1.0170   -8.8332  49.5641
 8VV  C3   C  C      0   0.397  1.5461   -8.1235  51.9110
 8VV  C9   C  CR5    0   0.209  2.3516  -10.5291  47.9370
 8VV  C12  C  CR5    0   0.133  2.1592  -11.0229  45.8777
 8VV  C13  C  CR15   0  -0.096  2.1241  -12.2042  46.5724
 8VV  C14  C  CH2    0  -0.577  2.0568  -10.8213  44.3996
 8VV  C15  C  CH1    0  -0.189  3.1707  -11.4520  43.5563
 8VV  C16  C  C      0   0.413  2.6566  -11.7561  42.1116
 8VV  O4   O  O      0  -0.602  0.6645   -8.5588  52.6725
 8VV  O5   O  OC    -1  -0.600  2.7741   -8.0713  52.1254
 8VV  N6   N  NH2    0  -0.793  1.9290   -6.6101  49.9149
 8VV  S7   S  S3     0   0.753  2.6313   -9.6846  49.4777
 8VV  O8   O  O      0  -0.768  2.6257  -10.7943  50.5012
 8VV  N10  N  NR15   0  -0.564  2.2557  -11.8660  47.8859
 8VV  N11  N  N      0  -0.433  2.3063   -9.9823  46.7525
 8VV  O17  O  OC    -1  -0.574  2.9029  -12.8916  41.6785
 8VV  O18  O  O      0  -0.571  2.0294  -10.8399  41.5541
 8VV  N19  N  NT     1  -0.392  4.4609  -10.6319  43.5070
 8VV  H1   H  HCH1   0   0.250  0.0707   -7.2515  50.5821
 8VV  H2   H  HCH2   0   0.290  0.7801   -8.4944  48.5546
 8VV  H3   H  HCH2   0   0.297  0.2948   -9.5896  49.8773
 8VV  H4   H  HCR5   0   0.296  2.0172  -13.2267  46.2512
 8VV  H5   H  HCH2   0   0.274  1.9322   -9.7600  44.1825
 8VV  H6   H  HCH2   0   0.292  1.1313  -11.2882  44.0566
 8VV  H7   H  HCH1   0   0.290  3.4826  -12.3890  44.0203
 8VV  H8   H  HCH3   0   0.284  3.5236   -8.7397  43.3011
 8VV  H9   H  HCH3   0   0.282  5.2452   -8.7809  42.9040
 8VV  H10  H  HCH3   0   0.294  4.0614   -9.4687  41.7745
 8VV  H11  H  HCH3   0   0.291  5.6746  -12.3539  43.3155
 8VV  H12  H  HCH3   0   0.297  5.1893  -11.6224  41.7715
 8VV  H13  H  HCH3   0   0.285  6.4239  -10.8383  42.7728
 8VV  H15  H  HCH3   0   0.295  4.3139   -9.6603  45.3885
 8VV  H16  H  HCH3   0   0.289  5.0075  -11.2973  45.4442
 8VV  H17  H  HCH3   0   0.296  5.9639   -9.9406  44.8099
 8VV  H18  H  HNH2   0   0.347  1.7084   -5.7214  50.3467
 8VV  H19  H  HNH2   0   0.335  2.8878   -6.7977  50.1883
 8VV  H22  H  HNR5   0   0.426  2.2587  -12.4922  48.6775
 8VV  C20  C  CH3    0  -0.542  4.3046   -9.3191  42.8191
 8VV  C22  C  CH3    0  -0.547  5.5056  -11.4188  42.7885
 8VV  C23  C  CH3    0  -0.553  4.9662  -10.3662  44.8853

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
 8VV  C22  N19  single    1.492  0.020  1.492
 8VV  O18  C16  deloc     1.242  0.020  1.242
 8VV  O17  C16  deloc     1.240  0.020  1.240
 8VV  C16  C15  single    1.563  0.020  1.563
 8VV  C20  N19  single    1.490  0.020  1.490
 8VV  N19  C15  single    1.530  0.020  1.530
 8VV  N19  C23  single    1.492  0.020  1.492
 8VV  C15  C14  single    1.533  0.020  1.533
 8VV  C14  C12  single    1.495  0.020  1.495
 8VV  C12  C13  aromatic  1.371  0.020  1.371
 8VV  C12  N11  aromatic  1.367  0.020  1.367
 8VV  C13  N10  aromatic  1.363  0.020  1.363
 8VV  N11  C9   aromatic  1.305  0.020  1.305
 8VV  N10  C9   aromatic  1.341  0.020  1.341
 8VV  C9   S7   single    1.779  0.020  1.779
 8VV  S7   C2   single    1.827  0.020  1.827
 8VV  S7   O8   double    1.510  0.020  1.510
 8VV  C2   C1   single    1.526  0.020  1.526
 8VV  N6   C1   single    1.455  0.020  1.455
 8VV  C1   C3   single    1.549  0.020  1.549
 8VV  C3   O4   deloc     1.244  0.020  1.244
 8VV  C3   O5   deloc     1.248  0.020  1.248
 8VV  C1   H1   single    0.970  0.020  1.090
 8VV  C2   H2   single    0.970  0.020  1.090
 8VV  C2   H3   single    0.970  0.020  1.090
 8VV  C13  H4   single    0.930  0.020  1.080
 8VV  C14  H5   single    0.970  0.020  1.090
 8VV  C14  H6   single    0.970  0.020  1.090
 8VV  C15  H7   single    0.970  0.020  1.090
 8VV  C20  H8   single    0.970  0.020  1.090
 8VV  C20  H9   single    0.970  0.020  1.090
 8VV  C20  H10  single    0.970  0.020  1.090
 8VV  C22  H11  single    0.970  0.020  1.090
 8VV  C22  H12  single    0.970  0.020  1.090
 8VV  C22  H13  single    0.970  0.020  1.090
 8VV  C23  H15  single    0.970  0.020  1.090
 8VV  C23  H16  single    0.970  0.020  1.090
 8VV  C23  H17  single    0.970  0.020  1.090
 8VV  N6   H18  single    0.890  0.020  1.040
 8VV  N6   H19  single    0.890  0.020  1.040
 8VV  N10  H22  single    0.860  0.020  1.020

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
 8VV  H1   C1   N6   108.26  3.000
 8VV  H1   C1   C3   109.09  3.000
 8VV  N6   C1   C3   114.98  3.000
 8VV  H1   C1   C2   105.79  3.000
 8VV  C3   C1   C2   109.28  3.000
 8VV  N6   C1   C2   109.04  3.000
 8VV  H3   C2   H2   109.69  3.000
 8VV  H3   C2   S7   105.97  3.000
 8VV  H2   C2   S7   107.02  3.000
 8VV  H3   C2   C1   113.33  3.000
 8VV  H2   C2   C1   110.00  3.000
 8VV  S7   C2   C1   110.57  3.000
 8VV  O5   C3   O4   127.39  3.000
 8VV  O5   C3   C1   115.55  3.000
 8VV  O4   C3   C1   117.01  3.000
 8VV  N11  C9   N10  112.36  3.000
 8VV  N10  C9   S7   121.16  3.000
 8VV  N11  C9   S7   126.33  3.000
 8VV  N11  C12  C14  122.49  3.000
 8VV  N11  C12  C13  109.53  3.000
 8VV  C14  C12  C13  127.97  3.000
 8VV  H4   C13  N10  122.18  3.000
 8VV  H4   C13  C12  132.03  3.000
 8VV  N10  C13  C12  105.79  3.000
 8VV  H6   C14  H5   104.88  3.000
 8VV  H6   C14  C15  105.50  3.000
 8VV  H5   C14  C15  111.96  3.000
 8VV  H6   C14  C12  108.12  3.000
 8VV  H5   C14  C12  109.62  3.000
 8VV  C15  C14  C12  116.01  3.000
 8VV  H7   C15  N19  103.47  3.000
 8VV  H7   C15  C16  108.66  3.000
 8VV  N19  C15  C16  110.60  3.000
 8VV  H7   C15  C14  109.09  3.000
 8VV  N19  C15  C14  114.21  3.000
 8VV  C16  C15  C14  110.46  3.000
 8VV  O18  C16  O17  128.23  3.000
 8VV  O17  C16  C15  115.82  3.000
 8VV  O18  C16  C15  115.93  3.000
 8VV  H19  N6   H18  104.67  3.000
 8VV  H19  N6   C1   107.65  3.000
 8VV  H18  N6   C1   108.67  3.000
 8VV  O8   S7   C9   103.75  3.000
 8VV  O8   S7   C2   107.89  3.000
 8VV  C9   S7   C2    97.08  3.000
 8VV  H22  N10  C13  127.03  3.000
 8VV  H22  N10  C9   126.04  3.000
 8VV  C13  N10  C9   106.92  3.000
 8VV  C12  N11  C9   105.39  3.000
 8VV  C23  N19  C22  107.56  3.000
 8VV  C23  N19  C20  107.76  3.000
 8VV  C22  N19  C20  108.40  3.000
 8VV  C23  N19  C15  110.57  3.000
 8VV  C20  N19  C15  113.49  3.000
 8VV  C22  N19  C15  108.86  3.000
 8VV  H10  C20  H9   109.76  3.000
 8VV  H10  C20  H8   109.91  3.000
 8VV  H9   C20  H8   108.88  3.000
 8VV  H10  C20  N19  110.31  3.000
 8VV  H9   C20  N19  108.02  3.000
 8VV  H8   C20  N19  109.92  3.000
 8VV  H13  C22  H12  109.47  3.000
 8VV  H13  C22  H11  109.59  3.000
 8VV  H12  C22  H11  109.80  3.000
 8VV  H13  C22  N19  108.48  3.000
 8VV  H12  C22  N19  110.27  3.000
 8VV  H11  C22  N19  109.22  3.000
 8VV  H17  C23  H16  109.65  3.000
 8VV  H17  C23  H15  109.22  3.000
 8VV  H16  C23  H15  109.98  3.000
 8VV  H17  C23  N19  108.45  3.000
 8VV  H16  C23  N19  109.60  3.000
 8VV  H15  C23  N19  109.92  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
 8VV  CONST_01  C13  C12  N11  C9      0.00   0.0  0
 8VV  CONST_02  C12  C13  N10  C9      0.00   0.0  0
 8VV  CONST_03  N10  C9   N11  C12     0.00   0.0  0
 8VV  CONST_04  N11  C9   N10  C13     0.00   0.0  0
 8VV  CONST_05  N11  C12  C13  N10     0.00   0.0  0
 8VV  CONST_06  C14  C12  N11  C9    180.00   0.0  0
 8VV  CONST_07  S7   C9   N11  C12   180.00   0.0  0
 8VV  CONST_08  S7   C9   N10  C13   180.00   0.0  0
 8VV  CONST_09  N10  C13  C12  C14   180.00   0.0  0
 8VV  CONST_10  H4   C13  N10  C9    180.00   0.0  0
 8VV  CONST_11  H22  N10  C13  C12   180.00   0.0  0
 8VV  Var_01    N11  C9   S7   C2     71.32  30.0  2
 8VV  Var_02    C15  C14  C12  C13   -62.51  30.0  2
 8VV  Var_03    C9   S7   C2   C1   -160.05  30.0  1
 8VV  Var_04    H11  C22  N19  C15   -59.60  30.0  3
 8VV  Var_05    H8   C20  N19  C15    56.90  30.0  3
 8VV  Var_06    H15  C23  N19  C15   -70.56  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
 8VV  chir_01  C1   C2   N6   C3   positiv
 8VV  chir_02  C15  C16  N19  C14  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
 8VV  plan-1  C9   0.020
 8VV  plan-1  C12  0.020
 8VV  plan-1  C13  0.020
 8VV  plan-1  C14  0.020
 8VV  plan-1  S7   0.020
 8VV  plan-1  N10  0.020
 8VV  plan-1  N11  0.020
 8VV  plan-1  H4   0.020
 8VV  plan-1  H22  0.020
 8VV  plan-2  C1   0.020
 8VV  plan-2  C3   0.020
 8VV  plan-2  O4   0.020
 8VV  plan-2  O5   0.020
 8VV  plan-3  C15  0.020
 8VV  plan-3  C16  0.020
 8VV  plan-3  O17  0.020
 8VV  plan-3  O18  0.020
 8VV  plan-4  C2   0.020
 8VV  plan-4  C9   0.020
 8VV  plan-4  S7   0.020
 8VV  plan-4  O8   0.020

