# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Mon Apr 13 14:30:01 2020
#   Inital geometry file: a 116 line input string
#   Ligand name: trans-4-({[(E)-1-amino-2-sulfanylethenyl](4-carboxybutyl)carbamoyl}oxy)cyclohexanecarboxylic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: N\C(=C/S)N(CCCCC(O)=O)C(=O)O[C@H]1CC[C@@H](CC1)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
 7BB  7BB  'trans-4-({[(E)-1-amino-2-sulfanylethenyl](4-carboxybutyl)carbamoyl}oxy)cyclohexanecarboxylic acid'  peptide  46  24  .  2022-03-10  2022-03-10
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_7BB
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
 7BB  N     N  NH2    0  -0.795  -1.2046  -2.0009   1.3900
 7BB  O8    O  O      0  -0.512  -0.0222   1.2768  -0.9778
 7BB  O9    O  O2     0  -0.491   1.0720  -0.4754  -0.0756
 7BB  CA    C  C      0   0.528  -1.0160  -1.9755   0.0410
 7BB  CB    C  C1     0  -0.542  -0.8915  -3.0478  -0.7610
 7BB  SG    S  S2     0  -0.236  -0.7761  -4.6838  -0.1175
 7BB  O10   O  O      0  -0.613   7.2291   0.7964   1.2114
 7BB  O11   O  OC    -1  -0.609   7.1052   1.6003  -0.8565
 7BB  O12   O  OC    -1  -0.634  -7.2915   2.8819   1.2793
 7BB  N13   N  NT     0  -0.559  -1.0828  -0.6866  -0.5525
 7BB  O13   O  O      0  -0.609  -7.0432   2.1472  -0.8081
 7BB  C48   C  C      0   0.756  -0.0001   0.1359  -0.5661
 7BB  C49   C  CH2    0  -0.295  -2.3874  -0.1796  -0.9682
 7BB  C50   C  CH2    0  -0.425  -3.1401   0.5597   0.1300
 7BB  C51   C  CH2    0  -0.410  -4.5036   1.0480  -0.3438
 7BB  C52   C  CH2    0  -0.427   4.4828   0.2362   1.2737
 7BB  C53   C  CH2    0  -0.453   3.1331  -0.4526   1.0964
 7BB  C54   C  CH1    0   0.072   2.3037   0.2580   0.0418
 7BB  C55   C  CH2    0  -0.462   3.0458   0.3208  -1.2829
 7BB  C56   C  CH2    0  -0.424   4.3950   1.0129  -1.1031
 7BB  C57   C  CH1    0  -0.390   5.2532   0.3301  -0.0420
 7BB  C58   C  C      0   0.433   6.6459   0.9772   0.1225
 7BB  C59   C  CH2    0  -0.582  -5.2654   1.7790   0.7493
 7BB  C60   C  C      0   0.412  -6.6571   2.3121   0.3657
 7BB  HN    H  HNH2   0   0.390  -0.9258  -1.1824   1.9060
 7BB  H2    H  HNH2   0   0.385  -0.9862  -2.8696   1.8549
 7BB  HB    H  H      0   0.270  -0.8131  -2.9067  -1.8295
 7BB  HSG   H  HSH1   0   0.221  -2.0772  -5.0101  -0.0615
 7BB  H49   H  HCH2   0   0.250  -2.2470   0.4685  -1.8338
 7BB  H49A  H  HCH2   0   0.249  -2.9694  -1.0362  -1.3115
 7BB  H50   H  HCH2   0   0.218  -3.2631  -0.1029   0.9912
 7BB  H50A  H  HCH2   0   0.219  -2.5422   1.4101   0.4715
 7BB  H51   H  HCH2   0   0.207  -4.3748   1.7066  -1.2071
 7BB  H51A  H  HCH2   0   0.206  -5.0902   0.1955  -0.6994
 7BB  H52   H  HCH2   0   0.205   4.3256   1.2442   1.6763
 7BB  H52A  H  HCH2   0   0.229   5.0703  -0.3019   2.0172
 7BB  H53   H  HCH2   0   0.219   3.2903  -1.4930   0.7908
 7BB  H53A  H  HCH2   0   0.235   2.5893  -0.4760   2.0445
 7BB  H54   H  HCH1   0   0.224   2.0827   1.2747   0.3838
 7BB  H55   H  HCH2   0   0.217   3.1990  -0.6985  -1.6555
 7BB  H55A  H  HCH2   0   0.238   2.4509   0.8513  -2.0292
 7BB  H56   H  HCH2   0   0.227   4.9213   1.0387  -2.0570
 7BB  H56A  H  HCH2   0   0.205   4.2280   2.0583  -0.8176
 7BB  H57   H  HCH1   0   0.217   5.4359  -0.7012  -0.3839
 7BB  H59   H  HCH2   0   0.217  -5.3758   1.1238   1.6210
 7BB  H59A  H  HCH2   0   0.219  -4.6673   2.6251   1.1088

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
 7BB  N    CA    single  1.458  0.019  1.458
 7BB  N    HN    single  0.890  0.020  1.040
 7BB  O9   C54   single  1.438  0.020  1.438
 7BB  CA   N13   single  1.421  0.020  1.421
 7BB  CB   CA    double  1.521  0.033  1.521
 7BB  SG   CB    single  1.762  0.020  1.762
 7BB  N13  C49   single  1.460  0.020  1.460
 7BB  N13  C48   single  1.360  0.020  1.360
 7BB  O13  C60   deloc   1.247  0.020  1.247
 7BB  C48  O8    double  1.213  0.020  1.213
 7BB  C48  O9    single  1.328  0.020  1.328
 7BB  C50  C49   single  1.523  0.020  1.523
 7BB  C50  C51   single  1.524  0.020  1.524
 7BB  C52  C57   single  1.528  0.020  1.528
 7BB  C53  C52   single  1.526  0.020  1.526
 7BB  C53  C54   single  1.518  0.020  1.518
 7BB  C54  C55   single  1.520  0.020  1.520
 7BB  C55  C56   single  1.527  0.020  1.527
 7BB  C56  C57   single  1.526  0.020  1.526
 7BB  C57  C58   single  1.544  0.020  1.544
 7BB  C58  O10   deloc   1.248  0.020  1.248
 7BB  C58  O11   deloc   1.248  0.020  1.248
 7BB  C59  C51   single  1.520  0.020  1.520
 7BB  C60  O12   deloc   1.250  0.020  1.250
 7BB  C60  C59   single  1.539  0.020  1.539
 7BB  N    H2    single  0.890  0.020  1.040
 7BB  CB   HB    single  0.930  0.020  1.080
 7BB  SG   HSG   single  1.200  0.020  1.300
 7BB  C49  H49   single  0.970  0.020  1.090
 7BB  C49  H49A  single  0.970  0.020  1.090
 7BB  C50  H50   single  0.970  0.020  1.090
 7BB  C50  H50A  single  0.970  0.020  1.090
 7BB  C51  H51   single  0.970  0.020  1.090
 7BB  C51  H51A  single  0.970  0.020  1.090
 7BB  C52  H52   single  0.970  0.020  1.090
 7BB  C52  H52A  single  0.970  0.020  1.090
 7BB  C53  H53   single  0.970  0.020  1.090
 7BB  C53  H53A  single  0.970  0.020  1.090
 7BB  C54  H54   single  0.970  0.020  1.090
 7BB  C55  H55   single  0.970  0.020  1.090
 7BB  C55  H55A  single  0.970  0.020  1.090
 7BB  C56  H56   single  0.970  0.020  1.090
 7BB  C56  H56A  single  0.970  0.020  1.090
 7BB  C57  H57   single  0.970  0.020  1.090
 7BB  C59  H59   single  0.970  0.020  1.090
 7BB  C59  H59A  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
 7BB  H2    N    HN   113.80  3.000
 7BB  H2    N    CA   116.25  3.000
 7BB  HN    N    CA   117.00  3.000
 7BB  C54   O9   C48  119.13  3.000
 7BB  N13   CA   CB   118.60  3.000
 7BB  CB    CA   N    110.40  1.500
 7BB  N13   CA   N    115.09  3.000
 7BB  HB    CB   SG   118.53  3.000
 7BB  HB    CB   CA   119.49  3.000
 7BB  SG    CB   CA   121.92  3.000
 7BB  HSG   SG   CB   100.22  3.000
 7BB  C49   N13  C48  119.91  3.000
 7BB  C48   N13  CA   121.04  3.000
 7BB  C49   N13  CA   118.42  3.000
 7BB  N13   C48  O9   111.14  3.000
 7BB  O9    C48  O8   124.96  3.000
 7BB  N13   C48  O8   123.90  3.000
 7BB  H49A  C49  H49  106.59  3.000
 7BB  H49A  C49  C50  110.15  3.000
 7BB  H49   C49  C50  110.34  3.000
 7BB  H49A  C49  N13  107.08  3.000
 7BB  H49   C49  N13  108.50  3.000
 7BB  C50   C49  N13  113.89  3.000
 7BB  H50A  C50  H50  106.65  3.000
 7BB  H50A  C50  C51  109.69  3.000
 7BB  H50   C50  C51  109.78  3.000
 7BB  H50A  C50  C49  109.41  3.000
 7BB  H50   C50  C49  109.22  3.000
 7BB  C51   C50  C49  111.94  3.000
 7BB  H51A  C51  H51  106.01  3.000
 7BB  H51A  C51  C59  109.86  3.000
 7BB  H51   C51  C59  109.71  3.000
 7BB  H51A  C51  C50  109.33  3.000
 7BB  H51   C51  C50  109.46  3.000
 7BB  C59   C51  C50  112.27  3.000
 7BB  H52A  C52  H52  106.30  3.000
 7BB  H52A  C52  C57  110.25  3.000
 7BB  H52   C52  C57  109.39  3.000
 7BB  H52A  C52  C53  109.47  3.000
 7BB  H52   C52  C53  109.32  3.000
 7BB  C57   C52  C53  111.95  3.000
 7BB  H53A  C53  H53  107.04  3.000
 7BB  H53A  C53  C54  109.92  3.000
 7BB  H53   C53  C54  109.21  3.000
 7BB  H53A  C53  C52  110.42  3.000
 7BB  H53   C53  C52  109.52  3.000
 7BB  C54   C53  C52  110.65  3.000
 7BB  H54   C54  C55  109.42  3.000
 7BB  H54   C54  C53  109.14  3.000
 7BB  C55   C54  C53  110.98  3.000
 7BB  H54   C54  O9   109.03  3.000
 7BB  C55   C54  O9   111.59  3.000
 7BB  C53   C54  O9   106.61  3.000
 7BB  H55A  C55  H55  107.19  3.000
 7BB  H55A  C55  C56  109.98  3.000
 7BB  H55   C55  C56  109.76  3.000
 7BB  H55A  C55  C54  110.48  3.000
 7BB  H55   C55  C54  109.04  3.000
 7BB  C56   C55  C54  110.34  3.000
 7BB  H56A  C56  H56  106.20  3.000
 7BB  H56A  C56  C57  109.34  3.000
 7BB  H56   C56  C57  110.34  3.000
 7BB  H56A  C56  C55  109.16  3.000
 7BB  H56   C56  C55  109.53  3.000
 7BB  C57   C56  C55  112.08  3.000
 7BB  H57   C57  C58  106.00  3.000
 7BB  H57   C57  C56  107.24  3.000
 7BB  C58   C57  C56  113.18  3.000
 7BB  H57   C57  C52  107.06  3.000
 7BB  C58   C57  C52  112.88  3.000
 7BB  C56   C57  C52  110.05  3.000
 7BB  C57   C58  O11  117.22  3.000
 7BB  O11   C58  O10  125.77  3.000
 7BB  C57   C58  O10  116.97  3.000
 7BB  H59A  C59  H59  104.81  3.000
 7BB  H59A  C59  C60  107.92  3.000
 7BB  H59   C59  C60  108.32  3.000
 7BB  H59A  C59  C51  109.48  3.000
 7BB  H59   C59  C51  109.57  3.000
 7BB  C60   C59  C51  116.14  3.000
 7BB  C59   C60  O13  117.97  3.000
 7BB  C59   C60  O12  115.77  3.000
 7BB  O13   C60  O12  126.25  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
 7BB  Var_01  C57  C52  C53  C54   -56.15  30.0  1
 7BB  Var_02  C57  C56  C55  C54    56.41  30.0  1
 7BB  Var_03  SG   CB   CA   N      -7.11   0.0  2
 7BB  Var_04  CA   N13  C48  O8   -174.93  30.0  2
 7BB  Var_05  C50  C49  N13  CA     87.84  30.0  3
 7BB  Var_06  C51  C59  C60  O12   178.24  30.0  3
 7BB  Var_07  C51  C50  C49  N13  -179.01  30.0  1
 7BB  Var_08  C59  C51  C50  C49   179.61  30.0  3
 7BB  Var_09  C60  C59  C51  C50   179.97  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
 7BB  chir_01  C54  O9   C53  C55  negativ
 7BB  chir_02  C57  C58  C56  C52  positiv

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
 7BB  plan-1  N    0.020
 7BB  plan-1  CA   0.020
 7BB  plan-1  CB   0.020
 7BB  plan-1  SG   0.020
 7BB  plan-1  N13  0.020
 7BB  plan-1  C48  0.020
 7BB  plan-1  C49  0.020
 7BB  plan-1  HN   0.020
 7BB  plan-1  H2   0.020
 7BB  plan-1  HB   0.020
 7BB  plan-2  O10  0.020
 7BB  plan-2  O11  0.020
 7BB  plan-2  C57  0.020
 7BB  plan-2  C58  0.020
 7BB  plan-3  O12  0.020
 7BB  plan-3  O13  0.020
 7BB  plan-3  C59  0.020
 7BB  plan-3  C60  0.020
 7BB  plan-4  O8   0.020
 7BB  plan-4  O9   0.020
 7BB  plan-4  N13  0.020
 7BB  plan-4  C48  0.020

