# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Apr 28 01:44:21 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  48  24  .  2022-03-10  2022-11-17
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

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  -0.797  -1.3121  -1.9465   1.3378
 7BB  O8    O  O     0  -0.509  -0.0337   1.3862  -0.9433
 7BB  O9    O  O2    0  -0.491   1.0101  -0.3774  -0.0041
 7BB  CA    C  C     0   0.518  -1.0830  -1.8759  -0.0051
 7BB  CB    C  C1    0  -0.534  -0.9374  -2.9136  -0.8466
 7BB  SG    S  S2    0  -0.232  -1.0207  -4.5833  -0.2887
 7BB  O10   O  O     0  -0.440   6.9273   1.5835   1.0298
 7BB  O11   O  OH1   0  -0.596   7.3406   0.5208  -0.8833
 7BB  O12   O  OH1   0  -0.598  -7.2771   2.9207   1.4548
 7BB  N13   N  NT    0  -0.559  -1.1288  -0.5665  -0.5566
 7BB  O13   O  O     0  -0.445  -7.1370   2.2745  -0.6738
 7BB  C48   C  C     0   0.759  -0.0390   0.2450  -0.5333
 7BB  C49   C  CH2   0  -0.298  -2.4223  -0.0354  -0.9738
 7BB  C50   C  CH2   0  -0.431  -3.1776   0.6681   0.1466
 7BB  C51   C  CH2   0  -0.427  -4.5397   1.1668  -0.3172
 7BB  C52   C  CH2   0  -0.436   4.4190   0.3204   1.3457
 7BB  C53   C  CH2   0  -0.462   3.0459  -0.3293   1.2096
 7BB  C54   C  CH1   0   0.072   2.2623   0.3177   0.0812
 7BB  C55   C  CH2   0  -0.468   3.0187   0.2283  -1.2347
 7BB  C56   C  CH2   0  -0.440   4.4011   0.8621  -1.1099
 7BB  C57   C  CH1   0  -0.384   5.1970   0.2208   0.0387
 7BB  C58   C  C     0   0.566   6.5629   0.8510   0.1433
 7BB  C59   C  CH2   0  -0.580  -5.2878   1.8526   0.8138
 7BB  C60   C  C     0   0.551  -6.6499   2.3561   0.4263
 7BB  HN    H  HNH2  0   0.390  -1.0235  -1.1542   1.8887
 7BB  H2    H  HNH2  0   0.385  -1.1123  -2.8335   1.7753
 7BB  HB    H  H     0   0.271  -0.8436  -2.7265  -1.9070
 7BB  HSG   H  HSH1  0   0.223   0.2854  -4.8903  -0.3022
 7BB  HO11  H  HOH1  0   0.479   8.1987   0.9637  -0.8046
 7BB  HO12  H  HOH1  0   0.478  -8.1480   3.2407   1.1761
 7BB  H49   H  HCH2  0   0.255  -2.2651   0.6452  -1.8107
 7BB  H49A  H  HCH2  0   0.254  -3.0070  -0.8735  -1.3548
 7BB  H50   H  HCH2  0   0.229  -3.3027  -0.0216   0.9852
 7BB  H50A  H  HCH2  0   0.230  -2.5821   1.5091   0.5135
 7BB  H51   H  HCH2  0   0.233  -4.4134   1.8605  -1.1520
 7BB  H51A  H  HCH2  0   0.231  -5.1273   0.3264  -0.6963
 7BB  H52   H  HCH2  0   0.231   4.3023   1.3708   1.6275
 7BB  H52A  H  HCH2  0   0.251   4.9691  -0.1618   2.1557
 7BB  H53   H  HCH2  0   0.231   3.1608  -1.3998   1.0092
 7BB  H53A  H  HCH2  0   0.249   2.4953  -0.2360   2.1482
 7BB  H54   H  HCH1  0   0.234   2.0788   1.3680   0.3287
 7BB  H55   H  HCH2  0   0.232   3.1209  -0.8238  -1.5197
 7BB  H55A  H  HCH2  0   0.253   2.4624   0.7282  -2.0298
 7BB  H56   H  HCH2  0   0.257   4.9325   0.7566  -2.0561
 7BB  H56A  H  HCH2  0   0.236   4.2983   1.9362  -0.9226
 7BB  H57   H  HCH1  0   0.271   5.3434  -0.8379  -0.2074
 7BB  H59   H  HCH2  0   0.277  -5.4023   1.1745   1.6652
 7BB  H59A  H  HCH2  0   0.279  -4.7105   2.7016   1.1941

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  1.435  0.020  1.435
 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  1.459  0.020  1.459
 7BB  N13  C48   single  1.359  0.020  1.359
 7BB  O13  C60   double  1.206  0.020  1.206
 7BB  C48  O8    double  1.213  0.020  1.213
 7BB  C48  O9    single  1.330  0.020  1.330
 7BB  C50  C49   single  1.523  0.020  1.523
 7BB  C50  C51   single  1.523  0.020  1.523
 7BB  C52  C57   single  1.524  0.020  1.524
 7BB  C53  C52   single  1.525  0.020  1.525
 7BB  C53  C54   single  1.519  0.020  1.519
 7BB  C54  C55   single  1.520  0.020  1.520
 7BB  C55  C56   single  1.526  0.020  1.526
 7BB  C56  C57   single  1.537  0.020  1.537
 7BB  C57  C58   single  1.508  0.020  1.508
 7BB  C58  O10   double  1.206  0.020  1.206
 7BB  C58  O11   single  1.330  0.020  1.330
 7BB  C59  C51   single  1.520  0.020  1.520
 7BB  C60  O12   single  1.330  0.020  1.330
 7BB  C60  C59   single  1.503  0.020  1.503
 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  O11  HO11  single  0.850  0.020  0.980
 7BB  O12  HO12  single  0.850  0.020  0.980
 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   113.43  3.000
 7BB  H2    N    CA   116.04  3.000
 7BB  HN    N    CA   116.71  3.000
 7BB  C54   O9   C48  119.05  3.000
 7BB  N13   CA   CB   118.15  3.000
 7BB  CB    CA   N    110.40  1.500
 7BB  N13   CA   N    115.10  3.000
 7BB  HB    CB   SG   118.60  3.000
 7BB  HB    CB   CA   119.34  3.000
 7BB  SG    CB   CA   121.88  3.000
 7BB  HSG   SG   CB    99.64  3.000
 7BB  HO11  O11  C58  109.99  3.000
 7BB  HO12  O12  C60  109.98  3.000
 7BB  C49   N13  C48  119.89  3.000
 7BB  C48   N13  CA   121.17  3.000
 7BB  C49   N13  CA   118.35  3.000
 7BB  N13   C48  O9   111.10  3.000
 7BB  O9    C48  O8   124.86  3.000
 7BB  N13   C48  O8   124.03  3.000
 7BB  H49A  C49  H49  106.79  3.000
 7BB  H49A  C49  C50  110.24  3.000
 7BB  H49   C49  C50  110.35  3.000
 7BB  H49A  C49  N13  107.19  3.000
 7BB  H49   C49  N13  108.60  3.000
 7BB  C50   C49  N13  113.41  3.000
 7BB  H50A  C50  H50  106.87  3.000
 7BB  H50A  C50  C51  109.72  3.000
 7BB  H50   C50  C51  109.75  3.000
 7BB  H50A  C50  C49  109.38  3.000
 7BB  H50   C50  C49  109.25  3.000
 7BB  C51   C50  C49  111.76  3.000
 7BB  H51A  C51  H51  106.57  3.000
 7BB  H51A  C51  C59  109.90  3.000
 7BB  H51   C51  C59  109.82  3.000
 7BB  H51A  C51  C50  109.55  3.000
 7BB  H51   C51  C50  109.70  3.000
 7BB  C59   C51  C50  111.19  3.000
 7BB  H52A  C52  H52  106.67  3.000
 7BB  H52A  C52  C57  110.50  3.000
 7BB  H52   C52  C57  109.76  3.000
 7BB  H52A  C52  C53  109.37  3.000
 7BB  H52   C52  C53  109.63  3.000
 7BB  C57   C52  C53  110.80  3.000
 7BB  H53A  C53  H53  107.09  3.000
 7BB  H53A  C53  C54  110.00  3.000
 7BB  H53   C53  C54  109.55  3.000
 7BB  H53A  C53  C52  109.92  3.000
 7BB  H53   C53  C52  109.77  3.000
 7BB  C54   C53  C52  110.45  3.000
 7BB  H54   C54  C55  109.61  3.000
 7BB  H54   C54  C53  109.11  3.000
 7BB  C55   C54  C53  111.18  3.000
 7BB  H54   C54  O9   109.39  3.000
 7BB  C55   C54  O9   110.75  3.000
 7BB  C53   C54  O9   106.74  3.000
 7BB  H55A  C55  H55  107.34  3.000
 7BB  H55A  C55  C56  109.33  3.000
 7BB  H55   C55  C56  109.63  3.000
 7BB  H55A  C55  C54  110.49  3.000
 7BB  H55   C55  C54  109.17  3.000
 7BB  C56   C55  C54  110.82  3.000
 7BB  H56A  C56  H56  106.80  3.000
 7BB  H56A  C56  C57  109.26  3.000
 7BB  H56   C56  C57  110.83  3.000
 7BB  H56A  C56  C55  109.66  3.000
 7BB  H56   C56  C55  109.29  3.000
 7BB  C57   C56  C55  110.91  3.000
 7BB  H57   C57  C58  107.34  3.000
 7BB  H57   C57  C56  107.71  3.000
 7BB  C58   C57  C56  110.27  3.000
 7BB  H57   C57  C52  108.88  3.000
 7BB  C58   C57  C52  112.06  3.000
 7BB  C56   C57  C52  110.43  3.000
 7BB  C57   C58  O11  111.87  3.000
 7BB  O11   C58  O10  122.78  3.000
 7BB  C57   C58  O10  125.34  3.000
 7BB  H59A  C59  H59  105.39  3.000
 7BB  H59A  C59  C60  107.91  3.000
 7BB  H59   C59  C60  108.26  3.000
 7BB  H59A  C59  C51  110.42  3.000
 7BB  H59   C59  C51  110.55  3.000
 7BB  C60   C59  C51  113.92  3.000
 7BB  C59   C60  O13  125.35  3.000
 7BB  C59   C60  O12  111.73  3.000
 7BB  O13   C60  O12  122.92  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
 7BB  CONST_01  HO11  O11  C58  C57   180.00   0.0  0
 7BB  CONST_08  HO12  O12  C60  O13     0.00   0.0  0
 7BB  Var_01    C57   C52  C53  C54   -57.55  30.0  1
 7BB  Var_02    C57   C56  C55  C54    55.76  30.0  1
 7BB  Var_03    SG    CB   CA   N      -0.33   0.0  2
 7BB  Var_04    CA    N13  C48  O8   -177.18  30.0  1
 7BB  Var_05    C50   C49  N13  CA     87.69  30.0  3
 7BB  Var_06    C51   C59  C60  O12   178.59  30.0  3
 7BB  Var_07    C51   C50  C49  N13  -178.12  30.0  1
 7BB  Var_08    C59   C51  C50  C49   179.38  30.0  3
 7BB  Var_09    C60   C59  C51  C50  -179.35  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-2  HO11  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-3  HO12  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

