# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sat Apr 11 22:10:32 2020
#   Inital geometry file: a 139 line input string
#   Ligand name: 3-({cis-4-[(2-{[2-(acetylamino)ethyl]disulfanyl}ethyl)carbamoyl]cyclohexyl}carbamoyl)pyrazine-2-carboxylic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CC(=O)NCCSSCCNC(=O)[C@H]1CC[C@H](CC1)NC(=O)c2nccnc2C(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
 964  964  '3-({cis-4-[(2-{[2-(acetylamino)ethyl]disulfanyl}ethyl)carbamoyl]cyclohexyl}carbamoyl)pyrazine-2-carboxylic acid'  ligand  57  31  .  2022-03-11  2022-03-11
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_964
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
 964  O31   O  O      0  -0.569   0.4061  -2.7840  -5.2200
 964  C1    C  CH3    0  -0.776   2.3897  -3.0622   9.6013
 964  C2    C  C      0   0.520   1.8588  -1.8416   8.8923
 964  N4    N  NH1    0  -0.621   0.5785  -1.5269   9.1614
 964  O3    O  O      0  -0.503   2.5577  -1.1760   8.1403
 964  C29   C  C      0   0.382   1.4721  -2.6333  -5.8432
 964  O30   O  OC    -1  -0.580   2.5445  -3.2371  -5.7023
 964  C24   C  CR6    0   0.052   1.4209  -1.5670  -6.9330
 964  N25   N  N      0  -0.360   2.2160  -1.7074  -7.9879
 964  C26   C  CR16   0  -0.117   2.1037  -0.8282  -8.9707
 964  C27   C  CR16   0  -0.111   1.1914   0.2151  -8.9116
 964  N28   N  N      0  -0.364   0.4120   0.3846  -7.8549
 964  C22   C  CR6    0   0.072   0.5269  -0.4950  -6.8684
 964  C21   C  C      0   0.530  -0.3800  -0.2317  -5.6950
 964  O23   O  O      0  -0.495  -1.5929  -0.3026  -5.8172
 964  N20   N  NH1    0  -0.624   0.2548   0.2105  -4.6025
 964  C17   C  CH1    0  -0.055  -0.4018   0.4852  -3.3400
 964  C18   C  CH2    0  -0.425  -0.5179  -0.7661  -2.4709
 964  C19   C  CH2    0  -0.425  -1.1826  -0.4458  -1.1369
 964  C16   C  CH2    0  -0.450   0.3501   1.5880  -2.6029
 964  C15   C  CH2    0  -0.424  -0.3040   1.9042  -1.2640
 964  C13   C  CH1    0  -0.391  -0.4201   0.6478  -0.3911
 964  C12   C  C      0   0.581  -1.0951   1.0056   0.9178
 964  O14   O  O      0  -0.502  -2.3044   1.1765   1.0055
 964  N11   N  NH1    0  -0.643  -0.2703   1.1533   1.9682
 964  C10   C  CH2    0  -0.225  -0.7241   1.6050   3.2656
 964  C9    C  CH2    0  -0.611   0.3548   1.3628   4.3049
 964  S7    S  S2     0  -0.041  -1.6274   0.5973   6.4560
 964  C5    C  CH2    0  -0.270  -0.1066  -0.4107   8.5552
 964  C6    C  CH2    0  -0.571  -0.7061  -0.7782   7.2042
 964  S8    S  S2     0  -0.032  -0.1441   1.9264   5.9560
 964  H11A  H  HCH3   0   0.267   3.1678  -2.7608  10.3033
 964  H12   H  HCH3   0   0.248   1.6303  -3.6145  10.1513
 964  H13A  H  HCH3   0   0.264   2.8505  -3.7316   8.8759
 964  H4    H  HNH1   0   0.403   0.0394  -2.1421   9.7474
 964  H26   H  HCR6   0   0.274   2.7498  -0.9501  -9.8321
 964  H27   H  HCR6   0   0.277   1.0960   0.9223  -9.7263
 964  H20   H  HNH1   0   0.396   1.2627   0.1722  -4.5932
 964  H17   H  HCH1   0   0.240  -1.4077   0.8475  -3.5690
 964  H181  H  HCH2   0   0.214   0.4834  -1.1761  -2.3008
 964  H182  H  HCH2   0   0.245  -1.0823  -1.5326  -3.0039
 964  H191  H  HCH2   0   0.242  -1.2404  -1.3499  -0.5263
 964  H192  H  HCH2   0   0.225  -2.2108  -0.1154  -1.3087
 964  H161  H  HCH2   0   0.224   1.3858   1.2701  -2.4351
 964  H162  H  HCH2   0   0.247   0.3893   2.4881  -3.2204
 964  H151  H  HCH2   0   0.229  -1.3032   2.3186  -1.4318
 964  H152  H  HCH2   0   0.246   0.2745   2.6727  -0.7462
 964  H13   H  HCH1   0   0.249   0.5933   0.2830  -0.1858
 964  H11   H  HNH1   0   0.403   0.7217   1.0666   1.8143
 964  H101  H  HCH2   0   0.244  -1.6267   1.0579   3.5423
 964  H102  H  HCH2   0   0.242  -0.9796   2.6682   3.2439
 964  H91   H  HCH2   0   0.296   1.2543   1.9420   4.0790
 964  H92   H  HCH2   0   0.288   0.6420   0.3113   4.3500
 964  H51   H  HCH2   0   0.260  -0.8964  -0.0855   9.2318
 964  H52   H  HCH2   0   0.251   0.5902   0.4188   8.4387
 964  H61   H  HCH2   0   0.284   0.0591  -1.1285   6.5108
 964  H62   H  HCH2   0   0.290  -1.4458  -1.5749   7.3131

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
 964  O31  C29   deloc     1.244  0.020  1.244
 964  C1   C2    single    1.508  0.020  1.508
 964  C1   H11A  single    0.970  0.020  1.090
 964  C1   H12   single    0.970  0.020  1.090
 964  C1   H13A  single    0.970  0.020  1.090
 964  C2   N4    single    1.346  0.020  1.346
 964  C2   O3    double    1.224  0.020  1.224
 964  N4   C5    single    1.443  0.020  1.443
 964  N4   H4    single    0.860  0.020  1.020
 964  C29  O30   deloc     1.239  0.020  1.239
 964  C29  C24   single    1.526  0.020  1.526
 964  C24  N25   aromatic  1.328  0.020  1.328
 964  C24  C22   aromatic  1.397  0.020  1.397
 964  N25  C26   aromatic  1.324  0.020  1.324
 964  C26  C27   aromatic  1.387  0.020  1.387
 964  C26  H26   single    0.930  0.020  1.080
 964  C27  N28   aromatic  1.324  0.020  1.324
 964  C27  H27   single    0.930  0.020  1.080
 964  N28  C22   aromatic  1.327  0.020  1.327
 964  C22  C21   single    1.506  0.020  1.506
 964  C21  O23   double    1.221  0.020  1.221
 964  C21  N20   single    1.339  0.020  1.339
 964  N20  C17   single    1.449  0.020  1.449
 964  N20  H20   single    0.860  0.020  1.020
 964  C17  C18   single    1.528  0.020  1.528
 964  C17  C16   single    1.525  0.020  1.525
 964  C17  H17   single    0.970  0.020  1.090
 964  C18  C19   single    1.524  0.020  1.524
 964  C18  H181  single    0.970  0.020  1.090
 964  C18  H182  single    0.970  0.020  1.090
 964  C19  C13   single    1.528  0.020  1.528
 964  C19  H191  single    0.970  0.020  1.090
 964  C19  H192  single    0.970  0.020  1.090
 964  C16  C15   single    1.523  0.020  1.523
 964  C16  H161  single    0.970  0.020  1.090
 964  C16  H162  single    0.970  0.020  1.090
 964  C15  C13   single    1.534  0.020  1.534
 964  C15  H151  single    0.970  0.020  1.090
 964  C15  H152  single    0.970  0.020  1.090
 964  C13  C12   single    1.516  0.020  1.516
 964  C13  H13   single    0.970  0.020  1.090
 964  C12  O14   double    1.224  0.020  1.224
 964  C12  N11   single    1.344  0.020  1.344
 964  N11  C10   single    1.447  0.020  1.447
 964  N11  H11   single    0.860  0.020  1.020
 964  C10  C9    single    1.517  0.020  1.517
 964  C10  H101  single    0.970  0.020  1.090
 964  C10  H102  single    0.970  0.020  1.090
 964  C9   S8    single    1.815  0.020  1.815
 964  C9   H91   single    0.970  0.020  1.090
 964  C9   H92   single    0.970  0.020  1.090
 964  S7   C6    single    1.817  0.020  1.817
 964  S7   S8    single    2.053  0.020  2.053
 964  C5   C6    single    1.523  0.020  1.523
 964  C5   H51   single    0.970  0.020  1.090
 964  C5   H52   single    0.970  0.020  1.090
 964  C6   H61   single    0.970  0.020  1.090
 964  C6   H62   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
 964  H13A  C1   H12   108.66  3.000
 964  H13A  C1   H11A  107.25  3.000
 964  H12   C1   H11A  108.23  3.000
 964  H13A  C1   C2    109.46  3.000
 964  H12   C1   C2    113.75  3.000
 964  H11A  C1   C2    109.28  3.000
 964  O3    C2   N4    122.63  3.000
 964  O3    C2   C1    121.88  3.000
 964  N4    C2   C1    115.48  3.000
 964  H4    N4   C5    117.59  3.000
 964  H4    N4   C2    118.90  3.000
 964  C5    N4   C2    123.27  3.000
 964  C24   C29  O30   116.81  3.000
 964  C24   C29  O31   114.44  3.000
 964  O30   C29  O31   128.75  3.000
 964  C22   C24  N25   120.05  3.000
 964  C22   C24  C29   121.65  3.000
 964  N25   C24  C29   118.25  3.000
 964  C26   N25  C24   117.95  3.000
 964  H26   C26  C27   120.71  3.000
 964  H26   C26  N25   117.71  3.000
 964  C27   C26  N25   121.59  3.000
 964  H27   C27  N28   117.71  3.000
 964  H27   C27  C26   121.13  3.000
 964  N28   C27  C26   121.17  3.000
 964  C22   N28  C27   117.23  3.000
 964  C21   C22  N28   114.28  3.000
 964  C21   C22  C24   123.73  3.000
 964  N28   C22  C24   121.99  3.000
 964  N20   C21  O23   124.88  3.000
 964  N20   C21  C22   114.08  3.000
 964  O23   C21  C22   120.66  3.000
 964  H20   N20  C17   116.86  3.000
 964  H20   N20  C21   117.96  3.000
 964  C17   N20  C21   123.96  3.000
 964  H17   C17  C16   108.38  3.000
 964  H17   C17  C18   108.69  3.000
 964  C16   C17  C18   110.78  3.000
 964  H17   C17  N20   107.29  3.000
 964  C16   C17  N20   109.56  3.000
 964  C18   C17  N20   112.01  3.000
 964  H182  C18  H181  106.61  3.000
 964  H182  C18  C19   110.46  3.000
 964  H181  C18  C19   109.96  3.000
 964  H182  C18  C17   109.68  3.000
 964  H181  C18  C17   108.99  3.000
 964  C19   C18  C17   111.03  3.000
 964  H192  C19  H191  106.75  3.000
 964  H192  C19  C13   109.25  3.000
 964  H191  C19  C13   110.24  3.000
 964  H192  C19  C18   109.63  3.000
 964  H191  C19  C18   109.77  3.000
 964  C13   C19  C18   111.10  3.000
 964  H162  C16  H161  106.96  3.000
 964  H162  C16  C15   109.95  3.000
 964  H161  C16  C15   109.35  3.000
 964  H162  C16  C17   109.90  3.000
 964  H161  C16  C17   109.28  3.000
 964  C15   C16  C17   111.30  3.000
 964  H152  C15  H151  106.84  3.000
 964  H152  C15  C13   110.28  3.000
 964  H151  C15  C13   109.16  3.000
 964  H152  C15  C16   109.59  3.000
 964  H151  C15  C16   109.62  3.000
 964  C13   C15  C16   111.26  3.000
 964  H13   C13  C12   109.18  3.000
 964  H13   C13  C15   108.00  3.000
 964  C12   C13  C15   109.37  3.000
 964  H13   C13  C19   108.34  3.000
 964  C12   C13  C19   111.61  3.000
 964  C15   C13  C19   110.26  3.000
 964  N11   C12  O14   122.34  3.000
 964  N11   C12  C13   115.32  3.000
 964  O14   C12  C13   122.32  3.000
 964  H11   N11  C10   118.21  3.000
 964  H11   N11  C12   118.39  3.000
 964  C10   N11  C12   122.87  3.000
 964  H102  C10  H101  107.41  3.000
 964  H102  C10  C9    109.56  3.000
 964  H101  C10  C9    109.54  3.000
 964  H102  C10  N11   111.04  3.000
 964  H101  C10  N11   109.29  3.000
 964  C9    C10  N11   109.96  3.000
 964  H92   C9   H91   107.61  3.000
 964  H92   C9   S8    109.52  3.000
 964  H91   C9   S8    104.45  3.000
 964  H92   C9   C10   111.67  3.000
 964  H91   C9   C10   111.03  3.000
 964  S8    C9   C10   112.22  3.000
 964  S8    S7   C6    102.94  3.000
 964  H52   C5   H51   107.62  3.000
 964  H52   C5   C6    109.91  3.000
 964  H51   C5   C6    109.72  3.000
 964  H52   C5   N4    109.28  3.000
 964  H51   C5   N4    108.31  3.000
 964  C6    C5   N4    111.89  3.000
 964  H62   C6   H61   107.71  3.000
 964  H62   C6   C5    110.73  3.000
 964  H61   C6   C5    111.43  3.000
 964  H62   C6   S7    104.47  3.000
 964  H61   C6   S7    109.71  3.000
 964  C5    C6   S7    112.47  3.000
 964  S7    S8   C9    102.65  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
 964  CONST_01  C27   C26  N25  C24     0.00   0.0  0
 964  CONST_02  C27   N28  C22  C24     0.00   0.0  0
 964  CONST_03  N28   C22  C24  N25     0.00   0.0  0
 964  CONST_04  N28   C27  C26  N25     0.00   0.0  0
 964  CONST_05  C22   C24  N25  C26     0.00   0.0  0
 964  CONST_06  C22   N28  C27  C26     0.00   0.0  0
 964  CONST_07  C26   N25  C24  C29   180.00   0.0  0
 964  CONST_08  N28   C22  C24  C29   180.00   0.0  0
 964  CONST_09  C21   C22  C24  N25   180.00   0.0  0
 964  CONST_10  C21   C22  N28  C27   180.00   0.0  0
 964  CONST_11  H26   C26  N25  C24   180.00   0.0  0
 964  CONST_12  H27   C27  C26  N25   180.00   0.0  0
 964  CONST_13  C17   N20  C21  C22   180.00   0.0  0
 964  CONST_14  C17   N20  C21  O23     0.00   0.0  0
 964  CONST_15  C10   N11  C12  C13   180.00   0.0  0
 964  CONST_16  H20   N20  C21  C22     0.00   0.0  0
 964  CONST_17  H11   N11  C12  C13     0.00   0.0  0
 964  CONST_18  C5    N4   C2   C1    180.00   0.0  0
 964  CONST_19  C5    N4   C2   O3      0.00   0.0  0
 964  CONST_20  C10   N11  C12  O14     0.00   0.0  0
 964  CONST_21  H4    N4   C2   C1      0.00   0.0  0
 964  Var_01    C13   C19  C18  C17   -56.89  30.0  1
 964  Var_02    C13   C15  C16  C17    55.94  30.0  1
 964  Var_03    N25   C24  C29  O31  -151.10  30.0  2
 964  Var_04    O23   C21  C22  C24  -115.07  30.0  2
 964  Var_05    C6    C5   N4   C2     85.28  30.0  3
 964  Var_06    S7    C6   C5   N4    177.79  30.0  3
 964  Var_07    C9    C10  N11  C12   166.94  30.0  3
 964  Var_08    S8    C9   C10  N11   179.33  30.0  3
 964  Var_09    H11A  C1   C2   N4   -113.78  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
 964  chir_01  C17  N20  C18  C16  negativ
 964  chir_02  C13  C19  C15  C12  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
 964  plan-1  C29  0.020
 964  plan-1  C24  0.020
 964  plan-1  N25  0.020
 964  plan-1  C26  0.020
 964  plan-1  C27  0.020
 964  plan-1  N28  0.020
 964  plan-1  C22  0.020
 964  plan-1  C21  0.020
 964  plan-1  H26  0.020
 964  plan-1  H27  0.020
 964  plan-2  C1   0.020
 964  plan-2  C2   0.020
 964  plan-2  N4   0.020
 964  plan-2  O3   0.020
 964  plan-2  C5   0.020
 964  plan-2  H4   0.020
 964  plan-3  C22  0.020
 964  plan-3  C21  0.020
 964  plan-3  O23  0.020
 964  plan-3  N20  0.020
 964  plan-3  C17  0.020
 964  plan-3  H20  0.020
 964  plan-4  C13  0.020
 964  plan-4  C12  0.020
 964  plan-4  O14  0.020
 964  plan-4  N11  0.020
 964  plan-4  C10  0.020
 964  plan-4  H11  0.020
 964  plan-5  O31  0.020
 964  plan-5  C29  0.020
 964  plan-5  O30  0.020
 964  plan-5  C24  0.020

