# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Mar 18 17:48:23 2022
#   Inital geometry file: a 136 line input string
#   Ligand name: methyl N-(carboxymethyl)-N-(3-phenylpropyl)glycyl-L-histidinate
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: COC(=O)[C@H](Cc1[nH]cnc1)NC(=O)CN(CCCc2ccccc2)CC(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
 MGK  MGK  'methyl N-(carboxymethyl)-N-(3-phenylpropyl)glycyl-L-histidinate'  ligand  54  29  .  2022-03-22  2022-03-22
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_MGK
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
 MGK  C10   C  CR15   0   0.084  -5.5066   3.5027  -1.5821
 MGK  N12   N  NH1    0  -0.631  -2.5424   0.3833  -0.3098
 MGK  C13   C  C      0   0.532  -1.3933   0.5999   0.3569
 MGK  C15   C  CH2    0  -0.390  -0.1899   0.8811  -0.5264
 MGK  C17   C  CH2    0  -0.242   2.2106   0.8579  -0.5230
 MGK  C20   C  CR6    0   0.138   5.9719   0.5858   0.3005
 MGK  C21   C  CR16   0  -0.315   6.7357  -0.3409  -0.4061
 MGK  C22   C  CR16   0  -0.240   7.8853  -0.8898   0.1472
 MGK  C24   C  CR16   0  -0.240   7.5382   0.4038   2.1378
 MGK  C26   C  CH2    0  -0.472   0.9586  -1.2045  -0.0813
 MGK  O29   O  OC    -1  -0.626   1.2381  -3.1441  -1.3915
 MGK  C27   C  C      0   0.398   1.0770  -1.9076  -1.4521
 MGK  O28   O  O      0  -0.597   0.9789  -1.2233  -2.4895
 MGK  N16   N  NT     0  -0.420   0.9961   0.2441  -0.0163
 MGK  C18   C  CH2    0  -0.447   3.4775   0.3208   0.1277
 MGK  C19   C  CH2    0  -0.505   4.7024   1.1403  -0.2820
 MGK  C25   C  CR16   0  -0.313   6.3897   0.9492   1.5796
 MGK  C23   C  CR16   0  -0.275   8.2910  -0.5192   1.4227
 MGK  O14   O  O      0  -0.489  -1.3456   0.6059   1.5771
 MGK  C05   C  CH1    0  -0.174  -3.7581   0.0701   0.3812
 MGK  C03   C  C      0   0.593  -3.6527  -1.2907   1.0591
 MGK  O04   O  O      0  -0.433  -2.8997  -2.1645   0.7191
 MGK  O02   O  O2     0  -0.451  -4.5324  -1.3989   2.0398
 MGK  C01   C  CH3    0  -0.425  -4.6078  -2.6518   2.7241
 MGK  C06   C  CH2    0  -0.568  -4.9398   0.0588  -0.6050
 MGK  C07   C  CR5    0   0.315  -5.1097   1.3625  -1.2973
 MGK  N11   N  NR15   0  -0.610  -5.4798   2.5160  -0.6633
 MGK  N09   N  N      0  -0.441  -5.1768   3.0629  -2.7682
 MGK  C08   C  CR15   0  -0.265  -4.9258   1.7298  -2.6018
 MGK  H10   H  HCR5   0   0.277  -5.7762   4.5165  -1.3295
 MGK  HN12  H  HNH1   0   0.400  -2.5144   0.2798  -1.3117
 MGK  H15   H  HCH2   0   0.228  -0.4087   0.6226  -1.5696
 MGK  H15A  H  HCH2   0   0.262  -0.0436   1.9668  -0.5010
 MGK  H17   H  HCH2   0   0.192   2.3060   0.7645  -1.6133
 MGK  H17A  H  HCH2   0   0.215   2.1458   1.9309  -0.3112
 MGK  H21   H  HCR6   0   0.245   6.4298  -0.6342  -1.4040
 MGK  H22   H  HCR6   0   0.252   8.4660  -1.6056  -0.4208
 MGK  H24   H  HCR6   0   0.252   7.8459   0.7014   3.1322
 MGK  H26   H  HCH2   0   0.246   0.0202  -1.5455   0.3714
 MGK  H26A  H  HCH2   0   0.237   1.7338  -1.6074   0.5759
 MGK  H18   H  HCH2   0   0.223   3.3682   0.3409   1.2164
 MGK  H18A  H  HCH2   0   0.230   3.6434  -0.7227  -0.1537
 MGK  H19   H  HCH2   0   0.238   4.5670   2.1775   0.0366
 MGK  H19A  H  HCH2   0   0.238   4.7762   1.1562  -1.3730
 MGK  H25   H  HCR6   0   0.244   5.8095   1.6696   2.1452
 MGK  H23   H  HCR6   0   0.252   9.1876  -0.9444   1.8549
 MGK  H05   H  HCH1   0   0.289  -3.9482   0.8223   1.1517
 MGK  H01   H  HCH3   0   0.242  -4.8607  -3.4621   2.0411
 MGK  H01A  H  HCH3   0   0.243  -3.6691  -2.8830   3.2266
 MGK  H01B  H  HCH3   0   0.254  -5.3954  -2.5417   3.4628
 MGK  H06   H  HCH2   0   0.283  -4.7808  -0.7170  -1.3575
 MGK  H06A  H  HCH2   0   0.292  -5.8478  -0.2101  -0.0614
 MGK  H08   H  HCR5   0   0.256  -4.6277   1.0943  -3.4228
 MGK  HN11  H  HNR5   0   0.419  -5.7067   2.6177   0.3138

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
 MGK  N11  C10   aromatic  1.348  0.020  1.348
 MGK  C10  N09   aromatic  1.307  0.020  1.307
 MGK  C10  H10   single    0.930  0.020  1.080
 MGK  C05  N12   single    1.433  0.020  1.433
 MGK  C13  N12   single    1.346  0.020  1.346
 MGK  N12  HN12  single    0.860  0.020  1.020
 MGK  C15  C13   single    1.519  0.020  1.519
 MGK  C13  O14   double    1.221  0.020  1.221
 MGK  C15  N16   single    1.440  0.020  1.440
 MGK  C15  H15   single    0.970  0.020  1.090
 MGK  C15  H15A  single    0.970  0.020  1.090
 MGK  C18  C17   single    1.522  0.020  1.522
 MGK  N16  C17   single    1.452  0.020  1.452
 MGK  C17  H17   single    0.970  0.020  1.090
 MGK  C17  H17A  single    0.970  0.020  1.090
 MGK  C25  C20   aromatic  1.394  0.020  1.394
 MGK  C20  C19   single    1.503  0.020  1.503
 MGK  C20  C21   aromatic  1.393  0.020  1.393
 MGK  C22  C21   aromatic  1.389  0.020  1.389
 MGK  C21  H21   single    0.930  0.020  1.080
 MGK  C23  C22   aromatic  1.389  0.020  1.389
 MGK  C22  H22   single    0.930  0.020  1.080
 MGK  C24  C25   aromatic  1.389  0.020  1.389
 MGK  C24  C23   aromatic  1.389  0.020  1.389
 MGK  C24  H24   single    0.930  0.020  1.080
 MGK  N16  C26   single    1.451  0.020  1.451
 MGK  C26  C27   single    1.545  0.020  1.545
 MGK  C26  H26   single    0.970  0.020  1.090
 MGK  C26  H26A  single    0.970  0.020  1.090
 MGK  C27  O29   deloc     1.248  0.020  1.248
 MGK  C27  O28   deloc     1.247  0.020  1.247
 MGK  C18  C19   single    1.530  0.020  1.530
 MGK  C18  H18   single    0.970  0.020  1.090
 MGK  C18  H18A  single    0.970  0.020  1.090
 MGK  C19  H19   single    0.970  0.020  1.090
 MGK  C19  H19A  single    0.970  0.020  1.090
 MGK  C25  H25   single    0.930  0.020  1.080
 MGK  C23  H23   single    0.930  0.020  1.080
 MGK  C06  C05   single    1.539  0.020  1.539
 MGK  C05  C03   single    1.524  0.020  1.524
 MGK  C05  H05   single    0.970  0.020  1.090
 MGK  O02  C03   single    1.322  0.020  1.322
 MGK  C03  O04   double    1.202  0.020  1.202
 MGK  O02  C01   single    1.430  0.020  1.430
 MGK  C01  H01   single    0.970  0.020  1.090
 MGK  C01  H01A  single    0.970  0.020  1.090
 MGK  C01  H01B  single    0.970  0.020  1.090
 MGK  C06  C07   single    1.486  0.020  1.486
 MGK  C06  H06   single    0.970  0.020  1.090
 MGK  C06  H06A  single    0.970  0.020  1.090
 MGK  N11  C07   aromatic  1.367  0.020  1.367
 MGK  C07  C08   aromatic  1.368  0.020  1.368
 MGK  C08  N09   aromatic  1.367  0.020  1.367
 MGK  C08  H08   single    0.930  0.020  1.080
 MGK  N11  HN11  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
 MGK  H10   C10  N09   126.26  3.000
 MGK  H10   C10  N11   122.21  3.000
 MGK  N09   C10  N11   111.53  3.000
 MGK  HN12  N12  C05   118.72  3.000
 MGK  HN12  N12  C13   119.04  3.000
 MGK  C05   N12  C13   121.37  3.000
 MGK  O14   C13  C15   123.31  3.000
 MGK  O14   C13  N12   121.94  3.000
 MGK  C15   C13  N12   114.72  3.000
 MGK  H15A  C15  H15   106.39  3.000
 MGK  H15A  C15  N16   108.68  3.000
 MGK  H15   C15  N16   113.40  3.000
 MGK  H15A  C15  C13   106.00  3.000
 MGK  H15   C15  C13   110.57  3.000
 MGK  N16   C15  C13   111.39  3.000
 MGK  H17A  C17  H17   106.28  3.000
 MGK  H17A  C17  C18   108.19  3.000
 MGK  H17   C17  C18   108.79  3.000
 MGK  H17A  C17  N16   107.28  3.000
 MGK  H17   C17  N16   112.52  3.000
 MGK  C18   C17  N16   113.44  3.000
 MGK  C25   C20  C19   120.85  3.000
 MGK  C19   C20  C21   120.79  3.000
 MGK  C25   C20  C21   118.32  3.000
 MGK  H21   C21  C22   119.55  3.000
 MGK  H21   C21  C20   119.47  3.000
 MGK  C22   C21  C20   120.97  3.000
 MGK  H22   C22  C23   120.11  3.000
 MGK  H22   C22  C21   119.75  3.000
 MGK  C23   C22  C21   120.14  3.000
 MGK  H24   C24  C23   120.10  3.000
 MGK  H24   C24  C25   119.76  3.000
 MGK  C23   C24  C25   120.14  3.000
 MGK  H26A  C26  H26   104.13  3.000
 MGK  H26A  C26  N16   108.83  3.000
 MGK  H26   C26  N16   108.32  3.000
 MGK  H26A  C26  C27   108.13  3.000
 MGK  H26   C26  C27   106.88  3.000
 MGK  N16   C26  C27   119.48  3.000
 MGK  O28   C27  O29   126.46  3.000
 MGK  O28   C27  C26   118.85  3.000
 MGK  O29   C27  C26   114.67  3.000
 MGK  C26   N16  C17   115.35  3.000
 MGK  C26   N16  C15   113.87  3.000
 MGK  C17   N16  C15   112.23  3.000
 MGK  H18A  C18  H18   106.78  3.000
 MGK  H18A  C18  C19   108.71  3.000
 MGK  H18   C18  C19   109.67  3.000
 MGK  H18A  C18  C17   110.67  3.000
 MGK  H18   C18  C17   109.61  3.000
 MGK  C19   C18  C17   111.28  3.000
 MGK  H19A  C19  H19   106.58  3.000
 MGK  H19A  C19  C18   109.21  3.000
 MGK  H19   C19  C18   109.33  3.000
 MGK  H19A  C19  C20   109.57  3.000
 MGK  H19   C19  C20   109.97  3.000
 MGK  C18   C19  C20   112.02  3.000
 MGK  H25   C25  C24   119.59  3.000
 MGK  H25   C25  C20   119.45  3.000
 MGK  C24   C25  C20   120.96  3.000
 MGK  H23   C23  C24   120.28  3.000
 MGK  H23   C23  C22   120.26  3.000
 MGK  C24   C23  C22   119.46  3.000
 MGK  H05   C05  C06   108.85  3.000
 MGK  H05   C05  C03   108.23  3.000
 MGK  C06   C05  C03   109.36  3.000
 MGK  H05   C05  N12   109.69  3.000
 MGK  C03   C05  N12   110.54  3.000
 MGK  C06   C05  N12   110.12  3.000
 MGK  O02   C03  O04   124.54  3.000
 MGK  O04   C03  C05   124.50  3.000
 MGK  O02   C03  C05   110.92  3.000
 MGK  C01   O02  C03   117.51  3.000
 MGK  H01B  C01  H01A  109.44  3.000
 MGK  H01B  C01  H01   109.48  3.000
 MGK  H01A  C01  H01   109.35  3.000
 MGK  H01B  C01  O02   105.97  3.000
 MGK  H01A  C01  O02   111.18  3.000
 MGK  H01   C01  O02   111.35  3.000
 MGK  H06A  C06  H06   106.80  3.000
 MGK  H06A  C06  C07   110.67  3.000
 MGK  H06   C06  C07   108.59  3.000
 MGK  H06A  C06  C05   108.73  3.000
 MGK  H06   C06  C05   109.56  3.000
 MGK  C07   C06  C05   112.33  3.000
 MGK  C08   C07  N11   104.60  3.000
 MGK  C08   C07  C06   131.66  3.000
 MGK  N11   C07  C06   123.72  3.000
 MGK  HN11  N11  C07   126.54  3.000
 MGK  HN11  N11  C10   125.59  3.000
 MGK  C07   N11  C10   107.86  3.000
 MGK  C08   N09  C10   105.31  3.000
 MGK  H08   C08  N09   122.14  3.000
 MGK  H08   C08  C07   127.16  3.000
 MGK  N09   C08  C07   110.70  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
 MGK  CONST_01  C08   C07  N11  C10     0.00   0.0  0
 MGK  CONST_02  C07   C08  N09  C10     0.00   0.0  0
 MGK  CONST_03  C23   C24  C25  C20     0.00   0.0  0
 MGK  CONST_04  C23   C22  C21  C20     0.00   0.0  0
 MGK  CONST_05  C24   C25  C20  C21     0.00   0.0  0
 MGK  CONST_06  C24   C23  C22  C21     0.00   0.0  0
 MGK  CONST_07  C25   C20  C21  C22     0.00   0.0  0
 MGK  CONST_08  C25   C24  C23  C22     0.00   0.0  0
 MGK  CONST_09  N09   C10  N11  C07     0.00   0.0  0
 MGK  CONST_10  C08   N09  C10  N11     0.00   0.0  0
 MGK  CONST_11  N09   C08  C07  N11     0.00   0.0  0
 MGK  CONST_12  C06   C07  N11  C10   180.00   0.0  0
 MGK  CONST_13  C19   C20  C21  C22   180.00   0.0  0
 MGK  CONST_14  C19   C20  C25  C24   180.00   0.0  0
 MGK  CONST_15  N09   C08  C07  C06   180.00   0.0  0
 MGK  CONST_16  H08   C08  N09  C10   180.00   0.0  0
 MGK  CONST_17  H24   C24  C25  C20   180.00   0.0  0
 MGK  CONST_18  H22   C22  C21  C20   180.00   0.0  0
 MGK  CONST_19  H25   C25  C20  C21   180.00   0.0  0
 MGK  CONST_20  H23   C23  C22  C21   180.00   0.0  0
 MGK  CONST_21  H21   C21  C20  C25   180.00   0.0  0
 MGK  CONST_22  H10   C10  N11  C07   180.00   0.0  0
 MGK  CONST_23  HN11  N11  C10  N09   180.00   0.0  0
 MGK  CONST_24  C05   N12  C13  C15   180.00   0.0  0
 MGK  CONST_25  C05   N12  C13  O14     0.00   0.0  0
 MGK  CONST_26  HN12  N12  C13  C15     0.00   0.0  0
 MGK  Var_01    C18   C19  C20  C21    91.91  30.0  2
 MGK  Var_02    N11   C07  C06  C05   -66.53  30.0  2
 MGK  Var_03    C20   C19  C18  C17  -177.36  30.0  3
 MGK  Var_04    N16   C15  C13  N12  -140.76  30.0  1
 MGK  Var_05    C17   N16  C15  C13  -159.21  30.0  3
 MGK  Var_06    C18   C17  N16  C15   172.90  30.0  3
 MGK  Var_07    C27   C26  N16  C15    71.77  30.0  3
 MGK  Var_08    N16   C26  C27  O29   169.65  30.0  2
 MGK  Var_09    C19   C18  C17  N16  -171.41  30.0  2
 MGK  Var_10    H01   C01  O02  C03   -59.61  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
 MGK  chir_01  C05  N12  C06  C03  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
 MGK  plan-1  C10   0.020
 MGK  plan-1  C06   0.020
 MGK  plan-1  C07   0.020
 MGK  plan-1  N11   0.020
 MGK  plan-1  N09   0.020
 MGK  plan-1  C08   0.020
 MGK  plan-1  H10   0.020
 MGK  plan-1  H08   0.020
 MGK  plan-1  HN11  0.020
 MGK  plan-2  C20   0.020
 MGK  plan-2  C21   0.020
 MGK  plan-2  C22   0.020
 MGK  plan-2  C24   0.020
 MGK  plan-2  C19   0.020
 MGK  plan-2  C25   0.020
 MGK  plan-2  C23   0.020
 MGK  plan-2  H21   0.020
 MGK  plan-2  H22   0.020
 MGK  plan-2  H24   0.020
 MGK  plan-2  H25   0.020
 MGK  plan-2  H23   0.020
 MGK  plan-3  N12   0.020
 MGK  plan-3  C13   0.020
 MGK  plan-3  C15   0.020
 MGK  plan-3  O14   0.020
 MGK  plan-3  C05   0.020
 MGK  plan-3  HN12  0.020
 MGK  plan-4  C26   0.020
 MGK  plan-4  O29   0.020
 MGK  plan-4  C27   0.020
 MGK  plan-4  O28   0.020
 MGK  plan-5  C05   0.020
 MGK  plan-5  C03   0.020
 MGK  plan-5  O04   0.020
 MGK  plan-5  O02   0.020

