# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Fri Mar 18 17:48:20 2022
#   Inital geometry file: a 138 line input string
#   Ligand name: N-(carboxymethyl)-N-(3-phenylpropyl)glycyl-N-methyl-L-histidinamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CNC(=O)[C@H](Cc1c[nH]cn1)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
 MGJ  MGJ  N-(carboxymethyl)-N-(3-phenylpropyl)glycyl-N-methyl-L-histidinamide  ligand  55  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_MGJ
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
 MGJ  C10   C  CR15   0   0.089   5.7543  -3.5027  -1.2056
 MGJ  N12   N  NH1    0  -0.619   2.5724  -0.4929  -0.3473
 MGJ  C13   C  C      0   0.530   1.4299  -0.7383   0.3185
 MGJ  C15   C  CH2    0  -0.391   0.2180  -0.9824  -0.5656
 MGJ  C17   C  CH2    0  -0.249  -2.1776  -0.9260  -0.5441
 MGJ  C20   C  CR6    0   0.145  -5.9358  -0.5500   0.2511
 MGJ  C21   C  CR16   0  -0.305  -6.6561   0.4132  -0.4520
 MGJ  C22   C  CR16   0  -0.227  -7.7880   1.0013   0.0964
 MGJ  C24   C  CR16   0  -0.226  -7.5109  -0.3253   2.0757
 MGJ  C26   C  CH2    0  -0.485  -0.8991   1.1113  -0.0657
 MGJ  C03   C  C      0   0.545   3.5855   1.2916   0.9636
 MGJ  N02   N  NH1    0  -0.628   4.3930   1.5477   2.0076
 MGJ  C01   C  CH3    0  -0.503   4.4014   2.8260   2.6785
 MGJ  C05   C  CH1    0  -0.190   3.7684  -0.0982   0.3412
 MGJ  C06   C  CH2    0  -0.551   4.9517  -0.0827  -0.6355
 MGJ  C07   C  CR5    0   0.169   5.2286  -1.4334  -1.1995
 MGJ  C08   C  CR15   0  -0.122   5.1290  -1.8509  -2.4968
 MGJ  N09   N  NR15   0  -0.556   5.4691  -3.1732  -2.4791
 MGJ  N11   N  N      0  -0.460   5.6196  -2.4767  -0.4053
 MGJ  O14   O  O      0  -0.493   1.3857  -0.8012   1.5372
 MGJ  N16   N  NT     0  -0.418  -0.9539  -0.3386  -0.0308
 MGJ  C27   C  C      0   0.399  -1.0718   1.8366  -1.4168
 MGJ  O28   O  OC    -1  -0.631  -1.3199   3.0582  -1.3322
 MGJ  O29   O  O      0  -0.599  -0.9235   1.1847  -2.4689
 MGJ  C18   C  CH2    0  -0.435  -3.4338  -0.3654   0.1067
 MGJ  C19   C  CH2    0  -0.496  -4.6796  -1.1410  -0.3235
 MGJ  C23   C  CR16   0  -0.259  -8.2190   0.6341   1.3641
 MGJ  C25   C  CR16   0  -0.298  -6.3802  -0.9099   1.5216
 MGJ  H10   H  HCR5   0   0.279   6.0567  -4.4980  -0.9189
 MGJ  HN12  H  HNH1   0   0.390   2.5118  -0.2932  -1.3328
 MGJ  H15   H  HCH2   0   0.227   0.4310  -0.7008  -1.6043
 MGJ  H15A  H  HCH2   0   0.255   0.0482  -2.0647  -0.5659
 MGJ  H17   H  HCH2   0   0.188  -2.2709  -0.8190  -1.6340
 MGJ  H17A  H  HCH2   0   0.230  -2.1329  -2.0018  -0.3407
 MGJ  H21   H  HCR6   0   0.234  -6.3301   0.7054  -1.4437
 MGJ  H22   H  HCR6   0   0.242  -8.3341   1.7455  -0.4688
 MGJ  H24   H  HCR6   0   0.241  -7.8387  -0.6199   3.0643
 MGJ  H26   H  HCH2   0   0.230  -1.6361   1.5102   0.6368
 MGJ  H26A  H  HCH2   0   0.272   0.0675   1.4316   0.3401
 MGJ  HN02  H  HNH1   0   0.379   4.9530   0.8071   2.3920
 MGJ  H01   H  HCH3   0   0.235   3.4712   3.0100   3.2186
 MGJ  H01A  H  HCH3   0   0.237   5.2213   2.8370   3.3910
 MGJ  H01B  H  HCH3   0   0.245   4.5496   3.6389   1.9688
 MGJ  H05   H  HCH1   0   0.266   3.9820  -0.8287   1.1269
 MGJ  H06   H  HCH2   0   0.262   4.7551   0.6301  -1.4411
 MGJ  H06A  H  HCH2   0   0.264   5.8323   0.2877  -0.1053
 MGJ  H08   H  HCR5   0   0.274   4.8526  -1.3354  -3.4007
 MGJ  HN09  H  HNR5   0   0.400   5.5125  -3.7870  -3.2746
 MGJ  H18   H  HCH2   0   0.213  -3.3338  -0.4039   1.1957
 MGJ  H18A  H  HCH2   0   0.225  -3.5691   0.6866  -0.1578
 MGJ  H19   H  HCH2   0   0.229  -4.5800  -2.1857  -0.0167
 MGJ  H19A  H  HCH2   0   0.228  -4.7417  -1.1440  -1.4153
 MGJ  H23   H  HCR6   0   0.232  -9.1005   1.0914   1.7937
 MGJ  H25   H  HCR6   0   0.226  -5.8351  -1.6577   2.0861
 MGJ  O04   O  O      0  -0.437   2.8090   2.1066   0.5065

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
 MGJ  C10  N09   aromatic  1.346  0.020  1.346
 MGJ  C10  N11   aromatic  1.308  0.020  1.308
 MGJ  C10  H10   single    0.930  0.020  1.080
 MGJ  N12  C13   single    1.345  0.020  1.345
 MGJ  N12  C05   single    1.435  0.020  1.435
 MGJ  N12  HN12  single    0.890  0.020  1.040
 MGJ  C13  C15   single    1.520  0.020  1.520
 MGJ  C13  O14   double    1.221  0.020  1.221
 MGJ  C15  N16   single    1.440  0.020  1.440
 MGJ  C15  H15   single    0.970  0.020  1.090
 MGJ  C15  H15A  single    0.970  0.020  1.090
 MGJ  C17  N16   single    1.451  0.020  1.451
 MGJ  C17  C18   single    1.522  0.020  1.522
 MGJ  C17  H17   single    0.970  0.020  1.090
 MGJ  C17  H17A  single    0.970  0.020  1.090
 MGJ  C20  C21   aromatic  1.393  0.020  1.393
 MGJ  C20  C19   single    1.502  0.020  1.502
 MGJ  C20  C25   aromatic  1.393  0.020  1.393
 MGJ  C21  C22   aromatic  1.388  0.020  1.388
 MGJ  C21  H21   single    0.930  0.020  1.080
 MGJ  C22  C23   aromatic  1.388  0.020  1.388
 MGJ  C22  H22   single    0.930  0.020  1.080
 MGJ  C24  C23   aromatic  1.389  0.020  1.389
 MGJ  C24  C25   aromatic  1.388  0.020  1.388
 MGJ  C24  H24   single    0.930  0.020  1.080
 MGJ  C26  N16   single    1.451  0.020  1.451
 MGJ  C26  C27   single    1.543  0.020  1.543
 MGJ  C26  H26   single    0.970  0.020  1.090
 MGJ  C26  H26A  single    0.970  0.020  1.090
 MGJ  O04  C03   double    1.215  0.020  1.215
 MGJ  C03  N02   single    1.344  0.020  1.344
 MGJ  C03  C05   single    1.534  0.020  1.534
 MGJ  N02  C01   single    1.444  0.020  1.444
 MGJ  N02  HN02  single    0.860  0.020  1.020
 MGJ  C01  H01   single    0.970  0.020  1.090
 MGJ  C01  H01A  single    0.970  0.020  1.090
 MGJ  C01  H01B  single    0.970  0.020  1.090
 MGJ  C05  C06   single    1.534  0.020  1.534
 MGJ  C05  H05   single    0.970  0.020  1.090
 MGJ  C06  C07   single    1.490  0.020  1.490
 MGJ  C06  H06   single    0.970  0.020  1.090
 MGJ  C06  H06A  single    0.970  0.020  1.090
 MGJ  C07  C08   aromatic  1.366  0.020  1.366
 MGJ  C07  N11   aromatic  1.368  0.020  1.368
 MGJ  C08  N09   aromatic  1.365  0.020  1.365
 MGJ  C08  H08   single    0.930  0.020  1.080
 MGJ  N09  HN09  single    0.860  0.020  1.020
 MGJ  C27  O28   deloc     1.249  0.020  1.249
 MGJ  C27  O29   deloc     1.247  0.020  1.247
 MGJ  C18  C19   single    1.529  0.020  1.529
 MGJ  C18  H18   single    0.970  0.020  1.090
 MGJ  C18  H18A  single    0.970  0.020  1.090
 MGJ  C19  H19   single    0.970  0.020  1.090
 MGJ  C19  H19A  single    0.970  0.020  1.090
 MGJ  C23  H23   single    0.930  0.020  1.080
 MGJ  C25  H25   single    0.930  0.020  1.080

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
 MGJ  H10   C10  N11   126.14  3.000
 MGJ  H10   C10  N09   122.46  3.000
 MGJ  N11   C10  N09   111.40  3.000
 MGJ  HN12  N12  C05   117.70  3.000
 MGJ  HN12  N12  C13   117.99  3.000
 MGJ  C05   N12  C13   121.37  3.000
 MGJ  O14   C13  C15   122.91  3.000
 MGJ  O14   C13  N12   122.29  3.000
 MGJ  C15   C13  N12   114.75  3.000
 MGJ  H15A  C15  H15   106.46  3.000
 MGJ  H15A  C15  N16   108.40  3.000
 MGJ  H15   C15  N16   113.26  3.000
 MGJ  H15A  C15  C13   106.40  3.000
 MGJ  H15   C15  C13   110.77  3.000
 MGJ  N16   C15  C13   111.16  3.000
 MGJ  H17A  C17  H17   106.44  3.000
 MGJ  H17A  C17  C18   108.42  3.000
 MGJ  H17   C17  C18   108.55  3.000
 MGJ  H17A  C17  N16   107.30  3.000
 MGJ  H17   C17  N16   112.51  3.000
 MGJ  C18   C17  N16   113.31  3.000
 MGJ  C25   C20  C19   120.92  3.000
 MGJ  C25   C20  C21   118.28  3.000
 MGJ  C19   C20  C21   120.75  3.000
 MGJ  H21   C21  C22   119.49  3.000
 MGJ  H21   C21  C20   119.50  3.000
 MGJ  C22   C21  C20   121.00  3.000
 MGJ  H22   C22  C23   120.14  3.000
 MGJ  H22   C22  C21   119.76  3.000
 MGJ  C23   C22  C21   120.11  3.000
 MGJ  H24   C24  C25   119.78  3.000
 MGJ  H24   C24  C23   120.11  3.000
 MGJ  C25   C24  C23   120.11  3.000
 MGJ  H26A  C26  H26   104.47  3.000
 MGJ  H26A  C26  C27   106.59  3.000
 MGJ  H26   C26  C27   108.40  3.000
 MGJ  H26A  C26  N16   108.44  3.000
 MGJ  H26   C26  N16   108.87  3.000
 MGJ  C27   C26  N16   119.10  3.000
 MGJ  C05   C03  N02   114.59  3.000
 MGJ  C05   C03  O04   122.10  3.000
 MGJ  N02   C03  O04   123.25  3.000
 MGJ  HN02  N02  C01   118.13  3.000
 MGJ  HN02  N02  C03   119.43  3.000
 MGJ  C01   N02  C03   122.21  3.000
 MGJ  H01B  C01  H01A  108.48  3.000
 MGJ  H01B  C01  H01   108.22  3.000
 MGJ  H01A  C01  H01   108.49  3.000
 MGJ  H01B  C01  N02   111.02  3.000
 MGJ  H01A  C01  N02   108.55  3.000
 MGJ  H01   C01  N02   111.99  3.000
 MGJ  H05   C05  C06   108.26  3.000
 MGJ  H05   C05  C03   109.69  3.000
 MGJ  C06   C05  C03   109.94  3.000
 MGJ  H05   C05  N12   108.88  3.000
 MGJ  C06   C05  N12   109.88  3.000
 MGJ  C03   C05  N12   110.15  3.000
 MGJ  H06A  C06  H06   106.34  3.000
 MGJ  H06A  C06  C07   109.96  3.000
 MGJ  H06   C06  C07   110.21  3.000
 MGJ  H06A  C06  C05   108.43  3.000
 MGJ  H06   C06  C05   109.69  3.000
 MGJ  C07   C06  C05   112.03  3.000
 MGJ  N11   C07  C08   109.81  3.000
 MGJ  N11   C07  C06   121.65  3.000
 MGJ  C08   C07  C06   128.54  3.000
 MGJ  H08   C08  N09   122.58  3.000
 MGJ  H08   C08  C07   132.02  3.000
 MGJ  N09   C08  C07   105.39  3.000
 MGJ  HN09  N09  C08   126.27  3.000
 MGJ  HN09  N09  C10   126.14  3.000
 MGJ  C08   N09  C10   107.59  3.000
 MGJ  C07   N11  C10   105.81  3.000
 MGJ  C26   N16  C17   115.32  3.000
 MGJ  C26   N16  C15   114.01  3.000
 MGJ  C17   N16  C15   111.96  3.000
 MGJ  O29   C27  O28   126.30  3.000
 MGJ  O29   C27  C26   118.68  3.000
 MGJ  O28   C27  C26   114.99  3.000
 MGJ  H18A  C18  H18   106.62  3.000
 MGJ  H18A  C18  C19   108.61  3.000
 MGJ  H18   C18  C19   109.67  3.000
 MGJ  H18A  C18  C17   110.69  3.000
 MGJ  H18   C18  C17   109.71  3.000
 MGJ  C19   C18  C17   111.43  3.000
 MGJ  H19A  C19  H19   106.42  3.000
 MGJ  H19A  C19  C18   109.18  3.000
 MGJ  H19   C19  C18   109.36  3.000
 MGJ  H19A  C19  C20   109.60  3.000
 MGJ  H19   C19  C20   110.16  3.000
 MGJ  C18   C19  C20   111.96  3.000
 MGJ  H23   C23  C24   120.26  3.000
 MGJ  H23   C23  C22   120.24  3.000
 MGJ  C24   C23  C22   119.50  3.000
 MGJ  H25   C25  C24   119.48  3.000
 MGJ  H25   C25  C20   119.52  3.000
 MGJ  C24   C25  C20   121.00  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
 MGJ  CONST_01  C07   C08  N09  C10     0.00   0.0  0
 MGJ  CONST_02  C08   C07  N11  C10     0.00   0.0  0
 MGJ  CONST_03  C23   C22  C21  C20     0.00   0.0  0
 MGJ  CONST_04  C23   C24  C25  C20     0.00   0.0  0
 MGJ  CONST_05  C24   C25  C20  C21     0.00   0.0  0
 MGJ  CONST_06  C24   C23  C22  C21     0.00   0.0  0
 MGJ  CONST_07  C25   C20  C21  C22     0.00   0.0  0
 MGJ  CONST_08  C25   C24  C23  C22     0.00   0.0  0
 MGJ  CONST_09  N09   C10  N11  C07     0.00   0.0  0
 MGJ  CONST_10  N11   C10  N09  C08     0.00   0.0  0
 MGJ  CONST_11  N11   C07  C08  N09     0.00   0.0  0
 MGJ  CONST_12  C06   C07  N11  C10   180.00   0.0  0
 MGJ  CONST_13  C19   C20  C21  C22   180.00   0.0  0
 MGJ  CONST_14  C19   C20  C25  C24   180.00   0.0  0
 MGJ  CONST_15  N09   C08  C07  C06   180.00   0.0  0
 MGJ  CONST_16  H08   C08  N09  C10   180.00   0.0  0
 MGJ  CONST_17  H22   C22  C21  C20   180.00   0.0  0
 MGJ  CONST_18  H24   C24  C25  C20   180.00   0.0  0
 MGJ  CONST_19  H25   C25  C20  C21   180.00   0.0  0
 MGJ  CONST_20  H23   C23  C22  C21   180.00   0.0  0
 MGJ  CONST_21  HN09  N09  C08  C07   180.00   0.0  0
 MGJ  CONST_22  H10   C10  N11  C07   180.00   0.0  0
 MGJ  CONST_23  H21   C21  C22  C23   180.00   0.0  0
 MGJ  CONST_24  C05   N12  C13  C15   180.00   0.0  0
 MGJ  CONST_25  C01   N02  C03  O04     0.00   0.0  0
 MGJ  CONST_26  C05   C03  N02  C01   180.00   0.0  0
 MGJ  CONST_27  O14   C13  N12  C05     0.00   0.0  0
 MGJ  CONST_28  HN12  N12  C13  C15     0.00   0.0  0
 MGJ  CONST_29  HN02  N02  C03  O04   180.00   0.0  0
 MGJ  Var_01    C18   C19  C20  C21    91.53  30.0  2
 MGJ  Var_02    C08   C07  C06  C05   115.42  30.0  2
 MGJ  Var_03    C20   C19  C18  C17  -176.80  30.0  3
 MGJ  Var_04    N16   C15  C13  N12  -139.34  30.0  3
 MGJ  Var_05    C17   N16  C15  C13  -159.13  30.0  3
 MGJ  Var_06    C18   C17  N16  C15   174.13  30.0  1
 MGJ  Var_07    C27   C26  N16  C15    73.86  30.0  2
 MGJ  Var_08    C19   C18  C17  N16  -172.29  30.0  3
 MGJ  Var_09    O28   C27  C26  N16   164.24  30.0  3
 MGJ  Var_10    H01   C01  N02  C03    67.91  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
 MGJ  chir_01  C05  N12  C03  C06  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
 MGJ  plan-1  C10   0.020
 MGJ  plan-1  C06   0.020
 MGJ  plan-1  C07   0.020
 MGJ  plan-1  C08   0.020
 MGJ  plan-1  N09   0.020
 MGJ  plan-1  N11   0.020
 MGJ  plan-1  H10   0.020
 MGJ  plan-1  H08   0.020
 MGJ  plan-1  HN09  0.020
 MGJ  plan-2  C20   0.020
 MGJ  plan-2  C21   0.020
 MGJ  plan-2  C22   0.020
 MGJ  plan-2  C24   0.020
 MGJ  plan-2  C19   0.020
 MGJ  plan-2  C23   0.020
 MGJ  plan-2  C25   0.020
 MGJ  plan-2  H21   0.020
 MGJ  plan-2  H22   0.020
 MGJ  plan-2  H24   0.020
 MGJ  plan-2  H23   0.020
 MGJ  plan-2  H25   0.020
 MGJ  plan-3  N12   0.020
 MGJ  plan-3  C13   0.020
 MGJ  plan-3  C15   0.020
 MGJ  plan-3  C05   0.020
 MGJ  plan-3  O14   0.020
 MGJ  plan-3  HN12  0.020
 MGJ  plan-4  C03   0.020
 MGJ  plan-4  N02   0.020
 MGJ  plan-4  C01   0.020
 MGJ  plan-4  C05   0.020
 MGJ  plan-4  HN02  0.020
 MGJ  plan-4  O04   0.020
 MGJ  plan-5  C26   0.020
 MGJ  plan-5  C27   0.020
 MGJ  plan-5  O28   0.020
 MGJ  plan-5  O29   0.020

