# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Apr 23 16:13:18 2020
#   Inital geometry file: a 137 line input string
#   Ligand name: methyl N-(carboxymethyl)-N-(3-phenylpropanoyl)glycyl-D-histidinate
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: COC(=O)[C@@H](Cc1c[nH]cn1)NC(=O)CN(CC(O)=O)C(=O)CCc2ccccc2
#
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
 MGH  MGH  'methyl N-(carboxymethyl)-N-(3-phenylpropanoyl)glycyl-D-histidinate'  ligand  53  30  .  2021-08-14  2021-08-14  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_MGH
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
 MGH  C01   C  CH3    0  -0.426  -3.1808   4.4755   1.0988
 MGH  O02   O  O2     0  -0.449  -3.5629   3.0999   1.0670
 MGH  C03   C  C      0   0.581  -3.0454   2.3461   0.1110
 MGH  O04   O  O      0  -0.445  -2.2875   2.7453  -0.7337
 MGH  C05   C  CH1    0  -0.142  -3.6051   0.9329   0.1585
 MGH  C06   C  CH2    0  -0.559  -4.7495   0.8279  -0.8639
 MGH  C07   C  CR5    0   0.153  -5.3486  -0.5357  -0.9125
 MGH  C08   C  CR15   0  -0.122  -6.5614  -0.9575  -0.4450
 MGH  N09   N  NR15   0  -0.562  -6.6080  -2.2949  -0.7116
 MGH  C10   C  CR15   0   0.105  -5.4540  -2.6348  -1.3118
 MGH  N11   N  N      0  -0.477  -4.6686  -1.5966  -1.4524
 MGH  N12   N  NH1    0  -0.662  -2.5720  -0.0199  -0.1537
 MGH  C13   C  C      0   0.573  -1.4527  -0.0800   0.5812
 MGH  O14   O  O      0  -0.493  -1.2002   0.7341   1.4557
 MGH  C15   C  CH2    0  -0.450  -0.5511  -1.2680   0.2916
 MGH  N16   N  NT     0  -0.419   0.8152  -0.9988   0.6444
 MGH  C17   C  CH2    0  -0.482   1.3623  -1.6694   1.8006
 MGH  C18   C  C      0   0.414   1.8999  -3.0905   1.5173
 MGH  O19   O  OC    -1  -0.617   2.2727  -3.7167   2.5278
 MGH  O20   O  O      0  -0.595   1.9188  -3.4685   0.3344
 MGH  C21   C  C      0   0.583   1.5353  -0.2480  -0.2100
 MGH  O22   O  O      0  -0.510   1.0175   0.2516  -1.2032
 MGH  C23   C  CH2    0  -0.591   2.9984  -0.0304   0.1150
 MGH  C24   C  CH2    0  -0.499   3.7507   0.7058  -0.9896
 MGH  C25   C  CR6    0   0.126   5.1859   0.9278  -0.5983
 MGH  C26   C  CR16   0  -0.310   5.5670   2.0727   0.0985
 MGH  C27   C  CR16   0  -0.240   6.8850   2.2619   0.4929
 MGH  C28   C  CR16   0  -0.274   7.8461   1.3039   0.1961
 MGH  C29   C  CR16   0  -0.240   7.4787   0.1584  -0.4982
 MGH  C30   C  CR16   0  -0.309   6.1592  -0.0256  -0.8899
 MGH  H101  H  HCH3   0   0.240  -3.4567   4.9886   0.1780
 MGH  H201  H  HCH3   0   0.252  -3.7197   4.9156   1.9323
 MGH  H301  H  HCH3   0   0.241  -2.1091   4.5836   1.2640
 MGH  H05   H  HCH1   0   0.280  -4.0096   0.7444   1.1577
 MGH  H106  H  HCH2   0   0.277  -5.5171   1.5574  -0.6022
 MGH  H206  H  HCH2   0   0.266  -4.3672   1.1013  -1.8510
 MGH  H08   H  HCR5   0   0.288  -7.3688  -0.4335   0.0376
 MGH  HN09  H  HNR5   0   0.424  -7.3715  -2.9172  -0.4987
 MGH  H10   H  HCR5   0   0.283  -5.2377  -3.6431  -1.6284
 MGH  HN12  H  HNH1   0   0.410  -2.7882  -0.7497  -0.8222
 MGH  H115  H  HCH2   0   0.293  -0.9097  -2.1051   0.8951
 MGH  H215  H  HCH2   0   0.271  -0.6452  -1.5785  -0.7508
 MGH  H117  H  HCH2   0   0.267   2.1583  -1.0683   2.2431
 MGH  H217  H  HCH2   0   0.264   0.5859  -1.7215   2.5668
 MGH  H123  H  HCH2   0   0.274   3.0708   0.5356   1.0498
 MGH  H223  H  HCH2   0   0.270   3.4791  -0.9918   0.3117
 MGH  H124  H  HCH2   0   0.246   3.7076   0.1252  -1.9132
 MGH  H224  H  HCH2   0   0.247   3.2696   1.6635  -1.1935
 MGH  H26   H  HCR6   0   0.246   4.8239   2.8271   0.3316
 MGH  H27   H  HCR6   0   0.252   7.1628   3.1600   1.0300
 MGH  H28   H  HCR6   0   0.253   8.8743   1.4506   0.5007
 MGH  H29   H  HCR6   0   0.252   8.2216  -0.5916  -0.7390
 MGH  H30   H  HCR6   0   0.245   5.8806  -0.9206  -1.4348

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
 MGH  C01  H101  single    0.970  0.020  1.090
 MGH  C01  H201  single    0.970  0.020  1.090
 MGH  C01  H301  single    0.970  0.020  1.090
 MGH  O02  C03   single    1.323  0.020  1.323
 MGH  O02  C01   single    1.428  0.020  1.428
 MGH  C03  C05   single    1.521  0.020  1.521
 MGH  C03  O04   double    1.203  0.020  1.203
 MGH  C05  N12   single    1.440  0.020  1.440
 MGH  C05  H05   single    0.970  0.020  1.090
 MGH  C06  C07   single    1.490  0.020  1.490
 MGH  C06  C05   single    1.538  0.020  1.538
 MGH  C06  H106  single    0.970  0.020  1.090
 MGH  C06  H206  single    0.970  0.020  1.090
 MGH  C07  N11   aromatic  1.371  0.020  1.371
 MGH  C08  N09   aromatic  1.365  0.020  1.365
 MGH  C08  C07   aromatic  1.367  0.020  1.367
 MGH  C08  H08   single    0.930  0.020  1.080
 MGH  N09  C10   aromatic  1.344  0.020  1.344
 MGH  N09  HN09  single    0.860  0.020  1.020
 MGH  C10  N11   aromatic  1.309  0.020  1.309
 MGH  C10  H10   single    0.930  0.020  1.080
 MGH  N12  HN12  single    0.860  0.020  1.020
 MGH  C13  N12   single    1.340  0.020  1.340
 MGH  C13  C15   single    1.519  0.020  1.519
 MGH  O14  C13   double    1.221  0.020  1.221
 MGH  C15  H115  single    0.970  0.020  1.090
 MGH  C15  H215  single    0.970  0.020  1.090
 MGH  N16  C15   single    1.437  0.020  1.437
 MGH  N16  C17   single    1.444  0.020  1.444
 MGH  C17  C18   single    1.546  0.020  1.546
 MGH  C17  H117  single    0.970  0.020  1.090
 MGH  C17  H217  single    0.970  0.020  1.090
 MGH  C18  O19   deloc     1.246  0.020  1.246
 MGH  C18  O20   deloc     1.242  0.020  1.242
 MGH  C21  N16   single    1.346  0.020  1.346
 MGH  O22  C21   double    1.226  0.020  1.226
 MGH  C23  C21   single    1.514  0.020  1.514
 MGH  C23  H123  single    0.970  0.020  1.090
 MGH  C23  H223  single    0.970  0.020  1.090
 MGH  C24  C25   single    1.504  0.020  1.504
 MGH  C24  C23   single    1.526  0.020  1.526
 MGH  C24  H124  single    0.970  0.020  1.090
 MGH  C24  H224  single    0.970  0.020  1.090
 MGH  C25  C30   aromatic  1.393  0.020  1.393
 MGH  C26  C27   aromatic  1.389  0.020  1.389
 MGH  C26  C25   aromatic  1.393  0.020  1.393
 MGH  C26  H26   single    0.930  0.020  1.080
 MGH  C27  C28   aromatic  1.389  0.020  1.389
 MGH  C27  H27   single    0.930  0.020  1.080
 MGH  C28  C29   aromatic  1.389  0.020  1.389
 MGH  C28  H28   single    0.930  0.020  1.080
 MGH  C29  H29   single    0.930  0.020  1.080
 MGH  C30  C29   aromatic  1.389  0.020  1.389
 MGH  C30  H30   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
 MGH  H301  C01  H201  109.36  3.000
 MGH  H301  C01  H101  109.30  3.000
 MGH  H201  C01  H101  109.40  3.000
 MGH  H301  C01  O02   111.23  3.000
 MGH  H201  C01  O02   105.95  3.000
 MGH  H101  C01  O02   111.53  3.000
 MGH  C03   O02  C01   117.41  3.000
 MGH  C05   C03  O04   124.20  3.000
 MGH  O04   C03  O02   124.39  3.000
 MGH  C05   C03  O02   111.29  3.000
 MGH  H05   C05  N12   110.43  3.000
 MGH  H05   C05  C06   108.67  3.000
 MGH  N12   C05  C06   110.16  3.000
 MGH  C06   C05  C03   108.46  3.000
 MGH  H05   C05  C03   108.94  3.000
 MGH  N12   C05  C03   110.13  3.000
 MGH  H206  C06  H106  107.18  3.000
 MGH  H206  C06  C07   109.87  3.000
 MGH  H106  C06  C07   109.69  3.000
 MGH  H206  C06  C05   108.83  3.000
 MGH  H106  C06  C05   108.57  3.000
 MGH  C07   C06  C05   112.54  3.000
 MGH  N11   C07  C08   109.64  3.000
 MGH  C08   C07  C06   128.91  3.000
 MGH  N11   C07  C06   121.44  3.000
 MGH  H08   C08  N09   122.61  3.000
 MGH  H08   C08  C07   131.96  3.000
 MGH  N09   C08  C07   105.43  3.000
 MGH  HN09  N09  C10   126.05  3.000
 MGH  HN09  N09  C08   126.15  3.000
 MGH  C10   N09  C08   107.80  3.000
 MGH  H10   C10  N11   126.10  3.000
 MGH  H10   C10  N09   122.65  3.000
 MGH  N11   C10  N09   111.25  3.000
 MGH  C10   N11  C07   105.89  3.000
 MGH  HN12  N12  C13   120.51  3.000
 MGH  C13   N12  C05   120.67  3.000
 MGH  HN12  N12  C05   117.82  3.000
 MGH  C15   C13  O14   122.36  3.000
 MGH  O14   C13  N12   122.37  3.000
 MGH  C15   C13  N12   115.22  3.000
 MGH  H215  C15  H115  106.34  3.000
 MGH  H215  C15  N16   111.71  3.000
 MGH  H115  C15  N16   108.67  3.000
 MGH  N16   C15  C13   111.78  3.000
 MGH  H215  C15  C13   110.68  3.000
 MGH  H115  C15  C13   107.40  3.000
 MGH  C21   N16  C17   124.36  3.000
 MGH  C21   N16  C15   117.22  3.000
 MGH  C17   N16  C15   118.03  3.000
 MGH  H217  C17  H117  105.09  3.000
 MGH  H217  C17  C18   109.39  3.000
 MGH  H117  C17  C18   109.09  3.000
 MGH  H217  C17  N16   108.34  3.000
 MGH  H117  C17  N16   110.20  3.000
 MGH  C18   C17  N16   114.33  3.000
 MGH  O20   C18  O19   127.95  3.000
 MGH  O20   C18  C17   117.37  3.000
 MGH  O19   C18  C17   114.68  3.000
 MGH  C23   C21  O22   121.55  3.000
 MGH  C23   C21  N16   117.43  3.000
 MGH  O22   C21  N16   121.02  3.000
 MGH  H223  C23  H123  105.79  3.000
 MGH  H223  C23  C24   109.75  3.000
 MGH  H123  C23  C24   109.63  3.000
 MGH  C24   C23  C21   112.97  3.000
 MGH  H223  C23  C21   109.71  3.000
 MGH  H123  C23  C21   108.74  3.000
 MGH  H224  C24  H124  106.94  3.000
 MGH  H224  C24  C25   109.87  3.000
 MGH  H124  C24  C25   109.65  3.000
 MGH  H224  C24  C23   109.96  3.000
 MGH  H124  C24  C23   109.66  3.000
 MGH  C25   C24  C23   110.70  3.000
 MGH  C30   C25  C26   118.41  3.000
 MGH  C26   C25  C24   120.82  3.000
 MGH  C30   C25  C24   120.74  3.000
 MGH  H26   C26  C27   119.64  3.000
 MGH  H26   C26  C25   119.46  3.000
 MGH  C27   C26  C25   120.90  3.000
 MGH  H27   C27  C28   120.04  3.000
 MGH  H27   C27  C26   119.83  3.000
 MGH  C28   C27  C26   120.13  3.000
 MGH  H28   C28  C29   120.25  3.000
 MGH  H28   C28  C27   120.24  3.000
 MGH  C29   C28  C27   119.51  3.000
 MGH  H29   C29  C30   119.83  3.000
 MGH  C30   C29  C28   120.10  3.000
 MGH  H29   C29  C28   120.06  3.000
 MGH  H30   C30  C29   119.68  3.000
 MGH  H30   C30  C25   119.38  3.000
 MGH  C29   C30  C25   120.94  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
 MGH  CONST_01  N09   C10  N11  C07     0.00   0.0  0
 MGH  CONST_02  C10   N09  C08  C07     0.00   0.0  0
 MGH  CONST_03  N11   C10  N09  C08     0.00   0.0  0
 MGH  CONST_04  C10   N11  C07  C08     0.00   0.0  0
 MGH  CONST_05  N11   C07  C08  N09     0.00   0.0  0
 MGH  CONST_06  C28   C29  C30  C25     0.00   0.0  0
 MGH  CONST_07  C28   C27  C26  C25     0.00   0.0  0
 MGH  CONST_08  C29   C28  C27  C26     0.00   0.0  0
 MGH  CONST_09  C29   C30  C25  C26     0.00   0.0  0
 MGH  CONST_10  C30   C25  C26  C27     0.00   0.0  0
 MGH  CONST_11  C30   C29  C28  C27     0.00   0.0  0
 MGH  CONST_12  C10   N11  C07  C06   180.00   0.0  0
 MGH  CONST_13  N09   C08  C07  C06   180.00   0.0  0
 MGH  CONST_14  C29   C30  C25  C24   180.00   0.0  0
 MGH  CONST_15  C27   C26  C25  C24   180.00   0.0  0
 MGH  CONST_16  H10   C10  N11  C07   180.00   0.0  0
 MGH  CONST_17  HN09  N09  C08  C07   180.00   0.0  0
 MGH  CONST_18  H08   C08  N09  C10   180.00   0.0  0
 MGH  CONST_19  H29   C29  C30  C25   180.00   0.0  0
 MGH  CONST_20  H27   C27  C26  C25   180.00   0.0  0
 MGH  CONST_21  H28   C28  C27  C26   180.00   0.0  0
 MGH  CONST_22  H30   C30  C25  C26   180.00   0.0  0
 MGH  CONST_23  H26   C26  C27  C28   180.00   0.0  0
 MGH  CONST_24  C15   C13  N12  C05   180.00   0.0  0
 MGH  CONST_25  O14   C13  N12  C05     0.00   0.0  0
 MGH  CONST_26  O22   C21  N16  C15     0.00   0.0  0
 MGH  CONST_27  C23   C21  N16  C15   180.00   0.0  0
 MGH  CONST_28  O22   C21  N16  C17   180.00   0.0  0
 MGH  CONST_29  C23   C21  N16  C17     0.00   0.0  0
 MGH  CONST_30  HN12  N12  C13  O14   180.00   0.0  0
 MGH  Var_01    N11   C07  C06  C05   -71.17  30.0  2
 MGH  Var_02    C30   C25  C24  C23    88.94  30.0  2
 MGH  Var_03    C25   C24  C23  C21   178.43  30.0  1
 MGH  Var_04    C05   C03  O02  C01  -176.73  30.0  3
 MGH  Var_05    N16   C15  C13  N12   155.17  30.0  3
 MGH  Var_06    C17   N16  C15  C13   108.56  30.0  3
 MGH  Var_07    C18   C17  N16  C15    84.28  30.0  3
 MGH  Var_08    O19   C18  C17  N16  -174.41  30.0  3
 MGH  Var_09    C24   C23  C21  N16   173.87  30.0  1
 MGH  Var_10    H101  C01  O02  C03    60.05  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
 MGH  chir_01  C05  C03  N12  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
 MGH  plan-1  C06   0.020
 MGH  plan-1  C07   0.020
 MGH  plan-1  C08   0.020
 MGH  plan-1  N09   0.020
 MGH  plan-1  C10   0.020
 MGH  plan-1  N11   0.020
 MGH  plan-1  H08   0.020
 MGH  plan-1  HN09  0.020
 MGH  plan-1  H10   0.020
 MGH  plan-2  C24   0.020
 MGH  plan-2  C25   0.020
 MGH  plan-2  C26   0.020
 MGH  plan-2  C27   0.020
 MGH  plan-2  C28   0.020
 MGH  plan-2  C29   0.020
 MGH  plan-2  C30   0.020
 MGH  plan-2  H26   0.020
 MGH  plan-2  H27   0.020
 MGH  plan-2  H28   0.020
 MGH  plan-2  H29   0.020
 MGH  plan-2  H30   0.020
 MGH  plan-3  C05   0.020
 MGH  plan-3  N12   0.020
 MGH  plan-3  C13   0.020
 MGH  plan-3  O14   0.020
 MGH  plan-3  C15   0.020
 MGH  plan-3  HN12  0.020
 MGH  plan-4  C15   0.020
 MGH  plan-4  N16   0.020
 MGH  plan-4  C17   0.020
 MGH  plan-4  C21   0.020
 MGH  plan-4  O22   0.020
 MGH  plan-4  C23   0.020
 MGH  plan-5  C17   0.020
 MGH  plan-5  C18   0.020
 MGH  plan-5  O19   0.020
 MGH  plan-5  O20   0.020
 MGH  plan-6  O02   0.020
 MGH  plan-6  C03   0.020
 MGH  plan-6  O04   0.020
 MGH  plan-6  C05   0.020

