# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun May 17 03:34:34 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  54  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  -3.0626   4.3755   1.3874
 MGH  O02   O  O2    0  -0.449  -3.4610   3.0075   1.2878
 MGH  C03   C  C     0   0.581  -2.9863   2.3076   0.2708
 MGH  O04   O  O     0  -0.443  -2.2457   2.7454  -0.5697
 MGH  C05   C  CH1   0  -0.144  -3.5726   0.9045   0.2478
 MGH  C06   C  CH2   0  -0.559  -4.7836   0.8988  -0.7014
 MGH  C07   C  CR5   0   0.152  -5.4056  -0.4497  -0.8244
 MGH  C08   C  CR15  0  -0.121  -6.5830  -0.9029  -0.2992
 MGH  N09   N  NR15  0  -0.562  -6.6711  -2.2100  -0.6804
 MGH  C10   C  CR15  0   0.104  -5.5747  -2.5029  -1.4012
 MGH  N11   N  N     0  -0.477  -4.7874  -1.4623  -1.5113
 MGH  N12   N  NH1   0  -0.661  -2.5840  -0.0383  -0.2068
 MGH  C13   C  C     0   0.578  -1.4238  -0.1819   0.4462
 MGH  O14   O  O     0  -0.490  -1.0982   0.5363   1.3781
 MGH  C15   C  CH2   0  -0.460  -0.5574  -1.3412  -0.0209
 MGH  N16   N  NT    0  -0.440   0.8227  -1.1405   0.3340
 MGH  C17   C  CH2   0  -0.472   1.3298  -1.8188   1.4920
 MGH  C18   C  C     0   0.549   1.8752  -3.1922   1.1559
 MGH  O19   O  OH1   0  -0.588   2.2504  -3.8367   2.2501
 MGH  O20   O  O     0  -0.431   1.9608  -3.6345   0.0411
 MGH  C21   C  C     0   0.594   1.5422  -0.2641  -0.4094
 MGH  O22   O  O     0  -0.485   1.0255   0.3236  -1.3464
 MGH  C23   C  CH2   0  -0.599   2.9896  -0.0445  -0.0247
 MGH  C24   C  CH2   0  -0.500   3.7571   0.7853  -1.0506
 MGH  C25   C  CR6   0   0.124   5.1724   1.0143  -0.5956
 MGH  C26   C  CR16  0  -0.310   5.5030   2.1302   0.1700
 MGH  C27   C  CR16  0  -0.239   6.8016   2.3256   0.6218
 MGH  C28   C  CR16  0  -0.273   7.7927   1.4024   0.3141
 MGH  C29   C  CR16  0  -0.239   7.4753   0.2857  -0.4487
 MGH  C30   C  CR16  0  -0.307   6.1752   0.0955  -0.8978
 MGH  H101  H  HCH3  0   0.240  -3.3542   4.9417   0.5033
 MGH  H201  H  HCH3  0   0.253  -3.5773   4.7734   2.2567
 MGH  H301  H  HCH3  0   0.241  -1.9863   4.4634   1.5327
 MGH  H05   H  HCH1  0   0.283  -3.9162   0.6453   1.2539
 MGH  H106  H  HCH2  0   0.278  -5.5203   1.6104  -0.3271
 MGH  H206  H  HCH2  0   0.267  -4.4631   1.2516  -1.6853
 MGH  H08   H  HCR5  0   0.288  -7.3412  -0.4181   0.2921
 MGH  HN09  H  HNR5  0   0.424  -7.4247  -2.8428  -0.4633
 MGH  H10   H  HCR5  0   0.283  -5.4007  -3.4795  -1.8250
 MGH  HN12  H  HNH1  0   0.412  -2.8548  -0.6970  -0.9274
 MGH  H115  H  HCH2  0   0.304  -0.9191  -2.2481   0.4682
 MGH  H215  H  HCH2  0   0.286  -0.6684  -1.5035  -1.0937
 MGH  H117  H  HCH2  0   0.317   2.1107  -1.2398   1.9872
 MGH  H217  H  HCH2  0   0.321   0.5375  -1.9221   2.2366
 MGH  H123  H  HCH2  0   0.285   3.0195   0.4578   0.9484
 MGH  H223  H  HCH2  0   0.271   3.4944  -1.0031   0.1194
 MGH  H124  H  HCH2  0   0.251   3.7567   0.2702  -2.0131
 MGH  H224  H  HCH2  0   0.252   3.2572   1.7429  -1.2019
 MGH  H26   H  HCR6  0   0.247   4.7357   2.8568   0.4127
 MGH  H27   H  HCR6  0   0.253   7.0404   3.2016   1.2116
 MGH  H28   H  HCR6  0   0.253   8.8060   1.5535   0.6636
 MGH  H29   H  HCR6  0   0.253   8.2423  -0.4364  -0.6984
 MGH  H30   H  HCR6  0   0.246   5.9361  -0.7764  -1.4962
 MGH  H24   H  HOH1  0   0.487   2.6123  -4.7061   2.0210

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    1.539  0.020  1.539
 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  1.364  0.020  1.364
 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    1.339  0.020  1.339
 MGH  C13  C15   single    1.521  0.020  1.521
 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    1.439  0.020  1.439
 MGH  N16  C17   single    1.435  0.020  1.435
 MGH  C17  C18   single    1.515  0.020  1.515
 MGH  C17  H117  single    0.970  0.020  1.090
 MGH  C17  H217  single    0.970  0.020  1.090
 MGH  C18  O19   single    1.324  0.020  1.324
 MGH  C18  O20   double    1.202  0.020  1.202
 MGH  C21  N16   single    1.356  0.020  1.356
 MGH  O22  C21   double    1.221  0.020  1.221
 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    1.527  0.020  1.527
 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
 MGH  O19  H24   single    0.850  0.020  0.980

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  109.39  3.000
 MGH  H301  C01  H101  109.31  3.000
 MGH  H201  C01  H101  109.41  3.000
 MGH  H301  C01  O02   111.22  3.000
 MGH  H201  C01  O02   105.94  3.000
 MGH  H101  C01  O02   111.50  3.000
 MGH  C03   O02  C01   117.41  3.000
 MGH  C05   C03  O04   124.24  3.000
 MGH  O04   C03  O02   124.45  3.000
 MGH  C05   C03  O02   111.19  3.000
 MGH  H05   C05  N12   110.54  3.000
 MGH  H05   C05  C06   108.61  3.000
 MGH  N12   C05  C06   110.07  3.000
 MGH  C06   C05  C03   108.43  3.000
 MGH  H05   C05  C03   109.01  3.000
 MGH  N12   C05  C03   110.13  3.000
 MGH  H206  C06  H106  107.23  3.000
 MGH  H206  C06  C07   109.89  3.000
 MGH  H106  C06  C07   109.69  3.000
 MGH  H206  C06  C05   108.86  3.000
 MGH  H106  C06  C05   108.51  3.000
 MGH  C07   C06  C05   112.51  3.000
 MGH  N11   C07  C08   109.65  3.000
 MGH  C08   C07  C06   128.90  3.000
 MGH  N11   C07  C06   121.43  3.000
 MGH  H08   C08  N09   122.63  3.000
 MGH  H08   C08  C07   131.95  3.000
 MGH  N09   C08  C07   105.43  3.000
 MGH  HN09  N09  C10   126.06  3.000
 MGH  HN09  N09  C08   126.14  3.000
 MGH  C10   N09  C08   107.81  3.000
 MGH  H10   C10  N11   126.12  3.000
 MGH  H10   C10  N09   122.64  3.000
 MGH  N11   C10  N09   111.24  3.000
 MGH  C10   N11  C07   105.88  3.000
 MGH  HN12  N12  C13   120.58  3.000
 MGH  C13   N12  C05   120.74  3.000
 MGH  HN12  N12  C05   117.83  3.000
 MGH  C15   C13  O14   122.07  3.000
 MGH  O14   C13  N12   122.70  3.000
 MGH  C15   C13  N12   115.19  3.000
 MGH  H215  C15  H115  106.46  3.000
 MGH  H215  C15  N16   111.16  3.000
 MGH  H115  C15  N16   108.85  3.000
 MGH  N16   C15  C13   111.36  3.000
 MGH  H215  C15  C13   110.95  3.000
 MGH  H115  C15  C13   107.86  3.000
 MGH  C21   N16  C17   124.10  3.000
 MGH  C21   N16  C15   117.63  3.000
 MGH  C17   N16  C15   118.17  3.000
 MGH  H217  C17  H117  105.08  3.000
 MGH  H217  C17  C18   109.06  3.000
 MGH  H117  C17  C18   108.90  3.000
 MGH  H217  C17  N16   109.79  3.000
 MGH  H117  C17  N16   111.62  3.000
 MGH  C18   C17  N16   112.12  3.000
 MGH  O20   C18  O19   124.54  3.000
 MGH  O20   C18  C17   124.38  3.000
 MGH  O19   C18  C17   111.09  3.000
 MGH  H24   O19  C18   110.30  3.000
 MGH  C23   C21  O22   122.00  3.000
 MGH  C23   C21  N16   117.50  3.000
 MGH  O22   C21  N16   120.49  3.000
 MGH  H223  C23  H123  105.81  3.000
 MGH  H223  C23  C24   109.46  3.000
 MGH  H123  C23  C24   109.51  3.000
 MGH  C24   C23  C21   112.88  3.000
 MGH  H223  C23  C21   110.37  3.000
 MGH  H123  C23  C21   108.57  3.000
 MGH  H224  C24  H124  106.96  3.000
 MGH  H224  C24  C25   109.85  3.000
 MGH  H124  C24  C25   109.81  3.000
 MGH  H224  C24  C23   109.88  3.000
 MGH  H124  C24  C23   109.62  3.000
 MGH  C25   C24  C23   110.65  3.000
 MGH  C30   C25  C26   118.46  3.000
 MGH  C26   C25  C24   120.76  3.000
 MGH  C30   C25  C24   120.75  3.000
 MGH  H26   C26  C27   119.65  3.000
 MGH  H26   C26  C25   119.46  3.000
 MGH  C27   C26  C25   120.89  3.000
 MGH  H27   C27  C28   120.07  3.000
 MGH  H27   C27  C26   119.82  3.000
 MGH  C28   C27  C26   120.11  3.000
 MGH  H28   C28  C29   120.23  3.000
 MGH  H28   C28  C27   120.24  3.000
 MGH  C29   C28  C27   119.53  3.000
 MGH  H29   C29  C30   119.82  3.000
 MGH  C30   C29  C28   120.11  3.000
 MGH  H29   C29  C28   120.07  3.000
 MGH  H30   C30  C29   119.68  3.000
 MGH  H30   C30  C25   119.43  3.000
 MGH  C29   C30  C25   120.89  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  CONST_31  H24   O19  C18  C17   180.00   0.0  0
 MGH  Var_01    N11   C07  C06  C05   -72.07  30.0  2
 MGH  Var_02    C30   C25  C24  C23    87.78  30.0  2
 MGH  Var_03    C25   C24  C23  C21   177.96  30.0  1
 MGH  Var_04    C05   C03  O02  C01  -176.11  30.0  3
 MGH  Var_05    N16   C15  C13  N12   157.97  30.0  3
 MGH  Var_06    C17   N16  C15  C13    99.95  30.0  2
 MGH  Var_07    C18   C17  N16  C15    89.03  30.0  3
 MGH  Var_08    O19   C18  C17  N16  -175.58  30.0  3
 MGH  Var_09    C24   C23  C21  N16   170.99  30.0  1
 MGH  Var_10    H101  C01  O02  C03    59.31  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-5  H24   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

