FMODB

FMODB: The database of quantum mechanical data based on the FMO method

Last updated: 2025-10-17

All entries: 77277

Number of unique PDB entries: 32023

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FMODB ID: 2G5GR

Calculation Name: 1XSS-B-Xray547

Preferred Name:

Target Type:

Ligand Name: (3s)-3-amino-3-[(4z)-1-(carboxymethyl)-4-[(4-hydroxyphenyl)methylidene]-5-oxo-imidazol-2-yl]propanoic acid

Ligand 3-letter code: DYG

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 1XSS

Chain ID: B

ChEMBL ID:

UniProt ID: Q53UG7

Base Structure: X-ray

Registration Date: 2025-10-06

Reference: Sci Data 11, 1164 (2024).

DOI: https://doi.org/10.1038/s41597-024-03999-2

Apendix: None


IFIE MAP

IFIE Diagram


Modeling method
Optimization MOE:Amber10:EHT
Restraint OptAll
Protonation MOE:Protonate 3D
Complement MOE:Homology Modeling
Water No
Procedure Manual calculation
Remarks
ac.sh, 23 2024 Oct; Missing atoms/residues were imported from a 100% homology model, which was constructed by MOE.
FMO calculation
FMO method FMO2-MP2/6-31G(d)
Fragmentation Auto
Number of fragment 225
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922
Total energy (hartree)
FMO2-HF: Electronic energy -2906851.356548
FMO2-HF: Nuclear repulsion 2815676.905046
FMO2-HF: Total energy -91174.451502
FMO2-MP2: Total energy -91436.611644


3D Structure Molmil
Snapshot
 
Ligand structure

ligand structure
Ligand Interaction
ligand interaction
Ligand binding energy
IFIE [kcal/mol] PIEDA [kcal/mol] Charge transfer value [e]
IFIE SUMIFIE SUM at MP2 level. ESElectro static interaction energy. EXExchange-repulsion energy. CT+mixCharge transfer and mixing terms energy. DI(MP2)Dispersion energy. q(I=>J)Charge transfer value from I to J fragments.
N/AN/AN/AN/AN/AN/A


Interactive mode: IFIE and PIEDA for fragment #1(B:1:VAL)


Summations of interaction energy for fragment #1(B:1:VAL)
IFIE [kcal/mol] PIEDA [kcal/mol] Charge transfer value [e]
IFIE SUMIFIE SUM at MP2 level. ESElectro static interaction energy. EXExchange-repulsion energy. CT+mixCharge transfer and mixing terms energy. DI(MP2)Dispersion energy. q(I=>J)Charge transfer value from I to J fragments.
-49.113-45.8840.675-1.682-2.222-0.014
Interaction energy analysis for fragmet #1(B:1:VAL)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 1 / q_Mulliken : 0.855 / q_NPA : 0.914
Distance from base fragment(s) [Å]
Dist
Interaction energy by IFIE and PIEDA
[kcal/mol]
| Total | > | ES | > | EX | >
| CT+mix | > | DI(MP2) | >
Fragment charge [e]
FCHARGE q_Mulliken
q_NPA q(I=>J)
Residue
Res #    RES   
Sort
Graph Options
X Axis Label
Y Axis Max Y Axis Min
Display   
frag_NumFragment number. ChainChain species. Res #Residue number. RES3-letter code of amino acid residue, ligand and solvent molecule. FCHARGEFormal charge [e]. q_MullikenFragment charge evaluated by Mulliken charge [e]. q_NPAFragment charge evaluated by natural population analysis(NPA) charge [e]. DISTDistance from Ligand [Å]. TotalIFIE at MP2 level [kcal/mol]. ESElectro static interaction energy by PIEDA [kcal/mol]. EXExchange-repulsion energy by PIEDA [kcal/mol]. CT+mixCharge transfer and mixing terms energy by PIEDA [kcal/mol]. DI(MP2)Dispersion energy by PIEDA [kcal/mol]. q(I=>J)Charge transfer value from I to J fragmens [e].
3B3VAL00.0190.0002.678-2.1920.7600.677-1.630-1.999-0.014
4B4ILE0-0.035-0.0054.9615.2185.302-0.001-0.006-0.0770.000
79B81GLN0-0.064-0.0403.752-10.067-9.874-0.001-0.046-0.1460.000
5B5THR00.0190.0017.682-0.885-0.8850.0000.0000.0000.000
6B6SER00.0460.00010.247-0.036-0.0360.0000.0000.0000.000
7B7GLU-1-0.962-0.96713.666-13.998-13.9980.0000.0000.0000.000
8B8MET0-0.048-0.00511.320-1.431-1.4310.0000.0000.0000.000
9B9LYS10.9500.96815.56414.88014.8800.0000.0000.0000.000
10B10MET0-0.0060.02317.479-0.677-0.6770.0000.0000.0000.000
11B11GLU-1-0.858-0.93519.983-12.194-12.1940.0000.0000.0000.000
12B12LEU0-0.033-0.00422.276-0.538-0.5380.0000.0000.0000.000
13B13ARG10.8610.90824.85410.56010.5600.0000.0000.0000.000
14B14MET0-0.0010.03027.238-0.212-0.2120.0000.0000.0000.000
15B15GLU-1-0.827-0.89729.473-9.536-9.5360.0000.0000.0000.000
16B16GLY00.0430.00231.702-0.292-0.2920.0000.0000.0000.000
17B17ALA0-0.032-0.02034.2780.3080.3080.0000.0000.0000.000
18B18VAL00.0100.01536.928-0.188-0.1880.0000.0000.0000.000
19B19ASN0-0.027-0.02939.3460.0770.0770.0000.0000.0000.000
20B20GLY00.0020.00941.1940.2000.2000.0000.0000.0000.000
21B21HIS0-0.068-0.03640.9800.1520.1520.0000.0000.0000.000
22B22LYS10.9530.96839.0797.4907.4900.0000.0000.0000.000
23B23PHE0-0.016-0.01333.5800.1760.1760.0000.0000.0000.000
24B24VAL00.0250.02033.091-0.255-0.2550.0000.0000.0000.000
25B25ILE0-0.0060.00030.6280.2310.2310.0000.0000.0000.000
26B26THR0-0.025-0.00429.350-0.290-0.2900.0000.0000.0000.000
27B27GLY00.0420.00627.8280.3450.3450.0000.0000.0000.000
28B28LYS10.8610.93324.48111.43811.4380.0000.0000.0000.000
29B29GLY00.0040.00023.2110.5520.5520.0000.0000.0000.000
30B30SER0-0.073-0.04520.158-0.292-0.2920.0000.0000.0000.000
31B31GLY00.0680.03418.8160.5530.5530.0000.0000.0000.000
32B32GLN00.0280.01816.550-0.489-0.4890.0000.0000.0000.000
33B33PRO0-0.006-0.00812.3580.2940.2940.0000.0000.0000.000
34B34PHE0-0.0040.0018.636-0.563-0.5630.0000.0000.0000.000
35B35GLU-1-0.858-0.92014.427-16.598-16.5980.0000.0000.0000.000
36B36GLY0-0.028-0.00117.5260.7030.7030.0000.0000.0000.000
37B37ILE00.0040.01718.8250.8260.8260.0000.0000.0000.000
38B38GLN00.0210.00020.010-1.165-1.1650.0000.0000.0000.000
39B39ASN00.001-0.00421.9480.2770.2770.0000.0000.0000.000
40B40MET0-0.006-0.00223.708-0.268-0.2680.0000.0000.0000.000
41B41ASP-1-0.862-0.89826.358-9.726-9.7260.0000.0000.0000.000
42B42LEU0-0.012-0.00828.148-0.270-0.2700.0000.0000.0000.000
43B43THR0-0.016-0.01631.0880.4310.4310.0000.0000.0000.000
44B44VAL00.0050.01333.705-0.214-0.2140.0000.0000.0000.000
45B45ILE0-0.069-0.03433.6790.1570.1570.0000.0000.0000.000
46B46GLU-1-0.894-0.95137.126-8.411-8.4110.0000.0000.0000.000
47B47GLY00.0400.01338.646-0.166-0.1660.0000.0000.0000.000
48B48GLY00.0020.03140.9620.0080.0080.0000.0000.0000.000
49B49PRO0-0.026-0.01841.6780.1190.1190.0000.0000.0000.000
50B50LEU00.0270.01137.1010.0460.0460.0000.0000.0000.000
51B51PRO0-0.053-0.01941.7760.0710.0710.0000.0000.0000.000
52B52PHE00.029-0.00936.4690.1080.1080.0000.0000.0000.000
53B53ALA0-0.005-0.00238.907-0.058-0.0580.0000.0000.0000.000
54B54PHE00.0680.01332.280-0.191-0.1910.0000.0000.0000.000
55B55ASP-1-0.799-0.88234.075-9.220-9.2200.0000.0000.0000.000
56B56ILE0-0.0230.00632.628-0.358-0.3580.0000.0000.0000.000
57B57LEU0-0.025-0.00231.163-0.226-0.2260.0000.0000.0000.000
58B58THR0-0.043-0.03929.330-0.461-0.4610.0000.0000.0000.000
59B59THR00.0200.02226.372-0.307-0.3070.0000.0000.0000.000
60B60VAL00.016-0.01025.453-0.342-0.3420.0000.0000.0000.000
61B61PHE0-0.019-0.01824.852-0.349-0.3490.0000.0000.0000.000
62B64TYR-1-0.853-0.92122.498-13.721-13.7210.0000.0000.0000.000
63B65ASN00.0710.02815.553-1.120-1.1200.0000.0000.0000.000
64B66ARG00.0640.03316.178-0.934-0.9340.0000.0000.0000.000
65B67VAL0-0.002-0.00111.955-1.247-1.2470.0000.0000.0000.000
66B68PHE0-0.092-0.04314.125-0.990-0.9900.0000.0000.0000.000
67B69VAL00.0290.03015.6411.2371.2370.0000.0000.0000.000
68B70LYS10.8090.89615.05216.12516.1250.0000.0000.0000.000
69B71TYR0-0.010-0.04412.6230.9910.9910.0000.0000.0000.000
70B72PRO0-0.057-0.00313.758-0.675-0.6750.0000.0000.0000.000
71B73GLU-1-0.892-0.95811.904-20.407-20.4070.0000.0000.0000.000
72B74GLU-1-0.932-0.96912.267-19.162-19.1620.0000.0000.0000.000
73B75ILE0-0.079-0.02613.6510.2050.2050.0000.0000.0000.000
74B76VAL0-0.007-0.0058.312-1.657-1.6570.0000.0000.0000.000
75B77ASP-1-0.730-0.8578.559-26.878-26.8780.0000.0000.0000.000
76B78TYR00.0170.0067.935-4.275-4.2750.0000.0000.0000.000
77B79PHE00.0310.0209.395-1.414-1.4140.0000.0000.0000.000
78B80LYS10.8100.8977.91223.98523.9850.0000.0000.0000.000
80B82SER0-0.046-0.0325.297-2.994-2.9940.0000.0000.0000.000
81B83PHE0-0.0160.0297.5922.9652.9650.0000.0000.0000.000
82B84PRO00.004-0.0206.364-6.645-6.6450.0000.0000.0000.000
83B85GLU-1-0.829-0.9128.239-33.715-33.7150.0000.0000.0000.000
84B86GLY00.019-0.00310.2172.6032.6030.0000.0000.0000.000
85B87TYR0-0.040-0.05311.823-0.407-0.4070.0000.0000.0000.000
86B88SER0-0.019-0.00314.1081.2951.2950.0000.0000.0000.000
87B89TRP0-0.023-0.01817.669-0.318-0.3180.0000.0000.0000.000
88B90GLU-1-0.793-0.87120.217-13.139-13.1390.0000.0000.0000.000
89B91ARG10.8370.90122.36712.99012.9900.0000.0000.0000.000
90B92SER00.0020.02026.1010.3260.3260.0000.0000.0000.000
91B93MET0-0.028-0.02329.169-0.284-0.2840.0000.0000.0000.000
92B94SER00.0350.01931.4520.3100.3100.0000.0000.0000.000
93B95TYR00.033-0.01133.509-0.139-0.1390.0000.0000.0000.000
94B96GLU-1-0.862-0.92137.516-7.703-7.7030.0000.0000.0000.000
95B97ASP-1-0.861-0.92340.440-7.531-7.5310.0000.0000.0000.000
96B98GLY0-0.0060.00441.3350.1740.1740.0000.0000.0000.000
97B99GLY0-0.0180.00340.060-0.040-0.0400.0000.0000.0000.000
98B100ILE0-0.026-0.01734.264-0.201-0.2010.0000.0000.0000.000
99B101CYS0-0.0280.01632.6730.1960.1960.0000.0000.0000.000
100B102LEU0-0.0050.00230.545-0.223-0.2230.0000.0000.0000.000
101B103ALA0-0.014-0.00727.5130.1570.1570.0000.0000.0000.000
102B104THR0-0.005-0.00524.339-0.312-0.3120.0000.0000.0000.000
103B105ASN00.0320.01221.3030.2270.2270.0000.0000.0000.000
104B106ASN00.0060.00118.883-1.793-1.7930.0000.0000.0000.000
105B107ILE0-0.0060.01115.6180.2740.2740.0000.0000.0000.000
106B108THR0-0.024-0.00914.775-1.033-1.0330.0000.0000.0000.000
107B109MET00.0270.0209.500-0.436-0.4360.0000.0000.0000.000
108B110LYS10.8370.93114.15615.28415.2840.0000.0000.0000.000
109B111LYS10.9290.95314.66415.27815.2780.0000.0000.0000.000
110B112ASP-1-0.779-0.87316.061-15.835-15.8350.0000.0000.0000.000
111B113GLY00.0320.02813.2560.2470.2470.0000.0000.0000.000
112B114SER0-0.105-0.07914.313-0.156-0.1560.0000.0000.0000.000
113B115ASN0-0.014-0.01512.145-0.781-0.7810.0000.0000.0000.000
114B116CYS0-0.043-0.00114.0640.6090.6090.0000.0000.0000.000
115B117PHE00.0390.00912.140-0.557-0.5570.0000.0000.0000.000
116B118VAL0-0.021-0.01916.5951.1651.1650.0000.0000.0000.000
117B119TYR00.002-0.00818.008-1.116-1.1160.0000.0000.0000.000
118B120GLU-1-0.881-0.92821.671-12.666-12.6660.0000.0000.0000.000
119B121ILE0-0.003-0.01023.576-0.306-0.3060.0000.0000.0000.000
120B122ARG10.8160.88825.97910.21610.2160.0000.0000.0000.000
121B123PHE00.023-0.01328.535-0.248-0.2480.0000.0000.0000.000
122B124ASP-1-0.793-0.85831.154-9.170-9.1700.0000.0000.0000.000
123B125GLY00.000-0.01034.297-0.139-0.1390.0000.0000.0000.000
124B126VAL00.004-0.01036.7080.2490.2490.0000.0000.0000.000
125B127ASN00.0310.00539.8590.0030.0030.0000.0000.0000.000
126B128PHE00.0350.03636.6590.1050.1050.0000.0000.0000.000
127B129PRO00.0360.02842.6770.1420.1420.0000.0000.0000.000
128B130ALA00.0190.00746.139-0.057-0.0570.0000.0000.0000.000
129B131ASN0-0.030-0.02248.473-0.068-0.0680.0000.0000.0000.000
130B132GLY00.0890.05445.1370.0270.0270.0000.0000.0000.000
131B133PRO0-0.005-0.00341.9900.0240.0240.0000.0000.0000.000
132B134VAL00.0380.02638.944-0.030-0.0300.0000.0000.0000.000
133B135MET00.0110.00841.483-0.097-0.0970.0000.0000.0000.000
134B136GLN0-0.073-0.03044.2230.1420.1420.0000.0000.0000.000
135B137ARG10.8510.93542.6887.3647.3640.0000.0000.0000.000
136B138LYS10.8940.95043.8476.7956.7950.0000.0000.0000.000
137B139THR0-0.028-0.02938.8820.1200.1200.0000.0000.0000.000
138B140VAL0-0.056-0.02439.7180.1070.1070.0000.0000.0000.000
139B141LYS10.8850.93834.2309.1749.1740.0000.0000.0000.000
140B142TRP00.0180.00331.5790.2130.2130.0000.0000.0000.000
141B143GLU-1-0.838-0.91933.561-8.751-8.7510.0000.0000.0000.000
142B144PRO0-0.084-0.03829.790-0.291-0.2910.0000.0000.0000.000
143B145SER0-0.019-0.02427.6900.1850.1850.0000.0000.0000.000
144B146THR00.017-0.02024.627-0.089-0.0890.0000.0000.0000.000
145B147GLU-1-0.767-0.84721.388-14.437-14.4370.0000.0000.0000.000
146B148LYS10.8940.94822.62411.15611.1560.0000.0000.0000.000
147B149MET0-0.0040.01717.6220.0660.0660.0000.0000.0000.000
148B150TYR0-0.082-0.07119.300-0.014-0.0140.0000.0000.0000.000
149B151VAL00.0390.02915.792-0.052-0.0520.0000.0000.0000.000
150B152ARG10.8880.93918.57013.47813.4780.0000.0000.0000.000
151B153ASP-1-0.878-0.95020.109-13.571-13.5710.0000.0000.0000.000
152B154GLY0-0.0050.00716.846-0.064-0.0640.0000.0000.0000.000
153B155VAL0-0.061-0.02015.526-1.335-1.3350.0000.0000.0000.000
154B156LEU00.0070.01014.0790.3770.3770.0000.0000.0000.000
155B157LYS10.8820.93116.99913.85913.8590.0000.0000.0000.000
156B158GLY00.0820.02919.860-0.603-0.6030.0000.0000.0000.000
157B159ASP-1-0.861-0.89821.668-11.862-11.8620.0000.0000.0000.000
158B160VAL00.020-0.00425.385-0.061-0.0610.0000.0000.0000.000
159B161ASN0-0.0310.00127.5460.1880.1880.0000.0000.0000.000
160B162MET00.0010.02628.806-0.134-0.1340.0000.0000.0000.000
161B163ALA00.0290.00232.0050.3360.3360.0000.0000.0000.000
162B164LEU0-0.0050.00834.782-0.163-0.1630.0000.0000.0000.000
163B165LEU00.0050.00836.9750.2260.2260.0000.0000.0000.000
164B166LEU0-0.004-0.01339.606-0.025-0.0250.0000.0000.0000.000
165B167GLN00.000-0.01643.0070.2160.2160.0000.0000.0000.000
166B168GLY0-0.065-0.02045.6930.1170.1170.0000.0000.0000.000
167B169GLY00.0080.01445.5790.1190.1190.0000.0000.0000.000
168B170GLY00.0030.00144.1320.0390.0390.0000.0000.0000.000
169B171HIS0-0.069-0.06838.4320.0180.0180.0000.0000.0000.000
170B172TYR0-0.038-0.03438.8120.0800.0800.0000.0000.0000.000
171B173ARG10.7740.85734.0668.7658.7650.0000.0000.0000.000
172B174CYS0-0.043-0.01233.229-0.002-0.0020.0000.0000.0000.000
173B175ASP-1-0.817-0.87931.820-9.681-9.6810.0000.0000.0000.000
174B176PHE00.028-0.00326.3030.0590.0590.0000.0000.0000.000
175B177ARG10.8690.94126.46310.65110.6510.0000.0000.0000.000
176B178THR00.0210.03021.1770.3180.3180.0000.0000.0000.000
177B179THR0-0.042-0.01620.134-0.014-0.0140.0000.0000.0000.000
178B180TYR0-0.015-0.04415.965-0.098-0.0980.0000.0000.0000.000
179B181LYS10.8240.88315.88914.21214.2120.0000.0000.0000.000
180B182ALA00.0310.00610.5150.0530.0530.0000.0000.0000.000
181B183LYS10.7800.89512.06220.67620.6760.0000.0000.0000.000
182B184LYS10.8050.9085.32047.66247.6620.0000.0000.0000.000
183B185VAL00.0090.0059.6860.2700.2700.0000.0000.0000.000
184B186VAL0-0.033-0.0116.274-4.684-4.6840.0000.0000.0000.000
185B187GLN0-0.005-0.0026.4891.4341.4340.0000.0000.0000.000
186B188LEU00.001-0.0098.351-0.066-0.0660.0000.0000.0000.000
187B189PRO0-0.0020.00511.776-0.240-0.2400.0000.0000.0000.000
188B190ASP-1-0.870-0.92913.447-17.278-17.2780.0000.0000.0000.000
189B191TYR0-0.064-0.03616.957-0.089-0.0890.0000.0000.0000.000
190B192HIS0-0.023-0.00215.281-0.346-0.3460.0000.0000.0000.000
191B193PHE0-0.020-0.01219.7500.6740.6740.0000.0000.0000.000
192B194VAL00.0310.01018.084-0.875-0.8750.0000.0000.0000.000
193B195ASP-1-0.862-0.88320.920-11.881-11.8810.0000.0000.0000.000
194B196HIS0-0.012-0.02421.133-0.129-0.1290.0000.0000.0000.000
195B197ARG10.8900.93625.21510.88510.8850.0000.0000.0000.000
196B198ILE00.0160.02726.453-0.229-0.2290.0000.0000.0000.000
197B199GLU-1-0.849-0.93328.502-9.457-9.4570.0000.0000.0000.000
198B200ILE00.0130.00330.933-0.203-0.2030.0000.0000.0000.000
199B201THR0-0.004-0.00130.8480.3110.3110.0000.0000.0000.000
200B202SER0-0.018-0.01433.7570.3140.3140.0000.0000.0000.000
201B203HIS10.9040.94835.2847.8967.8960.0000.0000.0000.000
202B204ASP-1-0.772-0.86637.816-7.804-7.8040.0000.0000.0000.000
203B205LYS10.9310.96340.8616.6406.6400.0000.0000.0000.000
204B206ASP-1-0.899-0.95942.822-7.026-7.0260.0000.0000.0000.000
205B207TYR0-0.039-0.01337.141-0.031-0.0310.0000.0000.0000.000
206B208ASN00.0370.01237.634-0.238-0.2380.0000.0000.0000.000
207B209LYS10.8740.93334.1258.7968.7960.0000.0000.0000.000
208B210VAL0-0.015-0.01032.8770.2210.2210.0000.0000.0000.000
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