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: 2G52R

Calculation Name: 3MGF-A-Xray547

Preferred Name:

Target Type:

Ligand Name: [(4z)-2-{(2r)-2-[(1s)-1-amino-2-phenylethyl]-2-hydroxy-2,5-dihydro-1,3-thiazol-4-yl}-4-(4-hydroxybenzylidene)-5-oxo-4,5-dihydro-1h-imidazol-1-yl]acetic acid

Ligand 3-letter code: CFY

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 3MGF

Chain ID: A

ChEMBL ID:

UniProt ID: Q6I7B2

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 213
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922
Total energy (hartree)
FMO2-HF: Electronic energy -2600888.855964
FMO2-HF: Nuclear repulsion 2516084.376461
FMO2-HF: Total energy -84804.479503
FMO2-MP2: Total energy -85049.04252


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(A:3:SER)


Summations of interaction energy for fragment #1(A:3:SER)
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.
40.00146.5182.604-3.915-5.206-0.005
Interaction energy analysis for fragmet #1(A:3:SER)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 1 / q_Mulliken : 0.896 / q_NPA : 0.941
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].
3A5ILE00.0420.0392.3511.9594.8762.125-2.085-2.9570.010
4A6LYS10.9020.9403.11847.73449.3310.165-0.786-0.975-0.005
33A35TYR0-0.022-0.0412.545-5.304-3.3660.315-1.039-1.215-0.010
78A83LYS10.7740.8764.35628.04728.112-0.001-0.005-0.0590.000
5A7PRO00.040-0.0045.7192.0022.0020.0000.0000.0000.000
6A8GLU-1-0.835-0.9048.448-18.183-18.1830.0000.0000.0000.000
7A9MET0-0.0590.0097.010-3.197-3.1970.0000.0000.0000.000
8A10LYS10.9580.98710.95719.44719.4470.0000.0000.0000.000
9A11MET0-0.0430.00313.498-1.490-1.4900.0000.0000.0000.000
10A12ARG10.9170.96616.00314.51514.5150.0000.0000.0000.000
11A13TYR00.017-0.00117.440-0.766-0.7660.0000.0000.0000.000
12A14TYR0-0.017-0.02321.1920.3520.3520.0000.0000.0000.000
13A15MET00.0010.01023.884-0.201-0.2010.0000.0000.0000.000
14A16ASP-1-0.811-0.89026.571-10.105-10.1050.0000.0000.0000.000
15A17GLY0-0.004-0.01629.549-0.222-0.2220.0000.0000.0000.000
16A18SER0-0.0020.02231.6550.1670.1670.0000.0000.0000.000
17A19VAL00.0350.01434.483-0.166-0.1660.0000.0000.0000.000
18A20ASN0-0.033-0.02436.7600.0440.0440.0000.0000.0000.000
19A21GLY00.0110.01839.5530.1840.1840.0000.0000.0000.000
20A22HIS0-0.039-0.01738.8310.0410.0410.0000.0000.0000.000
21A23GLU-1-0.878-0.97036.584-8.329-8.3290.0000.0000.0000.000
22A24PHE0-0.028-0.01730.1150.0980.0980.0000.0000.0000.000
23A25THR00.0010.00830.550-0.183-0.1830.0000.0000.0000.000
24A26ILE0-0.008-0.00426.7110.1550.1550.0000.0000.0000.000
25A27GLU-1-0.892-0.94724.374-12.465-12.4650.0000.0000.0000.000
26A28GLY00.0330.00624.0770.3710.3710.0000.0000.0000.000
27A29GLU-1-0.836-0.87520.400-12.795-12.7950.0000.0000.0000.000
28A30GLY00.0470.02218.7700.5400.5400.0000.0000.0000.000
29A31THR0-0.053-0.03015.283-0.937-0.9370.0000.0000.0000.000
30A32GLY00.0660.02613.5270.9490.9490.0000.0000.0000.000
31A33ARG10.8280.90411.10819.88619.8860.0000.0000.0000.000
32A34PRO0-0.040-0.0266.7430.6290.6290.0000.0000.0000.000
34A36GLU-1-0.862-0.9288.980-18.715-18.7150.0000.0000.0000.000
35A37GLY00.0020.00511.8601.2281.2280.0000.0000.0000.000
36A38HIS10.7920.88913.42915.88415.8840.0000.0000.0000.000
37A39GLN00.001-0.02114.264-1.291-1.2910.0000.0000.0000.000
38A40GLU-1-0.860-0.91616.620-12.922-12.9220.0000.0000.0000.000
39A41MET0-0.045-0.01818.780-0.781-0.7810.0000.0000.0000.000
40A42THR00.0100.00821.4020.3380.3380.0000.0000.0000.000
41A43LEU0-0.063-0.03522.835-0.330-0.3300.0000.0000.0000.000
42A44ARG10.8190.86625.76911.57911.5790.0000.0000.0000.000
43A45VAL00.0240.00629.595-0.115-0.1150.0000.0000.0000.000
44A46THR0-0.012-0.00831.8930.3230.3230.0000.0000.0000.000
45A47MET00.0100.02934.428-0.171-0.1710.0000.0000.0000.000
46A48ALA0-0.013-0.01637.0980.1020.1020.0000.0000.0000.000
47A49LYS10.9080.94938.6777.2677.2670.0000.0000.0000.000
48A50GLY00.0070.01640.1670.1710.1710.0000.0000.0000.000
49A51GLY00.002-0.00341.0970.0450.0450.0000.0000.0000.000
50A52PRO00.0040.00139.119-0.199-0.1990.0000.0000.0000.000
51A53MET0-0.008-0.00832.296-0.024-0.0240.0000.0000.0000.000
52A54PRO0-0.045-0.01237.5580.0190.0190.0000.0000.0000.000
53A55PHE00.025-0.01732.2370.0330.0330.0000.0000.0000.000
54A56ALA00.0570.04234.749-0.112-0.1120.0000.0000.0000.000
55A57PHE00.030-0.00126.602-0.251-0.2510.0000.0000.0000.000
56A58ASP-1-0.754-0.83129.455-9.735-9.7350.0000.0000.0000.000
57A59LEU0-0.0230.00029.426-0.232-0.2320.0000.0000.0000.000
58A60VAL0-0.020-0.02727.528-0.155-0.1550.0000.0000.0000.000
59A61SER00.0210.02525.602-0.517-0.5170.0000.0000.0000.000
60A62HIS00.0130.01723.275-0.644-0.6440.0000.0000.0000.000
61A63VAL00.021-0.01519.520-0.244-0.2440.0000.0000.0000.000
62A66PHE0-0.011-0.02018.455-0.631-0.6310.0000.0000.0000.000
63A68HIS00.0760.06212.3800.4290.4290.0000.0000.0000.000
64A69ARG10.7960.86013.44415.40715.4070.0000.0000.0000.000
65A70PRO0-0.0270.0038.332-0.594-0.5940.0000.0000.0000.000
66A71PHE0-0.042-0.0098.944-2.444-2.4440.0000.0000.0000.000
67A72THR00.0260.00710.5952.3012.3010.0000.0000.0000.000
68A73LYS10.8980.96510.53715.84715.8470.0000.0000.0000.000
69A74TYR0-0.006-0.03410.0551.3181.3180.0000.0000.0000.000
70A75PRO0-0.0230.00711.308-1.493-1.4930.0000.0000.0000.000
71A76GLU-1-0.944-0.97811.120-23.481-23.4810.0000.0000.0000.000
72A77GLU-1-0.901-0.95212.693-17.813-17.8130.0000.0000.0000.000
73A78ILE0-0.046-0.01714.0780.8830.8830.0000.0000.0000.000
74A79PRO0-0.039-0.02511.449-1.403-1.4030.0000.0000.0000.000
75A80ASP-1-0.738-0.8637.828-26.150-26.1500.0000.0000.0000.000
76A81TYR00.004-0.0178.959-2.161-2.1610.0000.0000.0000.000
77A82PHE00.012-0.00110.138-0.447-0.4470.0000.0000.0000.000
79A84GLN0-0.056-0.0525.681-2.692-2.6920.0000.0000.0000.000
80A85ALA0-0.0210.0117.6640.3940.3940.0000.0000.0000.000
81A86PHE0-0.030-0.0016.4261.5531.5530.0000.0000.0000.000
82A87PRO0-0.035-0.0345.757-4.417-4.4170.0000.0000.0000.000
83A88GLU-1-0.860-0.9328.190-26.008-26.0080.0000.0000.0000.000
84A89GLY00.0160.01611.2641.6941.6940.0000.0000.0000.000
85A90LEU0-0.033-0.00912.306-0.032-0.0320.0000.0000.0000.000
86A91SER00.0040.00714.1940.6240.6240.0000.0000.0000.000
87A92TRP0-0.049-0.01917.522-0.146-0.1460.0000.0000.0000.000
88A93GLU-1-0.788-0.87620.043-11.806-11.8060.0000.0000.0000.000
89A94ARG10.8470.91720.87412.18412.1840.0000.0000.0000.000
90A95SER0-0.0040.01725.7700.2770.2770.0000.0000.0000.000
91A96LEU0-0.014-0.01327.663-0.250-0.2500.0000.0000.0000.000
92A97GLU-1-0.912-0.95331.138-8.394-8.3940.0000.0000.0000.000
93A98PHE00.014-0.02232.114-0.169-0.1690.0000.0000.0000.000
94A99GLU-1-0.884-0.93936.477-7.400-7.4000.0000.0000.0000.000
95A100ASP-1-0.842-0.92239.527-7.376-7.3760.0000.0000.0000.000
96A101GLY0-0.0070.00140.5630.1590.1590.0000.0000.0000.000
97A102GLY00.0060.00538.420-0.024-0.0240.0000.0000.0000.000
98A103SER0-0.053-0.01835.215-0.137-0.1370.0000.0000.0000.000
99A104ALA00.021-0.00231.5030.0560.0560.0000.0000.0000.000
100A105SER0-0.028-0.00829.902-0.117-0.1170.0000.0000.0000.000
101A106VAL0-0.018-0.00224.7530.0480.0480.0000.0000.0000.000
102A107SER0-0.025-0.00623.962-0.166-0.1660.0000.0000.0000.000
103A108ALA00.0330.01120.2970.2220.2220.0000.0000.0000.000
104A109HIS0-0.049-0.02818.5170.1100.1100.0000.0000.0000.000
105A110ILE00.0030.01413.1820.0670.0670.0000.0000.0000.000
106A111SER0-0.015-0.00513.545-0.786-0.7860.0000.0000.0000.000
107A112LEU00.0180.0007.527-0.297-0.2970.0000.0000.0000.000
108A113ARG10.9410.96811.87418.02118.0210.0000.0000.0000.000
109A114GLY00.0310.02411.6890.8770.8770.0000.0000.0000.000
110A115ASN0-0.021-0.0269.720-1.336-1.3360.0000.0000.0000.000
111A116THR00.0070.01310.7390.9410.9410.0000.0000.0000.000
112A117PHE00.002-0.0098.191-0.471-0.4710.0000.0000.0000.000
113A118TYR0-0.022-0.01413.3361.4881.4880.0000.0000.0000.000
114A119HIS0-0.024-0.02116.6590.1050.1050.0000.0000.0000.000
115A120LYS10.8750.94618.30712.09512.0950.0000.0000.0000.000
116A121SER0-0.009-0.01221.720-0.097-0.0970.0000.0000.0000.000
117A122LYS10.9260.95623.85710.52810.5280.0000.0000.0000.000
118A123PHE00.0420.00927.417-0.199-0.1990.0000.0000.0000.000
119A124THR0-0.013-0.01229.4960.2270.2270.0000.0000.0000.000
120A125GLY00.0070.01233.027-0.120-0.1200.0000.0000.0000.000
121A126VAL00.007-0.01335.0030.1780.1780.0000.0000.0000.000
122A127ASN00.004-0.01038.568-0.006-0.0060.0000.0000.0000.000
123A128PHE00.0380.03734.6200.0430.0430.0000.0000.0000.000
124A129PRO00.0370.03140.7540.0870.0870.0000.0000.0000.000
125A130ALA0-0.028-0.02143.104-0.117-0.1170.0000.0000.0000.000
126A131ASP-1-0.918-0.96244.987-6.478-6.4780.0000.0000.0000.000
127A132GLY00.0490.02942.4420.0040.0040.0000.0000.0000.000
128A133PRO00.0120.00339.020-0.058-0.0580.0000.0000.0000.000
129A134ILE0-0.0060.00234.188-0.141-0.1410.0000.0000.0000.000
130A135MET0-0.029-0.01437.789-0.187-0.1870.0000.0000.0000.000
131A136GLN00.0020.01040.417-0.018-0.0180.0000.0000.0000.000
132A137ASN0-0.075-0.03836.660-0.186-0.1860.0000.0000.0000.000
133A138GLN00.0680.04338.843-0.029-0.0290.0000.0000.0000.000
134A139SER0-0.053-0.04234.0390.0910.0910.0000.0000.0000.000
135A140VAL0-0.042-0.02834.285-0.041-0.0410.0000.0000.0000.000
136A141ASP-1-0.813-0.90629.450-9.947-9.9470.0000.0000.0000.000
137A142TRP00.010-0.00527.2050.2870.2870.0000.0000.0000.000
138A143GLU-1-0.909-0.96129.365-8.845-8.8450.0000.0000.0000.000
139A144PRO0-0.092-0.05226.100-0.363-0.3630.0000.0000.0000.000
140A145SER00.0430.01425.0100.1310.1310.0000.0000.0000.000
141A146THR0-0.045-0.03923.027-0.467-0.4670.0000.0000.0000.000
142A147GLU-1-0.778-0.84620.343-13.208-13.2080.0000.0000.0000.000
143A148LYS10.9370.96721.99010.65310.6530.0000.0000.0000.000
144A149ILE0-0.012-0.00117.6430.0530.0530.0000.0000.0000.000
145A150THR00.010-0.00820.9490.2670.2670.0000.0000.0000.000
146A151ALA00.007-0.00219.468-0.386-0.3860.0000.0000.0000.000
147A152SER00.002-0.02721.2760.5060.5060.0000.0000.0000.000
148A153ASP-1-0.884-0.91522.353-12.006-12.0060.0000.0000.0000.000
149A154GLY0-0.042-0.01218.939-0.196-0.1960.0000.0000.0000.000
150A155VAL0-0.035-0.00917.987-0.937-0.9370.0000.0000.0000.000
151A156LEU00.0070.00315.2870.0840.0840.0000.0000.0000.000
152A157LYS10.8690.92319.39011.94911.9490.0000.0000.0000.000
153A158GLY00.0330.02121.707-0.370-0.3700.0000.0000.0000.000
154A159ASP-1-0.866-0.90622.557-10.517-10.5170.0000.0000.0000.000
155A160VAL00.017-0.00724.545-0.219-0.2190.0000.0000.0000.000
156A161THR0-0.030-0.00926.9090.1270.1270.0000.0000.0000.000
157A162MET0-0.070-0.00725.883-0.293-0.2930.0000.0000.0000.000
158A163TYR00.0380.01029.9840.3640.3640.0000.0000.0000.000
159A164LEU0-0.0160.00231.763-0.296-0.2960.0000.0000.0000.000
160A165LYS10.8810.93131.7779.3539.3530.0000.0000.0000.000
161A166LEU00.003-0.00135.275-0.078-0.0780.0000.0000.0000.000
162A167GLU-1-0.898-0.95738.525-7.293-7.2930.0000.0000.0000.000
163A168GLY0-0.057-0.03340.8340.1040.1040.0000.0000.0000.000
164A169GLY0-0.041-0.01740.1730.1160.1160.0000.0000.0000.000
165A170GLY00.0040.01040.9120.0110.0110.0000.0000.0000.000
166A171ASN00.001-0.01435.327-0.257-0.2570.0000.0000.0000.000
167A172HIS00.008-0.00136.8250.0280.0280.0000.0000.0000.000
168A173LYS10.9290.97434.6507.6887.6880.0000.0000.0000.000
169A174CYS0-0.045-0.01231.6410.0170.0170.0000.0000.0000.000
170A175GLN00.0250.03529.671-0.061-0.0610.0000.0000.0000.000
171A176PHE00.018-0.00324.986-0.125-0.1250.0000.0000.0000.000
172A177LYS10.8510.91325.57010.89410.8940.0000.0000.0000.000
173A178THR0-0.0020.00721.0890.1140.1140.0000.0000.0000.000
174A179THR0-0.029-0.01121.8510.2220.2220.0000.0000.0000.000
175A180TYR0-0.028-0.05716.651-0.259-0.2590.0000.0000.0000.000
176A181LYS10.8360.89417.86812.53712.5370.0000.0000.0000.000
177A182ALA00.0340.01813.323-0.339-0.3390.0000.0000.0000.000
178A183ALA0-0.016-0.00214.4130.9650.9650.0000.0000.0000.000
179A184LYS10.8660.92710.80724.92124.9210.0000.0000.0000.000
180A185LYS10.9660.98214.33815.82515.8250.0000.0000.0000.000
181A186ILE00.0400.02611.097-1.012-1.0120.0000.0000.0000.000
182A187LEU0-0.008-0.00310.3851.3771.3770.0000.0000.0000.000
183A188LYS10.8790.93511.72521.63721.6370.0000.0000.0000.000
184A189MET00.0340.03913.065-1.163-1.1630.0000.0000.0000.000
185A190PRO00.0140.02714.0150.2390.2390.0000.0000.0000.000
186A191GLY00.0380.01616.4020.6280.6280.0000.0000.0000.000
187A192SER0-0.042-0.03419.413-0.441-0.4410.0000.0000.0000.000
188A193HIS0-0.0150.01516.590-0.561-0.5610.0000.0000.0000.000
189A194TYR00.0180.02120.0150.7290.7290.0000.0000.0000.000
190A195ILE00.003-0.00215.835-0.883-0.8830.0000.0000.0000.000
191A196SER00.0230.03119.1360.6390.6390.0000.0000.0000.000
192A197HIS10.7910.86118.80012.95112.9510.0000.0000.0000.000
193A198ARG10.9560.97621.16912.85312.8530.0000.0000.0000.000
194A199LEU0-0.017-0.00221.972-0.570-0.5700.0000.0000.0000.000
195A200VAL0-0.014-0.00323.8790.4110.4110.0000.0000.0000.000
196A201ARG10.8100.87625.5158.7848.7840.0000.0000.0000.000
197A202LYS10.9090.95028.04210.10210.1020.0000.0000.0000.000
198A203THR00.012-0.00230.172-0.242-0.2420.0000.0000.0000.000
199A204GLU-1-0.892-0.93332.464-8.162-8.1620.0000.0000.0000.000
200A205GLY0-0.010-0.00934.981-0.028-0.0280.0000.0000.0000.000
201A206ASN0-0.007-0.00734.1600.0000.0000.0000.0000.0000.000
202A207ILE0-0.0140.00130.136-0.324-0.3240.0000.0000.0000.000
203A208THR0-0.031-0.00627.3480.2710.2710.0000.0000.0000.000
204A209GLU-1-0.780-0.85325.939-11.018-11.0180.0000.0000.0000.000
205A210LEU0-0.052-0.03822.5210.3030.3030.0000.0000.0000.000
206A211VAL00.018-0.00420.906-0.607-0.6070.0000.0000.0000.000
207A212GLU-1-0.753-0.85418.087-14.542-14.5420.0000.0000.0000.000
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209A214ALA0-0.020-0.01115.5380.6580.6580.0000.0000.0000.000
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211A216ALA0-0.0130.00014.5280.8770.8770.0000.0000.0000.000
212A217HIS0-0.061-0.04716.439-0.201-0.2010.0000.0000.0000.000
213A218SER-1-0.801-0.89718.989-12.420-12.4200.0000.0000.0000.000