FMODB

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

Last updated: 2025-04-23

All entries: 37539

Number of unique PDB entries: 7791

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FMODB ID: 6GYYZ

Calculation Name: 1UEB-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1UEB

Chain ID: A

ChEMBL ID:

UniProt ID: Q76G20

Base Structure: X-ray

Registration Date: 2023-09-27

Reference: C. Watanabe, N. Tani, K. Kamisaka, T. Honma et al., Interaction energy analysis of Apo structure dataset on FMODB, To be published.

DOI:

Apendix: None


IFIE MAP

IFIE Diagram


Modeling method
Optimization MOE:Amber10:EHT
Restraint OptHSide
Protonation MOE:Protonate 3D
Complement MOE:Structure Preparation
Water No
Procedure Auto-FMO protocol ver. 2.20220422
FMO calculation
FMO method FMO2-MP2/6-31G(d)
Fragmentation Auto
Number of fragment 184
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -1706312.41068
FMO2-HF: Nuclear repulsion 1634954.270077
FMO2-HF: Total energy -71358.140603
FMO2-MP2: Total energy -71564.837668


3D Structure
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:1:MET)


Summations of interaction energy for fragment #1(A:1:MET)
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.
-22.068-19.99119.303-6.773-14.605-0.076
Interaction energy analysis for fragmet #1(A:1:MET)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.046 / q_NPA : -0.009
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].
3A3SER0-0.027-0.0203.801-0.4752.500-0.022-1.587-1.3650.009
4A4VAL00.0410.0236.248-0.094-0.0940.0000.0000.0000.000
5A5THR0-0.024-0.0238.2180.1370.1370.0000.0000.0000.000
6A6ASP-1-0.860-0.9328.036-1.963-1.9630.0000.0000.0000.000
7A7LEU0-0.0300.0158.231-0.045-0.0450.0000.0000.0000.000
8A8ARG10.8470.90510.8041.0631.0630.0000.0000.0000.000
9A9PRO00.0220.00913.568-0.048-0.0480.0000.0000.0000.000
10A10GLY00.0320.02315.124-0.028-0.0280.0000.0000.0000.000
11A11THR0-0.042-0.0408.542-0.085-0.0850.0000.0000.0000.000
12A12LYS10.9090.95910.1120.7060.7060.0000.0000.0000.000
13A13VAL00.003-0.0046.224-0.433-0.4330.0000.0000.0000.000
14A14LYS10.8680.9327.037-2.431-2.4310.0000.0000.0000.000
15A15MET0-0.083-0.0426.7760.3330.3330.0000.0000.0000.000
16A16ASP-1-0.842-0.9128.6820.4810.4810.0000.0000.0000.000
17A17GLY0-0.012-0.00710.240-0.104-0.1040.0000.0000.0000.000
18A18GLY0-0.0030.01511.891-0.073-0.0730.0000.0000.0000.000
19A19LEU00.0450.02511.4250.1190.1190.0000.0000.0000.000
20A20TRP0-0.050-0.04411.080-0.134-0.1340.0000.0000.0000.000
21A21GLU-1-0.759-0.86711.928-0.466-0.4660.0000.0000.0000.000
22A22CYS0-0.071-0.01512.1470.0680.0680.0000.0000.0000.000
23A23VAL00.003-0.01214.028-0.023-0.0230.0000.0000.0000.000
24A24GLU-1-0.860-0.91517.061-0.177-0.1770.0000.0000.0000.000
25A25TYR0-0.039-0.03712.9470.0240.0240.0000.0000.0000.000
26A26GLN00.0200.01816.4040.0330.0330.0000.0000.0000.000
27A27HIS00.0310.03415.4450.0180.0180.0000.0000.0000.000
28A28GLN0-0.003-0.01117.1150.0380.0380.0000.0000.0000.000
29A29LYS10.9120.93718.8310.1750.1750.0000.0000.0000.000
30A30LEU00.0380.03921.1190.0030.0030.0000.0000.0000.000
31A31GLY00.0130.00524.5140.0150.0150.0000.0000.0000.000
32A32ARG10.9700.96524.5740.0590.0590.0000.0000.0000.000
33A33GLY0-0.0120.01522.7360.0090.0090.0000.0000.0000.000
34A34GLY00.0240.01318.366-0.020-0.0200.0000.0000.0000.000
35A35ALA0-0.010-0.01516.1950.0080.0080.0000.0000.0000.000
36A36LYS10.9040.95914.8960.0930.0930.0000.0000.0000.000
37A37VAL00.0170.01011.934-0.028-0.0280.0000.0000.0000.000
38A38VAL0-0.0110.00313.9380.0460.0460.0000.0000.0000.000
39A39ALA0-0.006-0.00912.894-0.049-0.0490.0000.0000.0000.000
40A40LYS10.8690.92415.0470.2000.2000.0000.0000.0000.000
41A41PHE00.013-0.00910.576-0.061-0.0610.0000.0000.0000.000
42A42LYS10.8960.94515.7430.2990.2990.0000.0000.0000.000
43A43ASN00.0100.00115.952-0.029-0.0290.0000.0000.0000.000
44A44LEU00.0220.01013.584-0.038-0.0380.0000.0000.0000.000
45A45GLU-1-0.797-0.86217.1030.2330.2330.0000.0000.0000.000
46A46THR0-0.037-0.02919.457-0.013-0.0130.0000.0000.0000.000
47A47GLY00.0250.00621.609-0.022-0.0220.0000.0000.0000.000
48A48ALA0-0.038-0.00619.305-0.013-0.0130.0000.0000.0000.000
49A49THR00.008-0.00918.547-0.021-0.0210.0000.0000.0000.000
50A50VAL0-0.015-0.00114.1200.0290.0290.0000.0000.0000.000
51A51GLU-1-0.882-0.92916.202-0.151-0.1510.0000.0000.0000.000
52A52ARG10.8600.9269.000-0.255-0.2550.0000.0000.0000.000
53A53THR0-0.004-0.01114.136-0.065-0.0650.0000.0000.0000.000
54A54PHE00.0010.0088.2290.0350.0350.0000.0000.0000.000
55A55ASN0-0.066-0.06211.312-0.051-0.0510.0000.0000.0000.000
56A56SER00.007-0.02010.536-0.009-0.0090.0000.0000.0000.000
57A57GLY0-0.039-0.0169.997-0.116-0.1160.0000.0000.0000.000
58A58GLU-1-0.821-0.8906.8270.0830.0830.0000.0000.0000.000
59A59LYS10.9140.9522.398-0.4300.4361.415-0.559-1.7220.003
60A60LEU00.0030.0012.923-1.440-0.1580.869-0.446-1.705-0.004
61A61GLU-1-0.751-0.8692.4220.4352.1768.288-4.491-5.538-0.027
62A62ASP-1-0.902-0.9431.900-17.622-22.6348.7540.323-4.065-0.057
63A63ILE0-0.0050.0004.5760.4160.641-0.001-0.013-0.2100.000
64A64TYR0-0.072-0.0527.178-0.365-0.3650.0000.0000.0000.000
65A65VAL0-0.033-0.0319.7170.2140.2140.0000.0000.0000.000
66A66GLU-1-0.834-0.87313.250-0.383-0.3830.0000.0000.0000.000
67A67THR0-0.019-0.01816.2630.0380.0380.0000.0000.0000.000
68A68ARG10.7790.87918.9350.1150.1150.0000.0000.0000.000
69A69GLU-1-0.916-0.96322.661-0.124-0.1240.0000.0000.0000.000
70A70LEU0-0.023-0.00524.1990.0100.0100.0000.0000.0000.000
71A71GLN0-0.023-0.02327.9880.0000.0000.0000.0000.0000.000
72A72TYR0-0.034-0.02331.7430.0100.0100.0000.0000.0000.000
73A73LEU0-0.019-0.01533.286-0.003-0.0030.0000.0000.0000.000
74A74TYR0-0.039-0.02035.401-0.003-0.0030.0000.0000.0000.000
75A75PRO0-0.035-0.00335.4940.0030.0030.0000.0000.0000.000
76A76GLU-1-0.870-0.94735.0480.0460.0460.0000.0000.0000.000
77A77GLY0-0.0080.00335.4530.0070.0070.0000.0000.0000.000
78A78GLU-1-0.937-0.98033.5760.0530.0530.0000.0000.0000.000
79A79GLU-1-0.985-0.99129.9790.0920.0920.0000.0000.0000.000
80A80MET0-0.073-0.03331.112-0.006-0.0060.0000.0000.0000.000
81A81VAL00.0170.02430.5770.0020.0020.0000.0000.0000.000
82A82PHE00.000-0.01328.398-0.010-0.0100.0000.0000.0000.000
83A83MET00.0000.01229.9070.0080.0080.0000.0000.0000.000
84A84ASP-1-0.781-0.88224.043-0.111-0.1110.0000.0000.0000.000
85A85LEU0-0.044-0.03327.4790.0040.0040.0000.0000.0000.000
86A86GLU-1-0.969-0.96724.358-0.166-0.1660.0000.0000.0000.000
87A87THR0-0.092-0.09823.0830.0020.0020.0000.0000.0000.000
88A88TYR0-0.072-0.03226.5240.0170.0170.0000.0000.0000.000
89A89GLU-1-0.847-0.87723.325-0.025-0.0250.0000.0000.0000.000
90A90GLN0-0.012-0.01527.614-0.011-0.0110.0000.0000.0000.000
91A91PHE00.000-0.01022.9290.0130.0130.0000.0000.0000.000
92A92ALA00.0120.02427.548-0.010-0.0100.0000.0000.0000.000
93A93VAL00.009-0.01225.4990.0130.0130.0000.0000.0000.000
94A94PRO00.0630.03426.043-0.006-0.0060.0000.0000.0000.000
95A95ARG11.0291.00028.334-0.034-0.0340.0000.0000.0000.000
96A96SER0-0.050-0.01527.790-0.010-0.0100.0000.0000.0000.000
97A97ARG10.7600.85220.258-0.150-0.1500.0000.0000.0000.000
98A98VAL0-0.017-0.00625.515-0.018-0.0180.0000.0000.0000.000
99A99VAL0-0.037-0.02126.3880.0050.0050.0000.0000.0000.000
100A100GLY00.0690.02429.152-0.005-0.0050.0000.0000.0000.000
101A101ALA00.0140.00532.041-0.003-0.0030.0000.0000.0000.000
102A102GLU-1-0.969-0.98033.4880.0010.0010.0000.0000.0000.000
103A103PHE00.0050.00735.835-0.002-0.0020.0000.0000.0000.000
104A104PHE00.029-0.00230.030-0.007-0.0070.0000.0000.0000.000
105A105LYS10.8550.88536.1360.0370.0370.0000.0000.0000.000
106A106GLU-1-0.895-0.96137.318-0.007-0.0070.0000.0000.0000.000
107A107GLY0-0.008-0.00736.793-0.002-0.0020.0000.0000.0000.000
108A108MET0-0.0480.02834.433-0.006-0.0060.0000.0000.0000.000
109A109THR00.0030.00629.9470.0080.0080.0000.0000.0000.000
110A110ALA0-0.064-0.02828.444-0.001-0.0010.0000.0000.0000.000
111A111LEU00.0120.01023.834-0.006-0.0060.0000.0000.0000.000
112A112GLY00.0200.00922.9120.0150.0150.0000.0000.0000.000
113A113ASP-1-0.907-0.94617.824-0.209-0.2090.0000.0000.0000.000
114A114MET0-0.020-0.01117.5360.0590.0590.0000.0000.0000.000
115A115TYR0-0.052-0.06210.237-0.045-0.0450.0000.0000.0000.000
116A116GLU-1-0.891-0.93812.3380.6940.6940.0000.0000.0000.000
117A117GLY0-0.007-0.00414.8190.0240.0240.0000.0000.0000.000
118A118GLN00.0100.01417.946-0.015-0.0150.0000.0000.0000.000
119A119PRO00.0520.02418.802-0.008-0.0080.0000.0000.0000.000
120A120ILE0-0.063-0.02315.8270.0350.0350.0000.0000.0000.000
121A121LYS10.8550.92620.0420.0130.0130.0000.0000.0000.000
122A122VAL00.0310.03322.392-0.022-0.0220.0000.0000.0000.000
123A123THR0-0.028-0.01924.1830.0150.0150.0000.0000.0000.000
124A124PRO00.0270.03426.781-0.014-0.0140.0000.0000.0000.000
125A125PRO00.0190.00529.680-0.008-0.0080.0000.0000.0000.000
126A126THR0-0.010-0.01130.8690.0070.0070.0000.0000.0000.000
127A127VAL00.0010.01732.4950.0080.0080.0000.0000.0000.000
128A128VAL0-0.0030.01634.946-0.005-0.0050.0000.0000.0000.000
129A129GLU-1-0.843-0.93537.550-0.056-0.0560.0000.0000.0000.000
130A130LEU0-0.0090.00939.4300.0020.0020.0000.0000.0000.000
131A131LYS10.8560.91743.0320.0270.0270.0000.0000.0000.000
132A132VAL00.0170.02146.6460.0030.0030.0000.0000.0000.000
133A133VAL0-0.046-0.03348.404-0.001-0.0010.0000.0000.0000.000
134A134ASP-1-0.925-0.96050.807-0.004-0.0040.0000.0000.0000.000
135A135THR00.020-0.00251.662-0.001-0.0010.0000.0000.0000.000
136A136PRO0-0.0180.00653.8810.0000.0000.0000.0000.0000.000
137A137PRO0-0.003-0.00357.063-0.001-0.0010.0000.0000.0000.000
138A138GLY00.0170.00559.1150.0010.0010.0000.0000.0000.000
139A139VAL0-0.039-0.03458.5510.0000.0000.0000.0000.0000.000
140A140ARG10.8980.95859.4170.0080.0080.0000.0000.0000.000
141A141GLY00.0650.02656.3340.0000.0000.0000.0000.0000.000
142A142ASP-1-0.845-0.92353.134-0.006-0.0060.0000.0000.0000.000
143A143THR0-0.028-0.01254.7630.0010.0010.0000.0000.0000.000
144A144VAL0-0.035-0.02657.414-0.001-0.0010.0000.0000.0000.000
145A145SER0-0.017-0.02258.9990.0000.0000.0000.0000.0000.000
146A146GLY00.0080.03355.087-0.001-0.0010.0000.0000.0000.000
147A147GLY00.0230.00353.9200.0000.0000.0000.0000.0000.000
148A148SER0-0.074-0.04250.402-0.002-0.0020.0000.0000.0000.000
149A149LYS10.8140.90851.8550.0190.0190.0000.0000.0000.000
150A150PRO00.0330.03549.665-0.002-0.0020.0000.0000.0000.000
151A151ALA0-0.024-0.00948.5560.0000.0000.0000.0000.0000.000
152A152THR00.0310.02447.4050.0000.0000.0000.0000.0000.000
153A153LEU0-0.006-0.01542.374-0.003-0.0030.0000.0000.0000.000
154A154GLU-1-0.812-0.90543.389-0.025-0.0250.0000.0000.0000.000
155A155THR0-0.015-0.01539.6610.0010.0010.0000.0000.0000.000
156A156GLY0-0.026-0.00542.2270.0040.0040.0000.0000.0000.000
157A157ALA00.0060.01940.7850.0020.0020.0000.0000.0000.000
158A158VAL0-0.018-0.01342.864-0.002-0.0020.0000.0000.0000.000
159A159VAL00.0150.01442.0340.0000.0000.0000.0000.0000.000
160A160GLN0-0.027-0.02045.0630.0020.0020.0000.0000.0000.000
161A161VAL0-0.001-0.00446.685-0.004-0.0040.0000.0000.0000.000
162A162PRO00.0050.00048.6950.0020.0020.0000.0000.0000.000
163A163LEU00.0120.00251.8640.0010.0010.0000.0000.0000.000
164A164PHE0-0.052-0.03251.4230.0010.0010.0000.0000.0000.000
165A165VAL0-0.0160.01050.020-0.001-0.0010.0000.0000.0000.000
166A166GLU-1-0.812-0.89653.257-0.015-0.0150.0000.0000.0000.000
167A167PRO00.002-0.00653.168-0.001-0.0010.0000.0000.0000.000
168A168GLY0-0.020-0.00752.118-0.001-0.0010.0000.0000.0000.000
169A169GLU-1-0.891-0.94750.278-0.034-0.0340.0000.0000.0000.000
170A170VAL0-0.018-0.01045.0140.0010.0010.0000.0000.0000.000
171A171ILE0-0.018-0.00944.257-0.002-0.0020.0000.0000.0000.000
172A172LYS10.8560.92441.1470.0600.0600.0000.0000.0000.000
173A173VAL00.004-0.00738.5700.0030.0030.0000.0000.0000.000
174A174ASP-1-0.802-0.90034.795-0.069-0.0690.0000.0000.0000.000
175A175THR0-0.024-0.04232.6120.0060.0060.0000.0000.0000.000
176A176ARG10.8350.92026.7140.0980.0980.0000.0000.0000.000
177A177THR0-0.077-0.07032.5320.0060.0060.0000.0000.0000.000
178A178GLY00.0170.01735.6790.0060.0060.0000.0000.0000.000
179A179GLU-1-0.896-0.92337.840-0.027-0.0270.0000.0000.0000.000
180A180TYR00.0190.00640.501-0.006-0.0060.0000.0000.0000.000
181A181VAL0-0.004-0.01239.400-0.001-0.0010.0000.0000.0000.000
182A182GLY0-0.017-0.01442.737-0.003-0.0030.0000.0000.0000.000
183A183ARG10.9050.97445.3500.0380.0380.0000.0000.0000.000
184A184ALA0-0.032-0.00644.905-0.005-0.0050.0000.0000.0000.000