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: 8NVRY

Calculation Name: 3UEB-A-Xray540

Preferred Name:

Target Type:

Ligand Name:

Ligand 3-letter code:

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 3UEB

Chain ID: A

ChEMBL ID:

UniProt ID: B6YTZ3

Base Structure: X-ray

Registration Date: 2025-07-09

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 OptH
Protonation MOE:Protonate 3D
Complement MOE:Structure Preparation
Water No
Procedure Auto-FMO protocol ver. 2.20220422
Remarks
FMO calculation
FMO method FMO2-MP2/6-31G(d)
Fragmentation Auto
Number of fragment 198
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -780276.172089
FMO2-HF: Nuclear repulsion 739359.92467
FMO2-HF: Total energy -40916.24742
FMO2-MP2: Total energy -41037.393732


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:4:GLY)


Summations of interaction energy for fragment #1(A:4:GLY)
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.
-0.8871.347-0.014-0.944-1.275-0.001
Interaction energy analysis for fragmet #1(A:4:GLY)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.001 / q_NPA : -0.018
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].
3A5SER0-0.0310.0754.4260.2480.502-0.001-0.093-0.1600.000
4A6SER00.023-0.1083.578-1.891-0.045-0.012-0.835-0.999-0.001
5A6SER0-0.0230.0836.1580.5400.5400.0000.0000.0000.000
6A7GLY00.047-0.0524.4890.1270.261-0.001-0.016-0.1160.000
7A8LYS00.142-0.0066.9920.0030.0030.0000.0000.0000.000
8A8LYS10.7161.0319.856-0.262-0.2620.0000.0000.0000.000
9A9ARG00.052-0.14210.428-0.014-0.0140.0000.0000.0000.000
10A9ARG10.7961.03712.2650.0430.0430.0000.0000.0000.000
11A10VAL00.056-0.11513.336-0.004-0.0040.0000.0000.0000.000
12A10VAL0-0.0410.11815.6950.0090.0090.0000.0000.0000.000
13A11ILE00.015-0.09716.9780.0020.0020.0000.0000.0000.000
14A11ILE0-0.0960.10817.665-0.003-0.0030.0000.0000.0000.000
15A12HIS00.168-0.09119.8130.0020.0020.0000.0000.0000.000
16A12HIS0-0.1260.09522.278-0.004-0.0040.0000.0000.0000.000
17A13ILE00.025-0.12923.459-0.005-0.0050.0000.0000.0000.000
18A13ILE0-0.0660.11323.358-0.001-0.0010.0000.0000.0000.000
19A14GLY0-0.002-0.08226.2670.0040.0040.0000.0000.0000.000
20A15LEU0-0.041-0.05329.982-0.004-0.0040.0000.0000.0000.000
21A15LEU0-0.0420.12329.1770.0000.0000.0000.0000.0000.000
22A16PRO00.067-0.10832.4810.0000.0000.0000.0000.0000.000
23A17GLU00.081-0.02135.9790.0020.0020.0000.0000.0000.000
24A17GLU-1-1.030-0.85036.798-0.004-0.0040.0000.0000.0000.000
25A18LEU00.013-0.12035.556-0.001-0.0010.0000.0000.0000.000
26A18LEU0-0.0450.11833.0260.0000.0000.0000.0000.0000.000
27A19SER00.077-0.02636.9570.0030.0030.0000.0000.0000.000
28A19SER00.0100.05839.2340.0000.0000.0000.0000.0000.000
29A20GLU00.117-0.10535.843-0.002-0.0020.0000.0000.0000.000
30A20GLU-1-0.997-0.85736.2610.0210.0210.0000.0000.0000.000
31A21GLU00.083-0.12535.2380.0020.0020.0000.0000.0000.000
32A21GLU-1-1.057-0.85637.8630.0020.0020.0000.0000.0000.000
33A22GLN00.102-0.08535.2860.0000.0000.0000.0000.0000.000
34A22GLN0-0.0280.10835.7360.0010.0010.0000.0000.0000.000
35A23LEU00.106-0.10232.295-0.004-0.0040.0000.0000.0000.000
36A23LEU0-0.1180.11031.1690.0000.0000.0000.0000.0000.000
37A24ILE00.027-0.10530.7080.0000.0000.0000.0000.0000.000
38A24ILE0-0.0880.09131.8390.0010.0010.0000.0000.0000.000
39A25GLU00.180-0.08030.4710.0000.0000.0000.0000.0000.000
40A25GLU-1-1.014-0.84532.758-0.012-0.0120.0000.0000.0000.000
41A26ILE00.004-0.12929.801-0.005-0.0050.0000.0000.0000.000
42A26ILE0-0.0600.11328.2550.0000.0000.0000.0000.0000.000
43A27GLY0-0.015-0.12126.651-0.003-0.0030.0000.0000.0000.000
44A28GLU00.061-0.06425.6820.0000.0000.0000.0000.0000.000
45A28GLU-1-0.956-0.80928.806-0.001-0.0010.0000.0000.0000.000
46A29LEU00.145-0.07426.188-0.005-0.0050.0000.0000.0000.000
47A29LEU0-0.1010.09627.3850.0000.0000.0000.0000.0000.000
48A30ALA00.071-0.09124.097-0.012-0.0120.0000.0000.0000.000
49A30ALA0-0.0910.09923.2910.0020.0020.0000.0000.0000.000
50A31GLN00.131-0.11021.396-0.013-0.0130.0000.0000.0000.000
51A31GLN0-0.1370.08121.650-0.003-0.0030.0000.0000.0000.000
52A32GLU00.027-0.15621.185-0.009-0.0090.0000.0000.0000.000
53A32GLU-1-0.965-0.79725.031-0.021-0.0210.0000.0000.0000.000
54A33THR00.020-0.06922.805-0.011-0.0110.0000.0000.0000.000
55A33THR0-0.0710.01721.734-0.002-0.0020.0000.0000.0000.000
56A34ILE00.065-0.09318.643-0.022-0.0220.0000.0000.0000.000
57A34ILE0-0.0920.08916.5820.0000.0000.0000.0000.0000.000
58A35ILE00.066-0.11517.872-0.031-0.0310.0000.0000.0000.000
59A35ILE0-0.0880.08819.5650.0010.0010.0000.0000.0000.000
60A36ASP00.085-0.12419.232-0.022-0.0220.0000.0000.0000.000
61A36ASP-1-1.005-0.82922.574-0.070-0.0700.0000.0000.0000.000
62A37TYR00.092-0.09018.562-0.015-0.0150.0000.0000.0000.000
63A37TYR0-0.1330.07416.0480.0150.0150.0000.0000.0000.000
64A38VAL00.040-0.09515.373-0.034-0.0340.0000.0000.0000.000
65A38VAL0-0.0470.10913.981-0.006-0.0060.0000.0000.0000.000
66A39PHE0-0.004-0.11116.139-0.045-0.0450.0000.0000.0000.000
67A39PHE0-0.0920.07218.5980.0010.0010.0000.0000.0000.000
68A40ASP00.113-0.09318.641-0.005-0.0050.0000.0000.0000.000
69A40ASP-1-1.022-0.86120.523-0.121-0.1210.0000.0000.0000.000
70A41HIS0-0.053-0.12416.6660.0070.0070.0000.0000.0000.000
71A41HIS10.7140.97016.0170.2110.2110.0000.0000.0000.000
72A42LEU00.071-0.10614.565-0.044-0.0440.0000.0000.0000.000
73A42LEU0-0.0290.12411.433-0.021-0.0210.0000.0000.0000.000
74A43THR00.076-0.03315.7220.0440.0440.0000.0000.0000.000
75A43THR0-0.1130.03015.8490.0150.0150.0000.0000.0000.000
76A44ARG00.119-0.07616.354-0.024-0.0240.0000.0000.0000.000
77A44ARG10.8811.05819.9650.1020.1020.0000.0000.0000.000
78A45SER00.068-0.05816.8300.0110.0110.0000.0000.0000.000
79A45SER0-0.0700.04116.897-0.007-0.0070.0000.0000.0000.000
80A46GLU00.016-0.14312.9090.0250.0250.0000.0000.0000.000
81A46GLU-1-0.937-0.83012.367-0.460-0.4600.0000.0000.0000.000
82A47VAL00.098-0.11011.747-0.114-0.1140.0000.0000.0000.000
83A47VAL0-0.0990.12713.943-0.001-0.0010.0000.0000.0000.000
84A48LYS00.136-0.06412.0280.0460.0460.0000.0000.0000.000
85A48LYS10.7361.00810.056-0.182-0.1820.0000.0000.0000.000
86A49ASP00.057-0.15312.3350.0120.0120.0000.0000.0000.000
87A49ASP-1-0.941-0.81512.5080.1760.1760.0000.0000.0000.000
88A50ILE00.093-0.08012.488-0.010-0.0100.0000.0000.0000.000
89A50ILE0-0.1050.07614.496-0.011-0.0110.0000.0000.0000.000
90A51GLU00.038-0.15314.624-0.011-0.0110.0000.0000.0000.000
91A51GLU-1-1.000-0.81615.3150.2130.2130.0000.0000.0000.000
92A52VAL00.107-0.12815.8930.0130.0130.0000.0000.0000.000
93A52VAL0-0.1000.12516.650-0.004-0.0040.0000.0000.0000.000
94A53THR00.024-0.08118.409-0.009-0.0090.0000.0000.0000.000
95A53THR0-0.0210.06419.5750.0000.0000.0000.0000.0000.000
96A54MET00.093-0.08320.930-0.002-0.0020.0000.0000.0000.000
97A54MET0-0.0310.13824.226-0.001-0.0010.0000.0000.0000.000
98A55ARG00.088-0.10323.9330.0030.0030.0000.0000.0000.000
99A55ARG10.7871.03824.683-0.071-0.0710.0000.0000.0000.000
100A56ILE00.070-0.10626.062-0.001-0.0010.0000.0000.0000.000
101A56ILE0-0.0600.12327.7170.0000.0000.0000.0000.0000.000
102A57ASN00.135-0.09029.5370.0010.0010.0000.0000.0000.000
103A57ASN0-0.2110.02330.011-0.002-0.0020.0000.0000.0000.000
104A58ARG00.163-0.04831.5180.0030.0030.0000.0000.0000.000
105A58ARG10.6960.96434.360-0.015-0.0150.0000.0000.0000.000
106A59GLU00.031-0.13533.828-0.001-0.0010.0000.0000.0000.000
107A59GLU-1-1.056-0.86136.1500.0300.0300.0000.0000.0000.000
108A60GLU00.049-0.09832.486-0.001-0.0010.0000.0000.0000.000
109A60GLU-1-0.997-0.85331.8850.0550.0550.0000.0000.0000.000
110A61THR0-0.047-0.10128.7640.0060.0060.0000.0000.0000.000
111A61THR0-0.0640.01027.7850.0000.0000.0000.0000.0000.000
112A62LEU00.097-0.06728.466-0.002-0.0020.0000.0000.0000.000
113A62LEU0-0.1030.07626.6830.0000.0000.0000.0000.0000.000
114A63ASP00.154-0.06329.267-0.003-0.0030.0000.0000.0000.000
115A63ASP-1-0.876-0.81130.3570.0180.0180.0000.0000.0000.000
116A64LEU00.093-0.09527.2140.0030.0030.0000.0000.0000.000
117A64LEU0-0.1100.11825.235-0.001-0.0010.0000.0000.0000.000
118A65GLU00.022-0.12123.421-0.005-0.0050.0000.0000.0000.000
119A65GLU-1-0.943-0.84422.7520.0790.0790.0000.0000.0000.000
120A66ILE00.085-0.12320.8340.0040.0040.0000.0000.0000.000
121A66ILE0-0.0610.11718.835-0.002-0.0020.0000.0000.0000.000
122A67GLU00.089-0.12517.278-0.004-0.0040.0000.0000.0000.000
123A67GLU-1-0.975-0.82116.3090.1940.1940.0000.0000.0000.000
124A68VAL00.050-0.11414.5870.0010.0010.0000.0000.0000.000
125A68VAL0-0.0600.09813.222-0.008-0.0080.0000.0000.0000.000
126A69TYR00.083-0.09611.4990.0220.0220.0000.0000.0000.000
127A69TYR0-0.1290.0569.5320.1440.1440.0000.0000.0000.000
128A70LEU00.112-0.0929.9610.0000.0000.0000.0000.0000.000
129A70LEU0-0.1220.0969.509-0.021-0.0210.0000.0000.0000.000
130A71GLU00.129-0.1047.830-0.019-0.0190.0000.0000.0000.000
131A71GLU-1-0.983-0.8007.6580.5880.5880.0000.0000.0000.000
132A72VAL0-0.018-0.1187.2930.1340.1340.0000.0000.0000.000
133A72VAL0-0.0460.1116.358-0.041-0.0410.0000.0000.0000.000
134A73PRO0-0.048-0.1347.8270.0680.0680.0000.0000.0000.000
135A74ILE00.152-0.0016.313-0.340-0.3400.0000.0000.0000.000
136A74ILE0-0.0870.1016.4710.0440.0440.0000.0000.0000.000
137A75PHE00.026-0.0767.122-0.231-0.2310.0000.0000.0000.000
138A75PHE0-0.0930.06411.2530.0260.0260.0000.0000.0000.000
139A76VAL0-0.029-0.1538.6740.1220.1220.0000.0000.0000.000
140A76VAL0-0.0200.1438.7380.0240.0240.0000.0000.0000.000
141A77LYS00.060-0.0736.845-0.439-0.4390.0000.0000.0000.000
142A77LYS10.8271.0307.6520.6660.6660.0000.0000.0000.000
143A78VAL00.057-0.1256.5730.3280.3280.0000.0000.0000.000
144A78VAL00.0070.1408.1620.0240.0240.0000.0000.0000.000
145A79ASP00.130-0.0845.880-0.777-0.7770.0000.0000.0000.000
146A79ASP-1-1.022-0.8627.279-0.719-0.7190.0000.0000.0000.000
147A80VAL00.093-0.1095.4330.4530.4530.0000.0000.0000.000
148A80VAL0-0.0820.1224.942-0.023-0.0230.0000.0000.0000.000
149A81ASP00.154-0.0866.0110.2570.2570.0000.0000.0000.000
150A81ASP-1-0.961-0.8395.812-0.330-0.3300.0000.0000.0000.000
151A82LYS00.151-0.0427.8820.1470.1470.0000.0000.0000.000
152A82LYS10.7751.0369.5530.4350.4350.0000.0000.0000.000
153A83LEU00.070-0.1169.7200.1120.1120.0000.0000.0000.000
154A83LEU0-0.1110.09510.148-0.018-0.0180.0000.0000.0000.000
155A84ILE00.085-0.09610.3200.0610.0610.0000.0000.0000.000
156A84ILE0-0.0820.0969.2580.0170.0170.0000.0000.0000.000
157A85ASP00.043-0.13711.7640.0640.0640.0000.0000.0000.000
158A85ASP-1-0.909-0.79611.755-0.179-0.1790.0000.0000.0000.000
159A86GLU00.055-0.11713.7720.0450.0450.0000.0000.0000.000
160A86GLU-1-0.988-0.85214.820-0.297-0.2970.0000.0000.0000.000
161A87ALA00.099-0.10215.0580.0260.0260.0000.0000.0000.000
162A87ALA0-0.0710.11015.366-0.001-0.0010.0000.0000.0000.000
163A88VAL00.046-0.09516.0940.0200.0200.0000.0000.0000.000
164A88VAL0-0.0800.08815.5400.0050.0050.0000.0000.0000.000
165A89GLU00.086-0.10917.8370.0210.0210.0000.0000.0000.000
166A89GLU-1-1.033-0.86417.986-0.075-0.0750.0000.0000.0000.000
167A90ARG00.064-0.12519.5990.0150.0150.0000.0000.0000.000
168A90ARG10.8511.09020.3730.1110.1110.0000.0000.0000.000
169A91ALA00.124-0.09920.7070.0060.0060.0000.0000.0000.000
170A91ALA0-0.0630.11720.7850.0020.0020.0000.0000.0000.000
171A92TYR00.076-0.10622.1480.0090.0090.0000.0000.0000.000
172A92TYR0-0.0510.09620.1640.0020.0020.0000.0000.0000.000
173A93GLU00.096-0.10724.0350.0090.0090.0000.0000.0000.000
174A93GLU-1-0.974-0.81324.857-0.077-0.0770.0000.0000.0000.000
175A94ILE00.006-0.12525.4300.0050.0050.0000.0000.0000.000
176A94ILE0-0.0660.11124.342-0.001-0.0010.0000.0000.0000.000
177A95VAL00.084-0.11026.4030.0030.0030.0000.0000.0000.000
178A95VAL0-0.0450.11025.7640.0010.0010.0000.0000.0000.000
179A96GLU00.138-0.08928.0140.0050.0050.0000.0000.0000.000
180A96GLU-1-1.009-0.86028.664-0.022-0.0220.0000.0000.0000.000
181A97ARG0-0.022-0.14329.9610.0030.0030.0000.0000.0000.000
182A97ARG10.7500.99728.9440.0560.0560.0000.0000.0000.000
183A98LYS00.102-0.08531.2080.0010.0010.0000.0000.0000.000
184A98LYS10.8081.08031.0260.0230.0230.0000.0000.0000.000
185A99LEU00.071-0.09432.2530.0020.0020.0000.0000.0000.000
186A99LEU0-0.0540.10230.5390.0010.0010.0000.0000.0000.000
187A100ARG00.110-0.06934.0140.0030.0030.0000.0000.0000.000
188A100ARG10.8071.02331.9950.0290.0290.0000.0000.0000.000
189A101GLU00.116-0.09635.7040.0020.0020.0000.0000.0000.000
190A101GLU-1-1.012-0.85436.127-0.025-0.0250.0000.0000.0000.000
191A102ILE00.098-0.09536.7040.0010.0010.0000.0000.0000.000
192A102ILE0-0.0980.08734.9870.0000.0000.0000.0000.0000.000
193A103ALA00.080-0.10038.0830.0020.0020.0000.0000.0000.000
194A103ALA0-0.1000.08838.5280.0000.0000.0000.0000.0000.000
195A104ASN0-0.055-0.14340.0020.0020.0020.0000.0000.0000.000
196A104ASN0-0.1550.05139.928-0.002-0.0020.0000.0000.0000.000
197A105GLU0-0.138-0.15041.6940.0010.0010.0000.0000.0000.000
198A105GLU-1-0.886-0.92140.971-0.014-0.0140.0000.0000.0000.000