FMODB

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

Last updated: 2025-07-23

All entries: 44592

Number of unique PDB entries: 7794

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FMODB ID: QN9RY

Calculation Name: 3N3E-A-Xray540

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3N3E

Chain ID: A

ChEMBL ID:

UniProt ID: Q8UUZ6

Base Structure: X-ray

Registration Date: 2025-07-11

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 199
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -778075.734845
FMO2-HF: Nuclear repulsion 736247.745731
FMO2-HF: Total energy -41827.989114
FMO2-MP2: Total energy -41950.196419


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:61:GLY)


Summations of interaction energy for fragment #1(A:61: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.
-1.4431.646-0.006-1.644-1.4370.004
Interaction energy analysis for fragmet #1(A:61:GLY)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.041 / q_NPA : 0.012
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].
3A62VAL0-0.1420.1034.1770.0280.4150.001-0.191-0.1970.000
4A63SER00.085-0.0473.382-0.9391.538-0.005-1.389-1.0830.004
5A63SER0-0.0500.0385.4680.5520.5520.0000.0000.0000.000
6A64GLU00.066-0.1254.094-0.387-0.200-0.001-0.062-0.1230.000
7A64GLU-1-0.876-0.7334.755-1.704-1.666-0.001-0.002-0.0340.000
8A65VAL00.060-0.1045.9230.1110.1110.0000.0000.0000.000
9A65VAL0-0.0800.1048.9130.0360.0360.0000.0000.0000.000
10A66ARG00.046-0.1069.5280.1020.1020.0000.0000.0000.000
11A66ARG10.7670.9798.3041.1501.1500.0000.0000.0000.000
12A67SER00.119-0.05612.053-0.010-0.0100.0000.0000.0000.000
13A67SER0-0.0620.06215.0550.0090.0090.0000.0000.0000.000
14A68ASP00.024-0.07415.6820.0340.0340.0000.0000.0000.000
15A68ASP-1-0.854-0.78617.987-0.315-0.3150.0000.0000.0000.000
16A69ARG00.099-0.08018.800-0.009-0.0090.0000.0000.0000.000
17A69ARG10.7840.99823.0970.1490.1490.0000.0000.0000.000
18A70GLU00.083-0.09421.6620.0180.0180.0000.0000.0000.000
19A70GLU-1-0.918-0.82621.887-0.196-0.1960.0000.0000.0000.000
20A71LYS00.058-0.07919.6650.0180.0180.0000.0000.0000.000
21A71LYS10.8071.00517.9330.3320.3320.0000.0000.0000.000
22A72PHE00.116-0.08316.2200.0040.0040.0000.0000.0000.000
23A72PHE0-0.0850.08014.3070.0020.0020.0000.0000.0000.000
24A73THR00.016-0.07514.0330.0300.0300.0000.0000.0000.000
25A73THR0-0.0430.06212.7750.0220.0220.0000.0000.0000.000
26A74VAL00.083-0.09210.577-0.026-0.0260.0000.0000.0000.000
27A74VAL0-0.1000.0919.9450.0130.0130.0000.0000.0000.000
28A75TYR00.066-0.0888.8300.2380.2380.0000.0000.0000.000
29A75TYR0-0.0690.0947.9410.0640.0640.0000.0000.0000.000
30A76LEU00.136-0.0767.354-0.709-0.7090.0000.0000.0000.000
31A76LEU0-0.1630.0607.5100.0930.0930.0000.0000.0000.000
32A77ASP00.092-0.0617.1210.5740.5740.0000.0000.0000.000
33A77ASP-1-0.892-0.8156.444-2.287-2.2870.0000.0000.0000.000
34A78VAL00.027-0.1118.491-0.062-0.0620.0000.0000.0000.000
35A78VAL0-0.1030.08411.3440.0360.0360.0000.0000.0000.000
36A79LYS00.165-0.06610.9070.2000.2000.0000.0000.0000.000
37A79LYS10.7781.0047.9101.4681.4680.0000.0000.0000.000
38A80HIS00.039-0.11312.7770.0370.0370.0000.0000.0000.000
39A80HIS0-0.1030.03715.156-0.024-0.0240.0000.0000.0000.000
40A81PHE00.061-0.07015.4490.0870.0870.0000.0000.0000.000
41A81PHE0-0.1190.07513.6910.0010.0010.0000.0000.0000.000
42A82SER00.008-0.09017.160-0.053-0.0530.0000.0000.0000.000
43A82SER0-0.0510.05621.5960.0180.0180.0000.0000.0000.000
44A83PRO0-0.010-0.13219.972-0.016-0.0160.0000.0000.0000.000
45A84ASP00.107-0.01021.315-0.013-0.0130.0000.0000.0000.000
46A84ASP-1-1.001-0.83724.625-0.267-0.2670.0000.0000.0000.000
47A85GLU00.033-0.09620.7330.0320.0320.0000.0000.0000.000
48A85GLU-1-0.849-0.74819.997-0.356-0.3560.0000.0000.0000.000
49A86LEU00.077-0.11618.602-0.002-0.0020.0000.0000.0000.000
50A86LEU0-0.1100.08315.584-0.024-0.0240.0000.0000.0000.000
51A87SER00.091-0.06619.4310.0190.0190.0000.0000.0000.000
52A87SER0-0.0970.07121.2500.0200.0200.0000.0000.0000.000
53A88VAL00.099-0.11519.392-0.017-0.0170.0000.0000.0000.000
54A88VAL0-0.0950.11017.706-0.010-0.0100.0000.0000.0000.000
55A89LYS00.061-0.11920.2360.0200.0200.0000.0000.0000.000
56A89LYS10.9191.09322.6190.2320.2320.0000.0000.0000.000
57A90VAL00.026-0.11420.837-0.034-0.0340.0000.0000.0000.000
58A90VAL0-0.0480.11721.710-0.003-0.0030.0000.0000.0000.000
59A91THR00.009-0.06322.2810.0180.0180.0000.0000.0000.000
60A91THR0-0.0840.02123.166-0.002-0.0020.0000.0000.0000.000
61A92ASP00.189-0.05622.986-0.013-0.0130.0000.0000.0000.000
62A92ASP-1-1.021-0.85224.876-0.107-0.1070.0000.0000.0000.000
63A93ASP00.005-0.09923.0260.0020.0020.0000.0000.0000.000
64A93ASP-1-0.882-0.77023.008-0.137-0.1370.0000.0000.0000.000
65A94TYR00.070-0.11819.164-0.003-0.0030.0000.0000.0000.000
66A94TYR0-0.0590.09217.4740.0170.0170.0000.0000.0000.000
67A95VAL00.115-0.09417.6160.0290.0290.0000.0000.0000.000
68A95VAL0-0.0700.11216.552-0.011-0.0110.0000.0000.0000.000
69A96GLU00.078-0.11716.778-0.050-0.0500.0000.0000.0000.000
70A96GLU-1-0.926-0.79719.434-0.208-0.2080.0000.0000.0000.000
71A97ILE00.062-0.10015.3060.0280.0280.0000.0000.0000.000
72A97ILE0-0.0740.07813.185-0.027-0.0270.0000.0000.0000.000
73A98GLN00.031-0.10615.895-0.021-0.0210.0000.0000.0000.000
74A98GLN0-0.0850.09818.8040.0190.0190.0000.0000.0000.000
75A99GLY00.064-0.07216.480-0.021-0.0210.0000.0000.0000.000
76A100LYS00.120-0.01917.4150.0120.0120.0000.0000.0000.000
77A100LYS10.8161.07120.2970.2010.2010.0000.0000.0000.000
78A101HIS00.074-0.08218.4400.0130.0130.0000.0000.0000.000
79A101HIS10.6980.96417.4860.3500.3500.0000.0000.0000.000
80A102GLY0-0.025-0.11519.3440.0120.0120.0000.0000.0000.000
81A103GLU00.036-0.02821.470-0.008-0.0080.0000.0000.0000.000
82A103GLU-1-0.830-0.74418.023-0.339-0.3390.0000.0000.0000.000
83A104ARG00.128-0.07022.5790.0130.0130.0000.0000.0000.000
84A104ARG10.9071.07225.9660.1210.1210.0000.0000.0000.000
85A105GLN00.010-0.09223.195-0.025-0.0250.0000.0000.0000.000
86A105GLN0-0.1180.04619.9540.0090.0090.0000.0000.0000.000
87A106ASP00.100-0.09224.0740.0000.0000.0000.0000.0000.000
88A106ASP-1-0.940-0.83825.273-0.066-0.0660.0000.0000.0000.000
89A107ASP00.005-0.12626.355-0.001-0.0010.0000.0000.0000.000
90A107ASP-1-0.954-0.82529.029-0.037-0.0370.0000.0000.0000.000
91A108HIS0-0.025-0.12929.6410.0040.0040.0000.0000.0000.000
92A108HIS0-0.1040.08631.260-0.004-0.0040.0000.0000.0000.000
93A109GLY00.090-0.07525.8270.0030.0030.0000.0000.0000.000
94A110TYR00.080-0.02624.272-0.012-0.0120.0000.0000.0000.000
95A110TYR0-0.1070.09423.909-0.005-0.0050.0000.0000.0000.000
96A111ILE00.070-0.10919.8300.0240.0240.0000.0000.0000.000
97A111ILE0-0.1150.11517.808-0.001-0.0010.0000.0000.0000.000
98A112SER00.130-0.07020.279-0.024-0.0240.0000.0000.0000.000
99A112SER0-0.0690.06620.6300.0000.0000.0000.0000.0000.000
100A113ARG0-0.007-0.11515.7470.0460.0460.0000.0000.0000.000
101A113ARG10.7981.01513.7890.2980.2980.0000.0000.0000.000
102A114GLU00.144-0.11216.504-0.039-0.0390.0000.0000.0000.000
103A114GLU-1-0.951-0.79718.357-0.187-0.1870.0000.0000.0000.000
104A115PHE00.016-0.10713.4760.0490.0490.0000.0000.0000.000
105A115PHE0-0.0950.07712.894-0.046-0.0460.0000.0000.0000.000
106A116HIS00.120-0.07814.905-0.031-0.0310.0000.0000.0000.000
107A116HIS0-0.1120.08417.154-0.006-0.0060.0000.0000.0000.000
108A117ARG00.085-0.11212.6800.0720.0720.0000.0000.0000.000
109A117ARG10.8361.0676.8520.9410.9410.0000.0000.0000.000
110A118ARG00.120-0.07413.906-0.019-0.0190.0000.0000.0000.000
111A118ARG10.8251.04316.7320.1860.1860.0000.0000.0000.000
112A119TYR0-0.017-0.14513.9500.0290.0290.0000.0000.0000.000
113A119TYR0-0.0310.1229.366-0.082-0.0820.0000.0000.0000.000
114A120ARG00.178-0.05114.6230.0060.0060.0000.0000.0000.000
115A120ARG10.7991.03916.3910.0930.0930.0000.0000.0000.000
116A121LEU00.028-0.16716.295-0.039-0.0390.0000.0000.0000.000
117A121LEU0-0.0530.13817.584-0.005-0.0050.0000.0000.0000.000
118A122PRO0-0.064-0.11017.3960.0360.0360.0000.0000.0000.000
119A123SER00.1150.04220.435-0.018-0.0180.0000.0000.0000.000
120A123SER0-0.0540.06225.1470.0020.0020.0000.0000.0000.000
121A124ASN00.073-0.03123.4330.0020.0020.0000.0000.0000.000
122A124ASN0-0.1120.04422.547-0.009-0.0090.0000.0000.0000.000
123A125VAL00.106-0.07821.2980.0050.0050.0000.0000.0000.000
124A125VAL0-0.1070.07819.231-0.010-0.0100.0000.0000.0000.000
125A126ASP00.143-0.08422.6700.0100.0100.0000.0000.0000.000
126A126ASP-1-0.892-0.76825.577-0.192-0.1920.0000.0000.0000.000
127A127GLN00.159-0.11923.452-0.027-0.0270.0000.0000.0000.000
128A127GLN0-0.1000.09923.0890.0070.0070.0000.0000.0000.000
129A128SER0-0.025-0.09424.532-0.028-0.0280.0000.0000.0000.000
130A128SER0-0.0650.04728.3780.0070.0070.0000.0000.0000.000
131A129ALA00.082-0.11725.560-0.001-0.0010.0000.0000.0000.000
132A129ALA0-0.0850.12025.3270.0020.0020.0000.0000.0000.000
133A130ILE00.007-0.12721.334-0.014-0.0140.0000.0000.0000.000
134A130ILE0-0.1110.09219.275-0.005-0.0050.0000.0000.0000.000
135A131THR0-0.024-0.09020.6190.0250.0250.0000.0000.0000.000
136A131THR0-0.0250.08621.309-0.014-0.0140.0000.0000.0000.000
137A132CYS00.155-0.10718.050-0.044-0.0440.0000.0000.0000.000
138A132CYS0-0.1450.10316.753-0.003-0.0030.0000.0000.0000.000
139A133THR00.029-0.07117.5450.0600.0600.0000.0000.0000.000
140A133THR0-0.0490.05318.037-0.019-0.0190.0000.0000.0000.000
141A134LEU00.170-0.06016.373-0.108-0.1080.0000.0000.0000.000
142A134LEU0-0.1220.09715.1130.0100.0100.0000.0000.0000.000
143A135SER00.012-0.09415.7910.1140.1140.0000.0000.0000.000
144A135SER0-0.0400.05115.156-0.051-0.0510.0000.0000.0000.000
145A136ALA00.100-0.09417.087-0.032-0.0320.0000.0000.0000.000
146A136ALA0-0.0790.09919.1200.0130.0130.0000.0000.0000.000
147A137ASP0-0.030-0.13914.6350.0590.0590.0000.0000.0000.000
148A137ASP-1-0.911-0.82013.771-0.694-0.6940.0000.0000.0000.000
149A138GLY00.013-0.09413.133-0.103-0.1030.0000.0000.0000.000
150A139LEU00.115-0.00411.238-0.184-0.1840.0000.0000.0000.000
151A139LEU0-0.1170.1069.030-0.022-0.0220.0000.0000.0000.000
152A140LEU00.130-0.08011.6910.2050.2050.0000.0000.0000.000
153A140LEU0-0.1210.08312.4850.0130.0130.0000.0000.0000.000
154A141THR0-0.005-0.11711.887-0.239-0.2390.0000.0000.0000.000
155A141THR0-0.0450.08413.681-0.023-0.0230.0000.0000.0000.000
156A142LEU00.029-0.12013.6460.1090.1090.0000.0000.0000.000
157A142LEU0-0.0210.11813.9900.0070.0070.0000.0000.0000.000
158A143CYS00.086-0.10315.106-0.061-0.0610.0000.0000.0000.000
159A143CYS0-0.1290.11117.8950.0090.0090.0000.0000.0000.000
160A144GLY00.067-0.08817.8200.0360.0360.0000.0000.0000.000
161A145PRO00.0250.00519.7530.0040.0040.0000.0000.0000.000
162A146LYS00.1490.03122.6460.0020.0020.0000.0000.0000.000
163A146LYS10.7121.00318.2930.2470.2470.0000.0000.0000.000
164A147THR0-0.094-0.11623.7880.0010.0010.0000.0000.0000.000
165A147THR00.0200.10126.8720.0000.0000.0000.0000.0000.000
166A148SER00.026-0.07627.4950.0020.0020.0000.0000.0000.000
167A148SER0-0.0430.06529.4810.0050.0050.0000.0000.0000.000
168A149GLY0-0.007-0.11130.197-0.002-0.0020.0000.0000.0000.000
169A150ILE00.0660.01432.941-0.001-0.0010.0000.0000.0000.000
170A150ILE0-0.0720.08536.5300.0010.0010.0000.0000.0000.000
171A151ASP00.085-0.10133.4660.0020.0020.0000.0000.0000.000
172A151ASP-1-0.989-0.85233.374-0.105-0.1050.0000.0000.0000.000
173A152ALA00.108-0.09829.631-0.007-0.0070.0000.0000.0000.000
174A152ALA0-0.0740.10529.1870.0010.0010.0000.0000.0000.000
175A153GLY0-0.015-0.10128.256-0.011-0.0110.0000.0000.0000.000
176A154ARG00.076-0.01327.500-0.018-0.0180.0000.0000.0000.000
177A154ARG10.7370.97627.0970.1260.1260.0000.0000.0000.000
178A155GLY0-0.018-0.11727.3600.0130.0130.0000.0000.0000.000
179A156ASP00.152-0.00226.488-0.020-0.0200.0000.0000.0000.000
180A156ASP-1-0.971-0.81027.058-0.158-0.1580.0000.0000.0000.000
181A157ARG0-0.021-0.12726.0710.0150.0150.0000.0000.0000.000
182A157ARG10.7841.01524.0830.2650.2650.0000.0000.0000.000
183A158THR00.043-0.08725.024-0.017-0.0170.0000.0000.0000.000
184A158THR0-0.0260.08525.0610.0020.0020.0000.0000.0000.000
185A159ILE0-0.002-0.13022.2470.0270.0270.0000.0000.0000.000
186A159ILE0-0.0920.10220.298-0.005-0.0050.0000.0000.0000.000
187A160PRO00.006-0.10322.862-0.018-0.0180.0000.0000.0000.000
188A161VAL00.095-0.00620.943-0.016-0.0160.0000.0000.0000.000
189A161VAL0-0.0610.12619.061-0.008-0.0080.0000.0000.0000.000
190A162THR00.058-0.09821.5250.0190.0190.0000.0000.0000.000
191A162THR0-0.0580.08422.6220.0160.0160.0000.0000.0000.000
192A163ARG00.114-0.08520.842-0.055-0.0550.0000.0000.0000.000
193A163ARG10.7711.02019.8160.4270.4270.0000.0000.0000.000
194A164GLU00.086-0.07620.5800.0470.0470.0000.0000.0000.000
195A164GLU-1-0.890-0.77918.244-0.568-0.5680.0000.0000.0000.000
196A165ASP0-0.018-0.14022.017-0.031-0.0310.0000.0000.0000.000
197A165ASP-1-0.969-0.81125.787-0.279-0.2790.0000.0000.0000.000
198A166LYS00.025-0.11018.8580.0070.0070.0000.0000.0000.000
199A166LYS10.8650.91018.7070.5120.5120.0000.0000.0000.000