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: K21Y3

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 OptAll
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 -779088.312173
FMO2-HF: Nuclear repulsion 737260.129326
FMO2-HF: Total energy -41828.182848
FMO2-MP2: Total energy -41950.443232


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.
-0.6892.0910.008-1.507-1.2810.001
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 : 0.049 / q_NPA : 0.015
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].
3A62VAL0-0.1050.1054.2710.0810.3730.000-0.128-0.1640.000
4A63SER00.063-0.0713.1920.1812.2070.001-1.114-0.9130.003
5A63SER0-0.0670.0305.4660.5850.5850.0000.0000.0000.000
6A64GLU00.045-0.1113.556-1.748-1.2860.007-0.265-0.204-0.002
7A64GLU-1-0.868-0.7404.915-1.589-1.5890.0000.0000.0000.000
8A65VAL00.042-0.1125.8350.1910.1910.0000.0000.0000.000
9A65VAL0-0.0580.1068.4070.0380.0380.0000.0000.0000.000
10A66ARG00.059-0.0909.3980.1170.1170.0000.0000.0000.000
11A66ARG10.7630.9748.0851.1391.1390.0000.0000.0000.000
12A67SER00.092-0.07012.213-0.019-0.0190.0000.0000.0000.000
13A67SER0-0.0340.06914.9930.0090.0090.0000.0000.0000.000
14A68ASP00.010-0.06315.7660.0380.0380.0000.0000.0000.000
15A68ASP-1-0.884-0.80317.852-0.314-0.3140.0000.0000.0000.000
16A69ARG00.111-0.08218.948-0.005-0.0050.0000.0000.0000.000
17A69ARG10.7820.99422.9200.1510.1510.0000.0000.0000.000
18A70GLU00.080-0.10721.7120.0190.0190.0000.0000.0000.000
19A70GLU-1-0.848-0.78322.301-0.211-0.2110.0000.0000.0000.000
20A71LYS00.035-0.07719.7200.0150.0150.0000.0000.0000.000
21A71LYS10.7760.98718.1000.3150.3150.0000.0000.0000.000
22A72PHE00.132-0.06916.4140.0210.0210.0000.0000.0000.000
23A72PHE0-0.0390.09314.054-0.003-0.0030.0000.0000.0000.000
24A73THR00.006-0.07414.2660.0370.0370.0000.0000.0000.000
25A73THR0-0.0230.05212.8390.0170.0170.0000.0000.0000.000
26A74VAL00.027-0.09410.591-0.020-0.0200.0000.0000.0000.000
27A74VAL0-0.0730.0969.8840.0170.0170.0000.0000.0000.000
28A75TYR00.086-0.0718.6220.2800.2800.0000.0000.0000.000
29A75TYR0-0.0660.0957.7540.0300.0300.0000.0000.0000.000
30A76LEU00.118-0.0977.816-0.608-0.6080.0000.0000.0000.000
31A76LEU0-0.1380.0777.8780.0770.0770.0000.0000.0000.000
32A77ASP00.154-0.0517.2890.5510.5510.0000.0000.0000.000
33A77ASP-1-0.929-0.8046.725-1.965-1.9650.0000.0000.0000.000
34A78VAL0-0.005-0.1148.678-0.055-0.0550.0000.0000.0000.000
35A78VAL0-0.0800.08911.7730.0280.0280.0000.0000.0000.000
36A79LYS00.153-0.05911.3110.1890.1890.0000.0000.0000.000
37A79LYS10.7780.9948.2711.2961.2960.0000.0000.0000.000
38A80HIS00.060-0.10513.1660.0210.0210.0000.0000.0000.000
39A80HIS0-0.1210.02415.371-0.015-0.0150.0000.0000.0000.000
40A81PHE00.027-0.09915.8620.0850.0850.0000.0000.0000.000
41A81PHE0-0.1260.07814.056-0.009-0.0090.0000.0000.0000.000
42A82SER00.020-0.07317.593-0.053-0.0530.0000.0000.0000.000
43A82SER0-0.0390.05721.9600.0170.0170.0000.0000.0000.000
44A83PRO0-0.020-0.13420.127-0.024-0.0240.0000.0000.0000.000
45A84ASP00.038-0.02521.506-0.015-0.0150.0000.0000.0000.000
46A84ASP-1-0.928-0.81824.600-0.285-0.2850.0000.0000.0000.000
47A85GLU00.019-0.08820.9670.0320.0320.0000.0000.0000.000
48A85GLU-1-0.832-0.74620.254-0.357-0.3570.0000.0000.0000.000
49A86LEU00.043-0.13118.761-0.016-0.0160.0000.0000.0000.000
50A86LEU0-0.0950.09015.786-0.024-0.0240.0000.0000.0000.000
51A87SER00.170-0.03519.6730.0050.0050.0000.0000.0000.000
52A87SER0-0.1080.06321.8480.0210.0210.0000.0000.0000.000
53A88VAL00.074-0.11319.493-0.017-0.0170.0000.0000.0000.000
54A88VAL0-0.0920.10717.791-0.011-0.0110.0000.0000.0000.000
55A89LYS00.041-0.12020.1750.0280.0280.0000.0000.0000.000
56A89LYS10.8901.06122.0870.2790.2790.0000.0000.0000.000
57A90VAL00.023-0.12020.534-0.049-0.0490.0000.0000.0000.000
58A90VAL0-0.0390.12121.767-0.002-0.0020.0000.0000.0000.000
59A91THR00.022-0.06022.2350.0220.0220.0000.0000.0000.000
60A91THR0-0.1040.01022.6240.0000.0000.0000.0000.0000.000
61A92ASP00.135-0.07022.796-0.020-0.0200.0000.0000.0000.000
62A92ASP-1-0.954-0.82025.182-0.143-0.1430.0000.0000.0000.000
63A93ASP00.040-0.08122.9170.0000.0000.0000.0000.0000.000
64A93ASP-1-0.891-0.79022.782-0.173-0.1730.0000.0000.0000.000
65A94TYR00.075-0.11818.999-0.007-0.0070.0000.0000.0000.000
66A94TYR0-0.0740.08217.3580.0120.0120.0000.0000.0000.000
67A95VAL00.119-0.08917.5380.0390.0390.0000.0000.0000.000
68A95VAL0-0.0670.11416.460-0.011-0.0110.0000.0000.0000.000
69A96GLU00.074-0.11916.701-0.060-0.0600.0000.0000.0000.000
70A96GLU-1-0.898-0.78219.353-0.270-0.2700.0000.0000.0000.000
71A97ILE00.060-0.08815.3140.0350.0350.0000.0000.0000.000
72A97ILE0-0.0710.08312.989-0.030-0.0300.0000.0000.0000.000
73A98GLN00.049-0.09616.230-0.037-0.0370.0000.0000.0000.000
74A98GLN0-0.0920.08719.4900.0210.0210.0000.0000.0000.000
75A99GLY00.060-0.07816.6470.0050.0050.0000.0000.0000.000
76A100LYS00.113-0.01517.479-0.005-0.0050.0000.0000.0000.000
77A100LYS10.8071.06020.4980.2350.2350.0000.0000.0000.000
78A101HIS00.103-0.06618.4700.0240.0240.0000.0000.0000.000
79A101HIS10.6950.95117.6920.3550.3550.0000.0000.0000.000
80A102GLY0-0.034-0.11819.5610.0100.0100.0000.0000.0000.000
81A103GLU00.041-0.01621.690-0.005-0.0050.0000.0000.0000.000
82A103GLU-1-0.822-0.72618.512-0.331-0.3310.0000.0000.0000.000
83A104ARG00.112-0.06922.8430.0100.0100.0000.0000.0000.000
84A104ARG10.9171.06826.3520.1190.1190.0000.0000.0000.000
85A105GLN0-0.007-0.08523.422-0.025-0.0250.0000.0000.0000.000
86A105GLN0-0.1220.03320.1880.0080.0080.0000.0000.0000.000
87A106ASP00.137-0.07624.331-0.003-0.0030.0000.0000.0000.000
88A106ASP-1-0.948-0.83325.474-0.056-0.0560.0000.0000.0000.000
89A107ASP00.007-0.12926.672-0.004-0.0040.0000.0000.0000.000
90A107ASP-1-0.965-0.83429.874-0.036-0.0360.0000.0000.0000.000
91A108HIS00.012-0.12830.1480.0030.0030.0000.0000.0000.000
92A108HIS0-0.0990.09031.654-0.005-0.0050.0000.0000.0000.000
93A109GLY00.046-0.09126.267-0.002-0.0020.0000.0000.0000.000
94A110TYR00.070-0.02524.638-0.010-0.0100.0000.0000.0000.000
95A110TYR0-0.0940.09124.405-0.003-0.0030.0000.0000.0000.000
96A111ILE00.053-0.10720.3160.0230.0230.0000.0000.0000.000
97A111ILE0-0.0960.11318.331-0.001-0.0010.0000.0000.0000.000
98A112SER00.115-0.07220.421-0.019-0.0190.0000.0000.0000.000
99A112SER0-0.0620.06920.5940.0010.0010.0000.0000.0000.000
100A113ARG00.019-0.11015.8570.0450.0450.0000.0000.0000.000
101A113ARG10.7651.00114.0320.3190.3190.0000.0000.0000.000
102A114GLU00.128-0.11216.399-0.038-0.0380.0000.0000.0000.000
103A114GLU-1-0.935-0.79618.402-0.235-0.2350.0000.0000.0000.000
104A115PHE00.020-0.10813.6770.0460.0460.0000.0000.0000.000
105A115PHE0-0.0900.08313.152-0.056-0.0560.0000.0000.0000.000
106A116HIS00.107-0.07515.152-0.025-0.0250.0000.0000.0000.000
107A116HIS0-0.1040.08117.717-0.006-0.0060.0000.0000.0000.000
108A117ARG00.082-0.11012.9400.0720.0720.0000.0000.0000.000
109A117ARG10.8371.0546.9611.3821.3820.0000.0000.0000.000
110A118ARG00.096-0.07914.245-0.017-0.0170.0000.0000.0000.000
111A118ARG10.8311.02616.6410.2650.2650.0000.0000.0000.000
112A119TYR0-0.005-0.11913.8910.0290.0290.0000.0000.0000.000
113A119TYR0-0.0430.1229.364-0.094-0.0940.0000.0000.0000.000
114A120ARG00.182-0.05514.5650.0100.0100.0000.0000.0000.000
115A120ARG10.8021.03616.5980.1780.1780.0000.0000.0000.000
116A121LEU00.045-0.14516.428-0.038-0.0380.0000.0000.0000.000
117A121LEU0-0.0730.13417.910-0.003-0.0030.0000.0000.0000.000
118A122PRO0-0.037-0.11917.2000.0400.0400.0000.0000.0000.000
119A123SER00.0710.03420.217-0.019-0.0190.0000.0000.0000.000
120A123SER0-0.0470.06224.6130.0020.0020.0000.0000.0000.000
121A124ASN00.064-0.03923.3290.0090.0090.0000.0000.0000.000
122A124ASN0-0.0910.05522.883-0.011-0.0110.0000.0000.0000.000
123A125VAL00.105-0.08621.4590.0110.0110.0000.0000.0000.000
124A125VAL0-0.1100.08119.423-0.011-0.0110.0000.0000.0000.000
125A126ASP00.141-0.08022.8660.0050.0050.0000.0000.0000.000
126A126ASP-1-0.893-0.76925.824-0.208-0.2080.0000.0000.0000.000
127A127GLN00.128-0.12723.655-0.027-0.0270.0000.0000.0000.000
128A127GLN0-0.0970.10223.1470.0080.0080.0000.0000.0000.000
129A128SER00.012-0.07724.720-0.025-0.0250.0000.0000.0000.000
130A128SER0-0.0770.04428.6470.0070.0070.0000.0000.0000.000
131A129ALA00.098-0.11325.865-0.004-0.0040.0000.0000.0000.000
132A129ALA0-0.0850.11625.5970.0020.0020.0000.0000.0000.000
133A130ILE00.005-0.11321.634-0.013-0.0130.0000.0000.0000.000
134A130ILE0-0.0970.09619.589-0.007-0.0070.0000.0000.0000.000
135A131THR0-0.030-0.10420.7640.0270.0270.0000.0000.0000.000
136A131THR0-0.0220.08321.556-0.013-0.0130.0000.0000.0000.000
137A132CYS00.131-0.10518.249-0.045-0.0450.0000.0000.0000.000
138A132CYS0-0.1330.10016.843-0.002-0.0020.0000.0000.0000.000
139A133THR0-0.004-0.07417.6100.0680.0680.0000.0000.0000.000
140A133THR0-0.0420.04917.701-0.020-0.0200.0000.0000.0000.000
141A134LEU00.156-0.07416.256-0.108-0.1080.0000.0000.0000.000
142A134LEU0-0.0980.10815.3130.0050.0050.0000.0000.0000.000
143A135SER00.032-0.08715.7860.1080.1080.0000.0000.0000.000
144A135SER0-0.0530.05415.338-0.056-0.0560.0000.0000.0000.000
145A136ALA00.124-0.09116.959-0.045-0.0450.0000.0000.0000.000
146A136ALA0-0.0690.09719.5740.0130.0130.0000.0000.0000.000
147A137ASP0-0.021-0.13414.8830.0480.0480.0000.0000.0000.000
148A137ASP-1-0.869-0.77914.192-0.598-0.5980.0000.0000.0000.000
149A138GLY00.001-0.09913.417-0.065-0.0650.0000.0000.0000.000
150A139LEU00.104-0.00911.267-0.170-0.1700.0000.0000.0000.000
151A139LEU0-0.1220.1029.052-0.028-0.0280.0000.0000.0000.000
152A140LEU00.144-0.07811.9470.1890.1890.0000.0000.0000.000
153A140LEU0-0.1080.08512.5380.0040.0040.0000.0000.0000.000
154A141THR0-0.017-0.12511.804-0.280-0.2800.0000.0000.0000.000
155A141THR0-0.0420.08513.355-0.021-0.0210.0000.0000.0000.000
156A142LEU00.046-0.10113.6640.1140.1140.0000.0000.0000.000
157A142LEU0-0.0360.11113.8260.0070.0070.0000.0000.0000.000
158A143CYS00.096-0.11215.138-0.073-0.0730.0000.0000.0000.000
159A143CYS0-0.1220.11417.9480.0110.0110.0000.0000.0000.000
160A144GLY00.054-0.09117.9100.0320.0320.0000.0000.0000.000
161A145PRO00.0370.00119.8360.0060.0060.0000.0000.0000.000
162A146LYS00.1140.02822.732-0.003-0.0030.0000.0000.0000.000
163A146LYS10.6920.98118.5290.2770.2770.0000.0000.0000.000
164A147THR0-0.065-0.08924.0700.0040.0040.0000.0000.0000.000
165A147THR0-0.0180.07027.1850.0000.0000.0000.0000.0000.000
166A148SER00.023-0.09527.584-0.001-0.0010.0000.0000.0000.000
167A148SER0-0.0210.07029.4190.0060.0060.0000.0000.0000.000
168A149GLY00.000-0.09330.4280.0000.0000.0000.0000.0000.000
169A150ILE00.0710.01033.396-0.001-0.0010.0000.0000.0000.000
170A150ILE0-0.0610.09736.3210.0010.0010.0000.0000.0000.000
171A151ASP00.058-0.09933.1110.0000.0000.0000.0000.0000.000
172A151ASP-1-0.973-0.84233.167-0.117-0.1170.0000.0000.0000.000
173A152ALA00.129-0.11429.227-0.010-0.0100.0000.0000.0000.000
174A152ALA0-0.0650.11128.9170.0020.0020.0000.0000.0000.000
175A153GLY0-0.034-0.11328.009-0.012-0.0120.0000.0000.0000.000
176A154ARG00.064-0.01327.272-0.017-0.0170.0000.0000.0000.000
177A154ARG10.7040.96626.7960.1610.1610.0000.0000.0000.000
178A155GLY0-0.013-0.11927.2040.0160.0160.0000.0000.0000.000
179A156ASP00.1190.00226.359-0.023-0.0230.0000.0000.0000.000
180A156ASP-1-0.930-0.81327.207-0.186-0.1860.0000.0000.0000.000
181A157ARG0-0.031-0.12325.9820.0180.0180.0000.0000.0000.000
182A157ARG10.7540.99524.4540.2880.2880.0000.0000.0000.000
183A158THR00.047-0.06624.889-0.020-0.0200.0000.0000.0000.000
184A158THR0-0.0080.08125.0120.0020.0020.0000.0000.0000.000
185A159ILE0-0.012-0.13922.1210.0310.0310.0000.0000.0000.000
186A159ILE0-0.0770.11620.165-0.006-0.0060.0000.0000.0000.000
187A160PRO00.007-0.11022.582-0.021-0.0210.0000.0000.0000.000
188A161VAL00.1070.00720.637-0.011-0.0110.0000.0000.0000.000
189A161VAL0-0.0670.12318.772-0.007-0.0070.0000.0000.0000.000
190A162THR00.056-0.10021.3960.0180.0180.0000.0000.0000.000
191A162THR0-0.0720.08522.2240.0170.0170.0000.0000.0000.000
192A163ARG00.127-0.08520.842-0.054-0.0540.0000.0000.0000.000
193A163ARG10.7311.00119.9350.4000.4000.0000.0000.0000.000
194A164GLU00.091-0.06820.5220.0500.0500.0000.0000.0000.000
195A164GLU-1-0.882-0.78418.146-0.554-0.5540.0000.0000.0000.000
196A165ASP0-0.024-0.13221.668-0.034-0.0340.0000.0000.0000.000
197A165ASP-1-0.927-0.79925.452-0.279-0.2790.0000.0000.0000.000
198A166LYS0-0.054-0.15518.3560.0140.0140.0000.0000.0000.000
199A166LYS10.8590.90618.4250.4990.4990.0000.0000.0000.000