FMODB

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

Last updated: 2024-05-02

All entries: 37386

Number of unique PDB entries: 7781

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FMODB ID: 7MG4K

Calculation Name: 3FB2-A-Xray372

Preferred Name:
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Target Type:
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Ligand Name:
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ligand 3-letter code:
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PDB ID: 3FB2

Chain ID: A

ChEMBL ID:
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UniProt ID: Q13813

Base Structure: X-ray

Registration Date: 2023-09-26

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

DOI:


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 188
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -1822054.561805
FMO2-HF: Nuclear repulsion 1744807.046985
FMO2-HF: Total energy -77247.51482
FMO2-MP2: Total energy -77472.010891


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:1334:HIS)


Summations of interaction energy for fragment #1(A:1334:HIS)
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.
-20.141-17.647.37-3.549-6.323-0.028
Interaction energy analysis for fragmet #1(A:1334:HIS)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.021 / q_NPA : 0.005
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].
3A1336HIS0-0.056-0.0163.330-5.278-2.1000.040-1.174-2.0440.006
4A1337ASP-1-0.822-0.9124.512-0.766-0.5170.000-0.029-0.2210.000
5A1338SER0-0.0230.0036.552-0.219-0.2190.0000.0000.0000.000
6A1339HIS00.021-0.0102.114-13.463-14.3897.330-2.346-4.058-0.034
7A1340ASP-1-0.831-0.9246.517-0.966-0.9660.0000.0000.0000.000
8A1341LEU0-0.027-0.0059.3760.1900.1900.0000.0000.0000.000
9A1342GLN00.004-0.0037.165-0.553-0.5530.0000.0000.0000.000
10A1343ARG10.8570.92910.1111.2061.2060.0000.0000.0000.000
11A1344PHE00.0140.01611.8030.1790.1790.0000.0000.0000.000
12A1345LEU0-0.012-0.02514.2130.1350.1350.0000.0000.0000.000
13A1346SER0-0.044-0.01314.2290.0560.0560.0000.0000.0000.000
14A1347ASP-1-0.795-0.89815.864-0.783-0.7830.0000.0000.0000.000
15A1348PHE0-0.011-0.01317.8690.0870.0870.0000.0000.0000.000
16A1349ARG10.9340.97519.1410.5240.5240.0000.0000.0000.000
17A1350ASP-1-0.820-0.90018.290-0.686-0.6860.0000.0000.0000.000
18A1351LEU0-0.017-0.01421.3890.0570.0570.0000.0000.0000.000
19A1352MET0-0.019-0.00123.5940.0500.0500.0000.0000.0000.000
20A1353SER0-0.058-0.03123.7010.0370.0370.0000.0000.0000.000
21A1354TRP0-0.0090.00125.8890.0230.0230.0000.0000.0000.000
22A1355ILE00.0050.00527.8140.0240.0240.0000.0000.0000.000
23A1356ASN0-0.056-0.04028.5620.0340.0340.0000.0000.0000.000
24A1357GLY00.0090.01630.3390.0170.0170.0000.0000.0000.000
25A1358ILE0-0.013-0.00631.9020.0190.0190.0000.0000.0000.000
26A1359ARG10.8460.88832.7670.2230.2230.0000.0000.0000.000
27A1360GLY00.0260.01734.9420.0130.0130.0000.0000.0000.000
28A1361LEU0-0.040-0.00636.4810.0120.0120.0000.0000.0000.000
29A1362VAL0-0.035-0.02638.0780.0120.0120.0000.0000.0000.000
30A1363SER0-0.090-0.05339.4790.0100.0100.0000.0000.0000.000
31A1364SER0-0.0070.01241.2510.0080.0080.0000.0000.0000.000
32A1365ASP-1-0.833-0.92743.852-0.119-0.1190.0000.0000.0000.000
33A1366GLU-1-1.003-0.99246.973-0.110-0.1100.0000.0000.0000.000
34A1367LEU00.0280.01948.8950.0000.0000.0000.0000.0000.000
35A1368ALA0-0.029-0.01252.0480.0010.0010.0000.0000.0000.000
36A1369LYS10.8820.92553.7670.0990.0990.0000.0000.0000.000
37A1370ASP-1-0.762-0.88257.692-0.081-0.0810.0000.0000.0000.000
38A1371VAL00.0050.00957.298-0.002-0.0020.0000.0000.0000.000
39A1372THR00.0300.02155.749-0.002-0.0020.0000.0000.0000.000
40A1373GLY0-0.020-0.01553.759-0.004-0.0040.0000.0000.0000.000
41A1374ALA00.009-0.01352.378-0.005-0.0050.0000.0000.0000.000
42A1375GLU-1-0.943-0.96351.781-0.090-0.0900.0000.0000.0000.000
43A1376ALA00.0450.01950.352-0.004-0.0040.0000.0000.0000.000
44A1377LEU0-0.061-0.04048.006-0.007-0.0070.0000.0000.0000.000
45A1378LEU00.0070.00746.974-0.007-0.0070.0000.0000.0000.000
46A1379GLU-1-0.965-0.97746.636-0.118-0.1180.0000.0000.0000.000
47A1380ARG10.9600.96843.7210.1330.1330.0000.0000.0000.000
48A1381HIS0-0.049-0.01941.837-0.012-0.0120.0000.0000.0000.000
49A1382GLN00.0310.01142.025-0.003-0.0030.0000.0000.0000.000
50A1383GLU-1-0.857-0.90940.150-0.163-0.1630.0000.0000.0000.000
51A1384HIS10.8080.86537.2620.1720.1720.0000.0000.0000.000
52A1385ARG10.7540.88737.2270.1440.1440.0000.0000.0000.000
53A1386THR00.020-0.00137.187-0.005-0.0050.0000.0000.0000.000
54A1387GLU-1-0.922-0.94633.271-0.239-0.2390.0000.0000.0000.000
55A1388ILE00.0220.01032.820-0.022-0.0220.0000.0000.0000.000
56A1389ASP-1-0.811-0.90032.555-0.178-0.1780.0000.0000.0000.000
57A1390ALA0-0.047-0.02632.200-0.004-0.0040.0000.0000.0000.000
58A1391ARG10.8400.91627.3410.2680.2680.0000.0000.0000.000
59A1392ALA00.0170.01927.946-0.017-0.0170.0000.0000.0000.000
60A1393GLY00.0130.00227.348-0.004-0.0040.0000.0000.0000.000
61A1394THR0-0.007-0.01323.214-0.007-0.0070.0000.0000.0000.000
62A1395PHE00.0340.01223.278-0.033-0.0330.0000.0000.0000.000
63A1396GLN0-0.007-0.01124.232-0.011-0.0110.0000.0000.0000.000
64A1397ALA0-0.0060.00220.4950.0060.0060.0000.0000.0000.000
65A1398PHE0-0.0020.00218.837-0.016-0.0160.0000.0000.0000.000
66A1399GLU-1-0.809-0.88720.219-0.217-0.2170.0000.0000.0000.000
67A1400GLN0-0.049-0.02220.0300.0230.0230.0000.0000.0000.000
68A1401PHE0-0.019-0.01311.9990.0340.0340.0000.0000.0000.000
69A1402GLY00.0600.01616.8830.0080.0080.0000.0000.0000.000
70A1403GLN0-0.033-0.02018.8290.0500.0500.0000.0000.0000.000
71A1404GLN00.0110.01115.4840.0460.0460.0000.0000.0000.000
72A1405LEU0-0.0080.01512.3740.0620.0620.0000.0000.0000.000
73A1406LEU0-0.012-0.01415.6490.0580.0580.0000.0000.0000.000
74A1407ALA0-0.047-0.01518.3740.0400.0400.0000.0000.0000.000
75A1408HIS0-0.085-0.04613.0980.0920.0920.0000.0000.0000.000
76A1409GLY0-0.023-0.00113.9230.0510.0510.0000.0000.0000.000
77A1410HIS00.0100.00410.8490.1060.1060.0000.0000.0000.000
78A1411TYR00.0340.0109.619-0.059-0.0590.0000.0000.0000.000
79A1412ALA00.0020.00713.5570.0070.0070.0000.0000.0000.000
80A1413SER00.007-0.02116.007-0.041-0.0410.0000.0000.0000.000
81A1414PRO0-0.015-0.00918.155-0.012-0.0120.0000.0000.0000.000
82A1415GLU-1-0.854-0.92718.543-0.228-0.2280.0000.0000.0000.000
83A1416ILE00.0380.02614.884-0.026-0.0260.0000.0000.0000.000
84A1417LYS10.8170.88919.3010.1510.1510.0000.0000.0000.000
85A1418GLN0-0.012-0.02122.863-0.027-0.0270.0000.0000.0000.000
86A1419LYS10.7980.89620.1350.3570.3570.0000.0000.0000.000
87A1420LEU00.0250.02321.405-0.006-0.0060.0000.0000.0000.000
88A1421ASP-1-0.766-0.85524.322-0.163-0.1630.0000.0000.0000.000
89A1422ILE0-0.052-0.02925.0860.0070.0070.0000.0000.0000.000
90A1423LEU00.0210.00523.5360.0040.0040.0000.0000.0000.000
91A1424ASP-1-0.854-0.91126.924-0.216-0.2160.0000.0000.0000.000
92A1425GLN0-0.088-0.05029.6330.0170.0170.0000.0000.0000.000
93A1426GLU-1-0.818-0.89529.197-0.226-0.2260.0000.0000.0000.000
94A1427ARG10.7660.86227.6710.2370.2370.0000.0000.0000.000
95A1428ALA00.0080.00931.7440.0110.0110.0000.0000.0000.000
96A1429ASP-1-0.818-0.90034.564-0.149-0.1490.0000.0000.0000.000
97A1430LEU0-0.022-0.00332.3160.0050.0050.0000.0000.0000.000
98A1431GLU-1-0.831-0.88435.498-0.142-0.1420.0000.0000.0000.000
99A1432LYS10.8340.89537.4510.1520.1520.0000.0000.0000.000
100A1433ALA0-0.0060.00738.3230.0070.0070.0000.0000.0000.000
101A1434TRP00.0350.00338.8190.0080.0080.0000.0000.0000.000
102A1435VAL00.0200.00740.7400.0070.0070.0000.0000.0000.000
103A1436GLN0-0.031-0.01143.4280.0080.0080.0000.0000.0000.000
104A1437ARG10.8670.92743.1780.1340.1340.0000.0000.0000.000
105A1438ARG10.7690.84544.8320.1100.1100.0000.0000.0000.000
106A1439MET00.0380.01846.4550.0040.0040.0000.0000.0000.000
107A1440MET00.0040.00448.6030.0060.0060.0000.0000.0000.000
108A1441LEU00.002-0.00946.7060.0040.0040.0000.0000.0000.000
109A1442ASP-1-0.809-0.86450.168-0.096-0.0960.0000.0000.0000.000
110A1443GLN00.0700.03352.5550.0030.0030.0000.0000.0000.000
111A1444CYS0-0.074-0.00553.0930.0030.0030.0000.0000.0000.000
112A1445LEU00.0490.01354.3300.0030.0030.0000.0000.0000.000
113A1446GLU-1-0.840-0.93656.079-0.071-0.0710.0000.0000.0000.000
114A1447LEU0-0.038-0.00758.1340.0030.0030.0000.0000.0000.000
115A1448GLN0-0.004-0.00657.5780.0050.0050.0000.0000.0000.000
116A1449LEU0-0.023-0.01459.1940.0020.0020.0000.0000.0000.000
117A1450PHE00.0430.01762.0660.0030.0030.0000.0000.0000.000
118A1451HIS00.0330.01861.9980.0040.0040.0000.0000.0000.000
119A1452ARG10.9470.97063.5380.0670.0670.0000.0000.0000.000
120A1453ASP-1-0.870-0.93066.225-0.058-0.0580.0000.0000.0000.000
121A1454CYS0-0.080-0.03767.8510.0030.0030.0000.0000.0000.000
122A1455GLU-1-0.920-0.96466.883-0.062-0.0620.0000.0000.0000.000
123A1456GLN0-0.040-0.00868.2570.0000.0000.0000.0000.0000.000
124A1457ALA00.0090.00872.0710.0020.0020.0000.0000.0000.000
125A1458GLU-1-0.842-0.91273.179-0.049-0.0490.0000.0000.0000.000
126A1459ASN0-0.034-0.03472.2970.0020.0020.0000.0000.0000.000
127A1460TRP0-0.017-0.00176.0060.0020.0020.0000.0000.0000.000
128A1461MET0-0.021-0.01476.5260.0020.0020.0000.0000.0000.000
129A1462ALA00.0510.03478.5720.0010.0010.0000.0000.0000.000
130A1463ALA0-0.036-0.01980.1830.0010.0010.0000.0000.0000.000
131A1464ARG10.8590.93480.3950.0430.0430.0000.0000.0000.000
132A1465GLU-1-0.789-0.86981.607-0.042-0.0420.0000.0000.0000.000
133A1466ALA0-0.0250.01084.0100.0010.0010.0000.0000.0000.000
134A1467PHE0-0.065-0.02585.5180.0010.0010.0000.0000.0000.000
135A1468LEU0-0.058-0.03288.1240.0020.0020.0000.0000.0000.000
136A1488GLU-1-0.879-0.94692.446-0.031-0.0310.0000.0000.0000.000
137A1489ASP-1-0.901-0.95787.540-0.035-0.0350.0000.0000.0000.000
138A1490PHE00.0320.00887.024-0.001-0.0010.0000.0000.0000.000
139A1491ASP-1-0.824-0.92286.880-0.034-0.0340.0000.0000.0000.000
140A1492LYS10.8230.91885.3000.0320.0320.0000.0000.0000.000
141A1493ALA00.000-0.00682.631-0.001-0.0010.0000.0000.0000.000
142A1494ILE0-0.0010.00582.056-0.001-0.0010.0000.0000.0000.000
143A1495ASN0-0.069-0.03882.348-0.001-0.0010.0000.0000.0000.000
144A1496VAL00.002-0.00177.901-0.001-0.0010.0000.0000.0000.000
145A1497GLN00.0290.02375.649-0.002-0.0020.0000.0000.0000.000
146A1498GLU-1-0.788-0.87877.739-0.039-0.0390.0000.0000.0000.000
147A1499GLU-1-0.843-0.90174.572-0.047-0.0470.0000.0000.0000.000
148A1500LYS10.8160.89173.5620.0460.0460.0000.0000.0000.000
149A1501ILE00.0040.00873.120-0.002-0.0020.0000.0000.0000.000
150A1502ALA0-0.029-0.01374.086-0.001-0.0010.0000.0000.0000.000
151A1503ALA0-0.007-0.00370.358-0.001-0.0010.0000.0000.0000.000
152A1504LEU00.0150.00668.615-0.001-0.0010.0000.0000.0000.000
153A1505GLN0-0.032-0.01969.398-0.001-0.0010.0000.0000.0000.000
154A1506ALA00.0210.00769.573-0.001-0.0010.0000.0000.0000.000
155A1507PHE0-0.033-0.00661.803-0.001-0.0010.0000.0000.0000.000
156A1508ALA00.0350.00665.034-0.002-0.0020.0000.0000.0000.000
157A1509ASP-1-0.843-0.91965.596-0.051-0.0510.0000.0000.0000.000
158A1510GLN0-0.070-0.02860.360-0.001-0.0010.0000.0000.0000.000
159A1511LEU00.0140.02659.881-0.001-0.0010.0000.0000.0000.000
160A1512ILE0-0.029-0.01561.340-0.002-0.0020.0000.0000.0000.000
161A1513ALA0-0.043-0.02163.2110.0000.0000.0000.0000.0000.000
162A1514ALA0-0.019-0.01158.4210.0000.0000.0000.0000.0000.000
163A1515GLY0-0.072-0.04157.618-0.002-0.0020.0000.0000.0000.000
164A1516HIS0-0.013-0.00757.166-0.002-0.0020.0000.0000.0000.000
165A1517TYR00.0420.00154.2590.0030.0030.0000.0000.0000.000
166A1518ALA00.0060.00857.0680.0000.0000.0000.0000.0000.000
167A1519LYS10.8750.94560.3910.0650.0650.0000.0000.0000.000
168A1520GLY0-0.0170.00263.0770.0020.0020.0000.0000.0000.000
169A1521ASP-1-0.867-0.94363.462-0.064-0.0640.0000.0000.0000.000
170A1522ILE00.0040.00861.2730.0020.0020.0000.0000.0000.000
171A1523SER00.005-0.00865.6760.0020.0020.0000.0000.0000.000
172A1524SER0-0.076-0.02568.2730.0030.0030.0000.0000.0000.000
173A1525ARG10.9130.94067.4450.0590.0590.0000.0000.0000.000
174A1526ARG10.8550.91269.4750.0500.0500.0000.0000.0000.000
175A1527ASN00.001-0.00671.2420.0020.0020.0000.0000.0000.000
176A1528GLU-1-0.880-0.92472.368-0.051-0.0510.0000.0000.0000.000
177A1529VAL00.0460.02072.5160.0020.0020.0000.0000.0000.000
178A1530LEU00.0040.00774.2100.0020.0020.0000.0000.0000.000
179A1531ASP-1-0.829-0.90677.155-0.040-0.0400.0000.0000.0000.000
180A1532ARG10.7020.82876.7760.0480.0480.0000.0000.0000.000
181A1533TRP00.0340.00078.8090.0010.0010.0000.0000.0000.000
182A1534ARG10.7950.87679.6460.0410.0410.0000.0000.0000.000
183A1535ARG10.9050.93879.4740.0430.0430.0000.0000.0000.000
184A1536LEU00.0110.02382.4260.0010.0010.0000.0000.0000.000
185A1537LYS10.8740.90183.0740.0380.0380.0000.0000.0000.000
186A1538ALA0-0.059-0.02286.1770.0010.0010.0000.0000.0000.000
187A1539GLN0-0.072-0.04187.1030.0010.0010.0000.0000.0000.000
188A1540MET0-0.089-0.00985.1390.0010.0010.0000.0000.0000.000