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: M93ZZ

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 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 188
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -1818166.401704
FMO2-HF: Nuclear repulsion 1740919.508692
FMO2-HF: Total energy -77246.893012
FMO2-MP2: Total energy -77471.419442


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.
-18.46-13.5493.959-2.901-5.967-0.016
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 : 0.013 / q_NPA : 0.000
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].
3A1336HIS0-0.038-0.0153.062-6.194-2.6010.130-1.250-2.4730.009
4A1337ASP-1-0.805-0.8994.327-0.322-0.0040.002-0.043-0.2760.000
5A1338SER0-0.035-0.0036.808-0.425-0.4250.0000.0000.0000.000
6A1339HIS00.021-0.0162.314-11.348-10.3483.827-1.608-3.218-0.025
7A1340ASP-1-0.827-0.9166.799-0.366-0.3660.0000.0000.0000.000
8A1341LEU0-0.035-0.0089.4330.0670.0670.0000.0000.0000.000
9A1342GLN0-0.015-0.0137.755-0.401-0.4010.0000.0000.0000.000
10A1343ARG10.8850.93710.4510.8500.8500.0000.0000.0000.000
11A1344PHE00.0210.02112.2110.1190.1190.0000.0000.0000.000
12A1345LEU0-0.006-0.02414.6780.0750.0750.0000.0000.0000.000
13A1346SER0-0.0150.00514.3100.0360.0360.0000.0000.0000.000
14A1347ASP-1-0.814-0.89916.171-0.620-0.6200.0000.0000.0000.000
15A1348PHE0-0.006-0.01118.1330.0640.0640.0000.0000.0000.000
16A1349ARG10.9250.96419.5920.4030.4030.0000.0000.0000.000
17A1350ASP-1-0.847-0.92618.858-0.557-0.5570.0000.0000.0000.000
18A1351LEU0-0.040-0.02221.8430.0430.0430.0000.0000.0000.000
19A1352MET0-0.043-0.02023.9460.0370.0370.0000.0000.0000.000
20A1353SER0-0.056-0.03524.1150.0260.0260.0000.0000.0000.000
21A1354TRP0-0.0040.01126.3130.0190.0190.0000.0000.0000.000
22A1355ILE00.0180.00528.1710.0190.0190.0000.0000.0000.000
23A1356ASN0-0.020-0.01128.5560.0300.0300.0000.0000.0000.000
24A1357GLY00.0040.01330.8560.0140.0140.0000.0000.0000.000
25A1358ILE00.0070.00532.3580.0150.0150.0000.0000.0000.000
26A1359ARG10.8760.93333.9140.1660.1660.0000.0000.0000.000
27A1360GLY00.0030.00235.4360.0100.0100.0000.0000.0000.000
28A1361LEU0-0.047-0.00536.8620.0100.0100.0000.0000.0000.000
29A1362VAL0-0.048-0.04238.4700.0090.0090.0000.0000.0000.000
30A1363SER0-0.098-0.04740.0860.0080.0080.0000.0000.0000.000
31A1364SER0-0.023-0.00241.7780.0070.0070.0000.0000.0000.000
32A1365ASP-1-0.825-0.92244.359-0.095-0.0950.0000.0000.0000.000
33A1366GLU-1-1.023-1.00047.581-0.093-0.0930.0000.0000.0000.000
34A1367LEU00.0060.00649.5190.0000.0000.0000.0000.0000.000
35A1368ALA0-0.048-0.01552.5020.0000.0000.0000.0000.0000.000
36A1369LYS10.9210.94454.8230.0790.0790.0000.0000.0000.000
37A1370ASP-1-0.765-0.89157.462-0.067-0.0670.0000.0000.0000.000
38A1371VAL00.0180.00958.1380.0000.0000.0000.0000.0000.000
39A1372THR00.0100.00756.327-0.001-0.0010.0000.0000.0000.000
40A1373GLY0-0.011-0.01554.243-0.003-0.0030.0000.0000.0000.000
41A1374ALA0-0.003-0.02352.800-0.004-0.0040.0000.0000.0000.000
42A1375GLU-1-0.938-0.95852.431-0.072-0.0720.0000.0000.0000.000
43A1376ALA00.0350.02050.639-0.003-0.0030.0000.0000.0000.000
44A1377LEU0-0.059-0.03848.403-0.006-0.0060.0000.0000.0000.000
45A1378LEU00.0110.01247.222-0.005-0.0050.0000.0000.0000.000
46A1379GLU-1-0.960-0.97246.863-0.096-0.0960.0000.0000.0000.000
47A1380ARG10.9580.97344.0650.1100.1100.0000.0000.0000.000
48A1381HIS0-0.048-0.02242.241-0.011-0.0110.0000.0000.0000.000
49A1382GLN00.0340.00842.198-0.002-0.0020.0000.0000.0000.000
50A1383GLU-1-0.893-0.93440.556-0.129-0.1290.0000.0000.0000.000
51A1384HIS10.8580.90437.5980.1400.1400.0000.0000.0000.000
52A1385ARG10.7740.88537.4510.1080.1080.0000.0000.0000.000
53A1386THR00.009-0.00637.394-0.002-0.0020.0000.0000.0000.000
54A1387GLU-1-0.915-0.94233.602-0.195-0.1950.0000.0000.0000.000
55A1388ILE00.005-0.00633.023-0.017-0.0170.0000.0000.0000.000
56A1389ASP-1-0.813-0.91132.685-0.135-0.1350.0000.0000.0000.000
57A1390ALA0-0.060-0.01932.219-0.002-0.0020.0000.0000.0000.000
58A1391ARG10.8660.92727.3990.2150.2150.0000.0000.0000.000
59A1392ALA00.0070.01627.924-0.011-0.0110.0000.0000.0000.000
60A1393GLY00.0320.00627.3070.0010.0010.0000.0000.0000.000
61A1394THR0-0.008-0.01123.126-0.003-0.0030.0000.0000.0000.000
62A1395PHE00.0370.01023.254-0.022-0.0220.0000.0000.0000.000
63A1396GLN0-0.009-0.00724.264-0.004-0.0040.0000.0000.0000.000
64A1397ALA0-0.0110.00520.5040.0110.0110.0000.0000.0000.000
65A1398PHE0-0.0080.00018.949-0.003-0.0030.0000.0000.0000.000
66A1399GLU-1-0.802-0.88620.115-0.135-0.1350.0000.0000.0000.000
67A1400GLN0-0.047-0.02419.8590.0200.0200.0000.0000.0000.000
68A1401PHE0-0.041-0.02211.9150.0350.0350.0000.0000.0000.000
69A1402GLY00.0610.01316.7930.0260.0260.0000.0000.0000.000
70A1403GLN0-0.027-0.00818.6850.0560.0560.0000.0000.0000.000
71A1404GLN00.0020.00815.2480.0370.0370.0000.0000.0000.000
72A1405LEU00.0030.01712.3080.0790.0790.0000.0000.0000.000
73A1406LEU0-0.008-0.01315.0860.0540.0540.0000.0000.0000.000
74A1407ALA0-0.042-0.01417.7670.0310.0310.0000.0000.0000.000
75A1408HIS0-0.113-0.06012.7770.0650.0650.0000.0000.0000.000
76A1409GLY0-0.0140.00213.3080.0640.0640.0000.0000.0000.000
77A1410HIS00.0290.01510.3970.0470.0470.0000.0000.0000.000
78A1411TYR00.0470.0168.707-0.076-0.0760.0000.0000.0000.000
79A1412ALA0-0.0070.00013.265-0.022-0.0220.0000.0000.0000.000
80A1413SER00.003-0.02615.409-0.042-0.0420.0000.0000.0000.000
81A1414PRO0-0.026-0.00517.677-0.019-0.0190.0000.0000.0000.000
82A1415GLU-1-0.848-0.93518.387-0.126-0.1260.0000.0000.0000.000
83A1416ILE00.0250.01614.789-0.032-0.0320.0000.0000.0000.000
84A1417LYS10.8440.89919.4430.0630.0630.0000.0000.0000.000
85A1418GLN0-0.025-0.01622.563-0.027-0.0270.0000.0000.0000.000
86A1419LYS10.8010.90120.3620.2320.2320.0000.0000.0000.000
87A1420LEU00.0240.02321.573-0.008-0.0080.0000.0000.0000.000
88A1421ASP-1-0.768-0.85724.469-0.091-0.0910.0000.0000.0000.000
89A1422ILE0-0.054-0.02725.3070.0000.0000.0000.0000.0000.000
90A1423LEU00.0180.00123.811-0.001-0.0010.0000.0000.0000.000
91A1424ASP-1-0.876-0.93227.190-0.134-0.1340.0000.0000.0000.000
92A1425GLN0-0.096-0.05429.7000.0120.0120.0000.0000.0000.000
93A1426GLU-1-0.834-0.92829.354-0.172-0.1720.0000.0000.0000.000
94A1427ARG10.7910.89227.8150.1630.1630.0000.0000.0000.000
95A1428ALA0-0.0010.00531.9850.0070.0070.0000.0000.0000.000
96A1429ASP-1-0.818-0.90434.909-0.108-0.1080.0000.0000.0000.000
97A1430LEU0-0.0030.01032.6970.0030.0030.0000.0000.0000.000
98A1431GLU-1-0.829-0.88135.896-0.105-0.1050.0000.0000.0000.000
99A1432LYS10.8550.90537.8940.1060.1060.0000.0000.0000.000
100A1433ALA0-0.021-0.00238.6830.0050.0050.0000.0000.0000.000
101A1434TRP00.015-0.00839.1090.0050.0050.0000.0000.0000.000
102A1435VAL00.0120.00541.0260.0050.0050.0000.0000.0000.000
103A1436GLN0-0.029-0.01143.7410.0060.0060.0000.0000.0000.000
104A1437ARG10.8850.94243.6810.1060.1060.0000.0000.0000.000
105A1438ARG10.8010.87545.2980.0840.0840.0000.0000.0000.000
106A1439MET00.0240.01346.9020.0030.0030.0000.0000.0000.000
107A1440MET00.0100.00649.0030.0050.0050.0000.0000.0000.000
108A1441LEU0-0.014-0.02046.8380.0020.0020.0000.0000.0000.000
109A1442ASP-1-0.822-0.87850.699-0.074-0.0740.0000.0000.0000.000
110A1443GLN00.0290.01152.8820.0020.0020.0000.0000.0000.000
111A1444CYS0-0.0430.01153.5340.0020.0020.0000.0000.0000.000
112A1445LEU00.0750.01954.7340.0020.0020.0000.0000.0000.000
113A1446GLU-1-0.876-0.95456.504-0.055-0.0550.0000.0000.0000.000
114A1447LEU0-0.047-0.01858.5800.0030.0030.0000.0000.0000.000
115A1448GLN0-0.002-0.00857.8650.0030.0030.0000.0000.0000.000
116A1449LEU0-0.021-0.01559.4370.0010.0010.0000.0000.0000.000
117A1450PHE00.0200.01162.4680.0020.0020.0000.0000.0000.000
118A1451HIS00.0420.01762.3990.0030.0030.0000.0000.0000.000
119A1452ARG10.9340.97363.6270.0540.0540.0000.0000.0000.000
120A1453ASP-1-0.897-0.94866.437-0.045-0.0450.0000.0000.0000.000
121A1454CYS0-0.100-0.05468.2360.0020.0020.0000.0000.0000.000
122A1455GLU-1-0.908-0.95567.295-0.051-0.0510.0000.0000.0000.000
123A1456GLN0-0.062-0.02068.5840.0000.0000.0000.0000.0000.000
124A1457ALA0-0.008-0.01172.3890.0010.0010.0000.0000.0000.000
125A1458GLU-1-0.820-0.89673.423-0.040-0.0400.0000.0000.0000.000
126A1459ASN0-0.027-0.02372.1090.0010.0010.0000.0000.0000.000
127A1460TRP0-0.015-0.00176.0390.0010.0010.0000.0000.0000.000
128A1461MET0-0.022-0.01276.8940.0020.0020.0000.0000.0000.000
129A1462ALA00.0500.02778.8430.0010.0010.0000.0000.0000.000
130A1463ALA0-0.053-0.02380.6320.0010.0010.0000.0000.0000.000
131A1464ARG10.8860.93581.1640.0340.0340.0000.0000.0000.000
132A1465GLU-1-0.812-0.88881.809-0.034-0.0340.0000.0000.0000.000
133A1466ALA0-0.0130.01684.7710.0000.0000.0000.0000.0000.000
134A1467PHE0-0.088-0.03285.5840.0010.0010.0000.0000.0000.000
135A1468LEU0-0.019-0.00488.2880.0010.0010.0000.0000.0000.000
136A1488GLU-1-0.902-0.95692.784-0.024-0.0240.0000.0000.0000.000
137A1489ASP-1-0.907-0.95488.059-0.028-0.0280.0000.0000.0000.000
138A1490PHE00.010-0.01687.447-0.001-0.0010.0000.0000.0000.000
139A1491ASP-1-0.840-0.94487.176-0.026-0.0260.0000.0000.0000.000
140A1492LYS10.8830.94885.5000.0250.0250.0000.0000.0000.000
141A1493ALA0-0.016-0.00582.936-0.001-0.0010.0000.0000.0000.000
142A1494ILE0-0.012-0.00282.797-0.001-0.0010.0000.0000.0000.000
143A1495ASN0-0.064-0.04282.8160.0000.0000.0000.0000.0000.000
144A1496VAL00.0100.01178.258-0.001-0.0010.0000.0000.0000.000
145A1497GLN00.0080.00976.000-0.001-0.0010.0000.0000.0000.000
146A1498GLU-1-0.790-0.88378.219-0.031-0.0310.0000.0000.0000.000
147A1499GLU-1-0.847-0.90675.157-0.036-0.0360.0000.0000.0000.000
148A1500LYS10.8440.90573.8130.0360.0360.0000.0000.0000.000
149A1501ILE0-0.007-0.00173.327-0.001-0.0010.0000.0000.0000.000
150A1502ALA0-0.0150.00574.8110.0000.0000.0000.0000.0000.000
151A1503ALA0-0.006-0.00170.3170.0000.0000.0000.0000.0000.000
152A1504LEU00.012-0.00669.166-0.001-0.0010.0000.0000.0000.000
153A1505GLN0-0.022-0.01170.1000.0000.0000.0000.0000.0000.000
154A1506ALA00.0140.00369.9430.0000.0000.0000.0000.0000.000
155A1507PHE0-0.027-0.00962.1350.0000.0000.0000.0000.0000.000
156A1508ALA00.0410.01465.341-0.001-0.0010.0000.0000.0000.000
157A1509ASP-1-0.868-0.93166.277-0.039-0.0390.0000.0000.0000.000
158A1510GLN0-0.051-0.01661.0660.0000.0000.0000.0000.0000.000
159A1511LEU00.0280.02860.079-0.001-0.0010.0000.0000.0000.000
160A1512ILE0-0.018-0.00861.475-0.001-0.0010.0000.0000.0000.000
161A1513ALA0-0.056-0.03263.2610.0000.0000.0000.0000.0000.000
162A1514ALA0-0.0010.01358.6430.0000.0000.0000.0000.0000.000
163A1515GLY0-0.099-0.05357.943-0.002-0.0020.0000.0000.0000.000
164A1516HIS00.0250.01357.374-0.001-0.0010.0000.0000.0000.000
165A1517TYR00.0660.02154.8670.0010.0010.0000.0000.0000.000
166A1518ALA00.004-0.00257.4560.0000.0000.0000.0000.0000.000
167A1519LYS10.8920.96760.7470.0480.0480.0000.0000.0000.000
168A1520GLY0-0.038-0.02163.1520.0020.0020.0000.0000.0000.000
169A1521ASP-1-0.865-0.94563.726-0.050-0.0500.0000.0000.0000.000
170A1522ILE0-0.019-0.00561.4910.0010.0010.0000.0000.0000.000
171A1523SER00.001-0.00865.8400.0020.0020.0000.0000.0000.000
172A1524SER0-0.068-0.02368.3960.0020.0020.0000.0000.0000.000
173A1525ARG10.9490.97267.7470.0470.0470.0000.0000.0000.000
174A1526ARG10.8640.92269.9340.0380.0380.0000.0000.0000.000
175A1527ASN0-0.015-0.01371.7150.0010.0010.0000.0000.0000.000
176A1528GLU-1-0.887-0.93172.726-0.041-0.0410.0000.0000.0000.000
177A1529VAL00.0330.00972.9700.0010.0010.0000.0000.0000.000
178A1530LEU00.005-0.00574.4520.0010.0010.0000.0000.0000.000
179A1531ASP-1-0.847-0.90677.490-0.031-0.0310.0000.0000.0000.000
180A1532ARG10.7140.82977.0650.0380.0380.0000.0000.0000.000
181A1533TRP00.0250.00779.1260.0000.0000.0000.0000.0000.000
182A1534ARG10.8060.87680.3900.0310.0310.0000.0000.0000.000
183A1535ARG10.9270.97280.0220.0340.0340.0000.0000.0000.000
184A1536LEU00.0250.02382.7940.0010.0010.0000.0000.0000.000
185A1537LYS10.8390.90283.3950.0290.0290.0000.0000.0000.000
186A1538ALA0-0.028-0.01286.4800.0010.0010.0000.0000.0000.000
187A1539GLN0-0.059-0.03387.7910.0010.0010.0000.0000.0000.000
188A1540MET0-0.0700.00485.1340.0010.0010.0000.0000.0000.000