Manual

About

FMODB

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

Last updated: 2024-04-05

All entries: 36946

Number of unique PDB entries: 7781

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FMODB ID: 6NG4Z

Calculation Name: 3THF-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3THF

Chain ID: A

ChEMBL ID:

UniProt ID: A1Z9P3

Base Structure: X-ray

Registration Date: 2023-06-22

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 175
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -1183395.608602
FMO2-HF: Nuclear repulsion 1113780.433711
FMO2-HF: Total energy -69615.17489
FMO2-MP2: Total energy -69816.805797


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:1396:THR)


Summations of interaction energy for fragment #1(A:1396:THR)
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.
-8.373-4.7080.017-1.533-2.1480.002
Interaction energy analysis for fragmet #1(A:1396:THR)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.016 / q_NPA : 0.002
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].
3A1398LEU00.0520.0163.809-0.7961.185-0.016-0.923-1.0420.005
4A1399ILE00.0450.0215.295-0.155-0.059-0.001-0.005-0.0890.000
5A1400LYS10.9620.9794.684-3.163-3.047-0.001-0.007-0.1070.000
6A1401GLN00.0250.0133.132-4.615-3.2080.036-0.596-0.848-0.003
7A1402LYS10.9700.9785.0420.1610.226-0.001-0.002-0.0620.000
8A1403MET0-0.026-0.0038.541-0.109-0.1090.0000.0000.0000.000
9A1404ASP-1-0.898-0.9426.4810.6020.6020.0000.0000.0000.000
10A1405GLU-1-0.905-0.9587.686-1.623-1.6230.0000.0000.0000.000
11A1406LEU00.0130.00910.4050.0380.0380.0000.0000.0000.000
12A1407ILE00.0320.00912.160-0.013-0.0130.0000.0000.0000.000
13A1408LYS10.9480.99612.1610.6250.6250.0000.0000.0000.000
14A1409HIS0-0.019-0.01414.238-0.020-0.0200.0000.0000.0000.000
15A1410LEU0-0.001-0.00816.5040.0160.0160.0000.0000.0000.000
16A1411ASN0-0.022-0.02316.4460.0170.0170.0000.0000.0000.000
17A1412GLN0-0.013-0.00716.619-0.011-0.0110.0000.0000.0000.000
18A1413LYS10.9980.99820.1400.0990.0990.0000.0000.0000.000
19A1414ILE00.0090.01222.0770.0140.0140.0000.0000.0000.000
20A1415VAL0-0.023-0.00622.5240.0080.0080.0000.0000.0000.000
21A1416SER0-0.026-0.02724.4540.0010.0010.0000.0000.0000.000
22A1417LEU00.0110.01026.0060.0060.0060.0000.0000.0000.000
23A1418LYS10.9630.98226.7630.0300.0300.0000.0000.0000.000
24A1419ARG10.9220.97026.2970.1300.1300.0000.0000.0000.000
25A1420GLU-1-0.898-0.94830.673-0.078-0.0780.0000.0000.0000.000
26A1421GLN00.006-0.00132.2350.0040.0040.0000.0000.0000.000
27A1422GLN0-0.077-0.04833.5210.0090.0090.0000.0000.0000.000
28A1423THR0-0.014-0.00935.0020.0000.0000.0000.0000.0000.000
29A1424ILE00.0660.02736.4370.0030.0030.0000.0000.0000.000
30A1425SER00.0170.02138.0290.0060.0060.0000.0000.0000.000
31A1426GLU-1-0.914-0.94938.323-0.055-0.0550.0000.0000.0000.000
32A1427GLU-1-0.946-0.97440.742-0.051-0.0510.0000.0000.0000.000
33A1428CYS0-0.047-0.03042.1200.0030.0030.0000.0000.0000.000
34A1429SER0-0.019-0.00743.6200.0030.0030.0000.0000.0000.000
35A1430ALA0-0.040-0.01745.6850.0020.0020.0000.0000.0000.000
36A1431ASN0-0.018-0.01147.2610.0010.0010.0000.0000.0000.000
37A1432ASP-1-0.855-0.93148.400-0.019-0.0190.0000.0000.0000.000
38A1433ARG10.8880.94749.5270.0320.0320.0000.0000.0000.000
39A1434LEU00.0270.02451.8090.0010.0010.0000.0000.0000.000
40A1435GLY00.0190.00853.1040.0010.0010.0000.0000.0000.000
41A1436GLN0-0.050-0.03651.6560.0010.0010.0000.0000.0000.000
42A1437ASP-1-0.888-0.93456.291-0.024-0.0240.0000.0000.0000.000
43A1438LEU0-0.059-0.03956.8410.0010.0010.0000.0000.0000.000
44A1439PHE0-0.036-0.02859.0010.0020.0020.0000.0000.0000.000
45A1440ALA00.0390.03160.5600.0010.0010.0000.0000.0000.000
46A1441LYS10.9500.96262.4320.0210.0210.0000.0000.0000.000
47A1442LEU0-0.041-0.01463.4730.0010.0010.0000.0000.0000.000
48A1443ALA0-0.009-0.01564.4270.0010.0010.0000.0000.0000.000
49A1444GLU-1-0.960-0.96866.192-0.014-0.0140.0000.0000.0000.000
50A1445LYS10.8410.92268.3700.0180.0180.0000.0000.0000.000
51A1446VAL0-0.033-0.00667.6940.0000.0000.0000.0000.0000.000
52A1447ARG10.8830.93570.4050.0070.0070.0000.0000.0000.000
53A1448PRO00.0900.03068.5590.0000.0000.0000.0000.0000.000
54A1449SER00.001-0.00367.4240.0000.0000.0000.0000.0000.000
55A1450GLU-1-0.827-0.90767.178-0.007-0.0070.0000.0000.0000.000
56A1451ALA00.0740.05164.7700.0000.0000.0000.0000.0000.000
57A1452SER00.005-0.01263.1200.0000.0000.0000.0000.0000.000
58A1453LYS10.9270.98262.4020.0040.0040.0000.0000.0000.000
59A1454PHE00.0380.02358.8850.0000.0000.0000.0000.0000.000
60A1455ARG10.9470.97557.8120.0060.0060.0000.0000.0000.000
61A1456THR00.004-0.01257.6000.0000.0000.0000.0000.0000.000
62A1457HIS0-0.013-0.00157.6370.0020.0020.0000.0000.0000.000
63A1458VAL0-0.004-0.01154.3040.0000.0000.0000.0000.0000.000
64A1459ASP-1-0.874-0.93153.321-0.007-0.0070.0000.0000.0000.000
65A1460ALA0-0.054-0.01652.7680.0010.0010.0000.0000.0000.000
66A1461VAL00.0230.01051.4410.0010.0010.0000.0000.0000.000
67A1462GLY00.0670.05349.1780.0000.0000.0000.0000.0000.000
68A1463ASN0-0.031-0.03548.5620.0020.0020.0000.0000.0000.000
69A1464ILE0-0.008-0.00549.1800.0020.0020.0000.0000.0000.000
70A1465THR0-0.010-0.01245.8140.0000.0000.0000.0000.0000.000
71A1466SER00.000-0.00744.7900.0000.0000.0000.0000.0000.000
72A1467LEU0-0.046-0.01344.9270.0020.0020.0000.0000.0000.000
73A1468LEU00.005-0.00846.3850.0020.0020.0000.0000.0000.000
74A1469LEU00.0350.03041.6490.0010.0010.0000.0000.0000.000
75A1470SER00.0750.05641.4930.0030.0030.0000.0000.0000.000
76A1471LEU0-0.067-0.03342.3180.0040.0040.0000.0000.0000.000
77A1472SER0-0.036-0.02142.6640.0020.0020.0000.0000.0000.000
78A1473GLU-1-0.904-0.96138.0740.0070.0070.0000.0000.0000.000
79A1474ARG10.8770.91639.301-0.018-0.0180.0000.0000.0000.000
80A1475LEU0-0.0130.02140.8800.0040.0040.0000.0000.0000.000
81A1476ALA00.0510.02238.3260.0030.0030.0000.0000.0000.000
82A1477GLN00.0110.00032.6880.0070.0070.0000.0000.0000.000
83A1478THR0-0.022-0.01037.4430.0070.0070.0000.0000.0000.000
84A1479GLU-1-0.898-0.95940.1560.0340.0340.0000.0000.0000.000
85A1480SER0-0.042-0.01134.9430.0020.0020.0000.0000.0000.000
86A1481SER0-0.025-0.01935.8610.0090.0090.0000.0000.0000.000
87A1482LEU0-0.019-0.01837.3050.0060.0060.0000.0000.0000.000
88A1483GLU-1-0.921-0.96835.2070.0380.0380.0000.0000.0000.000
89A1484THR0-0.030-0.00933.3580.0030.0030.0000.0000.0000.000
90A1485ARG10.7730.85234.859-0.083-0.0830.0000.0000.0000.000
91A1486GLN0-0.0040.01138.7510.0030.0030.0000.0000.0000.000
92A1487GLN0-0.016-0.01734.1420.0040.0040.0000.0000.0000.000
93A1488GLU-1-0.815-0.87234.2590.1010.1010.0000.0000.0000.000
94A1489ARG10.8390.89236.474-0.053-0.0530.0000.0000.0000.000
95A1490GLY00.0410.02539.7360.0000.0000.0000.0000.0000.000
96A1491ALA00.0040.00235.3950.0010.0010.0000.0000.0000.000
97A1492LEU0-0.039-0.03236.6820.0040.0040.0000.0000.0000.000
98A1493GLU-1-0.832-0.88839.0290.0610.0610.0000.0000.0000.000
99A1494SER00.0430.02538.792-0.002-0.0020.0000.0000.0000.000
100A1495LYS10.9050.95935.310-0.125-0.1250.0000.0000.0000.000
101A1496ARG10.8170.89139.425-0.067-0.0670.0000.0000.0000.000
102A1497ASP-1-0.805-0.88042.9080.0630.0630.0000.0000.0000.000
103A1498LEU00.0240.01238.3470.0000.0000.0000.0000.0000.000
104A1499LEU0-0.042-0.02539.9810.0010.0010.0000.0000.0000.000
105A1500TYR0-0.004-0.01043.189-0.001-0.0010.0000.0000.0000.000
106A1501GLU-1-0.888-0.93244.5630.0660.0660.0000.0000.0000.000
107A1502GLN0-0.050-0.04040.0260.0010.0010.0000.0000.0000.000
108A1503MET0-0.019-0.00845.2320.0010.0010.0000.0000.0000.000
109A1504GLU-1-0.877-0.92547.9860.0550.0550.0000.0000.0000.000
110A1505GLU-1-0.866-0.92046.9540.0640.0640.0000.0000.0000.000
111A1506ALA0-0.015-0.01747.157-0.001-0.0010.0000.0000.0000.000
112A1507GLN0-0.040-0.01949.1350.0010.0010.0000.0000.0000.000
113A1508ARG10.8440.91150.142-0.062-0.0620.0000.0000.0000.000
114A1509LEU00.001-0.00348.959-0.001-0.0010.0000.0000.0000.000
115A1510LYS10.8600.92952.293-0.066-0.0660.0000.0000.0000.000
116A1511SER00.0400.01854.032-0.002-0.0020.0000.0000.0000.000
117A1512ASP-1-0.858-0.90654.9100.0530.0530.0000.0000.0000.000
118A1513ILE0-0.068-0.04651.307-0.001-0.0010.0000.0000.0000.000
119A1514GLU-1-0.823-0.90155.9840.0590.0590.0000.0000.0000.000
120A1515ARG10.8520.90858.259-0.053-0.0530.0000.0000.0000.000
121A1516ARG10.9330.97052.771-0.067-0.0670.0000.0000.0000.000
122A1517GLY00.0330.01059.6710.0000.0000.0000.0000.0000.000
123A1518VAL00.0190.00960.648-0.001-0.0010.0000.0000.0000.000
124A1519SER0-0.050-0.02562.716-0.002-0.0020.0000.0000.0000.000
125A1520ILE0-0.035-0.01759.536-0.001-0.0010.0000.0000.0000.000
126A1521ALA00.0600.03463.031-0.001-0.0010.0000.0000.0000.000
127A1522GLY00.0090.01065.598-0.001-0.0010.0000.0000.0000.000
128A1523LEU0-0.093-0.04463.169-0.001-0.0010.0000.0000.0000.000
129A1524LEU00.0430.00762.968-0.001-0.0010.0000.0000.0000.000
130A1525ALA00.0180.01767.088-0.001-0.0010.0000.0000.0000.000
131A1526LYS10.8730.93770.261-0.041-0.0410.0000.0000.0000.000
132A1527ASN0-0.074-0.04468.256-0.001-0.0010.0000.0000.0000.000
133A1528LEU0-0.0190.00265.3600.0010.0010.0000.0000.0000.000
134A1529SER0-0.008-0.01970.121-0.001-0.0010.0000.0000.0000.000
135A1530ALA00.0640.01570.8020.0010.0010.0000.0000.0000.000
136A1531ASP-1-0.834-0.89970.8510.0450.0450.0000.0000.0000.000
137A1532MET00.0190.01467.2320.0020.0020.0000.0000.0000.000
138A1533CYS0-0.057-0.01666.2850.0020.0020.0000.0000.0000.000
139A1534ALA00.0230.01466.3020.0010.0010.0000.0000.0000.000
140A1535ASP-1-0.881-0.94464.6330.0570.0570.0000.0000.0000.000
141A1536TYR0-0.063-0.03059.4130.0040.0040.0000.0000.0000.000
142A1537ASP-1-0.876-0.94461.5740.0550.0550.0000.0000.0000.000
143A1538TYR0-0.026-0.00860.5870.0030.0030.0000.0000.0000.000
144A1539PHE00.001-0.00355.3280.0030.0030.0000.0000.0000.000
145A1540ILE0-0.020-0.00955.6680.0040.0040.0000.0000.0000.000
146A1541ASN0-0.038-0.03756.8870.0030.0030.0000.0000.0000.000
147A1542MET0-0.0080.00656.6740.0010.0010.0000.0000.0000.000
148A1543LYS10.9620.98649.953-0.085-0.0850.0000.0000.0000.000
149A1544ALA0-0.015-0.01052.7780.0040.0040.0000.0000.0000.000
150A1545LYS10.8370.89452.748-0.074-0.0740.0000.0000.0000.000
151A1546LEU00.0320.01451.7590.0030.0030.0000.0000.0000.000
152A1547ILE0-0.042-0.01647.4950.0050.0050.0000.0000.0000.000
153A1548ALA0-0.024-0.00948.3410.0050.0050.0000.0000.0000.000
154A1549ASP-1-0.791-0.87449.1630.0850.0850.0000.0000.0000.000
155A1550ALA00.0070.00546.2640.0040.0040.0000.0000.0000.000
156A1551ARG10.9190.95442.070-0.111-0.1110.0000.0000.0000.000
157A1552ASP-1-0.808-0.88444.7180.1030.1030.0000.0000.0000.000
158A1553LEU00.0210.00645.7150.0030.0030.0000.0000.0000.000
159A1554ALA0-0.019-0.00641.1690.0060.0060.0000.0000.0000.000
160A1555VAL0-0.065-0.03141.0620.0070.0070.0000.0000.0000.000
161A1556ARG10.8870.91341.532-0.095-0.0950.0000.0000.0000.000
162A1557ILE0-0.0080.01639.3750.0010.0010.0000.0000.0000.000
163A1558LYS10.9700.98936.901-0.148-0.1480.0000.0000.0000.000
164A1559GLY00.0570.03937.6260.0060.0060.0000.0000.0000.000
165A1560SER0-0.045-0.04239.1860.0000.0000.0000.0000.0000.000
166A1561GLU-1-0.951-0.97735.4550.1830.1830.0000.0000.0000.000
167A1562GLU-1-0.955-0.96934.4470.1720.1720.0000.0000.0000.000
168A1563GLN0-0.041-0.02335.4490.0020.0020.0000.0000.0000.000
169A1564LEU00.0060.01235.4490.0010.0010.0000.0000.0000.000
170A1565SER0-0.015-0.01631.5620.0050.0050.0000.0000.0000.000
171A1566SER0-0.030-0.00932.7470.0010.0010.0000.0000.0000.000
172A1567LEU0-0.037-0.03033.934-0.005-0.0050.0000.0000.0000.000
173A1568SER0-0.121-0.06532.339-0.004-0.0040.0000.0000.0000.000
174A1569ASP-1-0.960-0.95629.8700.2350.2350.0000.0000.0000.000
175A1570ALA0-0.048-0.02732.184-0.005-0.0050.0000.0000.0000.000