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: 2JLMR

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 OptH
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 -1183915.612148
FMO2-HF: Nuclear repulsion 1114301.551165
FMO2-HF: Total energy -69614.060983
FMO2-MP2: Total energy -69815.785572


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.
-10.836-6.6280.247-1.848-2.608-0.006
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 : 0.011 / 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].
3A1398LEU00.0700.0203.802-0.2921.650-0.007-0.887-1.0490.004
4A1399ILE00.0450.0205.682-0.170-0.084-0.001-0.005-0.0800.000
5A1400LYS10.9610.9804.767-3.461-3.353-0.001-0.006-0.1000.000
6A1401GLN00.0770.0542.667-7.015-5.0090.257-0.948-1.316-0.010
7A1402LYS10.9570.9695.036-0.257-0.191-0.001-0.002-0.0630.000
8A1403MET0-0.0240.0008.533-0.165-0.1650.0000.0000.0000.000
9A1404ASP-1-0.891-0.9406.5090.5690.5690.0000.0000.0000.000
10A1405GLU-1-0.947-0.9927.732-1.311-1.3110.0000.0000.0000.000
11A1406LEU00.0260.01310.3870.0160.0160.0000.0000.0000.000
12A1407ILE00.0060.00612.538-0.027-0.0270.0000.0000.0000.000
13A1408LYS10.9310.97312.3130.5550.5550.0000.0000.0000.000
14A1409HIS0-0.011-0.00913.569-0.003-0.0030.0000.0000.0000.000
15A1410LEU00.009-0.00416.5020.0100.0100.0000.0000.0000.000
16A1411ASN00.0210.00716.2260.0180.0180.0000.0000.0000.000
17A1412GLN0-0.023-0.01016.7560.0050.0050.0000.0000.0000.000
18A1413LYS11.0151.00020.1890.0800.0800.0000.0000.0000.000
19A1414ILE00.0350.03422.1510.0110.0110.0000.0000.0000.000
20A1415VAL0-0.037-0.00722.4010.0070.0070.0000.0000.0000.000
21A1416SER0-0.117-0.07424.4970.0040.0040.0000.0000.0000.000
22A1417LEU00.0780.03226.3860.0060.0060.0000.0000.0000.000
23A1418LYS10.9450.97526.7890.0300.0300.0000.0000.0000.000
24A1419ARG10.9310.97426.2880.1230.1230.0000.0000.0000.000
25A1420GLU-1-0.902-0.95330.716-0.072-0.0720.0000.0000.0000.000
26A1421GLN0-0.004-0.00432.3010.0030.0030.0000.0000.0000.000
27A1422GLN0-0.039-0.01233.6060.0080.0080.0000.0000.0000.000
28A1423THR0-0.003-0.00334.9900.0000.0000.0000.0000.0000.000
29A1424ILE00.0520.02136.6600.0030.0030.0000.0000.0000.000
30A1425SER0-0.036-0.00638.1140.0050.0050.0000.0000.0000.000
31A1426GLU-1-0.913-0.97138.483-0.054-0.0540.0000.0000.0000.000
32A1427GLU-1-0.946-0.97340.759-0.047-0.0470.0000.0000.0000.000
33A1428CYS0-0.052-0.03042.2670.0030.0030.0000.0000.0000.000
34A1429SER0-0.0050.00444.0180.0030.0030.0000.0000.0000.000
35A1430ALA0-0.043-0.01445.7600.0020.0020.0000.0000.0000.000
36A1431ASN00.006-0.00647.3160.0010.0010.0000.0000.0000.000
37A1432ASP-1-0.871-0.93448.617-0.017-0.0170.0000.0000.0000.000
38A1433ARG10.8910.94249.8560.0320.0320.0000.0000.0000.000
39A1434LEU00.0210.02751.8770.0010.0010.0000.0000.0000.000
40A1435GLY00.0170.00453.1730.0010.0010.0000.0000.0000.000
41A1436GLN0-0.044-0.03252.2130.0010.0010.0000.0000.0000.000
42A1437ASP-1-0.886-0.93556.193-0.023-0.0230.0000.0000.0000.000
43A1438LEU0-0.060-0.03656.8140.0010.0010.0000.0000.0000.000
44A1439PHE0-0.046-0.03659.0860.0020.0020.0000.0000.0000.000
45A1440ALA00.0390.03360.6560.0010.0010.0000.0000.0000.000
46A1441LYS10.9490.96062.5330.0200.0200.0000.0000.0000.000
47A1442LEU0-0.036-0.01863.8300.0010.0010.0000.0000.0000.000
48A1443ALA0-0.028-0.01864.5310.0010.0010.0000.0000.0000.000
49A1444GLU-1-0.944-0.96266.320-0.012-0.0120.0000.0000.0000.000
50A1445LYS10.8300.91768.0750.0170.0170.0000.0000.0000.000
51A1446VAL0-0.0170.00867.7390.0000.0000.0000.0000.0000.000
52A1447ARG10.9661.00170.5140.0060.0060.0000.0000.0000.000
53A1448PRO00.0910.03268.6970.0000.0000.0000.0000.0000.000
54A1449SER00.016-0.01467.5560.0000.0000.0000.0000.0000.000
55A1450GLU-1-0.933-0.97767.300-0.007-0.0070.0000.0000.0000.000
56A1451ALA00.0760.05564.8580.0000.0000.0000.0000.0000.000
57A1452SER0-0.004-0.02263.2360.0000.0000.0000.0000.0000.000
58A1453LYS10.9150.96562.5290.0030.0030.0000.0000.0000.000
59A1454PHE00.0340.02458.9750.0000.0000.0000.0000.0000.000
60A1455ARG10.9900.98658.1230.0050.0050.0000.0000.0000.000
61A1456THR00.0060.01257.7170.0000.0000.0000.0000.0000.000
62A1457HIS0-0.019-0.00557.7510.0020.0020.0000.0000.0000.000
63A1458VAL0-0.009-0.01154.3690.0000.0000.0000.0000.0000.000
64A1459ASP-1-0.886-0.93753.425-0.006-0.0060.0000.0000.0000.000
65A1460ALA0-0.077-0.03552.8820.0010.0010.0000.0000.0000.000
66A1461VAL00.0150.00751.3860.0010.0010.0000.0000.0000.000
67A1462GLY00.0590.03849.2620.0000.0000.0000.0000.0000.000
68A1463ASN00.015-0.00748.6600.0010.0010.0000.0000.0000.000
69A1464ILE0-0.015-0.01049.2920.0020.0020.0000.0000.0000.000
70A1465THR0-0.0130.00045.8060.0000.0000.0000.0000.0000.000
71A1466SER00.0110.00144.8830.0010.0010.0000.0000.0000.000
72A1467LEU0-0.052-0.01545.0290.0020.0020.0000.0000.0000.000
73A1468LEU00.016-0.00846.4850.0030.0030.0000.0000.0000.000
74A1469LEU00.0460.03341.7700.0010.0010.0000.0000.0000.000
75A1470SER00.0520.04841.5970.0040.0040.0000.0000.0000.000
76A1471LEU0-0.060-0.03842.4230.0040.0040.0000.0000.0000.000
77A1472SER0-0.045-0.02742.6050.0020.0020.0000.0000.0000.000
78A1473GLU-1-0.902-0.95838.3570.0120.0120.0000.0000.0000.000
79A1474ARG10.8850.92739.380-0.022-0.0220.0000.0000.0000.000
80A1475LEU0-0.0230.00640.9770.0040.0040.0000.0000.0000.000
81A1476ALA00.0510.02338.2960.0030.0030.0000.0000.0000.000
82A1477GLN00.011-0.00632.7490.0050.0050.0000.0000.0000.000
83A1478THR0-0.018-0.00337.5250.0070.0070.0000.0000.0000.000
84A1479GLU-1-0.873-0.95440.2350.0380.0380.0000.0000.0000.000
85A1480SER0-0.050-0.01035.1440.0030.0030.0000.0000.0000.000
86A1481SER0-0.012-0.00935.8970.0090.0090.0000.0000.0000.000
87A1482LEU0-0.043-0.02937.3530.0060.0060.0000.0000.0000.000
88A1483GLU-1-0.954-0.97634.7560.0480.0480.0000.0000.0000.000
89A1484THR00.0010.00833.5360.0040.0040.0000.0000.0000.000
90A1485ARG10.8710.93136.040-0.081-0.0810.0000.0000.0000.000
91A1486GLN0-0.0140.01338.7400.0020.0020.0000.0000.0000.000
92A1487GLN00.016-0.00334.3460.0070.0070.0000.0000.0000.000
93A1488GLU-1-0.931-0.96333.7510.1120.1120.0000.0000.0000.000
94A1489ARG10.8670.92836.443-0.057-0.0570.0000.0000.0000.000
95A1490GLY00.0380.01739.6820.0000.0000.0000.0000.0000.000
96A1491ALA00.0060.00235.3760.0010.0010.0000.0000.0000.000
97A1492LEU0-0.043-0.03636.4890.0040.0040.0000.0000.0000.000
98A1493GLU-1-0.879-0.93039.0020.0650.0650.0000.0000.0000.000
99A1494SER00.0500.03838.763-0.002-0.0020.0000.0000.0000.000
100A1495LYS10.8990.96034.966-0.130-0.1300.0000.0000.0000.000
101A1496ARG10.8830.94039.433-0.072-0.0720.0000.0000.0000.000
102A1497ASP-1-0.842-0.92042.9170.0680.0680.0000.0000.0000.000
103A1498LEU00.0360.01238.1880.0000.0000.0000.0000.0000.000
104A1499LEU0-0.055-0.03140.2670.0000.0000.0000.0000.0000.000
105A1500TYR0-0.006-0.01043.208-0.001-0.0010.0000.0000.0000.000
106A1501GLU-1-0.879-0.92844.7370.0700.0700.0000.0000.0000.000
107A1502GLN0-0.062-0.04340.4610.0020.0020.0000.0000.0000.000
108A1503MET0-0.018-0.00845.2570.0010.0010.0000.0000.0000.000
109A1504GLU-1-0.933-0.96248.0110.0590.0590.0000.0000.0000.000
110A1505GLU-1-0.940-0.97446.6920.0680.0680.0000.0000.0000.000
111A1506ALA00.000-0.00847.210-0.001-0.0010.0000.0000.0000.000
112A1507GLN0-0.043-0.01849.1670.0010.0010.0000.0000.0000.000
113A1508ARG10.9520.97850.316-0.064-0.0640.0000.0000.0000.000
114A1509LEU00.0250.01349.050-0.001-0.0010.0000.0000.0000.000
115A1510LYS10.8660.93652.331-0.068-0.0680.0000.0000.0000.000
116A1511SER00.0230.01354.069-0.002-0.0020.0000.0000.0000.000
117A1512ASP-1-0.904-0.96154.9220.0560.0560.0000.0000.0000.000
118A1513ILE0-0.072-0.05251.398-0.001-0.0010.0000.0000.0000.000
119A1514GLU-1-0.854-0.91956.0270.0580.0580.0000.0000.0000.000
120A1515ARG10.9220.97758.118-0.054-0.0540.0000.0000.0000.000
121A1516ARG10.9320.96952.801-0.068-0.0680.0000.0000.0000.000
122A1517GLY00.0230.00659.7240.0000.0000.0000.0000.0000.000
123A1518VAL00.0320.01660.694-0.001-0.0010.0000.0000.0000.000
124A1519SER0-0.049-0.02862.765-0.002-0.0020.0000.0000.0000.000
125A1520ILE0-0.037-0.01559.632-0.001-0.0010.0000.0000.0000.000
126A1521ALA00.0580.02963.082-0.001-0.0010.0000.0000.0000.000
127A1522GLY00.0100.01165.647-0.001-0.0010.0000.0000.0000.000
128A1523LEU0-0.088-0.04263.149-0.001-0.0010.0000.0000.0000.000
129A1524LEU00.036-0.00263.149-0.001-0.0010.0000.0000.0000.000
130A1525ALA00.0150.01767.142-0.001-0.0010.0000.0000.0000.000
131A1526LYS10.8730.93570.317-0.041-0.0410.0000.0000.0000.000
132A1527ASN0-0.062-0.03568.343-0.001-0.0010.0000.0000.0000.000
133A1528LEU0-0.0140.00865.4590.0000.0000.0000.0000.0000.000
134A1529SER00.0400.02470.177-0.001-0.0010.0000.0000.0000.000
135A1530ALA00.0560.00670.8560.0010.0010.0000.0000.0000.000
136A1531ASP-1-0.889-0.94070.9020.0460.0460.0000.0000.0000.000
137A1532MET00.0060.00767.2820.0020.0020.0000.0000.0000.000
138A1533CYS0-0.053-0.01866.3380.0020.0020.0000.0000.0000.000
139A1534ALA00.0340.02466.3520.0010.0010.0000.0000.0000.000
140A1535ASP-1-0.880-0.94364.7030.0560.0560.0000.0000.0000.000
141A1536TYR0-0.066-0.03559.2240.0040.0040.0000.0000.0000.000
142A1537ASP-1-0.887-0.94961.6230.0550.0550.0000.0000.0000.000
143A1538TYR0-0.030-0.01960.9070.0030.0030.0000.0000.0000.000
144A1539PHE0-0.011-0.01055.3010.0030.0030.0000.0000.0000.000
145A1540ILE0-0.020-0.00755.9900.0040.0040.0000.0000.0000.000
146A1541ASN00.013-0.00156.9310.0040.0040.0000.0000.0000.000
147A1542MET0-0.036-0.00956.3410.0020.0020.0000.0000.0000.000
148A1543LYS10.9670.99150.335-0.084-0.0840.0000.0000.0000.000
149A1544ALA0-0.008-0.01052.8210.0040.0040.0000.0000.0000.000
150A1545LYS10.9110.95852.786-0.072-0.0720.0000.0000.0000.000
151A1546LEU00.0260.01451.7780.0030.0030.0000.0000.0000.000
152A1547ILE0-0.036-0.01047.5720.0050.0050.0000.0000.0000.000
153A1548ALA0-0.038-0.01848.3790.0050.0050.0000.0000.0000.000
154A1549ASP-1-0.840-0.92849.1960.0860.0860.0000.0000.0000.000
155A1550ALA00.0010.00146.2450.0040.0040.0000.0000.0000.000
156A1551ARG10.9110.94941.869-0.112-0.1120.0000.0000.0000.000
157A1552ASP-1-0.871-0.93344.7490.1020.1020.0000.0000.0000.000
158A1553LEU00.026-0.00145.7420.0030.0030.0000.0000.0000.000
159A1554ALA0-0.014-0.00141.2150.0060.0060.0000.0000.0000.000
160A1555VAL0-0.053-0.03541.0900.0080.0080.0000.0000.0000.000
161A1556ARG10.9380.96441.555-0.095-0.0950.0000.0000.0000.000
162A1557ILE0-0.0010.00939.3090.0010.0010.0000.0000.0000.000
163A1558LYS10.9510.98437.218-0.143-0.1430.0000.0000.0000.000
164A1559GLY00.0510.03737.6450.0050.0050.0000.0000.0000.000
165A1560SER0-0.038-0.02939.1990.0000.0000.0000.0000.0000.000
166A1561GLU-1-0.961-0.97935.4910.1840.1840.0000.0000.0000.000
167A1562GLU-1-0.943-0.97134.4370.1800.1800.0000.0000.0000.000
168A1563GLN0-0.051-0.02835.4560.0030.0030.0000.0000.0000.000
169A1564LEU00.0150.01435.4070.0010.0010.0000.0000.0000.000
170A1565SER0-0.027-0.02231.6050.0060.0060.0000.0000.0000.000
171A1566SER0-0.0140.00232.7510.0010.0010.0000.0000.0000.000
172A1567LEU0-0.053-0.03533.934-0.005-0.0050.0000.0000.0000.000
173A1568SER0-0.124-0.05832.434-0.004-0.0040.0000.0000.0000.000
174A1569ASP-1-0.937-0.95430.6770.2180.2180.0000.0000.0000.000
175A1570ALA0-0.060-0.02632.177-0.005-0.0050.0000.0000.0000.000