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: 6Y25Z

Calculation Name: 3PVE-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3PVE

Chain ID: A

ChEMBL ID:

UniProt ID: A2ASQ1

Base Structure: X-ray

Registration Date: 2023-09-23

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 176
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -1809363.779291
FMO2-HF: Nuclear repulsion 1743529.015065
FMO2-HF: Total energy -65834.764226
FMO2-MP2: Total energy -66030.466719


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:1454:SER)


Summations of interaction energy for fragment #1(A:1454:SER)
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.
-11.678-6.94811.044-8.36-7.414-0.054
Interaction energy analysis for fragmet #1(A:1454:SER)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.005 / q_NPA : -0.003
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].
3A1456PRO00.0320.0073.827-1.465-0.055-0.008-0.585-0.8160.003
4A1457PHE0-0.045-0.0206.0950.6710.6710.0000.0000.0000.000
5A1458LEU00.0130.0259.117-0.208-0.2080.0000.0000.0000.000
6A1459ALA00.0000.00912.5420.0760.0760.0000.0000.0000.000
7A1460ASP-1-0.792-0.88814.0400.1200.1200.0000.0000.0000.000
8A1461PHE0-0.001-0.02214.9130.0310.0310.0000.0000.0000.000
9A1462ASN00.0770.01520.038-0.037-0.0370.0000.0000.0000.000
10A1463GLY00.0060.01623.355-0.009-0.0090.0000.0000.0000.000
11A1464PHE0-0.073-0.04224.751-0.021-0.0210.0000.0000.0000.000
12A1465SER00.009-0.00119.4470.0010.0010.0000.0000.0000.000
13A1466TYR0-0.053-0.03418.207-0.031-0.0310.0000.0000.0000.000
14A1467LEU00.0030.01411.6440.0600.0600.0000.0000.0000.000
15A1468GLU-1-0.915-0.96014.7650.0300.0300.0000.0000.0000.000
16A1469LEU00.0180.00310.3500.0610.0610.0000.0000.0000.000
17A1470LYS10.9910.98512.1540.2040.2040.0000.0000.0000.000
18A1471GLY00.0670.03114.070-0.034-0.0340.0000.0000.0000.000
19A1472LEU00.021-0.00215.385-0.061-0.0610.0000.0000.0000.000
20A1473HIS0-0.039-0.00916.919-0.066-0.0660.0000.0000.0000.000
21A1474THR0-0.075-0.04013.2770.0180.0180.0000.0000.0000.000
22A1475PHE0-0.0110.00010.222-0.064-0.0640.0000.0000.0000.000
23A1483MET0-0.033-0.02119.7860.0020.0020.0000.0000.0000.000
24A1484ALA00.0170.00119.0770.0260.0260.0000.0000.0000.000
25A1485LEU0-0.030-0.00316.422-0.060-0.0600.0000.0000.0000.000
26A1486GLU-1-0.886-0.93715.632-0.397-0.3970.0000.0000.0000.000
27A1487MET0-0.015-0.00815.537-0.032-0.0320.0000.0000.0000.000
28A1488VAL0-0.0020.01315.7040.0230.0230.0000.0000.0000.000
29A1489PHE00.009-0.00916.6330.0150.0150.0000.0000.0000.000
30A1490LEU00.0200.02719.148-0.007-0.0070.0000.0000.0000.000
31A1491ALA0-0.029-0.01021.9270.0180.0180.0000.0000.0000.000
32A1492ARG10.7970.86721.829-0.139-0.1390.0000.0000.0000.000
33A1493GLY00.0550.04126.5850.0000.0000.0000.0000.0000.000
34A1494PRO0-0.040-0.03327.660-0.010-0.0100.0000.0000.0000.000
35A1495SER0-0.008-0.02229.136-0.014-0.0140.0000.0000.0000.000
36A1496GLY00.0360.03526.1710.0130.0130.0000.0000.0000.000
37A1497LEU0-0.073-0.03422.322-0.016-0.0160.0000.0000.0000.000
38A1498LEU00.0270.01020.0610.0120.0120.0000.0000.0000.000
39A1499LEU0-0.0060.00016.698-0.005-0.0050.0000.0000.0000.000
40A1500TYR00.0520.02619.7080.0050.0050.0000.0000.0000.000
41A1501ASN00.0410.01418.688-0.030-0.0300.0000.0000.0000.000
42A1502GLY00.0500.02821.463-0.004-0.0040.0000.0000.0000.000
43A1503GLN00.0420.04123.885-0.009-0.0090.0000.0000.0000.000
44A1504LYS10.9190.95826.6350.0540.0540.0000.0000.0000.000
45A1505THR00.0440.03626.9650.0030.0030.0000.0000.0000.000
46A1506ASP-1-0.780-0.89929.561-0.035-0.0350.0000.0000.0000.000
47A1507GLY00.0220.01331.7880.0010.0010.0000.0000.0000.000
48A1508LYS10.8170.89033.1360.0280.0280.0000.0000.0000.000
49A1509GLY0-0.022-0.00930.9770.0010.0010.0000.0000.0000.000
50A1510ASP-1-0.753-0.87328.139-0.125-0.1250.0000.0000.0000.000
51A1511PHE0-0.070-0.04525.7510.0060.0060.0000.0000.0000.000
52A1512VAL0-0.016-0.00221.831-0.008-0.0080.0000.0000.0000.000
53A1513SER00.013-0.00923.3170.0090.0090.0000.0000.0000.000
54A1514LEU0-0.0110.00420.878-0.010-0.0100.0000.0000.0000.000
55A1515ALA00.0090.01023.3820.0120.0120.0000.0000.0000.000
56A1516LEU00.0090.01624.811-0.011-0.0110.0000.0000.0000.000
57A1517HIS00.0730.02927.5040.0060.0060.0000.0000.0000.000
58A1518ASN0-0.004-0.01631.264-0.010-0.0100.0000.0000.0000.000
59A1519ARG10.9350.94929.9850.0170.0170.0000.0000.0000.000
60A1520HIS10.8080.93130.1970.0500.0500.0000.0000.0000.000
61A1521LEU00.0360.03424.1410.0040.0040.0000.0000.0000.000
62A1522GLU-1-0.803-0.89527.420-0.064-0.0640.0000.0000.0000.000
63A1523PHE0-0.020-0.00724.328-0.004-0.0040.0000.0000.0000.000
64A1524ARG10.8280.88526.7770.0730.0730.0000.0000.0000.000
65A1525TYR0-0.026-0.04226.784-0.015-0.0150.0000.0000.0000.000
66A1526ASP-1-0.843-0.90628.560-0.082-0.0820.0000.0000.0000.000
67A1527LEU0-0.073-0.03428.709-0.008-0.0080.0000.0000.0000.000
68A1528GLY00.0850.03831.442-0.002-0.0020.0000.0000.0000.000
69A1529LYS10.8270.92834.4290.0830.0830.0000.0000.0000.000
70A1530GLY00.0380.02235.3760.0050.0050.0000.0000.0000.000
71A1531ALA0-0.033-0.03032.357-0.008-0.0080.0000.0000.0000.000
72A1532ALA0-0.0040.00831.1550.0050.0050.0000.0000.0000.000
73A1533ILE0-0.023-0.02231.646-0.001-0.0010.0000.0000.0000.000
74A1534ILE0-0.0080.01429.3690.0030.0030.0000.0000.0000.000
75A1535ARG10.8900.94930.0670.0480.0480.0000.0000.0000.000
76A1536SER00.003-0.01429.202-0.001-0.0010.0000.0000.0000.000
77A1537LYS10.9060.94231.1280.0880.0880.0000.0000.0000.000
78A1538GLU-1-0.827-0.90232.291-0.067-0.0670.0000.0000.0000.000
79A1539PRO0-0.074-0.02031.880-0.005-0.0050.0000.0000.0000.000
80A1540ILE00.0590.02226.313-0.002-0.0020.0000.0000.0000.000
81A1541ALA00.0250.01829.3970.0100.0100.0000.0000.0000.000
82A1542LEU0-0.025-0.01927.976-0.005-0.0050.0000.0000.0000.000
83A1543GLY00.0200.01326.3660.0010.0010.0000.0000.0000.000
84A1544THR0-0.049-0.02325.680-0.001-0.0010.0000.0000.0000.000
85A1545TRP00.0320.01017.576-0.010-0.0100.0000.0000.0000.000
86A1546VAL0-0.0140.00221.899-0.013-0.0130.0000.0000.0000.000
87A1547ARG10.9620.99019.0480.2230.2230.0000.0000.0000.000
88A1548VAL0-0.020-0.00720.2040.0200.0200.0000.0000.0000.000
89A1549PHE00.0230.01019.022-0.033-0.0330.0000.0000.0000.000
90A1550LEU0-0.028-0.01721.0870.0350.0350.0000.0000.0000.000
91A1551GLU-1-0.915-0.96621.821-0.306-0.3060.0000.0000.0000.000
92A1552ARG10.9050.94424.2500.2430.2430.0000.0000.0000.000
93A1553ASN0-0.0120.00925.540-0.027-0.0270.0000.0000.0000.000
94A1554GLY00.0390.01828.2520.0160.0160.0000.0000.0000.000
95A1555ARG10.8400.90429.9280.1120.1120.0000.0000.0000.000
96A1556LYS10.9310.99831.5240.1460.1460.0000.0000.0000.000
97A1557GLY00.0570.03028.502-0.018-0.0180.0000.0000.0000.000
98A1558ALA0-0.037-0.03127.4500.0120.0120.0000.0000.0000.000
99A1559LEU0-0.0020.01525.235-0.017-0.0170.0000.0000.0000.000
100A1560GLN0-0.005-0.00325.0510.0210.0210.0000.0000.0000.000
101A1561VAL00.0170.00224.630-0.013-0.0130.0000.0000.0000.000
102A1562GLY0-0.028-0.01824.2510.0110.0110.0000.0000.0000.000
103A1563ASP-1-0.925-0.95725.191-0.146-0.1460.0000.0000.0000.000
104A1564GLY00.0190.02327.4470.0060.0060.0000.0000.0000.000
105A1565PRO0-0.003-0.02129.378-0.012-0.0120.0000.0000.0000.000
106A1566ARG10.8930.95627.1110.2120.2120.0000.0000.0000.000
107A1567VAL0-0.0190.00130.1840.0100.0100.0000.0000.0000.000
108A1568LEU0-0.008-0.01730.821-0.012-0.0120.0000.0000.0000.000
109A1569GLY00.0300.01132.5570.0110.0110.0000.0000.0000.000
110A1570GLU-1-0.903-0.95133.016-0.123-0.1230.0000.0000.0000.000
111A1571SER00.0520.04532.8060.0040.0040.0000.0000.0000.000
112A1572PRO00.0310.01034.775-0.003-0.0030.0000.0000.0000.000
113A1573VAL00.0080.00437.362-0.006-0.0060.0000.0000.0000.000
114A1574PRO0-0.065-0.02439.1730.0050.0050.0000.0000.0000.000
115A1575HIS00.1050.04634.287-0.008-0.0080.0000.0000.0000.000
116A1576THR00.017-0.01132.522-0.003-0.0030.0000.0000.0000.000
117A1577MET0-0.025-0.02329.312-0.017-0.0170.0000.0000.0000.000
118A1578LEU00.0230.02523.6300.0080.0080.0000.0000.0000.000
119A1579ASN0-0.035-0.02226.080-0.030-0.0300.0000.0000.0000.000
120A1580LEU0-0.018-0.00920.9150.0150.0150.0000.0000.0000.000
121A1581LYS10.8340.90322.8510.1540.1540.0000.0000.0000.000
122A1582GLU-1-0.925-0.94721.927-0.034-0.0340.0000.0000.0000.000
123A1583PRO00.0180.00517.384-0.042-0.0420.0000.0000.0000.000
124A1584LEU0-0.047-0.00113.563-0.013-0.0130.0000.0000.0000.000
125A1585TYR0-0.036-0.02116.1190.0260.0260.0000.0000.0000.000
126A1586VAL00.006-0.01113.953-0.042-0.0420.0000.0000.0000.000
127A1587GLY00.021-0.00316.8810.0480.0480.0000.0000.0000.000
128A1588GLY00.0600.02919.1500.0160.0160.0000.0000.0000.000
129A1589ALA0-0.047-0.03420.822-0.016-0.0160.0000.0000.0000.000
130A1590PRO0-0.0060.01421.3380.0080.0080.0000.0000.0000.000
131A1591ASP-1-0.788-0.88123.9840.0450.0450.0000.0000.0000.000
132A1592PHE00.0360.00425.095-0.014-0.0140.0000.0000.0000.000
133A1593SER0-0.039-0.03028.762-0.014-0.0140.0000.0000.0000.000
134A1594LYS10.9290.97625.248-0.020-0.0200.0000.0000.0000.000
135A1595LEU0-0.037-0.00724.766-0.011-0.0110.0000.0000.0000.000
136A1596ALA00.0090.00228.2990.0040.0040.0000.0000.0000.000
137A1597ARG10.8800.91630.4110.0150.0150.0000.0000.0000.000
138A1598GLY0-0.0070.00532.9270.0020.0020.0000.0000.0000.000
139A1599ALA0-0.007-0.00527.833-0.006-0.0060.0000.0000.0000.000
140A1600ALA0-0.054-0.01829.8240.0000.0000.0000.0000.0000.000
141A1601VAL0-0.0040.00326.8100.0020.0020.0000.0000.0000.000
142A1602ALA0-0.009-0.01929.7760.0020.0020.0000.0000.0000.000
143A1603SER00.0240.02128.2630.0050.0050.0000.0000.0000.000
144A1604GLY00.0620.03224.157-0.015-0.0150.0000.0000.0000.000
145A1605PHE0-0.083-0.03919.607-0.008-0.0080.0000.0000.0000.000
146A1606ASP-1-0.790-0.88822.8900.1130.1130.0000.0000.0000.000
147A1607GLY00.028-0.00722.028-0.021-0.0210.0000.0000.0000.000
148A1608ALA00.0040.02317.4380.0270.0270.0000.0000.0000.000
149A1609ILE0-0.030-0.02714.151-0.048-0.0480.0000.0000.0000.000
150A1610GLN0-0.010-0.02013.1620.0290.0290.0000.0000.0000.000
151A1611LEU0-0.0190.00511.432-0.072-0.0720.0000.0000.0000.000
152A1612VAL00.0360.00511.3250.0910.0910.0000.0000.0000.000
153A1613SER0-0.026-0.00411.232-0.155-0.1550.0000.0000.0000.000
154A1614LEU00.0340.01912.4730.1410.1410.0000.0000.0000.000
155A1615ARG10.9210.93413.5340.3790.3790.0000.0000.0000.000
156A1616GLY00.0530.03313.232-0.032-0.0320.0000.0000.0000.000
157A1617HIS0-0.0090.0087.272-0.041-0.0410.0000.0000.0000.000
158A1618GLN00.0500.0066.3400.3660.3660.0000.0000.0000.000
159A1619LEU0-0.002-0.0136.846-0.406-0.4060.0000.0000.0000.000
160A1620LEU0-0.0500.0007.7340.1400.1400.0000.0000.0000.000
161A1621THR00.002-0.0322.5550.0490.6820.463-0.413-0.6840.001
162A1622GLN00.018-0.0013.6210.2120.9010.041-0.308-0.4220.002
163A1623GLU-1-0.835-0.9042.213-12.700-10.70210.548-7.054-5.492-0.060
164A1624HIS10.7990.9054.9311.1751.1750.0000.0000.0000.000
165A1625VAL0-0.0310.0017.373-0.167-0.1670.0000.0000.0000.000
166A1626LEU0-0.037-0.0089.8350.1070.1070.0000.0000.0000.000
167A1627ARG10.9540.97113.116-0.173-0.1730.0000.0000.0000.000
168A1628ALA00.0140.00313.254-0.045-0.0450.0000.0000.0000.000
169A1629VAL0-0.032-0.00815.2660.0340.0340.0000.0000.0000.000
170A1630ASP-1-0.812-0.91818.9550.2220.2220.0000.0000.0000.000
171A1631VAL0-0.0270.02014.209-0.030-0.0300.0000.0000.0000.000
172A1632ALA00.0240.02116.5890.0700.0700.0000.0000.0000.000
173A1633PRO0-0.025-0.01414.150-0.018-0.0180.0000.0000.0000.000
174A1634PHE0-0.023-0.01715.491-0.048-0.0480.0000.0000.0000.000
175A1635ALA0-0.0090.00317.7120.0290.0290.0000.0000.0000.000
176A1636GLY00.0080.00520.485-0.021-0.0210.0000.0000.0000.000