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: R8248

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 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 176
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -1810526.728422
FMO2-HF: Nuclear repulsion 1744691.163702
FMO2-HF: Total energy -65835.56472
FMO2-MP2: Total energy -66031.319466


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.
-15.116-9.1928.351-7.056-7.219-0.053
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 : 0.007 / q_NPA : 0.006
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].
3A1456PRO00.0350.0043.864-0.6050.636-0.006-0.505-0.7300.003
4A1457PHE0-0.039-0.0226.2230.5980.5980.0000.0000.0000.000
5A1458LEU00.0070.0219.438-0.196-0.1960.0000.0000.0000.000
6A1459ALA00.0090.01612.9320.0260.0260.0000.0000.0000.000
7A1460ASP-1-0.793-0.88414.4720.1930.1930.0000.0000.0000.000
8A1461PHE00.017-0.00515.3610.0470.0470.0000.0000.0000.000
9A1462ASN00.0670.00520.699-0.042-0.0420.0000.0000.0000.000
10A1463GLY0-0.0030.01324.155-0.016-0.0160.0000.0000.0000.000
11A1464PHE0-0.049-0.03925.379-0.022-0.0220.0000.0000.0000.000
12A1465SER0-0.010-0.00220.060-0.006-0.0060.0000.0000.0000.000
13A1466TYR0-0.036-0.01318.727-0.030-0.0300.0000.0000.0000.000
14A1467LEU00.0140.01712.3190.0750.0750.0000.0000.0000.000
15A1468GLU-1-0.782-0.85215.2310.1480.1480.0000.0000.0000.000
16A1469LEU00.0250.01210.3230.0990.0990.0000.0000.0000.000
17A1470LYS10.9890.99211.0210.0190.0190.0000.0000.0000.000
18A1471GLY00.0660.03514.116-0.036-0.0360.0000.0000.0000.000
19A1472LEU00.010-0.00215.037-0.058-0.0580.0000.0000.0000.000
20A1473HIS0-0.036-0.00816.548-0.070-0.0700.0000.0000.0000.000
21A1474THR0-0.068-0.04113.2990.0170.0170.0000.0000.0000.000
22A1475PHE0-0.021-0.00810.189-0.079-0.0790.0000.0000.0000.000
23A1483MET00.0020.01619.807-0.005-0.0050.0000.0000.0000.000
24A1484ALA00.0030.00619.8640.0250.0250.0000.0000.0000.000
25A1485LEU0-0.027-0.00916.371-0.049-0.0490.0000.0000.0000.000
26A1486GLU-1-0.885-0.93715.787-0.317-0.3170.0000.0000.0000.000
27A1487MET0-0.021-0.01415.499-0.013-0.0130.0000.0000.0000.000
28A1488VAL00.0060.01415.9250.0030.0030.0000.0000.0000.000
29A1489PHE00.016-0.00816.5440.0340.0340.0000.0000.0000.000
30A1490LEU00.0070.02219.167-0.017-0.0170.0000.0000.0000.000
31A1491ALA0-0.020-0.00621.9850.0250.0250.0000.0000.0000.000
32A1492ARG10.7680.85122.429-0.225-0.2250.0000.0000.0000.000
33A1493GLY00.0740.04126.812-0.009-0.0090.0000.0000.0000.000
34A1494PRO0-0.043-0.03428.036-0.009-0.0090.0000.0000.0000.000
35A1495SER0-0.015-0.03329.344-0.017-0.0170.0000.0000.0000.000
36A1496GLY00.0410.03626.2970.0130.0130.0000.0000.0000.000
37A1497LEU0-0.063-0.02422.327-0.019-0.0190.0000.0000.0000.000
38A1498LEU00.0250.01520.1110.0200.0200.0000.0000.0000.000
39A1499LEU0-0.016-0.00716.5360.0110.0110.0000.0000.0000.000
40A1500TYR00.0480.02019.773-0.015-0.0150.0000.0000.0000.000
41A1501ASN00.0200.01518.561-0.005-0.0050.0000.0000.0000.000
42A1502GLY00.0600.02521.351-0.009-0.0090.0000.0000.0000.000
43A1503GLN00.0130.01323.9350.0010.0010.0000.0000.0000.000
44A1504LYS10.8510.92226.7100.0150.0150.0000.0000.0000.000
45A1505THR00.0590.02827.3360.0000.0000.0000.0000.0000.000
46A1506ASP-1-0.782-0.86829.6730.0060.0060.0000.0000.0000.000
47A1507GLY00.0580.02631.821-0.001-0.0010.0000.0000.0000.000
48A1508LYS10.7950.88732.561-0.011-0.0110.0000.0000.0000.000
49A1509GLY00.0270.01531.2320.0020.0020.0000.0000.0000.000
50A1510ASP-1-0.818-0.90828.086-0.078-0.0780.0000.0000.0000.000
51A1511PHE0-0.039-0.02525.6910.0070.0070.0000.0000.0000.000
52A1512VAL0-0.011-0.00721.609-0.013-0.0130.0000.0000.0000.000
53A1513SER00.001-0.00722.8630.0110.0110.0000.0000.0000.000
54A1514LEU0-0.020-0.00220.478-0.014-0.0140.0000.0000.0000.000
55A1515ALA00.0040.00323.3520.0200.0200.0000.0000.0000.000
56A1516LEU00.0200.02524.782-0.015-0.0150.0000.0000.0000.000
57A1517HIS00.0750.03727.5520.0050.0050.0000.0000.0000.000
58A1518ASN00.0170.00431.347-0.012-0.0120.0000.0000.0000.000
59A1519ARG10.9460.95630.195-0.027-0.0270.0000.0000.0000.000
60A1520HIS10.7970.91330.1010.0060.0060.0000.0000.0000.000
61A1521LEU00.0520.03623.8730.0070.0070.0000.0000.0000.000
62A1522GLU-1-0.802-0.88227.222-0.022-0.0220.0000.0000.0000.000
63A1523PHE0-0.0090.00323.9270.0030.0030.0000.0000.0000.000
64A1524ARG10.8210.88926.4560.0200.0200.0000.0000.0000.000
65A1525TYR0-0.005-0.03026.446-0.010-0.0100.0000.0000.0000.000
66A1526ASP-1-0.780-0.87428.235-0.048-0.0480.0000.0000.0000.000
67A1527LEU0-0.064-0.02928.641-0.007-0.0070.0000.0000.0000.000
68A1528GLY00.0330.01831.339-0.003-0.0030.0000.0000.0000.000
69A1529LYS10.7830.89334.1940.0570.0570.0000.0000.0000.000
70A1530GLY00.014-0.00435.0870.0040.0040.0000.0000.0000.000
71A1531ALA0-0.016-0.01832.521-0.007-0.0070.0000.0000.0000.000
72A1532ALA00.0000.00930.7860.0020.0020.0000.0000.0000.000
73A1533ILE0-0.040-0.02831.4470.0040.0040.0000.0000.0000.000
74A1534ILE0-0.0080.01429.162-0.001-0.0010.0000.0000.0000.000
75A1535ARG10.8400.89729.7850.0080.0080.0000.0000.0000.000
76A1536SER00.020-0.00629.109-0.003-0.0030.0000.0000.0000.000
77A1537LYS10.9100.95831.0790.0550.0550.0000.0000.0000.000
78A1538GLU-1-0.839-0.91232.724-0.035-0.0350.0000.0000.0000.000
79A1539PRO0-0.072-0.01831.849-0.002-0.0020.0000.0000.0000.000
80A1540ILE00.0600.01926.036-0.001-0.0010.0000.0000.0000.000
81A1541ALA00.0180.01929.3450.0080.0080.0000.0000.0000.000
82A1542LEU0-0.019-0.01127.955-0.002-0.0020.0000.0000.0000.000
83A1543GLY00.0260.01326.584-0.002-0.0020.0000.0000.0000.000
84A1544THR0-0.060-0.03225.508-0.003-0.0030.0000.0000.0000.000
85A1545TRP00.0350.00317.655-0.004-0.0040.0000.0000.0000.000
86A1546VAL0-0.0040.00922.284-0.023-0.0230.0000.0000.0000.000
87A1547ARG10.9040.95419.3880.1740.1740.0000.0000.0000.000
88A1548VAL0-0.034-0.02220.1910.0140.0140.0000.0000.0000.000
89A1549PHE00.0300.01819.146-0.022-0.0220.0000.0000.0000.000
90A1550LEU0-0.012-0.00620.8290.0300.0300.0000.0000.0000.000
91A1551GLU-1-0.820-0.87321.925-0.231-0.2310.0000.0000.0000.000
92A1552ARG10.8850.93424.4080.1830.1830.0000.0000.0000.000
93A1553ASN0-0.021-0.00525.574-0.024-0.0240.0000.0000.0000.000
94A1554GLY00.0480.02828.3340.0140.0140.0000.0000.0000.000
95A1555ARG10.8370.89029.9180.0880.0880.0000.0000.0000.000
96A1556LYS10.8540.92931.8840.1080.1080.0000.0000.0000.000
97A1557GLY00.0520.01628.534-0.014-0.0140.0000.0000.0000.000
98A1558ALA0-0.039-0.01927.4760.0110.0110.0000.0000.0000.000
99A1559LEU0-0.0140.00425.247-0.008-0.0080.0000.0000.0000.000
100A1560GLN0-0.0020.00125.0730.0090.0090.0000.0000.0000.000
101A1561VAL00.020-0.00224.759-0.003-0.0030.0000.0000.0000.000
102A1562GLY00.0310.01724.5520.0070.0070.0000.0000.0000.000
103A1563ASP-1-0.913-0.94924.707-0.118-0.1180.0000.0000.0000.000
104A1564GLY00.0270.03427.3740.0020.0020.0000.0000.0000.000
105A1565PRO0-0.034-0.04229.643-0.010-0.0100.0000.0000.0000.000
106A1566ARG10.7920.86527.5410.1710.1710.0000.0000.0000.000
107A1567VAL00.0060.01930.4250.0050.0050.0000.0000.0000.000
108A1568LEU0-0.014-0.01730.669-0.011-0.0110.0000.0000.0000.000
109A1569GLY00.0440.01532.5020.0110.0110.0000.0000.0000.000
110A1570GLU-1-0.808-0.87332.860-0.100-0.1000.0000.0000.0000.000
111A1571SER00.0650.05432.7100.0050.0050.0000.0000.0000.000
112A1572PRO00.0120.00634.516-0.004-0.0040.0000.0000.0000.000
113A1573VAL00.0180.03437.223-0.005-0.0050.0000.0000.0000.000
114A1574PRO0-0.001-0.01138.9320.0070.0070.0000.0000.0000.000
115A1575HIS00.0510.01934.185-0.008-0.0080.0000.0000.0000.000
116A1576THR00.0410.00932.2480.0000.0000.0000.0000.0000.000
117A1577MET0-0.025-0.01928.933-0.016-0.0160.0000.0000.0000.000
118A1578LEU00.0320.01223.5210.0080.0080.0000.0000.0000.000
119A1579ASN0-0.0130.00525.323-0.024-0.0240.0000.0000.0000.000
120A1580LEU0-0.038-0.01520.6950.0170.0170.0000.0000.0000.000
121A1581LYS10.8390.89422.5270.1020.1020.0000.0000.0000.000
122A1582GLU-1-0.835-0.89721.8320.0530.0530.0000.0000.0000.000
123A1583PRO00.0200.00617.792-0.036-0.0360.0000.0000.0000.000
124A1584LEU0-0.0370.00713.289-0.026-0.0260.0000.0000.0000.000
125A1585TYR0-0.071-0.05516.2680.0430.0430.0000.0000.0000.000
126A1586VAL00.001-0.02014.436-0.048-0.0480.0000.0000.0000.000
127A1587GLY00.0250.00617.2650.0530.0530.0000.0000.0000.000
128A1588GLY00.0610.03219.5190.0040.0040.0000.0000.0000.000
129A1589ALA0-0.036-0.02521.011-0.008-0.0080.0000.0000.0000.000
130A1590PRO0-0.0190.00821.7650.0030.0030.0000.0000.0000.000
131A1591ASP-1-0.783-0.87424.4780.0900.0900.0000.0000.0000.000
132A1592PHE00.0280.00025.225-0.013-0.0130.0000.0000.0000.000
133A1593SER0-0.065-0.04328.882-0.017-0.0170.0000.0000.0000.000
134A1594LYS10.8710.93624.752-0.093-0.0930.0000.0000.0000.000
135A1595LEU0-0.0290.00424.738-0.012-0.0120.0000.0000.0000.000
136A1596ALA00.0090.00128.332-0.001-0.0010.0000.0000.0000.000
137A1597ARG10.8940.92030.337-0.034-0.0340.0000.0000.0000.000
138A1598GLY0-0.0090.00432.8040.0010.0010.0000.0000.0000.000
139A1599ALA0-0.002-0.00727.697-0.006-0.0060.0000.0000.0000.000
140A1600ALA0-0.052-0.02429.6390.0020.0020.0000.0000.0000.000
141A1601VAL0-0.0130.00626.4640.0050.0050.0000.0000.0000.000
142A1602ALA0-0.010-0.02529.5540.0000.0000.0000.0000.0000.000
143A1603SER00.0150.02228.2100.0020.0020.0000.0000.0000.000
144A1604GLY00.0710.03124.303-0.011-0.0110.0000.0000.0000.000
145A1605PHE0-0.082-0.03919.853-0.022-0.0220.0000.0000.0000.000
146A1606ASP-1-0.774-0.88423.3480.1890.1890.0000.0000.0000.000
147A1607GLY00.0340.01222.584-0.030-0.0300.0000.0000.0000.000
148A1608ALA0-0.0020.01017.8740.0370.0370.0000.0000.0000.000
149A1609ILE0-0.053-0.04214.298-0.059-0.0590.0000.0000.0000.000
150A1610GLN0-0.0030.00013.4650.0480.0480.0000.0000.0000.000
151A1611LEU0-0.0060.00011.490-0.039-0.0390.0000.0000.0000.000
152A1612VAL00.0340.00711.2690.0710.0710.0000.0000.0000.000
153A1613SER0-0.0250.00310.830-0.146-0.1460.0000.0000.0000.000
154A1614LEU00.0490.01812.5380.1150.1150.0000.0000.0000.000
155A1615ARG10.8790.89414.0330.2990.2990.0000.0000.0000.000
156A1616GLY00.0830.05913.550-0.021-0.0210.0000.0000.0000.000
157A1617HIS00.0090.0247.167-0.007-0.0070.0000.0000.0000.000
158A1618GLN00.031-0.0066.7970.3600.3600.0000.0000.0000.000
159A1619LEU0-0.009-0.0156.950-0.295-0.2950.0000.0000.0000.000
160A1620LEU0-0.0440.0057.8890.2100.2100.0000.0000.0000.000
161A1621THR0-0.001-0.0382.8140.3000.9610.222-0.296-0.5870.000
162A1622GLN00.029-0.0023.822-0.968-0.4090.030-0.234-0.3550.001
163A1623GLU-1-0.832-0.8952.456-14.935-11.4688.106-6.012-5.561-0.057
164A1624HIS10.7760.8835.0040.2990.295-0.001-0.0090.0140.000
165A1625VAL0-0.032-0.0027.930-0.262-0.2620.0000.0000.0000.000
166A1626LEU0-0.031-0.01510.4840.0640.0640.0000.0000.0000.000
167A1627ARG10.8060.85713.669-0.313-0.3130.0000.0000.0000.000
168A1628ALA00.0180.01313.843-0.014-0.0140.0000.0000.0000.000
169A1629VAL0-0.023-0.01215.8670.0100.0100.0000.0000.0000.000
170A1630ASP-1-0.799-0.89919.5930.3020.3020.0000.0000.0000.000
171A1631VAL0-0.0330.02015.015-0.028-0.0280.0000.0000.0000.000
172A1632ALA00.0120.01517.5100.0660.0660.0000.0000.0000.000
173A1633PRO0-0.036-0.02214.8570.0130.0130.0000.0000.0000.000
174A1634PHE00.001-0.01216.254-0.064-0.0640.0000.0000.0000.000
175A1635ALA00.005-0.00518.0580.0320.0320.0000.0000.0000.000
176A1636GLY0-0.0200.00720.821-0.028-0.0280.0000.0000.0000.000