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: 8969Y

Calculation Name: 1PGL-1-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1PGL

Chain ID: 1

ChEMBL ID:

UniProt ID: P23009

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 185
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -1926114.853422
FMO2-HF: Nuclear repulsion 1852852.599872
FMO2-HF: Total energy -73262.253549
FMO2-MP2: Total energy -73472.948291


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(1:1:SER)


Summations of interaction energy for fragment #1(1:1: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.
-4.959-3.3674.912-2.609-3.8940.016
Interaction energy analysis for fragmet #1(1:1:SER)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.021 / q_NPA : 0.001
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].
313SER0-0.0110.0023.143-0.1331.522-0.001-0.683-0.9720.002
414GLN00.006-0.0025.0900.1980.231-0.001-0.005-0.0260.000
515GLN00.0390.0198.5800.2370.2370.0000.0000.0000.000
616THR0-0.012-0.01711.2070.0690.0690.0000.0000.0000.000
717VAL0-0.0100.01111.0820.1050.1050.0000.0000.0000.000
818TRP00.0150.01612.8620.0430.0430.0000.0000.0000.000
919ASN0-0.049-0.03315.0030.0590.0590.0000.0000.0000.000
10110GLN00.0550.03017.3270.0250.0250.0000.0000.0000.000
11111MET0-0.0550.00020.4140.0150.0150.0000.0000.0000.000
12112ALA00.0510.01122.2250.0110.0110.0000.0000.0000.000
13113THR0-0.025-0.00825.903-0.011-0.0110.0000.0000.0000.000
14114VAL0-0.022-0.00928.7460.0080.0080.0000.0000.0000.000
15115ARG10.9020.94031.987-0.005-0.0050.0000.0000.0000.000
16116THR0-0.0120.00135.1770.0060.0060.0000.0000.0000.000
17117PRO00.0130.02638.178-0.003-0.0030.0000.0000.0000.000
18118LEU0-0.021-0.02041.217-0.003-0.0030.0000.0000.0000.000
19119ASN0-0.048-0.03043.418-0.002-0.0020.0000.0000.0000.000
20120PHE0-0.0050.01443.7250.0000.0000.0000.0000.0000.000
21121ASP-1-0.783-0.88945.8400.0050.0050.0000.0000.0000.000
22122SER0-0.044-0.02247.1790.0000.0000.0000.0000.0000.000
23123SER0-0.092-0.05649.2370.0000.0000.0000.0000.0000.000
24124LYN0-0.040-0.00347.3490.0000.0000.0000.0000.0000.000
25125GLN0-0.021-0.01744.1320.0020.0020.0000.0000.0000.000
26126SER0-0.026-0.02945.0800.0000.0000.0000.0000.0000.000
27127PHE0-0.020-0.00841.427-0.003-0.0030.0000.0000.0000.000
28128CYS0-0.0400.00339.3300.0010.0010.0000.0000.0000.000
29129GLN00.0170.00137.254-0.002-0.0020.0000.0000.0000.000
30130PHE00.0090.00130.1190.0010.0010.0000.0000.0000.000
31131SER0-0.003-0.00431.3830.0020.0020.0000.0000.0000.000
32132VAL00.0180.00125.988-0.001-0.0010.0000.0000.0000.000
33133ASP-1-0.744-0.82826.1700.1610.1610.0000.0000.0000.000
34134LEU0-0.007-0.02621.3680.0050.0050.0000.0000.0000.000
35135LEU0-0.036-0.00819.6520.0250.0250.0000.0000.0000.000
36136GLY00.0300.01922.4180.0220.0220.0000.0000.0000.000
37137GLY0-0.041-0.02324.619-0.002-0.0020.0000.0000.0000.000
38138GLY00.0180.00225.114-0.008-0.0080.0000.0000.0000.000
39139ILE0-0.015-0.01628.536-0.002-0.0020.0000.0000.0000.000
40140SER0-0.031-0.00731.1370.0020.0020.0000.0000.0000.000
41141VAL00.001-0.01234.529-0.003-0.0030.0000.0000.0000.000
42142ASP-1-0.765-0.88237.1430.0310.0310.0000.0000.0000.000
43143LYS10.9410.96040.545-0.039-0.0390.0000.0000.0000.000
44144THR0-0.019-0.00942.516-0.002-0.0020.0000.0000.0000.000
45145GLY00.0200.00944.089-0.004-0.0040.0000.0000.0000.000
46146ASP-1-0.895-0.93742.6160.0290.0290.0000.0000.0000.000
47147TRP0-0.034-0.03535.681-0.004-0.0040.0000.0000.0000.000
48148ILE0-0.0110.00235.3170.0010.0010.0000.0000.0000.000
49149THR0-0.022-0.01232.444-0.003-0.0030.0000.0000.0000.000
50150LEU0-0.030-0.01128.4430.0020.0020.0000.0000.0000.000
51151VAL00.0530.02725.345-0.003-0.0030.0000.0000.0000.000
52152GLN00.002-0.00623.7260.0170.0170.0000.0000.0000.000
53153ASN00.0240.02223.3260.0200.0200.0000.0000.0000.000
54154SER0-0.016-0.02118.9290.0150.0150.0000.0000.0000.000
55155PRO00.017-0.00715.0240.0240.0240.0000.0000.0000.000
56156ILE00.0340.02113.6410.0490.0490.0000.0000.0000.000
57157SER00.0320.02116.3170.0320.0320.0000.0000.0000.000
58158ASN0-0.044-0.03018.933-0.007-0.0070.0000.0000.0000.000
59159LEU00.0160.01512.8960.0090.0090.0000.0000.0000.000
60160LEU00.003-0.00216.4590.0220.0220.0000.0000.0000.000
61161ARG10.8320.92318.971-0.162-0.1620.0000.0000.0000.000
62162VAL0-0.0080.00319.209-0.014-0.0140.0000.0000.0000.000
63163ALA00.0150.01717.0980.0080.0080.0000.0000.0000.000
64164ALA0-0.037-0.00719.149-0.025-0.0250.0000.0000.0000.000
65165TRP0-0.008-0.01319.860-0.030-0.0300.0000.0000.0000.000
66166LYS10.8230.89116.997-0.261-0.2610.0000.0000.0000.000
67167LYS10.8790.93014.700-0.727-0.7270.0000.0000.0000.000
68168GLY00.0480.05013.1010.1000.1000.0000.0000.0000.000
69169CYS0-0.060-0.05712.047-0.121-0.1210.0000.0000.0000.000
70170LEU0-0.0360.00012.4910.0910.0910.0000.0000.0000.000
71171MET0-0.036-0.00213.333-0.035-0.0350.0000.0000.0000.000
72172VAL00.0340.00915.1940.0060.0060.0000.0000.0000.000
73173LYS10.8060.88618.7510.1030.1030.0000.0000.0000.000
74174VAL0-0.0060.00220.7900.0150.0150.0000.0000.0000.000
75175VAL0-0.019-0.01724.168-0.015-0.0150.0000.0000.0000.000
76176MET0-0.0340.02226.7760.0100.0100.0000.0000.0000.000
77177SER00.024-0.00330.163-0.012-0.0120.0000.0000.0000.000
78178GLY00.0460.01332.6130.0070.0070.0000.0000.0000.000
79179ASN0-0.065-0.03836.238-0.006-0.0060.0000.0000.0000.000
80180ALA00.016-0.00838.4250.0000.0000.0000.0000.0000.000
81181ALA0-0.0220.00440.134-0.002-0.0020.0000.0000.0000.000
82182VAL0-0.0230.01042.3230.0010.0010.0000.0000.0000.000
83183LYS10.8870.93243.1440.0210.0210.0000.0000.0000.000
84184ARG10.9040.93536.6750.0520.0520.0000.0000.0000.000
85185SER0-0.039-0.04143.2260.0000.0000.0000.0000.0000.000
86186ASP-1-0.794-0.85945.794-0.022-0.0220.0000.0000.0000.000
87187TRP0-0.0180.00137.3700.0010.0010.0000.0000.0000.000
88188ALA0-0.009-0.00843.3730.0000.0000.0000.0000.0000.000
89189SER0-0.016-0.00239.8340.0020.0020.0000.0000.0000.000
90190LEU00.0040.00537.766-0.004-0.0040.0000.0000.0000.000
91191VAL0-0.004-0.00333.0220.0030.0030.0000.0000.0000.000
92192GLN0-0.025-0.00534.2250.0000.0000.0000.0000.0000.000
93193VAL00.0060.00028.2790.0020.0020.0000.0000.0000.000
94194PHE00.012-0.00430.648-0.004-0.0040.0000.0000.0000.000
95195LEU00.0100.00723.5890.0010.0010.0000.0000.0000.000
96196THR00.0630.02427.9490.0050.0050.0000.0000.0000.000
97197ASN00.0340.02127.347-0.005-0.0050.0000.0000.0000.000
98198SER00.0720.05128.5170.0100.0100.0000.0000.0000.000
99199ASN0-0.031-0.03231.565-0.013-0.0130.0000.0000.0000.000
1001100SER0-0.043-0.02434.160-0.008-0.0080.0000.0000.0000.000
1011101THR0-0.005-0.02236.3210.0000.0000.0000.0000.0000.000
1021102GLU-1-0.907-0.92138.4460.0710.0710.0000.0000.0000.000
1031103HIS0-0.069-0.03631.9500.0000.0000.0000.0000.0000.000
1041104PHE00.008-0.00234.251-0.005-0.0050.0000.0000.0000.000
1051105ASP-1-0.818-0.88231.1300.0670.0670.0000.0000.0000.000
1061106ALA0-0.0030.00726.662-0.003-0.0030.0000.0000.0000.000
1071107CYS0-0.072-0.03126.166-0.007-0.0070.0000.0000.0000.000
1081108ARG10.8400.89828.598-0.039-0.0390.0000.0000.0000.000
1091109TRP00.0320.01924.629-0.006-0.0060.0000.0000.0000.000
1101110THR0-0.039-0.03631.3270.0050.0050.0000.0000.0000.000
1111111LYS10.8080.92028.6270.0380.0380.0000.0000.0000.000
1121112SER00.0550.01033.5230.0050.0050.0000.0000.0000.000
1131113GLU-1-0.856-0.91331.445-0.042-0.0420.0000.0000.0000.000
1141114PRO00.007-0.00435.6000.0000.0000.0000.0000.0000.000
1151115HIS0-0.030-0.01636.241-0.009-0.0090.0000.0000.0000.000
1161116SER0-0.001-0.01031.3330.0000.0000.0000.0000.0000.000
1171117TRP00.0070.02027.651-0.004-0.0040.0000.0000.0000.000
1181118GLU-1-0.781-0.89022.822-0.123-0.1230.0000.0000.0000.000
1191119LEU0-0.0090.00024.5720.0000.0000.0000.0000.0000.000
1201120ILE00.000-0.00318.3340.0000.0000.0000.0000.0000.000
1211121PHE00.002-0.00219.918-0.005-0.0050.0000.0000.0000.000
1221122PRO00.0360.01316.0150.0020.0020.0000.0000.0000.000
1231123ILE0-0.019-0.00517.153-0.015-0.0150.0000.0000.0000.000
1241124GLU-1-0.808-0.91114.9400.4840.4840.0000.0000.0000.000
1251125VAL0-0.0160.01717.091-0.042-0.0420.0000.0000.0000.000
1261126CYS00.002-0.01318.0130.0540.0540.0000.0000.0000.000
1271127GLY00.0010.00420.636-0.033-0.0330.0000.0000.0000.000
1281128PRO0-0.010-0.01323.0740.0160.0160.0000.0000.0000.000
1291129ASN0-0.103-0.02322.6120.0050.0050.0000.0000.0000.000
1301130ASN00.035-0.01020.177-0.013-0.0130.0000.0000.0000.000
1311131GLY00.0250.02319.1260.0510.0510.0000.0000.0000.000
1321132PHE0-0.020-0.00815.505-0.009-0.0090.0000.0000.0000.000
1331133GLU-1-0.819-0.90720.0240.1970.1970.0000.0000.0000.000
1341134MET0-0.079-0.02721.6520.0310.0310.0000.0000.0000.000
1351135TRP0-0.072-0.06124.037-0.017-0.0170.0000.0000.0000.000
1361136SER0-0.017-0.01625.598-0.009-0.0090.0000.0000.0000.000
1371137SER0-0.0210.01028.173-0.010-0.0100.0000.0000.0000.000
1381138GLU-1-0.883-0.96229.9150.1260.1260.0000.0000.0000.000
1391139TRP0-0.057-0.01628.578-0.007-0.0070.0000.0000.0000.000
1401140ALA0-0.014-0.00829.490-0.003-0.0030.0000.0000.0000.000
1411141ASN0-0.086-0.05131.355-0.007-0.0070.0000.0000.0000.000
1421142GLN00.0230.02625.7760.0170.0170.0000.0000.0000.000
1431143THR0-0.040-0.03927.226-0.016-0.0160.0000.0000.0000.000
1441144SER00.000-0.03025.1010.0230.0230.0000.0000.0000.000
1451145TRP0-0.020-0.02221.226-0.020-0.0200.0000.0000.0000.000
1461146HIS0-0.027-0.01625.105-0.003-0.0030.0000.0000.0000.000
1471147LEU0-0.0140.01524.206-0.010-0.0100.0000.0000.0000.000
1481148SER00.0070.00127.488-0.002-0.0020.0000.0000.0000.000
1491149PHE0-0.012-0.00927.750-0.007-0.0070.0000.0000.0000.000
1501150LEU0-0.0100.00633.4200.0030.0030.0000.0000.0000.000
1511151VAL0-0.011-0.00735.198-0.004-0.0040.0000.0000.0000.000
1521152ASP-1-0.770-0.88737.7980.0060.0060.0000.0000.0000.000
1531153ASN00.0100.00440.790-0.003-0.0030.0000.0000.0000.000
1541154PRO00.0200.00739.634-0.004-0.0040.0000.0000.0000.000
1551155LYS10.8520.91940.150-0.004-0.0040.0000.0000.0000.000
1561156GLN0-0.015-0.00440.836-0.003-0.0030.0000.0000.0000.000
1571157SER00.0320.00136.117-0.005-0.0050.0000.0000.0000.000
1581158THR0-0.044-0.02036.5960.0040.0040.0000.0000.0000.000
1591159THR0-0.004-0.02331.8700.0060.0060.0000.0000.0000.000
1601160PHE0-0.0010.00329.622-0.006-0.0060.0000.0000.0000.000
1611161ASP-1-0.845-0.89125.803-0.012-0.0120.0000.0000.0000.000
1621162VAL00.007-0.00222.687-0.008-0.0080.0000.0000.0000.000
1631163LEU0-0.021-0.02119.0700.0020.0020.0000.0000.0000.000
1641164LEU00.0330.01416.5590.0060.0060.0000.0000.0000.000
1651165GLY00.0080.00013.052-0.058-0.0580.0000.0000.0000.000
1661166ILE00.0030.0138.6980.0240.0240.0000.0000.0000.000
1671167SER0-0.012-0.0298.097-0.130-0.1300.0000.0000.0000.000
1681168GLN0-0.004-0.0302.140-6.608-6.7594.915-1.921-2.8420.014
1691169ASN0-0.0170.0095.7170.4360.491-0.0010.000-0.0540.000
1701170PHE0-0.033-0.0038.982-0.243-0.2430.0000.0000.0000.000
1711171GLU-1-0.827-0.9029.8841.0871.0870.0000.0000.0000.000
1721172ILE0-0.012-0.02412.243-0.153-0.1530.0000.0000.0000.000
1731173ALA00.0070.00214.8930.0460.0460.0000.0000.0000.000
1741174GLY00.0200.00917.658-0.048-0.0480.0000.0000.0000.000
1751175ASN0-0.024-0.01219.6640.0390.0390.0000.0000.0000.000
1761176THR00.0120.00321.871-0.016-0.0160.0000.0000.0000.000
1771177LEU0-0.026-0.00924.7350.0010.0010.0000.0000.0000.000
1781178MET00.0190.01225.226-0.012-0.0120.0000.0000.0000.000
1791179PRO0-0.014-0.00328.050-0.002-0.0020.0000.0000.0000.000
1801180ALA00.002-0.00728.4550.0070.0070.0000.0000.0000.000
1811181PHE0-0.003-0.00322.411-0.011-0.0110.0000.0000.0000.000
1821182SER00.0090.01127.945-0.005-0.0050.0000.0000.0000.000
1831183VAL00.003-0.00128.0070.0020.0020.0000.0000.0000.000
1841184PRO00.0060.00529.526-0.004-0.0040.0000.0000.0000.000
1851185GLN0-0.0040.00932.4050.0000.0000.0000.0000.0000.000