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: G5451

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 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 185
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -1926063.353111
FMO2-HF: Nuclear repulsion 1852801.613675
FMO2-HF: Total energy -73261.739437
FMO2-MP2: Total energy -73472.348045


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.
-4.518-3.5415.338-2.515-3.80.008
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 : 0.006 / q_NPA : -0.007
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].
313SER00.0010.0093.764-0.7630.739-0.015-0.661-0.8260.002
414GLN00.006-0.0045.4360.3250.3250.0000.0000.0000.000
515GLN00.0130.0079.0060.1880.1880.0000.0000.0000.000
616THR0-0.022-0.02111.4260.0800.0800.0000.0000.0000.000
717VAL00.0060.02111.2190.0820.0820.0000.0000.0000.000
818TRP00.0240.02512.5830.0080.0080.0000.0000.0000.000
919ASN0-0.035-0.02714.9680.0570.0570.0000.0000.0000.000
10110GLN00.0500.02417.3390.0210.0210.0000.0000.0000.000
11111MET0-0.0450.00720.5940.0150.0150.0000.0000.0000.000
12112ALA00.0600.01422.3290.0120.0120.0000.0000.0000.000
13113THR0-0.016-0.01325.976-0.011-0.0110.0000.0000.0000.000
14114VAL0-0.041-0.01228.8550.0070.0070.0000.0000.0000.000
15115ARG10.9040.93931.915-0.002-0.0020.0000.0000.0000.000
16116THR00.0150.00535.0560.0060.0060.0000.0000.0000.000
17117PRO0-0.0200.01337.872-0.003-0.0030.0000.0000.0000.000
18118LEU00.000-0.01241.147-0.003-0.0030.0000.0000.0000.000
19119ASN0-0.056-0.02943.352-0.002-0.0020.0000.0000.0000.000
20120PHE00.0040.01343.5290.0000.0000.0000.0000.0000.000
21121ASP-1-0.772-0.89045.6260.0040.0040.0000.0000.0000.000
22122SER0-0.037-0.02847.5950.0010.0010.0000.0000.0000.000
23123SER0-0.101-0.06349.0160.0010.0010.0000.0000.0000.000
24124LYN0-0.0190.01747.0320.0000.0000.0000.0000.0000.000
25125GLN0-0.025-0.02044.1510.0020.0020.0000.0000.0000.000
26126SER0-0.001-0.00445.2130.0000.0000.0000.0000.0000.000
27127PHE0-0.013-0.00141.290-0.003-0.0030.0000.0000.0000.000
28128CYS0-0.057-0.00239.4670.0010.0010.0000.0000.0000.000
29129GLN0-0.002-0.01637.225-0.002-0.0020.0000.0000.0000.000
30130PHE00.0120.01130.2300.0020.0020.0000.0000.0000.000
31131SER0-0.004-0.01131.4600.0010.0010.0000.0000.0000.000
32132VAL00.0110.00225.8820.0010.0010.0000.0000.0000.000
33133ASP-1-0.737-0.85226.3110.1520.1520.0000.0000.0000.000
34134LEU0-0.022-0.03021.6400.0070.0070.0000.0000.0000.000
35135LEU0-0.024-0.00719.6320.0200.0200.0000.0000.0000.000
36136GLY00.0150.01522.5100.0200.0200.0000.0000.0000.000
37137GLY0-0.046-0.02624.9010.0000.0000.0000.0000.0000.000
38138GLY00.0080.00825.465-0.010-0.0100.0000.0000.0000.000
39139ILE0-0.014-0.01828.717-0.002-0.0020.0000.0000.0000.000
40140SER0-0.025-0.00431.0800.0010.0010.0000.0000.0000.000
41141VAL0-0.012-0.02334.412-0.004-0.0040.0000.0000.0000.000
42142ASP-1-0.762-0.86937.1850.0300.0300.0000.0000.0000.000
43143LYS10.8860.94440.642-0.038-0.0380.0000.0000.0000.000
44144THR00.0380.00641.819-0.002-0.0020.0000.0000.0000.000
45145GLY00.0280.01343.743-0.004-0.0040.0000.0000.0000.000
46146ASP-1-0.904-0.94042.4740.0260.0260.0000.0000.0000.000
47147TRP0-0.011-0.02535.670-0.004-0.0040.0000.0000.0000.000
48148ILE0-0.007-0.00335.6610.0020.0020.0000.0000.0000.000
49149THR00.0010.00332.338-0.003-0.0030.0000.0000.0000.000
50150LEU0-0.024-0.01128.8380.0020.0020.0000.0000.0000.000
51151VAL00.0440.02925.244-0.005-0.0050.0000.0000.0000.000
52152GLN0-0.013-0.00123.6820.0160.0160.0000.0000.0000.000
53153ASN00.0170.01923.2250.0220.0220.0000.0000.0000.000
54154SER0-0.023-0.02919.2200.0130.0130.0000.0000.0000.000
55155PRO00.039-0.00515.0350.0240.0240.0000.0000.0000.000
56156ILE00.0240.01113.5860.0510.0510.0000.0000.0000.000
57157SER00.0150.01016.3440.0350.0350.0000.0000.0000.000
58158ASN0-0.039-0.02318.923-0.006-0.0060.0000.0000.0000.000
59159LEU00.0010.01412.8010.0120.0120.0000.0000.0000.000
60160LEU00.0120.00116.6800.0240.0240.0000.0000.0000.000
61161ARG10.8580.92018.901-0.154-0.1540.0000.0000.0000.000
62162VAL00.0020.01118.945-0.011-0.0110.0000.0000.0000.000
63163ALA0-0.0020.02017.0300.0150.0150.0000.0000.0000.000
64164ALA0-0.0210.00018.978-0.020-0.0200.0000.0000.0000.000
65165TRP0-0.015-0.00419.517-0.035-0.0350.0000.0000.0000.000
66166LYS10.8370.89716.744-0.263-0.2630.0000.0000.0000.000
67167LYS10.9230.95014.225-0.792-0.7920.0000.0000.0000.000
68168GLY00.0550.05312.9170.1280.1280.0000.0000.0000.000
69169CYS0-0.042-0.02312.290-0.093-0.0930.0000.0000.0000.000
70170LEU0-0.0110.01112.4820.0730.0730.0000.0000.0000.000
71171MET0-0.031-0.00213.602-0.025-0.0250.0000.0000.0000.000
72172VAL00.0300.00515.5180.0010.0010.0000.0000.0000.000
73173LYS10.8250.90319.0300.1270.1270.0000.0000.0000.000
74174VAL0-0.025-0.00520.9460.0100.0100.0000.0000.0000.000
75175VAL00.000-0.01324.033-0.014-0.0140.0000.0000.0000.000
76176MET0-0.0300.03026.7090.0090.0090.0000.0000.0000.000
77177SER00.0260.00530.063-0.012-0.0120.0000.0000.0000.000
78178GLY00.025-0.01132.4300.0070.0070.0000.0000.0000.000
79179ASN0-0.069-0.03436.104-0.005-0.0050.0000.0000.0000.000
80180ALA00.013-0.01238.3600.0000.0000.0000.0000.0000.000
81181ALA0-0.0140.00240.036-0.002-0.0020.0000.0000.0000.000
82182VAL0-0.0230.01342.5840.0020.0020.0000.0000.0000.000
83183LYS11.0001.00943.2650.0240.0240.0000.0000.0000.000
84184ARG10.9800.98036.5780.0570.0570.0000.0000.0000.000
85185SER0-0.068-0.05943.2260.0000.0000.0000.0000.0000.000
86186ASP-1-0.859-0.91646.038-0.025-0.0250.0000.0000.0000.000
87187TRP0-0.052-0.01237.3890.0010.0010.0000.0000.0000.000
88188ALA0-0.012-0.01743.3890.0000.0000.0000.0000.0000.000
89189SER0-0.030-0.01239.7180.0030.0030.0000.0000.0000.000
90190LEU0-0.0010.00537.541-0.004-0.0040.0000.0000.0000.000
91191VAL0-0.006-0.00632.8420.0030.0030.0000.0000.0000.000
92192GLN0-0.020-0.00134.344-0.001-0.0010.0000.0000.0000.000
93193VAL0-0.005-0.00528.0340.0030.0030.0000.0000.0000.000
94194PHE00.019-0.00330.737-0.003-0.0030.0000.0000.0000.000
95195LEU0-0.0020.01623.7790.0020.0020.0000.0000.0000.000
96196THR00.0500.01827.953-0.001-0.0010.0000.0000.0000.000
97197ASN00.0290.02927.306-0.005-0.0050.0000.0000.0000.000
98198SER00.0930.04128.4000.0090.0090.0000.0000.0000.000
99199ASN0-0.022-0.02131.429-0.013-0.0130.0000.0000.0000.000
1001100SER0-0.0300.01433.954-0.009-0.0090.0000.0000.0000.000
1011101THR00.021-0.00636.142-0.001-0.0010.0000.0000.0000.000
1021102GLU-1-0.963-0.98338.4970.0670.0670.0000.0000.0000.000
1031103HIS0-0.064-0.02232.0380.0000.0000.0000.0000.0000.000
1041104PHE00.010-0.00134.417-0.005-0.0050.0000.0000.0000.000
1051105ASP-1-0.816-0.88431.6130.0580.0580.0000.0000.0000.000
1061106ALA0-0.031-0.01126.717-0.001-0.0010.0000.0000.0000.000
1071107CYS0-0.064-0.03026.185-0.008-0.0080.0000.0000.0000.000
1081108ARG10.8530.90028.802-0.033-0.0330.0000.0000.0000.000
1091109TRP00.0170.00824.654-0.006-0.0060.0000.0000.0000.000
1101110THR0-0.026-0.02631.1950.0050.0050.0000.0000.0000.000
1111111LYS10.8080.92228.6050.0480.0480.0000.0000.0000.000
1121112SER00.0620.01533.4030.0040.0040.0000.0000.0000.000
1131113GLU-1-0.876-0.91531.422-0.050-0.0500.0000.0000.0000.000
1141114PRO00.001-0.01435.5210.0010.0010.0000.0000.0000.000
1151115HIS0-0.043-0.02236.056-0.009-0.0090.0000.0000.0000.000
1161116SER0-0.005-0.00831.2060.0000.0000.0000.0000.0000.000
1171117TRP0-0.0120.00928.007-0.004-0.0040.0000.0000.0000.000
1181118GLU-1-0.787-0.89322.998-0.138-0.1380.0000.0000.0000.000
1191119LEU0-0.028-0.01224.778-0.002-0.0020.0000.0000.0000.000
1201120ILE00.009-0.00218.3740.0020.0020.0000.0000.0000.000
1211121PHE0-0.0100.00020.138-0.004-0.0040.0000.0000.0000.000
1221122PRO00.0320.01316.227-0.001-0.0010.0000.0000.0000.000
1231123ILE0-0.0120.00017.277-0.008-0.0080.0000.0000.0000.000
1241124GLU-1-0.909-0.98515.9810.3810.3810.0000.0000.0000.000
1251125VAL0-0.0320.00217.106-0.032-0.0320.0000.0000.0000.000
1261126CYS00.0070.00418.0200.0510.0510.0000.0000.0000.000
1271127GLY00.024-0.01220.618-0.027-0.0270.0000.0000.0000.000
1281128PRO0-0.032-0.01622.8150.0080.0080.0000.0000.0000.000
1291129ASN0-0.086-0.02122.7080.0020.0020.0000.0000.0000.000
1301130ASN00.032-0.00520.232-0.020-0.0200.0000.0000.0000.000
1311131GLY00.0490.03319.4480.0430.0430.0000.0000.0000.000
1321132PHE0-0.061-0.02315.3490.0020.0020.0000.0000.0000.000
1331133GLU-1-0.824-0.92020.1030.1950.1950.0000.0000.0000.000
1341134MET0-0.100-0.03221.6390.0240.0240.0000.0000.0000.000
1351135TRP0-0.073-0.05323.894-0.016-0.0160.0000.0000.0000.000
1361136SER0-0.005-0.00625.452-0.009-0.0090.0000.0000.0000.000
1371137SER0-0.0290.00227.914-0.010-0.0100.0000.0000.0000.000
1381138GLU-1-0.860-0.94829.6900.1220.1220.0000.0000.0000.000
1391139TRP0-0.019-0.00828.193-0.007-0.0070.0000.0000.0000.000
1401140ALA0-0.079-0.01629.448-0.007-0.0070.0000.0000.0000.000
1411141ASN0-0.062-0.04631.379-0.010-0.0100.0000.0000.0000.000
1421142GLN00.0140.01425.6600.0180.0180.0000.0000.0000.000
1431143THR0-0.027-0.02526.744-0.018-0.0180.0000.0000.0000.000
1441144SER0-0.006-0.01524.9420.0240.0240.0000.0000.0000.000
1451145TRP0-0.027-0.02921.292-0.019-0.0190.0000.0000.0000.000
1461146HIS0-0.034-0.01825.058-0.002-0.0020.0000.0000.0000.000
1471147LEU0-0.0110.00024.415-0.006-0.0060.0000.0000.0000.000
1481148SER00.0160.01127.708-0.001-0.0010.0000.0000.0000.000
1491149PHE00.005-0.00327.437-0.007-0.0070.0000.0000.0000.000
1501150LEU0-0.0060.01433.2650.0030.0030.0000.0000.0000.000
1511151VAL0-0.020-0.02835.282-0.005-0.0050.0000.0000.0000.000
1521152ASP-1-0.790-0.89537.7940.0030.0030.0000.0000.0000.000
1531153ASN00.0010.01040.933-0.003-0.0030.0000.0000.0000.000
1541154PRO00.000-0.01339.609-0.004-0.0040.0000.0000.0000.000
1551155LYS10.8730.92840.205-0.001-0.0010.0000.0000.0000.000
1561156GLN00.0060.02040.698-0.004-0.0040.0000.0000.0000.000
1571157SER00.024-0.00935.816-0.006-0.0060.0000.0000.0000.000
1581158THR0-0.040-0.03136.3230.0040.0040.0000.0000.0000.000
1591159THR00.000-0.00631.7360.0070.0070.0000.0000.0000.000
1601160PHE0-0.007-0.00229.473-0.006-0.0060.0000.0000.0000.000
1611161ASP-1-0.837-0.87925.481-0.019-0.0190.0000.0000.0000.000
1621162VAL00.006-0.00222.274-0.008-0.0080.0000.0000.0000.000
1631163LEU0-0.019-0.01718.9880.0040.0040.0000.0000.0000.000
1641164LEU00.0240.00416.7080.0060.0060.0000.0000.0000.000
1651165GLY00.0030.00013.354-0.042-0.0420.0000.0000.0000.000
1661166ILE00.0000.0088.9770.0270.0270.0000.0000.0000.000
1671167SER0-0.007-0.0188.375-0.122-0.1220.0000.0000.0000.000
1681168GLN0-0.016-0.0422.224-5.924-6.5155.354-1.854-2.9090.006
1691169ASN00.0090.0075.6700.7800.846-0.0010.000-0.0650.000
1701170PHE0-0.0260.0098.466-0.218-0.2180.0000.0000.0000.000
1711171GLU-1-0.823-0.8979.6751.1901.1900.0000.0000.0000.000
1721172ILE0-0.011-0.02211.927-0.165-0.1650.0000.0000.0000.000
1731173ALA00.0080.00014.4910.0570.0570.0000.0000.0000.000
1741174GLY00.0110.00617.138-0.051-0.0510.0000.0000.0000.000
1751175ASN0-0.019-0.01419.4140.0340.0340.0000.0000.0000.000
1761176THR00.0120.00621.623-0.015-0.0150.0000.0000.0000.000
1771177LEU0-0.033-0.01824.3850.0000.0000.0000.0000.0000.000
1781178MET00.0230.01624.995-0.013-0.0130.0000.0000.0000.000
1791179PRO00.0010.00527.652-0.001-0.0010.0000.0000.0000.000
1801180ALA0-0.004-0.01128.4800.0070.0070.0000.0000.0000.000
1811181PHE0-0.0020.00222.437-0.008-0.0080.0000.0000.0000.000
1821182SER00.001-0.00328.051-0.004-0.0040.0000.0000.0000.000
1831183VAL00.0010.00027.618-0.001-0.0010.0000.0000.0000.000
1841184PRO00.0140.00729.376-0.004-0.0040.0000.0000.0000.000
1851185GLN0-0.0030.00831.968-0.001-0.0010.0000.0000.0000.000