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: QY58Y

Calculation Name: 1JRH-H-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1JRH

Chain ID: H

ChEMBL ID:

UniProt ID: P01869

Base Structure: X-ray

Registration Date: 2023-06-26

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 182
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -1730299.778723
FMO2-HF: Nuclear repulsion 1659718.947583
FMO2-HF: Total energy -70580.831141
FMO2-MP2: Total energy -70786.267845


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(H:1:ALA)


Summations of interaction energy for fragment #1(H:1:ALA)
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.
-0.7951.420.034-0.832-1.4170.003
Interaction energy analysis for fragmet #1(H:1:ALA)
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].
3H3LYS10.9500.9903.8650.5731.873-0.008-0.517-0.7750.002
4H4LEU00.014-0.0105.9210.2480.2480.0000.0000.0000.000
5H5GLN0-0.036-0.0189.644-0.100-0.1000.0000.0000.0000.000
6H6GLU-1-0.743-0.85911.891-0.274-0.2740.0000.0000.0000.000
7H7SER0-0.064-0.03715.693-0.022-0.0220.0000.0000.0000.000
8H8GLY00.0430.00918.3090.0190.0190.0000.0000.0000.000
9H9PRO0-0.0070.00522.131-0.009-0.0090.0000.0000.0000.000
10H10GLY00.0460.04924.5390.0030.0030.0000.0000.0000.000
11H11ILE0-0.048-0.04125.6260.0060.0060.0000.0000.0000.000
12H12LEU0-0.036-0.00229.125-0.001-0.0010.0000.0000.0000.000
13H13LYS10.8760.93631.4460.0630.0630.0000.0000.0000.000
14H14PRO00.040-0.00434.8120.0000.0000.0000.0000.0000.000
15H15SER0-0.014-0.00737.0450.0000.0000.0000.0000.0000.000
16H16GLN00.0100.02633.402-0.001-0.0010.0000.0000.0000.000
17H17THR0-0.004-0.01230.0670.0040.0040.0000.0000.0000.000
18H18LEU00.0130.01825.572-0.004-0.0040.0000.0000.0000.000
19H19SER0-0.042-0.02724.8760.0100.0100.0000.0000.0000.000
20H20LEU0-0.0030.01020.877-0.009-0.0090.0000.0000.0000.000
21H21THR0-0.013-0.00916.5670.0220.0220.0000.0000.0000.000
22H22CYS0-0.057-0.02414.400-0.017-0.0170.0000.0000.0000.000
23H23SER00.0440.03112.0500.0680.0680.0000.0000.0000.000
24H24PHE0-0.044-0.0158.885-0.093-0.0930.0000.0000.0000.000
25H25SER00.007-0.0033.9210.0490.252-0.001-0.046-0.1560.000
26H26GLY00.0340.0133.609-0.801-0.3610.041-0.221-0.2600.001
27H27PHE0-0.004-0.0134.146-0.0210.2510.002-0.048-0.2260.000
28H28SER00.0750.0437.976-0.271-0.2710.0000.0000.0000.000
29H29LEU00.0030.01011.1640.0220.0220.0000.0000.0000.000
30H30THR00.027-0.00414.399-0.031-0.0310.0000.0000.0000.000
31H31THR0-0.045-0.02113.1590.0220.0220.0000.0000.0000.000
32H32TYR00.0360.01215.776-0.026-0.0260.0000.0000.0000.000
33H33GLY00.0210.01717.8070.0330.0330.0000.0000.0000.000
34H34MET0-0.027-0.00611.441-0.029-0.0290.0000.0000.0000.000
35H35GLY00.0490.01015.631-0.026-0.0260.0000.0000.0000.000
36H35VAL0-0.057-0.02013.7410.0050.0050.0000.0000.0000.000
37H35GLY00.0520.03616.5140.0090.0090.0000.0000.0000.000
38H36TRP0-0.049-0.02418.028-0.034-0.0340.0000.0000.0000.000
39H37ILE0-0.007-0.00718.2450.0180.0180.0000.0000.0000.000
40H38ARG10.8080.89321.5630.0400.0400.0000.0000.0000.000
41H39GLN00.0480.02322.3240.0160.0160.0000.0000.0000.000
42H40SER0-0.008-0.01425.232-0.007-0.0070.0000.0000.0000.000
43H41SER00.008-0.01428.065-0.001-0.0010.0000.0000.0000.000
44H42GLY00.0040.00928.7970.0050.0050.0000.0000.0000.000
45H43LYS10.9150.96528.9210.0550.0550.0000.0000.0000.000
46H44GLY00.0540.03226.941-0.005-0.0050.0000.0000.0000.000
47H45LEU0-0.019-0.00921.434-0.002-0.0020.0000.0000.0000.000
48H46GLU-1-0.836-0.89225.113-0.037-0.0370.0000.0000.0000.000
49H47TRP00.007-0.00122.516-0.007-0.0070.0000.0000.0000.000
50H48LEU0-0.013-0.00624.1750.0040.0040.0000.0000.0000.000
51H49ALA00.019-0.00523.8130.0070.0070.0000.0000.0000.000
52H50HIS0-0.0080.00018.462-0.027-0.0270.0000.0000.0000.000
53H51ILE0-0.0380.00119.1670.0000.0000.0000.0000.0000.000
54H52TRP00.0540.02818.8890.0140.0140.0000.0000.0000.000
55H53TRP00.0410.01418.069-0.005-0.0050.0000.0000.0000.000
56H54ASP-1-0.893-0.95119.2820.0970.0970.0000.0000.0000.000
57H55ASP-1-0.813-0.87622.3930.0250.0250.0000.0000.0000.000
58H56ASP-1-0.804-0.87123.6180.0390.0390.0000.0000.0000.000
59H57LYS10.7610.84623.983-0.025-0.0250.0000.0000.0000.000
60H58TYR0-0.072-0.03025.081-0.001-0.0010.0000.0000.0000.000
61H59TYR00.0380.00025.969-0.008-0.0080.0000.0000.0000.000
62H60ASN00.0060.00028.2900.0090.0090.0000.0000.0000.000
63H61PRO00.004-0.01629.948-0.002-0.0020.0000.0000.0000.000
64H62SER00.0040.00733.5590.0010.0010.0000.0000.0000.000
65H63LEU0-0.0010.00130.353-0.002-0.0020.0000.0000.0000.000
66H64LYS10.9590.98831.571-0.006-0.0060.0000.0000.0000.000
67H65SER0-0.008-0.00332.628-0.001-0.0010.0000.0000.0000.000
68H66ARG10.7740.86732.5480.0420.0420.0000.0000.0000.000
69H67LEU0-0.0210.00227.294-0.006-0.0060.0000.0000.0000.000
70H68THR0-0.020-0.01727.1200.0070.0070.0000.0000.0000.000
71H69ILE0-0.0110.00620.630-0.012-0.0120.0000.0000.0000.000
72H70SER0-0.011-0.00922.3620.0080.0080.0000.0000.0000.000
73H71LYS10.8070.88517.515-0.098-0.0980.0000.0000.0000.000
74H72ASP-1-0.758-0.83317.539-0.012-0.0120.0000.0000.0000.000
75H73THR00.0340.00214.397-0.031-0.0310.0000.0000.0000.000
76H74SER0-0.080-0.04914.5620.0070.0070.0000.0000.0000.000
77H75ARG10.8410.89914.7080.0680.0680.0000.0000.0000.000
78H76ASN0-0.024-0.0029.931-0.004-0.0040.0000.0000.0000.000
79H77GLN0-0.008-0.00812.213-0.059-0.0590.0000.0000.0000.000
80H78VAL00.0250.01114.9710.0490.0490.0000.0000.0000.000
81H79PHE0-0.029-0.02317.387-0.035-0.0350.0000.0000.0000.000
82H80LEU0-0.0040.00020.6630.0180.0180.0000.0000.0000.000
83H81LYS10.9110.94523.5380.0580.0580.0000.0000.0000.000
84H82ILE00.0290.01226.1660.0060.0060.0000.0000.0000.000
85H82THR00.0440.01829.591-0.004-0.0040.0000.0000.0000.000
86H82SER00.0240.00833.1890.0000.0000.0000.0000.0000.000
87H82VAL0-0.043-0.00631.3100.0010.0010.0000.0000.0000.000
88H83ALA00.0630.02533.9830.0030.0030.0000.0000.0000.000
89H84THR00.0520.01733.856-0.003-0.0030.0000.0000.0000.000
90H85ALA00.0180.01433.621-0.004-0.0040.0000.0000.0000.000
91H86ASP-1-0.774-0.84830.068-0.052-0.0520.0000.0000.0000.000
92H87THR0-0.0010.00928.848-0.009-0.0090.0000.0000.0000.000
93H88ALA0-0.036-0.00225.9680.0050.0050.0000.0000.0000.000
94H89THR00.0040.00920.229-0.010-0.0100.0000.0000.0000.000
95H90TYR0-0.048-0.04621.4030.0150.0150.0000.0000.0000.000
96H91TYR00.0310.00616.555-0.014-0.0140.0000.0000.0000.000
97H93ALA00.0410.01413.611-0.049-0.0490.0000.0000.0000.000
98H94ARG10.8100.8837.848-0.432-0.4320.0000.0000.0000.000
99H95ARG10.8380.92313.717-0.182-0.1820.0000.0000.0000.000
100H96ALA00.0130.00113.3600.0470.0470.0000.0000.0000.000
101H97PRO0-0.042-0.00310.869-0.015-0.0150.0000.0000.0000.000
102H98PHE0-0.019-0.02412.5700.0390.0390.0000.0000.0000.000
103H99TYR00.0600.01917.188-0.030-0.0300.0000.0000.0000.000
104H100GLY00.0000.01120.925-0.003-0.0030.0000.0000.0000.000
105H100ASN0-0.010-0.01317.512-0.037-0.0370.0000.0000.0000.000
106H100HIS00.0480.01119.4610.0180.0180.0000.0000.0000.000
107H100ALA00.0040.01918.185-0.018-0.0180.0000.0000.0000.000
108H100MET00.0010.00315.6780.0140.0140.0000.0000.0000.000
109H101ASP-1-0.736-0.84411.0810.1900.1900.0000.0000.0000.000
110H102TYR0-0.029-0.0125.8880.0520.0520.0000.0000.0000.000
111H103TRP00.016-0.01910.7250.0370.0370.0000.0000.0000.000
112H104GLY00.0120.01710.449-0.107-0.1070.0000.0000.0000.000
113H105GLN0-0.034-0.01712.097-0.005-0.0050.0000.0000.0000.000
114H106GLY00.008-0.00113.8350.0420.0420.0000.0000.0000.000
115H107THR0-0.079-0.04517.152-0.009-0.0090.0000.0000.0000.000
116H108THR00.0150.01219.7040.0150.0150.0000.0000.0000.000
117H109VAL0-0.054-0.02723.266-0.004-0.0040.0000.0000.0000.000
118H110THR0-0.002-0.00526.2000.0080.0080.0000.0000.0000.000
119H111VAL0-0.024-0.01329.8260.0000.0000.0000.0000.0000.000
120H112SER0-0.025-0.03432.6550.0030.0030.0000.0000.0000.000
121H113SER00.016-0.01735.773-0.001-0.0010.0000.0000.0000.000
122H114ALA0-0.0090.02537.1820.0020.0020.0000.0000.0000.000
123H115LYS10.9540.96437.4910.0500.0500.0000.0000.0000.000
124H116THR0-0.0050.00034.4170.0010.0010.0000.0000.0000.000
125H117THR0-0.034-0.00736.6570.0040.0040.0000.0000.0000.000
126H118PRO00.0240.01438.104-0.002-0.0020.0000.0000.0000.000
127H142CYS0-0.044-0.01240.3490.0010.0010.0000.0000.0000.000
128H143LEU0-0.038-0.02542.215-0.001-0.0010.0000.0000.0000.000
129H144VAL0-0.017-0.00638.1100.0010.0010.0000.0000.0000.000
130H145LYS10.9470.95940.3890.0450.0450.0000.0000.0000.000
131H146GLY00.0130.00941.713-0.001-0.0010.0000.0000.0000.000
132H147TYR0-0.044-0.03334.0580.0020.0020.0000.0000.0000.000
133H148PHE00.0340.01133.851-0.001-0.0010.0000.0000.0000.000
134H149PRO0-0.0040.00931.0150.0020.0020.0000.0000.0000.000
135H150GLU-1-0.748-0.87529.737-0.084-0.0840.0000.0000.0000.000
136H151PRO0-0.049-0.03926.920-0.004-0.0040.0000.0000.0000.000
137H152VAL00.0180.03629.7220.0040.0040.0000.0000.0000.000
138H153THR0-0.036-0.02030.406-0.007-0.0070.0000.0000.0000.000
139H154VAL00.002-0.00232.6080.0030.0030.0000.0000.0000.000
140H156THR00.0320.03833.0860.0020.0020.0000.0000.0000.000
141H157TRP00.0730.00535.7340.0040.0040.0000.0000.0000.000
142H161ASN00.0230.00239.066-0.001-0.0010.0000.0000.0000.000
143H162SER00.013-0.01036.8140.0000.0000.0000.0000.0000.000
144H163GLY00.0130.01435.419-0.004-0.0040.0000.0000.0000.000
145H164SER0-0.068-0.03036.1890.0010.0010.0000.0000.0000.000
146H165LEU00.0110.01138.1920.0030.0030.0000.0000.0000.000
147H166SER0-0.0120.01634.019-0.002-0.0020.0000.0000.0000.000
148H167SER0-0.006-0.00735.9870.0000.0000.0000.0000.0000.000
149H168GLY00.0660.02237.7520.0000.0000.0000.0000.0000.000
150H171VAL0-0.056-0.02336.3320.0020.0020.0000.0000.0000.000
151H172HIS0-0.044-0.02036.866-0.001-0.0010.0000.0000.0000.000
152H173THR0-0.059-0.03434.0240.0010.0010.0000.0000.0000.000
153H174PHE00.0090.00534.641-0.002-0.0020.0000.0000.0000.000
154H175PRO00.006-0.00132.404-0.003-0.0030.0000.0000.0000.000
155H176ALA0-0.0010.00133.4620.0040.0040.0000.0000.0000.000
156H177VAL0-0.024-0.01234.9050.0000.0000.0000.0000.0000.000
157H178LEU0-0.045-0.01735.999-0.001-0.0010.0000.0000.0000.000
158H179GLN00.0600.04238.5810.0030.0030.0000.0000.0000.000
159H180SER00.001-0.03341.3280.0000.0000.0000.0000.0000.000
160H183ASP-1-0.823-0.89339.022-0.054-0.0540.0000.0000.0000.000
161H184LEU0-0.038-0.00438.602-0.004-0.0040.0000.0000.0000.000
162H185TYR00.0250.01731.7250.0020.0020.0000.0000.0000.000
163H186THR0-0.042-0.02937.6580.0030.0030.0000.0000.0000.000
164H187LEU00.0200.03034.5190.0000.0000.0000.0000.0000.000
165H188SER00.014-0.00238.5750.0030.0030.0000.0000.0000.000
166H189SER00.0250.01537.567-0.002-0.0020.0000.0000.0000.000
167H190SER00.0580.03339.4890.0020.0020.0000.0000.0000.000
168H191VAL00.0180.01240.400-0.002-0.0020.0000.0000.0000.000
169H192THR00.0020.01142.3880.0020.0020.0000.0000.0000.000
170H209ASN0-0.017-0.02137.3820.0020.0020.0000.0000.0000.000
171H210VAL00.0020.00836.844-0.004-0.0040.0000.0000.0000.000
172H211ALA00.005-0.00133.4740.0010.0010.0000.0000.0000.000
173H212HIS10.8290.88033.5330.0800.0800.0000.0000.0000.000
174H213PRO00.0610.02829.1990.0030.0030.0000.0000.0000.000
175H214ALA00.0140.01530.9240.0000.0000.0000.0000.0000.000
176H215SER00.009-0.00731.8480.0020.0020.0000.0000.0000.000
177H216SER0-0.009-0.01033.7860.0030.0030.0000.0000.0000.000
178H217THR0-0.0230.02034.8850.0030.0030.0000.0000.0000.000
179H218LYS10.8930.92236.1000.0700.0700.0000.0000.0000.000
180H219VAL00.0100.00038.1860.0030.0030.0000.0000.0000.000
181H220ASP-1-0.780-0.84839.377-0.069-0.0690.0000.0000.0000.000
182H221LYS10.9350.97041.6030.0520.0520.0000.0000.0000.000