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: 2J56R

Calculation Name: 5IFH-H-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 5IFH

Chain ID: H

ChEMBL ID:

UniProt ID:

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 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 176
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -1658470.247344
FMO2-HF: Nuclear repulsion 1590292.145943
FMO2-HF: Total energy -68178.101401
FMO2-MP2: Total energy -68374.968563


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:2:VAL)


Summations of interaction energy for fragment #1(H:2:VAL)
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.
-8.279-4.98614.324-6.057-11.558-0.034
Interaction energy analysis for fragmet #1(H:2:VAL)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.070 / q_NPA : -0.038
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].
3H4LEU0-0.001-0.0113.809-0.8101.692-0.039-1.283-1.1800.001
4H5VAL00.0290.0166.563-0.140-0.1400.0000.0000.0000.000
5H6GLU-1-0.764-0.86510.183-0.114-0.1140.0000.0000.0000.000
6H7SER0-0.037-0.02113.1540.0190.0190.0000.0000.0000.000
7H8GLY00.0330.00516.733-0.003-0.0030.0000.0000.0000.000
8H9GLY0-0.0030.01519.533-0.008-0.0080.0000.0000.0000.000
9H10GLY00.0350.00521.1780.0080.0080.0000.0000.0000.000
10H11LEU0-0.052-0.01324.659-0.009-0.0090.0000.0000.0000.000
11H12VAL0-0.005-0.00526.9860.0080.0080.0000.0000.0000.000
12H13LYS10.8730.94229.817-0.018-0.0180.0000.0000.0000.000
13H14PRO00.0400.00632.4190.0020.0020.0000.0000.0000.000
14H15GLY0-0.039-0.01332.9900.0020.0020.0000.0000.0000.000
15H16GLY0-0.0240.00231.8520.0040.0040.0000.0000.0000.000
16H17SER0-0.028-0.05328.451-0.005-0.0050.0000.0000.0000.000
17H18LEU0-0.025-0.01323.2150.0020.0020.0000.0000.0000.000
18H19ARG10.8820.96520.426-0.134-0.1340.0000.0000.0000.000
19H20LEU00.0080.02017.5660.0070.0070.0000.0000.0000.000
20H21SER0-0.014-0.01815.8140.0190.0190.0000.0000.0000.000
21H22CYS0-0.059-0.02810.0920.0350.0350.0000.0000.0000.000
22H23ALA0-0.0090.00610.1770.0430.0430.0000.0000.0000.000
23H24ALA00.0240.0086.200-0.071-0.0710.0000.0000.0000.000
24H25SER0-0.026-0.0174.3990.0710.272-0.001-0.076-0.1230.000
25H26GLY00.0900.0382.1520.4080.0038.263-4.815-3.043-0.018
26H27PHE0-0.018-0.0132.305-4.493-4.6674.2390.792-4.856-0.015
27H28THR00.003-0.0013.932-0.1070.0280.005-0.051-0.0900.000
28H29PHE00.0800.0377.517-0.169-0.1690.0000.0000.0000.000
29H30ARG10.9720.9778.397-0.398-0.3980.0000.0000.0000.000
30H31SER0-0.051-0.0299.356-0.048-0.0480.0000.0000.0000.000
31H32TYR00.0350.0326.448-0.006-0.0060.0000.0000.0000.000
32H33SER0-0.014-0.0099.6400.0670.0670.0000.0000.0000.000
33H34MET0-0.040-0.0047.8890.0010.0010.0000.0000.0000.000
34H35ASN0-0.026-0.01411.2110.0380.0380.0000.0000.0000.000
35H36TRP00.0190.00412.690-0.012-0.0120.0000.0000.0000.000
36H37VAL0-0.0030.00114.4610.0060.0060.0000.0000.0000.000
37H38ARG10.7940.87916.1440.0560.0560.0000.0000.0000.000
38H39GLN00.0370.01618.816-0.029-0.0290.0000.0000.0000.000
39H40ALA00.0370.03320.8280.0060.0060.0000.0000.0000.000
40H41PRO00.0560.00924.181-0.012-0.0120.0000.0000.0000.000
41H42GLY00.0230.01824.8080.0070.0070.0000.0000.0000.000
42H43LYS10.8380.92324.9880.0950.0950.0000.0000.0000.000
43H44GLY00.0480.02522.756-0.013-0.0130.0000.0000.0000.000
44H45LEU0-0.009-0.00316.2510.0110.0110.0000.0000.0000.000
45H46GLU-1-0.802-0.87619.881-0.068-0.0680.0000.0000.0000.000
46H47TRP0-0.014-0.01616.8560.0020.0020.0000.0000.0000.000
47H48VAL0-0.0120.00018.5090.0150.0150.0000.0000.0000.000
48H49SER0-0.009-0.03318.3290.0200.0200.0000.0000.0000.000
49H50SER00.009-0.00215.741-0.017-0.0170.0000.0000.0000.000
50H51ILE0-0.035-0.00714.5960.0150.0150.0000.0000.0000.000
51H52ILE00.0200.01214.599-0.001-0.0010.0000.0000.0000.000
52H53SER00.0270.01912.7050.0250.0250.0000.0000.0000.000
53H54SER0-0.051-0.01714.739-0.021-0.0210.0000.0000.0000.000
54H55SER0-0.003-0.01717.4680.0080.0080.0000.0000.0000.000
55H56SER0-0.053-0.01818.2280.0100.0100.0000.0000.0000.000
56H57TYR00.0360.02219.154-0.001-0.0010.0000.0000.0000.000
57H58ILE00.000-0.01019.593-0.002-0.0020.0000.0000.0000.000
58H59TYR00.0010.00919.844-0.005-0.0050.0000.0000.0000.000
59H60TYR00.0140.00121.2810.0050.0050.0000.0000.0000.000
60H61ALA00.0750.04923.181-0.003-0.0030.0000.0000.0000.000
61H62ASP-1-0.854-0.93824.756-0.030-0.0300.0000.0000.0000.000
62H63SER0-0.048-0.00426.2280.0070.0070.0000.0000.0000.000
63H64VAL0-0.007-0.01723.3360.0040.0040.0000.0000.0000.000
64H65LYS10.8980.94726.7720.0350.0350.0000.0000.0000.000
65H66GLY00.0080.00728.160-0.001-0.0010.0000.0000.0000.000
66H67ARG10.7020.82727.9750.0150.0150.0000.0000.0000.000
67H68PHE00.015-0.00722.3550.0080.0080.0000.0000.0000.000
68H69THR0-0.035-0.01723.1700.0010.0010.0000.0000.0000.000
69H70ILE00.0110.03115.7580.0110.0110.0000.0000.0000.000
70H71SER0-0.019-0.02117.9680.0090.0090.0000.0000.0000.000
71H72ARG10.8530.93011.002-0.200-0.2000.0000.0000.0000.000
72H73ASP-1-0.797-0.88514.9320.3170.3170.0000.0000.0000.000
73H74ASN0-0.023-0.04313.3140.0710.0710.0000.0000.0000.000
74H75ALA00.0070.02413.4640.0620.0620.0000.0000.0000.000
75H76LYS10.8470.91414.027-0.307-0.3070.0000.0000.0000.000
76H77ASN0-0.036-0.0048.761-0.062-0.0620.0000.0000.0000.000
77H78SER00.0600.04410.1150.0310.0310.0000.0000.0000.000
78H79LEU00.005-0.00111.628-0.032-0.0320.0000.0000.0000.000
79H80TYR0-0.029-0.04313.670-0.012-0.0120.0000.0000.0000.000
80H81LEU00.029-0.00117.193-0.018-0.0180.0000.0000.0000.000
81H82GLN0-0.022-0.00519.4000.0110.0110.0000.0000.0000.000
82H83MET0-0.0170.00422.317-0.014-0.0140.0000.0000.0000.000
83H84ASN00.0740.04424.9720.0080.0080.0000.0000.0000.000
84H85SER00.0420.01628.771-0.005-0.0050.0000.0000.0000.000
85H86LEU0-0.0160.02125.880-0.007-0.0070.0000.0000.0000.000
86H87ARG10.9490.97029.7310.0220.0220.0000.0000.0000.000
87H88ALA00.0580.02329.920-0.001-0.0010.0000.0000.0000.000
88H89GLU-1-0.860-0.94729.750-0.031-0.0310.0000.0000.0000.000
89H90ASP-1-0.762-0.84225.748-0.029-0.0290.0000.0000.0000.000
90H91THR0-0.0010.02124.7720.0010.0010.0000.0000.0000.000
91H92ALA0-0.020-0.01321.743-0.009-0.0090.0000.0000.0000.000
92H93LEU0-0.0240.00716.8570.0210.0210.0000.0000.0000.000
93H94TYR0-0.044-0.05017.064-0.016-0.0160.0000.0000.0000.000
94H95TYR00.013-0.01012.2790.0060.0060.0000.0000.0000.000
95H97ALA00.0600.0218.222-0.106-0.1060.0000.0000.0000.000
96H98ARG10.7740.8563.274-0.1560.6970.165-0.248-0.770-0.001
97H99ASP-1-0.860-0.9227.950-0.372-0.3720.0000.0000.0000.000
98H100GLN00.0360.0259.8220.0350.0350.0000.0000.0000.000
99H101ASN0-0.043-0.01612.886-0.026-0.0260.0000.0000.0000.000
100H102ALA00.006-0.01112.3850.0060.0060.0000.0000.0000.000
101H103MET0-0.0120.00810.029-0.011-0.0110.0000.0000.0000.000
102H104ASP-1-0.747-0.8415.160-1.200-1.126-0.0010.000-0.0720.000
103H105VAL0-0.034-0.0122.387-0.765-0.6581.693-0.376-1.424-0.001
104H106TRP0-0.007-0.0275.4580.3720.3720.0000.0000.0000.000
105H107GLY00.0340.0286.962-0.263-0.2630.0000.0000.0000.000
106H108GLN0-0.058-0.0428.8260.0210.0210.0000.0000.0000.000
107H109GLY00.0180.01811.9840.0390.0390.0000.0000.0000.000
108H110THR0-0.051-0.02713.9500.0340.0340.0000.0000.0000.000
109H111THR00.0250.00017.162-0.013-0.0130.0000.0000.0000.000
110H112VAL0-0.0170.00120.7150.0200.0200.0000.0000.0000.000
111H113THR0-0.032-0.02423.271-0.012-0.0120.0000.0000.0000.000
112H114VAL0-0.006-0.00126.9000.0090.0090.0000.0000.0000.000
113H115SER00.014-0.01429.618-0.005-0.0050.0000.0000.0000.000
114H116SER00.0400.00732.9470.0050.0050.0000.0000.0000.000
115H117ASP-1-0.871-0.89735.015-0.006-0.0060.0000.0000.0000.000
116H118SER0-0.031-0.03534.7910.0020.0020.0000.0000.0000.000
117H119ALA00.0250.01931.849-0.003-0.0030.0000.0000.0000.000
118H120SER0-0.034-0.02633.2300.0010.0010.0000.0000.0000.000
119H121ALA0-0.001-0.00132.819-0.002-0.0020.0000.0000.0000.000
120H122PRO00.0090.01831.569-0.002-0.0020.0000.0000.0000.000
121H123THR0-0.010-0.00334.5770.0060.0060.0000.0000.0000.000
122H124LEU0-0.006-0.01533.533-0.003-0.0030.0000.0000.0000.000
123H125PHE0-0.025-0.01737.7230.0030.0030.0000.0000.0000.000
124H126PRO00.0050.01039.472-0.003-0.0030.0000.0000.0000.000
125H127LEU0-0.0120.00138.9060.0000.0000.0000.0000.0000.000
126H128VAL00.013-0.00841.4510.0000.0000.0000.0000.0000.000
127H129SER00.0260.02743.694-0.001-0.0010.0000.0000.0000.000
128H142VAL0-0.025-0.01737.4290.0000.0000.0000.0000.0000.000
129H143GLY00.0470.01436.964-0.004-0.0040.0000.0000.0000.000
130H144CYS0-0.060-0.02232.7520.0030.0030.0000.0000.0000.000
131H145LEU00.0200.02135.548-0.004-0.0040.0000.0000.0000.000
132H146ALA00.0320.02533.5270.0050.0050.0000.0000.0000.000
133H147GLN00.0140.00435.566-0.007-0.0070.0000.0000.0000.000
134H148ASP-1-0.822-0.93236.621-0.003-0.0030.0000.0000.0000.000
135H149PHE0-0.0340.01729.9170.0060.0060.0000.0000.0000.000
136H150LEU0-0.0270.00131.217-0.006-0.0060.0000.0000.0000.000
137H151PRO00.0630.00926.6750.0070.0070.0000.0000.0000.000
138H152ASP-1-0.792-0.88627.579-0.043-0.0430.0000.0000.0000.000
139H153SER0-0.066-0.03823.586-0.007-0.0070.0000.0000.0000.000
140H154ILE00.0020.01125.1880.0120.0120.0000.0000.0000.000
141H155THR0-0.0130.01122.318-0.015-0.0150.0000.0000.0000.000
142H156PHE00.022-0.00625.3700.0110.0110.0000.0000.0000.000
143H157SER0-0.035-0.00625.552-0.001-0.0010.0000.0000.0000.000
144H158TRP00.0580.01127.3150.0050.0050.0000.0000.0000.000
145H171GLY0-0.016-0.02227.9010.0030.0030.0000.0000.0000.000
146H172PHE0-0.019-0.00428.936-0.007-0.0070.0000.0000.0000.000
147H173PRO0-0.0110.00328.5020.0030.0030.0000.0000.0000.000
148H174SER0-0.032-0.04429.0190.0060.0060.0000.0000.0000.000
149H175VAL0-0.037-0.00831.163-0.004-0.0040.0000.0000.0000.000
150H176LEU0-0.021-0.00833.6280.0040.0040.0000.0000.0000.000
151H177ARG10.8970.92635.4740.0190.0190.0000.0000.0000.000
152H178GLY00.0380.02238.9880.0020.0020.0000.0000.0000.000
153H179GLY00.0230.01537.0370.0030.0030.0000.0000.0000.000
154H180LYS10.8320.91535.0540.0010.0010.0000.0000.0000.000
155H181TYR00.0510.02330.250-0.001-0.0010.0000.0000.0000.000
156H182ALA0-0.044-0.01633.9020.0050.0050.0000.0000.0000.000
157H183ALA00.0290.01331.128-0.006-0.0060.0000.0000.0000.000
158H184THR00.0230.00433.1340.0070.0070.0000.0000.0000.000
159H185SER0-0.0090.01330.268-0.004-0.0040.0000.0000.0000.000
160H186GLN00.027-0.01132.3860.0010.0010.0000.0000.0000.000
161H187VAL0-0.0070.02131.546-0.004-0.0040.0000.0000.0000.000
162H203VAL0-0.043-0.03033.4040.0000.0000.0000.0000.0000.000
163H205LYS10.8800.92229.569-0.039-0.0390.0000.0000.0000.000
164H206VAL00.0210.02328.475-0.006-0.0060.0000.0000.0000.000
165H207GLN0-0.035-0.04623.7720.0020.0020.0000.0000.0000.000
166H208HIS00.0410.00526.272-0.004-0.0040.0000.0000.0000.000
167H209PRO00.0200.01924.8210.0090.0090.0000.0000.0000.000
168H210ASN0-0.018-0.01326.5880.0040.0040.0000.0000.0000.000
169H211GLY0-0.017-0.01629.6640.0020.0020.0000.0000.0000.000
170H212ASN0-0.035-0.00326.116-0.002-0.0020.0000.0000.0000.000
171H213LYS10.9530.98730.213-0.027-0.0270.0000.0000.0000.000
172H214GLU-1-0.838-0.90032.0700.0380.0380.0000.0000.0000.000
173H215LYS10.9170.95734.212-0.009-0.0090.0000.0000.0000.000
174H216ASN00.0000.00336.584-0.001-0.0010.0000.0000.0000.000
175H217VAL00.0140.00537.316-0.001-0.0010.0000.0000.0000.000
176H218PRO00.0120.02640.0360.0000.0000.0000.0000.0000.000