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: 4JK3N

Calculation Name: 1KA9-H-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1KA9

Chain ID: H

ChEMBL ID:

UniProt ID: Q7SIC0

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 195
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2152197.225346
FMO2-HF: Nuclear repulsion 2078589.058787
FMO2-HF: Total energy -73608.166559
FMO2-MP2: Total energy -73825.347506


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:3:MET)


Summations of interaction energy for fragment #1(H:3:MET)
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.
-21.068-9.6498.759-6.592-13.583-0.015
Interaction energy analysis for fragmet #1(H:3:MET)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.026 / q_NPA : 0.021
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].
3H5ALA0-0.005-0.0053.646-1.5471.020-0.013-1.249-1.3050.005
4H6LEU0-0.032-0.0115.6580.1410.1410.0000.0000.0000.000
5H7LEU0-0.074-0.0469.0330.2330.2330.0000.0000.0000.000
6H8ILE00.003-0.01811.594-0.030-0.0300.0000.0000.0000.000
7H9ASP-1-0.896-0.94114.373-0.229-0.2290.0000.0000.0000.000
8H10TYR0-0.022-0.05117.742-0.008-0.0080.0000.0000.0000.000
9H11GLY00.0540.03220.6230.0160.0160.0000.0000.0000.000
10H12SER0-0.045-0.01221.3140.0310.0310.0000.0000.0000.000
11H13GLY00.0700.02418.440-0.020-0.0200.0000.0000.0000.000
12H14ASN0-0.068-0.04318.0000.0250.0250.0000.0000.0000.000
13H15LEU00.0500.01715.9600.0190.0190.0000.0000.0000.000
14H16ARG11.0011.02315.5480.1470.1470.0000.0000.0000.000
15H17SER00.0360.00716.097-0.025-0.0250.0000.0000.0000.000
16H18ALA00.0460.02813.3970.0380.0380.0000.0000.0000.000
17H19ALA00.0340.02411.6900.0470.0470.0000.0000.0000.000
18H20LYS10.7880.85611.4030.3920.3920.0000.0000.0000.000
19H21ALA0-0.0020.00112.5190.0270.0270.0000.0000.0000.000
20H22LEU00.000-0.0047.0040.1720.1720.0000.0000.0000.000
21H23GLU-1-0.777-0.8707.712-0.425-0.4250.0000.0000.0000.000
22H24ALA0-0.052-0.0208.9840.0530.0530.0000.0000.0000.000
23H25ALA0-0.025-0.0078.1230.0600.0600.0000.0000.0000.000
24H26GLY0-0.015-0.0135.8670.5770.5770.0000.0000.0000.000
25H27PHE0-0.028-0.0072.286-2.628-1.5872.618-0.970-2.6890.008
26H28SER00.0340.0333.8460.4190.870-0.001-0.125-0.3250.000
27H29VAL0-0.019-0.0225.514-0.522-0.5220.0000.0000.0000.000
28H30ALA0-0.022-0.0038.4160.0370.0370.0000.0000.0000.000
29H31VAL0-0.0020.02311.1170.0340.0340.0000.0000.0000.000
30H32ALA00.024-0.01313.899-0.082-0.0820.0000.0000.0000.000
31H33GLN0-0.023-0.01415.9690.0290.0290.0000.0000.0000.000
32H34ASP-1-0.835-0.90817.942-0.443-0.4430.0000.0000.0000.000
33H35PRO0-0.019-0.00816.946-0.088-0.0880.0000.0000.0000.000
34H36LYS10.8130.89016.2020.5700.5700.0000.0000.0000.000
35H37ALA00.0130.02015.501-0.045-0.0450.0000.0000.0000.000
36H38HIS0-0.029-0.03510.814-0.187-0.1870.0000.0000.0000.000
37H39GLU-1-0.813-0.88611.564-0.814-0.8140.0000.0000.0000.000
38H40GLU-1-0.924-0.9708.738-1.410-1.4100.0000.0000.0000.000
39H41ALA0-0.092-0.0306.582-0.577-0.5770.0000.0000.0000.000
40H42ASP-1-0.797-0.8862.180-10.730-8.7533.957-2.692-3.242-0.024
41H43LEU0-0.061-0.0322.663-0.2020.9840.304-0.300-1.189-0.001
42H44LEU0-0.0170.0104.2330.0590.1020.001-0.019-0.0250.000
43H45VAL0-0.002-0.0227.9260.3360.3360.0000.0000.0000.000
44H46LEU00.0450.03810.056-0.100-0.1000.0000.0000.0000.000
45H47PRO0-0.0140.01313.5830.1140.1140.0000.0000.0000.000
46H48GLY00.0920.03216.050-0.029-0.0290.0000.0000.0000.000
47H49GLN0-0.071-0.05019.7600.0550.0550.0000.0000.0000.000
48H50GLY00.0280.01123.284-0.021-0.0210.0000.0000.0000.000
49H51HIS00.000-0.00125.752-0.001-0.0010.0000.0000.0000.000
50H52PHE00.0730.03923.570-0.013-0.0130.0000.0000.0000.000
51H53GLY00.0270.00425.709-0.011-0.0110.0000.0000.0000.000
52H54GLN0-0.054-0.03325.628-0.024-0.0240.0000.0000.0000.000
53H55VAL0-0.001-0.00421.130-0.015-0.0150.0000.0000.0000.000
54H56MET00.0090.00421.376-0.019-0.0190.0000.0000.0000.000
55H57ARG10.8160.87924.0220.0860.0860.0000.0000.0000.000
56H58ALA00.0060.01224.617-0.015-0.0150.0000.0000.0000.000
57H59PHE0-0.014-0.01716.589-0.026-0.0260.0000.0000.0000.000
58H60GLN0-0.071-0.03421.112-0.018-0.0180.0000.0000.0000.000
59H61GLU-1-0.809-0.86823.737-0.128-0.1280.0000.0000.0000.000
60H62SER00.0190.01120.579-0.013-0.0130.0000.0000.0000.000
61H63GLY00.0280.01320.972-0.035-0.0350.0000.0000.0000.000
62H64PHE00.026-0.01013.777-0.020-0.0200.0000.0000.0000.000
63H65VAL0-0.0030.02216.774-0.028-0.0280.0000.0000.0000.000
64H66GLU-1-0.868-0.93917.721-0.241-0.2410.0000.0000.0000.000
65H67ARG10.7710.88210.8461.0261.0260.0000.0000.0000.000
66H68VAL00.0530.02112.755-0.057-0.0570.0000.0000.0000.000
67H69ARG10.9150.97113.4850.1020.1020.0000.0000.0000.000
68H70ARG10.9500.96514.7780.4140.4140.0000.0000.0000.000
69H71HIS0-0.065-0.0316.0320.1980.1980.0000.0000.0000.000
70H72LEU0-0.024-0.02010.4940.0050.0050.0000.0000.0000.000
71H73GLU-1-0.929-0.95912.309-0.046-0.0460.0000.0000.0000.000
72H74ARG10.8790.94511.5530.6890.6890.0000.0000.0000.000
73H75GLY00.0330.02810.764-0.030-0.0300.0000.0000.0000.000
74H76LEU0-0.040-0.0096.4970.0690.0690.0000.0000.0000.000
75H77PRO0-0.0070.0022.420-0.3780.1500.497-0.161-0.863-0.001
76H78PHE00.0580.0254.967-0.402-0.374-0.001-0.002-0.0240.000
77H79LEU0-0.002-0.0067.7190.3480.3480.0000.0000.0000.000
78H80GLY00.0210.0169.386-0.201-0.2010.0000.0000.0000.000
79H81ILE0-0.019-0.02912.1130.0740.0740.0000.0000.0000.000
80H82CYS0-0.028-0.00715.504-0.080-0.0800.0000.0000.0000.000
81H83VAL00.0490.03219.2850.0070.0070.0000.0000.0000.000
82H84GLY00.0120.01016.304-0.017-0.0170.0000.0000.0000.000
83H85MET0-0.071-0.02916.344-0.013-0.0130.0000.0000.0000.000
84H86GLN00.008-0.02917.488-0.024-0.0240.0000.0000.0000.000
85H87VAL00.0210.01518.332-0.007-0.0070.0000.0000.0000.000
86H88LEU0-0.034-0.00214.518-0.022-0.0220.0000.0000.0000.000
87H89TYR0-0.036-0.02518.7520.0170.0170.0000.0000.0000.000
88H90GLU-1-0.837-0.91522.2740.0350.0350.0000.0000.0000.000
89H91GLY00.0420.02925.227-0.018-0.0180.0000.0000.0000.000
90H92SER00.0160.00826.5610.0180.0180.0000.0000.0000.000
91H93GLU-1-0.696-0.80528.5130.0520.0520.0000.0000.0000.000
92H94GLU-1-0.922-0.95728.3040.0190.0190.0000.0000.0000.000
93H95ALA0-0.047-0.02229.191-0.009-0.0090.0000.0000.0000.000
94H96PRO00.013-0.00230.841-0.003-0.0030.0000.0000.0000.000
95H97GLY00.0350.03133.0180.0030.0030.0000.0000.0000.000
96H98VAL0-0.080-0.03126.945-0.006-0.0060.0000.0000.0000.000
97H99ARG10.9610.98626.0210.0330.0330.0000.0000.0000.000
98H100GLY00.0330.01223.426-0.012-0.0120.0000.0000.0000.000
99H101LEU0-0.039-0.04116.720-0.011-0.0110.0000.0000.0000.000
100H102GLY0-0.019-0.00420.871-0.008-0.0080.0000.0000.0000.000
101H103LEU0-0.027-0.00716.000-0.001-0.0010.0000.0000.0000.000
102H104VAL0-0.051-0.02218.3490.0310.0310.0000.0000.0000.000
103H105PRO00.0110.01621.112-0.016-0.0160.0000.0000.0000.000
104H106GLY00.013-0.00824.9330.0170.0170.0000.0000.0000.000
105H107GLU-1-0.863-0.91726.2340.0420.0420.0000.0000.0000.000
106H108VAL0-0.026-0.02524.0030.0110.0110.0000.0000.0000.000
107H109ARG10.8010.87427.150-0.080-0.0800.0000.0000.0000.000
108H110ARG10.9420.97029.652-0.039-0.0390.0000.0000.0000.000
109H111PHE00.0070.00228.3340.0000.0000.0000.0000.0000.000
110H112ARG10.7760.84633.277-0.071-0.0710.0000.0000.0000.000
111H113ALA00.0510.02236.492-0.002-0.0020.0000.0000.0000.000
112H114GLY00.0520.04636.3090.0040.0040.0000.0000.0000.000
113H115ARG10.9320.96236.043-0.083-0.0830.0000.0000.0000.000
114H116VAL00.0230.05333.2520.0080.0080.0000.0000.0000.000
115H117PRO0-0.040-0.04529.975-0.009-0.0090.0000.0000.0000.000
116H118GLN00.0060.02226.5930.0050.0050.0000.0000.0000.000
117H119MET0-0.044-0.03728.6650.0050.0050.0000.0000.0000.000
118H120GLY00.0110.00827.624-0.007-0.0070.0000.0000.0000.000
119H121TRP0-0.066-0.03522.4850.0210.0210.0000.0000.0000.000
120H122ASN00.0150.00525.732-0.007-0.0070.0000.0000.0000.000
121H123ALA00.0080.01624.9030.0270.0270.0000.0000.0000.000
122H124LEU0-0.025-0.00120.853-0.010-0.0100.0000.0000.0000.000
123H125GLU-1-0.808-0.88423.6420.3560.3560.0000.0000.0000.000
124H126PHE0-0.029-0.02017.4380.0220.0220.0000.0000.0000.000
125H127GLY00.1010.05619.639-0.025-0.0250.0000.0000.0000.000
126H128GLY00.002-0.01817.1570.0610.0610.0000.0000.0000.000
127H129ALA0-0.010-0.01713.086-0.023-0.0230.0000.0000.0000.000
128H130PHE00.009-0.00110.3560.0390.0390.0000.0000.0000.000
129H131ALA00.0200.02915.855-0.058-0.0580.0000.0000.0000.000
130H132PRO0-0.015-0.01816.992-0.048-0.0480.0000.0000.0000.000
131H133LEU0-0.076-0.02614.969-0.031-0.0310.0000.0000.0000.000
132H134THR00.0310.02219.484-0.034-0.0340.0000.0000.0000.000
133H135GLY00.0090.01422.653-0.010-0.0100.0000.0000.0000.000
134H136ARG10.8760.94618.400-0.483-0.4830.0000.0000.0000.000
135H137HIS00.0350.00823.3100.0070.0070.0000.0000.0000.000
136H138PHE0-0.039-0.03417.2240.0350.0350.0000.0000.0000.000
137H139TYR0-0.006-0.00221.690-0.032-0.0320.0000.0000.0000.000
138H140PHE00.006-0.00622.1440.0220.0220.0000.0000.0000.000
139H141ALA00.0510.00724.598-0.017-0.0170.0000.0000.0000.000
140H142ASN0-0.032-0.00424.787-0.005-0.0050.0000.0000.0000.000
141H143SER00.0650.02626.8930.0010.0010.0000.0000.0000.000
142H144TYR00.0160.00827.202-0.004-0.0040.0000.0000.0000.000
143H145TYR00.0020.01025.5140.0110.0110.0000.0000.0000.000
144H146GLY00.0840.04523.766-0.016-0.0160.0000.0000.0000.000
145H147PRO00.0010.00724.8320.0160.0160.0000.0000.0000.000
146H148LEU00.0100.00225.0480.0140.0140.0000.0000.0000.000
147H149THR00.0220.01122.022-0.015-0.0150.0000.0000.0000.000
148H150PRO00.004-0.00222.7920.0160.0160.0000.0000.0000.000
149H151TYR00.0660.02418.0050.0010.0010.0000.0000.0000.000
150H152SER0-0.015-0.01518.5400.0440.0440.0000.0000.0000.000
151H153LEU00.0020.00115.404-0.006-0.0060.0000.0000.0000.000
152H154GLY0-0.005-0.00319.2310.0140.0140.0000.0000.0000.000
153H155LYS10.8050.88220.099-0.377-0.3770.0000.0000.0000.000
154H156GLY00.0650.02223.7550.0160.0160.0000.0000.0000.000
155H157GLU-1-0.900-0.94426.4130.1470.1470.0000.0000.0000.000
156H158TYR0-0.017-0.03329.7140.0060.0060.0000.0000.0000.000
157H159GLU-1-0.911-0.95531.5030.0940.0940.0000.0000.0000.000
158H160GLY00.0140.01134.402-0.009-0.0090.0000.0000.0000.000
159H161THR0-0.076-0.02731.084-0.005-0.0050.0000.0000.0000.000
160H162PRO00.001-0.00729.9280.0110.0110.0000.0000.0000.000
161H163PHE0-0.060-0.02623.859-0.008-0.0080.0000.0000.0000.000
162H164THR00.0030.01620.4020.0260.0260.0000.0000.0000.000
163H165ALA0-0.028-0.01021.214-0.010-0.0100.0000.0000.0000.000
164H166LEU0-0.048-0.02513.7170.0260.0260.0000.0000.0000.000
165H167LEU00.0100.01915.956-0.012-0.0120.0000.0000.0000.000
166H168ALA0-0.036-0.04313.7700.0940.0940.0000.0000.0000.000
167H169LYS10.8710.94513.263-0.233-0.2330.0000.0000.0000.000
168H170GLU-1-0.881-0.95112.2840.3340.3340.0000.0000.0000.000
169H171ASN00.013-0.0026.1750.4380.4380.0000.0000.0000.000
170H172LEU00.0250.0317.895-0.114-0.1140.0000.0000.0000.000
171H173LEU0-0.032-0.0138.3090.0720.0720.0000.0000.0000.000
172H174ALA00.0250.00011.171-0.079-0.0790.0000.0000.0000.000
173H175PRO0-0.0260.01313.268-0.032-0.0320.0000.0000.0000.000
174H176GLN00.0310.00916.274-0.070-0.0700.0000.0000.0000.000
175H177PHE00.0020.01315.985-0.045-0.0450.0000.0000.0000.000
176H178HIS00.0440.01217.7190.0370.0370.0000.0000.0000.000
177H179PRO00.0070.01813.368-0.014-0.0140.0000.0000.0000.000
178H180GLU-1-0.806-0.90814.8850.1990.1990.0000.0000.0000.000
179H181LYS10.7880.89216.291-0.152-0.1520.0000.0000.0000.000
180H182SER00.0310.01018.346-0.015-0.0150.0000.0000.0000.000
181H183GLY00.0170.01219.9360.0230.0230.0000.0000.0000.000
182H184LYS10.9800.96717.744-0.219-0.2190.0000.0000.0000.000
183H185ALA00.0260.02816.9950.0680.0680.0000.0000.0000.000
184H186GLY00.0520.01916.3340.0770.0770.0000.0000.0000.000
185H187LEU0-0.016-0.00812.7460.0980.0980.0000.0000.0000.000
186H188ALA0-0.027-0.01312.2090.1520.1520.0000.0000.0000.000
187H189PHE00.0470.01711.9670.1830.1830.0000.0000.0000.000
188H190LEU00.0220.0049.2390.2270.2270.0000.0000.0000.000
189H191ALA0-0.0050.0068.2290.5730.5730.0000.0000.0000.000
190H192LEU0-0.031-0.0287.9440.4200.4200.0000.0000.0000.000
191H193ALA00.0020.0017.8080.1610.1610.0000.0000.0000.000
192H194ARG10.8860.9522.809-3.985-2.4010.387-0.368-1.6030.002
193H195ARG10.8950.9564.007-1.226-0.2870.042-0.365-0.615-0.003
194H196TYR0-0.051-0.0176.472-0.213-0.2130.0000.0000.0000.000
195H197PHE00.0240.0163.222-2.143-1.0680.968-0.341-1.703-0.001