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: 5JQ3Z

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 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 195
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2161716.112065
FMO2-HF: Nuclear repulsion 2088107.393204
FMO2-HF: Total energy -73608.718861
FMO2-MP2: Total energy -73825.934423


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.
-24.369-13.21912.831-7.483-16.496-0.026
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 : 0.038 / q_NPA : 0.029
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].
3H5ALA0-0.0100.0003.880-0.7191.166-0.006-0.841-1.0370.004
4H6LEU0-0.024-0.0185.0880.0260.071-0.001-0.004-0.0400.000
5H7LEU0-0.061-0.0308.7730.2510.2510.0000.0000.0000.000
6H8ILE00.013-0.00411.337-0.038-0.0380.0000.0000.0000.000
7H9ASP-1-0.853-0.93613.981-0.190-0.1900.0000.0000.0000.000
8H10TYR0-0.044-0.04917.496-0.012-0.0120.0000.0000.0000.000
9H11GLY00.0370.03120.6130.0210.0210.0000.0000.0000.000
10H12SER0-0.040-0.02021.0420.0380.0380.0000.0000.0000.000
11H13GLY00.0500.02418.526-0.021-0.0210.0000.0000.0000.000
12H14ASN0-0.075-0.06118.0560.0220.0220.0000.0000.0000.000
13H15LEU00.0830.04015.8810.0360.0360.0000.0000.0000.000
14H16ARG10.9870.99515.5230.1100.1100.0000.0000.0000.000
15H17SER00.0220.00516.140-0.018-0.0180.0000.0000.0000.000
16H18ALA00.0400.02013.3990.0600.0600.0000.0000.0000.000
17H19ALA00.0400.02511.3330.0940.0940.0000.0000.0000.000
18H20LYS10.8040.87411.0170.3820.3820.0000.0000.0000.000
19H21ALA00.0100.00912.5860.0470.0470.0000.0000.0000.000
20H22LEU00.0100.0047.1250.2270.2270.0000.0000.0000.000
21H23GLU-1-0.764-0.8707.506-0.244-0.2440.0000.0000.0000.000
22H24ALA0-0.043-0.0148.9720.0660.0660.0000.0000.0000.000
23H25ALA0-0.013-0.0018.1290.0510.0510.0000.0000.0000.000
24H26GLY0-0.0040.0076.5600.6840.6840.0000.0000.0000.000
25H27PHE0-0.028-0.0232.339-2.775-2.1193.598-1.137-3.1180.009
26H28SER00.0230.0163.2670.2380.8670.003-0.189-0.4420.000
27H29VAL0-0.011-0.0035.135-0.571-0.538-0.001-0.009-0.0230.000
28H30ALA0-0.0090.0068.042-0.144-0.1440.0000.0000.0000.000
29H31VAL0-0.019-0.00910.4550.1110.1110.0000.0000.0000.000
30H32ALA0-0.012-0.00613.321-0.045-0.0450.0000.0000.0000.000
31H33GLN0-0.017-0.00915.7540.0260.0260.0000.0000.0000.000
32H34ASP-1-0.804-0.89817.681-0.481-0.4810.0000.0000.0000.000
33H35PRO0-0.004-0.00416.507-0.088-0.0880.0000.0000.0000.000
34H36LYS10.8210.90215.6500.5700.5700.0000.0000.0000.000
35H37ALA00.0310.02815.790-0.070-0.0700.0000.0000.0000.000
36H38HIS0-0.036-0.03010.587-0.179-0.1790.0000.0000.0000.000
37H39GLU-1-0.809-0.88511.135-0.968-0.9680.0000.0000.0000.000
38H40GLU-1-0.925-0.9568.582-1.499-1.4990.0000.0000.0000.000
39H41ALA0-0.064-0.0336.573-0.619-0.6190.0000.0000.0000.000
40H42ASP-1-0.829-0.9062.341-12.893-10.0284.647-3.416-4.096-0.036
41H43LEU0-0.051-0.0112.442-0.3010.8410.908-0.391-1.6580.000
42H44LEU00.0010.0194.1490.2250.2970.002-0.025-0.0490.000
43H45VAL00.000-0.0177.5020.3390.3390.0000.0000.0000.000
44H46LEU00.0390.0329.680-0.105-0.1050.0000.0000.0000.000
45H47PRO00.0080.01313.3410.1130.1130.0000.0000.0000.000
46H48GLY00.0790.03115.643-0.048-0.0480.0000.0000.0000.000
47H49GLN0-0.065-0.04719.3640.0650.0650.0000.0000.0000.000
48H50GLY00.0240.01722.884-0.022-0.0220.0000.0000.0000.000
49H51HIS00.002-0.00425.234-0.004-0.0040.0000.0000.0000.000
50H52PHE00.0580.02322.888-0.015-0.0150.0000.0000.0000.000
51H53GLY00.0190.00325.159-0.012-0.0120.0000.0000.0000.000
52H54GLN0-0.041-0.02225.179-0.027-0.0270.0000.0000.0000.000
53H55VAL00.0140.01020.850-0.017-0.0170.0000.0000.0000.000
54H56MET00.0040.00421.213-0.025-0.0250.0000.0000.0000.000
55H57ARG10.8000.87323.4780.0870.0870.0000.0000.0000.000
56H58ALA00.0550.02623.825-0.016-0.0160.0000.0000.0000.000
57H59PHE0-0.019-0.00316.116-0.031-0.0310.0000.0000.0000.000
58H60GLN0-0.024-0.01220.918-0.018-0.0180.0000.0000.0000.000
59H61GLU-1-0.822-0.87923.514-0.146-0.1460.0000.0000.0000.000
60H62SER0-0.038-0.03120.481-0.019-0.0190.0000.0000.0000.000
61H63GLY00.0290.01220.835-0.038-0.0380.0000.0000.0000.000
62H64PHE00.003-0.01013.325-0.034-0.0340.0000.0000.0000.000
63H65VAL0-0.0030.01416.518-0.043-0.0430.0000.0000.0000.000
64H66GLU-1-0.851-0.93317.532-0.276-0.2760.0000.0000.0000.000
65H67ARG10.7230.84410.4881.1221.1220.0000.0000.0000.000
66H68VAL00.0330.00712.656-0.067-0.0670.0000.0000.0000.000
67H69ARG10.8210.89913.1500.1200.1200.0000.0000.0000.000
68H70ARG10.9460.97615.0580.4460.4460.0000.0000.0000.000
69H71HIS0-0.040-0.0256.1920.2420.2420.0000.0000.0000.000
70H72LEU0-0.007-0.00910.4990.0000.0000.0000.0000.0000.000
71H73GLU-1-0.833-0.91212.211-0.124-0.1240.0000.0000.0000.000
72H74ARG10.8650.95211.4730.8370.8370.0000.0000.0000.000
73H75GLY00.0280.02310.786-0.051-0.0510.0000.0000.0000.000
74H76LEU0-0.043-0.0086.9490.0210.0210.0000.0000.0000.000
75H77PRO0-0.0190.0012.567-0.4320.0060.997-0.230-1.205-0.002
76H78PHE00.0420.0024.582-0.223-0.171-0.001-0.008-0.0420.000
77H79LEU0-0.006-0.0077.1500.3740.3740.0000.0000.0000.000
78H80GLY00.0390.0288.872-0.153-0.1530.0000.0000.0000.000
79H81ILE0-0.038-0.03111.8230.0860.0860.0000.0000.0000.000
80H82CYS0-0.045-0.01114.967-0.088-0.0880.0000.0000.0000.000
81H83VAL00.0230.01518.702-0.002-0.0020.0000.0000.0000.000
82H84GLY00.0290.01416.044-0.023-0.0230.0000.0000.0000.000
83H85MET0-0.086-0.02115.760-0.023-0.0230.0000.0000.0000.000
84H86GLN0-0.020-0.04616.742-0.035-0.0350.0000.0000.0000.000
85H87VAL00.0100.00217.944-0.010-0.0100.0000.0000.0000.000
86H88LEU0-0.027-0.00213.953-0.025-0.0250.0000.0000.0000.000
87H89TYR0-0.011-0.00318.1430.0090.0090.0000.0000.0000.000
88H90GLU-1-0.830-0.91921.6700.0130.0130.0000.0000.0000.000
89H91GLY00.0210.01724.680-0.018-0.0180.0000.0000.0000.000
90H92SER00.0060.00625.8630.0190.0190.0000.0000.0000.000
91H93GLU-1-0.687-0.79127.7490.0570.0570.0000.0000.0000.000
92H94GLU-1-0.937-0.96027.9020.0290.0290.0000.0000.0000.000
93H95ALA0-0.045-0.02728.783-0.009-0.0090.0000.0000.0000.000
94H96PRO00.0450.01430.528-0.006-0.0060.0000.0000.0000.000
95H97GLY00.0220.03232.3460.0020.0020.0000.0000.0000.000
96H98VAL0-0.090-0.03626.415-0.008-0.0080.0000.0000.0000.000
97H99ARG10.9630.98425.6520.0460.0460.0000.0000.0000.000
98H100GLY00.0130.00022.964-0.011-0.0110.0000.0000.0000.000
99H101LEU0-0.031-0.02316.086-0.013-0.0130.0000.0000.0000.000
100H102GLY00.0080.00520.300-0.016-0.0160.0000.0000.0000.000
101H103LEU0-0.013-0.00415.192-0.003-0.0030.0000.0000.0000.000
102H104VAL0-0.051-0.02017.4940.0300.0300.0000.0000.0000.000
103H105PRO00.0110.01720.276-0.014-0.0140.0000.0000.0000.000
104H106GLY00.002-0.00724.1360.0190.0190.0000.0000.0000.000
105H107GLU-1-0.858-0.91325.5280.0410.0410.0000.0000.0000.000
106H108VAL0-0.020-0.01423.1680.0140.0140.0000.0000.0000.000
107H109ARG10.7980.86326.227-0.082-0.0820.0000.0000.0000.000
108H110ARG10.9350.95928.849-0.048-0.0480.0000.0000.0000.000
109H111PHE0-0.001-0.00227.3840.0010.0010.0000.0000.0000.000
110H112ARG10.7900.84532.389-0.079-0.0790.0000.0000.0000.000
111H113ALA00.0300.02835.468-0.005-0.0050.0000.0000.0000.000
112H114GLY00.0380.02035.3740.0060.0060.0000.0000.0000.000
113H115ARG10.8420.92835.178-0.112-0.1120.0000.0000.0000.000
114H116VAL00.0190.03232.3580.0090.0090.0000.0000.0000.000
115H117PRO0-0.049-0.03929.352-0.010-0.0100.0000.0000.0000.000
116H118GLN00.0230.02725.6900.0060.0060.0000.0000.0000.000
117H119MET0-0.044-0.02428.0910.0070.0070.0000.0000.0000.000
118H120GLY00.0120.01527.636-0.009-0.0090.0000.0000.0000.000
119H121TRP0-0.055-0.02522.0960.0260.0260.0000.0000.0000.000
120H122ASN0-0.001-0.01225.450-0.013-0.0130.0000.0000.0000.000
121H123ALA00.0060.01224.7360.0340.0340.0000.0000.0000.000
122H124LEU0-0.024-0.00320.448-0.010-0.0100.0000.0000.0000.000
123H125GLU-1-0.828-0.89723.2030.3850.3850.0000.0000.0000.000
124H126PHE0-0.002-0.00716.8380.0190.0190.0000.0000.0000.000
125H127GLY00.0910.04919.209-0.024-0.0240.0000.0000.0000.000
126H128GLY00.014-0.01216.9820.0720.0720.0000.0000.0000.000
127H129ALA0-0.027-0.02212.567-0.016-0.0160.0000.0000.0000.000
128H130PHE00.0210.00810.0040.0840.0840.0000.0000.0000.000
129H131ALA00.0230.02815.586-0.057-0.0570.0000.0000.0000.000
130H132PRO0-0.024-0.02316.937-0.053-0.0530.0000.0000.0000.000
131H133LEU0-0.064-0.01914.711-0.015-0.0150.0000.0000.0000.000
132H134THR00.0290.01819.253-0.042-0.0420.0000.0000.0000.000
133H135GLY0-0.0020.01122.527-0.007-0.0070.0000.0000.0000.000
134H136ARG10.8440.92918.265-0.607-0.6070.0000.0000.0000.000
135H137HIS00.0360.01223.3610.0010.0010.0000.0000.0000.000
136H138PHE0-0.031-0.03316.7400.0460.0460.0000.0000.0000.000
137H139TYR00.000-0.00521.360-0.040-0.0400.0000.0000.0000.000
138H140PHE00.005-0.00821.7550.0260.0260.0000.0000.0000.000
139H141ALA00.0550.00824.207-0.017-0.0170.0000.0000.0000.000
140H142ASN0-0.019-0.00424.237-0.006-0.0060.0000.0000.0000.000
141H143SER00.0520.01126.3680.0010.0010.0000.0000.0000.000
142H144TYR00.0180.01526.621-0.005-0.0050.0000.0000.0000.000
143H145TYR0-0.0030.00924.5490.0130.0130.0000.0000.0000.000
144H146GLY00.0970.05222.460-0.020-0.0200.0000.0000.0000.000
145H147PRO00.0140.01423.5280.0200.0200.0000.0000.0000.000
146H148LEU00.0090.01323.7980.0160.0160.0000.0000.0000.000
147H149THR00.018-0.00221.103-0.020-0.0200.0000.0000.0000.000
148H150PRO00.009-0.00622.1080.0230.0230.0000.0000.0000.000
149H151TYR00.0780.03616.987-0.002-0.0020.0000.0000.0000.000
150H152SER0-0.035-0.02317.3850.0460.0460.0000.0000.0000.000
151H153LEU00.004-0.00114.515-0.003-0.0030.0000.0000.0000.000
152H154GLY0-0.011-0.01318.1880.0270.0270.0000.0000.0000.000
153H155LYS10.7870.88319.263-0.419-0.4190.0000.0000.0000.000
154H156GLY00.0750.02422.7840.0260.0260.0000.0000.0000.000
155H157GLU-1-0.878-0.93425.5930.1600.1600.0000.0000.0000.000
156H158TYR0-0.015-0.02328.9090.0120.0120.0000.0000.0000.000
157H159GLU-1-0.831-0.91530.8510.1040.1040.0000.0000.0000.000
158H160GLY00.0350.02333.908-0.011-0.0110.0000.0000.0000.000
159H161THR0-0.062-0.01930.325-0.008-0.0080.0000.0000.0000.000
160H162PRO0-0.007-0.01628.8200.0130.0130.0000.0000.0000.000
161H163PHE0-0.069-0.02522.911-0.010-0.0100.0000.0000.0000.000
162H164THR00.0110.01519.2690.0300.0300.0000.0000.0000.000
163H165ALA0-0.002-0.00420.331-0.011-0.0110.0000.0000.0000.000
164H166LEU0-0.057-0.03712.7000.0400.0400.0000.0000.0000.000
165H167LEU00.0220.02715.158-0.014-0.0140.0000.0000.0000.000
166H168ALA0-0.045-0.04312.6320.1000.1000.0000.0000.0000.000
167H169LYS10.8770.94512.162-0.177-0.1770.0000.0000.0000.000
168H170GLU-1-0.862-0.93711.8080.2570.2570.0000.0000.0000.000
169H171ASN00.021-0.0035.6080.2270.2270.0000.0000.0000.000
170H172LEU00.0060.0126.862-0.077-0.0770.0000.0000.0000.000
171H173LEU0-0.050-0.0257.6020.1620.1620.0000.0000.0000.000
172H174ALA00.0280.00010.215-0.102-0.1020.0000.0000.0000.000
173H175PRO0-0.0420.01012.324-0.023-0.0230.0000.0000.0000.000
174H176GLN00.0550.02815.335-0.083-0.0830.0000.0000.0000.000
175H177PHE00.0250.01715.609-0.044-0.0440.0000.0000.0000.000
176H178HIS00.0600.02617.5080.0300.0300.0000.0000.0000.000
177H179PRO00.0030.02013.478-0.008-0.0080.0000.0000.0000.000
178H180GLU-1-0.801-0.90514.8680.2850.2850.0000.0000.0000.000
179H181LYS10.7870.89316.173-0.214-0.2140.0000.0000.0000.000
180H182SER00.0060.01118.012-0.019-0.0190.0000.0000.0000.000
181H183GLY00.0450.02219.0160.0300.0300.0000.0000.0000.000
182H184LYS10.9520.96117.389-0.297-0.2970.0000.0000.0000.000
183H185ALA00.0220.03418.3470.0510.0510.0000.0000.0000.000
184H186GLY00.0370.00315.9490.0960.0960.0000.0000.0000.000
185H187LEU0-0.009-0.00712.7790.1350.1350.0000.0000.0000.000
186H188ALA0-0.0090.00112.0880.2020.2020.0000.0000.0000.000
187H189PHE00.0520.02411.2960.2170.2170.0000.0000.0000.000
188H190LEU0-0.003-0.0059.0350.2630.2630.0000.0000.0000.000
189H191ALA00.0080.0017.8790.8210.8210.0000.0000.0000.000
190H192LEU0-0.039-0.0228.3490.4870.4870.0000.0000.0000.000
191H193ALA00.006-0.0017.4040.1790.1790.0000.0000.0000.000
192H194ARG10.8400.9193.268-5.204-3.6780.531-0.452-1.6050.003
193H195ARG10.9110.9664.310-1.472-0.7800.033-0.213-0.513-0.002
194H196TYR0-0.042-0.0036.887-0.745-0.7450.0000.0000.0000.000
195H197PHE00.0170.0032.271-2.215-1.1002.121-0.568-2.668-0.002