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: K9QR3

Calculation Name: 1JN6-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1JN6

Chain ID: A

ChEMBL ID:

UniProt ID: P01843

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 OptH
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 208
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2025990.542075
FMO2-HF: Nuclear repulsion 1946418.096225
FMO2-HF: Total energy -79572.445849
FMO2-MP2: Total energy -79804.149443


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(A:1:GLN)


Summations of interaction energy for fragment #1(A:1:GLN)
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.
-8.244-0.6315.539-5.23-7.92-0.006
Interaction energy analysis for fragmet #1(A:1:GLN)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.028 / q_NPA : 0.012
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].
3A3VAL00.0380.0123.6270.1603.945-0.023-2.116-1.6450.007
4A4VAL00.0050.0096.376-0.766-0.7660.0000.0000.0000.000
5A5THR0-0.043-0.0278.9970.0110.0110.0000.0000.0000.000
6A6GLN00.032-0.01112.4470.0410.0410.0000.0000.0000.000
7A7GLU-1-0.811-0.90915.8100.4760.4760.0000.0000.0000.000
8A8SER00.0210.00519.147-0.004-0.0040.0000.0000.0000.000
9A9ALA0-0.020-0.02420.0390.0060.0060.0000.0000.0000.000
10A10LEU00.0050.02922.821-0.017-0.0170.0000.0000.0000.000
11A11THR00.0090.00725.6090.0010.0010.0000.0000.0000.000
12A12THR00.003-0.00529.233-0.007-0.0070.0000.0000.0000.000
13A13SER00.0340.03631.710-0.002-0.0020.0000.0000.0000.000
14A14PRO00.007-0.00634.4870.0040.0040.0000.0000.0000.000
15A15GLY0-0.058-0.02435.092-0.008-0.0080.0000.0000.0000.000
16A16GLU-1-0.935-0.95533.0680.1490.1490.0000.0000.0000.000
17A17THR0-0.029-0.02430.3640.0040.0040.0000.0000.0000.000
18A18VAL00.0100.02225.9800.0000.0000.0000.0000.0000.000
19A19THR0-0.023-0.02823.286-0.005-0.0050.0000.0000.0000.000
20A20LEU00.0100.01820.3320.0100.0100.0000.0000.0000.000
21A21THR0-0.055-0.01218.7280.0050.0050.0000.0000.0000.000
22A22CYS0-0.039-0.02413.0420.0250.0250.0000.0000.0000.000
23A23ARG10.9840.98813.067-0.497-0.4970.0000.0000.0000.000
24A24SER00.0690.0276.9940.0270.0270.0000.0000.0000.000
25A25SER00.0100.0116.9220.0020.0020.0000.0000.0000.000
26A26SER0-0.053-0.0285.743-0.239-0.2390.0000.0000.0000.000
27A27GLY00.0330.0167.330-0.007-0.0070.0000.0000.0000.000
28A28ALA0-0.021-0.00211.0660.1130.1130.0000.0000.0000.000
29A29ILE0-0.038-0.00111.129-0.006-0.0060.0000.0000.0000.000
30A30THR00.0040.00412.861-0.031-0.0310.0000.0000.0000.000
31A31THR00.0680.01314.3720.0430.0430.0000.0000.0000.000
32A32SER0-0.057-0.01413.0560.0100.0100.0000.0000.0000.000
33A33HIS00.0530.0377.9900.0120.0120.0000.0000.0000.000
34A34TYR0-0.076-0.04411.4820.0940.0940.0000.0000.0000.000
35A35ALA00.0510.03713.3740.0460.0460.0000.0000.0000.000
36A36ASN0-0.005-0.01214.294-0.153-0.1530.0000.0000.0000.000
37A37TRP00.0000.00015.3160.1270.1270.0000.0000.0000.000
38A38ILE00.0230.01714.493-0.076-0.0760.0000.0000.0000.000
39A39GLN00.0290.01518.1690.0420.0420.0000.0000.0000.000
40A40GLU-1-0.891-0.96218.2440.5040.5040.0000.0000.0000.000
41A41LYS10.8620.92821.019-0.256-0.2560.0000.0000.0000.000
42A42PRO0-0.022-0.03323.7360.0090.0090.0000.0000.0000.000
43A43ASP-1-0.871-0.92824.9340.1810.1810.0000.0000.0000.000
44A44HIS0-0.0100.00520.1350.0110.0110.0000.0000.0000.000
45A45LEU0-0.0030.00521.618-0.018-0.0180.0000.0000.0000.000
46A46PHE00.0060.01117.1010.0220.0220.0000.0000.0000.000
47A47THR0-0.038-0.02421.111-0.043-0.0430.0000.0000.0000.000
48A48GLY0-0.0110.00820.1560.0410.0410.0000.0000.0000.000
49A49LEU00.003-0.00320.655-0.033-0.0330.0000.0000.0000.000
50A50ILE0-0.0250.00719.747-0.034-0.0340.0000.0000.0000.000
51A51SER00.0170.01817.9450.0330.0330.0000.0000.0000.000
52A52GLY00.0300.00617.084-0.031-0.0310.0000.0000.0000.000
53A53THR0-0.040-0.02316.839-0.014-0.0140.0000.0000.0000.000
54A54ASN0-0.047-0.04118.3000.0090.0090.0000.0000.0000.000
55A55ASN0-0.0080.00521.538-0.030-0.0300.0000.0000.0000.000
56A56ARG10.8660.93622.998-0.143-0.1430.0000.0000.0000.000
57A57ALA00.0180.02323.169-0.017-0.0170.0000.0000.0000.000
58A58PRO0-0.039-0.02825.014-0.008-0.0080.0000.0000.0000.000
59A59GLY00.0070.01428.2170.0020.0020.0000.0000.0000.000
60A60VAL00.0360.02025.6530.0090.0090.0000.0000.0000.000
61A61PRO00.0140.00229.085-0.007-0.0070.0000.0000.0000.000
62A62ALA00.0560.00430.0580.0130.0130.0000.0000.0000.000
63A63ARG10.7910.91230.079-0.173-0.1730.0000.0000.0000.000
64A64PHE00.0250.01525.5220.0090.0090.0000.0000.0000.000
65A65SER0-0.034-0.02925.991-0.010-0.0100.0000.0000.0000.000
66A66GLY00.0170.02821.7740.0210.0210.0000.0000.0000.000
67A67SER0-0.033-0.02921.224-0.037-0.0370.0000.0000.0000.000
68A68LEU00.0170.00516.0300.0360.0360.0000.0000.0000.000
69A69ILE00.0300.02019.547-0.030-0.0300.0000.0000.0000.000
70A70GLY0-0.020-0.01919.7830.0200.0200.0000.0000.0000.000
71A71ASP-1-0.897-0.95015.5590.1860.1860.0000.0000.0000.000
72A72LYS10.8560.92314.928-0.218-0.2180.0000.0000.0000.000
73A73ALA00.0220.02315.483-0.046-0.0460.0000.0000.0000.000
74A74ALA0-0.015-0.03517.1810.0120.0120.0000.0000.0000.000
75A75LEU0-0.0110.01820.341-0.029-0.0290.0000.0000.0000.000
76A76THR0-0.013-0.01522.1700.0010.0010.0000.0000.0000.000
77A77ILE00.0110.01225.049-0.010-0.0100.0000.0000.0000.000
78A78THR00.002-0.00728.260-0.005-0.0050.0000.0000.0000.000
79A79GLY00.0050.00831.839-0.008-0.0080.0000.0000.0000.000
80A80ALA0-0.035-0.00630.877-0.002-0.0020.0000.0000.0000.000
81A81GLN00.006-0.00232.299-0.018-0.0180.0000.0000.0000.000
82A82THR00.0540.00732.2580.0110.0110.0000.0000.0000.000
83A83GLU-1-0.977-0.98931.8650.1580.1580.0000.0000.0000.000
84A84ASP-1-0.789-0.87528.1190.2090.2090.0000.0000.0000.000
85A85GLU-1-0.919-0.94627.2600.2410.2410.0000.0000.0000.000
86A86ALA0-0.045-0.05823.844-0.014-0.0140.0000.0000.0000.000
87A87ILE00.0020.02018.3790.0100.0100.0000.0000.0000.000
88A88TYR0-0.002-0.00319.304-0.016-0.0160.0000.0000.0000.000
89A89ILE00.0120.02012.8890.0490.0490.0000.0000.0000.000
90A91ALA00.0100.01110.4640.2650.2650.0000.0000.0000.000
91A92LEU0-0.010-0.0228.138-0.340-0.3400.0000.0000.0000.000
92A93TRP00.0190.0177.8810.3600.3600.0000.0000.0000.000
93A94PHE00.013-0.0223.374-0.830-0.2420.020-0.140-0.468-0.001
94A95SER0-0.032-0.0244.670-0.588-0.373-0.001-0.008-0.2050.000
95A96ASN0-0.022-0.0204.884-0.111-0.1110.0000.0000.0000.000
96A97GLN00.0270.0262.413-2.964-1.4302.750-1.728-2.556-0.021
97A98PHE00.0190.0076.3600.4310.4310.0000.0000.0000.000
98A99ILE0-0.0270.0042.396-3.134-1.6432.793-1.238-3.0460.009
99A100PHE0-0.001-0.0145.884-1.135-1.1350.0000.0000.0000.000
100A101GLY00.0150.0158.6910.4310.4310.0000.0000.0000.000
101A102SER0-0.029-0.03311.112-0.075-0.0750.0000.0000.0000.000
102A103GLY00.0120.01913.023-0.098-0.0980.0000.0000.0000.000
103A104THR0-0.049-0.01816.1970.0090.0090.0000.0000.0000.000
104A105LYS10.9320.95519.570-0.540-0.5400.0000.0000.0000.000
105A106VAL00.0200.01322.604-0.017-0.0170.0000.0000.0000.000
106A107THR0-0.012-0.01725.295-0.013-0.0130.0000.0000.0000.000
107A108VAL00.0030.01128.746-0.009-0.0090.0000.0000.0000.000
108A109LEU0-0.005-0.00331.664-0.010-0.0100.0000.0000.0000.000
109A110GLY00.003-0.03134.838-0.003-0.0030.0000.0000.0000.000
110A111GLN0-0.014-0.01438.3350.0050.0050.0000.0000.0000.000
111A112PRO0-0.0130.02038.894-0.002-0.0020.0000.0000.0000.000
112A113LYS10.9280.98140.525-0.116-0.1160.0000.0000.0000.000
113A114SER0-0.029-0.04641.498-0.007-0.0070.0000.0000.0000.000
114A115SER00.0180.00842.3620.0060.0060.0000.0000.0000.000
115A116PRO0-0.0170.00041.966-0.002-0.0020.0000.0000.0000.000
116A117SER0-0.0010.02043.946-0.007-0.0070.0000.0000.0000.000
117A118VAL0-0.003-0.00644.7070.0030.0030.0000.0000.0000.000
118A119THR0-0.044-0.02145.647-0.006-0.0060.0000.0000.0000.000
119A120LEU0-0.024-0.01446.2290.0030.0030.0000.0000.0000.000
120A121PHE00.0290.02646.404-0.003-0.0030.0000.0000.0000.000
121A122PRO0-0.025-0.01648.6570.0020.0020.0000.0000.0000.000
122A123PRO00.0110.01048.9800.0000.0000.0000.0000.0000.000
123A124SER00.0480.03049.216-0.003-0.0030.0000.0000.0000.000
124A125SER00.056-0.00450.8970.0010.0010.0000.0000.0000.000
125A126GLU-1-0.916-0.95950.6600.0430.0430.0000.0000.0000.000
126A127GLU-1-0.865-0.91545.6770.0660.0660.0000.0000.0000.000
127A128LEU00.0000.01249.5020.0000.0000.0000.0000.0000.000
128A129GLU-1-0.962-0.96452.2010.0360.0360.0000.0000.0000.000
129A130THR0-0.069-0.04948.653-0.001-0.0010.0000.0000.0000.000
130A131ASN0-0.059-0.06249.4730.0020.0020.0000.0000.0000.000
131A132LYS10.8850.95644.997-0.060-0.0600.0000.0000.0000.000
132A133ALA00.0870.02447.471-0.003-0.0030.0000.0000.0000.000
133A134THR0-0.0150.01042.3800.0040.0040.0000.0000.0000.000
134A135LEU0-0.047-0.00245.595-0.002-0.0020.0000.0000.0000.000
135A136VAL00.0230.00942.3370.0050.0050.0000.0000.0000.000
136A137CYS0-0.041-0.00542.9580.0010.0010.0000.0000.0000.000
137A138THR00.0360.00341.4310.0050.0050.0000.0000.0000.000
138A139ILE0-0.008-0.00639.413-0.005-0.0050.0000.0000.0000.000
139A140THR00.045-0.00440.1750.0050.0050.0000.0000.0000.000
140A141ASP-1-0.876-0.95141.6060.0980.0980.0000.0000.0000.000
141A142PHE0-0.0320.04135.862-0.001-0.0010.0000.0000.0000.000
142A143TYR0-0.004-0.00835.4050.0080.0080.0000.0000.0000.000
143A144PRO00.0330.01434.596-0.009-0.0090.0000.0000.0000.000
144A145GLY00.029-0.01633.889-0.007-0.0070.0000.0000.0000.000
145A146VAL0-0.038-0.02432.8180.0150.0150.0000.0000.0000.000
146A147VAL00.0040.00634.589-0.010-0.0100.0000.0000.0000.000
147A148THR0-0.025-0.00835.8120.0110.0110.0000.0000.0000.000
148A149VAL0-0.046-0.02537.871-0.007-0.0070.0000.0000.0000.000
149A150ASP-1-0.876-0.92339.6340.1220.1220.0000.0000.0000.000
150A151TRP00.023-0.01841.526-0.008-0.0080.0000.0000.0000.000
151A152LYS10.8420.91045.088-0.080-0.0800.0000.0000.0000.000
152A153VAL00.0050.00548.562-0.001-0.0010.0000.0000.0000.000
153A154ASP-1-0.808-0.91751.1890.0550.0550.0000.0000.0000.000
154A155GLY0-0.0070.00752.744-0.002-0.0020.0000.0000.0000.000
155A156THR0-0.041-0.02350.0710.0010.0010.0000.0000.0000.000
156A157PRO00.000-0.00145.9290.0000.0000.0000.0000.0000.000
157A158VAL0-0.0150.00344.767-0.003-0.0030.0000.0000.0000.000
158A159THR00.0210.00140.2540.0020.0020.0000.0000.0000.000
159A160GLN0-0.035-0.01540.2330.0070.0070.0000.0000.0000.000
160A161GLY00.0400.00839.825-0.006-0.0060.0000.0000.0000.000
161A162MET0-0.048-0.01738.587-0.003-0.0030.0000.0000.0000.000
162A163GLU-1-0.895-0.94134.7070.1360.1360.0000.0000.0000.000
163A164THR0-0.019-0.00935.069-0.010-0.0100.0000.0000.0000.000
164A165THR00.0120.02432.5050.0070.0070.0000.0000.0000.000
165A166GLN00.009-0.00827.364-0.005-0.0050.0000.0000.0000.000
166A167PRO0-0.025-0.02130.696-0.010-0.0100.0000.0000.0000.000
167A168SER00.0370.03530.9850.0160.0160.0000.0000.0000.000
168A169LYS10.8630.95231.521-0.200-0.2000.0000.0000.0000.000
169A170GLN00.0240.01033.201-0.007-0.0070.0000.0000.0000.000
170A171SER00.061-0.00135.3420.0030.0030.0000.0000.0000.000
171A172ASN0-0.011-0.01136.3550.0090.0090.0000.0000.0000.000
172A173ASN00.006-0.01234.5530.0010.0010.0000.0000.0000.000
173A174LYS10.9720.99636.842-0.106-0.1060.0000.0000.0000.000
174A175TYR0-0.0430.00431.5920.0020.0020.0000.0000.0000.000
175A176MET0-0.038-0.01335.788-0.010-0.0100.0000.0000.0000.000
176A177ALA0-0.014-0.00835.4480.0120.0120.0000.0000.0000.000
177A178SER0-0.010-0.01336.440-0.010-0.0100.0000.0000.0000.000
178A179SER00.0320.02337.1830.0040.0040.0000.0000.0000.000
179A180TYR00.0160.00436.748-0.010-0.0100.0000.0000.0000.000
180A181LEU00.0350.04240.6690.0040.0040.0000.0000.0000.000
181A182THR0-0.002-0.00440.900-0.004-0.0040.0000.0000.0000.000
182A183LEU0-0.051-0.01543.5400.0000.0000.0000.0000.0000.000
183A184THR0-0.039-0.03846.977-0.001-0.0010.0000.0000.0000.000
184A185ALA00.0280.01449.4740.0000.0000.0000.0000.0000.000
185A186ARG10.9560.97152.608-0.042-0.0420.0000.0000.0000.000
186A187ALA0-0.028-0.01850.618-0.001-0.0010.0000.0000.0000.000
187A188TRP00.1000.04051.5410.0020.0020.0000.0000.0000.000
188A189GLU-1-0.888-0.95352.9790.0430.0430.0000.0000.0000.000
189A190ARG10.8610.94352.111-0.054-0.0540.0000.0000.0000.000
190A191HIS10.7630.89151.765-0.060-0.0600.0000.0000.0000.000
191A192SER00.0350.03656.224-0.002-0.0020.0000.0000.0000.000
192A193SER0-0.050-0.03554.8020.0000.0000.0000.0000.0000.000
193A194TYR00.0000.01049.6980.0020.0020.0000.0000.0000.000
194A195SER0-0.009-0.01549.6670.0000.0000.0000.0000.0000.000
195A197GLN0-0.004-0.02143.818-0.006-0.0060.0000.0000.0000.000
196A198VAL00.0420.01940.7450.0060.0060.0000.0000.0000.000
197A199THR0-0.008-0.01441.248-0.007-0.0070.0000.0000.0000.000
198A200HIS0-0.039-0.02938.5950.0020.0020.0000.0000.0000.000
199A201GLU-1-0.898-0.95438.3710.1400.1400.0000.0000.0000.000
200A202GLY0-0.0200.00041.412-0.005-0.0050.0000.0000.0000.000
201A203HIS00.0000.00143.943-0.005-0.0050.0000.0000.0000.000
202A204THR0-0.007-0.00845.0710.0030.0030.0000.0000.0000.000
203A205VAL0-0.0270.00046.132-0.005-0.0050.0000.0000.0000.000
204A206GLU-1-0.865-0.93846.7800.0820.0820.0000.0000.0000.000
205A207LYS10.9070.97149.001-0.077-0.0770.0000.0000.0000.000
206A208SER00.013-0.00449.9450.0030.0030.0000.0000.0000.000
207A209LEU0-0.0290.00450.421-0.002-0.0020.0000.0000.0000.000
208A210SER00.0430.02354.1740.0000.0000.0000.0000.0000.000