Manual

About

FMODB

FMODB: The database of quantum mechanical data based on the FMO method

Last updated: 2024-05-02

All entries: 37386

Number of unique PDB entries: 7781

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FMODB ID: GQKV1

Calculation Name: 1JSX-A-Xray309

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1JSX

Chain ID: A

ChEMBL ID:

UniProt ID: P0A6U5

Base Structure: X-ray

Registration Date: 2021-09-06

Reference: C. Watanabe, S. Koyama, K. Kamisaka, D. Takaya, T. Honma et. al., Interaction energy analysis of Apo structure dataset on FMODB, To be pubulished.

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. 1.20200116
FMO calculation
FMO method FMO2-MP2/6-31G(d)
Fragmentation Auto
Number of fragment 197
LigandCharge
Software ABINIT-MP - Open Ver.1 Rev. 15 / 20190524
Total energy (hartree)
FMO2-HF: Electronic energy -2246488.435373
FMO2-HF: Nuclear repulsion 2169365.262719
FMO2-HF: Total energy -77123.172655
FMO2-MP2: Total energy -77349.992614


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:MET )


Summations of interaction energy for fragment #1(A:1: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.
-13.766-9.575.115-3.935-5.3770.009
Interaction energy analysis for fragmet #1(A:1:MET )
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.014 / q_NPA : -0.014
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].
3A3ASN 00.0160.0092.563-4.3300.0530.480-2.213-2.650-0.005
4A4LYS 10.9410.9892.280-9.547-9.7344.635-1.722-2.7270.014
5A5LEU 00.0770.0394.881-0.471-0.4710.0000.0000.0000.000
6A6SER 00.0330.0257.408-0.036-0.0360.0000.0000.0000.000
7A7LEU 00.001-0.0168.494-0.003-0.0030.0000.0000.0000.000
8A8LEU 0-0.047-0.01210.004-0.069-0.0690.0000.0000.0000.000
9A9LEU 0-0.022-0.01411.536-0.077-0.0770.0000.0000.0000.000
10A10LYS 10.8970.94212.120-0.317-0.3170.0000.0000.0000.000
11A11ASP -1-0.874-0.93013.9390.5270.5270.0000.0000.0000.000
12A12ALA 0-0.0360.00016.464-0.033-0.0330.0000.0000.0000.000
13A13GLY 00.0300.01118.702-0.023-0.0230.0000.0000.0000.000
14A14ILE 0-0.071-0.03718.845-0.018-0.0180.0000.0000.0000.000
15A15SER 0-0.053-0.01419.2470.0230.0230.0000.0000.0000.000
16A16LEU 00.051-0.00315.1500.0270.0270.0000.0000.0000.000
17A17THR 00.0000.02218.2170.0020.0020.0000.0000.0000.000
18A18ASP -1-0.838-0.94216.3280.3210.3210.0000.0000.0000.000
19A19HIS 0-0.028-0.00815.8080.0640.0640.0000.0000.0000.000
20A20GLN 00.0900.04016.5570.0590.0590.0000.0000.0000.000
21A21LYS 10.9620.9909.651-0.908-0.9080.0000.0000.0000.000
22A22ASN 0-0.002-0.01111.9790.2300.2300.0000.0000.0000.000
23A23GLN 0-0.0030.00112.4560.0960.0960.0000.0000.0000.000
24A24LEU 00.0380.02311.7490.1040.1040.0000.0000.0000.000
25A25ILE 0-0.081-0.0497.0810.3810.3810.0000.0000.0000.000
26A26ALA 00.0520.0298.5170.3560.3560.0000.0000.0000.000
27A27TYR 00.008-0.01410.4180.0130.0130.0000.0000.0000.000
28A28VAL 0-0.013-0.0075.5960.0870.0870.0000.0000.0000.000
29A29ASN 0-0.073-0.0405.0440.0580.0580.0000.0000.0000.000
30A30MET 00.0040.0147.175-0.418-0.4180.0000.0000.0000.000
31A31LEU 0-0.010-0.0069.835-0.172-0.1720.0000.0000.0000.000
32A32HIS 0-0.054-0.0295.7420.0480.0480.0000.0000.0000.000
33A33LYS 10.9370.9727.962-0.176-0.1760.0000.0000.0000.000
34A34TRP 0-0.070-0.02110.219-0.088-0.0880.0000.0000.0000.000
35A35ASN 0-0.046-0.02310.162-0.062-0.0620.0000.0000.0000.000
36A36NME 00.0160.02112.351-0.060-0.0600.0000.0000.0000.000
37A47ACE 00.008-0.00710.062-0.003-0.0030.0000.0000.0000.000
38A48GLU -1-0.930-0.9718.7560.0210.0210.0000.0000.0000.000
39A49MET 00.008-0.00310.0470.0880.0880.0000.0000.0000.000
40A50LEU 00.0140.0187.5990.0460.0460.0000.0000.0000.000
41A51VAL 00.017-0.0037.6860.0840.0840.0000.0000.0000.000
42A52ARG 10.9610.98010.219-0.209-0.2090.0000.0000.0000.000
43A53HIS 00.0420.03013.452-0.027-0.0270.0000.0000.0000.000
44A54ILE 0-0.0230.00010.838-0.011-0.0110.0000.0000.0000.000
45A55LEU 00.0240.00913.928-0.032-0.0320.0000.0000.0000.000
46A56ASP -1-0.862-0.93615.5430.1920.1920.0000.0000.0000.000
47A57SER 0-0.055-0.05517.429-0.035-0.0350.0000.0000.0000.000
48A58ILE 00.0100.00515.182-0.018-0.0180.0000.0000.0000.000
49A59VAL 0-0.021-0.00819.123-0.029-0.0290.0000.0000.0000.000
50A60VAL 0-0.009-0.01121.428-0.024-0.0240.0000.0000.0000.000
51A61ALA 00.0400.02322.133-0.018-0.0180.0000.0000.0000.000
52A62PRO 0-0.039-0.01623.668-0.016-0.0160.0000.0000.0000.000
53A63TYR 0-0.009-0.00326.366-0.017-0.0170.0000.0000.0000.000
54A64LEU 0-0.0540.00625.530-0.010-0.0100.0000.0000.0000.000
55A65GLN 00.0080.00129.550-0.001-0.0010.0000.0000.0000.000
56A66GLY 00.014-0.00133.009-0.004-0.0040.0000.0000.0000.000
57A67GLU -1-0.970-0.98931.8060.1120.1120.0000.0000.0000.000
58A68ARG 10.8660.95931.553-0.083-0.0830.0000.0000.0000.000
59A69PHE 00.0020.00128.163-0.004-0.0040.0000.0000.0000.000
60A70ILE 00.0020.01028.6450.0030.0030.0000.0000.0000.000
61A71ASP -1-0.811-0.89422.6860.1920.1920.0000.0000.0000.000
62A72VAL 00.0410.01326.339-0.004-0.0040.0000.0000.0000.000
63A73GLY 0-0.040-0.01026.048-0.001-0.0010.0000.0000.0000.000
64A74THR 0-0.010-0.02521.7450.0120.0120.0000.0000.0000.000
65A75GLY 00.0160.00020.5480.0220.0220.0000.0000.0000.000
66A76PRO 0-0.087-0.06815.516-0.005-0.0050.0000.0000.0000.000
67A77GLY 00.0500.02516.7150.0520.0520.0000.0000.0000.000
68A78LEU 0-0.0700.00714.2280.0450.0450.0000.0000.0000.000
69A79PRO 00.0490.00118.486-0.030-0.0300.0000.0000.0000.000
70A80GLY 00.0680.01919.6060.0270.0270.0000.0000.0000.000
71A81ILE 0-0.018-0.00516.1250.0000.0000.0000.0000.0000.000
72A82PRO 0-0.026-0.01414.9590.0120.0120.0000.0000.0000.000
73A83LEU 00.0150.01017.262-0.009-0.0090.0000.0000.0000.000
74A84SER 0-0.043-0.01720.072-0.014-0.0140.0000.0000.0000.000
75A85ILE 0-0.026-0.00515.6620.0000.0000.0000.0000.0000.000
76A86VAL 0-0.031-0.02818.602-0.012-0.0120.0000.0000.0000.000
77A87ARG 10.7600.87021.158-0.187-0.1870.0000.0000.0000.000
78A88PRO 0-0.009-0.02122.964-0.009-0.0090.0000.0000.0000.000
79A89GLU -1-0.846-0.90325.3340.1590.1590.0000.0000.0000.000
80A90ALA 00.0050.02227.405-0.012-0.0120.0000.0000.0000.000
81A91HIS 0-0.003-0.01427.4440.0160.0160.0000.0000.0000.000
82A92PHE 0-0.018-0.01324.853-0.001-0.0010.0000.0000.0000.000
83A93THR 0-0.0020.00826.4090.0050.0050.0000.0000.0000.000
84A94LEU 0-0.046-0.02621.4790.0060.0060.0000.0000.0000.000
85A95LEU 00.0640.04025.435-0.008-0.0080.0000.0000.0000.000
86A96ASP -1-0.766-0.87924.0690.1060.1060.0000.0000.0000.000
87A97SER 00.0510.03226.602-0.010-0.0100.0000.0000.0000.000
88A98LEU 0-0.049-0.02724.980-0.010-0.0100.0000.0000.0000.000
89A99GLY 00.0860.04525.2370.0090.0090.0000.0000.0000.000
90A100LYS 10.8810.92919.9920.0050.0050.0000.0000.0000.000
91A101ARG 10.9030.95320.480-0.079-0.0790.0000.0000.0000.000
92A102VAL 00.0730.05421.1860.0170.0170.0000.0000.0000.000
93A103ARG 10.9170.95222.760-0.030-0.0300.0000.0000.0000.000
94A104PHE 0-0.0200.00313.326-0.010-0.0100.0000.0000.0000.000
95A105LEU 00.0440.01518.6420.0220.0220.0000.0000.0000.000
96A106ARG 10.9840.99220.135-0.076-0.0760.0000.0000.0000.000
97A107GLN 0-0.043-0.00917.4020.0160.0160.0000.0000.0000.000
98A108VAL 00.0090.00515.1330.0150.0150.0000.0000.0000.000
99A109GLN 00.0150.00717.3640.0120.0120.0000.0000.0000.000
100A110HIS 0-0.037-0.00720.3580.0000.0000.0000.0000.0000.000
101A111GLU -1-0.947-0.99115.2340.1890.1890.0000.0000.0000.000
102A112LEU 0-0.114-0.06014.0390.0270.0270.0000.0000.0000.000
103A113LYS 10.9430.97617.579-0.169-0.1690.0000.0000.0000.000
104A114LEU 0-0.025-0.00118.6370.0000.0000.0000.0000.0000.000
105A115GLU -1-0.937-0.97822.1400.1290.1290.0000.0000.0000.000
106A116ASN 0-0.0260.00123.842-0.004-0.0040.0000.0000.0000.000
107A117ILE 0-0.011-0.00721.3660.0040.0040.0000.0000.0000.000
108A118GLU -1-0.911-0.96725.3970.0880.0880.0000.0000.0000.000
109A119PRO 0-0.070-0.02923.464-0.004-0.0040.0000.0000.0000.000
110A120VAL 00.0390.02025.767-0.013-0.0130.0000.0000.0000.000
111A121GLN 0-0.088-0.05928.0820.0020.0020.0000.0000.0000.000
112A122SER 00.0560.00429.454-0.007-0.0070.0000.0000.0000.000
113A123ARG 10.8800.94131.012-0.039-0.0390.0000.0000.0000.000
114A124VAL 00.0430.00432.4980.0010.0010.0000.0000.0000.000
115A125GLU -1-0.876-0.93134.2600.0510.0510.0000.0000.0000.000
116A126GLU -1-1.052-0.99935.5650.0410.0410.0000.0000.0000.000
117A127PHE 0-0.046-0.02633.0620.0020.0020.0000.0000.0000.000
118A128PRO 00.0200.00135.8580.0000.0000.0000.0000.0000.000
119A129SER 00.030-0.00236.9600.0010.0010.0000.0000.0000.000
120A130GLU -1-0.928-0.92637.9050.0480.0480.0000.0000.0000.000
121A131PRO 0-0.078-0.03437.6620.0000.0000.0000.0000.0000.000
122A132PRO 00.0780.03237.6770.0060.0060.0000.0000.0000.000
123A133PHE 0-0.003-0.00131.9740.0040.0040.0000.0000.0000.000
124A134ASP -1-0.781-0.89133.7960.0900.0900.0000.0000.0000.000
125A135GLY 0-0.030-0.03231.745-0.001-0.0010.0000.0000.0000.000
126A136VAL 00.0020.01630.7530.0060.0060.0000.0000.0000.000
127A137ILE 0-0.020-0.00324.5580.0010.0010.0000.0000.0000.000
128A138SER 00.026-0.02025.612-0.002-0.0020.0000.0000.0000.000
129A139ARG 10.9500.98320.217-0.144-0.1440.0000.0000.0000.000
130A140ALA 0-0.095-0.05424.370-0.004-0.0040.0000.0000.0000.000
131A141PHE 0-0.0010.00826.132-0.010-0.0100.0000.0000.0000.000
132A142ALA 0-0.018-0.00228.4780.0050.0050.0000.0000.0000.000
133A143SER 0-0.048-0.03830.3150.0010.0010.0000.0000.0000.000
134A144LEU 00.005-0.01731.4550.0030.0030.0000.0000.0000.000
135A145ASN 00.003-0.00833.6060.0010.0010.0000.0000.0000.000
136A146ASP -1-0.842-0.90733.1600.0500.0500.0000.0000.0000.000
137A147MET 0-0.042-0.02630.3330.0030.0030.0000.0000.0000.000
138A148VAL 0-0.0010.00533.0380.0010.0010.0000.0000.0000.000
139A149SER 00.0150.00336.158-0.002-0.0020.0000.0000.0000.000
140A150TRP 0-0.065-0.02734.215-0.002-0.0020.0000.0000.0000.000
141A151CYS 0-0.060-0.02932.5280.0030.0030.0000.0000.0000.000
142A152HIS 0-0.010-0.02035.3270.0010.0010.0000.0000.0000.000
143A153HIS 00.0300.02136.2770.0000.0000.0000.0000.0000.000
144A154LEU 0-0.054-0.01933.0630.0020.0020.0000.0000.0000.000
145A155PRO 0-0.039-0.01835.6470.0030.0030.0000.0000.0000.000
146A156GLY 00.0630.02037.580-0.004-0.0040.0000.0000.0000.000
147A157GLU -1-0.915-0.95640.3550.0500.0500.0000.0000.0000.000
148A158GLN 00.013-0.02241.214-0.001-0.0010.0000.0000.0000.000
149A159GLY 0-0.0070.02337.2300.0040.0040.0000.0000.0000.000
150A160ARG 10.7900.86334.237-0.089-0.0890.0000.0000.0000.000
151A161PHE 00.0230.02732.7960.0060.0060.0000.0000.0000.000
152A162TYR 00.0330.00428.412-0.001-0.0010.0000.0000.0000.000
153A163ALA 00.0410.00927.7780.0050.0050.0000.0000.0000.000
154A164LEU 0-0.055-0.01221.840-0.001-0.0010.0000.0000.0000.000
155A165LYS 10.8780.94025.517-0.083-0.0830.0000.0000.0000.000
156A166GLY 00.0030.00325.2480.0090.0090.0000.0000.0000.000
157A167GLN 00.0110.00826.0570.0000.0000.0000.0000.0000.000
158A168MET 0-0.004-0.01129.3880.0050.0050.0000.0000.0000.000
159A169PRO 0-0.0130.00331.210-0.004-0.0040.0000.0000.0000.000
160A170GLU -1-0.921-0.98233.2350.0460.0460.0000.0000.0000.000
161A171ASP -1-0.868-0.93136.3620.0380.0380.0000.0000.0000.000
162A172GLU -1-0.811-0.92631.5300.0680.0680.0000.0000.0000.000
163A173ILE 0-0.035-0.01435.2420.0010.0010.0000.0000.0000.000
164A174ALA 0-0.0040.00737.762-0.001-0.0010.0000.0000.0000.000
165A175LEU 0-0.056-0.02038.277-0.003-0.0030.0000.0000.0000.000
166A176LEU 0-0.0320.00436.8910.0010.0010.0000.0000.0000.000
167A177PRO 0-0.025-0.00540.058-0.002-0.0020.0000.0000.0000.000
168A178GLU -1-0.912-0.94843.2000.0410.0410.0000.0000.0000.000
169A179GLU -1-0.829-0.91644.5500.0410.0410.0000.0000.0000.000
170A180TYR 0-0.066-0.03539.8890.0040.0040.0000.0000.0000.000
171A181GLN 0-0.025-0.01541.1430.0000.0000.0000.0000.0000.000
172A182VAL 0-0.007-0.01636.3520.0040.0040.0000.0000.0000.000
173A183GLU -1-0.818-0.88437.6470.0750.0750.0000.0000.0000.000
174A184SER 0-0.053-0.04035.1980.0020.0020.0000.0000.0000.000
175A185VAL 00.0360.01332.4840.0030.0030.0000.0000.0000.000
176A186VAL 0-0.0180.00229.299-0.003-0.0030.0000.0000.0000.000
177A187LYS 10.9780.99629.435-0.070-0.0700.0000.0000.0000.000
178A188LEU 0-0.033-0.02324.3940.0030.0030.0000.0000.0000.000
179A189GLN 0-0.047-0.03425.644-0.005-0.0050.0000.0000.0000.000
180A190VAL 00.0300.01620.324-0.001-0.0010.0000.0000.0000.000
181A191PRO 00.0030.01118.979-0.002-0.0020.0000.0000.0000.000
182A192ALA 00.0580.01218.277-0.005-0.0050.0000.0000.0000.000
183A193LEU 0-0.091-0.01915.647-0.009-0.0090.0000.0000.0000.000
184A194ASP -1-0.873-0.97020.3670.0540.0540.0000.0000.0000.000
185A195GLY 0-0.075-0.02621.1840.0100.0100.0000.0000.0000.000
186A196GLU -1-0.848-0.92022.0570.0790.0790.0000.0000.0000.000
187A197ARG 10.7990.89819.726-0.138-0.1380.0000.0000.0000.000
188A198HIS 00.0080.01025.431-0.006-0.0060.0000.0000.0000.000
189A199LEU 0-0.0160.00326.4990.0040.0040.0000.0000.0000.000
190A200VAL 00.0170.00228.675-0.007-0.0070.0000.0000.0000.000
191A201VAL 0-0.018-0.00131.4590.0060.0060.0000.0000.0000.000
192A202ILE 00.0150.00233.725-0.006-0.0060.0000.0000.0000.000
193A203LYS 10.8430.95536.421-0.066-0.0660.0000.0000.0000.000
194A204ALA 00.0580.03239.216-0.002-0.0020.0000.0000.0000.000
195A205ASN 0-0.047-0.02342.0490.0030.0030.0000.0000.0000.000
196A206LYS 10.8230.89644.606-0.054-0.0540.0000.0000.0000.000
197A207ILE -1-0.903-0.93847.8040.0370.0370.0000.0000.0000.000