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: 8249Y

Calculation Name: 1JSX-A-Xray372

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: 2023-06-19

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 -2242053.22789
FMO2-HF: Nuclear repulsion 2165097.167481
FMO2-HF: Total energy -76956.060409
FMO2-MP2: Total energy -77182.077834


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.
-12.883-11.7689.844-4.695-6.264-0.012
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 : 0.021 / 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].
3A3ASN00.0240.0101.999-5.539-4.7785.762-3.097-3.425-0.025
4A4LYS10.9180.9572.380-9.899-9.7494.084-1.595-2.6390.013
5A5LEU00.0150.0214.852-0.147-0.1470.0000.0000.0000.000
6A6SER0-0.016-0.0277.3810.1700.1700.0000.0000.0000.000
7A7LEU00.014-0.0108.2580.0730.0730.0000.0000.0000.000
8A8LEU0-0.037-0.0169.805-0.007-0.0070.0000.0000.0000.000
9A9LEU0-0.0050.00611.592-0.023-0.0230.0000.0000.0000.000
10A10LYS10.8190.89611.484-0.048-0.0480.0000.0000.0000.000
11A11ASP-1-0.812-0.89214.1190.3600.3600.0000.0000.0000.000
12A12ALA0-0.0150.00116.034-0.006-0.0060.0000.0000.0000.000
13A13GLY0-0.025-0.02118.566-0.017-0.0170.0000.0000.0000.000
14A14ILE0-0.044-0.01518.932-0.010-0.0100.0000.0000.0000.000
15A15SER0-0.0220.00019.2230.0200.0200.0000.0000.0000.000
16A16LEU00.009-0.00615.4480.0120.0120.0000.0000.0000.000
17A17THR00.011-0.00618.5800.0020.0020.0000.0000.0000.000
18A18ASP-1-0.855-0.93816.3520.2580.2580.0000.0000.0000.000
19A19HIS0-0.0100.01315.7680.0580.0580.0000.0000.0000.000
20A20GLN00.0760.05416.4930.0370.0370.0000.0000.0000.000
21A21LYS10.8690.93110.818-0.466-0.4660.0000.0000.0000.000
22A22ASN0-0.048-0.04711.9530.2000.2000.0000.0000.0000.000
23A23GLN00.020-0.00112.1660.1250.1250.0000.0000.0000.000
24A24LEU00.0400.02611.2820.0800.0800.0000.0000.0000.000
25A25ILE0-0.049-0.0316.8220.3870.3870.0000.0000.0000.000
26A26ALA00.0110.0067.7660.5790.5790.0000.0000.0000.000
27A27TYR00.014-0.0159.7840.0220.0220.0000.0000.0000.000
28A28VAL0-0.004-0.0025.0940.0010.0010.0000.0000.0000.000
29A29ASN0-0.015-0.0054.7121.5561.665-0.001-0.001-0.1070.000
30A30MET0-0.0250.0056.659-0.499-0.4990.0000.0000.0000.000
31A31LEU00.0070.0029.638-0.188-0.1880.0000.0000.0000.000
32A32HIS0-0.013-0.0055.237-0.329-0.234-0.001-0.002-0.0930.000
33A33LYS10.9330.9657.826-0.117-0.1170.0000.0000.0000.000
34A34TRP0-0.045-0.0089.968-0.057-0.0570.0000.0000.0000.000
35A35ASN0-0.084-0.03610.566-0.070-0.0700.0000.0000.0000.000
36A48GLU-1-0.772-0.8729.325-0.088-0.0880.0000.0000.0000.000
37A49MET00.0340.02310.5540.0670.0670.0000.0000.0000.000
38A50LEU0-0.0030.0137.1720.0330.0330.0000.0000.0000.000
39A51VAL00.0250.0057.4350.0790.0790.0000.0000.0000.000
40A52ARG10.8430.8919.979-0.033-0.0330.0000.0000.0000.000
41A53HIS00.0660.03713.4140.0110.0110.0000.0000.0000.000
42A54ILE0-0.0160.01410.3440.0110.0110.0000.0000.0000.000
43A55LEU00.0360.01813.546-0.008-0.0080.0000.0000.0000.000
44A56ASP-1-0.799-0.88515.3690.0820.0820.0000.0000.0000.000
45A57SER0-0.053-0.04716.854-0.015-0.0150.0000.0000.0000.000
46A58ILE0-0.005-0.00714.833-0.006-0.0060.0000.0000.0000.000
47A59VAL0-0.013-0.00918.691-0.013-0.0130.0000.0000.0000.000
48A60VAL00.0140.00021.178-0.014-0.0140.0000.0000.0000.000
49A61ALA00.0270.01421.831-0.010-0.0100.0000.0000.0000.000
50A62PRO0-0.020-0.01023.582-0.007-0.0070.0000.0000.0000.000
51A63TYR00.0020.00625.943-0.009-0.0090.0000.0000.0000.000
52A64LEU0-0.0240.01525.061-0.007-0.0070.0000.0000.0000.000
53A65GLN0-0.011-0.00629.1590.0010.0010.0000.0000.0000.000
54A66GLY00.015-0.00932.580-0.004-0.0040.0000.0000.0000.000
55A67GLU-1-0.954-0.97131.5530.0780.0780.0000.0000.0000.000
56A68ARG10.8560.93631.090-0.056-0.0560.0000.0000.0000.000
57A69PHE0-0.0110.00127.759-0.005-0.0050.0000.0000.0000.000
58A70ILE0-0.009-0.00128.0260.0020.0020.0000.0000.0000.000
59A71ASP-1-0.786-0.86522.0990.1130.1130.0000.0000.0000.000
60A72VAL00.0290.01825.705-0.003-0.0030.0000.0000.0000.000
61A73GLY0-0.0030.01625.394-0.003-0.0030.0000.0000.0000.000
62A74THR00.007-0.02121.3010.0040.0040.0000.0000.0000.000
63A75GLY00.0050.00719.8730.0120.0120.0000.0000.0000.000
64A76PRO0-0.050-0.04215.166-0.001-0.0010.0000.0000.0000.000
65A77GLY00.0330.02616.5700.0410.0410.0000.0000.0000.000
66A78LEU0-0.051-0.00313.9410.0300.0300.0000.0000.0000.000
67A79PRO00.0850.02318.088-0.024-0.0240.0000.0000.0000.000
68A80GLY00.0500.00019.2160.0210.0210.0000.0000.0000.000
69A81ILE0-0.024-0.00115.7020.0010.0010.0000.0000.0000.000
70A82PRO0-0.016-0.01414.4600.0160.0160.0000.0000.0000.000
71A83LEU00.0010.01516.851-0.002-0.0020.0000.0000.0000.000
72A84SER0-0.021-0.01419.654-0.003-0.0030.0000.0000.0000.000
73A85ILE0-0.016-0.00314.9690.0040.0040.0000.0000.0000.000
74A86VAL0-0.035-0.02918.062-0.003-0.0030.0000.0000.0000.000
75A87ARG10.7470.86620.683-0.131-0.1310.0000.0000.0000.000
76A88PRO00.008-0.00522.371-0.006-0.0060.0000.0000.0000.000
77A89GLU-1-0.838-0.90024.6650.1160.1160.0000.0000.0000.000
78A90ALA00.0150.02427.160-0.010-0.0100.0000.0000.0000.000
79A91HIS0-0.037-0.03126.8180.0140.0140.0000.0000.0000.000
80A92PHE00.004-0.00524.468-0.002-0.0020.0000.0000.0000.000
81A93THR0-0.022-0.03425.9930.0040.0040.0000.0000.0000.000
82A94LEU0-0.050-0.02521.2200.0050.0050.0000.0000.0000.000
83A95LEU00.0460.03125.029-0.005-0.0050.0000.0000.0000.000
84A96ASP-1-0.772-0.88523.7620.0470.0470.0000.0000.0000.000
85A97SER00.0390.00226.261-0.004-0.0040.0000.0000.0000.000
86A98LEU0-0.059-0.01925.269-0.007-0.0070.0000.0000.0000.000
87A99GLY00.0490.01924.7250.0050.0050.0000.0000.0000.000
88A100LYS10.8840.94218.7850.0400.0400.0000.0000.0000.000
89A101ARG10.9020.94020.315-0.027-0.0270.0000.0000.0000.000
90A102VAL00.0570.03420.8360.0150.0150.0000.0000.0000.000
91A103ARG10.9420.96922.571-0.006-0.0060.0000.0000.0000.000
92A104PHE0-0.0130.00413.079-0.004-0.0040.0000.0000.0000.000
93A105LEU00.0500.01618.1660.0240.0240.0000.0000.0000.000
94A106ARG10.9110.94719.824-0.050-0.0500.0000.0000.0000.000
95A107GLN0-0.036-0.01617.5380.0070.0070.0000.0000.0000.000
96A108VAL00.003-0.00914.6610.0180.0180.0000.0000.0000.000
97A109GLN0-0.026-0.01617.0850.0140.0140.0000.0000.0000.000
98A110HIS0-0.034-0.00819.424-0.001-0.0010.0000.0000.0000.000
99A111GLU-1-0.954-0.99215.3670.1690.1690.0000.0000.0000.000
100A112LEU0-0.078-0.03913.3970.0280.0280.0000.0000.0000.000
101A113LYS10.9260.97117.309-0.156-0.1560.0000.0000.0000.000
102A114LEU00.0000.01217.9290.0000.0000.0000.0000.0000.000
103A115GLU-1-0.912-0.96821.8880.1020.1020.0000.0000.0000.000
104A116ASN0-0.0380.00123.427-0.001-0.0010.0000.0000.0000.000
105A117ILE0-0.007-0.00820.9170.0020.0020.0000.0000.0000.000
106A118GLU-1-0.801-0.86525.1450.0620.0620.0000.0000.0000.000
107A119PRO0-0.0220.00323.035-0.006-0.0060.0000.0000.0000.000
108A120VAL00.0160.01425.456-0.010-0.0100.0000.0000.0000.000
109A121GLN0-0.064-0.04027.7460.0010.0010.0000.0000.0000.000
110A122SER00.033-0.00229.247-0.004-0.0040.0000.0000.0000.000
111A123ARG10.8620.92830.949-0.016-0.0160.0000.0000.0000.000
112A124VAL00.0520.01831.7280.0020.0020.0000.0000.0000.000
113A125GLU-1-0.799-0.88233.9300.0290.0290.0000.0000.0000.000
114A126GLU-1-0.911-0.93035.3110.0210.0210.0000.0000.0000.000
115A127PHE00.0000.00232.4180.0010.0010.0000.0000.0000.000
116A128PRO00.005-0.01335.3710.0000.0000.0000.0000.0000.000
117A129SER0-0.006-0.01636.5300.0000.0000.0000.0000.0000.000
118A130GLU-1-0.921-0.93437.4280.0300.0300.0000.0000.0000.000
119A131PRO0-0.035-0.00237.081-0.001-0.0010.0000.0000.0000.000
120A132PRO00.0370.01337.0770.0030.0030.0000.0000.0000.000
121A133PHE0-0.032-0.01431.4610.0030.0030.0000.0000.0000.000
122A134ASP-1-0.761-0.88233.2510.0600.0600.0000.0000.0000.000
123A135GLY0-0.037-0.03231.318-0.002-0.0020.0000.0000.0000.000
124A136VAL0-0.0090.00530.1570.0050.0050.0000.0000.0000.000
125A137ILE0-0.021-0.00924.2340.0000.0000.0000.0000.0000.000
126A138SER00.038-0.01725.035-0.003-0.0030.0000.0000.0000.000
127A139ARG10.8240.91419.538-0.072-0.0720.0000.0000.0000.000
128A140ALA0-0.091-0.04823.549-0.005-0.0050.0000.0000.0000.000
129A141PHE00.0080.01025.599-0.006-0.0060.0000.0000.0000.000
130A142ALA0-0.0050.00928.1770.0020.0020.0000.0000.0000.000
131A143SER0-0.037-0.05129.9710.0010.0010.0000.0000.0000.000
132A144LEU00.022-0.00731.1620.0020.0020.0000.0000.0000.000
133A145ASN00.0090.01633.2810.0020.0020.0000.0000.0000.000
134A146ASP-1-0.829-0.88432.5770.0220.0220.0000.0000.0000.000
135A147MET0-0.043-0.02029.3730.0020.0020.0000.0000.0000.000
136A148VAL00.0110.01332.3480.0020.0020.0000.0000.0000.000
137A149SER00.0200.00435.4940.0000.0000.0000.0000.0000.000
138A150TRP0-0.072-0.03833.560-0.001-0.0010.0000.0000.0000.000
139A151CYS0-0.062-0.02732.2610.0020.0020.0000.0000.0000.000
140A152HIS10.8130.89134.988-0.026-0.0260.0000.0000.0000.000
141A153HIS00.007-0.00836.0500.0000.0000.0000.0000.0000.000
142A154LEU0-0.0350.00432.3430.0010.0010.0000.0000.0000.000
143A155PRO0-0.0080.00735.5500.0030.0030.0000.0000.0000.000
144A156GLY00.0640.02336.816-0.003-0.0030.0000.0000.0000.000
145A157GLU-1-0.845-0.90939.9220.0320.0320.0000.0000.0000.000
146A158GLN00.001-0.00840.790-0.002-0.0020.0000.0000.0000.000
147A159GLY00.0260.03536.7360.0020.0020.0000.0000.0000.000
148A160ARG10.7730.85833.780-0.058-0.0580.0000.0000.0000.000
149A161PHE00.0100.00832.2830.0020.0020.0000.0000.0000.000
150A162TYR00.009-0.00528.019-0.001-0.0010.0000.0000.0000.000
151A163ALA00.0380.00727.3780.0020.0020.0000.0000.0000.000
152A164LEU0-0.043-0.00821.6240.0000.0000.0000.0000.0000.000
153A165LYS10.8270.89925.523-0.038-0.0380.0000.0000.0000.000
154A166GLY00.0230.01525.0920.0050.0050.0000.0000.0000.000
155A167GLN00.019-0.00525.9060.0020.0020.0000.0000.0000.000
156A168MET00.0210.02029.4070.0040.0040.0000.0000.0000.000
157A169PRO0-0.0090.00030.990-0.003-0.0030.0000.0000.0000.000
158A170GLU-1-0.927-0.97933.0180.0250.0250.0000.0000.0000.000
159A171ASP-1-0.887-0.94436.2670.0180.0180.0000.0000.0000.000
160A172GLU-1-0.808-0.90831.2420.0310.0310.0000.0000.0000.000
161A173ILE0-0.028-0.02034.9410.0010.0010.0000.0000.0000.000
162A174ALA0-0.016-0.00337.7420.0000.0000.0000.0000.0000.000
163A175LEU0-0.023-0.00438.383-0.002-0.0020.0000.0000.0000.000
164A176LEU0-0.052-0.00936.4600.0000.0000.0000.0000.0000.000
165A177PRO0-0.022-0.00240.035-0.001-0.0010.0000.0000.0000.000
166A178GLU-1-0.907-0.95242.8450.0240.0240.0000.0000.0000.000
167A179GLU-1-0.884-0.94344.1710.0220.0220.0000.0000.0000.000
168A180TYR0-0.052-0.03439.7260.0030.0030.0000.0000.0000.000
169A181GLN0-0.023-0.00340.9380.0000.0000.0000.0000.0000.000
170A182VAL00.003-0.01535.8480.0020.0020.0000.0000.0000.000
171A183GLU-1-0.799-0.85436.5610.0500.0500.0000.0000.0000.000
172A184SER0-0.027-0.02634.7660.0010.0010.0000.0000.0000.000
173A185VAL00.017-0.00331.8950.0010.0010.0000.0000.0000.000
174A186VAL0-0.0010.01329.107-0.002-0.0020.0000.0000.0000.000
175A187LYS10.8560.92829.005-0.040-0.0400.0000.0000.0000.000
176A188LEU0-0.045-0.02224.1390.0030.0030.0000.0000.0000.000
177A189GLN0-0.004-0.01425.299-0.007-0.0070.0000.0000.0000.000
178A190VAL00.0210.01620.6200.0010.0010.0000.0000.0000.000
179A191PRO0-0.0210.00818.188-0.001-0.0010.0000.0000.0000.000
180A192ALA00.0530.01818.753-0.006-0.0060.0000.0000.0000.000
181A193LEU0-0.089-0.04316.4950.0050.0050.0000.0000.0000.000
182A194ASP-1-0.819-0.91820.2990.0270.0270.0000.0000.0000.000
183A195GLY0-0.054-0.03821.4670.0020.0020.0000.0000.0000.000
184A196GLU-1-0.849-0.89922.5130.0440.0440.0000.0000.0000.000
185A197ARG10.8040.88519.330-0.065-0.0650.0000.0000.0000.000
186A198HIS00.002-0.01225.379-0.002-0.0020.0000.0000.0000.000
187A199LEU0-0.0130.00126.0700.0010.0010.0000.0000.0000.000
188A200VAL00.0020.00228.153-0.002-0.0020.0000.0000.0000.000
189A201VAL0-0.014-0.00330.7520.0040.0040.0000.0000.0000.000
190A202ILE00.002-0.00233.177-0.004-0.0040.0000.0000.0000.000
191A203LYS10.8130.89935.971-0.039-0.0390.0000.0000.0000.000
192A204ALA00.0620.03138.786-0.002-0.0020.0000.0000.0000.000
193A205ASN0-0.011-0.00641.6650.0020.0020.0000.0000.0000.000
194A206LYS10.8000.89144.472-0.033-0.0330.0000.0000.0000.000
195A207ILE0-0.020-0.00947.570-0.002-0.0020.0000.0000.0000.000