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: 2JQ3R

Calculation Name: 1A58-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1A58

Chain ID: A

ChEMBL ID:

UniProt ID: Q27450

Base Structure: X-ray

Registration Date: 2023-09-20

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 177
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -1883000.268301
FMO2-HF: Nuclear repulsion 1813192.62389
FMO2-HF: Total energy -69807.644411
FMO2-MP2: Total energy -70006.06498


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.
-14.275-15.94817.488-8.757-7.059-0.055
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 : -0.005 / q_NPA : -0.008
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].
3A3LYS11.0191.0023.611-1.8260.830-0.017-1.613-1.0260.008
4A4LYS10.9030.9456.2112.3382.3380.0000.0000.0000.000
5A5ASP-1-0.804-0.9031.757-14.449-20.38616.702-6.609-4.158-0.062
6A6ARG10.7330.8574.8302.7092.824-0.001-0.008-0.1060.000
7A7ARG10.9080.9557.0790.8160.8160.0000.0000.0000.000
8A8ARG10.8680.9229.9500.7610.7610.0000.0000.0000.000
9A9VAL00.0180.01313.5760.0410.0410.0000.0000.0000.000
10A10PHE0-0.023-0.02016.2460.0010.0010.0000.0000.0000.000
11A11LEU00.0360.01220.0120.0240.0240.0000.0000.0000.000
12A12ASP-1-0.793-0.84923.054-0.202-0.2020.0000.0000.0000.000
13A13VAL0-0.012-0.02126.3430.0130.0130.0000.0000.0000.000
14A14THR0-0.019-0.00628.9280.0010.0010.0000.0000.0000.000
15A15ILE00.005-0.01032.7090.0010.0010.0000.0000.0000.000
16A16ASP-1-0.829-0.91735.205-0.071-0.0710.0000.0000.0000.000
17A17GLY0-0.018-0.00836.6310.0020.0020.0000.0000.0000.000
18A18ASN0-0.042-0.01437.039-0.003-0.0030.0000.0000.0000.000
19A19LEU0-0.026-0.02030.191-0.003-0.0030.0000.0000.0000.000
20A20ALA0-0.017-0.00531.0220.0010.0010.0000.0000.0000.000
21A21GLY00.0320.01329.332-0.005-0.0050.0000.0000.0000.000
22A22ARG10.8290.88522.6560.2430.2430.0000.0000.0000.000
23A23ILE00.0120.01721.061-0.008-0.0080.0000.0000.0000.000
24A24VAL0-0.025-0.01317.434-0.003-0.0030.0000.0000.0000.000
25A25MET0-0.025-0.00915.9010.0090.0090.0000.0000.0000.000
26A26GLU-1-0.855-0.91610.894-1.007-1.0070.0000.0000.0000.000
27A27LEU0-0.016-0.0229.6840.0670.0670.0000.0000.0000.000
28A28TYR00.016-0.0137.410-0.303-0.3030.0000.0000.0000.000
29A29ASN00.024-0.0194.900-0.016-0.0160.0000.0000.0000.000
30A30ASP-1-0.777-0.8512.416-3.434-2.0390.782-0.771-1.4060.000
31A31ILE0-0.039-0.0163.1550.7000.7980.0220.244-0.363-0.001
32A32ALA00.0230.0236.8170.3170.3170.0000.0000.0000.000
33A33PRO00.0560.0335.891-0.167-0.1670.0000.0000.0000.000
34A34ARG10.9250.9697.504-0.578-0.5780.0000.0000.0000.000
35A35THR00.002-0.02911.250-0.091-0.0910.0000.0000.0000.000
36A36CYS0-0.042-0.0048.645-0.113-0.1130.0000.0000.0000.000
37A37ASN0-0.035-0.01310.023-0.133-0.1330.0000.0000.0000.000
38A38ASN00.0180.00511.470-0.022-0.0220.0000.0000.0000.000
39A39PHE00.0460.01214.050-0.025-0.0250.0000.0000.0000.000
40A40LEU00.0130.00911.992-0.005-0.0050.0000.0000.0000.000
41A41MET00.001-0.00914.419-0.019-0.0190.0000.0000.0000.000
42A42LEU0-0.0180.01616.6660.0050.0050.0000.0000.0000.000
43A43CYS0-0.043-0.00217.656-0.003-0.0030.0000.0000.0000.000
44A44THR0-0.007-0.01517.2350.0130.0130.0000.0000.0000.000
45A45GLY0-0.0020.00619.9230.0060.0060.0000.0000.0000.000
46A46MET0-0.043-0.02518.5400.0220.0220.0000.0000.0000.000
47A47ALA00.0160.00418.6390.0140.0140.0000.0000.0000.000
48A48GLY0-0.0060.01420.5790.0210.0210.0000.0000.0000.000
49A49THR00.009-0.00524.368-0.011-0.0110.0000.0000.0000.000
50A50GLY0-0.036-0.02125.2760.0120.0120.0000.0000.0000.000
51A51LYS10.9360.97321.985-0.126-0.1260.0000.0000.0000.000
52A52ILE0-0.007-0.00926.974-0.001-0.0010.0000.0000.0000.000
53A53SER0-0.072-0.05627.912-0.009-0.0090.0000.0000.0000.000
54A54GLY00.0250.01729.540-0.006-0.0060.0000.0000.0000.000
55A55LYS10.8510.93129.4460.0070.0070.0000.0000.0000.000
56A56PRO00.0190.00227.1430.0070.0070.0000.0000.0000.000
57A57LEU0-0.0080.01321.553-0.003-0.0030.0000.0000.0000.000
58A58HIS0-0.017-0.03822.330-0.003-0.0030.0000.0000.0000.000
59A59TYR0-0.044-0.03218.9880.0070.0070.0000.0000.0000.000
60A60LYS10.9120.97024.2350.1120.1120.0000.0000.0000.000
61A61GLY00.0090.01026.6770.0110.0110.0000.0000.0000.000
62A62SER0-0.081-0.04126.4160.0060.0060.0000.0000.0000.000
63A63THR00.019-0.01128.968-0.006-0.0060.0000.0000.0000.000
64A64PHE00.0020.00724.117-0.001-0.0010.0000.0000.0000.000
65A65HIS0-0.015-0.01427.874-0.001-0.0010.0000.0000.0000.000
66A66ARG10.8950.93630.2750.0580.0580.0000.0000.0000.000
67A67VAL00.0100.01730.090-0.009-0.0090.0000.0000.0000.000
68A68ILE0-0.042-0.01631.0230.0090.0090.0000.0000.0000.000
69A69LYS10.8920.95831.7590.0760.0760.0000.0000.0000.000
70A70ASN00.0230.02332.5100.0030.0030.0000.0000.0000.000
71A71PHE0-0.0200.01127.159-0.002-0.0020.0000.0000.0000.000
72A72MET00.0170.02125.951-0.012-0.0120.0000.0000.0000.000
73A73ILE00.0070.02525.7200.0120.0120.0000.0000.0000.000
74A74GLN00.032-0.00225.523-0.008-0.0080.0000.0000.0000.000
75A75GLY00.0610.03025.0220.0050.0050.0000.0000.0000.000
76A76GLY00.0390.02023.7060.0040.0040.0000.0000.0000.000
77A77ASP-1-0.755-0.86724.528-0.014-0.0140.0000.0000.0000.000
78A78PHE00.0790.02123.325-0.003-0.0030.0000.0000.0000.000
79A79THR0-0.048-0.00828.2150.0020.0020.0000.0000.0000.000
80A80LYS10.9040.93330.7000.0050.0050.0000.0000.0000.000
81A81GLY00.0320.04731.241-0.001-0.0010.0000.0000.0000.000
82A82ASP-1-0.842-0.91432.235-0.026-0.0260.0000.0000.0000.000
83A83GLY0-0.0110.01529.8510.0000.0000.0000.0000.0000.000
84A84THR0-0.056-0.03330.1810.0070.0070.0000.0000.0000.000
85A85GLY0-0.0040.00429.9490.0080.0080.0000.0000.0000.000
86A86GLY0-0.015-0.00626.023-0.003-0.0030.0000.0000.0000.000
87A87GLU-1-0.766-0.85524.2190.0650.0650.0000.0000.0000.000
88A88SER0-0.004-0.00119.069-0.007-0.0070.0000.0000.0000.000
89A89ILE00.017-0.00915.1470.0040.0040.0000.0000.0000.000
90A90TYR0-0.092-0.06513.3010.0490.0490.0000.0000.0000.000
91A91GLY0-0.041-0.00719.6170.0130.0130.0000.0000.0000.000
92A92GLY00.011-0.00323.1870.0120.0120.0000.0000.0000.000
93A93MET0-0.066-0.01822.494-0.015-0.0150.0000.0000.0000.000
94A94PHE0-0.031-0.01915.1410.0190.0190.0000.0000.0000.000
95A95ASP-1-0.847-0.93917.6170.2230.2230.0000.0000.0000.000
96A96ASP-1-0.849-0.90717.2210.0720.0720.0000.0000.0000.000
97A97GLU-1-0.785-0.86810.6760.4380.4380.0000.0000.0000.000
98A98GLU-1-0.890-0.95111.9450.1460.1460.0000.0000.0000.000
99A99PHE00.0130.00913.135-0.057-0.0570.0000.0000.0000.000
100A100VAL0-0.010-0.00810.045-0.040-0.0400.0000.0000.0000.000
101A101MET0-0.0260.00511.447-0.058-0.0580.0000.0000.0000.000
102A102LYS10.8710.93914.1810.2070.2070.0000.0000.0000.000
103A103HIS00.001-0.00417.911-0.034-0.0340.0000.0000.0000.000
104A104ASP-1-0.890-0.96418.662-0.274-0.2740.0000.0000.0000.000
105A105GLU-1-0.836-0.90818.393-0.371-0.3710.0000.0000.0000.000
106A106PRO0-0.030-0.00121.6810.0030.0030.0000.0000.0000.000
107A107PHE0-0.001-0.01921.525-0.029-0.0290.0000.0000.0000.000
108A108VAL00.0350.04616.709-0.042-0.0420.0000.0000.0000.000
109A109VAL0-0.029-0.02816.0840.0400.0400.0000.0000.0000.000
110A110SER00.019-0.01216.359-0.012-0.0120.0000.0000.0000.000
111A111MET00.0210.02316.727-0.003-0.0030.0000.0000.0000.000
112A112ALA0-0.030-0.01319.4530.0070.0070.0000.0000.0000.000
113A113ASN0-0.035-0.02521.8280.0000.0000.0000.0000.0000.000
114A114LYS10.8400.90524.628-0.001-0.0010.0000.0000.0000.000
115A115GLY00.0560.03926.4560.0050.0050.0000.0000.0000.000
116A116PRO0-0.0160.00123.907-0.002-0.0020.0000.0000.0000.000
117A117ASN0-0.001-0.00820.754-0.007-0.0070.0000.0000.0000.000
118A118THR00.014-0.01322.525-0.002-0.0020.0000.0000.0000.000
119A119ASN0-0.044-0.02618.560-0.051-0.0510.0000.0000.0000.000
120A120GLY00.0590.02520.9970.0200.0200.0000.0000.0000.000
121A121SER0-0.003-0.01720.2230.0050.0050.0000.0000.0000.000
122A122GLN0-0.092-0.05321.712-0.028-0.0280.0000.0000.0000.000
123A123PHE00.0220.02419.7910.0040.0040.0000.0000.0000.000
124A124PHE0-0.040-0.03221.2470.0060.0060.0000.0000.0000.000
125A125ILE00.0300.02120.695-0.018-0.0180.0000.0000.0000.000
126A126THR0-0.001-0.00522.2270.0110.0110.0000.0000.0000.000
127A127THR0-0.027-0.04124.076-0.019-0.0190.0000.0000.0000.000
128A128THR0-0.010-0.01026.1410.0010.0010.0000.0000.0000.000
129A129PRO0-0.0160.00724.167-0.003-0.0030.0000.0000.0000.000
130A130ALA0-0.013-0.01724.0200.0170.0170.0000.0000.0000.000
131A131PRO00.0520.00923.5420.0050.0050.0000.0000.0000.000
132A132HIS00.0150.01324.5120.0060.0060.0000.0000.0000.000
133A133LEU0-0.004-0.00123.5310.0150.0150.0000.0000.0000.000
134A134ASN00.0520.03120.750-0.013-0.0130.0000.0000.0000.000
135A135ASN0-0.024-0.02119.8820.0050.0050.0000.0000.0000.000
136A136ILE0-0.0190.02020.9690.0190.0190.0000.0000.0000.000
137A137HIS10.8260.91220.5890.0550.0550.0000.0000.0000.000
138A138VAL00.0720.03914.176-0.023-0.0230.0000.0000.0000.000
139A139VAL00.0010.00714.645-0.012-0.0120.0000.0000.0000.000
140A140PHE00.006-0.01811.631-0.005-0.0050.0000.0000.0000.000
141A141GLY00.0550.01711.308-0.110-0.1100.0000.0000.0000.000
142A142LYS10.7800.90313.4570.4210.4210.0000.0000.0000.000
143A143VAL0-0.012-0.00515.963-0.034-0.0340.0000.0000.0000.000
144A144VAL0-0.064-0.03815.603-0.009-0.0090.0000.0000.0000.000
145A145SER00.002-0.00918.7960.0030.0030.0000.0000.0000.000
146A146GLY00.0660.04122.122-0.003-0.0030.0000.0000.0000.000
147A147GLN0-0.016-0.01522.2780.0180.0180.0000.0000.0000.000
148A148GLU-1-0.826-0.92625.159-0.198-0.1980.0000.0000.0000.000
149A149VAL0-0.0020.00626.4050.0160.0160.0000.0000.0000.000
150A150VAL0-0.012-0.00623.8770.0130.0130.0000.0000.0000.000
151A151THR00.0350.00727.3140.0130.0130.0000.0000.0000.000
152A152LYS10.9340.98030.2660.1240.1240.0000.0000.0000.000
153A153ILE00.001-0.01028.2210.0110.0110.0000.0000.0000.000
154A154GLU-1-0.807-0.89629.963-0.119-0.1190.0000.0000.0000.000
155A155TYR0-0.086-0.07831.8280.0100.0100.0000.0000.0000.000
156A156LEU0-0.0030.02234.0580.0060.0060.0000.0000.0000.000
157A157LYS10.9510.97136.9150.0560.0560.0000.0000.0000.000
158A158THR00.0270.02436.1510.0000.0000.0000.0000.0000.000
159A159ASN00.0150.00039.3130.0030.0030.0000.0000.0000.000
160A160SER00.0460.00740.170-0.002-0.0020.0000.0000.0000.000
161A161LYS10.8650.94436.4960.0300.0300.0000.0000.0000.000
162A162ASN0-0.052-0.04035.002-0.004-0.0040.0000.0000.0000.000
163A163ARG10.9170.95734.3630.0460.0460.0000.0000.0000.000
164A164PRO0-0.015-0.01133.5220.0030.0030.0000.0000.0000.000
165A165LEU0-0.055-0.03736.6950.0030.0030.0000.0000.0000.000
166A166ALA0-0.0030.02537.4300.0020.0020.0000.0000.0000.000
167A167ASP-1-0.891-0.95736.151-0.064-0.0640.0000.0000.0000.000
168A168VAL0-0.056-0.01830.286-0.006-0.0060.0000.0000.0000.000
169A169VAL00.017-0.00230.9080.0020.0020.0000.0000.0000.000
170A170ILE00.0110.01524.234-0.011-0.0110.0000.0000.0000.000
171A171LEU0-0.0040.01127.9260.0070.0070.0000.0000.0000.000
172A172ASN0-0.038-0.03126.1510.0170.0170.0000.0000.0000.000
173A173CYS0-0.035-0.01321.6780.0020.0020.0000.0000.0000.000
174A174GLY00.0300.03019.8600.0190.0190.0000.0000.0000.000
175A175GLU-1-0.827-0.90012.940-0.550-0.5500.0000.0000.0000.000
176A176LEU0-0.041-0.02615.9400.0360.0360.0000.0000.0000.000
177A177VAL0-0.0030.00714.791-0.117-0.1170.0000.0000.0000.000