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: 5292Z

Calculation Name: 5J1B-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 5J1B

Chain ID: A

ChEMBL ID:

UniProt ID: P32566

Base Structure: X-ray

Registration Date: 2023-06-21

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 226
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2842125.678557
FMO2-HF: Nuclear repulsion 2752685.468711
FMO2-HF: Total energy -89440.209846
FMO2-MP2: Total energy -89704.902409


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:84:ASN)


Summations of interaction energy for fragment #1(A:84:ASN)
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.
3.4937.4770.068-1.81-2.2410.003
Interaction energy analysis for fragmet #1(A:84:ASN)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.022 / q_NPA : 0.006
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].
3A86GLY00.0440.0242.7700.5823.6880.067-1.611-1.5620.003
4A87VAL0-0.0100.0003.2412.8893.4230.003-0.155-0.3820.000
5A88SER00.002-0.0054.1811.6441.769-0.001-0.003-0.1200.000
6A89GLU-1-0.849-0.9294.287-6.636-6.417-0.001-0.041-0.1770.000
7A90THR00.007-0.0187.4950.9350.9350.0000.0000.0000.000
8A91LEU0-0.061-0.0188.5430.5690.5690.0000.0000.0000.000
9A92LEU0-0.0180.00110.2670.3810.3810.0000.0000.0000.000
10A93ALA00.0130.00711.6410.2960.2960.0000.0000.0000.000
11A94TRP00.0380.00812.8650.2540.2540.0000.0000.0000.000
12A95ARG10.9090.97114.7180.9480.9480.0000.0000.0000.000
13A96HIS0-0.068-0.05615.0520.1000.1000.0000.0000.0000.000
14A97ILE00.0070.01116.4040.1030.1030.0000.0000.0000.000
15A98ASP-1-0.822-0.88719.081-0.808-0.8080.0000.0000.0000.000
16A99PHE0-0.101-0.03820.7090.0680.0680.0000.0000.0000.000
17A100TRP00.0770.04522.0790.0420.0420.0000.0000.0000.000
18A101THR00.024-0.01523.0020.0540.0540.0000.0000.0000.000
19A102SER0-0.094-0.04925.0380.0460.0460.0000.0000.0000.000
20A103GLU-1-0.959-0.97026.818-0.328-0.3280.0000.0000.0000.000
21A104HIS0-0.097-0.05926.4430.0580.0580.0000.0000.0000.000
22A105ASN0-0.047-0.03828.4950.0200.0200.0000.0000.0000.000
23A106PRO00.0640.02628.954-0.028-0.0280.0000.0000.0000.000
24A107ASP-1-0.863-0.91830.104-0.355-0.3550.0000.0000.0000.000
25A108LEU00.0100.00925.852-0.020-0.0200.0000.0000.0000.000
26A109ASN0-0.079-0.04524.376-0.012-0.0120.0000.0000.0000.000
27A110ALA00.0120.00526.114-0.027-0.0270.0000.0000.0000.000
28A111THR0-0.026-0.00126.760-0.011-0.0110.0000.0000.0000.000
29A112LEU0-0.057-0.02821.493-0.035-0.0350.0000.0000.0000.000
30A113SER00.0220.00523.0750.0230.0230.0000.0000.0000.000
31A114ASP-1-0.887-0.93222.215-0.583-0.5830.0000.0000.0000.000
32A115PRO0-0.066-0.02918.257-0.043-0.0430.0000.0000.0000.000
33A116CYS0-0.0220.00218.4330.0470.0470.0000.0000.0000.000
34A117THR0-0.061-0.06718.848-0.034-0.0340.0000.0000.0000.000
35A118GLN00.007-0.01415.553-0.165-0.1650.0000.0000.0000.000
36A119ASN0-0.0120.01418.666-0.022-0.0220.0000.0000.0000.000
37A120ASP-1-0.747-0.83521.425-0.537-0.5370.0000.0000.0000.000
38A121ILE00.007-0.00315.300-0.025-0.0250.0000.0000.0000.000
39A122THR0-0.051-0.04318.942-0.011-0.0110.0000.0000.0000.000
40A123HIS0-0.030-0.02920.0550.0310.0310.0000.0000.0000.000
41A124ALA00.0580.03820.3490.0230.0230.0000.0000.0000.000
42A125GLU-1-0.811-0.89215.456-0.972-0.9720.0000.0000.0000.000
43A126GLU-1-0.916-0.95619.975-0.316-0.3160.0000.0000.0000.000
44A127ASP-1-0.897-0.94623.435-0.373-0.3730.0000.0000.0000.000
45A128LEU0-0.097-0.04920.9790.0120.0120.0000.0000.0000.000
46A129GLU-1-1.000-0.98622.915-0.306-0.3060.0000.0000.0000.000
47A130VAL0-0.058-0.02617.6400.0140.0140.0000.0000.0000.000
48A131SER0-0.0060.00014.2310.0180.0180.0000.0000.0000.000
49A132PHE00.0160.00113.854-0.113-0.1130.0000.0000.0000.000
50A133PRO00.004-0.0139.211-0.082-0.0820.0000.0000.0000.000
51A134ASN0-0.023-0.0194.8270.8560.8560.0000.0000.0000.000
52A135PRO00.0050.0085.8010.3080.3080.0000.0000.0000.000
53A136VAL00.0350.0207.8690.4500.4500.0000.0000.0000.000
54A137LYS10.7930.88110.9441.4161.4160.0000.0000.0000.000
55A138ALA0-0.025-0.0158.6760.2100.2100.0000.0000.0000.000
56A139SER00.0310.01410.7460.2280.2280.0000.0000.0000.000
57A140PHE00.0510.02213.1380.1400.1400.0000.0000.0000.000
58A141LYS10.8280.92812.9271.3271.3270.0000.0000.0000.000
59A142ILE0-0.062-0.02712.6530.0180.0180.0000.0000.0000.000
60A143HIS10.8240.87616.5540.9750.9750.0000.0000.0000.000
61A144ASP-1-0.764-0.86918.603-0.821-0.8210.0000.0000.0000.000
62A145GLY0-0.022-0.00920.0820.0720.0720.0000.0000.0000.000
63A146GLN0-0.030-0.02921.839-0.060-0.0600.0000.0000.0000.000
64A147GLU-1-0.780-0.89924.967-0.432-0.4320.0000.0000.0000.000
65A148ASP-1-0.905-0.95828.445-0.367-0.3670.0000.0000.0000.000
66A149LEU0-0.065-0.01432.1580.0250.0250.0000.0000.0000.000
67A150GLU-1-0.869-0.91634.129-0.259-0.2590.0000.0000.0000.000
68A151SER0-0.160-0.09937.6250.0090.0090.0000.0000.0000.000
69A152MET0-0.041-0.01036.1700.0180.0180.0000.0000.0000.000
70A153THR0-0.021-0.03633.083-0.004-0.0040.0000.0000.0000.000
71A154GLY0-0.040-0.00134.2330.0030.0030.0000.0000.0000.000
72A155THR0-0.059-0.04927.998-0.015-0.0150.0000.0000.0000.000
73A156SER0-0.019-0.03129.067-0.031-0.0310.0000.0000.0000.000
74A157GLY0-0.0040.00726.692-0.025-0.0250.0000.0000.0000.000
75A158LEU0-0.006-0.00620.0630.0040.0040.0000.0000.0000.000
76A159PHE0-0.028-0.02617.808-0.024-0.0240.0000.0000.0000.000
77A160TYR0-0.088-0.08022.7120.0100.0100.0000.0000.0000.000
78A161GLY00.0720.04626.2680.0370.0370.0000.0000.0000.000
79A162PHE0-0.060-0.01924.4520.0150.0150.0000.0000.0000.000
80A163GLN00.0590.04024.528-0.028-0.0280.0000.0000.0000.000
81A164LEU0-0.055-0.02717.947-0.050-0.0500.0000.0000.0000.000
82A165MET0-0.057-0.01921.8330.0710.0710.0000.0000.0000.000
83A166THR00.0520.02421.509-0.069-0.0690.0000.0000.0000.000
84A167LEU00.001-0.01519.004-0.012-0.0120.0000.0000.0000.000
85A168ASP-1-0.846-0.92322.035-0.512-0.5120.0000.0000.0000.000
86A169GLN00.0040.01425.128-0.002-0.0020.0000.0000.0000.000
87A170VAL0-0.0040.00719.5020.0100.0100.0000.0000.0000.000
88A171VAL00.0190.02222.9150.0130.0130.0000.0000.0000.000
89A172ALA00.0250.00924.5750.0320.0320.0000.0000.0000.000
90A173MET00.007-0.00525.3390.0450.0450.0000.0000.0000.000
91A174THR0-0.014-0.02222.6850.0030.0030.0000.0000.0000.000
92A175GLN0-0.037-0.02025.1200.0480.0480.0000.0000.0000.000
93A176ALA0-0.029-0.00428.3140.0360.0360.0000.0000.0000.000
94A177TRP00.012-0.01526.1750.0560.0560.0000.0000.0000.000
95A178ARG10.8370.91822.7830.5100.5100.0000.0000.0000.000
96A179ASN0-0.007-0.00929.1040.0400.0400.0000.0000.0000.000
97A180VAL0-0.0100.00631.2660.0280.0280.0000.0000.0000.000
98A181ALA00.0360.02029.2200.0240.0240.0000.0000.0000.000
99A182LYS10.9290.96131.3670.3090.3090.0000.0000.0000.000
100A183ASN0-0.025-0.01234.1790.0340.0340.0000.0000.0000.000
101A184LEU00.0120.00832.8540.0160.0160.0000.0000.0000.000
102A185ASN0-0.025-0.01431.9370.0100.0100.0000.0000.0000.000
103A186LYS10.8430.91135.7170.2140.2140.0000.0000.0000.000
104A187ARG10.8880.95338.3990.2110.2110.0000.0000.0000.000
105A188SER00.0250.03636.329-0.003-0.0030.0000.0000.0000.000
106A218PRO00.0340.00134.0200.0090.0090.0000.0000.0000.000
107A219ASP-1-0.902-0.93732.143-0.213-0.2130.0000.0000.0000.000
108A220GLN0-0.055-0.03528.217-0.042-0.0420.0000.0000.0000.000
109A221LYS10.8330.90126.7380.2520.2520.0000.0000.0000.000
110A222SER0-0.007-0.00220.784-0.045-0.0450.0000.0000.0000.000
111A223ILE0-0.046-0.00620.9210.0560.0560.0000.0000.0000.000
112A224PRO00.1290.03716.566-0.055-0.0550.0000.0000.0000.000
113A225PRO0-0.0010.01119.780-0.016-0.0160.0000.0000.0000.000
114A226ASN0-0.012-0.00820.8560.0010.0010.0000.0000.0000.000
115A227ALA00.0550.04316.3900.0190.0190.0000.0000.0000.000
116A228VAL00.0560.04117.325-0.068-0.0680.0000.0000.0000.000
117A229GLN0-0.019-0.01019.7990.0860.0860.0000.0000.0000.000
118A230PRO00.0000.00822.781-0.021-0.0210.0000.0000.0000.000
119A231VAL0-0.025-0.02325.2780.0360.0360.0000.0000.0000.000
120A232TYR0-0.018-0.02026.897-0.025-0.0250.0000.0000.0000.000
121A233ALA00.0120.00726.765-0.026-0.0260.0000.0000.0000.000
122A234HIS00.025-0.00323.1460.0140.0140.0000.0000.0000.000
123A235PRO0-0.033-0.02424.395-0.036-0.0360.0000.0000.0000.000
124A236ALA00.0440.03019.781-0.012-0.0120.0000.0000.0000.000
125A237TRP0-0.080-0.02319.267-0.060-0.0600.0000.0000.0000.000
126A238ILE00.0530.03217.6120.0640.0640.0000.0000.0000.000
127A239PRO0-0.049-0.01118.674-0.119-0.1190.0000.0000.0000.000
128A240LEU00.007-0.01715.040-0.026-0.0260.0000.0000.0000.000
129A241ILE00.0010.01618.9230.0040.0040.0000.0000.0000.000
130A242THR0-0.039-0.03321.8230.0290.0290.0000.0000.0000.000
131A243ASP-1-0.781-0.90925.605-0.456-0.4560.0000.0000.0000.000
132A244ASN0-0.0140.00528.2650.0200.0200.0000.0000.0000.000
133A245ALA0-0.0050.02030.8140.0320.0320.0000.0000.0000.000
134A246GLY0-0.066-0.05030.9510.0250.0250.0000.0000.0000.000
135A247ASN0-0.082-0.04827.1120.0030.0030.0000.0000.0000.000
136A248HIS00.0530.01822.8160.0250.0250.0000.0000.0000.000
137A249ILE00.0320.02417.9690.0110.0110.0000.0000.0000.000
138A250GLY00.0290.01118.2050.0160.0160.0000.0000.0000.000
139A251VAL0-0.0110.00912.661-0.093-0.0930.0000.0000.0000.000
140A252ASP-1-0.793-0.90414.980-0.634-0.6340.0000.0000.0000.000
141A253LEU0-0.019-0.01714.179-0.146-0.1460.0000.0000.0000.000
142A254ALA0-0.038-0.02616.4150.1180.1180.0000.0000.0000.000
143A255PRO00.0270.04014.3500.0410.0410.0000.0000.0000.000
144A256GLY0-0.034-0.02017.2670.0920.0920.0000.0000.0000.000
145A257PRO0-0.034-0.03217.465-0.023-0.0230.0000.0000.0000.000
146A258ASN0-0.085-0.04217.1560.0820.0820.0000.0000.0000.000
147A259GLY00.0150.00714.556-0.042-0.0420.0000.0000.0000.000
148A260LYS10.8730.9585.2673.2213.2210.0000.0000.0000.000
149A261TYR00.0170.00310.829-0.053-0.0530.0000.0000.0000.000
150A262ALA0-0.011-0.0189.379-0.327-0.3270.0000.0000.0000.000
151A263GLN0-0.048-0.01610.811-0.374-0.3740.0000.0000.0000.000
152A264ILE0-0.023-0.01011.7710.1160.1160.0000.0000.0000.000
153A265ILE0-0.030-0.01914.4180.1100.1100.0000.0000.0000.000
154A266THR00.0110.00717.936-0.006-0.0060.0000.0000.0000.000
155A267PHE0-0.023-0.02721.3800.0560.0560.0000.0000.0000.000
156A268GLY00.0570.02024.227-0.021-0.0210.0000.0000.0000.000
157A269ARG10.8370.90627.7440.3470.3470.0000.0000.0000.000
158A270ASP-1-0.820-0.88230.378-0.321-0.3210.0000.0000.0000.000
159A271PHE0-0.008-0.00224.592-0.011-0.0110.0000.0000.0000.000
160A272ASP-1-0.786-0.87427.192-0.322-0.3220.0000.0000.0000.000
161A273THR0-0.076-0.03825.3500.0100.0100.0000.0000.0000.000
162A274LYS10.8270.92822.1020.4170.4170.0000.0000.0000.000
163A275PHE00.007-0.01820.4780.0430.0430.0000.0000.0000.000
164A276VAL00.0140.00413.898-0.045-0.0450.0000.0000.0000.000
165A277ILE0-0.024-0.00215.5490.0120.0120.0000.0000.0000.000
166A278ALA0-0.0070.00011.293-0.011-0.0110.0000.0000.0000.000
167A279GLU-1-0.880-0.9517.206-1.638-1.6380.0000.0000.0000.000
168A280ASN00.0190.0125.1410.3210.3210.0000.0000.0000.000
169A281TRP00.0710.0098.9340.2760.2760.0000.0000.0000.000
170A282GLY00.0590.0338.1420.3820.3820.0000.0000.0000.000
171A283GLU-1-0.927-0.9766.754-2.619-2.6190.0000.0000.0000.000
172A284PHE0-0.035-0.0109.5860.5070.5070.0000.0000.0000.000
173A285LEU00.0430.03511.7600.2540.2540.0000.0000.0000.000
174A286LEU00.0270.0099.8960.2760.2760.0000.0000.0000.000
175A287SER0-0.098-0.05013.0450.3110.3110.0000.0000.0000.000
176A288PHE00.0470.01614.9810.1470.1470.0000.0000.0000.000
177A289ALA00.0390.01215.6570.1200.1200.0000.0000.0000.000
178A290ASN0-0.058-0.04614.5640.2310.2310.0000.0000.0000.000
179A291ASP-1-0.747-0.81218.222-0.615-0.6150.0000.0000.0000.000
180A292LEU00.0240.02120.4780.0780.0780.0000.0000.0000.000
181A293GLU-1-0.793-0.88819.491-0.565-0.5650.0000.0000.0000.000
182A294ALA0-0.060-0.01821.8640.0670.0670.0000.0000.0000.000
183A295GLY0-0.010-0.01023.5470.0650.0650.0000.0000.0000.000
184A296ASN0-0.095-0.05722.6850.0840.0840.0000.0000.0000.000
185A297TRP0-0.039-0.00725.592-0.020-0.0200.0000.0000.0000.000
186A298TYR0-0.061-0.03028.4260.0370.0370.0000.0000.0000.000
187A299LEU00.0640.03930.727-0.029-0.0290.0000.0000.0000.000
188A300VAL0-0.028-0.00433.6170.0290.0290.0000.0000.0000.000
189A310ASP-1-0.940-0.97733.157-0.312-0.3120.0000.0000.0000.000
190A311GLY0-0.013-0.01833.7110.0170.0170.0000.0000.0000.000
191A312GLU-1-0.862-0.89532.274-0.428-0.4280.0000.0000.0000.000
192A313LEU00.0140.01525.7920.0170.0170.0000.0000.0000.000
193A314VAL0-0.014-0.01429.104-0.021-0.0210.0000.0000.0000.000
194A315PHE00.0270.01723.4150.0110.0110.0000.0000.0000.000
195A316ARG10.8520.91427.6000.3410.3410.0000.0000.0000.000
196A317ASP-1-0.802-0.85526.145-0.390-0.3900.0000.0000.0000.000
197A318LYS10.9310.97227.6180.3890.3890.0000.0000.0000.000
198A319LYS10.8310.90024.4040.3910.3910.0000.0000.0000.000
199A320SER0-0.068-0.05629.0060.0260.0260.0000.0000.0000.000
200A321ASN0-0.028-0.01531.5490.0030.0030.0000.0000.0000.000
201A322GLY00.0230.03031.6990.0110.0110.0000.0000.0000.000
202A323PRO0-0.010-0.01532.737-0.005-0.0050.0000.0000.0000.000
203A324ILE00.0350.00531.653-0.016-0.0160.0000.0000.0000.000
204A325GLN0-0.069-0.02528.7830.0090.0090.0000.0000.0000.000
205A326ASP-1-0.708-0.85427.944-0.508-0.5080.0000.0000.0000.000
206A327TYR00.019-0.01219.784-0.019-0.0190.0000.0000.0000.000
207A328PHE00.0430.02123.203-0.053-0.0530.0000.0000.0000.000
208A329GLU-1-0.889-0.93924.282-0.389-0.3890.0000.0000.0000.000
209A330VAL0-0.0290.00222.2160.0100.0100.0000.0000.0000.000
210A331LEU00.0340.01818.147-0.010-0.0100.0000.0000.0000.000
211A332LYS10.8430.94420.4820.4250.4250.0000.0000.0000.000
212A333ARG10.8340.89322.7370.4020.4020.0000.0000.0000.000
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