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: 49N9N

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 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 226
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2834605.258891
FMO2-HF: Nuclear repulsion 2745165.555062
FMO2-HF: Total energy -89439.703829
FMO2-MP2: Total energy -89704.363454


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.
3.3657.2680.073-1.784-2.1920.004
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 : 0.012 / q_NPA : 0.000
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].
3A86GLY00.0390.0322.5590.5073.8170.074-1.703-1.6810.004
4A87VAL0-0.008-0.0123.3343.0153.4110.001-0.078-0.3200.000
5A88SER00.006-0.0054.3311.5981.708-0.001-0.001-0.1070.000
6A89GLU-1-0.847-0.9254.997-5.830-5.743-0.001-0.002-0.0840.000
7A90THR00.006-0.0017.8370.8220.8220.0000.0000.0000.000
8A91LEU0-0.052-0.0168.7060.5300.5300.0000.0000.0000.000
9A92LEU0-0.026-0.00710.3930.3690.3690.0000.0000.0000.000
10A93ALA00.0070.00312.0480.2920.2920.0000.0000.0000.000
11A94TRP00.0430.00913.2690.2470.2470.0000.0000.0000.000
12A95ARG10.9340.99415.1510.9090.9090.0000.0000.0000.000
13A96HIS0-0.068-0.05915.4030.0730.0730.0000.0000.0000.000
14A97ILE00.0100.01216.8020.1040.1040.0000.0000.0000.000
15A98ASP-1-0.837-0.90419.286-0.795-0.7950.0000.0000.0000.000
16A99PHE0-0.095-0.04820.9750.0720.0720.0000.0000.0000.000
17A100TRP00.0720.03622.4320.0450.0450.0000.0000.0000.000
18A101THR00.013-0.00223.5180.0520.0520.0000.0000.0000.000
19A102SER0-0.083-0.04025.6500.0460.0460.0000.0000.0000.000
20A103GLU-1-0.976-0.97727.196-0.334-0.3340.0000.0000.0000.000
21A104HIS0-0.070-0.04626.8580.0560.0560.0000.0000.0000.000
22A105ASN0-0.046-0.03228.8140.0190.0190.0000.0000.0000.000
23A106PRO00.0600.02129.256-0.026-0.0260.0000.0000.0000.000
24A107ASP-1-0.853-0.91830.270-0.356-0.3560.0000.0000.0000.000
25A108LEU0-0.0070.00926.226-0.016-0.0160.0000.0000.0000.000
26A109ASN0-0.075-0.04124.644-0.011-0.0110.0000.0000.0000.000
27A110ALA00.0100.00426.295-0.024-0.0240.0000.0000.0000.000
28A111THR0-0.0130.00527.045-0.013-0.0130.0000.0000.0000.000
29A112LEU0-0.063-0.02221.801-0.033-0.0330.0000.0000.0000.000
30A113SER00.0120.01323.1280.0360.0360.0000.0000.0000.000
31A114ASP-1-0.891-0.93722.580-0.545-0.5450.0000.0000.0000.000
32A115PRO0-0.088-0.04718.860-0.032-0.0320.0000.0000.0000.000
33A116CYS0-0.0080.02318.6060.0420.0420.0000.0000.0000.000
34A117THR0-0.038-0.05419.303-0.024-0.0240.0000.0000.0000.000
35A118GLN00.010-0.01515.884-0.147-0.1470.0000.0000.0000.000
36A119ASN0-0.0020.00618.968-0.017-0.0170.0000.0000.0000.000
37A120ASP-1-0.749-0.82521.598-0.503-0.5030.0000.0000.0000.000
38A121ILE0-0.010-0.01415.601-0.024-0.0240.0000.0000.0000.000
39A122THR0-0.051-0.04319.380-0.001-0.0010.0000.0000.0000.000
40A123HIS0-0.020-0.02020.5990.0320.0320.0000.0000.0000.000
41A124ALA00.0630.04620.8660.0180.0180.0000.0000.0000.000
42A125GLU-1-0.810-0.89515.823-0.888-0.8880.0000.0000.0000.000
43A126GLU-1-0.928-0.96320.510-0.284-0.2840.0000.0000.0000.000
44A127ASP-1-0.934-0.95723.862-0.352-0.3520.0000.0000.0000.000
45A128LEU0-0.117-0.06421.4280.0180.0180.0000.0000.0000.000
46A129GLU-1-0.970-0.96523.136-0.282-0.2820.0000.0000.0000.000
47A130VAL0-0.079-0.04017.645-0.005-0.0050.0000.0000.0000.000
48A131SER0-0.017-0.00214.4010.0370.0370.0000.0000.0000.000
49A132PHE00.010-0.01114.068-0.108-0.1080.0000.0000.0000.000
50A133PRO00.007-0.0069.651-0.076-0.0760.0000.0000.0000.000
51A134ASN0-0.009-0.0145.2620.7570.7570.0000.0000.0000.000
52A135PRO00.0030.0035.9890.3440.3440.0000.0000.0000.000
53A136VAL00.0350.0218.0350.3890.3890.0000.0000.0000.000
54A137LYS10.8180.89811.2431.3221.3220.0000.0000.0000.000
55A138ALA0-0.032-0.0218.9500.2130.2130.0000.0000.0000.000
56A139SER00.0260.01210.9960.1930.1930.0000.0000.0000.000
57A140PHE00.0370.01413.3330.1310.1310.0000.0000.0000.000
58A141LYS10.8440.93313.2221.1881.1880.0000.0000.0000.000
59A142ILE0-0.051-0.01212.8930.0410.0410.0000.0000.0000.000
60A143HIS10.8150.86816.8150.9600.9600.0000.0000.0000.000
61A144ASP-1-0.759-0.87318.728-0.796-0.7960.0000.0000.0000.000
62A145GLY0-0.025-0.01520.3720.0680.0680.0000.0000.0000.000
63A146GLN0-0.024-0.02622.167-0.047-0.0470.0000.0000.0000.000
64A147GLU-1-0.835-0.93325.374-0.424-0.4240.0000.0000.0000.000
65A148ASP-1-0.815-0.93128.748-0.361-0.3610.0000.0000.0000.000
66A149LEU0-0.092-0.02032.3800.0210.0210.0000.0000.0000.000
67A150GLU-1-0.862-0.91734.450-0.256-0.2560.0000.0000.0000.000
68A151SER0-0.159-0.09737.9180.0090.0090.0000.0000.0000.000
69A152MET0-0.040-0.00936.5400.0180.0180.0000.0000.0000.000
70A153THR0-0.024-0.04033.555-0.002-0.0020.0000.0000.0000.000
71A154GLY0-0.0240.01034.494-0.001-0.0010.0000.0000.0000.000
72A155THR0-0.096-0.04228.362-0.025-0.0250.0000.0000.0000.000
73A156SER00.002-0.02229.722-0.025-0.0250.0000.0000.0000.000
74A157GLY0-0.027-0.00527.059-0.021-0.0210.0000.0000.0000.000
75A158LEU00.0020.00120.5390.0070.0070.0000.0000.0000.000
76A159PHE0-0.015-0.02418.022-0.022-0.0220.0000.0000.0000.000
77A160TYR0-0.087-0.08023.1030.0090.0090.0000.0000.0000.000
78A161GLY00.0610.04126.8210.0270.0270.0000.0000.0000.000
79A162PHE0-0.056-0.01924.6950.0120.0120.0000.0000.0000.000
80A163GLN00.0370.02824.957-0.021-0.0210.0000.0000.0000.000
81A164LEU0-0.043-0.02518.228-0.051-0.0510.0000.0000.0000.000
82A165MET0-0.072-0.02321.8440.0730.0730.0000.0000.0000.000
83A166THR00.0710.03621.549-0.072-0.0720.0000.0000.0000.000
84A167LEU00.011-0.01519.351-0.012-0.0120.0000.0000.0000.000
85A168ASP-1-0.880-0.93522.359-0.471-0.4710.0000.0000.0000.000
86A169GLN00.0050.00625.335-0.006-0.0060.0000.0000.0000.000
87A170VAL0-0.0030.00819.9350.0130.0130.0000.0000.0000.000
88A171VAL00.0240.02723.3000.0110.0110.0000.0000.0000.000
89A172ALA00.0000.00225.0800.0330.0330.0000.0000.0000.000
90A173MET00.001-0.01625.8000.0440.0440.0000.0000.0000.000
91A174THR0-0.008-0.02523.2400.0030.0030.0000.0000.0000.000
92A175GLN0-0.023-0.01525.6230.0390.0390.0000.0000.0000.000
93A176ALA0-0.0240.00028.8290.0320.0320.0000.0000.0000.000
94A177TRP0-0.007-0.01426.8380.0460.0460.0000.0000.0000.000
95A178ARG10.8280.91022.9580.5130.5130.0000.0000.0000.000
96A179ASN0-0.045-0.03329.5000.0380.0380.0000.0000.0000.000
97A180VAL0-0.0160.00431.5750.0280.0280.0000.0000.0000.000
98A181ALA00.0450.01529.3320.0210.0210.0000.0000.0000.000
99A182LYS10.9680.99431.4530.2960.2960.0000.0000.0000.000
100A183ASN0-0.036-0.02834.1840.0310.0310.0000.0000.0000.000
101A184LEU00.0050.00233.1720.0180.0180.0000.0000.0000.000
102A185ASN0-0.0260.00232.0690.0100.0100.0000.0000.0000.000
103A186LYS10.8720.92935.8760.2160.2160.0000.0000.0000.000
104A187ARG10.9030.96138.7560.2160.2160.0000.0000.0000.000
105A188SER00.0260.03436.603-0.006-0.0060.0000.0000.0000.000
106A218PRO00.0490.01834.5340.0080.0080.0000.0000.0000.000
107A219ASP-1-0.915-0.94332.545-0.230-0.2300.0000.0000.0000.000
108A220GLN0-0.049-0.04028.351-0.042-0.0420.0000.0000.0000.000
109A221LYS10.8300.89627.1040.2720.2720.0000.0000.0000.000
110A222SER0-0.006-0.00921.057-0.042-0.0420.0000.0000.0000.000
111A223ILE0-0.054-0.01121.2610.0560.0560.0000.0000.0000.000
112A224PRO00.1210.03016.853-0.051-0.0510.0000.0000.0000.000
113A225PRO00.0120.01820.076-0.012-0.0120.0000.0000.0000.000
114A226ASN0-0.040-0.02920.732-0.006-0.0060.0000.0000.0000.000
115A227ALA00.0510.04216.6360.0170.0170.0000.0000.0000.000
116A228VAL00.0610.04217.432-0.071-0.0710.0000.0000.0000.000
117A229GLN0-0.043-0.03119.9350.0980.0980.0000.0000.0000.000
118A230PRO0-0.0010.00922.894-0.023-0.0230.0000.0000.0000.000
119A231VAL0-0.015-0.02025.2800.0390.0390.0000.0000.0000.000
120A232TYR00.018-0.00126.998-0.027-0.0270.0000.0000.0000.000
121A233ALA00.0100.00127.114-0.024-0.0240.0000.0000.0000.000
122A234HIS00.0390.01822.9180.0130.0130.0000.0000.0000.000
123A235PRO0-0.016-0.01724.467-0.035-0.0350.0000.0000.0000.000
124A236ALA00.0260.01719.685-0.015-0.0150.0000.0000.0000.000
125A237TRP0-0.071-0.01719.444-0.060-0.0600.0000.0000.0000.000
126A238ILE00.0390.02118.0830.0650.0650.0000.0000.0000.000
127A239PRO0-0.047-0.00819.182-0.111-0.1110.0000.0000.0000.000
128A240LEU00.017-0.01415.340-0.026-0.0260.0000.0000.0000.000
129A241ILE00.0140.02219.0540.0030.0030.0000.0000.0000.000
130A242THR0-0.043-0.02822.0010.0280.0280.0000.0000.0000.000
131A243ASP-1-0.832-0.92325.731-0.479-0.4790.0000.0000.0000.000
132A244ASN0-0.025-0.00828.7140.0170.0170.0000.0000.0000.000
133A245ALA00.0150.00730.9450.0330.0330.0000.0000.0000.000
134A246GLY0-0.027-0.02131.1550.0160.0160.0000.0000.0000.000
135A247ASN0-0.042-0.03927.560-0.004-0.0040.0000.0000.0000.000
136A248HIS00.0440.01423.2400.0290.0290.0000.0000.0000.000
137A249ILE00.0250.02118.4080.0040.0040.0000.0000.0000.000
138A250GLY00.0220.00618.2840.0220.0220.0000.0000.0000.000
139A251VAL0-0.0060.01512.934-0.081-0.0810.0000.0000.0000.000
140A252ASP-1-0.789-0.89615.303-0.665-0.6650.0000.0000.0000.000
141A253LEU0-0.021-0.02014.277-0.138-0.1380.0000.0000.0000.000
142A254ALA0-0.026-0.01816.3550.1140.1140.0000.0000.0000.000
143A255PRO00.0020.03314.0480.0560.0560.0000.0000.0000.000
144A256GLY0-0.018-0.00917.0750.0930.0930.0000.0000.0000.000
145A257PRO0-0.023-0.02817.199-0.025-0.0250.0000.0000.0000.000
146A258ASN0-0.079-0.03016.5470.0820.0820.0000.0000.0000.000
147A259GLY00.0300.01814.857-0.053-0.0530.0000.0000.0000.000
148A260LYS10.8780.9595.3003.5803.5800.0000.0000.0000.000
149A261TYR0-0.001-0.01410.560-0.022-0.0220.0000.0000.0000.000
150A262ALA0-0.012-0.0189.840-0.392-0.3920.0000.0000.0000.000
151A263GLN0-0.040-0.01411.275-0.361-0.3610.0000.0000.0000.000
152A264ILE0-0.017-0.01212.1590.1480.1480.0000.0000.0000.000
153A265ILE0-0.025-0.01914.8280.0900.0900.0000.0000.0000.000
154A266THR00.0130.01218.282-0.006-0.0060.0000.0000.0000.000
155A267PHE0-0.017-0.03121.4110.0490.0490.0000.0000.0000.000
156A268GLY00.0740.02724.578-0.020-0.0200.0000.0000.0000.000
157A269ARG10.8700.94328.1590.3500.3500.0000.0000.0000.000
158A270ASP-1-0.870-0.91830.841-0.343-0.3430.0000.0000.0000.000
159A271PHE0-0.046-0.01125.041-0.016-0.0160.0000.0000.0000.000
160A272ASP-1-0.799-0.87827.579-0.337-0.3370.0000.0000.0000.000
161A273THR0-0.096-0.05025.4490.0140.0140.0000.0000.0000.000
162A274LYS10.8360.92922.3370.4400.4400.0000.0000.0000.000
163A275PHE00.015-0.00420.8700.0390.0390.0000.0000.0000.000
164A276VAL00.0250.01614.223-0.037-0.0370.0000.0000.0000.000
165A277ILE0-0.037-0.02116.1480.0360.0360.0000.0000.0000.000
166A278ALA0-0.0030.00211.752-0.033-0.0330.0000.0000.0000.000
167A279GLU-1-0.908-0.9537.572-1.887-1.8870.0000.0000.0000.000
168A280ASN00.0220.0115.7180.2830.2830.0000.0000.0000.000
169A281TRP00.0750.0069.4530.2320.2320.0000.0000.0000.000
170A282GLY00.0550.0318.3000.3690.3690.0000.0000.0000.000
171A283GLU-1-0.926-0.9816.863-3.188-3.1880.0000.0000.0000.000
172A284PHE0-0.042-0.01410.1640.4920.4920.0000.0000.0000.000
173A285LEU00.0530.03111.9190.2580.2580.0000.0000.0000.000
174A286LEU00.0230.01410.2870.2610.2610.0000.0000.0000.000
175A287SER0-0.105-0.05413.4850.3010.3010.0000.0000.0000.000
176A288PHE00.0420.01415.6480.1570.1570.0000.0000.0000.000
177A289ALA00.0510.02416.0780.1190.1190.0000.0000.0000.000
178A290ASN0-0.031-0.03114.6970.2150.2150.0000.0000.0000.000
179A291ASP-1-0.741-0.81718.567-0.655-0.6550.0000.0000.0000.000
180A292LEU00.0060.00821.0850.0800.0800.0000.0000.0000.000
181A293GLU-1-0.841-0.91119.662-0.594-0.5940.0000.0000.0000.000
182A294ALA0-0.092-0.03022.4970.0670.0670.0000.0000.0000.000
183A295GLY0-0.072-0.04824.1360.0520.0520.0000.0000.0000.000
184A296ASN0-0.051-0.02223.5300.0840.0840.0000.0000.0000.000
185A297TRP0-0.0050.01226.176-0.028-0.0280.0000.0000.0000.000
186A298TYR0-0.068-0.03728.7790.0360.0360.0000.0000.0000.000
187A299LEU00.0580.04231.377-0.023-0.0230.0000.0000.0000.000
188A300VAL0-0.0190.00633.9920.0280.0280.0000.0000.0000.000
189A310ASP-1-0.947-0.97833.907-0.309-0.3090.0000.0000.0000.000
190A311GLY0-0.023-0.02234.5560.0140.0140.0000.0000.0000.000
191A312GLU-1-0.877-0.93532.544-0.430-0.4300.0000.0000.0000.000
192A313LEU00.0000.02026.0040.0160.0160.0000.0000.0000.000
193A314VAL0-0.005-0.00929.800-0.015-0.0150.0000.0000.0000.000
194A315PHE00.0260.01124.0860.0060.0060.0000.0000.0000.000
195A316ARG10.9400.96528.5440.3720.3720.0000.0000.0000.000
196A317ASP-1-0.814-0.85126.538-0.437-0.4370.0000.0000.0000.000
197A318LYS10.9840.99828.2660.3960.3960.0000.0000.0000.000
198A319LYS10.8360.90225.1210.4370.4370.0000.0000.0000.000
199A320SER0-0.067-0.06229.9980.0260.0260.0000.0000.0000.000
200A321ASN0-0.062-0.03532.0370.0070.0070.0000.0000.0000.000
201A322GLY00.0140.02732.5140.0140.0140.0000.0000.0000.000
202A323PRO0-0.018-0.01833.622-0.003-0.0030.0000.0000.0000.000
203A324ILE00.0280.00532.538-0.018-0.0180.0000.0000.0000.000
204A325GLN0-0.072-0.02829.3770.0080.0080.0000.0000.0000.000
205A326ASP-1-0.751-0.87828.729-0.515-0.5150.0000.0000.0000.000
206A327TYR00.037-0.00520.666-0.022-0.0220.0000.0000.0000.000
207A328PHE00.0890.04623.733-0.056-0.0560.0000.0000.0000.000
208A329GLU-1-0.892-0.94024.835-0.426-0.4260.0000.0000.0000.000
209A330VAL0-0.046-0.00622.9380.0110.0110.0000.0000.0000.000
210A331LEU00.0190.00818.925-0.016-0.0160.0000.0000.0000.000
211A332LYS10.8570.94221.0620.4460.4460.0000.0000.0000.000
212A333ARG10.8580.91223.1030.4270.4270.0000.0000.0000.000
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