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: K9R93

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 OptH
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 -2834583.085732
FMO2-HF: Nuclear repulsion 2745144.212053
FMO2-HF: Total energy -89438.873679
FMO2-MP2: Total energy -89703.49699


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.
0.4953.7770.029-1.53-1.7810.003
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 : 0.023 / q_NPA : 0.004
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].
3A86GLY00.0470.0392.9270.0112.9290.031-1.507-1.4420.003
4A87VAL0-0.013-0.0173.8202.3952.646-0.001-0.021-0.2290.000
5A88SER0-0.006-0.0144.3171.3021.415-0.001-0.002-0.1100.000
6A89GLU-1-0.837-0.9175.305-5.641-5.6410.0000.0000.0000.000
7A90THR0-0.019-0.0078.0640.8260.8260.0000.0000.0000.000
8A91LEU0-0.043-0.0158.7600.5130.5130.0000.0000.0000.000
9A92LEU0-0.034-0.00910.3460.3720.3720.0000.0000.0000.000
10A93ALA00.0150.00512.1100.3040.3040.0000.0000.0000.000
11A94TRP00.0370.00213.5390.2410.2410.0000.0000.0000.000
12A95ARG10.9390.99715.1630.9910.9910.0000.0000.0000.000
13A96HIS0-0.021-0.02015.4860.0650.0650.0000.0000.0000.000
14A97ILE00.0180.01516.9920.1090.1090.0000.0000.0000.000
15A98ASP-1-0.853-0.92219.203-0.838-0.8380.0000.0000.0000.000
16A99PHE0-0.083-0.04420.9820.0730.0730.0000.0000.0000.000
17A100TRP00.0640.03722.4550.0550.0550.0000.0000.0000.000
18A101THR00.0110.00423.7000.0560.0560.0000.0000.0000.000
19A102SER0-0.089-0.05325.7260.0450.0450.0000.0000.0000.000
20A103GLU-1-0.990-0.97727.219-0.361-0.3610.0000.0000.0000.000
21A104HIS0-0.069-0.05127.0640.0590.0590.0000.0000.0000.000
22A105ASN0-0.034-0.02228.9610.0270.0270.0000.0000.0000.000
23A106PRO00.0550.01929.440-0.026-0.0260.0000.0000.0000.000
24A107ASP-1-0.848-0.92730.459-0.367-0.3670.0000.0000.0000.000
25A108LEU0-0.0020.01426.405-0.014-0.0140.0000.0000.0000.000
26A109ASN0-0.085-0.03224.868-0.020-0.0200.0000.0000.0000.000
27A110ALA00.0120.00426.530-0.024-0.0240.0000.0000.0000.000
28A111THR0-0.022-0.00627.365-0.013-0.0130.0000.0000.0000.000
29A112LEU0-0.054-0.02221.906-0.031-0.0310.0000.0000.0000.000
30A113SER00.0180.02123.6150.0300.0300.0000.0000.0000.000
31A114ASP-1-0.873-0.93422.880-0.566-0.5660.0000.0000.0000.000
32A115PRO0-0.104-0.05419.117-0.025-0.0250.0000.0000.0000.000
33A116CYS00.0210.04019.0700.0480.0480.0000.0000.0000.000
34A117THR0-0.041-0.02319.654-0.030-0.0300.0000.0000.0000.000
35A118GLN00.004-0.02016.162-0.136-0.1360.0000.0000.0000.000
36A119ASN00.001-0.00519.4690.0000.0000.0000.0000.0000.000
37A120ASP-1-0.762-0.85821.961-0.507-0.5070.0000.0000.0000.000
38A121ILE0-0.021-0.02316.071-0.017-0.0170.0000.0000.0000.000
39A122THR0-0.043-0.03119.9270.0020.0020.0000.0000.0000.000
40A123HIS00.0060.00121.2140.0340.0340.0000.0000.0000.000
41A124ALA00.0640.04821.4590.0200.0200.0000.0000.0000.000
42A125GLU-1-0.895-0.96116.445-0.778-0.7780.0000.0000.0000.000
43A126GLU-1-0.965-0.99021.168-0.258-0.2580.0000.0000.0000.000
44A127ASP-1-0.944-0.96324.504-0.330-0.3300.0000.0000.0000.000
45A128LEU0-0.129-0.07122.1810.0210.0210.0000.0000.0000.000
46A129GLU-1-0.958-0.96523.787-0.237-0.2370.0000.0000.0000.000
47A130VAL0-0.083-0.04318.0540.0030.0030.0000.0000.0000.000
48A131SER0-0.0080.00515.0740.0320.0320.0000.0000.0000.000
49A132PHE00.002-0.00614.585-0.088-0.0880.0000.0000.0000.000
50A133PRO0-0.009-0.01510.373-0.079-0.0790.0000.0000.0000.000
51A134ASN0-0.026-0.0186.3320.4660.4660.0000.0000.0000.000
52A135PRO00.0140.0116.7600.2450.2450.0000.0000.0000.000
53A136VAL00.0480.0268.6420.3040.3040.0000.0000.0000.000
54A137LYS10.9360.97611.7011.3541.3540.0000.0000.0000.000
55A138ALA0-0.034-0.0229.3170.1730.1730.0000.0000.0000.000
56A139SER00.0320.01911.4030.1640.1640.0000.0000.0000.000
57A140PHE00.0490.02213.7700.1130.1130.0000.0000.0000.000
58A141LYS10.8450.93613.6751.1941.1940.0000.0000.0000.000
59A142ILE0-0.058-0.01613.0090.0220.0220.0000.0000.0000.000
60A143HIS10.8290.89717.0740.9810.9810.0000.0000.0000.000
61A144ASP-1-0.767-0.87619.162-0.771-0.7710.0000.0000.0000.000
62A145GLY0-0.033-0.02820.8440.0650.0650.0000.0000.0000.000
63A146GLN0-0.036-0.04222.652-0.048-0.0480.0000.0000.0000.000
64A147GLU-1-0.853-0.93325.818-0.416-0.4160.0000.0000.0000.000
65A148ASP-1-0.821-0.93629.183-0.363-0.3630.0000.0000.0000.000
66A149LEU0-0.100-0.02832.8110.0220.0220.0000.0000.0000.000
67A150GLU-1-0.853-0.91334.958-0.256-0.2560.0000.0000.0000.000
68A151SER0-0.161-0.09938.4210.0100.0100.0000.0000.0000.000
69A152MET0-0.047-0.00936.8590.0190.0190.0000.0000.0000.000
70A153THR0-0.010-0.02234.332-0.004-0.0040.0000.0000.0000.000
71A154GLY0-0.025-0.00234.7610.0090.0090.0000.0000.0000.000
72A155THR0-0.062-0.02629.009-0.020-0.0200.0000.0000.0000.000
73A156SER0-0.004-0.00830.192-0.023-0.0230.0000.0000.0000.000
74A157GLY0-0.019-0.00127.511-0.022-0.0220.0000.0000.0000.000
75A158LEU00.0120.00520.8080.0090.0090.0000.0000.0000.000
76A159PHE0-0.021-0.02918.357-0.022-0.0220.0000.0000.0000.000
77A160TYR0-0.078-0.06223.0990.0110.0110.0000.0000.0000.000
78A161GLY00.0650.04326.7960.0280.0280.0000.0000.0000.000
79A162PHE0-0.045-0.02024.4680.0090.0090.0000.0000.0000.000
80A163GLN00.0130.01325.271-0.012-0.0120.0000.0000.0000.000
81A164LEU0-0.044-0.01618.758-0.045-0.0450.0000.0000.0000.000
82A165MET0-0.090-0.02322.4190.0680.0680.0000.0000.0000.000
83A166THR00.0900.03922.121-0.071-0.0710.0000.0000.0000.000
84A167LEU00.020-0.00920.057-0.008-0.0080.0000.0000.0000.000
85A168ASP-1-0.876-0.94122.959-0.462-0.4620.0000.0000.0000.000
86A169GLN00.0020.01425.968-0.005-0.0050.0000.0000.0000.000
87A170VAL00.0040.00920.6590.0170.0170.0000.0000.0000.000
88A171VAL00.0200.03723.9900.0160.0160.0000.0000.0000.000
89A172ALA0-0.0010.00425.7750.0340.0340.0000.0000.0000.000
90A173MET0-0.021-0.02226.5060.0430.0430.0000.0000.0000.000
91A174THR00.012-0.03423.8960.0060.0060.0000.0000.0000.000
92A175GLN0-0.007-0.00926.3680.0290.0290.0000.0000.0000.000
93A176ALA0-0.0250.00329.5750.0310.0310.0000.0000.0000.000
94A177TRP0-0.003-0.00627.3960.0450.0450.0000.0000.0000.000
95A178ARG10.8170.90623.4220.4570.4570.0000.0000.0000.000
96A179ASN0-0.045-0.02729.7160.0350.0350.0000.0000.0000.000
97A180VAL0-0.036-0.00731.4630.0270.0270.0000.0000.0000.000
98A181ALA00.0460.01429.2990.0200.0200.0000.0000.0000.000
99A182LYS10.9901.00131.4220.2550.2550.0000.0000.0000.000
100A183ASN0-0.041-0.03034.1560.0270.0270.0000.0000.0000.000
101A184LEU0-0.001-0.00133.1060.0160.0160.0000.0000.0000.000
102A185ASN0-0.0210.00331.9880.0090.0090.0000.0000.0000.000
103A186LYS10.8710.93335.8520.1900.1900.0000.0000.0000.000
104A187ARG10.9060.96138.8380.1880.1880.0000.0000.0000.000
105A188SER00.0220.03236.598-0.004-0.0040.0000.0000.0000.000
106A218PRO00.0500.01834.4840.0060.0060.0000.0000.0000.000
107A219ASP-1-0.949-0.98132.528-0.191-0.1910.0000.0000.0000.000
108A220GLN0-0.036-0.00128.249-0.041-0.0410.0000.0000.0000.000
109A221LYS10.8650.93027.0960.2360.2360.0000.0000.0000.000
110A222SER0-0.007-0.01421.023-0.039-0.0390.0000.0000.0000.000
111A223ILE0-0.050-0.01021.1840.0530.0530.0000.0000.0000.000
112A224PRO00.1180.02716.795-0.050-0.0500.0000.0000.0000.000
113A225PRO00.0140.02320.043-0.010-0.0100.0000.0000.0000.000
114A226ASN0-0.047-0.03320.7090.0020.0020.0000.0000.0000.000
115A227ALA00.0510.04416.6380.0230.0230.0000.0000.0000.000
116A228VAL00.0620.04017.404-0.060-0.0600.0000.0000.0000.000
117A229GLN0-0.049-0.03319.9040.0900.0900.0000.0000.0000.000
118A230PRO0-0.0050.00922.866-0.025-0.0250.0000.0000.0000.000
119A231VAL0-0.016-0.02025.2120.0350.0350.0000.0000.0000.000
120A232TYR00.0170.00126.961-0.025-0.0250.0000.0000.0000.000
121A233ALA00.0140.00227.071-0.024-0.0240.0000.0000.0000.000
122A234HIS00.0380.01822.6470.0090.0090.0000.0000.0000.000
123A235PRO0-0.007-0.01224.433-0.034-0.0340.0000.0000.0000.000
124A236ALA00.0340.01919.523-0.014-0.0140.0000.0000.0000.000
125A237TRP0-0.065-0.01119.412-0.054-0.0540.0000.0000.0000.000
126A238ILE00.0360.02218.7380.0570.0570.0000.0000.0000.000
127A239PRO0-0.046-0.00919.781-0.105-0.1050.0000.0000.0000.000
128A240LEU00.025-0.01915.992-0.025-0.0250.0000.0000.0000.000
129A241ILE00.0150.02119.1600.0000.0000.0000.0000.0000.000
130A242THR0-0.037-0.02722.4650.0330.0330.0000.0000.0000.000
131A243ASP-1-0.799-0.90926.152-0.466-0.4660.0000.0000.0000.000
132A244ASN0-0.035-0.01128.9380.0230.0230.0000.0000.0000.000
133A245ALA00.0130.00631.2600.0310.0310.0000.0000.0000.000
134A246GLY0-0.036-0.02631.5050.0160.0160.0000.0000.0000.000
135A247ASN0-0.045-0.02527.4550.0020.0020.0000.0000.0000.000
136A248HIS00.028-0.00623.5300.0280.0280.0000.0000.0000.000
137A249ILE00.0320.02318.4860.0080.0080.0000.0000.0000.000
138A250GLY00.0160.00118.6710.0170.0170.0000.0000.0000.000
139A251VAL0-0.0130.01513.289-0.070-0.0700.0000.0000.0000.000
140A252ASP-1-0.792-0.90215.270-0.558-0.5580.0000.0000.0000.000
141A253LEU0-0.017-0.02014.454-0.111-0.1110.0000.0000.0000.000
142A254ALA0-0.040-0.02716.3290.1120.1120.0000.0000.0000.000
143A255PRO00.0060.03514.1080.0420.0420.0000.0000.0000.000
144A256GLY0-0.019-0.01017.0530.0860.0860.0000.0000.0000.000
145A257PRO0-0.018-0.02817.186-0.016-0.0160.0000.0000.0000.000
146A258ASN0-0.069-0.02416.5120.0920.0920.0000.0000.0000.000
147A259GLY00.0250.01614.832-0.055-0.0550.0000.0000.0000.000
148A260LYS10.9050.9665.3292.6662.6660.0000.0000.0000.000
149A261TYR0-0.006-0.01410.420-0.035-0.0350.0000.0000.0000.000
150A262ALA0-0.011-0.0199.812-0.344-0.3440.0000.0000.0000.000
151A263GLN0-0.0210.00611.229-0.349-0.3490.0000.0000.0000.000
152A264ILE0-0.023-0.01712.1150.1380.1380.0000.0000.0000.000
153A265ILE0-0.029-0.02314.7760.0860.0860.0000.0000.0000.000
154A266THR00.0310.02418.233-0.014-0.0140.0000.0000.0000.000
155A267PHE0-0.019-0.03520.9490.0520.0520.0000.0000.0000.000
156A268GLY00.0650.02124.530-0.022-0.0220.0000.0000.0000.000
157A269ARG10.8980.95528.1100.3200.3200.0000.0000.0000.000
158A270ASP-1-0.870-0.91930.766-0.315-0.3150.0000.0000.0000.000
159A271PHE0-0.058-0.02125.123-0.015-0.0150.0000.0000.0000.000
160A272ASP-1-0.835-0.92327.534-0.301-0.3010.0000.0000.0000.000
161A273THR0-0.083-0.04225.3520.0170.0170.0000.0000.0000.000
162A274LYS10.8390.93422.1090.3840.3840.0000.0000.0000.000
163A275PHE00.004-0.00920.7470.0410.0410.0000.0000.0000.000
164A276VAL00.0270.01614.243-0.034-0.0340.0000.0000.0000.000
165A277ILE0-0.034-0.01916.2100.0350.0350.0000.0000.0000.000
166A278ALA0-0.013-0.00711.794-0.040-0.0400.0000.0000.0000.000
167A279GLU-1-0.906-0.9537.573-1.575-1.5750.0000.0000.0000.000
168A280ASN00.0170.0135.9660.1080.1080.0000.0000.0000.000
169A281TRP00.0580.0029.4930.1950.1950.0000.0000.0000.000
170A282GLY00.0520.0298.3420.3330.3330.0000.0000.0000.000
171A283GLU-1-0.918-0.9776.451-3.619-3.6190.0000.0000.0000.000
172A284PHE0-0.028-0.00910.1860.4630.4630.0000.0000.0000.000
173A285LEU00.0460.02612.4860.2440.2440.0000.0000.0000.000
174A286LEU00.0170.01510.3180.2290.2290.0000.0000.0000.000
175A287SER0-0.117-0.06713.5000.2900.2900.0000.0000.0000.000
176A288PHE00.0420.01715.6630.1510.1510.0000.0000.0000.000
177A289ALA00.0480.02016.1260.1120.1120.0000.0000.0000.000
178A290ASN0-0.006-0.01414.7700.1560.1560.0000.0000.0000.000
179A291ASP-1-0.773-0.87618.620-0.662-0.6620.0000.0000.0000.000
180A292LEU0-0.0020.00221.1180.0800.0800.0000.0000.0000.000
181A293GLU-1-0.901-0.95519.658-0.631-0.6310.0000.0000.0000.000
182A294ALA0-0.088-0.03022.5380.0650.0650.0000.0000.0000.000
183A295GLY0-0.071-0.04424.2050.0540.0540.0000.0000.0000.000
184A296ASN0-0.044-0.01123.5820.0840.0840.0000.0000.0000.000
185A297TRP0-0.0050.00326.571-0.029-0.0290.0000.0000.0000.000
186A298TYR0-0.065-0.03728.8020.0340.0340.0000.0000.0000.000
187A299LEU00.0560.03931.781-0.021-0.0210.0000.0000.0000.000
188A300VAL0-0.0280.00433.9880.0280.0280.0000.0000.0000.000
189A310ASP-1-0.969-0.99934.908-0.317-0.3170.0000.0000.0000.000
190A311GLY00.0090.00834.6510.0160.0160.0000.0000.0000.000
191A312GLU-1-0.894-0.96332.941-0.422-0.4220.0000.0000.0000.000
192A313LEU00.0110.02325.9320.0150.0150.0000.0000.0000.000
193A314VAL0-0.008-0.00929.811-0.012-0.0120.0000.0000.0000.000
194A315PHE00.0270.01124.0520.0050.0050.0000.0000.0000.000
195A316ARG10.9440.96228.5470.3820.3820.0000.0000.0000.000
196A317ASP-1-0.817-0.86526.837-0.423-0.4230.0000.0000.0000.000
197A318LYS10.9780.98928.2720.3940.3940.0000.0000.0000.000
198A319LYS10.8390.89925.1980.4160.4160.0000.0000.0000.000
199A320SER0-0.058-0.04430.0050.0280.0280.0000.0000.0000.000
200A321ASN0-0.059-0.02932.0490.0090.0090.0000.0000.0000.000
201A322GLY00.0060.02332.5340.0140.0140.0000.0000.0000.000
202A323PRO0-0.017-0.01233.516-0.003-0.0030.0000.0000.0000.000
203A324ILE00.0250.00232.452-0.017-0.0170.0000.0000.0000.000
204A325GLN0-0.110-0.05328.9810.0130.0130.0000.0000.0000.000
205A326ASP-1-0.755-0.87428.574-0.490-0.4900.0000.0000.0000.000
206A327TYR00.0500.01520.462-0.020-0.0200.0000.0000.0000.000
207A328PHE00.0960.04123.750-0.055-0.0550.0000.0000.0000.000
208A329GLU-1-0.894-0.93524.870-0.400-0.4000.0000.0000.0000.000
209A330VAL0-0.074-0.02322.9160.0130.0130.0000.0000.0000.000
210A331LEU00.0120.00419.154-0.012-0.0120.0000.0000.0000.000
211A332LYS10.8340.92021.0960.4060.4060.0000.0000.0000.000
212A333ARG10.9510.97023.1380.3970.3970.0000.0000.0000.000
213A334ARG10.8180.89419.4220.7490.7490.0000.0000.0000.000
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