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: 3JN9L

Calculation Name: 3F5C-B-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3F5C

Chain ID: B

ChEMBL ID:

UniProt ID: Q61066

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 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 183
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2054673.869948
FMO2-HF: Nuclear repulsion 1978541.801623
FMO2-HF: Total energy -76132.068325
FMO2-MP2: Total energy -76346.897581


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(B:251:LYS)


Summations of interaction energy for fragment #1(B:251:LYS)
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.
-54.229-50.670.536-1.653-2.442-0.004
Interaction energy analysis for fragmet #1(B:251:LYS)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 1 / q_Mulliken : 0.934 / q_NPA : 0.960
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].
3B253PRO0-0.003-0.0052.4242.6145.4860.529-1.550-1.851-0.004
4B254GLN00.0420.0093.720-1.314-0.9410.009-0.085-0.2970.000
5B255VAL00.0810.0325.0042.4292.4290.0000.0000.0000.000
6B256VAL00.0200.0266.1123.1713.1710.0000.0000.0000.000
7B257CYS0-0.0160.0078.4442.9022.9020.0000.0000.0000.000
8B258GLU-1-0.946-0.96410.011-19.349-19.3490.0000.0000.0000.000
9B259ALA00.012-0.00510.6461.7711.7710.0000.0000.0000.000
10B260ALA0-0.020-0.00312.2791.3671.3670.0000.0000.0000.000
11B261SER0-0.006-0.01114.1401.6641.6640.0000.0000.0000.000
12B262ALA0-0.034-0.02715.3871.1711.1710.0000.0000.0000.000
13B263GLY00.0150.00716.3990.9020.9020.0000.0000.0000.000
14B264LEU00.0480.03018.1840.8440.8440.0000.0000.0000.000
15B265LEU0-0.027-0.01820.0700.8870.8870.0000.0000.0000.000
16B266LYS10.9200.95617.71215.16715.1670.0000.0000.0000.000
17B267THR00.0540.03421.8410.4910.4910.0000.0000.0000.000
18B268LEU00.012-0.00924.2860.5400.5400.0000.0000.0000.000
19B269ARG10.9080.96123.22711.67011.6700.0000.0000.0000.000
20B270PHE0-0.0080.00626.9320.3850.3850.0000.0000.0000.000
21B271VAL00.011-0.00128.4100.3330.3330.0000.0000.0000.000
22B272LYS10.8240.91930.2949.6959.6950.0000.0000.0000.000
23B273TYR0-0.025-0.02130.6440.2390.2390.0000.0000.0000.000
24B274LEU00.0000.02732.8510.2640.2640.0000.0000.0000.000
25B275PRO00.0520.03235.4740.0970.0970.0000.0000.0000.000
26B276CYS0-0.038-0.02938.3760.0400.0400.0000.0000.0000.000
27B277PHE00.0390.06933.4140.0690.0690.0000.0000.0000.000
28B278GLN00.013-0.00336.8720.1110.1110.0000.0000.0000.000
29B279ILE0-0.049-0.01938.2510.1180.1180.0000.0000.0000.000
30B280LEU0-0.067-0.02138.4360.1790.1790.0000.0000.0000.000
31B281PRO00.0570.02940.462-0.084-0.0840.0000.0000.0000.000
32B282LEU00.0550.02835.288-0.140-0.1400.0000.0000.0000.000
33B283ASP-1-0.829-0.91537.227-7.368-7.3680.0000.0000.0000.000
34B284GLN00.0400.00537.646-0.185-0.1850.0000.0000.0000.000
35B285GLN0-0.036-0.02335.177-0.360-0.3600.0000.0000.0000.000
36B286LEU0-0.018-0.01831.848-0.298-0.2980.0000.0000.0000.000
37B287VAL00.0200.01432.618-0.293-0.2930.0000.0000.0000.000
38B288LEU00.0110.01132.791-0.253-0.2530.0000.0000.0000.000
39B289VAL00.0280.00928.480-0.303-0.3030.0000.0000.0000.000
40B290ARG10.8540.92428.4798.8818.8810.0000.0000.0000.000
41B291SER0-0.0030.01328.907-0.099-0.0990.0000.0000.0000.000
42B292CYS0-0.036-0.01727.654-0.298-0.2980.0000.0000.0000.000
43B293TRP00.0030.01320.359-0.594-0.5940.0000.0000.0000.000
44B294ALA00.0610.03622.488-0.481-0.4810.0000.0000.0000.000
45B295PRO0-0.023-0.01522.522-0.445-0.4450.0000.0000.0000.000
46B296LEU0-0.004-0.01623.769-0.277-0.2770.0000.0000.0000.000
47B297LEU00.0010.01517.804-0.201-0.2010.0000.0000.0000.000
48B298MET0-0.018-0.00417.147-0.766-0.7660.0000.0000.0000.000
49B299LEU0-0.012-0.01520.196-0.240-0.2400.0000.0000.0000.000
50B300GLU-1-0.915-0.95920.188-12.298-12.2980.0000.0000.0000.000
51B301LEU0-0.018-0.00415.215-0.363-0.3630.0000.0000.0000.000
52B302ALA00.0030.01416.748-0.598-0.5980.0000.0000.0000.000
53B303GLN00.0790.06418.774-0.036-0.0360.0000.0000.0000.000
54B304ASP-1-0.982-0.98616.428-14.298-14.2980.0000.0000.0000.000
55B305HIS0-0.080-0.04015.759-0.268-0.2680.0000.0000.0000.000
56B306LEU00.0050.01110.344-1.063-1.0630.0000.0000.0000.000
57B307HIS0-0.027-0.0209.6950.9080.9080.0000.0000.0000.000
58B308PHE0-0.020-0.0237.532-1.732-1.7320.0000.0000.0000.000
59B309GLU-1-1.016-1.0174.974-41.847-41.711-0.001-0.004-0.1300.000
60B310MET0-0.0130.0105.553-3.221-3.2210.0000.0000.0000.000
61B311MET0-0.077-0.0024.3472.0532.231-0.001-0.014-0.1640.000
62B312GLU-1-0.846-0.9527.946-26.663-26.6630.0000.0000.0000.000
63B313ILE0-0.065-0.0326.8172.3232.3230.0000.0000.0000.000
64B353HIS0-0.062-0.04117.2590.4080.4080.0000.0000.0000.000
65B354LEU00.010-0.00910.6650.0530.0530.0000.0000.0000.000
66B355LEU00.0680.03913.087-0.967-0.9670.0000.0000.0000.000
67B356PRO0-0.0330.01715.5031.0701.0700.0000.0000.0000.000
68B357ALA00.032-0.00616.924-0.685-0.6850.0000.0000.0000.000
69B358ALA00.0160.01417.804-0.507-0.5070.0000.0000.0000.000
70B359ALA00.0330.00718.7580.1080.1080.0000.0000.0000.000
71B360VAL00.0660.03012.7720.3320.3320.0000.0000.0000.000
72B361GLN00.0070.00315.486-1.490-1.4900.0000.0000.0000.000
73B362ALA0-0.015-0.01117.6820.0430.0430.0000.0000.0000.000
74B363ILE00.0450.02715.3610.4130.4130.0000.0000.0000.000
75B364LYS10.9781.00612.66720.80720.8070.0000.0000.0000.000
76B365SER0-0.023-0.02216.5660.4420.4420.0000.0000.0000.000
77B366PHE00.0030.00420.1730.4840.4840.0000.0000.0000.000
78B367PHE00.0330.01414.3780.5160.5160.0000.0000.0000.000
79B368PHE00.009-0.00614.7440.3430.3430.0000.0000.0000.000
80B369LYS10.9170.97319.75911.35511.3550.0000.0000.0000.000
81B370CYS0-0.014-0.00621.4210.6110.6110.0000.0000.0000.000
82B371TRP0-0.043-0.02814.3010.3390.3390.0000.0000.0000.000
83B372SER0-0.103-0.04721.6570.4580.4580.0000.0000.0000.000
84B373LEU0-0.010-0.00824.1050.4300.4300.0000.0000.0000.000
85B374ASN0-0.074-0.03125.1020.0390.0390.0000.0000.0000.000
86B375ILE0-0.0220.00125.1720.3560.3560.0000.0000.0000.000
87B376ASP-1-0.764-0.87325.804-9.787-9.7870.0000.0000.0000.000
88B377THR00.004-0.02625.7030.0600.0600.0000.0000.0000.000
89B378LYS10.8810.94727.7878.2708.2700.0000.0000.0000.000
90B379GLU-1-0.796-0.91329.739-9.415-9.4150.0000.0000.0000.000
91B380TYR00.0530.02522.3780.0100.0100.0000.0000.0000.000
92B381ALA0-0.035-0.00927.750-0.016-0.0160.0000.0000.0000.000
93B382TYR00.0390.01429.9500.1830.1830.0000.0000.0000.000
94B383LEU0-0.0110.01327.2850.1560.1560.0000.0000.0000.000
95B384LYS10.8260.89224.67811.29611.2960.0000.0000.0000.000
96B385GLY00.0000.00729.2150.1120.1120.0000.0000.0000.000
97B386THR0-0.046-0.05132.4150.2760.2760.0000.0000.0000.000
98B387VAL0-0.050-0.01828.2500.1220.1220.0000.0000.0000.000
99B388LEU0-0.029-0.01731.2880.0860.0860.0000.0000.0000.000
100B389PHE0-0.004-0.02732.4890.1610.1610.0000.0000.0000.000
101B390ASN00.0210.00833.9940.2550.2550.0000.0000.0000.000
102B391PRO00.016-0.01236.500-0.039-0.0390.0000.0000.0000.000
103B392ASP-1-0.906-0.94337.751-7.530-7.5300.0000.0000.0000.000
104B393LEU0-0.081-0.03433.195-0.043-0.0430.0000.0000.0000.000
105B394PRO00.0490.01635.5230.2170.2170.0000.0000.0000.000
106B395GLY00.0050.00237.292-0.148-0.1480.0000.0000.0000.000
107B396LEU0-0.045-0.00737.5780.1010.1010.0000.0000.0000.000
108B397GLN0-0.020-0.01740.7350.2460.2460.0000.0000.0000.000
109B398CYS0-0.101-0.04241.6590.1350.1350.0000.0000.0000.000
110B399VAL00.1070.04442.969-0.026-0.0260.0000.0000.0000.000
111B400LYS10.9850.97243.9765.9975.9970.0000.0000.0000.000
112B401TYR0-0.082-0.07241.3170.0700.0700.0000.0000.0000.000
113B402ILE00.0480.01238.497-0.045-0.0450.0000.0000.0000.000
114B403GLU-1-0.886-0.92341.402-6.956-6.9560.0000.0000.0000.000
115B404GLY00.0060.00543.071-0.058-0.0580.0000.0000.0000.000
116B405LEU0-0.048-0.01439.4710.0000.0000.0000.0000.0000.000
117B406GLN00.0910.09137.978-0.044-0.0440.0000.0000.0000.000
118B407TRP0-0.035-0.01739.696-0.076-0.0760.0000.0000.0000.000
119B408ARG10.9570.95241.8027.0067.0060.0000.0000.0000.000
120B409THR0-0.049-0.05535.593-0.083-0.0830.0000.0000.0000.000
121B410GLN00.0420.00836.267-0.031-0.0310.0000.0000.0000.000
122B411GLN0-0.0540.01039.3520.1430.1430.0000.0000.0000.000
123B412ILE0-0.008-0.01737.7210.0480.0480.0000.0000.0000.000
124B413LEU00.0020.01634.419-0.085-0.0850.0000.0000.0000.000
125B414THR0-0.010-0.03237.723-0.044-0.0440.0000.0000.0000.000
126B415GLU-1-0.869-0.91440.361-6.788-6.7880.0000.0000.0000.000
127B416HIS0-0.016-0.01933.7430.2220.2220.0000.0000.0000.000
128B417ILE0-0.003-0.00935.972-0.040-0.0400.0000.0000.0000.000
129B418ARG10.8490.92538.0476.8156.8150.0000.0000.0000.000
130B419MET0-0.103-0.05039.8760.1690.1690.0000.0000.0000.000
131B420MET0-0.0320.01234.0330.1030.1030.0000.0000.0000.000
132B421GLN00.0190.00334.8610.0430.0430.0000.0000.0000.000
133B422ARG10.9410.96238.6866.8816.8810.0000.0000.0000.000
134B423GLU-1-0.915-0.95739.722-7.495-7.4950.0000.0000.0000.000
135B424TYR0-0.007-0.00938.9800.1630.1630.0000.0000.0000.000
136B425GLN00.0320.01240.450-0.136-0.1360.0000.0000.0000.000
137B426ILE00.0300.01736.174-0.120-0.1200.0000.0000.0000.000
138B427ARG10.8740.93129.7649.3599.3590.0000.0000.0000.000
139B428SER00.0220.02034.288-0.306-0.3060.0000.0000.0000.000
140B429ALA00.0260.01234.967-0.186-0.1860.0000.0000.0000.000
141B430GLU-1-0.913-0.96831.335-9.516-9.5160.0000.0000.0000.000
142B431LEU00.0100.00430.137-0.372-0.3720.0000.0000.0000.000
143B432ASN0-0.005-0.01730.476-0.350-0.3500.0000.0000.0000.000
144B433SER0-0.069-0.01130.035-0.258-0.2580.0000.0000.0000.000
145B434ALA00.0530.01525.902-0.230-0.2300.0000.0000.0000.000
146B435LEU00.0250.01026.796-0.283-0.2830.0000.0000.0000.000
147B436PHE0-0.058-0.03728.699-0.081-0.0810.0000.0000.0000.000
148B437LEU0-0.016-0.00823.942-0.045-0.0450.0000.0000.0000.000
149B438LEU0-0.0120.01123.246-0.413-0.4130.0000.0000.0000.000
150B439ARG10.9010.95425.2899.1869.1860.0000.0000.0000.000
151B440PHE0-0.045-0.02225.5610.2100.2100.0000.0000.0000.000
152B441ILE00.0040.00520.340-0.403-0.4030.0000.0000.0000.000
153B442ASN00.009-0.01422.006-0.100-0.1000.0000.0000.0000.000
154B443SER00.0100.01322.3320.1700.1700.0000.0000.0000.000
155B444ASP-1-0.859-0.91121.820-11.705-11.7050.0000.0000.0000.000
156B445VAL0-0.011-0.02517.271-0.495-0.4950.0000.0000.0000.000
157B446VAL00.0140.01816.890-0.834-0.8340.0000.0000.0000.000
158B447THR0-0.022-0.01416.270-0.785-0.7850.0000.0000.0000.000
159B448GLU-1-0.855-0.94215.886-15.477-15.4770.0000.0000.0000.000
160B449LEU0-0.051-0.02211.154-0.745-0.7450.0000.0000.0000.000
161B450PHE0-0.014-0.01811.434-1.223-1.2230.0000.0000.0000.000
162B451PHE00.029-0.00212.682-0.336-0.3360.0000.0000.0000.000
163B452ARG10.8760.94215.08713.65913.6590.0000.0000.0000.000
164B453PRO0-0.002-0.00710.3810.4060.4060.0000.0000.0000.000
165B454ILE0-0.033-0.00812.5210.2320.2320.0000.0000.0000.000
166B455ILE0-0.084-0.02414.4590.6290.6290.0000.0000.0000.000
167B456GLY00.0580.03416.5890.7200.7200.0000.0000.0000.000
168B457ALA0-0.038-0.01217.9640.0360.0360.0000.0000.0000.000
169B458VAL00.0380.01521.4040.5330.5330.0000.0000.0000.000
170B459SER00.0000.01122.678-0.457-0.4570.0000.0000.0000.000
171B460MET00.0290.01121.068-0.087-0.0870.0000.0000.0000.000
172B461ASP-1-0.871-0.94923.863-10.271-10.2710.0000.0000.0000.000
173B462ASP-1-0.893-0.96127.151-9.575-9.5750.0000.0000.0000.000
174B463MET0-0.019-0.00421.7470.1620.1620.0000.0000.0000.000
175B464MET00.0060.00325.2250.0610.0610.0000.0000.0000.000
176B465LEU00.0260.01827.5070.1730.1730.0000.0000.0000.000
177B466GLU-1-0.822-0.91827.728-9.258-9.2580.0000.0000.0000.000
178B467MET0-0.070-0.00923.113-0.051-0.0510.0000.0000.0000.000
179B468LEU0-0.048-0.03127.9310.0310.0310.0000.0000.0000.000
180B469CYS0-0.058-0.02731.0020.3610.3610.0000.0000.0000.000
181B470ALA00.0400.01928.1510.0780.0780.0000.0000.0000.000
182B471LYS10.8340.91125.91210.55510.5550.0000.0000.0000.000
183B472LEU00.0150.02529.2460.2030.2030.0000.0000.0000.000