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: 395GL

Calculation Name: 3E9N-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3E9N

Chain ID: A

ChEMBL ID:

UniProt ID: Q8NMW9

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 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 189
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -1978671.385534
FMO2-HF: Nuclear repulsion 1908075.61999
FMO2-HF: Total energy -70595.765544
FMO2-MP2: Total energy -70805.767504


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:4:LYS)


Summations of interaction energy for fragment #1(A:4: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.
-316.301-309.06936.65-19.569-24.31-0.202
Interaction energy analysis for fragmet #1(A:4:LYS)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 1 / q_Mulliken : 0.847 / q_NPA : 0.923
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].
3A6ALA0-0.014-0.0143.872-4.122-1.893-0.008-1.164-1.0570.004
4A7VAL00.0050.0085.8763.8543.8540.0000.0000.0000.000
5A8VAL00.0100.0039.669-0.562-0.5620.0000.0000.0000.000
6A9THR00.0290.01812.5151.4811.4810.0000.0000.0000.000
7A10GLY00.0430.01716.151-0.192-0.1920.0000.0000.0000.000
8A11ALA0-0.0040.00115.3790.1480.1480.0000.0000.0000.000
9A12THR00.0310.02416.976-0.027-0.0270.0000.0000.0000.000
10A13GLY0-0.0100.00019.8600.9320.9320.0000.0000.0000.000
11A14GLY00.003-0.01119.464-0.677-0.6770.0000.0000.0000.000
12A15MET00.017-0.00317.158-0.605-0.6050.0000.0000.0000.000
13A16GLY00.0470.03515.317-1.280-1.2800.0000.0000.0000.000
14A17ILE00.0480.02414.808-1.522-1.5220.0000.0000.0000.000
15A18GLU-1-0.840-0.90214.998-19.307-19.3070.0000.0000.0000.000
16A19ILE0-0.035-0.01910.544-1.713-1.7130.0000.0000.0000.000
17A20VAL00.0200.00910.258-3.153-3.1530.0000.0000.0000.000
18A21LYS10.8490.91010.49417.25117.2510.0000.0000.0000.000
19A22ASP-1-0.846-0.8988.259-34.491-34.4910.0000.0000.0000.000
20A23LEU00.0260.0055.135-3.668-3.6680.0000.0000.0000.000
21A24SER0-0.005-0.0145.752-5.676-5.6760.0000.0000.0000.000
22A25ARG10.8320.9266.54537.72237.7220.0000.0000.0000.000
23A26ASP-1-0.794-0.8641.687-110.192-114.52015.673-6.672-4.673-0.074
24A27HIS0-0.022-0.0042.095-46.580-44.29117.377-7.549-12.116-0.088
25A28ILE00.0430.0353.3486.9757.6030.028-0.030-0.6260.000
26A29VAL0-0.048-0.0235.814-2.145-2.1450.0000.0000.0000.000
27A30TYR00.0370.0227.8102.6772.6770.0000.0000.0000.000
28A31ALA0-0.005-0.01411.232-0.515-0.5150.0000.0000.0000.000
29A32LEU00.0200.00614.0431.3611.3610.0000.0000.0000.000
30A33GLY0-0.055-0.04116.836-0.253-0.2530.0000.0000.0000.000
31A34ARG10.8460.91520.16112.41612.4160.0000.0000.0000.000
32A35ASN0-0.001-0.01023.3200.5430.5430.0000.0000.0000.000
33A36PRO00.0750.02923.179-0.507-0.5070.0000.0000.0000.000
34A37GLU-1-0.904-0.93023.758-11.991-11.9910.0000.0000.0000.000
35A38HIS0-0.029-0.02721.396-0.455-0.4550.0000.0000.0000.000
36A39LEU0-0.031-0.01018.123-0.876-0.8760.0000.0000.0000.000
37A40ALA0-0.0030.00719.210-0.630-0.6300.0000.0000.0000.000
38A41ALA00.007-0.00720.341-0.363-0.3630.0000.0000.0000.000
39A42LEU0-0.063-0.04415.327-0.682-0.6820.0000.0000.0000.000
40A43ALA0-0.011-0.00915.677-1.176-1.1760.0000.0000.0000.000
41A44GLU-1-0.964-0.96316.708-14.221-14.2210.0000.0000.0000.000
42A45ILE0-0.123-0.04812.306-0.173-0.1730.0000.0000.0000.000
43A46GLU-1-0.868-0.93910.595-21.004-21.0040.0000.0000.0000.000
44A47GLY0-0.008-0.0098.408-2.032-2.0320.0000.0000.0000.000
45A48VAL0-0.043-0.0198.780-2.755-2.7550.0000.0000.0000.000
46A49GLU-1-0.782-0.87811.237-16.784-16.7840.0000.0000.0000.000
47A50PRO00.0010.01613.093-0.302-0.3020.0000.0000.0000.000
48A51ILE0-0.052-0.04514.3960.7820.7820.0000.0000.0000.000
49A52GLU-1-0.851-0.94218.149-13.120-13.1200.0000.0000.0000.000
50A53SER0-0.051-0.05419.925-0.047-0.0470.0000.0000.0000.000
51A54ASP-1-0.842-0.91322.026-11.415-11.4150.0000.0000.0000.000
52A55ILE00.0300.00518.0090.1220.1220.0000.0000.0000.000
53A56VAL0-0.016-0.00722.111-0.132-0.1320.0000.0000.0000.000
54A57LYS10.8530.94325.15511.54211.5420.0000.0000.0000.000
55A58GLU-1-0.813-0.88521.826-13.320-13.3200.0000.0000.0000.000
56A59VAL0-0.077-0.02919.617-0.118-0.1180.0000.0000.0000.000
57A60LEU0-0.025-0.02122.3430.0630.0630.0000.0000.0000.000
58A61GLU-1-0.953-0.97325.891-9.766-9.7660.0000.0000.0000.000
59A62GLU-1-0.841-0.92525.152-11.194-11.1940.0000.0000.0000.000
60A63GLY0-0.024-0.00724.039-0.152-0.1520.0000.0000.0000.000
61A64GLY00.0160.00020.035-0.439-0.4390.0000.0000.0000.000
62A65VAL00.008-0.00817.3300.4570.4570.0000.0000.0000.000
63A66ASP-1-0.809-0.90117.550-13.811-13.8110.0000.0000.0000.000
64A67LYS10.7510.84415.81216.78316.7830.0000.0000.0000.000
65A68LEU00.0140.00912.008-1.043-1.0430.0000.0000.0000.000
66A69LYS10.7860.90813.42212.78512.7850.0000.0000.0000.000
67A70ASN0-0.081-0.03312.598-0.256-0.2560.0000.0000.0000.000
68A71LEU0-0.0130.0098.533-0.339-0.3390.0000.0000.0000.000
69A72ASP-1-0.848-0.9248.920-22.558-22.5580.0000.0000.0000.000
70A73HIS10.8030.8875.38025.97925.9790.0000.0000.0000.000
71A74VAL00.0100.0005.975-0.504-0.5040.0000.0000.0000.000
72A75ASP-1-0.791-0.8932.464-58.194-52.7823.579-3.857-5.134-0.044
73A76THR0-0.029-0.0123.4002.4892.8110.000-0.059-0.2620.000
74A77LEU0-0.010-0.0016.2722.2222.2220.0000.0000.0000.000
75A78VAL0-0.013-0.0099.2490.8140.8140.0000.0000.0000.000
76A79HIS00.004-0.00211.8711.3371.3370.0000.0000.0000.000
77A80ALA00.012-0.00815.6730.4280.4280.0000.0000.0000.000
78A81ALA0-0.049-0.01017.4440.9830.9830.0000.0000.0000.000
79A92GLY00.0860.03840.4190.1030.1030.0000.0000.0000.000
80A93SER00.011-0.02438.732-0.091-0.0910.0000.0000.0000.000
81A94VAL0-0.0150.00437.897-0.178-0.1780.0000.0000.0000.000
82A95ALA00.0400.02136.583-0.180-0.1800.0000.0000.0000.000
83A96GLU-1-0.863-0.91334.486-9.212-9.2120.0000.0000.0000.000
84A97TRP00.008-0.02033.162-0.378-0.3780.0000.0000.0000.000
85A98HIS00.0230.01832.359-0.428-0.4280.0000.0000.0000.000
86A99ALA00.0550.03630.506-0.344-0.3440.0000.0000.0000.000
87A100HIS0-0.015-0.01828.576-0.672-0.6720.0000.0000.0000.000
88A101LEU0-0.025-0.01727.473-0.436-0.4360.0000.0000.0000.000
89A102ASP-1-0.839-0.92427.008-11.187-11.1870.0000.0000.0000.000
90A103LEU0-0.037-0.01423.526-0.525-0.5250.0000.0000.0000.000
91A104ASN0-0.0050.00222.931-1.077-1.0770.0000.0000.0000.000
92A105VAL0-0.022-0.02323.241-0.226-0.2260.0000.0000.0000.000
93A106ILE0-0.006-0.00323.269-0.469-0.4690.0000.0000.0000.000
94A107VAL00.0380.02720.269-0.305-0.3050.0000.0000.0000.000
95A108PRO00.0120.00218.667-0.613-0.6130.0000.0000.0000.000
96A109ALA0-0.0070.01618.470-0.818-0.8180.0000.0000.0000.000
97A110GLU-1-0.742-0.82219.878-13.676-13.6760.0000.0000.0000.000
98A111LEU00.0230.01015.292-0.205-0.2050.0000.0000.0000.000
99A112SER0-0.009-0.02615.265-1.391-1.3910.0000.0000.0000.000
100A113ARG10.7780.85116.15013.04713.0470.0000.0000.0000.000
101A114GLN0-0.105-0.07117.838-0.499-0.4990.0000.0000.0000.000
102A115LEU00.0210.00611.737-0.051-0.0510.0000.0000.0000.000
103A116LEU0-0.0130.01413.068-1.185-1.1850.0000.0000.0000.000
104A117PRO0-0.024-0.02514.278-0.601-0.6010.0000.0000.0000.000
105A118ALA00.0480.0399.707-0.386-0.3860.0000.0000.0000.000
106A119LEU0-0.0060.0009.264-2.125-2.1250.0000.0000.0000.000
107A120ARG10.8090.85910.31415.18015.1800.0000.0000.0000.000
108A121ALA0-0.042-0.01010.272-0.370-0.3700.0000.0000.0000.000
109A122ALA0-0.033-0.0215.983-0.148-0.1480.0000.0000.0000.000
110A123SER0-0.041-0.0067.069-1.894-1.8940.0000.0000.0000.000
111A124GLY00.0180.0266.651-1.750-1.7500.0000.0000.0000.000
112A125CYS0-0.052-0.0186.5644.2774.2770.0000.0000.0000.000
113A126VAL00.0260.0168.548-1.085-1.0850.0000.0000.0000.000
114A127ILE0-0.036-0.0268.9181.5411.5410.0000.0000.0000.000
115A128TYR0-0.0060.00112.6860.2970.2970.0000.0000.0000.000
116A129ILE0-0.005-0.00214.8960.1260.1260.0000.0000.0000.000
117A130ASN0-0.050-0.04517.8391.2751.2750.0000.0000.0000.000
118A141ASN00.0460.02434.5930.1490.1490.0000.0000.0000.000
119A142THR0-0.028-0.02334.476-0.321-0.3210.0000.0000.0000.000
120A143ILE00.0380.03332.240-0.198-0.1980.0000.0000.0000.000
121A144TYR0-0.032-0.03330.254-0.315-0.3150.0000.0000.0000.000
122A145ALA0-0.0030.00629.600-0.357-0.3570.0000.0000.0000.000
123A146ALA00.0210.01730.356-0.262-0.2620.0000.0000.0000.000
124A147SER00.0160.00027.344-0.313-0.3130.0000.0000.0000.000
125A148LYS10.8990.95525.21912.00112.0010.0000.0000.0000.000
126A149HIS0-0.094-0.04625.538-0.294-0.2940.0000.0000.0000.000
127A150ALA0-0.014-0.00826.731-0.226-0.2260.0000.0000.0000.000
128A151LEU00.0140.02219.955-0.221-0.2210.0000.0000.0000.000
129A152ARG10.8470.91321.81613.36313.3630.0000.0000.0000.000
130A153GLY0-0.007-0.00722.945-0.241-0.2410.0000.0000.0000.000
131A154LEU00.0040.00420.8590.0120.0120.0000.0000.0000.000
132A155ALA00.0220.01618.450-0.309-0.3090.0000.0000.0000.000
133A156ASP-1-0.761-0.85919.678-14.737-14.7370.0000.0000.0000.000
134A157ALA0-0.078-0.01922.0270.3320.3320.0000.0000.0000.000
135A158PHE00.1150.05115.099-0.042-0.0420.0000.0000.0000.000
136A159ARG10.7900.87016.79516.72416.7240.0000.0000.0000.000
137A160LYS10.7990.87918.74712.64412.6440.0000.0000.0000.000
138A161GLU-1-0.960-0.97420.878-13.136-13.1360.0000.0000.0000.000
139A162GLU-1-0.722-0.82115.827-16.745-16.7450.0000.0000.0000.000
140A163ALA0-0.0010.01616.010-0.759-0.7590.0000.0000.0000.000
141A164ASN0-0.066-0.04116.546-0.354-0.3540.0000.0000.0000.000
142A165ASN0-0.090-0.05516.1020.7810.7810.0000.0000.0000.000
143A166GLY00.0240.01712.724-0.821-0.8210.0000.0000.0000.000
144A167ILE0-0.0200.00811.120-1.665-1.6650.0000.0000.0000.000
145A168ARG10.8140.8856.79036.09136.0910.0000.0000.0000.000
146A169VAL00.0050.00811.848-0.794-0.7940.0000.0000.0000.000
147A170SER0-0.037-0.03213.0331.2611.2610.0000.0000.0000.000
148A171THR0-0.017-0.01614.7500.2100.2100.0000.0000.0000.000
149A172VAL00.0250.02813.8500.4380.4380.0000.0000.0000.000
150A173SER00.021-0.01216.8940.3830.3830.0000.0000.0000.000
151A174PRO00.0030.01519.6430.5490.5490.0000.0000.0000.000
152A175GLY00.0600.02922.4700.3140.3140.0000.0000.0000.000
153A176PRO0-0.018-0.00826.258-0.070-0.0700.0000.0000.0000.000
154A177THR0-0.035-0.02329.3250.5390.5390.0000.0000.0000.000
155A194ARG10.9780.99131.1599.4069.4060.0000.0000.0000.000
156A195PRO0-0.022-0.03030.869-0.194-0.1940.0000.0000.0000.000
157A196GLU-1-0.792-0.92424.997-12.456-12.4560.0000.0000.0000.000
158A197ILE00.0180.01025.484-0.415-0.4150.0000.0000.0000.000
159A198TYR0-0.028-0.01126.8470.0590.0590.0000.0000.0000.000
160A199ILE0-0.077-0.02721.1080.0740.0740.0000.0000.0000.000
161A200GLU-1-0.858-0.93620.747-14.575-14.5750.0000.0000.0000.000
162A201PRO00.0060.01018.870-0.712-0.7120.0000.0000.0000.000
163A202LYS10.8920.93811.94922.76222.7620.0000.0000.0000.000
164A203GLU-1-0.868-0.93115.197-18.730-18.7300.0000.0000.0000.000
165A204ILE0-0.029-0.01515.246-0.612-0.6120.0000.0000.0000.000
166A205ALA00.0370.02211.909-1.284-1.2840.0000.0000.0000.000
167A206ASN0-0.040-0.02111.030-3.919-3.9190.0000.0000.0000.000
168A207ALA0-0.035-0.01212.028-1.135-1.1350.0000.0000.0000.000
169A208ILE00.021-0.0038.450-0.541-0.5410.0000.0000.0000.000
170A209ARG10.6980.8083.09655.65356.0750.002-0.205-0.2190.000
171A210PHE0-0.028-0.0227.954-2.142-2.1420.0000.0000.0000.000
172A211VAL0-0.046-0.0329.6410.3270.3270.0000.0000.0000.000
173A212ILE0-0.033-0.0163.6461.2641.4460.000-0.031-0.1510.000
174A213ASP-1-0.824-0.9054.853-56.834-56.758-0.001-0.002-0.0720.000
175A214ALA0-0.041-0.0046.5083.8473.8470.0000.0000.0000.000
176A215GLY00.0330.0208.494-2.142-2.1420.0000.0000.0000.000
177A216GLU-1-0.868-0.9528.586-30.243-30.2430.0000.0000.0000.000
178A217THR0-0.083-0.03411.4100.7210.7210.0000.0000.0000.000
179A218THR0-0.046-0.01212.9651.9021.9020.0000.0000.0000.000
180A219GLN00.0750.03212.449-1.683-1.6830.0000.0000.0000.000
181A220ILE00.0130.02012.4681.8951.8950.0000.0000.0000.000
182A221THR00.0070.01414.489-0.482-0.4820.0000.0000.0000.000
183A222ASN00.000-0.01116.8410.2460.2460.0000.0000.0000.000
184A223VAL00.0120.01414.9140.0520.0520.0000.0000.0000.000
185A224ASP-1-0.811-0.87418.129-13.551-13.5510.0000.0000.0000.000
186A225VAL0-0.0050.00318.7530.0480.0480.0000.0000.0000.000
187A226ARG10.8060.88122.04713.20113.2010.0000.0000.0000.000
188A227PRO00.0030.01925.031-0.254-0.2540.0000.0000.0000.000
189A228ARG10.9841.00925.68512.08712.0870.0000.0000.0000.000