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: 397LL

Calculation Name: 4FHR-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 4FHR

Chain ID: A

ChEMBL ID:

UniProt ID: Q9WY63

Base Structure: X-ray

Registration Date: 2023-06-22

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 182
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2079663.90218
FMO2-HF: Nuclear repulsion 2005975.017398
FMO2-HF: Total energy -73688.884782
FMO2-MP2: Total energy -73902.730268


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:45:THR)


Summations of interaction energy for fragment #1(A:45:THR)
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.
-18.261-14.88817.064-8.253-12.184-0.06
Interaction energy analysis for fragmet #1(A:45:THR)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.036 / q_NPA : -0.012
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].
3A47PHE00.0760.0443.904-0.9110.907-0.013-0.996-0.8090.003
4A48SER00.0040.0026.730-0.048-0.0480.0000.0000.0000.000
5A49LYS10.9580.9589.908-0.537-0.5370.0000.0000.0000.000
6A50GLU-1-0.919-0.94913.2680.2230.2230.0000.0000.0000.000
7A51GLN00.0690.0448.7720.1890.1890.0000.0000.0000.000
8A52LEU00.0350.0208.909-0.045-0.0450.0000.0000.0000.000
9A53ARG10.7940.89712.185-0.267-0.2670.0000.0000.0000.000
10A54THR00.022-0.00114.495-0.042-0.0420.0000.0000.0000.000
11A55PHE00.0630.0239.018-0.011-0.0110.0000.0000.0000.000
12A56GLN0-0.024-0.00414.3520.0030.0030.0000.0000.0000.000
13A57MET0-0.073-0.04216.842-0.028-0.0280.0000.0000.0000.000
14A58ILE00.0190.02315.672-0.014-0.0140.0000.0000.0000.000
15A59HIS00.0570.01114.265-0.040-0.0400.0000.0000.0000.000
16A60GLU-1-0.734-0.85218.9860.1590.1590.0000.0000.0000.000
17A61ASN0-0.0050.00821.869-0.008-0.0080.0000.0000.0000.000
18A62PHE00.0350.02120.418-0.011-0.0110.0000.0000.0000.000
19A63GLY00.0500.01722.729-0.007-0.0070.0000.0000.0000.000
20A64ARG10.8310.89824.150-0.119-0.1190.0000.0000.0000.000
21A65ALA00.0030.00726.383-0.007-0.0070.0000.0000.0000.000
22A66LEU0-0.020-0.00724.155-0.008-0.0080.0000.0000.0000.000
23A67SER00.014-0.00827.542-0.005-0.0050.0000.0000.0000.000
24A68THR0-0.036-0.01030.068-0.006-0.0060.0000.0000.0000.000
25A69TYR0-0.052-0.06529.935-0.007-0.0070.0000.0000.0000.000
26A70LEU00.018-0.01028.069-0.005-0.0050.0000.0000.0000.000
27A71SER00.0080.00032.222-0.002-0.0020.0000.0000.0000.000
28A72GLY0-0.029-0.00735.169-0.003-0.0030.0000.0000.0000.000
29A73ARG10.7320.83033.176-0.020-0.0200.0000.0000.0000.000
30A74LEU00.0290.00633.117-0.002-0.0020.0000.0000.0000.000
31A75ARG10.7920.90137.152-0.020-0.0200.0000.0000.0000.000
32A76THR0-0.0010.00237.550-0.001-0.0010.0000.0000.0000.000
33A77PHE0-0.033-0.01033.477-0.001-0.0010.0000.0000.0000.000
34A78VAL00.002-0.00131.0200.0010.0010.0000.0000.0000.000
35A79ASP-1-0.855-0.90230.3760.0910.0910.0000.0000.0000.000
36A80VAL0-0.056-0.04024.9110.0010.0010.0000.0000.0000.000
37A81GLU-1-0.889-0.90825.0110.1460.1460.0000.0000.0000.000
38A82ILE0-0.048-0.02819.2970.0010.0010.0000.0000.0000.000
39A83SER0-0.0120.00218.463-0.004-0.0040.0000.0000.0000.000
40A84ILE0-0.031-0.02012.378-0.010-0.0100.0000.0000.0000.000
41A85ASP-1-0.862-0.91812.8820.6330.6330.0000.0000.0000.000
42A86GLN0-0.057-0.0376.5400.1770.1770.0000.0000.0000.000
43A87LEU00.0170.0308.8950.0530.0530.0000.0000.0000.000
44A88THR0-0.031-0.0577.3610.3520.3520.0000.0000.0000.000
45A89TYR00.019-0.0258.880-0.173-0.1730.0000.0000.0000.000
46A90GLU-1-0.934-0.98110.7860.0230.0230.0000.0000.0000.000
47A91GLU-1-0.878-0.91310.7150.6330.6330.0000.0000.0000.000
48A92PHE00.0610.03612.664-0.061-0.0610.0000.0000.0000.000
49A93ILE00.0000.01814.365-0.057-0.0570.0000.0000.0000.000
50A94ARG10.8640.93116.578-0.196-0.1960.0000.0000.0000.000
51A95SER0-0.069-0.03817.459-0.009-0.0090.0000.0000.0000.000
52A96VAL0-0.029-0.00118.579-0.011-0.0110.0000.0000.0000.000
53A97MET00.0010.00521.231-0.011-0.0110.0000.0000.0000.000
54A98ILE0-0.0090.02124.772-0.009-0.0090.0000.0000.0000.000
55A99PRO0-0.049-0.03027.311-0.001-0.0010.0000.0000.0000.000
56A100SER0-0.006-0.03824.6700.0130.0130.0000.0000.0000.000
57A101PHE0-0.007-0.01026.075-0.013-0.0130.0000.0000.0000.000
58A102ILE00.0070.00820.4080.0130.0130.0000.0000.0000.000
59A103VAL0-0.002-0.00821.824-0.015-0.0150.0000.0000.0000.000
60A104ILE0-0.0120.00818.0440.0120.0120.0000.0000.0000.000
61A105PHE0-0.056-0.03516.921-0.004-0.0040.0000.0000.0000.000
62A106THR00.1110.03617.380-0.009-0.0090.0000.0000.0000.000
63A107GLY00.033-0.00618.8680.0370.0370.0000.0000.0000.000
64A108ASP-1-0.869-0.93319.827-0.174-0.1740.0000.0000.0000.000
65A109VAL0-0.055-0.01617.748-0.006-0.0060.0000.0000.0000.000
66A110PHE0-0.059-0.02515.285-0.038-0.0380.0000.0000.0000.000
67A111GLU-1-0.902-0.93814.057-0.436-0.4360.0000.0000.0000.000
68A112GLY0-0.021-0.02113.425-0.121-0.1210.0000.0000.0000.000
69A113SER0-0.062-0.03814.0180.0420.0420.0000.0000.0000.000
70A114ALA00.0150.00513.314-0.028-0.0280.0000.0000.0000.000
71A115ILE0-0.024-0.01114.877-0.001-0.0010.0000.0000.0000.000
72A116PHE00.0280.01416.8090.0340.0340.0000.0000.0000.000
73A117GLU-1-0.812-0.87719.6750.1200.1200.0000.0000.0000.000
74A118MET00.0120.00921.5060.0090.0090.0000.0000.0000.000
75A119ARG10.8700.92121.652-0.144-0.1440.0000.0000.0000.000
76A120LEU00.012-0.00727.163-0.006-0.0060.0000.0000.0000.000
77A121ASP-1-0.772-0.86430.3430.0670.0670.0000.0000.0000.000
78A122LEU00.0550.04727.733-0.006-0.0060.0000.0000.0000.000
79A123PHE0-0.027-0.01429.505-0.006-0.0060.0000.0000.0000.000
80A124TYR0-0.020-0.04431.556-0.007-0.0070.0000.0000.0000.000
81A125THR0-0.006-0.00634.427-0.003-0.0030.0000.0000.0000.000
82A126MET0-0.032-0.01830.556-0.001-0.0010.0000.0000.0000.000
83A127LEU0-0.002-0.00634.885-0.004-0.0040.0000.0000.0000.000
84A128ASP-1-0.834-0.91836.6320.0190.0190.0000.0000.0000.000
85A129ILE00.0490.05337.757-0.002-0.0020.0000.0000.0000.000
86A130ILE0-0.073-0.03134.801-0.003-0.0030.0000.0000.0000.000
87A131MET0-0.093-0.06139.374-0.003-0.0030.0000.0000.0000.000
88A132GLY0-0.069-0.02942.115-0.002-0.0020.0000.0000.0000.000
89A133GLY0-0.0180.01043.2450.0000.0000.0000.0000.0000.000
90A134PRO0-0.025-0.03343.0430.0010.0010.0000.0000.0000.000
91A135GLY0-0.008-0.00239.5880.0030.0030.0000.0000.0000.000
92A136GLU-1-0.972-0.98039.3130.0300.0300.0000.0000.0000.000
93A137ASN0-0.071-0.05140.218-0.001-0.0010.0000.0000.0000.000
94A138PRO00.0570.05235.785-0.003-0.0030.0000.0000.0000.000
95A139PRO0-0.033-0.01037.2350.0020.0020.0000.0000.0000.000
96A140ASN00.009-0.00832.3140.0030.0030.0000.0000.0000.000
97A141ARG10.7840.85134.308-0.016-0.0160.0000.0000.0000.000
98A142PRO00.0690.03231.6480.0020.0020.0000.0000.0000.000
99A143PRO0-0.0090.01931.277-0.001-0.0010.0000.0000.0000.000
100A144THR0-0.022-0.03534.143-0.004-0.0040.0000.0000.0000.000
101A145GLU-1-0.881-0.94435.425-0.020-0.0200.0000.0000.0000.000
102A146ILE00.0010.01236.343-0.001-0.0010.0000.0000.0000.000
103A147GLU-1-0.691-0.79135.8470.0100.0100.0000.0000.0000.000
104A148THR00.0180.00230.7920.0030.0030.0000.0000.0000.000
105A149SER0-0.040-0.03632.692-0.003-0.0030.0000.0000.0000.000
106A150ILE0-0.048-0.00535.178-0.002-0.0020.0000.0000.0000.000
107A151MET00.0590.03030.941-0.002-0.0020.0000.0000.0000.000
108A152ARG10.9700.98927.9210.0450.0450.0000.0000.0000.000
109A153LYS10.8480.94429.3260.0090.0090.0000.0000.0000.000
110A154GLU-1-0.722-0.79830.5510.0140.0140.0000.0000.0000.000
111A155VAL00.0310.00824.4020.0030.0030.0000.0000.0000.000
112A156THR00.000-0.00925.738-0.004-0.0040.0000.0000.0000.000
113A157ASN0-0.039-0.01426.976-0.008-0.0080.0000.0000.0000.000
114A158MET0-0.0160.00225.0750.0050.0050.0000.0000.0000.000
115A159LEU00.0290.00820.6190.0060.0060.0000.0000.0000.000
116A160THR0-0.039-0.01822.949-0.010-0.0100.0000.0000.0000.000
117A161LEU0-0.043-0.02125.195-0.001-0.0010.0000.0000.0000.000
118A162LEU0-0.048-0.00817.8510.0060.0060.0000.0000.0000.000
119A163ALA00.0300.01020.8210.0020.0020.0000.0000.0000.000
120A164GLN0-0.028-0.02321.8550.0010.0010.0000.0000.0000.000
121A165ALA0-0.037-0.00121.4810.0000.0000.0000.0000.0000.000
122A166TRP00.009-0.01312.3380.0040.0040.0000.0000.0000.000
123A167SER0-0.070-0.04019.615-0.014-0.0140.0000.0000.0000.000
124A168ASP-1-0.946-0.96221.8400.0020.0020.0000.0000.0000.000
125A169PHE0-0.067-0.03916.8470.0060.0060.0000.0000.0000.000
126A170GLN0-0.011-0.02516.219-0.055-0.0550.0000.0000.0000.000
127A171TYR00.0060.01718.4460.0160.0160.0000.0000.0000.000
128A172PHE00.0400.01818.410-0.025-0.0250.0000.0000.0000.000
129A173ILE0-0.042-0.01721.3330.0250.0250.0000.0000.0000.000
130A174PRO0-0.0120.00121.910-0.016-0.0160.0000.0000.0000.000
131A175SER0-0.063-0.03122.3400.0030.0030.0000.0000.0000.000
132A176ILE0-0.012-0.01722.397-0.004-0.0040.0000.0000.0000.000
133A177GLU-1-0.827-0.89419.146-0.180-0.1800.0000.0000.0000.000
134A178ASN0-0.037-0.03422.8950.0050.0050.0000.0000.0000.000
135A179VAL0-0.074-0.04223.6650.0070.0070.0000.0000.0000.000
136A180GLU-1-0.832-0.91123.151-0.034-0.0340.0000.0000.0000.000
137A181THR0-0.024-0.02025.4250.0100.0100.0000.0000.0000.000
138A182ASN00.014-0.01125.2670.0180.0180.0000.0000.0000.000
139A183PRO00.0690.03920.346-0.015-0.0150.0000.0000.0000.000
140A184GLN0-0.026-0.00720.352-0.010-0.0100.0000.0000.0000.000
141A185PHE0-0.047-0.00622.169-0.009-0.0090.0000.0000.0000.000
142A186VAL00.0340.02917.544-0.018-0.0180.0000.0000.0000.000
143A187GLN0-0.046-0.02015.5660.0210.0210.0000.0000.0000.000
144A188ILE00.0030.01012.875-0.030-0.0300.0000.0000.0000.000
145A189VAL00.0110.0249.040-0.070-0.0700.0000.0000.0000.000
146A190PRO0-0.020-0.0159.2140.1190.1190.0000.0000.0000.000
147A191PRO00.0410.0249.5780.0750.0750.0000.0000.0000.000
148A192ASN0-0.021-0.0238.3220.1890.1890.0000.0000.0000.000
149A193GLU-1-0.818-0.8734.654-1.056-0.978-0.001-0.007-0.0700.000
150A194ILE0-0.037-0.0202.888-1.650-0.2990.996-0.782-1.5660.007
151A195VAL0-0.005-0.0104.941-0.940-0.849-0.001-0.007-0.0820.000
152A196LEU0-0.045-0.0157.4860.2020.2020.0000.0000.0000.000
153A197LEU0-0.004-0.0029.159-0.189-0.1890.0000.0000.0000.000
154A198VAL0-0.003-0.00412.6720.0070.0070.0000.0000.0000.000
155A199THR0-0.002-0.01915.533-0.011-0.0110.0000.0000.0000.000
156A200ALA0-0.008-0.01018.901-0.001-0.0010.0000.0000.0000.000
157A201SER0-0.039-0.03522.388-0.009-0.0090.0000.0000.0000.000
158A202VAL0-0.0040.00125.299-0.008-0.0080.0000.0000.0000.000
159A203SER00.0160.00328.090-0.003-0.0030.0000.0000.0000.000
160A204TRP00.038-0.00430.781-0.003-0.0030.0000.0000.0000.000
161A205GLY0-0.0050.00735.114-0.002-0.0020.0000.0000.0000.000
162A206GLU-1-0.950-0.98036.7440.0580.0580.0000.0000.0000.000
163A207PHE0-0.0400.00134.3290.0030.0030.0000.0000.0000.000
164A208THR0-0.012-0.03228.8110.0040.0040.0000.0000.0000.000
165A209SER0-0.077-0.04728.2670.0030.0030.0000.0000.0000.000
166A210PHE0-0.010-0.01023.0850.0060.0060.0000.0000.0000.000
167A211ILE0-0.0050.00121.843-0.015-0.0150.0000.0000.0000.000
168A212ASN0-0.030-0.01617.7760.0360.0360.0000.0000.0000.000
169A213VAL0-0.013-0.01215.723-0.037-0.0370.0000.0000.0000.000
170A214CYS0-0.052-0.01612.4060.0840.0840.0000.0000.0000.000
171A215TRP00.0370.01210.290-0.110-0.1100.0000.0000.0000.000
172A216PRO00.0370.0157.9410.2980.2980.0000.0000.0000.000
173A217PHE00.0290.0132.235-10.131-10.30316.085-6.432-9.481-0.070
174A218SER0-0.047-0.0544.844-0.732-0.703-0.001-0.004-0.0250.000
175A219LEU0-0.0080.0106.9730.1200.1200.0000.0000.0000.000
176A220LEU0-0.022-0.0096.5880.1590.1590.0000.0000.0000.000
177A221GLU-1-0.931-0.9704.351-4.819-4.641-0.001-0.025-0.1510.000
178A222PRO0-0.020-0.0197.1250.3880.3880.0000.0000.0000.000
179A223LEU0-0.040-0.02510.3060.1990.1990.0000.0000.0000.000
180A224LEU0-0.052-0.0125.6370.2280.2280.0000.0000.0000.000
181A225GLU-1-0.972-0.98110.109-0.043-0.0430.0000.0000.0000.000
182A226LYS10.8670.95312.8760.3120.3120.0000.0000.0000.000