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: JL2N9

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 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 182
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2075150.581509
FMO2-HF: Nuclear repulsion 2001461.943389
FMO2-HF: Total energy -73688.63812
FMO2-MP2: Total energy -73902.51786


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.
-16.642-11.37811.93-7.156-10.037-0.057
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 : -0.049 / q_NPA : -0.013
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].
3A47PHE00.0570.0343.783-2.2730.252-0.029-1.429-1.0680.004
4A48SER00.0090.0016.499-0.047-0.0470.0000.0000.0000.000
5A49LYS10.9560.9629.663-0.538-0.5380.0000.0000.0000.000
6A50GLU-1-0.917-0.95813.0360.2250.2250.0000.0000.0000.000
7A51GLN00.0540.0318.2420.2070.2070.0000.0000.0000.000
8A52LEU00.0640.0349.091-0.042-0.0420.0000.0000.0000.000
9A53ARG10.8320.92711.918-0.299-0.2990.0000.0000.0000.000
10A54THR00.0230.00414.046-0.048-0.0480.0000.0000.0000.000
11A55PHE00.0480.0228.704-0.012-0.0120.0000.0000.0000.000
12A56GLN0-0.0010.00814.318-0.002-0.0020.0000.0000.0000.000
13A57MET0-0.058-0.02516.818-0.033-0.0330.0000.0000.0000.000
14A58ILE00.0240.02315.559-0.018-0.0180.0000.0000.0000.000
15A59HIS00.0500.00714.519-0.047-0.0470.0000.0000.0000.000
16A60GLU-1-0.779-0.88319.1860.1720.1720.0000.0000.0000.000
17A61ASN0-0.0160.00021.900-0.014-0.0140.0000.0000.0000.000
18A62PHE00.0280.01820.710-0.012-0.0120.0000.0000.0000.000
19A63GLY00.0380.00922.808-0.010-0.0100.0000.0000.0000.000
20A64ARG10.8540.92224.284-0.132-0.1320.0000.0000.0000.000
21A65ALA00.0150.00726.441-0.008-0.0080.0000.0000.0000.000
22A66LEU0-0.018-0.00424.414-0.009-0.0090.0000.0000.0000.000
23A67SER00.0120.00127.668-0.007-0.0070.0000.0000.0000.000
24A68THR0-0.026-0.00930.167-0.007-0.0070.0000.0000.0000.000
25A69TYR0-0.051-0.05430.190-0.008-0.0080.0000.0000.0000.000
26A70LEU00.018-0.01128.442-0.006-0.0060.0000.0000.0000.000
27A71SER00.0090.00232.547-0.003-0.0030.0000.0000.0000.000
28A72GLY0-0.034-0.00735.305-0.003-0.0030.0000.0000.0000.000
29A73ARG10.7590.84133.739-0.024-0.0240.0000.0000.0000.000
30A74LEU00.004-0.00633.245-0.003-0.0030.0000.0000.0000.000
31A75ARG10.8180.91637.412-0.024-0.0240.0000.0000.0000.000
32A76THR00.0100.00337.4970.0000.0000.0000.0000.0000.000
33A77PHE0-0.037-0.01133.762-0.001-0.0010.0000.0000.0000.000
34A78VAL0-0.019-0.00931.1140.0010.0010.0000.0000.0000.000
35A79ASP-1-0.860-0.91830.5890.0970.0970.0000.0000.0000.000
36A80VAL0-0.050-0.03625.1570.0000.0000.0000.0000.0000.000
37A81GLU-1-0.956-0.95325.0980.1450.1450.0000.0000.0000.000
38A82ILE0-0.041-0.02619.2250.0030.0030.0000.0000.0000.000
39A83SER0-0.0040.00018.676-0.003-0.0030.0000.0000.0000.000
40A84ILE0-0.038-0.02412.769-0.002-0.0020.0000.0000.0000.000
41A85ASP-1-0.872-0.92213.0280.5800.5800.0000.0000.0000.000
42A86GLN0-0.057-0.0296.1850.1770.1770.0000.0000.0000.000
43A87LEU00.0190.0198.900-0.093-0.0930.0000.0000.0000.000
44A88THR0-0.035-0.0467.2760.2520.2520.0000.0000.0000.000
45A89TYR00.026-0.0188.809-0.094-0.0940.0000.0000.0000.000
46A90GLU-1-0.954-0.98911.019-0.039-0.0390.0000.0000.0000.000
47A91GLU-1-0.859-0.90510.6940.4730.4730.0000.0000.0000.000
48A92PHE00.0480.02613.085-0.034-0.0340.0000.0000.0000.000
49A93ILE00.0080.02614.868-0.040-0.0400.0000.0000.0000.000
50A94ARG10.8920.94216.836-0.120-0.1200.0000.0000.0000.000
51A95SER0-0.095-0.04617.944-0.009-0.0090.0000.0000.0000.000
52A96VAL0-0.026-0.00218.857-0.009-0.0090.0000.0000.0000.000
53A97MET0-0.0060.00021.502-0.013-0.0130.0000.0000.0000.000
54A98ILE0-0.0380.03125.341-0.008-0.0080.0000.0000.0000.000
55A99PRO0-0.034-0.03827.4780.0000.0000.0000.0000.0000.000
56A100SER0-0.002-0.04324.6860.0110.0110.0000.0000.0000.000
57A101PHE0-0.020-0.01826.235-0.013-0.0130.0000.0000.0000.000
58A102ILE00.0190.01320.5590.0110.0110.0000.0000.0000.000
59A103VAL00.000-0.00322.282-0.016-0.0160.0000.0000.0000.000
60A104ILE0-0.0090.00718.1520.0140.0140.0000.0000.0000.000
61A105PHE0-0.031-0.01817.426-0.006-0.0060.0000.0000.0000.000
62A106THR00.1020.04017.419-0.007-0.0070.0000.0000.0000.000
63A107GLY00.025-0.00818.8290.0350.0350.0000.0000.0000.000
64A108ASP-1-0.874-0.93120.050-0.138-0.1380.0000.0000.0000.000
65A109VAL0-0.049-0.02317.401-0.011-0.0110.0000.0000.0000.000
66A110PHE0-0.092-0.03614.999-0.033-0.0330.0000.0000.0000.000
67A111GLU-1-0.896-0.93414.025-0.388-0.3880.0000.0000.0000.000
68A112GLY00.017-0.00513.253-0.105-0.1050.0000.0000.0000.000
69A113SER0-0.065-0.05214.2430.0330.0330.0000.0000.0000.000
70A114ALA00.002-0.00213.515-0.007-0.0070.0000.0000.0000.000
71A115ILE0-0.026-0.01315.085-0.012-0.0120.0000.0000.0000.000
72A116PHE00.0150.00417.3030.0340.0340.0000.0000.0000.000
73A117GLU-1-0.885-0.94220.1620.1060.1060.0000.0000.0000.000
74A118MET00.0060.01521.7640.0130.0130.0000.0000.0000.000
75A119ARG10.9951.00823.295-0.123-0.1230.0000.0000.0000.000
76A120LEU00.026-0.00727.159-0.005-0.0050.0000.0000.0000.000
77A121ASP-1-0.779-0.85830.2410.0660.0660.0000.0000.0000.000
78A122LEU00.0440.03527.987-0.005-0.0050.0000.0000.0000.000
79A123PHE0-0.013-0.00929.791-0.005-0.0050.0000.0000.0000.000
80A124TYR0-0.024-0.05431.748-0.006-0.0060.0000.0000.0000.000
81A125THR0-0.0050.00334.747-0.003-0.0030.0000.0000.0000.000
82A126MET0-0.022-0.01431.201-0.001-0.0010.0000.0000.0000.000
83A127LEU0-0.011-0.01035.349-0.004-0.0040.0000.0000.0000.000
84A128ASP-1-0.839-0.92536.9370.0200.0200.0000.0000.0000.000
85A129ILE00.0460.04337.954-0.002-0.0020.0000.0000.0000.000
86A130ILE0-0.085-0.03235.225-0.003-0.0030.0000.0000.0000.000
87A131MET0-0.101-0.05539.779-0.003-0.0030.0000.0000.0000.000
88A132GLY0-0.075-0.03342.534-0.002-0.0020.0000.0000.0000.000
89A133GLY0-0.0080.01543.5370.0000.0000.0000.0000.0000.000
90A134PRO0-0.018-0.02443.4330.0010.0010.0000.0000.0000.000
91A135GLY0-0.017-0.01039.9640.0030.0030.0000.0000.0000.000
92A136GLU-1-0.987-0.98539.6780.0290.0290.0000.0000.0000.000
93A137ASN0-0.082-0.05640.252-0.002-0.0020.0000.0000.0000.000
94A138PRO00.0680.04836.001-0.003-0.0030.0000.0000.0000.000
95A139PRO0-0.031-0.01037.4110.0010.0010.0000.0000.0000.000
96A140ASN00.005-0.00832.7820.0050.0050.0000.0000.0000.000
97A141ARG10.7820.86034.807-0.013-0.0130.0000.0000.0000.000
98A142PRO00.0640.03532.1930.0030.0030.0000.0000.0000.000
99A143PRO00.0090.02131.561-0.001-0.0010.0000.0000.0000.000
100A144THR0-0.032-0.04034.525-0.004-0.0040.0000.0000.0000.000
101A145GLU-1-0.869-0.94135.796-0.020-0.0200.0000.0000.0000.000
102A146ILE00.0010.00636.6360.0000.0000.0000.0000.0000.000
103A147GLU-1-0.693-0.79636.0600.0090.0090.0000.0000.0000.000
104A148THR00.0270.01031.0600.0030.0030.0000.0000.0000.000
105A149SER0-0.058-0.04532.836-0.002-0.0020.0000.0000.0000.000
106A150ILE0-0.053-0.02734.793-0.001-0.0010.0000.0000.0000.000
107A151MET00.0530.03431.4190.0000.0000.0000.0000.0000.000
108A152ARG10.9840.99928.5410.0370.0370.0000.0000.0000.000
109A153LYS10.9020.97729.8710.0060.0060.0000.0000.0000.000
110A154GLU-1-0.724-0.79831.2770.0200.0200.0000.0000.0000.000
111A155VAL00.011-0.00325.0570.0030.0030.0000.0000.0000.000
112A156THR0-0.010-0.01826.378-0.002-0.0020.0000.0000.0000.000
113A157ASN0-0.033-0.01727.418-0.005-0.0050.0000.0000.0000.000
114A158MET0-0.0110.00225.5820.0050.0050.0000.0000.0000.000
115A159LEU00.0320.01521.1650.0080.0080.0000.0000.0000.000
116A160THR0-0.040-0.01623.360-0.007-0.0070.0000.0000.0000.000
117A161LEU0-0.047-0.02225.5040.0000.0000.0000.0000.0000.000
118A162LEU0-0.039-0.00818.1360.0070.0070.0000.0000.0000.000
119A163ALA00.0290.00821.0220.0050.0050.0000.0000.0000.000
120A164GLN0-0.022-0.02022.1560.0020.0020.0000.0000.0000.000
121A165ALA0-0.0510.00021.0890.0010.0010.0000.0000.0000.000
122A166TRP0-0.012-0.02112.5410.0050.0050.0000.0000.0000.000
123A167SER0-0.081-0.04019.828-0.014-0.0140.0000.0000.0000.000
124A168ASP-1-0.929-0.95121.7450.0260.0260.0000.0000.0000.000
125A169PHE0-0.063-0.04116.7860.0020.0020.0000.0000.0000.000
126A170GLN0-0.004-0.01716.343-0.050-0.0500.0000.0000.0000.000
127A171TYR0-0.0010.01018.6310.0160.0160.0000.0000.0000.000
128A172PHE00.0440.01318.555-0.022-0.0220.0000.0000.0000.000
129A173ILE0-0.034-0.01421.6680.0220.0220.0000.0000.0000.000
130A174PRO0-0.0130.00321.972-0.014-0.0140.0000.0000.0000.000
131A175SER0-0.042-0.02222.5770.0030.0030.0000.0000.0000.000
132A176ILE0-0.025-0.02522.761-0.004-0.0040.0000.0000.0000.000
133A177GLU-1-0.854-0.90619.356-0.162-0.1620.0000.0000.0000.000
134A178ASN0-0.040-0.03822.9900.0030.0030.0000.0000.0000.000
135A179VAL0-0.079-0.03523.8510.0090.0090.0000.0000.0000.000
136A180GLU-1-0.837-0.89823.372-0.045-0.0450.0000.0000.0000.000
137A181THR0-0.029-0.02825.6440.0090.0090.0000.0000.0000.000
138A182ASN0-0.001-0.01425.6310.0160.0160.0000.0000.0000.000
139A183PRO00.0900.04220.780-0.014-0.0140.0000.0000.0000.000
140A184GLN0-0.022-0.00220.664-0.007-0.0070.0000.0000.0000.000
141A185PHE0-0.039-0.00822.155-0.011-0.0110.0000.0000.0000.000
142A186VAL00.0240.02417.743-0.013-0.0130.0000.0000.0000.000
143A187GLN0-0.037-0.01516.1250.0170.0170.0000.0000.0000.000
144A188ILE0-0.0090.00413.135-0.028-0.0280.0000.0000.0000.000
145A189VAL00.0080.0219.270-0.060-0.0600.0000.0000.0000.000
146A190PRO0-0.018-0.0199.5510.0950.0950.0000.0000.0000.000
147A191PRO00.0280.01410.0200.0370.0370.0000.0000.0000.000
148A192ASN0-0.006-0.0228.0510.1550.1550.0000.0000.0000.000
149A193GLU-1-0.824-0.8725.066-0.800-0.8000.0000.0000.0000.000
150A194ILE0-0.022-0.0132.789-1.1430.0900.442-0.598-1.0770.003
151A195VAL00.002-0.0055.336-0.480-0.417-0.001-0.002-0.0590.000
152A196LEU0-0.047-0.0217.7800.2020.2020.0000.0000.0000.000
153A197LEU0-0.008-0.0019.581-0.179-0.1790.0000.0000.0000.000
154A198VAL0-0.010-0.01013.0450.0110.0110.0000.0000.0000.000
155A199THR00.011-0.00816.008-0.023-0.0230.0000.0000.0000.000
156A200ALA0-0.008-0.00719.1300.0000.0000.0000.0000.0000.000
157A201SER0-0.003-0.00422.550-0.013-0.0130.0000.0000.0000.000
158A202VAL00.001-0.00225.311-0.005-0.0050.0000.0000.0000.000
159A203SER00.0200.00928.391-0.004-0.0040.0000.0000.0000.000
160A204TRP00.0490.00831.067-0.002-0.0020.0000.0000.0000.000
161A205GLY0-0.0120.00535.274-0.001-0.0010.0000.0000.0000.000
162A206GLU-1-0.939-0.97537.4020.0580.0580.0000.0000.0000.000
163A207PHE0-0.059-0.01334.3870.0020.0020.0000.0000.0000.000
164A208THR0-0.002-0.02528.7370.0050.0050.0000.0000.0000.000
165A209SER0-0.080-0.05528.4590.0020.0020.0000.0000.0000.000
166A210PHE0-0.008-0.01023.1460.0070.0070.0000.0000.0000.000
167A211ILE0-0.015-0.00422.115-0.015-0.0150.0000.0000.0000.000
168A212ASN0-0.041-0.02417.9310.0420.0420.0000.0000.0000.000
169A213VAL00.0040.00015.823-0.036-0.0360.0000.0000.0000.000
170A214CYS0-0.057-0.01812.6300.0810.0810.0000.0000.0000.000
171A215TRP00.0400.00510.803-0.106-0.1060.0000.0000.0000.000
172A216PRO00.0430.0248.2420.3110.3110.0000.0000.0000.000
173A217PHE00.0430.0052.350-7.755-6.49311.520-5.118-7.664-0.064
174A218SER0-0.057-0.0575.318-0.834-0.806-0.001-0.002-0.0240.000
175A219LEU0-0.0260.0106.8900.0800.0800.0000.0000.0000.000
176A220LEU0-0.023-0.0196.9930.0540.0540.0000.0000.0000.000
177A221GLU-1-0.937-0.9704.718-4.746-4.593-0.001-0.007-0.1450.000
178A222PRO0-0.009-0.0097.1470.2650.2650.0000.0000.0000.000
179A223LEU0-0.033-0.02610.2890.1760.1760.0000.0000.0000.000
180A224LEU0-0.058-0.0125.4220.2070.2070.0000.0000.0000.000
181A225GLU-1-0.984-0.99010.081-0.031-0.0310.0000.0000.0000.000
182A226LYS10.8600.94612.8650.2860.2860.0000.0000.0000.000