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: 5373Z

Calculation Name: 4FBD-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 4FBD

Chain ID: A

ChEMBL ID:

UniProt ID:

Base Structure: X-ray

Registration Date: 2023-06-20

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 204
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2135239.621129
FMO2-HF: Nuclear repulsion 2055841.777492
FMO2-HF: Total energy -79397.843638
FMO2-MP2: Total energy -79629.366464


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:14:ARG)


Summations of interaction energy for fragment #1(A:14:ARG)
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.
-67.161-73.18114.0182.313-10.312-0.063
Interaction energy analysis for fragmet #1(A:14:ARG)
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 : 0.911
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].
3A16ALA00.0350.0192.63110.4291.6940.1659.094-0.525-0.005
4A17PRO00.0360.0125.904-0.063-0.0630.0000.0000.0000.000
5A18ALA00.0090.0128.9790.7150.7150.0000.0000.0000.000
6A19ASP-1-0.998-0.9966.510-22.796-22.7960.0000.0000.0000.000
7A20LEU0-0.077-0.0336.968-2.149-2.1490.0000.0000.0000.000
8A21PRO00.0290.01910.0560.9120.9120.0000.0000.0000.000
9A22LEU0-0.018-0.0238.101-0.376-0.3760.0000.0000.0000.000
10A23GLY00.0710.01812.0501.2271.2270.0000.0000.0000.000
11A24LEU0-0.066-0.04814.808-0.910-0.9100.0000.0000.0000.000
12A25ASP-1-0.825-0.90817.415-13.152-13.1520.0000.0000.0000.000
13A26PRO0-0.051-0.04319.6150.0020.0020.0000.0000.0000.000
14A27PHE0-0.073-0.01322.7860.4390.4390.0000.0000.0000.000
15A28CYS00.0330.02620.5840.0470.0470.0000.0000.0000.000
16A29TYR0-0.027-0.00920.0740.5130.5130.0000.0000.0000.000
17A40SER00.0200.00621.298-0.155-0.1550.0000.0000.0000.000
18A41ARG10.9430.96623.12711.10511.1050.0000.0000.0000.000
19A42ILE00.0110.02021.188-0.003-0.0030.0000.0000.0000.000
20A43SER0-0.026-0.03124.7500.4330.4330.0000.0000.0000.000
21A44GLY00.001-0.00427.206-0.185-0.1850.0000.0000.0000.000
22A45VAL00.0350.03323.4490.0230.0230.0000.0000.0000.000
23A46THR00.0220.02025.899-0.222-0.2220.0000.0000.0000.000
24A47LYS10.9480.96422.44811.53411.5340.0000.0000.0000.000
25A48GLU-1-0.851-0.92921.206-12.003-12.0030.0000.0000.0000.000
26A49GLU-1-0.918-0.96121.322-11.932-11.9320.0000.0000.0000.000
27A50PHE0-0.043-0.02317.231-0.589-0.5890.0000.0000.0000.000
28A51LEU00.0070.00115.314-0.776-0.7760.0000.0000.0000.000
29A52GLU-1-0.938-0.95616.495-14.900-14.9000.0000.0000.0000.000
30A53LYS11.0511.00917.58012.05912.0590.0000.0000.0000.000
31A54VAL0-0.057-0.01412.710-0.876-0.8760.0000.0000.0000.000
32A55ASN00.001-0.01212.716-2.598-2.5980.0000.0000.0000.000
33A56GLU-1-0.926-0.93513.460-15.220-15.2200.0000.0000.0000.000
34A57LEU0-0.078-0.06814.253-0.358-0.3580.0000.0000.0000.000
35A58VAL0-0.061-0.0258.362-1.090-1.0900.0000.0000.0000.000
36A59THR0-0.039-0.03010.089-0.811-0.8110.0000.0000.0000.000
37A60ARG10.9060.97411.41016.67916.6790.0000.0000.0000.000
38A61ASP-1-0.897-0.93911.982-22.591-22.5910.0000.0000.0000.000
39A62ALA00.006-0.0088.505-1.871-1.8710.0000.0000.0000.000
40A63GLY0-0.025-0.0077.816-2.888-2.8880.0000.0000.0000.000
41A64ILE0-0.065-0.0227.653-1.380-1.3800.0000.0000.0000.000
42A65GLU-1-0.944-0.9603.933-47.095-46.946-0.001-0.027-0.1210.000
43A66PHE00.0300.0002.1521.7593.0872.118-1.261-2.185-0.003
44A67PHE0-0.019-0.0311.831-36.870-38.42611.410-4.699-5.155-0.056
45A68GLN0-0.086-0.0693.5577.5088.3040.039-0.213-0.6230.002
46A69GLY00.0330.0225.3810.9921.045-0.001-0.003-0.0490.000
47A70TYR00.007-0.0059.0311.6681.6680.0000.0000.0000.000
48A71ALA00.0290.04410.3910.6550.6550.0000.0000.0000.000
49A72PRO0-0.007-0.0209.313-2.051-2.0510.0000.0000.0000.000
50A73PHE00.0110.01010.042-0.916-0.9160.0000.0000.0000.000
51A74CYS0-0.0010.02811.1180.6310.6310.0000.0000.0000.000
52A75ARG10.9110.9473.03346.23348.1780.288-0.578-1.654-0.001
53A76HIS10.8300.9206.91035.42535.4250.0000.0000.0000.000
54A77LEU00.0530.0516.517-6.161-6.1610.0000.0000.0000.000
55A78TYR0-0.0040.0148.3442.3902.3900.0000.0000.0000.000
56A79ILE00.0380.02610.965-1.086-1.0860.0000.0000.0000.000
57A80PRO00.033-0.00413.6280.7660.7660.0000.0000.0000.000
58A81ASN0-0.030-0.02517.149-0.042-0.0420.0000.0000.0000.000
59A82PHE0-0.005-0.00417.4410.8240.8240.0000.0000.0000.000
60A83VAL0-0.013-0.00121.2630.5470.5470.0000.0000.0000.000
61A84GLY00.0000.00923.5400.5080.5080.0000.0000.0000.000
62A85ALA00.0020.01122.1120.4090.4090.0000.0000.0000.000
63A86LEU00.0360.01523.821-0.256-0.2560.0000.0000.0000.000
64A87PRO0-0.0120.00822.676-0.376-0.3760.0000.0000.0000.000
65A88GLY0-0.010-0.00723.1330.4620.4620.0000.0000.0000.000
66A89SER0-0.086-0.05523.7340.1810.1810.0000.0000.0000.000
67A90LEU00.0560.03425.841-0.236-0.2360.0000.0000.0000.000
68A91PRO00.0130.00126.444-0.066-0.0660.0000.0000.0000.000
69A92ILE0-0.047-0.00927.8940.3250.3250.0000.0000.0000.000
70A93THR0-0.042-0.03530.805-0.054-0.0540.0000.0000.0000.000
71A94ALA00.0380.00333.1190.1010.1010.0000.0000.0000.000
72A95ASP-1-0.868-0.92436.462-8.002-8.0020.0000.0000.0000.000
73A96ASN0-0.049-0.03532.1330.1960.1960.0000.0000.0000.000
74A97GLU-1-0.903-0.94635.420-8.590-8.5900.0000.0000.0000.000
75A98HIS00.000-0.00736.385-0.080-0.0800.0000.0000.0000.000
76A99LEU0-0.038-0.02137.1820.1720.1720.0000.0000.0000.000
77A100LEU0-0.075-0.01332.442-0.103-0.1030.0000.0000.0000.000
78A101ARG10.8710.94936.1968.0678.0670.0000.0000.0000.000
79A102SER0-0.014-0.02235.999-0.260-0.2600.0000.0000.0000.000
80A103GLY00.0490.01036.6220.2900.2900.0000.0000.0000.000
81A104TYR00.0040.00536.441-0.313-0.3130.0000.0000.0000.000
82A105ILE00.0200.01234.0040.1600.1600.0000.0000.0000.000
83A106ALA00.0590.03734.400-0.194-0.1940.0000.0000.0000.000
84A107ARG10.7620.83425.85811.26411.2640.0000.0000.0000.000
85A108ARG10.9650.98228.80910.38110.3810.0000.0000.0000.000
86A109PRO00.0010.00034.1940.0620.0620.0000.0000.0000.000
87A110ASN0-0.014-0.01534.4730.0830.0830.0000.0000.0000.000
88A111GLU-1-0.769-0.83230.668-10.541-10.5410.0000.0000.0000.000
89A112LEU0-0.007-0.02335.2580.2280.2280.0000.0000.0000.000
90A113PRO0-0.034-0.01134.945-0.282-0.2820.0000.0000.0000.000
91A114VAL0-0.017-0.01931.2340.0030.0030.0000.0000.0000.000
92A115LEU0-0.0300.00334.572-0.008-0.0080.0000.0000.0000.000
93A116THR0-0.060-0.02630.675-0.462-0.4620.0000.0000.0000.000
94A117ARG10.9150.93829.53210.34010.3400.0000.0000.0000.000
95A118TRP0-0.055-0.03631.254-0.436-0.4360.0000.0000.0000.000
96A119PHE00.0440.02330.4990.2820.2820.0000.0000.0000.000
97A120PRO00.0220.01033.683-0.247-0.2470.0000.0000.0000.000
98A121MET00.0610.01733.506-0.224-0.2240.0000.0000.0000.000
99A122SER0-0.082-0.04236.477-0.058-0.0580.0000.0000.0000.000
100A123TYR00.0430.02433.089-0.022-0.0220.0000.0000.0000.000
101A124ALA00.023-0.00332.240-0.094-0.0940.0000.0000.0000.000
102A125LYS10.8160.91433.3407.7397.7390.0000.0000.0000.000
103A126ASP-1-0.871-0.92335.267-8.189-8.1890.0000.0000.0000.000
104A127ALA0-0.048-0.02632.4020.0100.0100.0000.0000.0000.000
105A128LEU0-0.068-0.03827.672-0.355-0.3550.0000.0000.0000.000
106A129MET00.0320.01827.9390.3070.3070.0000.0000.0000.000
107A130PRO0-0.035-0.02724.994-0.379-0.3790.0000.0000.0000.000
108A131ALA0-0.0340.00220.689-0.026-0.0260.0000.0000.0000.000
109A132ALA00.0380.01318.874-0.064-0.0640.0000.0000.0000.000
110A133PHE0-0.052-0.03614.761-0.760-0.7600.0000.0000.0000.000
111A134LEU00.0240.01215.5660.9820.9820.0000.0000.0000.000
112A135ASP-1-0.838-0.91111.324-27.059-27.0590.0000.0000.0000.000
113A136LEU0-0.002-0.01211.3811.7491.7490.0000.0000.0000.000
114A137ILE0-0.005-0.01711.083-2.764-2.7640.0000.0000.0000.000
115A138LEU0-0.013-0.0137.5181.2261.2260.0000.0000.0000.000
116A139TYR00.0510.00711.422-0.865-0.8650.0000.0000.0000.000
117A140SER00.0080.01212.1250.2370.2370.0000.0000.0000.000
118A141ARG10.9420.97412.97117.55117.5510.0000.0000.0000.000
119A142GLU-1-0.898-0.96214.273-16.946-16.9460.0000.0000.0000.000
120A143GLN0-0.049-0.04115.9541.4381.4380.0000.0000.0000.000
121A144ILE00.0850.05415.9050.5540.5540.0000.0000.0000.000
122A145ALA0-0.0060.03318.9610.7850.7850.0000.0000.0000.000
123A146LYS10.9240.94819.20015.57415.5740.0000.0000.0000.000
124A147GLU-1-0.906-0.95120.263-14.594-14.5940.0000.0000.0000.000
125A148THR00.015-0.00522.3750.4860.4860.0000.0000.0000.000
126A149ALA0-0.034-0.01924.8630.5100.5100.0000.0000.0000.000
127A150ALA0-0.012-0.00826.1970.4710.4710.0000.0000.0000.000
128A151GLU-1-0.971-0.97927.000-10.444-10.4440.0000.0000.0000.000
129A152SER0-0.052-0.02528.7210.4290.4290.0000.0000.0000.000
130A153ASN0-0.107-0.06530.3270.3310.3310.0000.0000.0000.000
131A154THR0-0.0290.00330.0810.3670.3670.0000.0000.0000.000
132A155ALA0-0.003-0.00329.636-0.289-0.2890.0000.0000.0000.000
133A156VAL0-0.013-0.01423.547-0.041-0.0410.0000.0000.0000.000
134A157VAL0-0.0100.00125.5060.0800.0800.0000.0000.0000.000
135A158ILE0-0.018-0.01519.109-0.303-0.3030.0000.0000.0000.000
136A159ASP-1-0.822-0.90420.999-12.017-12.0170.0000.0000.0000.000
137A160PRO0-0.045-0.03018.515-0.644-0.6440.0000.0000.0000.000
138A161ASN0-0.025-0.02217.413-0.811-0.8110.0000.0000.0000.000
139A162ALA0-0.0130.01417.758-0.180-0.1800.0000.0000.0000.000
140A163PRO00.0440.01513.625-0.535-0.5350.0000.0000.0000.000
141A164ALA00.0040.0099.7670.1220.1220.0000.0000.0000.000
142A165TRP0-0.048-0.0236.800-1.378-1.3780.0000.0000.0000.000
143A166SER00.0080.00211.0990.9180.9180.0000.0000.0000.000
144A167ILE0-0.004-0.01812.978-0.665-0.6650.0000.0000.0000.000
145A168ILE00.0400.02414.4900.9850.9850.0000.0000.0000.000
146A169ALA0-0.005-0.00516.0280.9590.9590.0000.0000.0000.000
147A170VAL00.0160.01015.873-1.224-1.2240.0000.0000.0000.000
148A171LYS10.9180.96116.32217.17017.1700.0000.0000.0000.000
149A172ALA00.0420.03217.106-0.900-0.9000.0000.0000.0000.000
150A173GLN0-0.116-0.08414.4030.9960.9960.0000.0000.0000.000
151A174ASN00.0560.02518.297-0.355-0.3550.0000.0000.0000.000
152A175GLU-1-0.823-0.88015.837-16.008-16.0080.0000.0000.0000.000
153A176LYS10.9250.97710.05825.11725.1170.0000.0000.0000.000
154A177TYR00.0260.00910.562-1.690-1.6900.0000.0000.0000.000
155A178SER00.0290.01110.9990.5910.5910.0000.0000.0000.000
156A179LEU00.0090.01612.6610.6340.6340.0000.0000.0000.000
157A180PRO0-0.0160.01416.355-0.093-0.0930.0000.0000.0000.000
158A181MET00.0410.02817.9010.9460.9460.0000.0000.0000.000
159A182ALA00.0300.02720.4390.1510.1510.0000.0000.0000.000
160A183PRO00.0550.01524.011-0.063-0.0630.0000.0000.0000.000
161A184ILE00.0770.03125.458-0.042-0.0420.0000.0000.0000.000
162A185THR0-0.037-0.01523.5000.3430.3430.0000.0000.0000.000
163A186MET0-0.013-0.00321.090-0.125-0.1250.0000.0000.0000.000
164A187LEU0-0.0120.00324.2710.0430.0430.0000.0000.0000.000
165A188ARG11.0061.01727.29210.93610.9360.0000.0000.0000.000
166A189ASN0-0.003-0.00522.2950.4470.4470.0000.0000.0000.000
167A190THR0-0.084-0.04725.527-0.081-0.0810.0000.0000.0000.000
168A191LEU00.0050.01027.4560.2150.2150.0000.0000.0000.000
169A192ILE00.0580.02628.926-0.061-0.0610.0000.0000.0000.000
170A193GLU-1-0.995-0.99830.785-8.697-8.6970.0000.0000.0000.000
171A194GLU-1-0.833-0.88632.351-9.034-9.0340.0000.0000.0000.000
172A195GLY0-0.0570.00528.715-0.239-0.2390.0000.0000.0000.000
173A196GLY0-0.020-0.03525.6540.1190.1190.0000.0000.0000.000
174A197SER0-0.050-0.05221.6040.2190.2190.0000.0000.0000.000
175A198GLY00.0630.04324.6920.2650.2650.0000.0000.0000.000
176A199VAL0-0.080-0.03521.3870.2250.2250.0000.0000.0000.000
177A200ALA00.006-0.00424.6150.1130.1130.0000.0000.0000.000
178A201LEU00.013-0.00223.350-0.498-0.4980.0000.0000.0000.000
179A202ASP-1-0.808-0.88617.840-15.735-15.7350.0000.0000.0000.000
180A203ARG10.9540.93921.42910.72510.7250.0000.0000.0000.000
181A204GLU-1-0.917-0.95319.560-14.319-14.3190.0000.0000.0000.000
182A205ALA00.0340.03217.715-0.152-0.1520.0000.0000.0000.000
183A206TYR0-0.015-0.02219.2790.1420.1420.0000.0000.0000.000
184A207LYS10.9230.95522.80912.47312.4730.0000.0000.0000.000
185A208ALA00.0360.02918.3430.2720.2720.0000.0000.0000.000
186A209SER0-0.023-0.04320.4730.2560.2560.0000.0000.0000.000
187A210VAL0-0.010-0.02021.3810.3410.3410.0000.0000.0000.000
188A211ALA0-0.047-0.03322.1090.4200.4200.0000.0000.0000.000
189A212TYR0-0.022-0.02819.9220.3820.3820.0000.0000.0000.000
190A213TRP0-0.024-0.01321.4110.6650.6650.0000.0000.0000.000
191A214LYS10.9270.97425.32511.17311.1730.0000.0000.0000.000
192A215THR00.012-0.00425.3980.2800.2800.0000.0000.0000.000
193A216HIS10.9010.95522.84813.02713.0270.0000.0000.0000.000
194A217ALA00.0020.01026.6340.0300.0300.0000.0000.0000.000
195A218ILE00.0150.00925.787-0.184-0.1840.0000.0000.0000.000
196A219VAL00.0270.02328.0130.3500.3500.0000.0000.0000.000
197A220MET0-0.041-0.03030.400-0.103-0.1030.0000.0000.0000.000
198A221ASP-1-0.930-0.95633.071-8.233-8.2330.0000.0000.0000.000
199A222LYS10.9430.96636.2448.3948.3940.0000.0000.0000.000
200A223GLU-1-0.767-0.86738.550-8.036-8.0360.0000.0000.0000.000
201A224SER0-0.028-0.01841.1390.0320.0320.0000.0000.0000.000
202A225SER0-0.026-0.01540.480-0.051-0.0510.0000.0000.0000.000
203A226LEU0-0.043-0.01341.6260.0120.0120.0000.0000.0000.000
204A227GLU-1-0.947-0.96143.618-7.254-7.2540.0000.0000.0000.000