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: 4L98N

Calculation Name: 5F1S-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 5F1S

Chain ID: A

ChEMBL ID:

UniProt ID: A0A060

Base Structure: X-ray

Registration Date: 2023-09-26

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 202
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2116576.542613
FMO2-HF: Nuclear repulsion 2034061.336275
FMO2-HF: Total energy -82515.206339
FMO2-MP2: Total energy -82750.162404


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:1:ARG)


Summations of interaction energy for fragment #1(A:1: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.
-127.401-126.85927.412-13.224-14.727-0.098
Interaction energy analysis for fragmet #1(A:1:ARG)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 1 / q_Mulliken : 0.919 / q_NPA : 0.949
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].
3A3THR0-0.083-0.0432.468-12.271-9.6991.611-1.202-2.981-0.001
4A4THR00.005-0.0255.0465.2545.331-0.001-0.003-0.0730.000
5A5VAL0-0.025-0.0037.636-2.422-2.4220.0000.0000.0000.000
6A6GLY00.0290.01010.302-0.714-0.7140.0000.0000.0000.000
7A7ASP-1-0.842-0.92511.402-20.905-20.9050.0000.0000.0000.000
8A8LEU0-0.023-0.00614.5880.7410.7410.0000.0000.0000.000
9A9ALA0-0.014-0.01317.7640.4840.4840.0000.0000.0000.000
10A10VAL0-0.032-0.01421.4910.0040.0040.0000.0000.0000.000
11A11LEU0-0.046-0.01024.0110.2480.2480.0000.0000.0000.000
12A12GLU-1-0.785-0.89527.682-10.025-10.0250.0000.0000.0000.000
13A13GLY0-0.0140.01529.4820.3620.3620.0000.0000.0000.000
14A14ARG10.8270.90926.11510.72010.7200.0000.0000.0000.000
15A15SER00.0240.00624.7200.0660.0660.0000.0000.0000.000
16A16VAL0-0.0230.00119.557-0.098-0.0980.0000.0000.0000.000
17A17MET0-0.001-0.00817.5860.4380.4380.0000.0000.0000.000
18A18ILE00.0050.00313.030-0.406-0.4060.0000.0000.0000.000
19A19PRO0-0.0090.01611.4230.3040.3040.0000.0000.0000.000
20A20CYS0-0.0090.0288.976-0.164-0.1640.0000.0000.0000.000
21A21HIS00.0620.0276.4180.3360.3360.0000.0000.0000.000
22A22TYR0-0.033-0.0264.614-5.110-4.955-0.001-0.036-0.1170.000
23A23GLY00.0370.0283.7241.0771.6150.003-0.173-0.3670.000
24A24PRO00.0260.0044.3992.1202.221-0.001-0.016-0.0840.000
25A25GLN00.003-0.0074.3791.0671.241-0.001-0.039-0.1340.000
26A26TYR0-0.007-0.0161.980-3.465-3.2955.926-3.004-3.0920.014
27A27ALA00.0210.0187.6780.7170.7170.0000.0000.0000.000
28A28SER0-0.007-0.00711.1160.4140.4140.0000.0000.0000.000
29A29TYR0-0.0270.0079.8911.0711.0710.0000.0000.0000.000
30A30VAL00.0030.01412.092-0.448-0.4480.0000.0000.0000.000
31A31LYS10.7900.8879.85318.92018.9200.0000.0000.0000.000
32A32TYR0-0.033-0.02310.5401.4081.4080.0000.0000.0000.000
33A33TRP00.0370.00913.058-1.502-1.5020.0000.0000.0000.000
34A34CYS0-0.098-0.02814.8911.7991.7990.0000.0000.0000.000
35A35ARG10.8710.93916.59712.55012.5500.0000.0000.0000.000
36A36GLY00.0320.01218.6270.6840.6840.0000.0000.0000.000
37A37SER0-0.006-0.00617.604-0.917-0.9170.0000.0000.0000.000
38A38VAL00.0180.01116.573-0.756-0.7560.0000.0000.0000.000
39A39LYS10.9110.95511.07120.27120.2710.0000.0000.0000.000
40A40ASP-1-0.877-0.94314.421-18.407-18.4070.0000.0000.0000.000
41A41LEU0-0.024-0.01116.5650.8980.8980.0000.0000.0000.000
42A43THR00.0270.01718.4330.5530.5530.0000.0000.0000.000
43A44SER0-0.006-0.01917.147-0.331-0.3310.0000.0000.0000.000
44A45LEU0-0.017-0.01118.9220.7290.7290.0000.0000.0000.000
45A46VAL0-0.063-0.04118.3460.6960.6960.0000.0000.0000.000
46A47ARG10.7880.83016.69313.64113.6410.0000.0000.0000.000
47A48SER00.0210.00615.1820.6190.6190.0000.0000.0000.000
48A49ASP-1-0.785-0.88017.557-13.254-13.2540.0000.0000.0000.000
49A50ALA0-0.0090.01519.6360.6120.6120.0000.0000.0000.000
50A51PRO00.0110.00422.3930.0870.0870.0000.0000.0000.000
51A52ARG10.8710.94420.87812.69812.6980.0000.0000.0000.000
52A61LYS10.9550.99924.04512.31212.3120.0000.0000.0000.000
53A62VAL0-0.038-0.03520.163-0.251-0.2510.0000.0000.0000.000
54A63VAL0-0.008-0.01121.7280.4700.4700.0000.0000.0000.000
55A64MET0-0.0040.00914.748-0.866-0.8660.0000.0000.0000.000
56A65PHE0-0.018-0.00117.7620.8230.8230.0000.0000.0000.000
57A66ASP-1-0.753-0.88413.508-20.151-20.1510.0000.0000.0000.000
58A67ASP-1-0.820-0.88914.369-15.953-15.9530.0000.0000.0000.000
59A68PRO00.021-0.00812.933-1.198-1.1980.0000.0000.0000.000
60A69VAL0-0.055-0.01213.204-0.559-0.5590.0000.0000.0000.000
61A70GLN0-0.084-0.05613.738-0.596-0.5960.0000.0000.0000.000
62A71GLN0-0.068-0.0347.345-0.126-0.1260.0000.0000.0000.000
63A72VAL00.0170.0118.774-3.183-3.1830.0000.0000.0000.000
64A73PHE0-0.021-0.0049.0821.8931.8930.0000.0000.0000.000
65A74THR0-0.009-0.00712.526-1.370-1.3700.0000.0000.0000.000
66A75VAL00.0240.00814.4091.2721.2720.0000.0000.0000.000
67A76THR0-0.017-0.01216.806-0.198-0.1980.0000.0000.0000.000
68A77MET00.0110.01620.1580.1100.1100.0000.0000.0000.000
69A78THR0-0.026-0.02122.640-0.015-0.0150.0000.0000.0000.000
70A79GLU-1-0.830-0.90726.307-9.963-9.9630.0000.0000.0000.000
71A80LEU00.0010.02122.7480.1600.1600.0000.0000.0000.000
72A81GLN00.0350.00027.3820.6000.6000.0000.0000.0000.000
73A82LYS10.9300.96328.0159.5799.5790.0000.0000.0000.000
74A83GLU-1-0.879-0.93227.808-10.579-10.5790.0000.0000.0000.000
75A84ASP-1-0.857-0.92124.559-12.334-12.3340.0000.0000.0000.000
76A85SER0-0.041-0.01923.413-0.814-0.8140.0000.0000.0000.000
77A86GLY0-0.014-0.00921.5610.4130.4130.0000.0000.0000.000
78A87TRP0-0.036-0.00113.354-0.287-0.2870.0000.0000.0000.000
79A88TYR0-0.026-0.04316.3671.0151.0150.0000.0000.0000.000
80A89TRP0-0.014-0.02210.264-2.010-2.0100.0000.0000.0000.000
81A91GLY00.019-0.0088.607-1.608-1.6080.0000.0000.0000.000
82A92VAL00.0050.0116.5171.1671.1670.0000.0000.0000.000
83A93GLU-1-0.850-0.8888.893-15.312-15.3120.0000.0000.0000.000
84A94VAL00.000-0.0047.0700.7210.7210.0000.0000.0000.000
85A95GLY00.0020.00910.116-0.450-0.4500.0000.0000.0000.000
86A96GLY0-0.010-0.01411.1550.0310.0310.0000.0000.0000.000
87A97VAL0-0.0070.0024.943-0.282-0.2820.0000.0000.0000.000
88A98TRP00.0150.0136.2000.6090.6090.0000.0000.0000.000
89A99SER00.0630.0136.076-2.755-2.7550.0000.0000.0000.000
90A100ALA00.0000.0126.116-0.591-0.5910.0000.0000.0000.000
91A101ASP-1-0.862-0.9242.006-63.844-62.0387.817-4.924-4.699-0.055
92A102VAL0-0.010-0.0071.859-8.249-13.39412.060-3.803-3.112-0.056
93A103THR0-0.062-0.0514.6364.4504.544-0.001-0.024-0.0680.000
94A104ALA00.0020.0045.801-4.314-4.3140.0000.0000.0000.000
95A105SER0-0.0220.0018.0082.4632.4630.0000.0000.0000.000
96A106LEU0-0.011-0.00110.520-1.767-1.7670.0000.0000.0000.000
97A107HIS0-0.013-0.02313.1192.0282.0280.0000.0000.0000.000
98A108ILE00.0070.00716.643-0.309-0.3090.0000.0000.0000.000
99A109ASN0-0.003-0.00619.5060.9050.9050.0000.0000.0000.000
100A110VAL00.0200.01322.609-0.003-0.0030.0000.0000.0000.000
101A111ILE0-0.0010.00925.4510.5230.5230.0000.0000.0000.000
102A112GLN00.005-0.02627.8860.2110.2110.0000.0000.0000.000
103A113GLY00.0140.00731.6360.0850.0850.0000.0000.0000.000
104A114LEU0-0.007-0.00932.7760.0150.0150.0000.0000.0000.000
105A115SER0-0.024-0.01627.701-0.162-0.1620.0000.0000.0000.000
106A116VAL00.0220.00629.4250.3520.3520.0000.0000.0000.000
107A117VAL0-0.0180.00527.616-0.351-0.3510.0000.0000.0000.000
108A118ASN00.013-0.01127.542-0.479-0.4790.0000.0000.0000.000
109A119SER00.0180.02029.6920.2770.2770.0000.0000.0000.000
110A120MET0-0.023-0.00331.1180.3650.3650.0000.0000.0000.000
111A121VAL00.0140.01532.626-0.165-0.1650.0000.0000.0000.000
112A122SER00.001-0.00735.1740.1380.1380.0000.0000.0000.000
113A123GLY00.0210.01037.481-0.142-0.1420.0000.0000.0000.000
114A124GLU-1-0.802-0.85840.220-7.074-7.0740.0000.0000.0000.000
115A125GLU-1-0.778-0.85943.581-6.327-6.3270.0000.0000.0000.000
116A126GLY0-0.035-0.01346.9350.0560.0560.0000.0000.0000.000
117A127THR0-0.080-0.05043.266-0.038-0.0380.0000.0000.0000.000
118A128SER0-0.001-0.01943.3680.0720.0720.0000.0000.0000.000
119A129VAL0-0.037-0.01538.325-0.169-0.1690.0000.0000.0000.000
120A130THR0-0.009-0.00736.1970.1610.1610.0000.0000.0000.000
121A131VAL00.0070.01835.155-0.300-0.3000.0000.0000.0000.000
122A132GLN00.010-0.01131.722-0.076-0.0760.0000.0000.0000.000
123A133CYS00.0030.04732.640-0.132-0.1320.0000.0000.0000.000
124A134LEU0-0.017-0.00928.5540.0330.0330.0000.0000.0000.000
125A135TYR0-0.023-0.03732.467-0.025-0.0250.0000.0000.0000.000
126A136SER00.0510.03431.356-0.123-0.1230.0000.0000.0000.000
127A137GLN00.004-0.02532.6350.3340.3340.0000.0000.0000.000
128A138GLY0-0.015-0.00334.8100.2560.2560.0000.0000.0000.000
129A139TYR0-0.019-0.01735.4300.3040.3040.0000.0000.0000.000
130A140ARG10.7790.87733.1149.4759.4750.0000.0000.0000.000
131A141GLN0-0.001-0.00239.1290.2480.2480.0000.0000.0000.000
132A142HIS0-0.0280.00641.2430.2030.2030.0000.0000.0000.000
133A143GLU-1-0.842-0.89843.220-6.965-6.9650.0000.0000.0000.000
134A144LYS10.7770.86139.2547.6727.6720.0000.0000.0000.000
135A145ARG10.8370.90641.8087.4887.4880.0000.0000.0000.000
136A146TRP00.0510.01137.973-0.346-0.3460.0000.0000.0000.000
137A147CYS0-0.072-0.01942.5060.0670.0670.0000.0000.0000.000
138A148ARG10.9140.94342.7526.7176.7170.0000.0000.0000.000
139A149SER0-0.034-0.03341.1370.0840.0840.0000.0000.0000.000
140A150GLY0-0.014-0.00443.2860.0700.0700.0000.0000.0000.000
141A151ASP-1-0.834-0.89046.308-6.133-6.1330.0000.0000.0000.000
142A152TRP00.0070.00045.536-0.099-0.0990.0000.0000.0000.000
143A153SER0-0.085-0.05849.0720.0340.0340.0000.0000.0000.000
144A154SER0-0.045-0.02847.521-0.023-0.0230.0000.0000.0000.000
145A156LEU00.0510.04146.5580.1220.1220.0000.0000.0000.000
146A157VAL00.000-0.02645.960-0.212-0.2120.0000.0000.0000.000
147A158THR0-0.058-0.01143.7640.0370.0370.0000.0000.0000.000
148A159ASP-1-0.773-0.89546.967-6.434-6.4340.0000.0000.0000.000
149A160GLY0-0.019-0.02648.020-0.137-0.1370.0000.0000.0000.000
150A161GLU-1-0.904-0.94048.167-6.363-6.3630.0000.0000.0000.000
151A162GLY0-0.017-0.00444.475-0.154-0.1540.0000.0000.0000.000
152A163ARG10.7870.88044.4336.4346.4340.0000.0000.0000.000
153A164TYR00.012-0.02446.9200.0990.0990.0000.0000.0000.000
154A165GLU-1-0.901-0.94947.613-6.454-6.4540.0000.0000.0000.000
155A166ASP-1-0.762-0.83550.018-6.175-6.1750.0000.0000.0000.000
156A167GLN0-0.024-0.03251.244-0.019-0.0190.0000.0000.0000.000
157A168ALA0-0.030-0.01049.428-0.021-0.0210.0000.0000.0000.000
158A169VAL0-0.016-0.00544.846-0.183-0.1830.0000.0000.0000.000
159A170GLU-1-0.871-0.92344.517-7.054-7.0540.0000.0000.0000.000
160A171ILE0-0.059-0.03341.906-0.205-0.2050.0000.0000.0000.000
161A172ARG10.9590.98241.5107.6257.6250.0000.0000.0000.000
162A173ASP-1-0.711-0.83739.549-8.270-8.2700.0000.0000.0000.000
163A174ASP-1-0.792-0.87335.559-8.854-8.8540.0000.0000.0000.000
164A175LEU0-0.034-0.01239.228-0.005-0.0050.0000.0000.0000.000
165A176THR0-0.063-0.03535.408-0.144-0.1440.0000.0000.0000.000
166A177LYS10.8210.90331.1629.2509.2500.0000.0000.0000.000
167A178ALA00.023-0.00333.135-0.259-0.2590.0000.0000.0000.000
168A179PHE00.0220.01335.0050.1980.1980.0000.0000.0000.000
169A180THR0-0.013-0.00436.386-0.220-0.2200.0000.0000.0000.000
170A181VAL0-0.010-0.01338.3030.1900.1900.0000.0000.0000.000
171A182THR0-0.023-0.02240.156-0.235-0.2350.0000.0000.0000.000
172A183LEU0-0.0070.00140.9730.1950.1950.0000.0000.0000.000
173A184LYS10.8450.90243.7156.3786.3780.0000.0000.0000.000
174A185GLY00.0350.02746.3140.0400.0400.0000.0000.0000.000
175A186LEU0-0.0530.00241.6770.0850.0850.0000.0000.0000.000
176A187ALA00.0330.00746.3730.1140.1140.0000.0000.0000.000
177A188ARG10.8740.89746.3706.3296.3290.0000.0000.0000.000
178A189ARG10.8330.89546.8236.2036.2030.0000.0000.0000.000
179A190ASP-1-0.778-0.85545.526-6.617-6.6170.0000.0000.0000.000
180A191THR00.0080.01841.726-0.236-0.2360.0000.0000.0000.000
181A192GLY0-0.0140.00041.4680.1900.1900.0000.0000.0000.000
182A193TRP0-0.006-0.00233.299-0.147-0.1470.0000.0000.0000.000
183A194TYR0-0.048-0.02739.0900.3250.3250.0000.0000.0000.000
184A195TRP0-0.006-0.01336.024-0.362-0.3620.0000.0000.0000.000
185A197ALA0-0.006-0.01737.655-0.168-0.1680.0000.0000.0000.000
186A198ALA00.0730.03938.7860.0900.0900.0000.0000.0000.000
187A199GLY00.0530.04339.998-0.130-0.1300.0000.0000.0000.000
188A200GLN0-0.049-0.03441.1830.0010.0010.0000.0000.0000.000
189A201GLN0-0.0110.00835.818-0.253-0.2530.0000.0000.0000.000
190A202GLN00.004-0.00936.5410.2810.2810.0000.0000.0000.000
191A203VAL0-0.036-0.00731.297-0.243-0.2430.0000.0000.0000.000
192A204ALA00.0000.01234.0670.1980.1980.0000.0000.0000.000
193A205VAL0-0.014-0.02433.670-0.342-0.3420.0000.0000.0000.000
194A206TYR0-0.014-0.00835.0230.3420.3420.0000.0000.0000.000
195A207ILE00.0100.01336.400-0.170-0.1700.0000.0000.0000.000
196A208LEU0-0.005-0.02137.3540.1440.1440.0000.0000.0000.000
197A209VAL00.0160.01739.822-0.083-0.0830.0000.0000.0000.000
198A210THR00.0050.00239.9660.0590.0590.0000.0000.0000.000
199A211PRO0-0.025-0.04142.9510.1210.1210.0000.0000.0000.000
200A212PRO0-0.0160.01545.272-0.131-0.1310.0000.0000.0000.000
201A213SER0-0.051-0.04944.9890.1070.1070.0000.0000.0000.000
202A214HIS0-0.051-0.02147.0400.1340.1340.0000.0000.0000.000