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: G5G41

Calculation Name: 3SH4-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3SH4

Chain ID: A

ChEMBL ID:

UniProt ID: P98160

Base Structure: X-ray

Registration Date: 2023-09-23

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 194
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2022758.174154
FMO2-HF: Nuclear repulsion 1951446.354143
FMO2-HF: Total energy -71311.82001
FMO2-MP2: Total energy -71523.847575


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:ASP)


Summations of interaction energy for fragment #1(A:1:ASP)
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.
17.63120.2981.582-1.798-2.449-0.011
Interaction energy analysis for fragmet #1(A:1:ASP)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : -1 / q_Mulliken : -0.920 / q_NPA : -0.961
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].
3A3PRO0-0.028-0.0343.980-0.7360.458-0.009-0.579-0.6050.002
4A4GLY0-0.002-0.0087.208-1.329-1.3290.0000.0000.0000.000
5A5GLN0-0.020-0.0042.3311.2892.1251.569-0.976-1.429-0.015
6A6TYR00.0280.0013.447-6.089-5.4520.022-0.243-0.4150.002
7A7GLY00.0340.0038.038-2.056-2.0560.0000.0000.0000.000
8A8ALA0-0.0070.00311.1160.5070.5070.0000.0000.0000.000
9A9TYR0-0.039-0.03114.048-0.687-0.6870.0000.0000.0000.000
10A10PHE00.0060.01117.1190.0640.0640.0000.0000.0000.000
11A11HIS0-0.016-0.04920.4720.3240.3240.0000.0000.0000.000
12A12ASP-1-0.850-0.91023.65210.83310.8330.0000.0000.0000.000
13A13ASP-1-0.910-0.95226.6279.8959.8950.0000.0000.0000.000
14A14GLY0-0.062-0.02122.656-0.019-0.0190.0000.0000.0000.000
15A15PHE0-0.083-0.04321.145-0.060-0.0600.0000.0000.0000.000
16A16LEU00.0320.02114.7410.2810.2810.0000.0000.0000.000
17A17ALA00.0010.00018.965-0.409-0.4090.0000.0000.0000.000
18A18PHE00.0260.01613.7550.4810.4810.0000.0000.0000.000
19A19PRO00.0620.03517.846-0.768-0.7680.0000.0000.0000.000
20A20GLY00.0750.02620.2820.4670.4670.0000.0000.0000.000
21A21HIS0-0.040-0.01717.9350.2840.2840.0000.0000.0000.000
22A22VAL0-0.042-0.02516.3100.5480.5480.0000.0000.0000.000
23A23PHE00.0080.00318.2770.5490.5490.0000.0000.0000.000
24A24SER0-0.049-0.02621.021-0.853-0.8530.0000.0000.0000.000
25A25ARG10.8810.94023.289-11.697-11.6970.0000.0000.0000.000
26A26SER0-0.069-0.05426.321-0.047-0.0470.0000.0000.0000.000
27A27LEU00.0030.01029.102-0.274-0.2740.0000.0000.0000.000
28A28PRO00.025-0.00431.4090.2150.2150.0000.0000.0000.000
29A29GLU-1-0.940-0.98132.9018.5698.5690.0000.0000.0000.000
30A30VAL0-0.070-0.00827.0480.0550.0550.0000.0000.0000.000
31A31PRO00.0160.02327.0410.0560.0560.0000.0000.0000.000
32A32GLU-1-0.834-0.92124.29812.16412.1640.0000.0000.0000.000
33A33THR0-0.023-0.01420.453-0.411-0.4110.0000.0000.0000.000
34A34ILE0-0.018-0.00619.9700.4790.4790.0000.0000.0000.000
35A35GLU-1-0.861-0.90017.55115.68615.6860.0000.0000.0000.000
36A36LEU0-0.0200.00516.2890.9760.9760.0000.0000.0000.000
37A37GLU-1-0.859-0.92514.18819.34019.3400.0000.0000.0000.000
38A38VAL00.002-0.01216.8860.4570.4570.0000.0000.0000.000
39A39ARG10.9690.99517.563-15.440-15.4400.0000.0000.0000.000
40A40THR0-0.025-0.04320.828-0.030-0.0300.0000.0000.0000.000
41A41SER00.1180.06823.869-0.044-0.0440.0000.0000.0000.000
42A42THR0-0.057-0.02026.375-0.472-0.4720.0000.0000.0000.000
43A43ALA00.0200.01128.3930.1370.1370.0000.0000.0000.000
44A44SER00.015-0.00831.185-0.002-0.0020.0000.0000.0000.000
45A45GLY00.0230.02328.150-0.014-0.0140.0000.0000.0000.000
46A46LEU0-0.069-0.02925.1440.1060.1060.0000.0000.0000.000
47A47LEU00.0110.01121.4470.3310.3310.0000.0000.0000.000
48A48LEU00.008-0.00719.9770.6080.6080.0000.0000.0000.000
49A49TRP00.0290.01522.951-0.630-0.6300.0000.0000.0000.000
50A50GLN0-0.0030.00224.1520.4040.4040.0000.0000.0000.000
51A51GLY00.0290.00926.017-0.301-0.3010.0000.0000.0000.000
52A52VAL0-0.043-0.02129.0590.2990.2990.0000.0000.0000.000
53A53GLU-1-0.831-0.90129.39410.20210.2020.0000.0000.0000.000
54A54VAL0-0.007-0.00830.850-0.331-0.3310.0000.0000.0000.000
55A55GLY0-0.013-0.01832.8390.0180.0180.0000.0000.0000.000
56A56GLU-1-0.920-0.93533.6928.4268.4260.0000.0000.0000.000
57A57ALA0-0.006-0.02136.3070.0460.0460.0000.0000.0000.000
58A58GLY0-0.0170.00438.599-0.206-0.2060.0000.0000.0000.000
59A59GLN0-0.018-0.02731.6490.1170.1170.0000.0000.0000.000
60A60GLY00.0240.02435.5480.0960.0960.0000.0000.0000.000
61A61LYS10.9090.93236.022-7.824-7.8240.0000.0000.0000.000
62A62ASP-1-0.778-0.87733.0828.8228.8220.0000.0000.0000.000
63A63PHE0-0.074-0.04730.2170.0430.0430.0000.0000.0000.000
64A64ILE0-0.019-0.00326.017-0.226-0.2260.0000.0000.0000.000
65A65SER0-0.043-0.02126.4950.0980.0980.0000.0000.0000.000
66A66LEU00.0470.01122.258-0.175-0.1750.0000.0000.0000.000
67A67GLY00.009-0.00325.6910.1690.1690.0000.0000.0000.000
68A68LEU0-0.0110.01925.4790.0470.0470.0000.0000.0000.000
69A69GLN0-0.004-0.03028.899-0.218-0.2180.0000.0000.0000.000
70A70ASP-1-0.883-0.92732.6998.2918.2910.0000.0000.0000.000
71A71GLY00.015-0.01930.256-0.080-0.0800.0000.0000.0000.000
72A72HIS10.8090.93129.687-8.650-8.6500.0000.0000.0000.000
73A73LEU00.0330.02524.9990.0610.0610.0000.0000.0000.000
74A74VAL0-0.031-0.02128.535-0.421-0.4210.0000.0000.0000.000
75A75PHE00.0080.00927.0750.3820.3820.0000.0000.0000.000
76A76ARG10.8340.91029.309-9.157-9.1570.0000.0000.0000.000
77A77TYR0-0.003-0.01430.4230.3120.3120.0000.0000.0000.000
78A78GLN00.0360.02732.239-0.422-0.4220.0000.0000.0000.000
79A79LEU0-0.011-0.00932.7050.2110.2110.0000.0000.0000.000
80A80GLY00.0940.04835.821-0.070-0.0700.0000.0000.0000.000
81A81SER0-0.072-0.03639.092-0.170-0.1700.0000.0000.0000.000
82A82GLY0-0.021-0.01939.876-0.189-0.1890.0000.0000.0000.000
83A83GLU-1-0.799-0.88236.5938.5298.5290.0000.0000.0000.000
84A84ALA0-0.0070.00334.438-0.237-0.2370.0000.0000.0000.000
85A85ARG10.9320.95833.967-8.152-8.1520.0000.0000.0000.000
86A86LEU0-0.066-0.00331.445-0.265-0.2650.0000.0000.0000.000
87A87VAL0-0.009-0.02131.9030.2500.2500.0000.0000.0000.000
88A88SER00.009-0.01129.679-0.118-0.1180.0000.0000.0000.000
89A89GLU-1-0.879-0.92231.8498.3758.3750.0000.0000.0000.000
90A90ASP-1-0.849-0.91231.6778.8538.8530.0000.0000.0000.000
91A91PRO0-0.113-0.06531.1800.2780.2780.0000.0000.0000.000
92A92ILE00.0450.00824.4160.1530.1530.0000.0000.0000.000
93A93ASN0-0.090-0.03226.1200.3520.3520.0000.0000.0000.000
94A94ASP-1-0.750-0.86626.15911.10011.1000.0000.0000.0000.000
95A95GLY0-0.051-0.00624.4870.0070.0070.0000.0000.0000.000
96A96GLU-1-0.927-0.97322.73811.83511.8350.0000.0000.0000.000
97A97TRP0-0.170-0.10215.2180.5160.5160.0000.0000.0000.000
98A98HIS10.8460.88820.268-12.405-12.4050.0000.0000.0000.000
99A99ARG10.9220.97316.418-16.571-16.5710.0000.0000.0000.000
100A100VAL0-0.0250.00520.202-0.791-0.7910.0000.0000.0000.000
101A101THR00.040-0.02620.9200.6050.6050.0000.0000.0000.000
102A102ALA0-0.037-0.01522.938-0.689-0.6890.0000.0000.0000.000
103A103LEU0-0.011-0.00124.1290.3970.3970.0000.0000.0000.000
104A104ARG10.8540.91026.788-10.894-10.8940.0000.0000.0000.000
105A105GLU-1-0.915-0.95328.90510.15310.1530.0000.0000.0000.000
106A106GLY00.0600.03031.635-0.343-0.3430.0000.0000.0000.000
107A107ARG10.8880.93633.484-7.697-7.6970.0000.0000.0000.000
108A108ARG10.9110.98134.371-9.013-9.0130.0000.0000.0000.000
109A109GLY00.0620.03631.2260.3040.3040.0000.0000.0000.000
110A110SER0-0.049-0.05029.643-0.273-0.2730.0000.0000.0000.000
111A111ILE0-0.0040.00127.6270.3580.3580.0000.0000.0000.000
112A112GLN0-0.012-0.00625.1440.0490.0490.0000.0000.0000.000
113A113VAL00.009-0.01224.9650.4870.4870.0000.0000.0000.000
114A114ASP-1-0.732-0.85023.03512.53912.5390.0000.0000.0000.000
115A115GLY0-0.053-0.01624.105-0.080-0.0800.0000.0000.0000.000
116A116GLU-1-0.959-0.97624.98310.40510.4050.0000.0000.0000.000
117A117GLU-1-0.893-0.93528.6799.7189.7180.0000.0000.0000.000
118A118LEU0-0.062-0.03928.4790.0690.0690.0000.0000.0000.000
119A119VAL00.0290.03431.428-0.369-0.3690.0000.0000.0000.000
120A120SER0-0.033-0.03432.4280.1910.1910.0000.0000.0000.000
121A121GLY00.0380.01034.662-0.211-0.2110.0000.0000.0000.000
122A122ARG10.9250.95835.670-7.709-7.7090.0000.0000.0000.000
123A123SER00.0500.04936.519-0.036-0.0360.0000.0000.0000.000
124A124PRO00.0200.02238.276-0.053-0.0530.0000.0000.0000.000
125A125GLY0-0.036-0.00240.9820.1490.1490.0000.0000.0000.000
126A126PRO00.008-0.01142.690-0.117-0.1170.0000.0000.0000.000
127A127ASN0-0.011-0.01338.475-0.064-0.0640.0000.0000.0000.000
128A128VAL00.035-0.00136.5150.0830.0830.0000.0000.0000.000
129A129ALA0-0.020-0.01533.4060.2840.2840.0000.0000.0000.000
130A130VAL0-0.0210.00629.031-0.170-0.1700.0000.0000.0000.000
131A131ASN0-0.063-0.04231.3760.1740.1740.0000.0000.0000.000
132A132ALA0-0.044-0.00628.968-0.047-0.0470.0000.0000.0000.000
133A133LYS10.9370.96327.196-9.731-9.7310.0000.0000.0000.000
134A134GLY00.0400.02526.9010.1810.1810.0000.0000.0000.000
135A135SER0-0.029-0.03323.1460.2270.2270.0000.0000.0000.000
136A136VAL0-0.046-0.01019.825-0.408-0.4080.0000.0000.0000.000
137A137TYR0-0.012-0.01120.7130.4230.4230.0000.0000.0000.000
138A138ILE00.011-0.01617.036-0.039-0.0390.0000.0000.0000.000
139A139GLY00.009-0.00420.1220.0540.0540.0000.0000.0000.000
140A140GLY00.0590.02121.521-0.419-0.4190.0000.0000.0000.000
141A141ALA0-0.028-0.01824.1690.2890.2890.0000.0000.0000.000
142A142PRO00.0170.02125.620-0.210-0.2100.0000.0000.0000.000
143A143ASP-1-0.772-0.82928.4488.4108.4100.0000.0000.0000.000
144A144VAL0-0.034-0.01727.948-0.003-0.0030.0000.0000.0000.000
145A145ALA00.0430.04630.580-0.058-0.0580.0000.0000.0000.000
146A146THR0-0.033-0.07433.891-0.208-0.2080.0000.0000.0000.000
147A147LEU0-0.064-0.01027.018-0.045-0.0450.0000.0000.0000.000
148A148THR0-0.046-0.03629.943-0.101-0.1010.0000.0000.0000.000
149A149GLY0-0.032-0.01232.538-0.162-0.1620.0000.0000.0000.000
150A150GLY0-0.021-0.01935.594-0.227-0.2270.0000.0000.0000.000
151A151ARG10.7140.84333.721-8.667-8.6670.0000.0000.0000.000
152A152PHE00.0300.02029.8250.0540.0540.0000.0000.0000.000
153A153SER0-0.006-0.02432.670-0.024-0.0240.0000.0000.0000.000
154A154SER00.0660.03929.757-0.157-0.1570.0000.0000.0000.000
155A155GLY00.0660.03425.7350.0870.0870.0000.0000.0000.000
156A156ILE0-0.052-0.01520.874-0.359-0.3590.0000.0000.0000.000
157A157THR00.0150.01423.5870.1570.1570.0000.0000.0000.000
158A158GLY0-0.006-0.00921.219-0.260-0.2600.0000.0000.0000.000
159A159CYS0-0.185-0.06811.835-1.101-1.1010.0000.0000.0000.000
160A160VAL00.0550.03815.668-0.575-0.5750.0000.0000.0000.000
161A161LYS10.8950.94611.414-20.417-20.4170.0000.0000.0000.000
162A162ASN0-0.080-0.0549.8501.1131.1130.0000.0000.0000.000
163A163LEU00.0310.03411.981-1.073-1.0730.0000.0000.0000.000
164A164VAL00.0140.00613.5471.2201.2200.0000.0000.0000.000
165A165LEU0-0.006-0.00715.623-1.357-1.3570.0000.0000.0000.000
166A166HIS00.0290.00718.0930.8820.8820.0000.0000.0000.000
167A167SER00.0110.02120.158-0.671-0.6710.0000.0000.0000.000
168A168ALA0-0.020-0.02423.0160.4040.4040.0000.0000.0000.000
169A169ARG10.9610.98824.144-12.849-12.8490.0000.0000.0000.000
170A170PRO00.035-0.00525.1010.3720.3720.0000.0000.0000.000
171A171GLY0-0.0040.00225.481-0.072-0.0720.0000.0000.0000.000
172A172ALA0-0.069-0.01821.3990.3490.3490.0000.0000.0000.000
173A173PRO00.0130.00516.748-0.190-0.1900.0000.0000.0000.000
174A174PRO00.004-0.01215.526-0.402-0.4020.0000.0000.0000.000
175A175PRO00.0050.02415.5190.8830.8830.0000.0000.0000.000
176A176GLN0-0.007-0.0199.5191.0201.0200.0000.0000.0000.000
177A177PRO0-0.0040.0029.062-1.438-1.4380.0000.0000.0000.000
178A178LEU0-0.034-0.0049.6722.0802.0800.0000.0000.0000.000
179A179ASP-1-0.785-0.8917.03032.31432.3140.0000.0000.0000.000
180A180LEU0-0.041-0.0448.845-1.878-1.8780.0000.0000.0000.000
181A181GLN00.0170.0208.493-2.232-2.2320.0000.0000.0000.000
182A182HIS0-0.066-0.0286.588-1.612-1.6120.0000.0000.0000.000
183A183ARG10.8880.93610.809-22.702-22.7020.0000.0000.0000.000
184A184ALA00.0220.03713.288-0.920-0.9200.0000.0000.0000.000
185A185GLN0-0.046-0.02916.034-0.405-0.4050.0000.0000.0000.000
186A186ALA00.0070.00119.430-0.660-0.6600.0000.0000.0000.000
187A187GLY00.0390.01119.5770.6910.6910.0000.0000.0000.000
188A188ALA0-0.054-0.01920.735-0.339-0.3390.0000.0000.0000.000
189A189ASN00.0070.01821.7270.3890.3890.0000.0000.0000.000
190A190THR00.0380.01017.0500.3290.3290.0000.0000.0000.000
191A191ARG10.9440.98415.638-14.508-14.5080.0000.0000.0000.000
192A192PRO00.0520.03010.330-0.029-0.0290.0000.0000.0000.000
193A194PRO00.0060.01110.8251.5821.5820.0000.0000.0000.000
194A195SER00.006-0.00211.079-1.518-1.5180.0000.0000.0000.000