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: 943Y2

Calculation Name: 3V6M-F-Xray372

Preferred Name: Caspase-6

Target Type: SINGLE PROTEIN

Ligand Name:

ligand 3-letter code:

PDB ID: 3V6M

Chain ID: F

ChEMBL ID: CHEMBL3308

UniProt ID: P55212

Base Structure: X-ray

Registration Date: 2023-09-20

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 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 203
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2497320.884712
FMO2-HF: Nuclear repulsion 2413825.024193
FMO2-HF: Total energy -83495.860519
FMO2-MP2: Total energy -83734.351131


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(F:32:ASP)


Summations of interaction energy for fragment #1(F:32: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.
-132.518-125.6710.815-8.674-8.9910.094
Interaction energy analysis for fragmet #1(F:32:ASP)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : -1 / q_Mulliken : -0.818 / q_NPA : -0.923
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].
3F34ALA0-0.039-0.0261.876-36.434-33.1109.473-6.972-5.8260.080
4F35GLU-1-0.825-0.8892.47529.24432.2901.284-1.495-2.8360.011
5F36LYS10.8620.9293.694-49.888-49.4100.058-0.207-0.3290.003
6F37TYR0-0.001-0.0297.0970.1360.1360.0000.0000.0000.000
7F38LYS10.8290.8919.493-24.107-24.1070.0000.0000.0000.000
8F39MET0-0.030-0.01111.557-1.785-1.7850.0000.0000.0000.000
9F40ASP-1-0.821-0.87913.91420.66820.6680.0000.0000.0000.000
10F41HIS0-0.036-0.00815.426-1.009-1.0090.0000.0000.0000.000
11F42ARG10.8760.92218.770-11.993-11.9930.0000.0000.0000.000
12F43ARG10.8650.93022.326-12.177-12.1770.0000.0000.0000.000
13F44ARG10.8550.92716.966-15.965-15.9650.0000.0000.0000.000
14F45GLY00.0500.00821.0060.4940.4940.0000.0000.0000.000
15F46ILE0-0.051-0.02123.685-0.281-0.2810.0000.0000.0000.000
16F47ALA00.0090.00425.6270.4490.4490.0000.0000.0000.000
17F48LEU00.000-0.00427.468-0.422-0.4220.0000.0000.0000.000
18F49ILE00.0020.00630.2250.2120.2120.0000.0000.0000.000
19F50PHE00.006-0.00832.470-0.327-0.3270.0000.0000.0000.000
20F51ASN00.0310.00135.6300.2070.2070.0000.0000.0000.000
21F52HIS0-0.013-0.00637.932-0.075-0.0750.0000.0000.0000.000
22F53GLU-1-0.848-0.91540.9637.4767.4760.0000.0000.0000.000
23F54ARG10.9270.97543.748-6.536-6.5360.0000.0000.0000.000
24F55PHE0-0.020-0.01342.1550.1300.1300.0000.0000.0000.000
25F56PHE00.0350.00347.666-0.170-0.1700.0000.0000.0000.000
26F57TRP00.002-0.01550.1890.0000.0000.0000.0000.0000.000
27F58HIS0-0.024-0.00353.0450.0410.0410.0000.0000.0000.000
28F59LEU0-0.0110.00845.968-0.001-0.0010.0000.0000.0000.000
29F60THR0-0.067-0.02649.4290.0030.0030.0000.0000.0000.000
30F61LEU0-0.0040.01744.4180.0530.0530.0000.0000.0000.000
31F62PRO0-0.020-0.01246.410-0.089-0.0890.0000.0000.0000.000
32F63GLU-1-0.889-0.95446.4706.6436.6430.0000.0000.0000.000
33F64ARG10.8040.90837.561-8.269-8.2690.0000.0000.0000.000
34F65ARG10.9820.97843.310-6.625-6.6250.0000.0000.0000.000
35F66GLY00.0260.01742.0530.0980.0980.0000.0000.0000.000
36F67THR00.0140.00538.6320.3130.3130.0000.0000.0000.000
37F68CYS0-0.037-0.01938.2490.2720.2720.0000.0000.0000.000
38F69ALA00.0210.01738.7740.1330.1330.0000.0000.0000.000
39F70ASP-1-0.764-0.86235.0379.2949.2940.0000.0000.0000.000
40F71ARG10.8100.87334.144-7.853-7.8530.0000.0000.0000.000
41F72ASP-1-0.827-0.87634.2838.6128.6120.0000.0000.0000.000
42F73ASN0-0.0090.00533.1090.3050.3050.0000.0000.0000.000
43F74LEU00.036-0.00729.0070.3450.3450.0000.0000.0000.000
44F75THR0-0.003-0.01429.5720.3800.3800.0000.0000.0000.000
45F76ARG10.8810.95030.763-9.282-9.2820.0000.0000.0000.000
46F77ARG10.8730.95426.946-10.663-10.6630.0000.0000.0000.000
47F78PHE00.0470.01123.1140.4750.4750.0000.0000.0000.000
48F79SER00.004-0.00225.7800.3050.3050.0000.0000.0000.000
49F80ASP-1-0.867-0.91926.58511.24611.2460.0000.0000.0000.000
50F81LEU0-0.046-0.01020.8610.5100.5100.0000.0000.0000.000
51F82GLY0-0.051-0.03622.0200.7860.7860.0000.0000.0000.000
52F83PHE0-0.043-0.03520.8460.1030.1030.0000.0000.0000.000
53F84GLU-1-0.857-0.92125.64310.07110.0710.0000.0000.0000.000
54F85VAL0-0.006-0.01228.7750.1400.1400.0000.0000.0000.000
55F86LYS10.8430.93030.597-10.152-10.1520.0000.0000.0000.000
56F87CYS0-0.027-0.00733.3780.1980.1980.0000.0000.0000.000
57F88PHE00.0230.00434.880-0.213-0.2130.0000.0000.0000.000
58F89ASN00.0280.01738.4140.2560.2560.0000.0000.0000.000
59F90ASP-1-0.775-0.89341.1357.2617.2610.0000.0000.0000.000
60F91LEU0-0.0350.01438.528-0.113-0.1130.0000.0000.0000.000
61F92LYS11.0351.00242.348-6.505-6.5050.0000.0000.0000.000
62F93ALA0-0.006-0.02241.2730.1790.1790.0000.0000.0000.000
63F94GLU-1-0.920-0.95540.7307.0327.0320.0000.0000.0000.000
64F95GLU-1-0.850-0.92141.2577.3397.3390.0000.0000.0000.000
65F96LEU0-0.021-0.00935.5160.2160.2160.0000.0000.0000.000
66F97LEU00.0100.00036.2910.3080.3080.0000.0000.0000.000
67F98LEU00.0320.01436.5430.2410.2410.0000.0000.0000.000
68F99LYS10.8250.89736.161-8.255-8.2550.0000.0000.0000.000
69F100ILE0-0.038-0.01930.5180.3070.3070.0000.0000.0000.000
70F101HIS00.0280.00532.0450.3770.3770.0000.0000.0000.000
71F102GLU-1-0.795-0.84133.0918.8548.8540.0000.0000.0000.000
72F103VAL00.015-0.00228.9310.2840.2840.0000.0000.0000.000
73F104SER0-0.089-0.04128.3670.4320.4320.0000.0000.0000.000
74F105THR0-0.038-0.03728.5930.3210.3210.0000.0000.0000.000
75F106VAL0-0.0320.00928.737-0.068-0.0680.0000.0000.0000.000
76F107SER00.0100.00826.5040.4600.4600.0000.0000.0000.000
77F108HIS10.8890.90822.894-12.170-12.1700.0000.0000.0000.000
78F109ALA00.0660.03621.7510.6680.6680.0000.0000.0000.000
79F110ASP-1-0.835-0.88420.80812.77512.7750.0000.0000.0000.000
80F111ALA0-0.002-0.01021.433-0.180-0.1800.0000.0000.0000.000
81F112ASP-1-0.712-0.84016.83917.88817.8880.0000.0000.0000.000
82F113CYS0-0.044-0.00517.2260.8240.8240.0000.0000.0000.000
83F114PHE0-0.038-0.01819.490-0.763-0.7630.0000.0000.0000.000
84F115VAL00.0200.02122.2850.4360.4360.0000.0000.0000.000
85F116CYS0-0.035-0.00324.598-0.651-0.6510.0000.0000.0000.000
86F117VAL0-0.004-0.01027.8460.1960.1960.0000.0000.0000.000
87F118PHE0-0.006-0.00530.081-0.337-0.3370.0000.0000.0000.000
88F119LEU0-0.012-0.00132.9000.1320.1320.0000.0000.0000.000
89F120SER00.032-0.01135.799-0.321-0.3210.0000.0000.0000.000
90F121HIS00.001-0.00938.3800.2560.2560.0000.0000.0000.000
91F122GLY00.030-0.01037.3510.1020.1020.0000.0000.0000.000
92F123GLU-1-0.834-0.88238.3777.4777.4770.0000.0000.0000.000
93F124GLY00.0590.03137.332-0.020-0.0200.0000.0000.0000.000
94F125ASN0-0.034-0.00833.2520.0630.0630.0000.0000.0000.000
95F126HIS0-0.009-0.02134.5360.0570.0570.0000.0000.0000.000
96F127ILE0-0.042-0.01334.5480.0760.0760.0000.0000.0000.000
97F128TYR00.008-0.00336.982-0.188-0.1880.0000.0000.0000.000
98F129ALA00.0060.02839.9650.1410.1410.0000.0000.0000.000
99F130TYR00.001-0.01441.327-0.174-0.1740.0000.0000.0000.000
100F131ASP-1-0.801-0.92244.8106.9056.9050.0000.0000.0000.000
101F132ALA00.0140.01243.934-0.121-0.1210.0000.0000.0000.000
102F133LYS10.7960.91040.496-7.356-7.3560.0000.0000.0000.000
103F134ILE00.0120.00236.092-0.079-0.0790.0000.0000.0000.000
104F135GLU-1-0.892-0.93834.5628.8078.8070.0000.0000.0000.000
105F136ILE00.0300.00629.5870.1280.1280.0000.0000.0000.000
106F137GLN00.0330.01426.8920.4150.4150.0000.0000.0000.000
107F138THR0-0.039-0.02530.0020.1640.1640.0000.0000.0000.000
108F139LEU00.0210.01831.4550.0490.0490.0000.0000.0000.000
109F140THR00.013-0.00525.9500.1380.1380.0000.0000.0000.000
110F141GLY00.013-0.00626.2610.4510.4510.0000.0000.0000.000
111F142LEU0-0.032-0.00827.4560.1120.1120.0000.0000.0000.000
112F143PHE00.019-0.01724.1150.0680.0680.0000.0000.0000.000
113F144LYS10.8630.93922.538-10.837-10.8370.0000.0000.0000.000
114F145GLY00.0560.00920.981-0.170-0.1700.0000.0000.0000.000
115F146ASP-1-0.887-0.92821.80011.49211.4920.0000.0000.0000.000
116F147LYS10.8620.94224.915-10.832-10.8320.0000.0000.0000.000
117F148CYS0-0.069-0.02324.334-0.204-0.2040.0000.0000.0000.000
118F149HIS00.1040.04722.6340.5920.5920.0000.0000.0000.000
119F150SER0-0.039-0.01921.3770.5830.5830.0000.0000.0000.000
120F151LEU00.015-0.00220.1320.3700.3700.0000.0000.0000.000
121F152VAL0-0.0050.00616.6270.6490.6490.0000.0000.0000.000
122F153GLY00.0010.01214.0140.3000.3000.0000.0000.0000.000
123F154LYS10.7940.92013.618-14.723-14.7230.0000.0000.0000.000
124F155PRO00.0080.00714.518-0.780-0.7800.0000.0000.0000.000
125F156LYS10.8070.91416.924-16.798-16.7980.0000.0000.0000.000
126F157ILE00.0130.01218.6660.0930.0930.0000.0000.0000.000
127F158PHE00.013-0.00122.114-0.623-0.6230.0000.0000.0000.000
128F159ILE00.0050.00824.6870.2100.2100.0000.0000.0000.000
129F160ILE0-0.009-0.01127.506-0.417-0.4170.0000.0000.0000.000
130F161GLN0-0.024-0.00330.7270.0590.0590.0000.0000.0000.000
131F162ALA00.017-0.01333.465-0.225-0.2250.0000.0000.0000.000
132F163CYS00.0140.03336.2880.0270.0270.0000.0000.0000.000
133F198TYR00.0250.01825.5210.0510.0510.0000.0000.0000.000
134F199THR0-0.023-0.01728.257-0.296-0.2960.0000.0000.0000.000
135F200LEU00.0160.01124.2800.3230.3230.0000.0000.0000.000
136F201PRO00.018-0.01120.694-0.315-0.3150.0000.0000.0000.000
137F202ALA0-0.0020.00722.836-0.007-0.0070.0000.0000.0000.000
138F203GLY00.0150.00520.275-0.300-0.3000.0000.0000.0000.000
139F204ALA00.0130.00014.8120.2700.2700.0000.0000.0000.000
140F205ASP-1-0.817-0.88413.11020.19920.1990.0000.0000.0000.000
141F206PHE0-0.0130.00515.778-0.484-0.4840.0000.0000.0000.000
142F207LEU0-0.031-0.01518.0610.5750.5750.0000.0000.0000.000
143F208MET0-0.0340.00120.036-0.458-0.4580.0000.0000.0000.000
144F209CYS0-0.0070.00123.3430.4590.4590.0000.0000.0000.000
145F210TYR00.030-0.00925.473-0.548-0.5480.0000.0000.0000.000
146F211SER00.007-0.01528.8330.1610.1610.0000.0000.0000.000
147F212VAL0-0.024-0.01131.090-0.425-0.4250.0000.0000.0000.000
148F222THR00.0600.01542.099-0.061-0.0610.0000.0000.0000.000
149F223VAL0-0.025-0.02142.1800.1200.1200.0000.0000.0000.000
150F224ASN0-0.0040.00040.724-0.068-0.0680.0000.0000.0000.000
151F225GLY00.0350.03437.7980.2300.2300.0000.0000.0000.000
152F226SER0-0.060-0.06035.526-0.040-0.0400.0000.0000.0000.000
153F227TRP00.022-0.00935.2070.2180.2180.0000.0000.0000.000
154F228TYR00.0810.04126.8770.1170.1170.0000.0000.0000.000
155F229ILE00.0200.01830.6390.4030.4030.0000.0000.0000.000
156F230GLN00.0190.00831.1650.3190.3190.0000.0000.0000.000
157F231ASP-1-0.768-0.87429.82910.31510.3150.0000.0000.0000.000
158F232LEU00.0110.00724.6520.4390.4390.0000.0000.0000.000
159F233CYS0-0.042-0.02126.6920.4110.4110.0000.0000.0000.000
160F234GLU-1-0.840-0.89628.27910.74910.7490.0000.0000.0000.000
161F235MET0-0.028-0.01724.2670.3210.3210.0000.0000.0000.000
162F236LEU00.0190.01222.5180.5330.5330.0000.0000.0000.000
163F237GLY0-0.035-0.02824.1640.3040.3040.0000.0000.0000.000
164F238LYS10.8340.91725.472-11.092-11.0920.0000.0000.0000.000
165F239TYR00.037-0.00420.721-0.007-0.0070.0000.0000.0000.000
166F240GLY00.0350.03119.7440.9670.9670.0000.0000.0000.000
167F241SER0-0.035-0.01218.9100.8810.8810.0000.0000.0000.000
168F242SER0-0.012-0.02116.9370.6640.6640.0000.0000.0000.000
169F243LEU0-0.020-0.02215.3251.3711.3710.0000.0000.0000.000
170F244GLU-1-0.778-0.84611.63623.97223.9720.0000.0000.0000.000
171F245PHE00.036-0.00614.306-1.488-1.4880.0000.0000.0000.000
172F246THR0-0.019-0.04315.082-1.280-1.2800.0000.0000.0000.000
173F247GLU-1-0.842-0.90815.27520.60920.6090.0000.0000.0000.000
174F248LEU0-0.038-0.01417.758-1.167-1.1670.0000.0000.0000.000
175F249LEU0-0.004-0.01420.182-1.007-1.0070.0000.0000.0000.000
176F250THR0-0.025-0.02119.627-0.837-0.8370.0000.0000.0000.000
177F251LEU0-0.034-0.01721.699-0.765-0.7650.0000.0000.0000.000
178F252VAL0-0.025-0.00424.080-0.660-0.6600.0000.0000.0000.000
179F253ASN00.0160.00524.120-0.767-0.7670.0000.0000.0000.000
180F254ARG10.9901.00623.916-13.089-13.0890.0000.0000.0000.000
181F255LYS10.7670.86628.095-10.935-10.9350.0000.0000.0000.000
182F256VAL0-0.020-0.02830.133-0.416-0.4160.0000.0000.0000.000
183F257GLU-1-0.978-0.98130.39310.33810.3380.0000.0000.0000.000
184F258GLN0-0.066-0.01432.429-0.119-0.1190.0000.0000.0000.000
185F259ARG10.8080.90934.268-9.557-9.5570.0000.0000.0000.000
186F275VAL0-0.011-0.01729.564-0.084-0.0840.0000.0000.0000.000
187F276PRO0-0.0300.00828.6550.0250.0250.0000.0000.0000.000
188F277CYS00.016-0.00426.1740.4020.4020.0000.0000.0000.000
189F278PHE0-0.015-0.00318.670-0.081-0.0810.0000.0000.0000.000
190F279ALA00.0150.00921.4480.1350.1350.0000.0000.0000.000
191F280SER00.022-0.00315.492-0.059-0.0590.0000.0000.0000.000
192F281MET0-0.0050.01316.057-0.088-0.0880.0000.0000.0000.000
193F282LEU0-0.035-0.00813.1270.1340.1340.0000.0000.0000.000
194F283THR0-0.027-0.0279.2430.8720.8720.0000.0000.0000.000
195F284LYS10.8020.9006.568-31.166-31.1660.0000.0000.0000.000
196F285LYS10.8840.9406.414-45.458-45.4580.0000.0000.0000.000
197F286LEU0-0.014-0.0169.6920.4920.4920.0000.0000.0000.000
198F287HIS00.0340.02210.2622.4182.4180.0000.0000.0000.000
199F288PHE00.018-0.00813.778-0.231-0.2310.0000.0000.0000.000
200F289PHE00.0070.01410.892-0.590-0.5900.0000.0000.0000.000
201F290PRO00.0220.01016.578-0.217-0.2170.0000.0000.0000.000
202F291LYS10.7690.86417.537-16.070-16.0700.0000.0000.0000.000
203F292SER00.0020.01319.861-0.769-0.7690.0000.0000.0000.000