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: N943Q

Calculation Name: 3V6M-I-Xray372

Preferred Name: Caspase-6

Target Type: SINGLE PROTEIN

Ligand Name:

ligand 3-letter code:

PDB ID: 3V6M

Chain ID: I

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 204
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2517582.809801
FMO2-HF: Nuclear repulsion 2433612.027867
FMO2-HF: Total energy -83970.781933
FMO2-MP2: Total energy -84210.849499


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(I:31:PHE)


Summations of interaction energy for fragment #1(I:31:PHE)
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.
0.1192.993-0.03-1.179-1.6650.003
Interaction energy analysis for fragmet #1(I:31:PHE)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.005 / q_NPA : 0.001
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].
3I33PRO00.0280.0273.808-0.7342.013-0.029-1.173-1.5450.003
4I34ALA0-0.046-0.0275.8700.1540.281-0.001-0.006-0.1200.000
5I35GLU-1-0.835-0.8985.263-0.255-0.2550.0000.0000.0000.000
6I36LYS10.8680.9357.8640.5050.5050.0000.0000.0000.000
7I37TYR00.001-0.03210.1070.0120.0120.0000.0000.0000.000
8I38LYS10.8060.88211.5480.0670.0670.0000.0000.0000.000
9I39MET0-0.028-0.00514.0600.0130.0130.0000.0000.0000.000
10I40ASP-1-0.839-0.90017.334-0.062-0.0620.0000.0000.0000.000
11I41HIS0-0.0230.00016.3720.0370.0370.0000.0000.0000.000
12I42ARG10.9000.93621.2920.0010.0010.0000.0000.0000.000
13I43ARG10.8300.89424.3470.0150.0150.0000.0000.0000.000
14I44ARG10.8600.91820.7670.1240.1240.0000.0000.0000.000
15I45GLY00.0380.01122.024-0.005-0.0050.0000.0000.0000.000
16I46ILE0-0.034-0.01524.371-0.002-0.0020.0000.0000.0000.000
17I47ALA00.0020.00325.235-0.007-0.0070.0000.0000.0000.000
18I48LEU00.000-0.00627.3220.0060.0060.0000.0000.0000.000
19I49ILE00.0030.00129.033-0.007-0.0070.0000.0000.0000.000
20I50PHE00.015-0.00130.1810.0060.0060.0000.0000.0000.000
21I51ASN00.017-0.00333.946-0.007-0.0070.0000.0000.0000.000
22I52HIS0-0.013-0.00436.4870.0020.0020.0000.0000.0000.000
23I53GLU-1-0.850-0.91339.062-0.046-0.0460.0000.0000.0000.000
24I54ARG10.9240.96042.0630.0270.0270.0000.0000.0000.000
25I55PHE0-0.014-0.01439.433-0.001-0.0010.0000.0000.0000.000
26I56PHE0-0.0180.00144.9860.0010.0010.0000.0000.0000.000
27I57TRP00.0740.00847.296-0.001-0.0010.0000.0000.0000.000
28I58HIS0-0.007-0.00549.819-0.002-0.0020.0000.0000.0000.000
29I59LEU0-0.0170.00742.6770.0000.0000.0000.0000.0000.000
30I60THR0-0.069-0.02445.915-0.001-0.0010.0000.0000.0000.000
31I61LEU0-0.0050.01141.128-0.002-0.0020.0000.0000.0000.000
32I62PRO0-0.018-0.00343.3460.0010.0010.0000.0000.0000.000
33I63GLU-1-0.871-0.94843.766-0.035-0.0350.0000.0000.0000.000
34I64ARG10.8020.91335.6400.0530.0530.0000.0000.0000.000
35I65ARG10.9870.98541.8830.0430.0430.0000.0000.0000.000
36I66GLY00.007-0.00341.490-0.002-0.0020.0000.0000.0000.000
37I67THR00.0360.01937.546-0.005-0.0050.0000.0000.0000.000
38I68CYS0-0.047-0.02837.796-0.002-0.0020.0000.0000.0000.000
39I69ALA00.0210.01539.239-0.001-0.0010.0000.0000.0000.000
40I70ASP-1-0.776-0.86634.590-0.078-0.0780.0000.0000.0000.000
41I71ARG10.8080.87034.5100.0440.0440.0000.0000.0000.000
42I72ASP-1-0.816-0.87534.904-0.053-0.0530.0000.0000.0000.000
43I73ASN0-0.018-0.00434.475-0.003-0.0030.0000.0000.0000.000
44I74LEU00.0360.00029.061-0.005-0.0050.0000.0000.0000.000
45I75THR00.010-0.00830.818-0.002-0.0020.0000.0000.0000.000
46I76ARG10.8540.94732.5200.0790.0790.0000.0000.0000.000
47I77ARG10.8630.94229.1200.0960.0960.0000.0000.0000.000
48I78PHE00.0520.01624.067-0.006-0.0060.0000.0000.0000.000
49I79SER00.012-0.00227.9820.0010.0010.0000.0000.0000.000
50I80ASP-1-0.873-0.92129.711-0.086-0.0860.0000.0000.0000.000
51I81LEU0-0.052-0.01724.148-0.006-0.0060.0000.0000.0000.000
52I82GLY0-0.025-0.01824.986-0.006-0.0060.0000.0000.0000.000
53I83PHE0-0.044-0.03721.7470.0050.0050.0000.0000.0000.000
54I84GLU-1-0.860-0.92427.307-0.028-0.0280.0000.0000.0000.000
55I85VAL0-0.018-0.01729.4300.0000.0000.0000.0000.0000.000
56I86LYS10.8660.94231.3000.0330.0330.0000.0000.0000.000
57I87CYS0-0.029-0.00832.865-0.004-0.0040.0000.0000.0000.000
58I88PHE00.0210.00133.7850.0050.0050.0000.0000.0000.000
59I89ASN00.0250.01837.186-0.006-0.0060.0000.0000.0000.000
60I90ASP-1-0.789-0.90639.709-0.033-0.0330.0000.0000.0000.000
61I91LEU0-0.0490.00836.4900.0020.0020.0000.0000.0000.000
62I92LYS11.0270.99439.9550.0140.0140.0000.0000.0000.000
63I93ALA00.004-0.01138.3260.0000.0000.0000.0000.0000.000
64I94GLU-1-0.929-0.95737.835-0.007-0.0070.0000.0000.0000.000
65I95GLU-1-0.855-0.93338.327-0.018-0.0180.0000.0000.0000.000
66I96LEU0-0.011-0.00732.875-0.001-0.0010.0000.0000.0000.000
67I97LEU00.0270.00633.118-0.001-0.0010.0000.0000.0000.000
68I98LEU00.0220.00933.8170.0020.0020.0000.0000.0000.000
69I99LYS10.7920.89434.2720.0150.0150.0000.0000.0000.000
70I100ILE0-0.013-0.01027.8790.0000.0000.0000.0000.0000.000
71I101HIS0-0.006-0.01729.5570.0030.0030.0000.0000.0000.000
72I102GLU-1-0.805-0.84530.560-0.007-0.0070.0000.0000.0000.000
73I103VAL0-0.002-0.01227.2130.0020.0020.0000.0000.0000.000
74I104SER0-0.083-0.04226.0270.0010.0010.0000.0000.0000.000
75I105THR0-0.023-0.02425.9850.0050.0050.0000.0000.0000.000
76I106VAL0-0.0210.01427.4770.0060.0060.0000.0000.0000.000
77I107SER0-0.038-0.01825.8300.0020.0020.0000.0000.0000.000
78I108HIS00.042-0.01122.036-0.013-0.0130.0000.0000.0000.000
79I109ALA00.0230.01521.296-0.007-0.0070.0000.0000.0000.000
80I110ASP-1-0.813-0.86621.179-0.007-0.0070.0000.0000.0000.000
81I111ALA0-0.005-0.00821.901-0.008-0.0080.0000.0000.0000.000
82I112ASP-1-0.727-0.84118.317-0.090-0.0900.0000.0000.0000.000
83I113CYS0-0.052-0.01517.250-0.017-0.0170.0000.0000.0000.000
84I114PHE00.0120.01019.0980.0150.0150.0000.0000.0000.000
85I115VAL00.0020.01521.011-0.014-0.0140.0000.0000.0000.000
86I116CYS0-0.035-0.00223.6250.0140.0140.0000.0000.0000.000
87I117VAL0-0.007-0.01325.896-0.008-0.0080.0000.0000.0000.000
88I118PHE00.0080.00227.6360.0080.0080.0000.0000.0000.000
89I119LEU0-0.030-0.01331.059-0.006-0.0060.0000.0000.0000.000
90I120SER00.034-0.01133.8230.0050.0050.0000.0000.0000.000
91I121HIS00.004-0.00535.417-0.006-0.0060.0000.0000.0000.000
92I122GLY00.026-0.00933.8010.0010.0010.0000.0000.0000.000
93I123GLU-1-0.817-0.86034.827-0.033-0.0330.0000.0000.0000.000
94I124GLY00.0320.01333.0750.0030.0030.0000.0000.0000.000
95I125ASN0-0.037-0.01029.227-0.006-0.0060.0000.0000.0000.000
96I126HIS0-0.009-0.01930.5040.0050.0050.0000.0000.0000.000
97I127ILE0-0.0160.00331.370-0.005-0.0050.0000.0000.0000.000
98I128TYR0-0.024-0.03033.6780.0050.0050.0000.0000.0000.000
99I129ALA0-0.0120.01537.159-0.003-0.0030.0000.0000.0000.000
100I130TYR00.0070.00438.5450.0000.0000.0000.0000.0000.000
101I131ASP-1-0.796-0.92542.116-0.020-0.0200.0000.0000.0000.000
102I132ALA0-0.0010.00940.7000.0010.0010.0000.0000.0000.000
103I133LYS10.8500.93736.8300.0260.0260.0000.0000.0000.000
104I134ILE00.001-0.00532.6790.0040.0040.0000.0000.0000.000
105I135GLU-1-0.887-0.93630.660-0.027-0.0270.0000.0000.0000.000
106I136ILE00.0360.00626.0230.0020.0020.0000.0000.0000.000
107I137GLN00.0240.01122.8660.0000.0000.0000.0000.0000.000
108I138THR0-0.052-0.03226.4000.0040.0040.0000.0000.0000.000
109I139LEU00.0100.01328.2190.0040.0040.0000.0000.0000.000
110I140THR00.0150.00022.5660.0010.0010.0000.0000.0000.000
111I141GLY00.0210.00422.9570.0000.0000.0000.0000.0000.000
112I142LEU0-0.072-0.04323.8960.0110.0110.0000.0000.0000.000
113I143PHE00.0420.00221.3450.0040.0040.0000.0000.0000.000
114I144LYS10.8570.92518.996-0.022-0.0220.0000.0000.0000.000
115I145GLY00.0620.01717.5680.0060.0060.0000.0000.0000.000
116I146ASP-1-0.868-0.92118.4670.0470.0470.0000.0000.0000.000
117I147LYS10.8730.94221.400-0.011-0.0110.0000.0000.0000.000
118I148CYS0-0.0150.01921.562-0.004-0.0040.0000.0000.0000.000
119I149HIS00.0410.01520.051-0.009-0.0090.0000.0000.0000.000
120I150SER0-0.021-0.01219.138-0.001-0.0010.0000.0000.0000.000
121I151LEU00.0450.02118.511-0.008-0.0080.0000.0000.0000.000
122I152VAL0-0.023-0.00314.099-0.025-0.0250.0000.0000.0000.000
123I153GLY0-0.0060.00711.5650.0170.0170.0000.0000.0000.000
124I154LYS10.7770.90612.088-0.022-0.0220.0000.0000.0000.000
125I155PRO0-0.0040.00013.7810.0030.0030.0000.0000.0000.000
126I156LYS10.8320.93014.9330.1160.1160.0000.0000.0000.000
127I157ILE0-0.010-0.00218.170-0.014-0.0140.0000.0000.0000.000
128I158PHE00.0240.00520.2020.0170.0170.0000.0000.0000.000
129I159ILE0-0.007-0.00122.899-0.011-0.0110.0000.0000.0000.000
130I160ILE0-0.002-0.01025.3730.0110.0110.0000.0000.0000.000
131I161GLN0-0.0260.00027.902-0.005-0.0050.0000.0000.0000.000
132I162ALA00.023-0.01330.9040.0060.0060.0000.0000.0000.000
133I163CYS00.0090.03033.154-0.002-0.0020.0000.0000.0000.000
134I198TYR00.0500.02325.5010.0000.0000.0000.0000.0000.000
135I199THR0-0.040-0.02624.0050.0080.0080.0000.0000.0000.000
136I200LEU0-0.0020.01719.349-0.011-0.0110.0000.0000.0000.000
137I201PRO00.025-0.01216.5150.0130.0130.0000.0000.0000.000
138I202ALA00.0130.01018.6770.0070.0070.0000.0000.0000.000
139I203GLY00.005-0.00516.2560.0230.0230.0000.0000.0000.000
140I204ALA00.0130.00210.936-0.026-0.0260.0000.0000.0000.000
141I205ASP-1-0.818-0.88610.307-0.218-0.2180.0000.0000.0000.000
142I206PHE0-0.0140.00212.8400.0220.0220.0000.0000.0000.000
143I207LEU0-0.031-0.01515.199-0.032-0.0320.0000.0000.0000.000
144I208MET0-0.0200.01017.2540.0210.0210.0000.0000.0000.000
145I209CYS0-0.013-0.00520.331-0.020-0.0200.0000.0000.0000.000
146I210TYR00.016-0.01522.5020.0170.0170.0000.0000.0000.000
147I211SER00.008-0.01625.631-0.007-0.0070.0000.0000.0000.000
148I212VAL0-0.021-0.00127.2970.0050.0050.0000.0000.0000.000
149I222THR00.0410.01741.1980.0020.0020.0000.0000.0000.000
150I223VAL00.000-0.01541.587-0.001-0.0010.0000.0000.0000.000
151I224ASN0-0.013-0.00841.4380.0030.0030.0000.0000.0000.000
152I225GLY00.0430.03937.733-0.003-0.0030.0000.0000.0000.000
153I226SER0-0.062-0.06534.347-0.001-0.0010.0000.0000.0000.000
154I227TRP00.025-0.00534.115-0.003-0.0030.0000.0000.0000.000
155I228TYR00.0820.04124.7130.0000.0000.0000.0000.0000.000
156I229ILE00.0260.02129.769-0.007-0.0070.0000.0000.0000.000
157I230GLN00.011-0.00231.539-0.006-0.0060.0000.0000.0000.000
158I231ASP-1-0.770-0.87329.844-0.111-0.1110.0000.0000.0000.000
159I232LEU00.0150.00524.699-0.008-0.0080.0000.0000.0000.000
160I233CYS0-0.038-0.01827.789-0.005-0.0050.0000.0000.0000.000
161I234GLU-1-0.838-0.89330.177-0.114-0.1140.0000.0000.0000.000
162I235MET0-0.031-0.01525.824-0.006-0.0060.0000.0000.0000.000
163I236LEU00.002-0.00124.264-0.008-0.0080.0000.0000.0000.000
164I237GLY0-0.038-0.02726.844-0.002-0.0020.0000.0000.0000.000
165I238LYS10.8310.91828.8360.1230.1230.0000.0000.0000.000
166I239TYR00.039-0.00424.0000.0010.0010.0000.0000.0000.000
167I240GLY00.0370.03223.470-0.016-0.0160.0000.0000.0000.000
168I241SER0-0.034-0.01022.556-0.013-0.0130.0000.0000.0000.000
169I242SER0-0.019-0.02622.397-0.005-0.0050.0000.0000.0000.000
170I243LEU0-0.008-0.01319.882-0.019-0.0190.0000.0000.0000.000
171I244GLU-1-0.790-0.85213.114-0.397-0.3970.0000.0000.0000.000
172I245PHE00.035-0.00816.7010.0180.0180.0000.0000.0000.000
173I246THR0-0.022-0.04213.8470.0160.0160.0000.0000.0000.000
174I247GLU-1-0.829-0.90416.715-0.326-0.3260.0000.0000.0000.000
175I248LEU0-0.043-0.01418.2520.0250.0250.0000.0000.0000.000
176I249LEU00.012-0.00618.6650.0200.0200.0000.0000.0000.000
177I250THR0-0.038-0.02218.6890.0130.0130.0000.0000.0000.000
178I251LEU0-0.043-0.02521.3400.0150.0150.0000.0000.0000.000
179I252VAL0-0.033-0.00224.2400.0140.0140.0000.0000.0000.000
180I253ASN00.0250.00621.8120.0200.0200.0000.0000.0000.000
181I254ARG10.9851.00924.7130.1860.1860.0000.0000.0000.000
182I255LYS10.7750.86227.5350.1270.1270.0000.0000.0000.000
183I256VAL0-0.013-0.02029.4170.0080.0080.0000.0000.0000.000
184I257GLU-1-0.977-0.97929.297-0.131-0.1310.0000.0000.0000.000
185I258GLN0-0.059-0.02931.3040.0000.0000.0000.0000.0000.000
186I259ARG10.7970.91733.7430.0980.0980.0000.0000.0000.000
187I275VAL0-0.006-0.01626.7730.0020.0020.0000.0000.0000.000
188I276PRO0-0.044-0.00426.2130.0020.0020.0000.0000.0000.000
189I277CYS00.015-0.00822.497-0.012-0.0120.0000.0000.0000.000
190I278PHE0-0.019-0.00115.7220.0070.0070.0000.0000.0000.000
191I279ALA00.0230.01417.418-0.010-0.0100.0000.0000.0000.000
192I280SER00.015-0.00612.3180.0170.0170.0000.0000.0000.000
193I281MET0-0.0110.00511.9360.0000.0000.0000.0000.0000.000
194I282LEU0-0.037-0.00610.8790.0130.0130.0000.0000.0000.000
195I283THR0-0.030-0.0245.883-0.071-0.0710.0000.0000.0000.000
196I284LYS10.8080.9015.4200.1060.1060.0000.0000.0000.000
197I285LYS10.8760.9357.7550.8600.8600.0000.0000.0000.000
198I286LEU0-0.013-0.01610.8600.0360.0360.0000.0000.0000.000
199I287HIS00.0360.02014.075-0.049-0.0490.0000.0000.0000.000
200I288PHE00.012-0.00917.0880.0140.0140.0000.0000.0000.000
201I289PHE00.0050.01616.8570.0110.0110.0000.0000.0000.000
202I290PRO00.0230.01021.7000.0100.0100.0000.0000.0000.000
203I291LYS10.7860.88521.4420.0820.0820.0000.0000.0000.000
204I292SER00.0040.01124.9280.0050.0050.0000.0000.0000.000