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: 6NM3Z

Calculation Name: 3V6M-C-Xray372

Preferred Name: Caspase-6

Target Type: SINGLE PROTEIN

Ligand Name:

ligand 3-letter code:

PDB ID: 3V6M

Chain ID: C

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 205
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2541628.173247
FMO2-HF: Nuclear repulsion 2457129.657424
FMO2-HF: Total energy -84498.515823
FMO2-MP2: Total energy -84740.130864


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(C:31:PHE)


Summations of interaction energy for fragment #1(C: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.
2.0814.546-0.025-1.024-1.4160.003
Interaction energy analysis for fragmet #1(C:31:PHE)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.003 / 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].
3C33PRO00.0320.0263.831-0.1202.230-0.024-1.020-1.3070.003
4C34ALA0-0.047-0.0265.3360.5850.700-0.001-0.004-0.1090.000
5C35GLU-1-0.820-0.8875.7071.2301.2300.0000.0000.0000.000
6C36LYS10.9030.9487.8420.2110.2110.0000.0000.0000.000
7C37TYR00.006-0.03010.3970.0920.0920.0000.0000.0000.000
8C38LYS10.8450.91312.408-0.117-0.1170.0000.0000.0000.000
9C39MET0-0.041-0.02014.6760.0070.0070.0000.0000.0000.000
10C40ASP-1-0.841-0.89417.4110.0150.0150.0000.0000.0000.000
11C41HIS0-0.034-0.01716.7480.0380.0380.0000.0000.0000.000
12C42ARG10.9140.94821.735-0.034-0.0340.0000.0000.0000.000
13C43ARG10.7570.84724.793-0.024-0.0240.0000.0000.0000.000
14C44ARG10.8540.92721.3780.0840.0840.0000.0000.0000.000
15C45GLY00.0400.00822.6540.0010.0010.0000.0000.0000.000
16C46ILE0-0.045-0.01824.916-0.004-0.0040.0000.0000.0000.000
17C47ALA00.0140.01025.524-0.004-0.0040.0000.0000.0000.000
18C48LEU0-0.002-0.00527.5570.0030.0030.0000.0000.0000.000
19C49ILE00.0020.00429.053-0.006-0.0060.0000.0000.0000.000
20C50PHE00.013-0.00630.0150.0050.0050.0000.0000.0000.000
21C51ASN0-0.005-0.03033.737-0.007-0.0070.0000.0000.0000.000
22C52HIS00.0310.02335.4420.0060.0060.0000.0000.0000.000
23C53GLU-1-0.829-0.88938.757-0.036-0.0360.0000.0000.0000.000
24C54ARG10.8260.89241.8970.0250.0250.0000.0000.0000.000
25C55PHE0-0.028-0.01639.2120.0000.0000.0000.0000.0000.000
26C56PHE00.0120.01544.6280.0010.0010.0000.0000.0000.000
27C57TRP00.0530.00946.933-0.001-0.0010.0000.0000.0000.000
28C58HIS0-0.010-0.00749.224-0.001-0.0010.0000.0000.0000.000
29C59LEU0-0.0290.00342.3360.0000.0000.0000.0000.0000.000
30C60THR0-0.063-0.02545.686-0.001-0.0010.0000.0000.0000.000
31C61LEU0-0.0060.01140.897-0.002-0.0020.0000.0000.0000.000
32C62PRO0-0.015-0.00443.3460.0010.0010.0000.0000.0000.000
33C63GLU-1-0.769-0.86943.633-0.030-0.0300.0000.0000.0000.000
34C64ARG10.8240.91835.6180.0430.0430.0000.0000.0000.000
35C65ARG10.8700.90141.8540.0310.0310.0000.0000.0000.000
36C66GLY00.0350.01941.604-0.002-0.0020.0000.0000.0000.000
37C67THR00.0290.01537.498-0.005-0.0050.0000.0000.0000.000
38C68CYS0-0.029-0.01737.736-0.001-0.0010.0000.0000.0000.000
39C69ALA00.0040.00839.1370.0000.0000.0000.0000.0000.000
40C70ASP-1-0.766-0.85934.576-0.068-0.0680.0000.0000.0000.000
41C71ARG10.8620.92534.5450.0350.0350.0000.0000.0000.000
42C72ASP-1-0.801-0.86034.912-0.044-0.0440.0000.0000.0000.000
43C73ASN0-0.004-0.00634.639-0.002-0.0020.0000.0000.0000.000
44C74LEU00.0380.00029.098-0.004-0.0040.0000.0000.0000.000
45C75THR0-0.025-0.03231.0230.0000.0000.0000.0000.0000.000
46C76ARG10.8300.91632.8340.0520.0520.0000.0000.0000.000
47C77ARG10.9100.97329.3240.0840.0840.0000.0000.0000.000
48C78PHE00.0320.00724.108-0.005-0.0050.0000.0000.0000.000
49C79SER0-0.010-0.01228.4210.0040.0040.0000.0000.0000.000
50C80ASP-1-0.883-0.93130.323-0.071-0.0710.0000.0000.0000.000
51C81LEU0-0.049-0.00924.459-0.006-0.0060.0000.0000.0000.000
52C82GLY0-0.025-0.02125.633-0.002-0.0020.0000.0000.0000.000
53C83PHE0-0.039-0.02822.1050.0070.0070.0000.0000.0000.000
54C84GLU-1-0.818-0.90627.835-0.007-0.0070.0000.0000.0000.000
55C85VAL0-0.008-0.01229.9740.0020.0020.0000.0000.0000.000
56C86LYS10.9210.97131.5980.0080.0080.0000.0000.0000.000
57C87CYS0-0.0200.00432.992-0.003-0.0030.0000.0000.0000.000
58C88PHE00.0350.00433.9160.0040.0040.0000.0000.0000.000
59C89ASN00.006-0.00337.060-0.006-0.0060.0000.0000.0000.000
60C90ASP-1-0.779-0.89339.524-0.023-0.0230.0000.0000.0000.000
61C91LEU0-0.0420.00336.2350.0020.0020.0000.0000.0000.000
62C92LYS11.0030.99539.6450.0050.0050.0000.0000.0000.000
63C93ALA0-0.014-0.02737.9040.0010.0010.0000.0000.0000.000
64C94GLU-1-0.910-0.95237.5110.0050.0050.0000.0000.0000.000
65C95GLU-1-0.845-0.92638.181-0.005-0.0050.0000.0000.0000.000
66C96LEU0-0.023-0.00632.7780.0010.0010.0000.0000.0000.000
67C97LEU00.024-0.00132.5080.0000.0000.0000.0000.0000.000
68C98LEU00.0240.01733.6600.0030.0030.0000.0000.0000.000
69C99LYS10.7600.87033.4290.0010.0010.0000.0000.0000.000
70C100ILE0-0.024-0.02027.6720.0010.0010.0000.0000.0000.000
71C101HIS00.0390.02529.3920.0000.0000.0000.0000.0000.000
72C102GLU-1-0.768-0.83630.3380.0110.0110.0000.0000.0000.000
73C103VAL0-0.034-0.03427.3710.0040.0040.0000.0000.0000.000
74C104SER0-0.074-0.04226.0090.0030.0030.0000.0000.0000.000
75C105THR00.0070.00425.9710.0090.0090.0000.0000.0000.000
76C106VAL0-0.051-0.00527.5250.0040.0040.0000.0000.0000.000
77C107SER0-0.0020.00225.7790.0060.0060.0000.0000.0000.000
78C108HIS10.8910.91822.130-0.031-0.0310.0000.0000.0000.000
79C109ALA00.0570.02821.195-0.001-0.0010.0000.0000.0000.000
80C110ASP-1-0.818-0.86421.2460.0420.0420.0000.0000.0000.000
81C111ALA00.005-0.00322.060-0.011-0.0110.0000.0000.0000.000
82C112ASP-1-0.724-0.85018.996-0.015-0.0150.0000.0000.0000.000
83C113CYS0-0.064-0.01717.778-0.004-0.0040.0000.0000.0000.000
84C114PHE0-0.013-0.00219.5920.0080.0080.0000.0000.0000.000
85C115VAL00.0170.02521.100-0.012-0.0120.0000.0000.0000.000
86C116CYS0-0.030-0.00223.6510.0110.0110.0000.0000.0000.000
87C117VAL00.0130.00025.666-0.008-0.0080.0000.0000.0000.000
88C118PHE0-0.004-0.00427.3190.0080.0080.0000.0000.0000.000
89C119LEU0-0.015-0.00530.778-0.006-0.0060.0000.0000.0000.000
90C120SER00.001-0.02633.6370.0040.0040.0000.0000.0000.000
91C121HIS00.0230.00035.300-0.006-0.0060.0000.0000.0000.000
92C122GLY00.019-0.01233.5800.0020.0020.0000.0000.0000.000
93C123GLU-1-0.837-0.88034.604-0.025-0.0250.0000.0000.0000.000
94C124GLY00.0630.03432.8480.0030.0030.0000.0000.0000.000
95C125ASN0-0.040-0.01528.598-0.006-0.0060.0000.0000.0000.000
96C126HIS0-0.018-0.02530.1170.0070.0070.0000.0000.0000.000
97C127ILE0-0.037-0.01331.008-0.005-0.0050.0000.0000.0000.000
98C128TYR00.005-0.00333.3140.0050.0050.0000.0000.0000.000
99C129ALA00.0180.03536.755-0.002-0.0020.0000.0000.0000.000
100C130TYR0-0.004-0.01838.0110.0000.0000.0000.0000.0000.000
101C131ASP-1-0.797-0.92141.566-0.010-0.0100.0000.0000.0000.000
102C132ALA00.0110.01340.0980.0010.0010.0000.0000.0000.000
103C133LYS10.8030.91736.3340.0170.0170.0000.0000.0000.000
104C134ILE00.0120.00032.1120.0030.0030.0000.0000.0000.000
105C135GLU-1-0.866-0.92730.061-0.012-0.0120.0000.0000.0000.000
106C136ILE00.0400.00925.5040.0030.0030.0000.0000.0000.000
107C137GLN00.0000.00122.4010.0060.0060.0000.0000.0000.000
108C138THR0-0.040-0.02425.7700.0050.0050.0000.0000.0000.000
109C139LEU00.0170.01927.7440.0040.0040.0000.0000.0000.000
110C140THR0-0.027-0.03122.0660.0040.0040.0000.0000.0000.000
111C141GLY00.0240.00422.6380.0040.0040.0000.0000.0000.000
112C142LEU0-0.023-0.00823.4700.0110.0110.0000.0000.0000.000
113C143PHE00.003-0.01721.2350.0050.0050.0000.0000.0000.000
114C144LYS10.8730.94918.755-0.023-0.0230.0000.0000.0000.000
115C145GLY00.0620.01717.0280.0060.0060.0000.0000.0000.000
116C146ASP-1-0.893-0.94317.9650.0790.0790.0000.0000.0000.000
117C147LYS10.8450.90820.672-0.059-0.0590.0000.0000.0000.000
118C148CYS0-0.0150.01921.346-0.005-0.0050.0000.0000.0000.000
119C149HIS00.0560.02019.536-0.001-0.0010.0000.0000.0000.000
120C150SER0-0.038-0.01918.7590.0060.0060.0000.0000.0000.000
121C151LEU00.0240.00018.499-0.006-0.0060.0000.0000.0000.000
122C152VAL00.0050.01413.574-0.016-0.0160.0000.0000.0000.000
123C153GLY0-0.0070.00511.5130.0210.0210.0000.0000.0000.000
124C154LYS10.7880.91612.318-0.076-0.0760.0000.0000.0000.000
125C155PRO0-0.009-0.00114.017-0.005-0.0050.0000.0000.0000.000
126C156LYS10.8260.92614.9060.0140.0140.0000.0000.0000.000
127C157ILE00.010-0.00117.961-0.014-0.0140.0000.0000.0000.000
128C158PHE00.007-0.00420.0300.0130.0130.0000.0000.0000.000
129C159ILE0-0.008-0.00122.769-0.012-0.0120.0000.0000.0000.000
130C160ILE0-0.003-0.01425.2180.0100.0100.0000.0000.0000.000
131C161GLN0-0.0250.00027.752-0.006-0.0060.0000.0000.0000.000
132C162ALA00.014-0.01630.8460.0050.0050.0000.0000.0000.000
133C163CYS00.0230.03733.091-0.002-0.0020.0000.0000.0000.000
134C198TYR00.0370.02220.902-0.007-0.0070.0000.0000.0000.000
135C199THR0-0.031-0.01823.6200.0100.0100.0000.0000.0000.000
136C200LEU00.0140.00819.008-0.008-0.0080.0000.0000.0000.000
137C201PRO00.021-0.00516.2920.0140.0140.0000.0000.0000.000
138C202ALA00.0350.02618.0730.0070.0070.0000.0000.0000.000
139C203GLY00.004-0.00215.4550.0210.0210.0000.0000.0000.000
140C204ALA00.0380.02010.633-0.025-0.0250.0000.0000.0000.000
141C205ASP-1-0.812-0.88410.314-0.010-0.0100.0000.0000.0000.000
142C206PHE0-0.0190.00012.5970.0130.0130.0000.0000.0000.000
143C207LEU0-0.031-0.01314.856-0.030-0.0300.0000.0000.0000.000
144C208MET0-0.0230.00917.0280.0200.0200.0000.0000.0000.000
145C209CYS0-0.015-0.00220.325-0.021-0.0210.0000.0000.0000.000
146C210TYR00.0430.00022.4370.0160.0160.0000.0000.0000.000
147C211SER00.002-0.01625.741-0.008-0.0080.0000.0000.0000.000
148C212VAL0-0.024-0.00627.6600.0030.0030.0000.0000.0000.000
149C222THR00.0510.01141.5310.0010.0010.0000.0000.0000.000
150C223VAL0-0.002-0.00641.8570.0000.0000.0000.0000.0000.000
151C224ASN0-0.013-0.00541.7510.0030.0030.0000.0000.0000.000
152C225GLY00.0350.03237.935-0.003-0.0030.0000.0000.0000.000
153C226SER0-0.059-0.06034.561-0.002-0.0020.0000.0000.0000.000
154C227TRP00.025-0.01034.645-0.003-0.0030.0000.0000.0000.000
155C228TYR00.0900.04425.0010.0000.0000.0000.0000.0000.000
156C229ILE00.0130.01629.914-0.007-0.0070.0000.0000.0000.000
157C230GLN00.0240.00931.741-0.006-0.0060.0000.0000.0000.000
158C231ASP-1-0.770-0.87230.267-0.108-0.1080.0000.0000.0000.000
159C232LEU0-0.006-0.00724.939-0.008-0.0080.0000.0000.0000.000
160C233CYS0-0.042-0.01828.086-0.004-0.0040.0000.0000.0000.000
161C234GLU-1-0.829-0.88930.524-0.112-0.1120.0000.0000.0000.000
162C235MET0-0.036-0.01926.155-0.007-0.0070.0000.0000.0000.000
163C236LEU00.0090.00224.415-0.007-0.0070.0000.0000.0000.000
164C237GLY0-0.012-0.01227.227-0.001-0.0010.0000.0000.0000.000
165C238LYS10.8340.91729.1110.1210.1210.0000.0000.0000.000
166C239TYR00.031-0.00624.2060.0010.0010.0000.0000.0000.000
167C240GLY00.0230.03023.733-0.016-0.0160.0000.0000.0000.000
168C241SER0-0.016-0.00523.003-0.009-0.0090.0000.0000.0000.000
169C242SER0-0.014-0.02322.629-0.005-0.0050.0000.0000.0000.000
170C243LEU0-0.012-0.01820.010-0.019-0.0190.0000.0000.0000.000
171C244GLU-1-0.769-0.84113.638-0.350-0.3500.0000.0000.0000.000
172C245PHE00.031-0.01317.0720.0140.0140.0000.0000.0000.000
173C246THR0-0.031-0.04714.3370.0120.0120.0000.0000.0000.000
174C247GLU-1-0.831-0.90216.930-0.353-0.3530.0000.0000.0000.000
175C248LEU0-0.032-0.00718.4770.0230.0230.0000.0000.0000.000
176C249LEU00.009-0.01418.9410.0190.0190.0000.0000.0000.000
177C250THR0-0.034-0.02018.9810.0130.0130.0000.0000.0000.000
178C251LEU0-0.029-0.01921.6540.0150.0150.0000.0000.0000.000
179C252VAL0-0.033-0.00324.5610.0150.0150.0000.0000.0000.000
180C253ASN00.0220.00622.1660.0220.0220.0000.0000.0000.000
181C254ARG10.9680.99625.1320.1920.1920.0000.0000.0000.000
182C255LYS10.7700.86727.7670.1250.1250.0000.0000.0000.000
183C256VAL0-0.009-0.02129.7740.0090.0090.0000.0000.0000.000
184C257GLU-1-0.980-0.97129.706-0.122-0.1220.0000.0000.0000.000
185C258GLN0-0.007-0.01731.578-0.001-0.0010.0000.0000.0000.000
186C259ARG10.7710.89233.9950.0940.0940.0000.0000.0000.000
187C260ARG10.9530.99635.1890.1010.1010.0000.0000.0000.000
188C275VAL0-0.021-0.02427.2150.0020.0020.0000.0000.0000.000
189C276PRO0-0.0270.00726.5450.0020.0020.0000.0000.0000.000
190C277CYS0-0.002-0.00922.331-0.014-0.0140.0000.0000.0000.000
191C278PHE0-0.009-0.00916.2420.0140.0140.0000.0000.0000.000
192C279ALA00.0320.01417.669-0.013-0.0130.0000.0000.0000.000
193C280SER00.017-0.00212.5690.0280.0280.0000.0000.0000.000
194C281MET0-0.0100.00511.664-0.004-0.0040.0000.0000.0000.000
195C282LEU0-0.035-0.00610.6450.0300.0300.0000.0000.0000.000
196C283THR0-0.030-0.0275.809-0.049-0.0490.0000.0000.0000.000
197C284LYS10.8100.9025.565-0.551-0.5510.0000.0000.0000.000
198C285LYS10.8820.9458.0380.9890.9890.0000.0000.0000.000
199C286LEU0-0.022-0.02311.2440.0750.0750.0000.0000.0000.000
200C287HIS0-0.017-0.00214.454-0.057-0.0570.0000.0000.0000.000
201C288PHE0-0.014-0.02217.6690.0270.0270.0000.0000.0000.000
202C289PHE00.0060.01516.9830.0100.0100.0000.0000.0000.000
203C290PRO00.0260.00622.3140.0150.0150.0000.0000.0000.000
204C291LYS10.7730.87721.6380.0280.0280.0000.0000.0000.000
205C292SER00.0100.01524.9600.0000.0000.0000.0000.0000.000