Manual

About

FMODB

FMODB: The database of quantum mechanical data based on the FMO method

Last updated: 2024-05-02

All entries: 37386

Number of unique PDB entries: 7781

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FMODB ID: G61Y1

Calculation Name: 4JQZ-B-Xray372

Preferred Name: Caspase-3

Target Type: SINGLE PROTEIN

Ligand Name:

ligand 3-letter code:

PDB ID: 4JQZ

Chain ID: B

ChEMBL ID: CHEMBL2334

UniProt ID: P42574

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 188
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2261249.629573
FMO2-HF: Nuclear repulsion 2183189.910301
FMO2-HF: Total energy -78059.719271
FMO2-MP2: Total energy -78283.049957


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(B:33:ALA)


Summations of interaction energy for fragment #1(B:33:ALA)
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.
-2.890.1930.11-1.275-1.92-0.004
Interaction energy analysis for fragmet #1(B:33:ALA)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.024 / 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].
3B35ASN00.0260.0143.035-2.832-0.0900.110-1.213-1.640-0.004
4B36SER00.0250.0244.0820.2950.6360.000-0.062-0.2800.000
5B37TYR0-0.014-0.0375.4870.0730.0730.0000.0000.0000.000
6B38LYS10.8240.9017.0870.0000.0000.0000.0000.0000.000
7B39MET0-0.026-0.0187.9970.1480.1480.0000.0000.0000.000
8B40ASP-1-0.817-0.8948.605-0.145-0.1450.0000.0000.0000.000
9B41TYR0-0.064-0.02410.7510.0610.0610.0000.0000.0000.000
10B42PRO0-0.029-0.01813.719-0.005-0.0050.0000.0000.0000.000
11B43GLU-1-0.822-0.89717.092-0.068-0.0680.0000.0000.0000.000
12B44MET00.0420.03313.985-0.023-0.0230.0000.0000.0000.000
13B45GLY00.0560.01916.882-0.018-0.0180.0000.0000.0000.000
14B46LEU0-0.0290.00219.6140.0060.0060.0000.0000.0000.000
15B47CYS0-0.037-0.01422.343-0.012-0.0120.0000.0000.0000.000
16B48ILE00.0050.00524.4380.0090.0090.0000.0000.0000.000
17B49ILE00.0160.01327.533-0.004-0.0040.0000.0000.0000.000
18B50ILE0-0.011-0.00629.8220.0070.0070.0000.0000.0000.000
19B51ASN0-0.048-0.01932.920-0.004-0.0040.0000.0000.0000.000
20B52ASN0-0.0100.00935.6570.0040.0040.0000.0000.0000.000
21B53LYS10.8550.92838.5550.0520.0520.0000.0000.0000.000
22B54ASN0-0.023-0.00540.8750.0030.0030.0000.0000.0000.000
23B67THR00.053-0.00736.0570.0020.0020.0000.0000.0000.000
24B68ASP-1-0.782-0.87635.513-0.060-0.0600.0000.0000.0000.000
25B69VAL00.0110.00435.678-0.001-0.0010.0000.0000.0000.000
26B70ASP-1-0.773-0.87132.326-0.087-0.0870.0000.0000.0000.000
27B71ALA00.001-0.00331.333-0.006-0.0060.0000.0000.0000.000
28B72ALA0-0.005-0.00731.368-0.003-0.0030.0000.0000.0000.000
29B73ASN00.0330.01829.748-0.005-0.0050.0000.0000.0000.000
30B74LEU00.0240.01426.472-0.008-0.0080.0000.0000.0000.000
31B75ARG10.8410.90326.4310.0670.0670.0000.0000.0000.000
32B76GLU-1-0.831-0.91326.842-0.101-0.1010.0000.0000.0000.000
33B77THR00.0230.00723.084-0.004-0.0040.0000.0000.0000.000
34B78PHE00.041-0.00219.888-0.008-0.0080.0000.0000.0000.000
35B79ARG10.9210.96222.1950.0730.0730.0000.0000.0000.000
36B80ASN0-0.0280.00322.6540.0060.0060.0000.0000.0000.000
37B81LEU0-0.0370.00117.453-0.006-0.0060.0000.0000.0000.000
38B82LYS10.9010.94814.3840.1750.1750.0000.0000.0000.000
39B83TYR0-0.010-0.01216.495-0.005-0.0050.0000.0000.0000.000
40B84GLU-1-0.806-0.88321.341-0.060-0.0600.0000.0000.0000.000
41B85VAL0-0.034-0.01924.4080.0020.0020.0000.0000.0000.000
42B86ARG10.6970.81426.7970.0750.0750.0000.0000.0000.000
43B87ASN00.0370.03229.886-0.004-0.0040.0000.0000.0000.000
44B88LYS10.9270.96332.4900.0590.0590.0000.0000.0000.000
45B89ASN00.002-0.00934.942-0.005-0.0050.0000.0000.0000.000
46B90ASP-1-0.804-0.91338.132-0.046-0.0460.0000.0000.0000.000
47B91LEU0-0.0250.00535.4280.0020.0020.0000.0000.0000.000
48B92THR00.024-0.01839.461-0.002-0.0020.0000.0000.0000.000
49B93ARG10.8900.92339.0310.0360.0360.0000.0000.0000.000
50B94GLU-1-0.803-0.89238.769-0.039-0.0390.0000.0000.0000.000
51B95GLU-1-0.759-0.85538.784-0.040-0.0400.0000.0000.0000.000
52B96ILE0-0.038-0.01233.733-0.002-0.0020.0000.0000.0000.000
53B97VAL0-0.042-0.03434.043-0.003-0.0030.0000.0000.0000.000
54B98GLU-1-0.869-0.91034.510-0.035-0.0350.0000.0000.0000.000
55B99LEU00.0160.00731.5890.0000.0000.0000.0000.0000.000
56B100MET0-0.024-0.02327.203-0.002-0.0020.0000.0000.0000.000
57B101ARG10.7400.86129.6510.0340.0340.0000.0000.0000.000
58B102ASP-1-0.792-0.87631.179-0.036-0.0360.0000.0000.0000.000
59B103VAL00.0020.00326.0410.0000.0000.0000.0000.0000.000
60B104SER0-0.098-0.04426.358-0.001-0.0010.0000.0000.0000.000
61B105LYS10.9360.96126.9600.0350.0350.0000.0000.0000.000
62B106GLU-1-0.774-0.83926.388-0.056-0.0560.0000.0000.0000.000
63B107ASP-1-0.813-0.88423.439-0.032-0.0320.0000.0000.0000.000
64B108HIS0-0.067-0.05120.220-0.012-0.0120.0000.0000.0000.000
65B109SER0-0.022-0.04919.079-0.014-0.0140.0000.0000.0000.000
66B110LYS10.8440.91417.8820.0450.0450.0000.0000.0000.000
67B111ARG10.8040.90417.5640.0650.0650.0000.0000.0000.000
68B112SER00.0340.00112.941-0.003-0.0030.0000.0000.0000.000
69B113SER0-0.027-0.01714.426-0.030-0.0300.0000.0000.0000.000
70B114PHE0-0.009-0.00816.5520.0290.0290.0000.0000.0000.000
71B115VAL00.0190.02219.615-0.013-0.0130.0000.0000.0000.000
72B116CYS0-0.068-0.02821.9410.0170.0170.0000.0000.0000.000
73B117VAL00.016-0.00725.544-0.005-0.0050.0000.0000.0000.000
74B118LEU0-0.018-0.00927.8050.0090.0090.0000.0000.0000.000
75B119LEU0-0.0070.00331.000-0.003-0.0030.0000.0000.0000.000
76B120SER00.004-0.01633.9360.0040.0040.0000.0000.0000.000
77B121HIS00.0710.06037.099-0.003-0.0030.0000.0000.0000.000
78B122GLY00.007-0.04135.929-0.002-0.0020.0000.0000.0000.000
79B123GLU-1-0.865-0.93136.476-0.056-0.0560.0000.0000.0000.000
80B124GLU-1-0.884-0.92934.387-0.068-0.0680.0000.0000.0000.000
81B125GLY0-0.093-0.05031.793-0.006-0.0060.0000.0000.0000.000
82B126ILE0-0.098-0.03931.610-0.004-0.0040.0000.0000.0000.000
83B127ILE00.0160.00132.909-0.001-0.0010.0000.0000.0000.000
84B128PHE0-0.045-0.01335.5210.0040.0040.0000.0000.0000.000
85B129GLY00.009-0.00938.632-0.002-0.0020.0000.0000.0000.000
86B130THR0-0.026-0.01739.8130.0010.0010.0000.0000.0000.000
87B131ASN0-0.056-0.03542.8180.0020.0020.0000.0000.0000.000
88B132GLY00.0270.01242.7670.0020.0020.0000.0000.0000.000
89B133PRO0-0.0120.01240.113-0.002-0.0020.0000.0000.0000.000
90B134VAL0-0.018-0.01935.8330.0030.0030.0000.0000.0000.000
91B135ASP-1-0.819-0.91434.633-0.062-0.0620.0000.0000.0000.000
92B136LEU00.0290.01228.3140.0000.0000.0000.0000.0000.000
93B137LYS10.9190.94629.0580.0640.0640.0000.0000.0000.000
94B138LYS10.8830.94731.3720.0430.0430.0000.0000.0000.000
95B139ILE00.0030.00328.9660.0020.0020.0000.0000.0000.000
96B140THR00.0670.02826.513-0.001-0.0010.0000.0000.0000.000
97B141ASN0-0.030-0.01926.964-0.006-0.0060.0000.0000.0000.000
98B142PHE0-0.050-0.02328.6350.0060.0060.0000.0000.0000.000
99B143PHE00.0360.00923.3630.0030.0030.0000.0000.0000.000
100B144ARG10.8050.89323.1930.0430.0430.0000.0000.0000.000
101B145GLY00.0260.00721.5000.0040.0040.0000.0000.0000.000
102B146ASP-1-0.831-0.90422.272-0.036-0.0360.0000.0000.0000.000
103B147ARG10.8750.95625.0120.0480.0480.0000.0000.0000.000
104B148CYS0-0.0220.00323.5110.0030.0030.0000.0000.0000.000
105B149ARG10.9720.97518.5790.0000.0000.0000.0000.0000.000
106B150SER00.0310.02020.707-0.003-0.0030.0000.0000.0000.000
107B151LEU00.0410.00818.549-0.009-0.0090.0000.0000.0000.000
108B152THR0-0.031-0.02118.123-0.021-0.0210.0000.0000.0000.000
109B153GLY0-0.0060.01014.7500.0170.0170.0000.0000.0000.000
110B154LYS10.8220.94113.3580.0540.0540.0000.0000.0000.000
111B155PRO00.0040.01713.0090.0330.0330.0000.0000.0000.000
112B156LYS10.8130.90815.8500.1830.1830.0000.0000.0000.000
113B157LEU0-0.035-0.02216.6760.0000.0000.0000.0000.0000.000
114B158PHE00.0250.00620.6520.0190.0190.0000.0000.0000.000
115B159ILE0-0.027-0.00921.888-0.003-0.0030.0000.0000.0000.000
116B160ILE00.0250.00925.6940.0090.0090.0000.0000.0000.000
117B161GLN00.026-0.00129.175-0.008-0.0080.0000.0000.0000.000
118B162ALA00.0340.03632.0240.0040.0040.0000.0000.0000.000
119B185HIS0-0.006-0.01335.8900.0010.0010.0000.0000.0000.000
120B186LYS10.9690.98332.2780.0570.0570.0000.0000.0000.000
121B187ILE00.0620.03927.1060.0010.0010.0000.0000.0000.000
122B188PRO0-0.031-0.01626.9570.0020.0020.0000.0000.0000.000
123B189VAL00.0320.02323.762-0.011-0.0110.0000.0000.0000.000
124B190GLU-1-0.842-0.91323.081-0.064-0.0640.0000.0000.0000.000
125B191ALA00.0530.01517.976-0.014-0.0140.0000.0000.0000.000
126B192ASP-1-0.852-0.90214.770-0.239-0.2390.0000.0000.0000.000
127B193PHE00.0010.00217.016-0.002-0.0020.0000.0000.0000.000
128B194LEU00.003-0.00717.198-0.017-0.0170.0000.0000.0000.000
129B195TYR00.002-0.01320.4320.0120.0120.0000.0000.0000.000
130B196ALA00.0020.01722.396-0.005-0.0050.0000.0000.0000.000
131B197TYR0-0.003-0.00524.4040.0020.0020.0000.0000.0000.000
132B198SER00.0340.02728.2020.0000.0000.0000.0000.0000.000
133B199THR00.0100.00930.9540.0070.0070.0000.0000.0000.000
134B212GLY00.0110.00835.8810.0010.0010.0000.0000.0000.000
135B213SER0-0.069-0.06733.355-0.001-0.0010.0000.0000.0000.000
136B214TRP00.0690.01633.209-0.005-0.0050.0000.0000.0000.000
137B215PHE0-0.0020.01525.759-0.005-0.0050.0000.0000.0000.000
138B216ILE00.0150.00928.262-0.009-0.0090.0000.0000.0000.000
139B217GLN00.0230.01328.571-0.004-0.0040.0000.0000.0000.000
140B218SER0-0.058-0.04927.936-0.005-0.0050.0000.0000.0000.000
141B219LEU00.0330.02022.234-0.010-0.0100.0000.0000.0000.000
142B220CYS0-0.019-0.01023.927-0.014-0.0140.0000.0000.0000.000
143B221ALA0-0.0170.00325.020-0.004-0.0040.0000.0000.0000.000
144B222MET0-0.052-0.01921.869-0.007-0.0070.0000.0000.0000.000
145B223LEU0-0.006-0.00219.018-0.016-0.0160.0000.0000.0000.000
146B224LYS10.8260.90520.5080.0970.0970.0000.0000.0000.000
147B225GLN0-0.0070.00922.1210.0020.0020.0000.0000.0000.000
148B226TYR0-0.024-0.04718.079-0.002-0.0020.0000.0000.0000.000
149B227ALA00.0500.03816.428-0.031-0.0310.0000.0000.0000.000
150B228ASP-1-0.850-0.90814.212-0.248-0.2480.0000.0000.0000.000
151B229LYS10.7800.86814.3000.1980.1980.0000.0000.0000.000
152B230LEU0-0.039-0.01912.884-0.039-0.0390.0000.0000.0000.000
153B231GLU-1-0.695-0.83410.173-0.508-0.5080.0000.0000.0000.000
154B232PHE00.0480.00412.4270.0780.0780.0000.0000.0000.000
155B233MET00.0130.00714.2600.0700.0700.0000.0000.0000.000
156B234HIS0-0.0080.01313.2240.0750.0750.0000.0000.0000.000
157B235ILE0-0.058-0.03015.9190.0400.0400.0000.0000.0000.000
158B236LEU00.008-0.00618.6290.0310.0310.0000.0000.0000.000
159B237THR0-0.003-0.01019.2820.0250.0250.0000.0000.0000.000
160B238ARG10.8850.94319.6230.2190.2190.0000.0000.0000.000
161B239VAL00.0000.01622.9990.0150.0150.0000.0000.0000.000
162B240ASN00.0110.00724.4310.0090.0090.0000.0000.0000.000
163B241ARG10.9720.98823.3700.1560.1560.0000.0000.0000.000
164B242LYS10.9040.97527.0740.1140.1140.0000.0000.0000.000
165B243VAL00.0160.00428.8280.0070.0070.0000.0000.0000.000
166B244ALA00.0140.00430.2530.0070.0070.0000.0000.0000.000
167B245THR0-0.002-0.01730.8870.0050.0050.0000.0000.0000.000
168B246GLU-1-0.898-0.96732.652-0.090-0.0900.0000.0000.0000.000
169B247PHE0-0.058-0.04434.2700.0050.0050.0000.0000.0000.000
170B248GLU-1-1.001-0.97134.529-0.078-0.0780.0000.0000.0000.000
171B249SER0-0.066-0.01938.0110.0040.0040.0000.0000.0000.000
172B261GLN00.0210.00934.995-0.002-0.0020.0000.0000.0000.000
173B262ILE0-0.061-0.03728.379-0.002-0.0020.0000.0000.0000.000
174B263PRO0-0.026-0.00526.9260.0020.0020.0000.0000.0000.000
175B264CYS0-0.0060.01226.871-0.005-0.0050.0000.0000.0000.000
176B265ILE0-0.001-0.00820.103-0.004-0.0040.0000.0000.0000.000
177B266VAL0-0.004-0.00923.0550.0010.0010.0000.0000.0000.000
178B267SER00.017-0.00816.560-0.006-0.0060.0000.0000.0000.000
179B268MET0-0.016-0.00118.6920.0160.0160.0000.0000.0000.000
180B269LEU0-0.058-0.01813.4310.0100.0100.0000.0000.0000.000
181B270THR0-0.035-0.02412.853-0.014-0.0140.0000.0000.0000.000
182B271LYS10.7910.9086.9080.5220.5220.0000.0000.0000.000
183B272GLU-1-0.866-0.9106.793-1.101-1.1010.0000.0000.0000.000
184B273LEU0-0.027-0.0368.522-0.108-0.1080.0000.0000.0000.000
185B274TYR0-0.021-0.0316.4010.1850.1850.0000.0000.0000.000
186B275PHE0-0.043-0.02510.5280.0050.0050.0000.0000.0000.000
187B276TYR0-0.031-0.01610.0990.0530.0530.0000.0000.0000.000
188B277HIS00.0290.0248.397-0.053-0.0530.0000.0000.0000.000