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: 85LNY

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 OptAll
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 -2266474.261827
FMO2-HF: Nuclear repulsion 2188414.058543
FMO2-HF: Total energy -78060.203284
FMO2-MP2: Total energy -78283.61915


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.
-5.521-3.0142.6-2.142-2.966-0.019
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 : 0.027 / q_NPA : -0.006
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].
3B35ASN00.0130.0012.191-5.252-3.1052.600-2.054-2.694-0.019
4B36SER00.0060.0044.0910.5130.8730.000-0.088-0.2720.000
5B37TYR0-0.033-0.0495.6510.0820.0820.0000.0000.0000.000
6B38LYS10.8290.9077.465-0.019-0.0190.0000.0000.0000.000
7B39MET0-0.030-0.0218.3830.1370.1370.0000.0000.0000.000
8B40ASP-1-0.806-0.8919.142-0.116-0.1160.0000.0000.0000.000
9B41TYR0-0.049-0.01611.2480.0630.0630.0000.0000.0000.000
10B42PRO0-0.052-0.03114.178-0.008-0.0080.0000.0000.0000.000
11B43GLU-1-0.811-0.88517.535-0.070-0.0700.0000.0000.0000.000
12B44MET00.0350.04013.961-0.015-0.0150.0000.0000.0000.000
13B45GLY00.0670.02417.116-0.021-0.0210.0000.0000.0000.000
14B46LEU0-0.050-0.00819.8960.0090.0090.0000.0000.0000.000
15B47CYS0-0.041-0.01922.478-0.016-0.0160.0000.0000.0000.000
16B48ILE00.0000.00524.8170.0120.0120.0000.0000.0000.000
17B49ILE00.0190.01728.089-0.005-0.0050.0000.0000.0000.000
18B50ILE0-0.018-0.01930.2260.0080.0080.0000.0000.0000.000
19B51ASN0-0.033-0.02633.435-0.006-0.0060.0000.0000.0000.000
20B52ASN0-0.035-0.01635.9980.0050.0050.0000.0000.0000.000
21B53LYS10.8690.91738.7990.0620.0620.0000.0000.0000.000
22B54ASN0-0.041-0.01440.8370.0040.0040.0000.0000.0000.000
23B67THR00.049-0.00136.1280.0020.0020.0000.0000.0000.000
24B68ASP-1-0.796-0.87035.827-0.070-0.0700.0000.0000.0000.000
25B69VAL00.0140.00535.483-0.002-0.0020.0000.0000.0000.000
26B70ASP-1-0.769-0.86532.366-0.104-0.1040.0000.0000.0000.000
27B71ALA00.009-0.00231.626-0.007-0.0070.0000.0000.0000.000
28B72ALA0-0.015-0.00132.070-0.002-0.0020.0000.0000.0000.000
29B73ASN00.0210.00129.875-0.005-0.0050.0000.0000.0000.000
30B74LEU00.0350.01726.648-0.008-0.0080.0000.0000.0000.000
31B75ARG10.8380.89326.8720.0780.0780.0000.0000.0000.000
32B76GLU-1-0.823-0.89927.568-0.113-0.1130.0000.0000.0000.000
33B77THR00.0320.01123.351-0.005-0.0050.0000.0000.0000.000
34B78PHE00.042-0.00320.517-0.007-0.0070.0000.0000.0000.000
35B79ARG10.9300.97022.6550.0800.0800.0000.0000.0000.000
36B80ASN0-0.058-0.01723.1620.0060.0060.0000.0000.0000.000
37B81LEU0-0.049-0.00818.154-0.006-0.0060.0000.0000.0000.000
38B82LYS10.8710.91614.6830.1860.1860.0000.0000.0000.000
39B83TYR0-0.020-0.01316.698-0.004-0.0040.0000.0000.0000.000
40B84GLU-1-0.795-0.87621.820-0.067-0.0670.0000.0000.0000.000
41B85VAL0-0.031-0.01924.8120.0000.0000.0000.0000.0000.000
42B86ARG10.6860.80627.0110.0870.0870.0000.0000.0000.000
43B87ASN00.0390.03630.154-0.006-0.0060.0000.0000.0000.000
44B88LYS10.9200.96232.7900.0680.0680.0000.0000.0000.000
45B89ASN00.0140.00035.577-0.008-0.0080.0000.0000.0000.000
46B90ASP-1-0.824-0.91438.526-0.056-0.0560.0000.0000.0000.000
47B91LEU00.0220.03635.9230.0020.0020.0000.0000.0000.000
48B92THR00.032-0.00639.954-0.003-0.0030.0000.0000.0000.000
49B93ARG10.8760.91438.9030.0450.0450.0000.0000.0000.000
50B94GLU-1-0.794-0.87538.696-0.049-0.0490.0000.0000.0000.000
51B95GLU-1-0.773-0.86039.040-0.050-0.0500.0000.0000.0000.000
52B96ILE0-0.020-0.00533.841-0.003-0.0030.0000.0000.0000.000
53B97VAL0-0.043-0.03434.416-0.004-0.0040.0000.0000.0000.000
54B98GLU-1-0.868-0.90635.197-0.042-0.0420.0000.0000.0000.000
55B99LEU00.002-0.00332.0260.0000.0000.0000.0000.0000.000
56B100MET0-0.026-0.02127.686-0.003-0.0030.0000.0000.0000.000
57B101ARG10.7410.84030.2840.0410.0410.0000.0000.0000.000
58B102ASP-1-0.778-0.84231.274-0.046-0.0460.0000.0000.0000.000
59B103VAL00.0250.01126.7630.0000.0000.0000.0000.0000.000
60B104SER0-0.091-0.04726.674-0.002-0.0020.0000.0000.0000.000
61B105LYS10.8500.90927.6710.0580.0580.0000.0000.0000.000
62B106GLU-1-0.726-0.80826.596-0.067-0.0670.0000.0000.0000.000
63B107ASP-1-0.823-0.88523.244-0.042-0.0420.0000.0000.0000.000
64B108HIS0-0.023-0.03220.467-0.013-0.0130.0000.0000.0000.000
65B109SER0-0.036-0.04219.046-0.015-0.0150.0000.0000.0000.000
66B110LYS10.8540.91217.7580.0430.0430.0000.0000.0000.000
67B111ARG10.7880.89017.9020.0800.0800.0000.0000.0000.000
68B112SER00.0350.00813.0770.0010.0010.0000.0000.0000.000
69B113SER0-0.013-0.00314.484-0.031-0.0310.0000.0000.0000.000
70B114PHE0-0.0050.00016.7760.0360.0360.0000.0000.0000.000
71B115VAL0-0.0010.01120.010-0.022-0.0220.0000.0000.0000.000
72B116CYS0-0.075-0.02722.3220.0220.0220.0000.0000.0000.000
73B117VAL00.013-0.00225.636-0.011-0.0110.0000.0000.0000.000
74B118LEU0-0.0080.00127.9560.0100.0100.0000.0000.0000.000
75B119LEU00.0000.00131.126-0.004-0.0040.0000.0000.0000.000
76B120SER0-0.011-0.02834.0100.0040.0040.0000.0000.0000.000
77B121HIS00.0810.05837.110-0.003-0.0030.0000.0000.0000.000
78B122GLY00.002-0.02835.938-0.003-0.0030.0000.0000.0000.000
79B123GLU-1-0.866-0.92336.268-0.073-0.0730.0000.0000.0000.000
80B124GLU-1-0.885-0.93433.943-0.089-0.0890.0000.0000.0000.000
81B125GLY0-0.058-0.03631.461-0.008-0.0080.0000.0000.0000.000
82B126ILE0-0.103-0.03931.353-0.004-0.0040.0000.0000.0000.000
83B127ILE00.0250.01232.8600.0000.0000.0000.0000.0000.000
84B128PHE0-0.030-0.02135.5990.0050.0050.0000.0000.0000.000
85B129GLY00.0400.02138.589-0.002-0.0020.0000.0000.0000.000
86B130THR0-0.027-0.02839.9570.0020.0020.0000.0000.0000.000
87B131ASN0-0.060-0.03343.1190.0030.0030.0000.0000.0000.000
88B132GLY0-0.009-0.00243.2600.0020.0020.0000.0000.0000.000
89B133PRO0-0.007-0.00340.011-0.002-0.0020.0000.0000.0000.000
90B134VAL0-0.023-0.02835.8080.0040.0040.0000.0000.0000.000
91B135ASP-1-0.813-0.90234.332-0.081-0.0810.0000.0000.0000.000
92B136LEU00.0390.02828.0960.0000.0000.0000.0000.0000.000
93B137LYS10.8940.92628.6520.0860.0860.0000.0000.0000.000
94B138LYS10.8700.93331.4140.0570.0570.0000.0000.0000.000
95B139ILE00.0040.01429.2050.0040.0040.0000.0000.0000.000
96B140THR00.0440.00626.2590.0040.0040.0000.0000.0000.000
97B141ASN00.0210.01227.017-0.008-0.0080.0000.0000.0000.000
98B142PHE0-0.060-0.02429.2610.0090.0090.0000.0000.0000.000
99B143PHE00.026-0.00323.8770.0040.0040.0000.0000.0000.000
100B144ARG10.7950.88223.3520.0650.0650.0000.0000.0000.000
101B145GLY00.0060.00721.4270.0040.0040.0000.0000.0000.000
102B146ASP-1-0.818-0.89622.207-0.052-0.0520.0000.0000.0000.000
103B147ARG10.8830.94525.2080.0600.0600.0000.0000.0000.000
104B148CYS0-0.014-0.00423.9120.0040.0040.0000.0000.0000.000
105B149ARG10.9730.98918.7350.0060.0060.0000.0000.0000.000
106B150SER00.0260.01620.886-0.002-0.0020.0000.0000.0000.000
107B151LEU00.0210.00118.713-0.011-0.0110.0000.0000.0000.000
108B152THR0-0.042-0.04118.300-0.021-0.0210.0000.0000.0000.000
109B153GLY00.0040.01514.6320.0200.0200.0000.0000.0000.000
110B154LYS10.8330.94513.2790.0690.0690.0000.0000.0000.000
111B155PRO00.0120.01013.4060.0390.0390.0000.0000.0000.000
112B156LYS10.7940.90816.0790.2330.2330.0000.0000.0000.000
113B157LEU0-0.022-0.01016.645-0.001-0.0010.0000.0000.0000.000
114B158PHE00.027-0.00320.6010.0220.0220.0000.0000.0000.000
115B159ILE0-0.0070.00321.875-0.004-0.0040.0000.0000.0000.000
116B160ILE00.007-0.01125.5910.0120.0120.0000.0000.0000.000
117B161GLN00.0220.01829.205-0.010-0.0100.0000.0000.0000.000
118B162ALA00.0470.04132.1290.0060.0060.0000.0000.0000.000
119B185HIS00.000-0.01335.7630.0000.0000.0000.0000.0000.000
120B186LYS10.9410.97732.1640.0770.0770.0000.0000.0000.000
121B187ILE00.0590.04026.9340.0020.0020.0000.0000.0000.000
122B188PRO0-0.022-0.01327.1150.0010.0010.0000.0000.0000.000
123B189VAL00.0210.02323.524-0.014-0.0140.0000.0000.0000.000
124B190GLU-1-0.797-0.88423.289-0.086-0.0860.0000.0000.0000.000
125B191ALA00.0320.00618.304-0.018-0.0180.0000.0000.0000.000
126B192ASP-1-0.824-0.88715.014-0.286-0.2860.0000.0000.0000.000
127B193PHE0-0.007-0.00317.143-0.007-0.0070.0000.0000.0000.000
128B194LEU00.004-0.00417.490-0.025-0.0250.0000.0000.0000.000
129B195TYR0-0.010-0.01920.4680.0150.0150.0000.0000.0000.000
130B196ALA00.0060.00422.316-0.011-0.0110.0000.0000.0000.000
131B197TYR0-0.028-0.02824.3450.0040.0040.0000.0000.0000.000
132B198SER00.0050.01228.1420.0000.0000.0000.0000.0000.000
133B199THR00.0220.00831.0460.0070.0070.0000.0000.0000.000
134B212GLY00.0200.00935.1830.0010.0010.0000.0000.0000.000
135B213SER0-0.056-0.06333.3350.0010.0010.0000.0000.0000.000
136B214TRP00.0490.01532.709-0.007-0.0070.0000.0000.0000.000
137B215PHE00.0430.04325.575-0.007-0.0070.0000.0000.0000.000
138B216ILE00.0040.00628.157-0.011-0.0110.0000.0000.0000.000
139B217GLN0-0.041-0.03128.558-0.003-0.0030.0000.0000.0000.000
140B218SER0-0.055-0.04727.486-0.006-0.0060.0000.0000.0000.000
141B219LEU00.0170.00522.154-0.011-0.0110.0000.0000.0000.000
142B220CYS0-0.023-0.00623.784-0.015-0.0150.0000.0000.0000.000
143B221ALA00.0020.01424.874-0.005-0.0050.0000.0000.0000.000
144B222MET0-0.043-0.01921.854-0.008-0.0080.0000.0000.0000.000
145B223LEU0-0.001-0.00718.968-0.020-0.0200.0000.0000.0000.000
146B224LYS10.8330.89220.4690.1070.1070.0000.0000.0000.000
147B225GLN00.0120.03022.2590.0050.0050.0000.0000.0000.000
148B226TYR0-0.010-0.03717.7340.0000.0000.0000.0000.0000.000
149B227ALA00.0280.02716.297-0.041-0.0410.0000.0000.0000.000
150B228ASP-1-0.845-0.90614.818-0.273-0.2730.0000.0000.0000.000
151B229LYS10.7830.86514.1520.2220.2220.0000.0000.0000.000
152B230LEU0-0.038-0.02112.728-0.046-0.0460.0000.0000.0000.000
153B231GLU-1-0.695-0.83710.117-0.640-0.6400.0000.0000.0000.000
154B232PHE00.023-0.00812.0720.1000.1000.0000.0000.0000.000
155B233MET00.0080.00314.2970.0890.0890.0000.0000.0000.000
156B234HIS0-0.0010.01812.9720.1010.1010.0000.0000.0000.000
157B235ILE0-0.050-0.01715.8680.0500.0500.0000.0000.0000.000
158B236LEU00.0220.00318.5910.0380.0380.0000.0000.0000.000
159B237THR0-0.014-0.01619.1760.0320.0320.0000.0000.0000.000
160B238ARG10.8640.93819.2760.2670.2670.0000.0000.0000.000
161B239VAL0-0.0170.00322.7130.0180.0180.0000.0000.0000.000
162B240ASN00.0160.00024.3270.0140.0140.0000.0000.0000.000
163B241ARG10.9820.99423.4500.1890.1890.0000.0000.0000.000
164B242LYS10.8870.97527.0210.1340.1340.0000.0000.0000.000
165B243VAL00.0220.00628.7540.0090.0090.0000.0000.0000.000
166B244ALA0-0.0030.00330.1320.0080.0080.0000.0000.0000.000
167B245THR00.022-0.00830.8960.0070.0070.0000.0000.0000.000
168B246GLU-1-0.846-0.93831.993-0.109-0.1090.0000.0000.0000.000
169B247PHE0-0.036-0.03633.9840.0070.0070.0000.0000.0000.000
170B248GLU-1-1.003-0.98133.817-0.100-0.1000.0000.0000.0000.000
171B249SER0-0.080-0.02637.5610.0060.0060.0000.0000.0000.000
172B261GLN00.0120.00434.736-0.002-0.0020.0000.0000.0000.000
173B262ILE0-0.047-0.03128.097-0.003-0.0030.0000.0000.0000.000
174B263PRO0-0.0230.00026.7040.0030.0030.0000.0000.0000.000
175B264CYS0-0.0070.01727.171-0.011-0.0110.0000.0000.0000.000
176B265ILE00.014-0.00820.356-0.007-0.0070.0000.0000.0000.000
177B266VAL0-0.008-0.00322.9950.0010.0010.0000.0000.0000.000
178B267SER00.0160.00116.470-0.001-0.0010.0000.0000.0000.000
179B268MET0-0.026-0.00618.6820.0180.0180.0000.0000.0000.000
180B269LEU0-0.059-0.01913.4730.0130.0130.0000.0000.0000.000
181B270THR0-0.036-0.03012.640-0.040-0.0400.0000.0000.0000.000
182B271LYS10.7880.9076.8830.7360.7360.0000.0000.0000.000
183B272GLU-1-0.818-0.8866.069-1.847-1.8470.0000.0000.0000.000
184B273LEU0-0.035-0.0308.773-0.084-0.0840.0000.0000.0000.000
185B274TYR0-0.029-0.0256.4090.2420.2420.0000.0000.0000.000
186B275PHE0-0.021-0.02311.0760.0130.0130.0000.0000.0000.000
187B276TYR0-0.046-0.01710.5630.0600.0600.0000.0000.0000.000
188B277HIS00.0540.0388.762-0.059-0.0590.0000.0000.0000.000