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: 94932

Calculation Name: 1K88-B-Xray372

Preferred Name: Caspase-7

Target Type: SINGLE PROTEIN

Ligand Name:

ligand 3-letter code:

PDB ID: 1K88

Chain ID: B

ChEMBL ID: CHEMBL3468

UniProt ID: P55210

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 234
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -3053880.123779
FMO2-HF: Nuclear repulsion 2958609.030463
FMO2-HF: Total energy -95271.093317
FMO2-MP2: Total energy -95543.083952


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:56:PRO)


Summations of interaction energy for fragment #1(B:56:PRO)
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.
-24.366-17.1496.263-5.574-7.9050.007
Interaction energy analysis for fragmet #1(B:56:PRO)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.034 / q_NPA : 0.011
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].
3B58TYR00.003-0.0062.314-12.647-8.8893.861-2.987-4.6320.024
4B59GLN00.0180.0302.351-9.533-6.1462.404-2.577-3.214-0.017
5B60TYR0-0.004-0.0604.7880.1120.075-0.001-0.0070.0460.000
6B61ASN0-0.0080.0016.213-0.557-0.5570.0000.0000.0000.000
7B62MET00.0380.0157.7740.1990.1990.0000.0000.0000.000
8B63ASN0-0.063-0.0229.5400.0190.0190.0000.0000.0000.000
9B64PHE0-0.031-0.01811.3330.0800.0800.0000.0000.0000.000
10B65GLU-1-0.849-0.89614.728-0.143-0.1430.0000.0000.0000.000
11B66LYS10.8480.92017.5070.1330.1330.0000.0000.0000.000
12B67LEU00.0330.03414.6300.0000.0000.0000.0000.0000.000
13B68GLY00.1000.03616.1110.0150.0150.0000.0000.0000.000
14B69LYS10.8110.89818.8990.0470.0470.0000.0000.0000.000
15B70CYS0-0.047-0.01321.7510.0080.0080.0000.0000.0000.000
16B71ILE0-0.0100.00023.6300.0010.0010.0000.0000.0000.000
17B72ILE00.0400.02826.7370.0060.0060.0000.0000.0000.000
18B73ILE0-0.005-0.01529.0810.0020.0020.0000.0000.0000.000
19B74ASN00.0080.00332.3740.0030.0030.0000.0000.0000.000
20B75ASN0-0.006-0.01534.806-0.002-0.0020.0000.0000.0000.000
21B76LYS10.8600.92237.6400.0300.0300.0000.0000.0000.000
22B77ASN0-0.061-0.07040.1150.0010.0010.0000.0000.0000.000
23B78PHE0-0.023-0.00839.1770.0000.0000.0000.0000.0000.000
24B79ASP-1-0.801-0.88145.024-0.006-0.0060.0000.0000.0000.000
25B80LYS10.9840.97948.2810.0050.0050.0000.0000.0000.000
26B81VAL0-0.021-0.00750.2480.0010.0010.0000.0000.0000.000
27B82THR0-0.004-0.01244.9870.0010.0010.0000.0000.0000.000
28B83GLY0-0.0010.01047.1450.0010.0010.0000.0000.0000.000
29B84MET0-0.0370.00441.9650.0000.0000.0000.0000.0000.000
30B85GLY00.0090.00145.172-0.001-0.0010.0000.0000.0000.000
31B86VAL0-0.035-0.02143.6780.0000.0000.0000.0000.0000.000
32B87ARG10.9010.95834.8430.0180.0180.0000.0000.0000.000
33B88ASN0-0.038-0.03739.701-0.005-0.0050.0000.0000.0000.000
34B89GLY00.0820.04538.3890.0010.0010.0000.0000.0000.000
35B90THR00.0410.01335.383-0.003-0.0030.0000.0000.0000.000
36B91ASP-1-0.819-0.89034.902-0.037-0.0370.0000.0000.0000.000
37B92LYS10.7520.86233.9330.0540.0540.0000.0000.0000.000
38B93ASP-1-0.690-0.84331.356-0.044-0.0440.0000.0000.0000.000
39B94ALA00.0320.00730.265-0.006-0.0060.0000.0000.0000.000
40B95GLU-1-0.843-0.90530.467-0.077-0.0770.0000.0000.0000.000
41B96ALA00.0340.01828.958-0.007-0.0070.0000.0000.0000.000
42B97LEU00.0460.00525.351-0.010-0.0100.0000.0000.0000.000
43B98PHE0-0.032-0.01825.629-0.011-0.0110.0000.0000.0000.000
44B99LYS10.7910.90826.4480.0740.0740.0000.0000.0000.000
45B100CYS00.0200.03622.720-0.012-0.0120.0000.0000.0000.000
46B101PHE00.048-0.00220.079-0.017-0.0170.0000.0000.0000.000
47B102ARG10.9590.98521.1650.1110.1110.0000.0000.0000.000
48B103SER0-0.117-0.07722.311-0.017-0.0170.0000.0000.0000.000
49B104LEU0-0.045-0.01716.668-0.021-0.0210.0000.0000.0000.000
50B105GLY00.0300.02317.440-0.035-0.0350.0000.0000.0000.000
51B106PHE0-0.049-0.03317.0730.0040.0040.0000.0000.0000.000
52B107ASP-1-0.860-0.93820.641-0.122-0.1220.0000.0000.0000.000
53B108VAL0-0.068-0.04023.7930.0140.0140.0000.0000.0000.000
54B109ILE0-0.029-0.00625.8400.0030.0030.0000.0000.0000.000
55B110VAL0-0.014-0.01228.9940.0020.0020.0000.0000.0000.000
56B111TYR00.0070.00630.8010.0020.0020.0000.0000.0000.000
57B112ASN00.023-0.00434.496-0.001-0.0010.0000.0000.0000.000
58B113ASP-1-0.766-0.85637.361-0.018-0.0180.0000.0000.0000.000
59B114CYS0-0.030-0.00436.6500.0010.0010.0000.0000.0000.000
60B115SER00.0240.02038.7130.0010.0010.0000.0000.0000.000
61B116CYS0-0.014-0.01138.556-0.001-0.0010.0000.0000.0000.000
62B117ALA00.0040.00738.1900.0010.0010.0000.0000.0000.000
63B118LYS10.8400.92336.0620.0100.0100.0000.0000.0000.000
64B119MET00.0180.02334.264-0.002-0.0020.0000.0000.0000.000
65B120GLN00.0430.01333.6120.0000.0000.0000.0000.0000.000
66B121ASP-1-0.840-0.89734.097-0.003-0.0030.0000.0000.0000.000
67B122LEU0-0.038-0.00931.3960.0000.0000.0000.0000.0000.000
68B123LEU00.0230.00627.988-0.003-0.0030.0000.0000.0000.000
69B124LYS10.8030.89929.249-0.012-0.0120.0000.0000.0000.000
70B125LYS10.8920.93630.5080.0020.0020.0000.0000.0000.000
71B126ALA00.0320.02726.755-0.001-0.0010.0000.0000.0000.000
72B127SER0-0.078-0.04926.0230.0010.0010.0000.0000.0000.000
73B128GLU-1-0.808-0.89326.9460.0170.0170.0000.0000.0000.000
74B129GLU-1-0.805-0.86726.286-0.042-0.0420.0000.0000.0000.000
75B130ASP-1-0.811-0.89523.723-0.016-0.0160.0000.0000.0000.000
76B131HIS0-0.044-0.03020.166-0.020-0.0200.0000.0000.0000.000
77B132THR0-0.027-0.04419.360-0.005-0.0050.0000.0000.0000.000
78B133ASN0-0.060-0.04918.202-0.004-0.0040.0000.0000.0000.000
79B134ALA00.0110.00417.469-0.030-0.0300.0000.0000.0000.000
80B135ALA00.0250.01612.2430.0230.0230.0000.0000.0000.000
81B136CYS0-0.094-0.04913.8690.0370.0370.0000.0000.0000.000
82B137PHE00.0180.01315.969-0.004-0.0040.0000.0000.0000.000
83B138ALA00.0100.01119.0490.0090.0090.0000.0000.0000.000
84B139CYS0-0.076-0.03321.1650.0010.0010.0000.0000.0000.000
85B140ILE00.001-0.00123.5770.0040.0040.0000.0000.0000.000
86B141LEU00.0000.00426.804-0.001-0.0010.0000.0000.0000.000
87B142LEU0-0.035-0.01729.8660.0000.0000.0000.0000.0000.000
88B143SER0-0.029-0.04432.745-0.001-0.0010.0000.0000.0000.000
89B144HIS00.0230.01235.7550.0010.0010.0000.0000.0000.000
90B145GLY0-0.044-0.04335.8300.0010.0010.0000.0000.0000.000
91B146GLU-1-0.815-0.87436.8390.0140.0140.0000.0000.0000.000
92B147GLU-1-0.779-0.85835.8250.0320.0320.0000.0000.0000.000
93B148ASN0-0.049-0.03433.6770.0060.0060.0000.0000.0000.000
94B149VAL0-0.010-0.02434.7590.0010.0010.0000.0000.0000.000
95B150ILE00.0050.00632.847-0.002-0.0020.0000.0000.0000.000
96B151TYR00.015-0.01036.0410.0010.0010.0000.0000.0000.000
97B152GLY00.0310.02437.853-0.003-0.0030.0000.0000.0000.000
98B153LYS10.7850.86739.6750.0090.0090.0000.0000.0000.000
99B154ASP-1-0.793-0.89642.5190.0010.0010.0000.0000.0000.000
100B155GLY00.0130.01143.1240.0010.0010.0000.0000.0000.000
101B156VAL00.0180.01239.190-0.001-0.0010.0000.0000.0000.000
102B157THR00.0210.00336.5880.0000.0000.0000.0000.0000.000
103B158PRO0-0.009-0.00735.166-0.001-0.0010.0000.0000.0000.000
104B159ILE00.0470.02829.1930.0000.0000.0000.0000.0000.000
105B160LYS10.8650.92829.201-0.082-0.0820.0000.0000.0000.000
106B161ASP-1-0.813-0.90530.2020.0470.0470.0000.0000.0000.000
107B162LEU00.0120.03130.806-0.003-0.0030.0000.0000.0000.000
108B163THR0-0.010-0.01826.0780.0000.0000.0000.0000.0000.000
109B164ALA0-0.018-0.02226.3570.0060.0060.0000.0000.0000.000
110B165HIS0-0.022-0.00328.3520.0090.0090.0000.0000.0000.000
111B166PHE00.0700.01223.1310.0020.0020.0000.0000.0000.000
112B167ARG10.7750.91123.029-0.113-0.1130.0000.0000.0000.000
113B168GLY00.1120.04522.759-0.011-0.0110.0000.0000.0000.000
114B169ALA0-0.034-0.02123.402-0.006-0.0060.0000.0000.0000.000
115B170ARG10.8150.88826.606-0.063-0.0630.0000.0000.0000.000
116B171CYS0-0.0090.01523.820-0.009-0.0090.0000.0000.0000.000
117B172LYS10.8600.91422.712-0.074-0.0740.0000.0000.0000.000
118B173THR00.0280.02021.2120.0130.0130.0000.0000.0000.000
119B174LEU00.0150.00418.499-0.016-0.0160.0000.0000.0000.000
120B175LEU0-0.018-0.00318.4620.0220.0220.0000.0000.0000.000
121B176GLU-1-0.965-0.97813.5490.2470.2470.0000.0000.0000.000
122B177LYS10.8210.95212.8340.0450.0450.0000.0000.0000.000
123B178PRO0-0.039-0.00612.0380.0260.0260.0000.0000.0000.000
124B179LYS10.8180.92014.894-0.171-0.1710.0000.0000.0000.000
125B180LEU0-0.005-0.00715.5660.0200.0200.0000.0000.0000.000
126B181PHE0-0.009-0.00919.631-0.016-0.0160.0000.0000.0000.000
127B182PHE00.0410.01518.9350.0100.0100.0000.0000.0000.000
128B183ILE0-0.015-0.01924.548-0.002-0.0020.0000.0000.0000.000
129B184GLN00.0430.05328.153-0.001-0.0010.0000.0000.0000.000
130B185ALA00.0110.00530.667-0.002-0.0020.0000.0000.0000.000
131B186ALA00.0220.00333.032-0.001-0.0010.0000.0000.0000.000
132B187ARG10.8230.89135.816-0.020-0.0200.0000.0000.0000.000
133B188GLY00.0120.00039.198-0.002-0.0020.0000.0000.0000.000
134B189THR00.0200.02241.9830.0010.0010.0000.0000.0000.000
135B204ASP-1-0.801-0.89437.8390.0180.0180.0000.0000.0000.000
136B205THR00.0010.00532.971-0.002-0.0020.0000.0000.0000.000
137B206ASP-1-0.797-0.86732.0340.0290.0290.0000.0000.0000.000
138B207ALA0-0.008-0.00632.7430.0030.0030.0000.0000.0000.000
139B208ASN00.0490.01427.9390.0010.0010.0000.0000.0000.000
140B209PRO0-0.013-0.01527.8840.0100.0100.0000.0000.0000.000
141B210ARG10.9810.99120.229-0.178-0.1780.0000.0000.0000.000
142B211TYR00.0340.01027.698-0.002-0.0020.0000.0000.0000.000
143B212LYS10.8000.91430.557-0.051-0.0510.0000.0000.0000.000
144B213ILE00.0750.03924.328-0.005-0.0050.0000.0000.0000.000
145B214PRO0-0.046-0.01324.4390.0070.0070.0000.0000.0000.000
146B215VAL0-0.023-0.01023.2530.0070.0070.0000.0000.0000.000
147B216GLU-1-0.779-0.89121.9040.1320.1320.0000.0000.0000.000
148B217ALA00.0510.02416.863-0.001-0.0010.0000.0000.0000.000
149B218ASP-1-0.747-0.83213.8300.3590.3590.0000.0000.0000.000
150B219PHE0-0.0220.00016.132-0.055-0.0550.0000.0000.0000.000
151B220LEU0-0.004-0.01315.6640.0320.0320.0000.0000.0000.000
152B221PHE00.007-0.01118.828-0.024-0.0240.0000.0000.0000.000
153B222ALA00.0340.01821.3940.0090.0090.0000.0000.0000.000
154B223TYR0-0.087-0.04623.286-0.012-0.0120.0000.0000.0000.000
155B224SER0-0.003-0.01127.0760.0040.0040.0000.0000.0000.000
156B225THR0-0.027-0.03529.1770.0010.0010.0000.0000.0000.000
157B226VAL00.0350.01431.070-0.001-0.0010.0000.0000.0000.000
158B227PRO00.0260.02233.631-0.004-0.0040.0000.0000.0000.000
159B228GLY0-0.036-0.01335.991-0.003-0.0030.0000.0000.0000.000
160B229TYR0-0.071-0.06236.652-0.002-0.0020.0000.0000.0000.000
161B230TYR00.0350.02539.8390.0010.0010.0000.0000.0000.000
162B231SER0-0.065-0.05440.500-0.005-0.0050.0000.0000.0000.000
163B232TRP00.0590.04942.5010.0020.0020.0000.0000.0000.000
164B233ARG10.8580.91243.6060.0250.0250.0000.0000.0000.000
165B234SER0-0.0050.01843.1930.0000.0000.0000.0000.0000.000
166B235PRO00.0520.01638.6490.0000.0000.0000.0000.0000.000
167B236GLY00.0080.00740.0440.0020.0020.0000.0000.0000.000
168B237ARG10.9230.95637.4650.0350.0350.0000.0000.0000.000
169B238GLY00.0230.02434.638-0.004-0.0040.0000.0000.0000.000
170B239SER0-0.048-0.05231.6200.0010.0010.0000.0000.0000.000
171B240TRP00.0520.02231.644-0.007-0.0070.0000.0000.0000.000
172B241PHE00.0470.03224.327-0.007-0.0070.0000.0000.0000.000
173B242VAL00.0040.00826.894-0.007-0.0070.0000.0000.0000.000
174B243GLN0-0.003-0.01927.215-0.014-0.0140.0000.0000.0000.000
175B244ALA0-0.012-0.00225.972-0.011-0.0110.0000.0000.0000.000
176B245LEU0-0.003-0.00521.136-0.012-0.0120.0000.0000.0000.000
177B246CYS0-0.055-0.03722.731-0.015-0.0150.0000.0000.0000.000
178B247SER0-0.040-0.03624.041-0.012-0.0120.0000.0000.0000.000
179B248ILE0-0.015-0.00219.408-0.016-0.0160.0000.0000.0000.000
180B249LEU00.0070.00217.718-0.028-0.0280.0000.0000.0000.000
181B250GLU-1-0.809-0.91619.792-0.202-0.2020.0000.0000.0000.000
182B251GLU-1-0.822-0.87421.100-0.150-0.1500.0000.0000.0000.000
183B252HIS00.013-0.00716.9350.0280.0280.0000.0000.0000.000
184B253GLY0-0.0060.00215.669-0.038-0.0380.0000.0000.0000.000
185B254LYS10.7910.90914.1970.2370.2370.0000.0000.0000.000
186B255ASP-1-0.834-0.91012.130-0.458-0.4580.0000.0000.0000.000
187B256LEU0-0.054-0.01411.397-0.066-0.0660.0000.0000.0000.000
188B257GLU-1-0.735-0.8578.6000.0210.0210.0000.0000.0000.000
189B258ILE00.008-0.01110.9370.0720.0720.0000.0000.0000.000
190B259MET0-0.004-0.00512.9950.0220.0220.0000.0000.0000.000
191B260GLN00.0200.02910.079-0.031-0.0310.0000.0000.0000.000
192B261ILE0-0.020-0.00515.0090.0150.0150.0000.0000.0000.000
193B262LEU00.026-0.00717.1060.0150.0150.0000.0000.0000.000
194B263THR0-0.030-0.01717.5190.0190.0190.0000.0000.0000.000
195B264ARG10.8860.94818.0110.1840.1840.0000.0000.0000.000
196B265VAL0-0.039-0.00421.1150.0030.0030.0000.0000.0000.000
197B266ASN00.003-0.01322.397-0.001-0.0010.0000.0000.0000.000
198B267ASP-1-0.811-0.89223.826-0.034-0.0340.0000.0000.0000.000
199B268ARG10.7590.86324.8490.1010.1010.0000.0000.0000.000
200B269VAL00.001-0.00927.0540.0010.0010.0000.0000.0000.000
201B270ALA00.0060.00128.3290.0030.0030.0000.0000.0000.000
202B271ARG10.8280.88426.5620.0540.0540.0000.0000.0000.000
203B272HIS0-0.077-0.02531.163-0.006-0.0060.0000.0000.0000.000
204B273PHE00.0180.02533.3350.0000.0000.0000.0000.0000.000
205B274GLU-1-0.825-0.92935.132-0.018-0.0180.0000.0000.0000.000
206B275SER0-0.084-0.03134.9100.0030.0030.0000.0000.0000.000
207B276GLN0-0.010-0.03134.8770.0010.0010.0000.0000.0000.000
208B277SER00.0310.02538.7360.0010.0010.0000.0000.0000.000
209B278ASP-1-0.871-0.93441.6360.0000.0000.0000.0000.0000.000
210B279ASP-1-0.885-0.93545.007-0.011-0.0110.0000.0000.0000.000
211B280PRO00.008-0.01645.4410.0000.0000.0000.0000.0000.000
212B281HIS10.7790.89845.4620.0120.0120.0000.0000.0000.000
213B282PHE0-0.011-0.00840.841-0.002-0.0020.0000.0000.0000.000
214B283HIS0-0.0010.02141.1740.0010.0010.0000.0000.0000.000
215B284GLU-1-0.814-0.89540.537-0.004-0.0040.0000.0000.0000.000
216B285LYS10.7610.85439.182-0.010-0.0100.0000.0000.0000.000
217B286LYS10.8270.92433.8300.0020.0020.0000.0000.0000.000
218B287GLN0-0.028-0.01733.1200.0020.0020.0000.0000.0000.000
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