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: LZ419

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 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 234
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -3051007.763197
FMO2-HF: Nuclear repulsion 2955737.825423
FMO2-HF: Total energy -95269.937774
FMO2-MP2: Total energy -95542.104401


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.
-18.408-11.3934.761-5.16-6.6170.004
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 : 0.068 / q_NPA : 0.016
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].
3B58TYR0-0.033-0.0332.607-9.242-4.6871.226-2.218-3.5630.026
4B59GLN00.0220.0212.295-6.894-4.4163.536-2.938-3.077-0.022
5B60TYR0-0.005-0.0484.831-0.257-0.275-0.001-0.0040.0230.000
6B61ASN00.0190.0156.843-0.405-0.4050.0000.0000.0000.000
7B62MET00.0320.0138.0460.1950.1950.0000.0000.0000.000
8B63ASN0-0.064-0.0249.7270.0010.0010.0000.0000.0000.000
9B64PHE0-0.043-0.02111.5140.0720.0720.0000.0000.0000.000
10B65GLU-1-0.875-0.91315.013-0.145-0.1450.0000.0000.0000.000
11B66LYS10.8900.94618.3500.1310.1310.0000.0000.0000.000
12B67LEU00.0520.03514.877-0.001-0.0010.0000.0000.0000.000
13B68GLY00.0960.03916.5990.0100.0100.0000.0000.0000.000
14B69LYS10.7930.88719.3720.0590.0590.0000.0000.0000.000
15B70CYS0-0.041-0.00921.8920.0060.0060.0000.0000.0000.000
16B71ILE0-0.016-0.00923.6550.0030.0030.0000.0000.0000.000
17B72ILE00.0300.01526.6680.0030.0030.0000.0000.0000.000
18B73ILE0-0.001-0.00129.1270.0020.0020.0000.0000.0000.000
19B74ASN00.003-0.00332.2610.0020.0020.0000.0000.0000.000
20B75ASN0-0.018-0.01034.607-0.002-0.0020.0000.0000.0000.000
21B76LYS10.8720.92637.6200.0320.0320.0000.0000.0000.000
22B77ASN0-0.079-0.07940.2460.0020.0020.0000.0000.0000.000
23B78PHE0-0.011-0.00739.1610.0000.0000.0000.0000.0000.000
24B79ASP-1-0.812-0.88744.893-0.011-0.0110.0000.0000.0000.000
25B80LYS11.0060.98847.9800.0070.0070.0000.0000.0000.000
26B81VAL0-0.049-0.02750.1200.0010.0010.0000.0000.0000.000
27B82THR0-0.007-0.00745.0590.0010.0010.0000.0000.0000.000
28B83GLY00.0040.01547.2750.0010.0010.0000.0000.0000.000
29B84MET0-0.0240.01142.2500.0000.0000.0000.0000.0000.000
30B85GLY00.0060.00445.223-0.001-0.0010.0000.0000.0000.000
31B86VAL0-0.034-0.02443.780-0.001-0.0010.0000.0000.0000.000
32B87ARG10.8860.95934.9560.0230.0230.0000.0000.0000.000
33B88ASN0-0.012-0.02140.104-0.004-0.0040.0000.0000.0000.000
34B89GLY00.0630.02738.3990.0010.0010.0000.0000.0000.000
35B90THR00.0410.01835.527-0.003-0.0030.0000.0000.0000.000
36B91ASP-1-0.796-0.88534.901-0.039-0.0390.0000.0000.0000.000
37B92LYS10.8260.93034.2910.0550.0550.0000.0000.0000.000
38B93ASP-1-0.715-0.84831.519-0.048-0.0480.0000.0000.0000.000
39B94ALA0-0.0010.00230.523-0.006-0.0060.0000.0000.0000.000
40B95GLU-1-0.870-0.95130.598-0.077-0.0770.0000.0000.0000.000
41B96ALA00.0080.01729.138-0.007-0.0070.0000.0000.0000.000
42B97LEU00.0760.02225.513-0.010-0.0100.0000.0000.0000.000
43B98PHE0-0.017-0.00725.658-0.011-0.0110.0000.0000.0000.000
44B99LYS10.8050.90626.4900.0720.0720.0000.0000.0000.000
45B100CYS0-0.0060.01722.905-0.011-0.0110.0000.0000.0000.000
46B101PHE00.0610.00020.030-0.017-0.0170.0000.0000.0000.000
47B102ARG10.9630.98921.6070.1060.1060.0000.0000.0000.000
48B103SER0-0.115-0.06822.193-0.019-0.0190.0000.0000.0000.000
49B104LEU0-0.053-0.02916.875-0.019-0.0190.0000.0000.0000.000
50B105GLY00.0220.01917.624-0.033-0.0330.0000.0000.0000.000
51B106PHE0-0.045-0.02717.0140.0020.0020.0000.0000.0000.000
52B107ASP-1-0.895-0.94021.015-0.126-0.1260.0000.0000.0000.000
53B108VAL0-0.066-0.05324.2370.0100.0100.0000.0000.0000.000
54B109ILE0-0.023-0.00226.3730.0040.0040.0000.0000.0000.000
55B110VAL0-0.015-0.01029.5120.0020.0020.0000.0000.0000.000
56B111TYR0-0.002-0.00330.7490.0020.0020.0000.0000.0000.000
57B112ASN00.027-0.00534.656-0.001-0.0010.0000.0000.0000.000
58B113ASP-1-0.769-0.85037.472-0.023-0.0230.0000.0000.0000.000
59B114CYS0-0.046-0.01336.9670.0010.0010.0000.0000.0000.000
60B115SER00.0360.02439.0150.0010.0010.0000.0000.0000.000
61B116CYS00.025-0.00138.828-0.001-0.0010.0000.0000.0000.000
62B117ALA00.0010.00238.2190.0000.0000.0000.0000.0000.000
63B118LYS10.8350.92336.2670.0180.0180.0000.0000.0000.000
64B119MET00.0310.02734.146-0.003-0.0030.0000.0000.0000.000
65B120GLN00.0630.01933.630-0.001-0.0010.0000.0000.0000.000
66B121ASP-1-0.872-0.92034.049-0.013-0.0130.0000.0000.0000.000
67B122LEU0-0.051-0.01731.575-0.001-0.0010.0000.0000.0000.000
68B123LEU00.0190.00928.003-0.003-0.0030.0000.0000.0000.000
69B124LYS10.8040.90229.411-0.002-0.0020.0000.0000.0000.000
70B125LYS10.9390.96330.5860.0110.0110.0000.0000.0000.000
71B126ALA00.0540.04727.032-0.002-0.0020.0000.0000.0000.000
72B127SER0-0.110-0.06126.174-0.002-0.0020.0000.0000.0000.000
73B128GLU-1-0.815-0.90727.2550.0040.0040.0000.0000.0000.000
74B129GLU-1-0.828-0.87226.484-0.052-0.0520.0000.0000.0000.000
75B130ASP-1-0.813-0.89423.965-0.039-0.0390.0000.0000.0000.000
76B131HIS0-0.047-0.04320.412-0.019-0.0190.0000.0000.0000.000
77B132THR0-0.002-0.04219.532-0.010-0.0100.0000.0000.0000.000
78B133ASN0-0.096-0.05618.493-0.008-0.0080.0000.0000.0000.000
79B134ALA00.0220.00617.815-0.022-0.0220.0000.0000.0000.000
80B135ALA00.0050.01312.5360.0130.0130.0000.0000.0000.000
81B136CYS0-0.072-0.04214.1110.0280.0280.0000.0000.0000.000
82B137PHE00.0210.01416.0090.0000.0000.0000.0000.0000.000
83B138ALA00.0050.01219.3780.0100.0100.0000.0000.0000.000
84B139CYS0-0.054-0.01221.1530.0020.0020.0000.0000.0000.000
85B140ILE00.0130.00323.5970.0050.0050.0000.0000.0000.000
86B141LEU0-0.029-0.01626.7010.0010.0010.0000.0000.0000.000
87B142LEU00.0050.01229.6860.0020.0020.0000.0000.0000.000
88B143SER0-0.013-0.03632.722-0.001-0.0010.0000.0000.0000.000
89B144HIS00.0320.02335.9750.0010.0010.0000.0000.0000.000
90B145GLY0-0.026-0.02736.1390.0000.0000.0000.0000.0000.000
91B146GLU-1-0.814-0.87337.2080.0080.0080.0000.0000.0000.000
92B147GLU-1-0.784-0.85836.1860.0230.0230.0000.0000.0000.000
93B148ASN0-0.062-0.05534.0630.0040.0040.0000.0000.0000.000
94B149VAL0-0.005-0.02535.1510.0010.0010.0000.0000.0000.000
95B150ILE00.0040.00532.926-0.002-0.0020.0000.0000.0000.000
96B151TYR0-0.008-0.02836.1740.0010.0010.0000.0000.0000.000
97B152GLY00.0310.02837.975-0.003-0.0030.0000.0000.0000.000
98B153LYS10.8100.86539.7300.0140.0140.0000.0000.0000.000
99B154ASP-1-0.789-0.89242.792-0.005-0.0050.0000.0000.0000.000
100B155GLY0-0.007-0.00443.0200.0020.0020.0000.0000.0000.000
101B156VAL00.0190.01639.519-0.001-0.0010.0000.0000.0000.000
102B157THR00.0220.01236.7420.0010.0010.0000.0000.0000.000
103B158PRO00.0080.00035.385-0.001-0.0010.0000.0000.0000.000
104B159ILE00.0820.03529.5380.0000.0000.0000.0000.0000.000
105B160LYS10.8660.92829.919-0.060-0.0600.0000.0000.0000.000
106B161ASP-1-0.886-0.95230.4970.0300.0300.0000.0000.0000.000
107B162LEU0-0.0220.00130.604-0.001-0.0010.0000.0000.0000.000
108B163THR00.008-0.00825.9770.0000.0000.0000.0000.0000.000
109B164ALA0-0.026-0.01526.5270.0030.0030.0000.0000.0000.000
110B165HIS0-0.065-0.03327.7550.0080.0080.0000.0000.0000.000
111B166PHE00.0820.02423.2150.0000.0000.0000.0000.0000.000
112B167ARG10.8470.95323.190-0.077-0.0770.0000.0000.0000.000
113B168GLY00.1150.03522.738-0.007-0.0070.0000.0000.0000.000
114B169ALA0-0.095-0.05323.393-0.009-0.0090.0000.0000.0000.000
115B170ARG10.8850.92926.993-0.042-0.0420.0000.0000.0000.000
116B171CYS00.0600.04824.010-0.010-0.0100.0000.0000.0000.000
117B172LYS10.8870.92722.802-0.049-0.0490.0000.0000.0000.000
118B173THR00.0250.02321.2960.0070.0070.0000.0000.0000.000
119B174LEU0-0.0020.00318.713-0.015-0.0150.0000.0000.0000.000
120B175LEU0-0.021-0.00118.2570.0130.0130.0000.0000.0000.000
121B176GLU-1-0.959-0.97313.6920.1830.1830.0000.0000.0000.000
122B177LYS10.8290.95213.1890.0700.0700.0000.0000.0000.000
123B178PRO0-0.040-0.00411.9830.0290.0290.0000.0000.0000.000
124B179LYS10.8360.92915.011-0.100-0.1000.0000.0000.0000.000
125B180LEU0-0.008-0.01215.5540.0180.0180.0000.0000.0000.000
126B181PHE00.0150.00019.585-0.011-0.0110.0000.0000.0000.000
127B182PHE00.0420.01318.9260.0080.0080.0000.0000.0000.000
128B183ILE0-0.027-0.02024.561-0.002-0.0020.0000.0000.0000.000
129B184GLN00.0260.01528.188-0.002-0.0020.0000.0000.0000.000
130B185ALA0-0.003-0.00430.801-0.002-0.0020.0000.0000.0000.000
131B186ALA00.0510.00333.861-0.001-0.0010.0000.0000.0000.000
132B187ARG10.8430.90636.277-0.014-0.0140.0000.0000.0000.000
133B188GLY0-0.018-0.01839.528-0.002-0.0020.0000.0000.0000.000
134B189THR00.0230.02642.4430.0010.0010.0000.0000.0000.000
135B204ASP-1-0.837-0.92037.7890.0130.0130.0000.0000.0000.000
136B205THR0-0.039-0.01632.9510.0000.0000.0000.0000.0000.000
137B206ASP-1-0.810-0.89432.5150.0180.0180.0000.0000.0000.000
138B207ALA0-0.017-0.00832.9180.0030.0030.0000.0000.0000.000
139B208ASN00.0360.00228.102-0.002-0.0020.0000.0000.0000.000
140B209PRO00.0340.00428.2850.0060.0060.0000.0000.0000.000
141B210ARG10.9520.99120.487-0.137-0.1370.0000.0000.0000.000
142B211TYR00.013-0.01527.953-0.004-0.0040.0000.0000.0000.000
143B212LYS10.8110.95530.590-0.037-0.0370.0000.0000.0000.000
144B213ILE00.0690.01224.814-0.005-0.0050.0000.0000.0000.000
145B214PRO0-0.077-0.01824.7600.0080.0080.0000.0000.0000.000
146B215VAL0-0.020-0.02023.4710.0060.0060.0000.0000.0000.000
147B216GLU-1-0.857-0.92421.5870.0980.0980.0000.0000.0000.000
148B217ALA00.0410.01516.928-0.002-0.0020.0000.0000.0000.000
149B218ASP-1-0.768-0.84914.0580.2330.2330.0000.0000.0000.000
150B219PHE0-0.0150.00916.384-0.046-0.0460.0000.0000.0000.000
151B220LEU00.003-0.01116.1340.0240.0240.0000.0000.0000.000
152B221PHE0-0.020-0.01719.387-0.022-0.0220.0000.0000.0000.000
153B222ALA00.0350.02621.7350.0080.0080.0000.0000.0000.000
154B223TYR0-0.041-0.01123.603-0.010-0.0100.0000.0000.0000.000
155B224SER0-0.001-0.00627.3470.0030.0030.0000.0000.0000.000
156B225THR0-0.055-0.03829.4780.0030.0030.0000.0000.0000.000
157B226VAL00.0380.02131.2640.0000.0000.0000.0000.0000.000
158B227PRO00.0270.02533.896-0.004-0.0040.0000.0000.0000.000
159B228GLY0-0.054-0.01936.578-0.002-0.0020.0000.0000.0000.000
160B229TYR0-0.006-0.02737.319-0.001-0.0010.0000.0000.0000.000
161B230TYR00.0590.04240.5260.0000.0000.0000.0000.0000.000
162B231SER0-0.010-0.02841.241-0.003-0.0030.0000.0000.0000.000
163B232TRP0-0.0030.03743.1170.0010.0010.0000.0000.0000.000
164B233ARG10.8800.89143.8810.0270.0270.0000.0000.0000.000
165B234SER0-0.0230.03442.7900.0000.0000.0000.0000.0000.000
166B235PRO00.035-0.00138.5550.0000.0000.0000.0000.0000.000
167B236GLY00.0270.01739.2680.0000.0000.0000.0000.0000.000
168B237ARG10.9370.96037.6880.0350.0350.0000.0000.0000.000
169B238GLY00.0280.02034.730-0.004-0.0040.0000.0000.0000.000
170B239SER0-0.040-0.03432.1620.0020.0020.0000.0000.0000.000
171B240TRP00.0500.01831.807-0.006-0.0060.0000.0000.0000.000
172B241PHE00.0470.02924.549-0.007-0.0070.0000.0000.0000.000
173B242VAL00.0100.00727.239-0.007-0.0070.0000.0000.0000.000
174B243GLN0-0.002-0.01727.504-0.013-0.0130.0000.0000.0000.000
175B244ALA0-0.040-0.01026.180-0.009-0.0090.0000.0000.0000.000
176B245LEU0-0.002-0.00621.246-0.011-0.0110.0000.0000.0000.000
177B246CYS0-0.046-0.02922.943-0.015-0.0150.0000.0000.0000.000
178B247SER0-0.022-0.02024.063-0.009-0.0090.0000.0000.0000.000
179B248ILE00.002-0.00219.660-0.011-0.0110.0000.0000.0000.000
180B249LEU0-0.017-0.00617.898-0.024-0.0240.0000.0000.0000.000
181B250GLU-1-0.841-0.91119.859-0.189-0.1890.0000.0000.0000.000
182B251GLU-1-0.896-0.92120.966-0.144-0.1440.0000.0000.0000.000
183B252HIS00.015-0.02217.0070.0220.0220.0000.0000.0000.000
184B253GLY0-0.0100.01316.006-0.034-0.0340.0000.0000.0000.000
185B254LYS10.8320.90613.9830.2240.2240.0000.0000.0000.000
186B255ASP-1-0.814-0.89312.374-0.404-0.4040.0000.0000.0000.000
187B256LEU0-0.060-0.02611.543-0.063-0.0630.0000.0000.0000.000
188B257GLU-1-0.698-0.8308.763-0.031-0.0310.0000.0000.0000.000
189B258ILE00.002-0.01211.2160.0770.0770.0000.0000.0000.000
190B259MET0-0.007-0.00313.2090.0200.0200.0000.0000.0000.000
191B260GLN00.0180.02811.450-0.028-0.0280.0000.0000.0000.000
192B261ILE0-0.004-0.00115.2240.0240.0240.0000.0000.0000.000
193B262LEU00.034-0.01317.4440.0170.0170.0000.0000.0000.000
194B263THR0-0.040-0.01517.6580.0210.0210.0000.0000.0000.000
195B264ARG10.8630.93018.0950.1640.1640.0000.0000.0000.000
196B265VAL0-0.040-0.00721.3360.0050.0050.0000.0000.0000.000
197B266ASN0-0.013-0.01922.1720.0010.0010.0000.0000.0000.000
198B267ASP-1-0.808-0.89524.129-0.034-0.0340.0000.0000.0000.000
199B268ARG10.8280.90124.9500.0910.0910.0000.0000.0000.000
200B269VAL00.004-0.00627.4490.0010.0010.0000.0000.0000.000
201B270ALA00.0120.00628.7340.0030.0030.0000.0000.0000.000
202B271ARG10.8250.88326.4990.0520.0520.0000.0000.0000.000
203B272HIS0-0.058-0.02031.311-0.005-0.0050.0000.0000.0000.000
204B273PHE0-0.0340.00033.3080.0010.0010.0000.0000.0000.000
205B274GLU-1-0.839-0.93736.008-0.016-0.0160.0000.0000.0000.000
206B275SER0-0.117-0.04335.0360.0030.0030.0000.0000.0000.000
207B276GLN00.031-0.00835.0280.0000.0000.0000.0000.0000.000
208B277SER00.0640.03939.0060.0010.0010.0000.0000.0000.000
209B278ASP-1-0.882-0.93541.7840.0000.0000.0000.0000.0000.000
210B279ASP-1-0.898-0.95044.955-0.011-0.0110.0000.0000.0000.000
211B280PRO0-0.029-0.02445.8060.0000.0000.0000.0000.0000.000
212B281HIS10.7970.89545.9690.0110.0110.0000.0000.0000.000
213B282PHE00.0100.00341.048-0.001-0.0010.0000.0000.0000.000
214B283HIS0-0.0010.03241.5010.0000.0000.0000.0000.0000.000
215B284GLU-1-0.921-0.97840.703-0.009-0.0090.0000.0000.0000.000
216B285LYS10.7760.88039.555-0.007-0.0070.0000.0000.0000.000
217B286LYS10.8530.94834.3430.0010.0010.0000.0000.0000.000
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