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: 39R6L

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 OptH
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 -3052861.266927
FMO2-HF: Nuclear repulsion 2957593.790715
FMO2-HF: Total energy -95267.476212
FMO2-MP2: Total energy -95539.882693


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.
-18.737-11.6855.771-5.858-6.9630
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 : 0.066 / 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].
3B58TYR00.001-0.0272.598-8.514-4.0231.097-2.192-3.3960.025
4B59GLN00.0270.0212.179-7.701-5.1254.675-3.661-3.589-0.025
5B60TYR0-0.005-0.0314.898-0.032-0.047-0.001-0.0050.0220.000
6B61ASN00.0250.0166.858-0.373-0.3730.0000.0000.0000.000
7B62MET00.0340.0178.0180.1850.1850.0000.0000.0000.000
8B63ASN0-0.059-0.0259.9170.0010.0010.0000.0000.0000.000
9B64PHE0-0.074-0.03011.5550.0860.0860.0000.0000.0000.000
10B65GLU-1-0.926-0.96314.987-0.145-0.1450.0000.0000.0000.000
11B66LYS10.9270.97018.3180.1440.1440.0000.0000.0000.000
12B67LEU00.0520.03314.579-0.003-0.0030.0000.0000.0000.000
13B68GLY00.0920.03816.6050.0040.0040.0000.0000.0000.000
14B69LYS10.8160.91019.3780.0790.0790.0000.0000.0000.000
15B70CYS0-0.029-0.00321.9130.0020.0020.0000.0000.0000.000
16B71ILE0-0.028-0.01223.6750.0070.0070.0000.0000.0000.000
17B72ILE00.0340.01626.9390.0000.0000.0000.0000.0000.000
18B73ILE00.000-0.00129.1560.0050.0050.0000.0000.0000.000
19B74ASN00.0180.01732.2950.0010.0010.0000.0000.0000.000
20B75ASN0-0.008-0.00534.6410.0010.0010.0000.0000.0000.000
21B76LYS10.9210.97637.6580.0500.0500.0000.0000.0000.000
22B77ASN0-0.088-0.08540.2830.0030.0030.0000.0000.0000.000
23B78PHE0-0.028-0.02139.248-0.001-0.0010.0000.0000.0000.000
24B79ASP-1-0.864-0.91844.935-0.024-0.0240.0000.0000.0000.000
25B80LYS10.9880.97848.0270.0180.0180.0000.0000.0000.000
26B81VAL0-0.040-0.02350.1510.0010.0010.0000.0000.0000.000
27B82THR0-0.016-0.01845.2920.0010.0010.0000.0000.0000.000
28B83GLY00.0050.01947.2230.0010.0010.0000.0000.0000.000
29B84MET0-0.0210.01541.9990.0000.0000.0000.0000.0000.000
30B85GLY0-0.002-0.00245.2080.0000.0000.0000.0000.0000.000
31B86VAL0-0.028-0.02443.667-0.001-0.0010.0000.0000.0000.000
32B87ARG10.8840.95034.9850.0500.0500.0000.0000.0000.000
33B88ASN0-0.015-0.03140.142-0.004-0.0040.0000.0000.0000.000
34B89GLY00.0370.01238.4330.0000.0000.0000.0000.0000.000
35B90THR00.0380.01535.609-0.005-0.0050.0000.0000.0000.000
36B91ASP-1-0.841-0.92834.933-0.063-0.0630.0000.0000.0000.000
37B92LYS10.8360.93434.5830.0780.0780.0000.0000.0000.000
38B93ASP-1-0.725-0.86531.469-0.085-0.0850.0000.0000.0000.000
39B94ALA00.0020.00430.551-0.008-0.0080.0000.0000.0000.000
40B95GLU-1-0.944-1.00030.619-0.103-0.1030.0000.0000.0000.000
41B96ALA00.0300.03129.102-0.007-0.0070.0000.0000.0000.000
42B97LEU00.0510.00426.002-0.012-0.0120.0000.0000.0000.000
43B98PHE00.005-0.00225.676-0.014-0.0140.0000.0000.0000.000
44B99LYS10.8490.94326.4980.1020.1020.0000.0000.0000.000
45B100CYS00.0210.02922.842-0.012-0.0120.0000.0000.0000.000
46B101PHE00.034-0.01420.275-0.021-0.0210.0000.0000.0000.000
47B102ARG10.9620.99521.6120.1280.1280.0000.0000.0000.000
48B103SER0-0.043-0.01122.220-0.018-0.0180.0000.0000.0000.000
49B104LEU0-0.069-0.04016.573-0.021-0.0210.0000.0000.0000.000
50B105GLY00.0250.02617.617-0.035-0.0350.0000.0000.0000.000
51B106PHE0-0.051-0.02517.1370.0040.0040.0000.0000.0000.000
52B107ASP-1-0.894-0.94221.017-0.148-0.1480.0000.0000.0000.000
53B108VAL0-0.066-0.05224.2370.0090.0090.0000.0000.0000.000
54B109ILE0-0.0140.00226.3820.0080.0080.0000.0000.0000.000
55B110VAL0-0.011-0.01029.532-0.001-0.0010.0000.0000.0000.000
56B111TYR00.002-0.00130.6950.0070.0070.0000.0000.0000.000
57B112ASN00.007-0.02634.681-0.004-0.0040.0000.0000.0000.000
58B113ASP-1-0.795-0.85737.500-0.040-0.0400.0000.0000.0000.000
59B114CYS0-0.030-0.00836.7630.0020.0020.0000.0000.0000.000
60B115SER00.0590.03739.0500.0000.0000.0000.0000.0000.000
61B116CYS00.0140.00338.879-0.002-0.0020.0000.0000.0000.000
62B117ALA00.0140.00638.2610.0000.0000.0000.0000.0000.000
63B118LYS10.8910.95836.4960.0380.0380.0000.0000.0000.000
64B119MET00.0210.02034.224-0.004-0.0040.0000.0000.0000.000
65B120GLN00.0330.00233.669-0.001-0.0010.0000.0000.0000.000
66B121ASP-1-0.944-0.97334.087-0.028-0.0280.0000.0000.0000.000
67B122LEU0-0.032-0.00732.004-0.001-0.0010.0000.0000.0000.000
68B123LEU0-0.001-0.00927.900-0.004-0.0040.0000.0000.0000.000
69B124LYS10.8890.97029.4440.0110.0110.0000.0000.0000.000
70B125LYS10.9330.99930.6160.0240.0240.0000.0000.0000.000
71B126ALA00.0350.03827.024-0.001-0.0010.0000.0000.0000.000
72B127SER0-0.149-0.08626.202-0.002-0.0020.0000.0000.0000.000
73B128GLU-1-0.848-0.96127.285-0.011-0.0110.0000.0000.0000.000
74B129GLU-1-0.850-0.89726.564-0.069-0.0690.0000.0000.0000.000
75B130ASP-1-0.807-0.89623.942-0.044-0.0440.0000.0000.0000.000
76B131HIS0-0.034-0.04620.467-0.019-0.0190.0000.0000.0000.000
77B132THR00.004-0.03019.537-0.012-0.0120.0000.0000.0000.000
78B133ASN0-0.055-0.02318.486-0.006-0.0060.0000.0000.0000.000
79B134ALA00.001-0.00717.797-0.023-0.0230.0000.0000.0000.000
80B135ALA00.0090.01312.5340.0130.0130.0000.0000.0000.000
81B136CYS0-0.076-0.03814.1720.0150.0150.0000.0000.0000.000
82B137PHE00.0100.00716.0320.0100.0100.0000.0000.0000.000
83B138ALA00.0030.01319.4160.0020.0020.0000.0000.0000.000
84B139CYS0-0.028-0.00321.1870.0090.0090.0000.0000.0000.000
85B140ILE00.000-0.00223.9080.0020.0020.0000.0000.0000.000
86B141LEU0-0.020-0.01226.7410.0050.0050.0000.0000.0000.000
87B142LEU00.0030.00829.5860.0000.0000.0000.0000.0000.000
88B143SER0-0.026-0.03932.7660.0020.0020.0000.0000.0000.000
89B144HIS00.0430.03235.942-0.002-0.0020.0000.0000.0000.000
90B145GLY0-0.020-0.02435.9510.0000.0000.0000.0000.0000.000
91B146GLU-1-0.845-0.86037.017-0.014-0.0140.0000.0000.0000.000
92B147GLU-1-0.890-0.92535.968-0.001-0.0010.0000.0000.0000.000
93B148ASN0-0.025-0.05433.8420.0010.0010.0000.0000.0000.000
94B149VAL0-0.016-0.03134.9140.0010.0010.0000.0000.0000.000
95B150ILE00.0000.00433.110-0.003-0.0030.0000.0000.0000.000
96B151TYR0-0.030-0.08536.1580.0020.0020.0000.0000.0000.000
97B152GLY00.0180.01938.023-0.004-0.0040.0000.0000.0000.000
98B153LYS10.8840.91839.7750.0320.0320.0000.0000.0000.000
99B154ASP-1-0.773-0.89142.834-0.021-0.0210.0000.0000.0000.000
100B155GLY0-0.004-0.00543.0830.0020.0020.0000.0000.0000.000
101B156VAL00.0170.01839.899-0.002-0.0020.0000.0000.0000.000
102B157THR00.010-0.00236.7930.0010.0010.0000.0000.0000.000
103B158PRO00.0370.01835.358-0.002-0.0020.0000.0000.0000.000
104B159ILE00.1070.04529.5120.0010.0010.0000.0000.0000.000
105B160LYS10.8470.92729.893-0.029-0.0290.0000.0000.0000.000
106B161ASP-1-0.893-0.94130.5550.0050.0050.0000.0000.0000.000
107B162LEU0-0.042-0.01730.739-0.001-0.0010.0000.0000.0000.000
108B163THR00.007-0.00326.0770.0000.0000.0000.0000.0000.000
109B164ALA0-0.030-0.02026.5790.0020.0020.0000.0000.0000.000
110B165HIS0-0.041-0.01727.8050.0080.0080.0000.0000.0000.000
111B166PHE00.0690.01823.2000.0010.0010.0000.0000.0000.000
112B167ARG10.8450.95323.235-0.040-0.0400.0000.0000.0000.000
113B168GLY00.1200.04122.776-0.004-0.0040.0000.0000.0000.000
114B169ALA0-0.110-0.07123.437-0.005-0.0050.0000.0000.0000.000
115B170ARG10.8890.91927.006-0.020-0.0200.0000.0000.0000.000
116B171CYS00.1150.08122.784-0.011-0.0110.0000.0000.0000.000
117B172LYS10.8840.94622.834-0.042-0.0420.0000.0000.0000.000
118B173THR00.0210.03121.3200.0090.0090.0000.0000.0000.000
119B174LEU0-0.002-0.00518.529-0.015-0.0150.0000.0000.0000.000
120B175LEU0-0.0200.01118.2940.0030.0030.0000.0000.0000.000
121B176GLU-1-0.946-0.96213.7290.1700.1700.0000.0000.0000.000
122B177LYS10.8330.95813.2260.0810.0810.0000.0000.0000.000
123B178PRO0-0.0330.00712.3490.0340.0340.0000.0000.0000.000
124B179LYS10.8270.90115.059-0.021-0.0210.0000.0000.0000.000
125B180LEU0-0.011-0.01115.7060.0150.0150.0000.0000.0000.000
126B181PHE00.0110.00219.634-0.001-0.0010.0000.0000.0000.000
127B182PHE00.0290.00418.9360.0050.0050.0000.0000.0000.000
128B183ILE0-0.009-0.01024.5890.0020.0020.0000.0000.0000.000
129B184GLN00.006-0.00228.130-0.004-0.0040.0000.0000.0000.000
130B185ALA00.004-0.00430.6960.0000.0000.0000.0000.0000.000
131B186ALA00.017-0.01533.706-0.002-0.0020.0000.0000.0000.000
132B187ARG11.0191.02436.1180.0130.0130.0000.0000.0000.000
133B188GLY0-0.012-0.01839.358-0.003-0.0030.0000.0000.0000.000
134B189THR00.0240.02742.2880.0020.0020.0000.0000.0000.000
135B204ASP-1-0.965-0.99237.837-0.011-0.0110.0000.0000.0000.000
136B205THR0-0.049-0.01832.056-0.002-0.0020.0000.0000.0000.000
137B206ASP-1-0.838-0.91932.418-0.012-0.0120.0000.0000.0000.000
138B207ALA0-0.023-0.01232.6980.0040.0040.0000.0000.0000.000
139B208ASN00.0380.00327.815-0.007-0.0070.0000.0000.0000.000
140B209PRO00.0260.00328.0420.0030.0030.0000.0000.0000.000
141B210ARG10.9291.05320.407-0.048-0.0480.0000.0000.0000.000
142B211TYR00.006-0.01527.692-0.003-0.0030.0000.0000.0000.000
143B212LYS10.7580.94130.313-0.005-0.0050.0000.0000.0000.000
144B213ILE00.0660.01124.429-0.007-0.0070.0000.0000.0000.000
145B214PRO0-0.087-0.02024.6100.0100.0100.0000.0000.0000.000
146B215VAL0-0.020-0.03123.1230.0020.0020.0000.0000.0000.000
147B216GLU-1-0.853-0.91921.8040.0660.0660.0000.0000.0000.000
148B217ALA00.0450.01316.658-0.007-0.0070.0000.0000.0000.000
149B218ASP-1-0.785-0.86714.2760.1250.1250.0000.0000.0000.000
150B219PHE0-0.0110.01016.364-0.042-0.0420.0000.0000.0000.000
151B220LEU00.015-0.01215.9020.0150.0150.0000.0000.0000.000
152B221PHE0-0.017-0.01319.153-0.014-0.0140.0000.0000.0000.000
153B222ALA00.0300.02021.6320.0040.0040.0000.0000.0000.000
154B223TYR0-0.024-0.00423.429-0.005-0.0050.0000.0000.0000.000
155B224SER00.0080.00927.1700.0020.0020.0000.0000.0000.000
156B225THR0-0.016-0.01529.3320.0030.0030.0000.0000.0000.000
157B226VAL00.0190.01231.0410.0030.0030.0000.0000.0000.000
158B227PRO00.0020.01233.775-0.004-0.0040.0000.0000.0000.000
159B228GLY0-0.052-0.01936.494-0.003-0.0030.0000.0000.0000.000
160B229TYR00.012-0.01937.2690.0000.0000.0000.0000.0000.000
161B230TYR00.0670.04540.4410.0020.0020.0000.0000.0000.000
162B231SER0-0.050-0.04741.177-0.004-0.0040.0000.0000.0000.000
163B232TRP00.0370.05943.0660.0020.0020.0000.0000.0000.000
164B233ARG10.8800.89343.9350.0440.0440.0000.0000.0000.000
165B234SER0-0.0200.03642.8200.0000.0000.0000.0000.0000.000
166B235PRO00.0450.00538.6290.0010.0010.0000.0000.0000.000
167B236GLY00.0260.01539.293-0.001-0.0010.0000.0000.0000.000
168B237ARG10.9450.96337.6570.0600.0600.0000.0000.0000.000
169B238GLY00.0200.01934.757-0.005-0.0050.0000.0000.0000.000
170B239SER0-0.032-0.01431.6560.0020.0020.0000.0000.0000.000
171B240TRP00.0790.02331.635-0.007-0.0070.0000.0000.0000.000
172B241PHE00.0290.02124.429-0.009-0.0090.0000.0000.0000.000
173B242VAL00.0130.00827.171-0.010-0.0100.0000.0000.0000.000
174B243GLN00.013-0.00827.538-0.014-0.0140.0000.0000.0000.000
175B244ALA0-0.053-0.01626.049-0.011-0.0110.0000.0000.0000.000
176B245LEU00.0030.00021.301-0.014-0.0140.0000.0000.0000.000
177B246CYS0-0.011-0.00422.964-0.019-0.0190.0000.0000.0000.000
178B247SER0-0.0030.00424.085-0.008-0.0080.0000.0000.0000.000
179B248ILE0-0.021-0.01419.647-0.011-0.0110.0000.0000.0000.000
180B249LEU0-0.019-0.01817.944-0.030-0.0300.0000.0000.0000.000
181B250GLU-1-0.931-0.96719.874-0.229-0.2290.0000.0000.0000.000
182B251GLU-1-0.970-0.99420.860-0.202-0.2020.0000.0000.0000.000
183B252HIS0-0.011-0.03316.8170.0210.0210.0000.0000.0000.000
184B253GLY0-0.0170.00515.937-0.051-0.0510.0000.0000.0000.000
185B254LYS10.8490.91413.9720.2930.2930.0000.0000.0000.000
186B255ASP-1-0.795-0.88612.086-0.521-0.5210.0000.0000.0000.000
187B256LEU0-0.089-0.04211.275-0.093-0.0930.0000.0000.0000.000
188B257GLU-1-0.650-0.8218.645-0.316-0.3160.0000.0000.0000.000
189B258ILE0-0.006-0.01111.1830.1160.1160.0000.0000.0000.000
190B259MET00.0030.00113.0900.0550.0550.0000.0000.0000.000
191B260GLN00.0020.02811.833-0.028-0.0280.0000.0000.0000.000
192B261ILE0-0.0010.00315.1940.0480.0480.0000.0000.0000.000
193B262LEU00.025-0.01917.4140.0340.0340.0000.0000.0000.000
194B263THR0-0.038-0.01717.5340.0360.0360.0000.0000.0000.000
195B264ARG10.9040.95718.1880.2680.2680.0000.0000.0000.000
196B265VAL0-0.040-0.01021.3110.0150.0150.0000.0000.0000.000
197B266ASN00.007-0.01022.5260.0110.0110.0000.0000.0000.000
198B267ASP-1-0.871-0.94324.083-0.084-0.0840.0000.0000.0000.000
199B268ARG10.8840.94525.5400.1480.1480.0000.0000.0000.000
200B269VAL00.0220.00527.2500.0050.0050.0000.0000.0000.000
201B270ALA0-0.030-0.01528.6820.0080.0080.0000.0000.0000.000
202B271ARG10.9060.94326.7210.1070.1070.0000.0000.0000.000
203B272HIS0-0.066-0.02131.273-0.004-0.0040.0000.0000.0000.000
204B273PHE0-0.045-0.01033.2710.0030.0030.0000.0000.0000.000
205B274GLU-1-0.839-0.93535.990-0.043-0.0430.0000.0000.0000.000
206B275SER0-0.140-0.05335.0370.0040.0040.0000.0000.0000.000
207B276GLN0-0.004-0.02334.9840.0000.0000.0000.0000.0000.000
208B277SER00.0100.00338.9650.0030.0030.0000.0000.0000.000
209B278ASP-1-0.875-0.93641.759-0.020-0.0200.0000.0000.0000.000
210B279ASP-1-0.916-0.95444.882-0.028-0.0280.0000.0000.0000.000
211B280PRO0-0.033-0.02345.768-0.001-0.0010.0000.0000.0000.000
212B281HIS10.8020.88945.9420.0300.0300.0000.0000.0000.000
213B282PHE00.0560.03841.004-0.001-0.0010.0000.0000.0000.000
214B283HIS0-0.0020.03741.448-0.001-0.0010.0000.0000.0000.000
215B284GLU-1-0.928-0.99040.780-0.033-0.0330.0000.0000.0000.000
216B285LYS10.9070.96239.6780.0190.0190.0000.0000.0000.000
217B286LYS10.9941.00831.7940.0360.0360.0000.0000.0000.000
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