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

tag_button

FMODB ID: G6N81

Calculation Name: 3CDK-B-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3CDK

Chain ID: B

ChEMBL ID:

UniProt ID: P42315

Base Structure: X-ray

Registration Date: 2023-06-21

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 213
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2340357.12318
FMO2-HF: Nuclear repulsion 2257431.387675
FMO2-HF: Total energy -82925.735505
FMO2-MP2: Total energy -83159.757761


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:1:MET)


Summations of interaction energy for fragment #1(B:1:MET)
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.
-7.944-8.61114.243-6.424-7.1540.032
Interaction energy analysis for fragmet #1(B:1:MET)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.085 / q_NPA : 0.035
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].
3B3GLU-1-0.852-0.9253.6000.1572.223-0.003-0.904-1.1600.001
4B4ALA00.0340.0142.697-0.7190.1910.418-0.372-0.956-0.002
5B5ARG10.9780.9833.584-0.2600.8180.056-0.271-0.8640.000
6B6LYS10.9720.9906.0570.5820.5820.0000.0000.0000.000
7B7ARG10.7690.8496.9430.5880.5880.0000.0000.0000.000
8B8MET0-0.0190.0176.2560.1810.1810.0000.0000.0000.000
9B9VAL00.0170.0009.7760.0720.0720.0000.0000.0000.000
10B10LYS10.8240.89911.8680.1780.1780.0000.0000.0000.000
11B11ARG10.7510.85213.3220.0980.0980.0000.0000.0000.000
12B12ALA00.0150.00314.1940.0320.0320.0000.0000.0000.000
13B13VAL00.0110.01415.9790.0200.0200.0000.0000.0000.000
14B14GLN0-0.0160.00017.9720.0000.0000.0000.0000.0000.000
15B15GLU-1-0.713-0.83919.117-0.010-0.0100.0000.0000.0000.000
16B16ILE00.0150.01619.9970.0090.0090.0000.0000.0000.000
17B17LYS10.7750.86423.3260.0280.0280.0000.0000.0000.000
18B18ASP-1-0.815-0.91826.963-0.029-0.0290.0000.0000.0000.000
19B19GLY0-0.0020.00729.8310.0030.0030.0000.0000.0000.000
20B20MET0-0.089-0.00826.4200.0020.0020.0000.0000.0000.000
21B21ASN00.005-0.00128.898-0.004-0.0040.0000.0000.0000.000
22B22VAL0-0.019-0.01922.5440.0040.0040.0000.0000.0000.000
23B23ASN0-0.028-0.01021.4930.0030.0030.0000.0000.0000.000
24B24LEU0-0.010-0.00617.7090.0050.0050.0000.0000.0000.000
25B25GLY00.0370.02017.096-0.004-0.0040.0000.0000.0000.000
26B26ILE00.0260.00513.992-0.012-0.0120.0000.0000.0000.000
27B27GLY0-0.027-0.01010.9840.0420.0420.0000.0000.0000.000
28B28MET0-0.040-0.0327.819-0.045-0.0450.0000.0000.0000.000
29B29PRO00.0140.00410.442-0.054-0.0540.0000.0000.0000.000
30B30THR00.0550.03513.925-0.022-0.0220.0000.0000.0000.000
31B31LEU0-0.017-0.0119.136-0.029-0.0290.0000.0000.0000.000
32B32VAL0-0.003-0.00213.707-0.005-0.0050.0000.0000.0000.000
33B33ALA00.0420.01915.8340.0060.0060.0000.0000.0000.000
34B34ASN0-0.078-0.03315.6910.0150.0150.0000.0000.0000.000
35B35GLU-1-0.857-0.92115.324-0.145-0.1450.0000.0000.0000.000
36B36ILE00.0120.00518.5100.0020.0020.0000.0000.0000.000
37B37PRO0-0.024-0.01721.6730.0010.0010.0000.0000.0000.000
38B38ASP-1-0.849-0.92524.357-0.054-0.0540.0000.0000.0000.000
39B39GLY0-0.067-0.03027.7030.0040.0040.0000.0000.0000.000
40B40VAL0-0.086-0.04025.1570.0030.0030.0000.0000.0000.000
41B41HIS0-0.0100.00327.175-0.003-0.0030.0000.0000.0000.000
42B42VAL0-0.013-0.01324.8730.0030.0030.0000.0000.0000.000
43B43MET0-0.0040.00828.233-0.004-0.0040.0000.0000.0000.000
44B44LEU00.0090.00322.3640.0040.0040.0000.0000.0000.000
45B45GLN0-0.007-0.01325.3290.0000.0000.0000.0000.0000.000
46B46SER00.018-0.01023.796-0.001-0.0010.0000.0000.0000.000
47B47GLU-1-0.847-0.93422.0350.0080.0080.0000.0000.0000.000
48B48ASN0-0.069-0.02025.0530.0030.0030.0000.0000.0000.000
49B49GLY00.0000.00827.0030.0000.0000.0000.0000.0000.000
50B50LEU00.0200.02526.828-0.001-0.0010.0000.0000.0000.000
51B51LEU0-0.027-0.01528.2840.0010.0010.0000.0000.0000.000
52B52GLY00.035-0.00328.2290.0010.0010.0000.0000.0000.000
53B53ILE0-0.041-0.02322.306-0.002-0.0020.0000.0000.0000.000
54B54GLY00.0280.01725.555-0.001-0.0010.0000.0000.0000.000
55B55PRO0-0.025-0.02122.391-0.003-0.0030.0000.0000.0000.000
56B56TYR0-0.062-0.04416.702-0.003-0.0030.0000.0000.0000.000
57B57PRO00.0140.03922.6250.0000.0000.0000.0000.0000.000
58B58LEU0-0.055-0.02425.077-0.006-0.0060.0000.0000.0000.000
59B59GLU-1-0.940-0.97825.353-0.070-0.0700.0000.0000.0000.000
60B60GLY0-0.030-0.01927.4890.0030.0030.0000.0000.0000.000
61B61THR0-0.106-0.06029.4570.0050.0050.0000.0000.0000.000
62B62GLU-1-0.892-0.94126.353-0.055-0.0550.0000.0000.0000.000
63B63ASP-1-0.804-0.90928.119-0.027-0.0270.0000.0000.0000.000
64B64ALA0-0.077-0.03427.948-0.003-0.0030.0000.0000.0000.000
65B65ASP-1-0.930-0.95429.031-0.019-0.0190.0000.0000.0000.000
66B66LEU0-0.049-0.01327.8670.0020.0020.0000.0000.0000.000
67B67ILE0-0.020-0.01024.102-0.006-0.0060.0000.0000.0000.000
68B68ASN00.011-0.00618.9150.0110.0110.0000.0000.0000.000
69B69ALA00.0480.02819.9710.0020.0020.0000.0000.0000.000
70B70GLY0-0.076-0.05117.7370.0110.0110.0000.0000.0000.000
71B71LYS10.8030.89718.488-0.001-0.0010.0000.0000.0000.000
72B72GLU-1-0.842-0.88516.067-0.120-0.1200.0000.0000.0000.000
73B73THR00.001-0.00520.7080.0060.0060.0000.0000.0000.000
74B74ILE0-0.052-0.03821.991-0.010-0.0100.0000.0000.0000.000
75B75THR00.0160.00624.5070.0040.0040.0000.0000.0000.000
76B76GLU-1-0.862-0.89227.015-0.027-0.0270.0000.0000.0000.000
77B77VAL00.000-0.01028.082-0.003-0.0030.0000.0000.0000.000
78B78THR0-0.014-0.02731.0050.0030.0030.0000.0000.0000.000
79B79GLY0-0.0060.00234.1060.0000.0000.0000.0000.0000.000
80B80ALA0-0.0290.00231.6770.0010.0010.0000.0000.0000.000
81B81SER0-0.046-0.01732.8370.0020.0020.0000.0000.0000.000
82B82TYR00.001-0.03630.6550.0000.0000.0000.0000.0000.000
83B83PHE0-0.035-0.01630.3040.0010.0010.0000.0000.0000.000
84B84ASP-1-0.804-0.89433.1400.0020.0020.0000.0000.0000.000
85B85SER00.035-0.01330.6040.0010.0010.0000.0000.0000.000
86B86ALA0-0.058-0.02231.7060.0030.0030.0000.0000.0000.000
87B87GLU-1-0.872-0.94334.2210.0050.0050.0000.0000.0000.000
88B88SER0-0.059-0.04128.5540.0000.0000.0000.0000.0000.000
89B89PHE0-0.026-0.03125.7170.0020.0020.0000.0000.0000.000
90B90ALA0-0.0080.01230.7410.0030.0030.0000.0000.0000.000
91B91MET00.0070.00531.0080.0000.0000.0000.0000.0000.000
92B92ILE0-0.035-0.01526.3160.0010.0010.0000.0000.0000.000
93B93ARG10.8250.88529.649-0.025-0.0250.0000.0000.0000.000
94B94GLY0-0.0160.00331.6590.0010.0010.0000.0000.0000.000
95B95GLY0-0.0010.01731.822-0.001-0.0010.0000.0000.0000.000
96B96HIS0-0.022-0.01632.832-0.004-0.0040.0000.0000.0000.000
97B97ILE0-0.028-0.00926.232-0.003-0.0030.0000.0000.0000.000
98B98ASP-1-0.780-0.89628.333-0.002-0.0020.0000.0000.0000.000
99B99LEU0-0.050-0.02221.6420.0020.0020.0000.0000.0000.000
100B100ALA00.0380.02121.873-0.003-0.0030.0000.0000.0000.000
101B101ILE0-0.0020.01015.8950.0060.0060.0000.0000.0000.000
102B102LEU00.0150.00116.138-0.002-0.0020.0000.0000.0000.000
103B103GLY00.0580.03412.0110.0060.0060.0000.0000.0000.000
104B104GLY00.0390.00111.349-0.048-0.0480.0000.0000.0000.000
105B105MET0-0.149-0.06610.8450.1640.1640.0000.0000.0000.000
106B106GLU-1-0.696-0.83412.5070.4000.4000.0000.0000.0000.000
107B107VAL0-0.003-0.00515.269-0.036-0.0360.0000.0000.0000.000
108B108SER0-0.018-0.03218.0580.0090.0090.0000.0000.0000.000
109B109GLU-1-0.745-0.86621.3080.0910.0910.0000.0000.0000.000
110B110GLN0-0.043-0.02323.585-0.020-0.0200.0000.0000.0000.000
111B111GLY00.0600.04222.517-0.011-0.0110.0000.0000.0000.000
112B112ASP-1-0.839-0.88122.7880.1020.1020.0000.0000.0000.000
113B113LEU00.0200.00716.3860.0180.0180.0000.0000.0000.000
114B114ALA00.0470.04017.257-0.021-0.0210.0000.0000.0000.000
115B115ASN0-0.041-0.02414.2770.0400.0400.0000.0000.0000.000
116B116TRP00.0660.02815.030-0.012-0.0120.0000.0000.0000.000
117B117MET0-0.047-0.02416.778-0.021-0.0210.0000.0000.0000.000
118B118ILE00.0300.01712.4440.0290.0290.0000.0000.0000.000
119B119PRO00.0240.01216.582-0.026-0.0260.0000.0000.0000.000
120B120GLY00.0220.00818.8480.0150.0150.0000.0000.0000.000
121B121LYS10.9540.96413.190-0.299-0.2990.0000.0000.0000.000
122B122MET00.0010.00314.127-0.011-0.0110.0000.0000.0000.000
123B123VAL0-0.001-0.00617.140-0.015-0.0150.0000.0000.0000.000
124B124LYS10.8960.96415.908-0.072-0.0720.0000.0000.0000.000
125B125GLY00.0640.02919.181-0.013-0.0130.0000.0000.0000.000
126B126MET00.002-0.00619.2170.0050.0050.0000.0000.0000.000
127B127GLY0-0.0010.00220.681-0.002-0.0020.0000.0000.0000.000
128B128GLY00.0960.03222.0640.0010.0010.0000.0000.0000.000
129B129ALA0-0.0150.00119.285-0.001-0.0010.0000.0000.0000.000
130B130MET0-0.006-0.01121.308-0.001-0.0010.0000.0000.0000.000
131B131ASP-1-0.791-0.85124.1120.0330.0330.0000.0000.0000.000
132B132LEU00.001-0.00522.163-0.002-0.0020.0000.0000.0000.000
133B133VAL0-0.045-0.03520.978-0.002-0.0020.0000.0000.0000.000
134B134ASN0-0.067-0.05223.9740.0010.0010.0000.0000.0000.000
135B135GLY00.0090.02427.289-0.003-0.0030.0000.0000.0000.000
136B136ALA0-0.031-0.00525.455-0.004-0.0040.0000.0000.0000.000
137B137LYS10.8090.91227.6050.0010.0010.0000.0000.0000.000
138B138ARG10.8210.91822.401-0.005-0.0050.0000.0000.0000.000
139B139ILE00.0090.01821.433-0.001-0.0010.0000.0000.0000.000
140B140VAL00.004-0.00616.9990.0020.0020.0000.0000.0000.000
141B141VAL0-0.009-0.00214.4200.0070.0070.0000.0000.0000.000
142B142ILE00.0000.00511.371-0.017-0.0170.0000.0000.0000.000
143B143MET0-0.083-0.0369.9840.0870.0870.0000.0000.0000.000
144B144GLU-1-0.795-0.8734.4235.8767.3590.050-0.736-0.797-0.005
145B145HIS00.0470.0237.5170.0380.0380.0000.0000.0000.000
146B146VAL00.0250.0158.695-0.094-0.0940.0000.0000.0000.000
147B147ASN0-0.020-0.0067.7040.5660.5660.0000.0000.0000.000
148B148LYS10.7320.7982.245-13.080-19.28413.722-4.141-3.3770.038
149B149HIS0-0.023-0.0117.734-0.176-0.1760.0000.0000.0000.000
150B150GLY00.0200.02310.730-0.140-0.1400.0000.0000.0000.000
151B151GLU-1-0.921-0.94712.0390.2620.2620.0000.0000.0000.000
152B152SER0-0.023-0.03512.0900.1430.1430.0000.0000.0000.000
153B153LYS10.7860.8848.288-1.010-1.0100.0000.0000.0000.000
154B154VAL00.0160.00213.520-0.038-0.0380.0000.0000.0000.000
155B155LYS10.8450.92016.170-0.363-0.3630.0000.0000.0000.000
156B156LYS10.8300.89619.725-0.111-0.1110.0000.0000.0000.000
157B157THR0-0.041-0.01922.678-0.017-0.0170.0000.0000.0000.000
158B158CYS0-0.046-0.00518.6780.0100.0100.0000.0000.0000.000
159B159SER0-0.056-0.05717.973-0.019-0.0190.0000.0000.0000.000
160B160LEU0-0.064-0.03514.476-0.008-0.0080.0000.0000.0000.000
161B161PRO0-0.029-0.03419.025-0.014-0.0140.0000.0000.0000.000
162B162LEU00.0210.01519.8580.0120.0120.0000.0000.0000.000
163B163THR0-0.040-0.05218.473-0.003-0.0030.0000.0000.0000.000
164B164GLY00.0450.01521.438-0.016-0.0160.0000.0000.0000.000
165B165GLN0-0.043-0.02123.4210.0080.0080.0000.0000.0000.000
166B166LYS10.8680.92425.846-0.077-0.0770.0000.0000.0000.000
167B167VAL00.0170.03122.632-0.006-0.0060.0000.0000.0000.000
168B168VAL0-0.059-0.02219.325-0.006-0.0060.0000.0000.0000.000
169B169HIS00.0410.02622.500-0.007-0.0070.0000.0000.0000.000
170B170ARG10.7110.82618.5800.0020.0020.0000.0000.0000.000
171B171LEU0-0.0140.01014.0210.0120.0120.0000.0000.0000.000
172B172ILE0-0.025-0.00712.597-0.022-0.0220.0000.0000.0000.000
173B173THR00.031-0.00610.2870.0170.0170.0000.0000.0000.000
174B174ASP-1-0.885-0.9495.824-0.485-0.4850.0000.0000.0000.000
175B175LEU0-0.016-0.0088.162-0.091-0.0910.0000.0000.0000.000
176B176ALA00.014-0.00810.8640.0080.0080.0000.0000.0000.000
177B177VAL0-0.0090.00613.9280.0070.0070.0000.0000.0000.000
178B178PHE00.0490.00815.542-0.002-0.0020.0000.0000.0000.000
179B179ASP-1-0.747-0.83919.6360.0110.0110.0000.0000.0000.000
180B180PHE0-0.023-0.01919.7940.0050.0050.0000.0000.0000.000
181B181VAL0-0.002-0.00424.942-0.005-0.0050.0000.0000.0000.000
182B182ASN0-0.042-0.03528.7440.0000.0000.0000.0000.0000.000
183B183GLY00.0230.02028.1970.0000.0000.0000.0000.0000.000
184B184ARG10.9200.97727.565-0.028-0.0280.0000.0000.0000.000
185B185MET00.0410.03919.620-0.001-0.0010.0000.0000.0000.000
186B186THR0-0.061-0.04223.488-0.005-0.0050.0000.0000.0000.000
187B187LEU0-0.0010.01618.008-0.001-0.0010.0000.0000.0000.000
188B188THR0-0.048-0.03220.022-0.006-0.0060.0000.0000.0000.000
189B189GLU-1-0.806-0.87918.191-0.053-0.0530.0000.0000.0000.000
190B190LEU00.006-0.00415.7360.0110.0110.0000.0000.0000.000
191B191GLN0-0.0170.01410.949-0.047-0.0470.0000.0000.0000.000
192B192ASP-1-0.834-0.91412.535-0.188-0.1880.0000.0000.0000.000
193B193GLY0-0.054-0.01412.2050.0220.0220.0000.0000.0000.000
194B194VAL0-0.0020.02711.5920.0070.0070.0000.0000.0000.000
195B195THR00.013-0.00214.4420.0200.0200.0000.0000.0000.000
196B196ILE00.030-0.00417.4440.0030.0030.0000.0000.0000.000
197B197GLU-1-0.931-0.95919.9120.0150.0150.0000.0000.0000.000
198B198GLU-1-0.796-0.87712.318-0.134-0.1340.0000.0000.0000.000
199B199VAL0-0.027-0.02015.1520.0160.0160.0000.0000.0000.000
200B200TYR0-0.0080.00416.6940.0250.0250.0000.0000.0000.000
201B201GLU-1-0.953-0.97416.9970.0280.0280.0000.0000.0000.000
202B202LYS10.7990.89011.1500.1070.1070.0000.0000.0000.000
203B203THR0-0.055-0.05415.0150.0560.0560.0000.0000.0000.000
204B204GLU-1-0.749-0.82316.9850.2720.2720.0000.0000.0000.000
205B205ALA0-0.093-0.03719.902-0.014-0.0140.0000.0000.0000.000
206B206ASP-1-0.825-0.92221.8160.0700.0700.0000.0000.0000.000
207B207PHE0-0.012-0.03620.2590.0020.0020.0000.0000.0000.000
208B208ALA0-0.050-0.00924.457-0.005-0.0050.0000.0000.0000.000
209B209VAL00.0430.01823.5270.0010.0010.0000.0000.0000.000
210B210SER0-0.014-0.01424.5510.0020.0020.0000.0000.0000.000
211B211GLN0-0.002-0.00126.450-0.002-0.0020.0000.0000.0000.000
212B212SER0-0.062-0.03927.242-0.003-0.0030.0000.0000.0000.000
213B213VAL0-0.030-0.00720.789-0.004-0.0040.0000.0000.0000.000