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: V5RV1

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 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 213
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2337690.869897
FMO2-HF: Nuclear repulsion 2254767.812241
FMO2-HF: Total energy -82923.057655
FMO2-MP2: Total energy -83157.231673


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.
-3.1164.1091.499-3.478-5.247-0.013
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 : 0.062 / q_NPA : 0.014
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-1-0.873-0.9283.570-0.8452.065-0.030-1.398-1.4820.001
4B4ALA00.0320.0262.661-0.7540.0300.413-0.352-0.8450.000
5B5ARG10.9990.9772.6020.4171.4940.229-0.322-0.9850.003
6B6LYS10.9770.9965.9780.2930.2930.0000.0000.0000.000
7B7ARG10.8610.9387.6840.5790.5790.0000.0000.0000.000
8B8MET0-0.036-0.0066.0690.1190.1190.0000.0000.0000.000
9B9VAL00.0510.0119.8340.0750.0750.0000.0000.0000.000
10B10LYS10.9420.97311.9410.1120.1120.0000.0000.0000.000
11B11ARG10.7770.85613.4050.1780.1780.0000.0000.0000.000
12B12ALA00.0080.00514.4490.0250.0250.0000.0000.0000.000
13B13VAL00.0430.02816.2360.0180.0180.0000.0000.0000.000
14B14GLN0-0.061-0.03118.3950.0090.0090.0000.0000.0000.000
15B15GLU-1-0.789-0.87919.301-0.108-0.1080.0000.0000.0000.000
16B16ILE0-0.015-0.00520.0430.0060.0060.0000.0000.0000.000
17B17LYS10.8910.93623.6430.0600.0600.0000.0000.0000.000
18B18ASP-1-0.827-0.93527.160-0.025-0.0250.0000.0000.0000.000
19B19GLY0-0.029-0.00929.677-0.001-0.0010.0000.0000.0000.000
20B20MET0-0.095-0.01526.179-0.002-0.0020.0000.0000.0000.000
21B21ASN00.0410.02127.8740.0040.0040.0000.0000.0000.000
22B22VAL0-0.030-0.02421.629-0.004-0.0040.0000.0000.0000.000
23B23ASN0-0.0100.00720.865-0.001-0.0010.0000.0000.0000.000
24B24LEU0-0.002-0.00217.009-0.009-0.0090.0000.0000.0000.000
25B25GLY00.0660.03816.4190.0070.0070.0000.0000.0000.000
26B26ILE00.0420.01013.286-0.008-0.0080.0000.0000.0000.000
27B27GLY0-0.027-0.00910.427-0.017-0.0170.0000.0000.0000.000
28B28MET0-0.046-0.0406.673-0.054-0.0540.0000.0000.0000.000
29B29PRO00.0200.0099.691-0.004-0.0040.0000.0000.0000.000
30B30THR00.0320.02613.1400.0140.0140.0000.0000.0000.000
31B31LEU0-0.030-0.0209.0380.0050.0050.0000.0000.0000.000
32B32VAL0-0.036-0.02413.1500.0140.0140.0000.0000.0000.000
33B33ALA00.0290.01315.4820.0100.0100.0000.0000.0000.000
34B34ASN0-0.0070.00614.7950.0170.0170.0000.0000.0000.000
35B35GLU-1-0.983-0.98515.7700.0180.0180.0000.0000.0000.000
36B36ILE0-0.018-0.00718.553-0.012-0.0120.0000.0000.0000.000
37B37PRO0-0.032-0.01721.5460.0080.0080.0000.0000.0000.000
38B38ASP-1-0.826-0.92524.221-0.001-0.0010.0000.0000.0000.000
39B39GLY0-0.131-0.05327.7010.0000.0000.0000.0000.0000.000
40B40VAL0-0.081-0.03725.741-0.001-0.0010.0000.0000.0000.000
41B41HIS00.0320.02827.3740.0010.0010.0000.0000.0000.000
42B42VAL00.0090.01924.509-0.003-0.0030.0000.0000.0000.000
43B43MET0-0.009-0.00127.5870.0040.0040.0000.0000.0000.000
44B44LEU00.009-0.00521.533-0.005-0.0050.0000.0000.0000.000
45B45GLN0-0.006-0.01324.7200.0020.0020.0000.0000.0000.000
46B46SER00.002-0.05123.592-0.006-0.0060.0000.0000.0000.000
47B47GLU-1-0.892-0.94921.903-0.043-0.0430.0000.0000.0000.000
48B48ASN0-0.062-0.00924.984-0.003-0.0030.0000.0000.0000.000
49B49GLY0-0.016-0.00927.0020.0030.0030.0000.0000.0000.000
50B50LEU00.0370.01926.4020.0030.0030.0000.0000.0000.000
51B51LEU0-0.050-0.00727.739-0.004-0.0040.0000.0000.0000.000
52B52GLY00.033-0.00127.6840.0030.0030.0000.0000.0000.000
53B53ILE0-0.026-0.01221.9980.0030.0030.0000.0000.0000.000
54B54GLY00.0110.01325.017-0.001-0.0010.0000.0000.0000.000
55B55PRO0-0.028-0.02221.938-0.002-0.0020.0000.0000.0000.000
56B56TYR0-0.030-0.02516.8650.0010.0010.0000.0000.0000.000
57B57PRO00.0130.03722.7860.0030.0030.0000.0000.0000.000
58B58LEU0-0.021-0.02225.3630.0040.0040.0000.0000.0000.000
59B59GLU-1-0.948-0.98325.8500.0480.0480.0000.0000.0000.000
60B60GLY0-0.042-0.01827.5790.0010.0010.0000.0000.0000.000
61B61THR0-0.097-0.05229.702-0.003-0.0030.0000.0000.0000.000
62B62GLU-1-0.932-0.96326.6260.0220.0220.0000.0000.0000.000
63B63ASP-1-0.833-0.92128.5110.0050.0050.0000.0000.0000.000
64B64ALA0-0.063-0.02528.678-0.001-0.0010.0000.0000.0000.000
65B65ASP-1-0.979-0.97629.504-0.001-0.0010.0000.0000.0000.000
66B66LEU0-0.018-0.01127.669-0.003-0.0030.0000.0000.0000.000
67B67ILE00.008-0.00623.5890.0010.0010.0000.0000.0000.000
68B68ASN00.0240.01418.692-0.003-0.0030.0000.0000.0000.000
69B69ALA00.0480.01519.7720.0020.0020.0000.0000.0000.000
70B70GLY0-0.086-0.06117.436-0.002-0.0020.0000.0000.0000.000
71B71LYS10.8360.91818.2960.0290.0290.0000.0000.0000.000
72B72GLU-1-0.872-0.92216.141-0.014-0.0140.0000.0000.0000.000
73B73THR00.0600.03520.713-0.004-0.0040.0000.0000.0000.000
74B74ILE0-0.061-0.02521.7630.0010.0010.0000.0000.0000.000
75B75THR00.0210.01224.1890.0040.0040.0000.0000.0000.000
76B76GLU-1-0.905-0.90426.645-0.007-0.0070.0000.0000.0000.000
77B77VAL00.003-0.00827.3770.0030.0030.0000.0000.0000.000
78B78THR0-0.008-0.03730.1480.0000.0000.0000.0000.0000.000
79B79GLY0-0.019-0.00633.183-0.002-0.0020.0000.0000.0000.000
80B80ALA0-0.0190.01131.332-0.002-0.0020.0000.0000.0000.000
81B81SER0-0.024-0.01332.4410.0010.0010.0000.0000.0000.000
82B82TYR0-0.001-0.02630.233-0.002-0.0020.0000.0000.0000.000
83B83PHE0-0.037-0.01230.1450.0000.0000.0000.0000.0000.000
84B84ASP-1-0.841-0.91933.006-0.015-0.0150.0000.0000.0000.000
85B85SER00.037-0.01329.945-0.001-0.0010.0000.0000.0000.000
86B86ALA0-0.043-0.01931.386-0.002-0.0020.0000.0000.0000.000
87B87GLU-1-0.853-0.92834.024-0.021-0.0210.0000.0000.0000.000
88B88SER0-0.031-0.00428.071-0.002-0.0020.0000.0000.0000.000
89B89PHE0-0.022-0.03425.215-0.003-0.0030.0000.0000.0000.000
90B90ALA0-0.0270.00730.348-0.002-0.0020.0000.0000.0000.000
91B91MET00.0140.00929.603-0.001-0.0010.0000.0000.0000.000
92B92ILE0-0.049-0.01325.474-0.002-0.0020.0000.0000.0000.000
93B93ARG10.9540.96728.8470.0280.0280.0000.0000.0000.000
94B94GLY0-0.061-0.02130.8660.0000.0000.0000.0000.0000.000
95B95GLY00.0270.02930.8070.0010.0010.0000.0000.0000.000
96B96HIS0-0.065-0.04031.781-0.001-0.0010.0000.0000.0000.000
97B97ILE0-0.0230.00225.1940.0000.0000.0000.0000.0000.000
98B98ASP-1-0.786-0.90127.619-0.044-0.0440.0000.0000.0000.000
99B99LEU0-0.051-0.02721.205-0.005-0.0050.0000.0000.0000.000
100B100ALA00.0440.02620.7920.0040.0040.0000.0000.0000.000
101B101ILE0-0.0230.00215.238-0.010-0.0100.0000.0000.0000.000
102B102LEU00.008-0.00815.3020.0050.0050.0000.0000.0000.000
103B103GLY00.0500.02811.294-0.021-0.0210.0000.0000.0000.000
104B104GLY00.033-0.00510.5950.0240.0240.0000.0000.0000.000
105B105MET0-0.117-0.06610.165-0.013-0.0130.0000.0000.0000.000
106B106GLU-1-0.737-0.85011.671-0.075-0.0750.0000.0000.0000.000
107B107VAL0-0.016-0.00614.3590.0020.0020.0000.0000.0000.000
108B108SER00.0110.00616.946-0.003-0.0030.0000.0000.0000.000
109B109GLU-1-0.776-0.88820.353-0.090-0.0900.0000.0000.0000.000
110B110GLN0-0.054-0.02723.1930.0030.0030.0000.0000.0000.000
111B111GLY00.0420.02221.4910.0050.0050.0000.0000.0000.000
112B112ASP-1-0.850-0.90221.687-0.067-0.0670.0000.0000.0000.000
113B113LEU00.002-0.00615.402-0.011-0.0110.0000.0000.0000.000
114B114ALA00.0440.03316.6850.0100.0100.0000.0000.0000.000
115B115ASN0-0.087-0.03213.4930.0050.0050.0000.0000.0000.000
116B116TRP00.0770.03814.6720.0030.0030.0000.0000.0000.000
117B117MET0-0.052-0.01916.7920.0060.0060.0000.0000.0000.000
118B118ILE00.0050.00712.302-0.002-0.0020.0000.0000.0000.000
119B119PRO00.0150.00816.7100.0050.0050.0000.0000.0000.000
120B120GLY00.0230.01819.4330.0010.0010.0000.0000.0000.000
121B121LYS10.9710.97312.9490.0010.0010.0000.0000.0000.000
122B122MET0-0.083-0.06914.7240.0000.0000.0000.0000.0000.000
123B123VAL00.0730.05017.5400.0000.0000.0000.0000.0000.000
124B124LYS10.9210.98215.6650.0230.0230.0000.0000.0000.000
125B125GLY00.0470.01819.1920.0030.0030.0000.0000.0000.000
126B126MET00.009-0.00318.846-0.003-0.0030.0000.0000.0000.000
127B127GLY0-0.040-0.01320.289-0.004-0.0040.0000.0000.0000.000
128B128GLY00.1240.05721.5570.0010.0010.0000.0000.0000.000
129B129ALA0-0.009-0.00418.493-0.002-0.0020.0000.0000.0000.000
130B130MET0-0.010-0.01720.520-0.001-0.0010.0000.0000.0000.000
131B131ASP-1-0.931-0.94523.330-0.039-0.0390.0000.0000.0000.000
132B132LEU00.0560.00321.0120.0000.0000.0000.0000.0000.000
133B133VAL0-0.096-0.04020.450-0.002-0.0020.0000.0000.0000.000
134B134ASN0-0.078-0.06023.186-0.002-0.0020.0000.0000.0000.000
135B135GLY00.0080.02626.4460.0020.0020.0000.0000.0000.000
136B136ALA0-0.022-0.00324.4160.0020.0020.0000.0000.0000.000
137B137LYS10.8580.93726.4730.0380.0380.0000.0000.0000.000
138B138ARG10.8130.91122.3960.0900.0900.0000.0000.0000.000
139B139ILE00.0050.00220.124-0.003-0.0030.0000.0000.0000.000
140B140VAL0-0.002-0.00716.979-0.006-0.0060.0000.0000.0000.000
141B141VAL00.0190.01713.7080.0010.0010.0000.0000.0000.000
142B142ILE0-0.0210.00711.114-0.015-0.0150.0000.0000.0000.000
143B143MET0-0.103-0.0589.0050.0170.0170.0000.0000.0000.000
144B144GLU-1-0.929-0.9733.417-1.6670.7870.887-1.406-1.935-0.017
145B145HIS00.0480.0237.6020.0610.0610.0000.0000.0000.000
146B146VAL00.0500.0298.3020.0660.0660.0000.0000.0000.000
147B147ASN0-0.078-0.0306.9110.1250.1250.0000.0000.0000.000
148B148LYS10.9690.9565.675-0.344-0.3440.0000.0000.0000.000
149B149HIS0-0.035-0.0277.512-0.122-0.1220.0000.0000.0000.000
150B150GLY00.0360.03410.007-0.023-0.0230.0000.0000.0000.000
151B151GLU-1-0.899-0.93811.381-0.136-0.1360.0000.0000.0000.000
152B152SER0-0.011-0.01011.602-0.001-0.0010.0000.0000.0000.000
153B153LYS10.8410.9237.4710.1580.1580.0000.0000.0000.000
154B154VAL00.0190.01313.2280.0110.0110.0000.0000.0000.000
155B155LYS10.9360.96515.9410.1030.1030.0000.0000.0000.000
156B156LYS10.9621.00619.1530.0840.0840.0000.0000.0000.000
157B157THR0-0.020-0.01622.4190.0030.0030.0000.0000.0000.000
158B158CYS0-0.0160.00019.064-0.006-0.0060.0000.0000.0000.000
159B159SER0-0.083-0.06617.6740.0070.0070.0000.0000.0000.000
160B160LEU0-0.050-0.02814.3340.0080.0080.0000.0000.0000.000
161B161PRO0-0.024-0.02318.797-0.001-0.0010.0000.0000.0000.000
162B162LEU00.0240.01219.409-0.004-0.0040.0000.0000.0000.000
163B163THR0-0.054-0.06517.9070.0050.0050.0000.0000.0000.000
164B164GLY00.0550.02020.6770.0040.0040.0000.0000.0000.000
165B165GLN0-0.042-0.01422.731-0.002-0.0020.0000.0000.0000.000
166B166LYS10.8820.92524.6210.0590.0590.0000.0000.0000.000
167B167VAL0-0.006-0.00521.4750.0020.0020.0000.0000.0000.000
168B168VAL0-0.044-0.01018.726-0.001-0.0010.0000.0000.0000.000
169B169HIS00.0880.06721.565-0.002-0.0020.0000.0000.0000.000
170B170ARG10.7720.86618.8630.1160.1160.0000.0000.0000.000
171B171LEU0-0.032-0.01213.741-0.001-0.0010.0000.0000.0000.000
172B172ILE0-0.056-0.00912.350-0.001-0.0010.0000.0000.0000.000
173B173THR00.0320.01110.473-0.022-0.0220.0000.0000.0000.000
174B174ASP-1-0.868-0.9526.470-0.953-0.9530.0000.0000.0000.000
175B175LEU0-0.033-0.0318.668-0.018-0.0180.0000.0000.0000.000
176B176ALA00.0320.00111.3620.0590.0590.0000.0000.0000.000
177B177VAL0-0.0150.01514.334-0.015-0.0150.0000.0000.0000.000
178B178PHE00.0380.00515.8480.0140.0140.0000.0000.0000.000
179B179ASP-1-0.774-0.86419.629-0.109-0.1090.0000.0000.0000.000
180B180PHE0-0.021-0.01419.794-0.001-0.0010.0000.0000.0000.000
181B181VAL0-0.011-0.01425.1830.0050.0050.0000.0000.0000.000
182B182ASN0-0.047-0.03128.9670.0020.0020.0000.0000.0000.000
183B183GLY0-0.0030.00527.8720.0030.0030.0000.0000.0000.000
184B184ARG10.9530.99627.1740.0680.0680.0000.0000.0000.000
185B185MET00.0630.05020.366-0.003-0.0030.0000.0000.0000.000
186B186THR0-0.068-0.04723.6300.0070.0070.0000.0000.0000.000
187B187LEU0-0.0180.00018.351-0.004-0.0040.0000.0000.0000.000
188B188THR0-0.036-0.03920.3850.0130.0130.0000.0000.0000.000
189B189GLU-1-0.794-0.88618.243-0.132-0.1320.0000.0000.0000.000
190B190LEU0-0.042-0.01716.133-0.016-0.0160.0000.0000.0000.000
191B191GLN0-0.052-0.01611.4040.0300.0300.0000.0000.0000.000
192B192ASP-1-0.868-0.96111.981-0.149-0.1490.0000.0000.0000.000
193B193GLY0-0.116-0.04911.8160.0250.0250.0000.0000.0000.000
194B194VAL0-0.0100.03111.7640.0100.0100.0000.0000.0000.000
195B195THR00.0520.00914.4090.0350.0350.0000.0000.0000.000
196B196ILE00.021-0.01017.497-0.019-0.0190.0000.0000.0000.000
197B197GLU-1-0.910-0.95219.834-0.133-0.1330.0000.0000.0000.000
198B198GLU-1-0.816-0.89511.992-0.432-0.4320.0000.0000.0000.000
199B199VAL0-0.016-0.01515.473-0.020-0.0200.0000.0000.0000.000
200B200TYR0-0.0130.01116.9310.0090.0090.0000.0000.0000.000
201B201GLU-1-0.932-0.95617.669-0.189-0.1890.0000.0000.0000.000
202B202LYS10.8080.90310.3620.5300.5300.0000.0000.0000.000
203B203THR0-0.092-0.07214.980-0.019-0.0190.0000.0000.0000.000
204B204GLU-1-0.892-0.93717.268-0.104-0.1040.0000.0000.0000.000
205B205ALA0-0.126-0.06919.3270.0120.0120.0000.0000.0000.000
206B206ASP-1-0.844-0.92621.303-0.094-0.0940.0000.0000.0000.000
207B207PHE0-0.050-0.05820.1410.0000.0000.0000.0000.0000.000
208B208ALA0-0.045-0.00824.5240.0030.0030.0000.0000.0000.000
209B209VAL00.0220.00523.829-0.009-0.0090.0000.0000.0000.000
210B210SER0-0.056-0.04024.9960.0120.0120.0000.0000.0000.000
211B211GLN00.0060.00826.815-0.002-0.0020.0000.0000.0000.000
212B212SER0-0.040-0.01127.4780.0040.0040.0000.0000.0000.000
213B213VAL00.0320.03821.192-0.002-0.0020.0000.0000.0000.000