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

tag_button

FMODB ID: 5JMRZ

Calculation Name: 3VX8-B-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3VX8

Chain ID: B

ChEMBL ID:

UniProt ID: Q0WWQ1

Base Structure: X-ray

Registration Date: 2023-09-24

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 179
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2030421.686424
FMO2-HF: Nuclear repulsion 1957035.946907
FMO2-HF: Total energy -73385.739516
FMO2-MP2: Total energy -73596.592508


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:23:PRO)


Summations of interaction energy for fragment #1(B:23: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.
-16.105-12.08414.069-8.377-9.715-0.056
Interaction energy analysis for fragmet #1(B:23:PRO)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.009 / q_NPA : 0.002
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].
3B25MET00.0130.0183.418-2.0300.6200.024-1.215-1.4580.004
4B26ALA00.006-0.0042.176-1.0010.0802.358-1.131-2.3080.000
5B27PHE00.008-0.0013.7800.1440.8160.006-0.226-0.4520.001
6B28LYS10.8790.9095.4411.3701.3700.0000.0000.0000.000
7B29GLU-1-0.834-0.9106.4860.0240.0240.0000.0000.0000.000
8B30LYS10.8030.9015.6080.4920.4920.0000.0000.0000.000
9B31GLY00.0170.0378.1890.1220.1220.0000.0000.0000.000
10B32VAL0-0.047-0.0104.0350.0120.152-0.001-0.016-0.1230.000
11B33LEU00.0060.0014.641-0.765-0.715-0.001-0.009-0.0400.000
12B34SER0-0.014-0.0082.3981.0811.8090.456-0.316-0.8690.001
13B35VAL00.028-0.0074.354-0.0470.0010.000-0.020-0.0270.000
14B36SER0-0.0050.0035.3100.1250.1250.0000.0000.0000.000
15B37GLU-1-0.722-0.8361.856-17.372-18.91611.228-5.394-4.291-0.062
16B38PHE0-0.012-0.0056.2490.0450.0450.0000.0000.0000.000
17B39VAL00.0200.0099.2480.0710.0710.0000.0000.0000.000
18B40LEU00.0300.0188.7410.0120.0120.0000.0000.0000.000
19B41ALA00.022-0.0029.4670.0500.0500.0000.0000.0000.000
20B42GLY0-0.015-0.00511.2450.0600.0600.0000.0000.0000.000
21B43ASP-1-0.799-0.87213.919-0.095-0.0950.0000.0000.0000.000
22B44ASN0-0.021-0.02513.1150.1100.1100.0000.0000.0000.000
23B45LEU0-0.007-0.00815.2720.0250.0250.0000.0000.0000.000
24B46VAL00.0130.00617.1210.0280.0280.0000.0000.0000.000
25B47SER0-0.034-0.00418.3070.0160.0160.0000.0000.0000.000
26B48LYS10.7880.89517.7210.2710.2710.0000.0000.0000.000
27B49CYS0-0.033-0.00120.9740.0050.0050.0000.0000.0000.000
28B50PRO00.0500.01722.832-0.006-0.0060.0000.0000.0000.000
29B51THR00.002-0.00724.5340.0110.0110.0000.0000.0000.000
30B52TRP0-0.063-0.02620.741-0.004-0.0040.0000.0000.0000.000
31B53SER0-0.018-0.01722.0530.0150.0150.0000.0000.0000.000
32B54TRP0-0.044-0.02713.788-0.019-0.0190.0000.0000.0000.000
33B55GLU-1-0.821-0.89020.728-0.079-0.0790.0000.0000.0000.000
34B56SER0-0.005-0.03320.959-0.004-0.0040.0000.0000.0000.000
35B57GLY0-0.048-0.01922.8030.0000.0000.0000.0000.0000.000
36B58ASP-1-0.803-0.91824.928-0.043-0.0430.0000.0000.0000.000
37B59ALA00.0190.00624.9510.0020.0020.0000.0000.0000.000
38B60SER0-0.019-0.01625.4580.0060.0060.0000.0000.0000.000
39B61LYS10.8270.93022.9620.0640.0640.0000.0000.0000.000
40B62ARG10.8730.95218.578-0.039-0.0390.0000.0000.0000.000
41B63LYS10.9270.97215.4020.1040.1040.0000.0000.0000.000
42B64PRO00.004-0.00217.1690.0010.0010.0000.0000.0000.000
43B65TYR0-0.021-0.01511.9810.0280.0280.0000.0000.0000.000
44B66LEU00.0120.00711.632-0.006-0.0060.0000.0000.0000.000
45B67PRO00.0580.03713.9120.0190.0190.0000.0000.0000.000
46B68SER00.0020.00717.152-0.020-0.0200.0000.0000.0000.000
47B69ASP-1-0.870-0.93019.925-0.022-0.0220.0000.0000.0000.000
48B70LYS10.8170.89316.0760.0650.0650.0000.0000.0000.000
49B71GLN0-0.046-0.01416.080-0.014-0.0140.0000.0000.0000.000
50B72PHE0-0.031-0.03716.762-0.026-0.0260.0000.0000.0000.000
51B73LEU00.0220.02715.2560.0110.0110.0000.0000.0000.000
52B74ILE0-0.039-0.03119.434-0.004-0.0040.0000.0000.0000.000
53B75THR00.009-0.00222.8990.0020.0020.0000.0000.0000.000
54B76ARG10.8860.90525.3080.1000.1000.0000.0000.0000.000
55B77ASN0-0.015-0.01029.0440.0060.0060.0000.0000.0000.000
56B78VAL00.0190.03427.2720.0020.0020.0000.0000.0000.000
57B79PRO00.0340.01430.7240.0050.0050.0000.0000.0000.000
58B80CYS0-0.051-0.01832.152-0.009-0.0090.0000.0000.0000.000
59B81LEU00.0140.01234.1260.0080.0080.0000.0000.0000.000
60B82ARG10.9380.97735.3050.1160.1160.0000.0000.0000.000
61B83ARG10.8790.90635.3590.0920.0920.0000.0000.0000.000
62B84ALA00.0240.01932.0870.0000.0000.0000.0000.0000.000
63B85ALA0-0.0130.00233.926-0.002-0.0020.0000.0000.0000.000
64B86SER0-0.116-0.05235.9450.0080.0080.0000.0000.0000.000
65B190LEU0-0.007-0.01641.419-0.002-0.0020.0000.0000.0000.000
66B191ARG10.8650.92641.3660.0690.0690.0000.0000.0000.000
67B192THR00.0040.00339.260-0.003-0.0030.0000.0000.0000.000
68B193ARG10.8050.89435.2610.0960.0960.0000.0000.0000.000
69B194THR0-0.015-0.01134.175-0.003-0.0030.0000.0000.0000.000
70B195TYR0-0.023-0.05429.2650.0000.0000.0000.0000.0000.000
71B196ASP-1-0.808-0.85828.385-0.101-0.1010.0000.0000.0000.000
72B197LEU0-0.051-0.02523.8240.0000.0000.0000.0000.0000.000
73B198SER0-0.0030.00621.7930.0000.0000.0000.0000.0000.000
74B199ILE0-0.002-0.00815.770-0.018-0.0180.0000.0000.0000.000
75B200THR00.0460.03716.6050.0190.0190.0000.0000.0000.000
76B201TYR0-0.034-0.0496.6000.1290.1290.0000.0000.0000.000
77B202ASP-1-0.790-0.89912.930-0.154-0.1540.0000.0000.0000.000
78B203LYS10.9430.9559.067-0.129-0.1290.0000.0000.0000.000
79B204TYR0-0.0260.00711.1340.0430.0430.0000.0000.0000.000
80B205TYR00.029-0.00511.9640.0170.0170.0000.0000.0000.000
81B206GLN0-0.067-0.0146.347-0.061-0.0610.0000.0000.0000.000
82B207THR00.0240.0107.857-0.259-0.2590.0000.0000.0000.000
83B208PRO00.0050.01110.4130.1010.1010.0000.0000.0000.000
84B209ARG10.8010.89113.1750.2020.2020.0000.0000.0000.000
85B210VAL00.0340.02516.6770.0110.0110.0000.0000.0000.000
86B211TRP0-0.032-0.02319.0230.0240.0240.0000.0000.0000.000
87B212LEU00.007-0.00423.182-0.003-0.0030.0000.0000.0000.000
88B213THR00.0090.00026.5810.0100.0100.0000.0000.0000.000
89B214GLY00.0730.03730.024-0.004-0.0040.0000.0000.0000.000
90B215TYR0-0.079-0.05631.8820.0080.0080.0000.0000.0000.000
91B216ASP-1-0.818-0.92736.320-0.072-0.0720.0000.0000.0000.000
92B217GLU-1-0.789-0.86039.510-0.065-0.0650.0000.0000.0000.000
93B218SER0-0.083-0.05541.7300.0010.0010.0000.0000.0000.000
94B219ARG10.7880.88032.6890.0880.0880.0000.0000.0000.000
95B220MET00.0420.03038.8230.0000.0000.0000.0000.0000.000
96B221LEU0-0.030-0.01533.800-0.004-0.0040.0000.0000.0000.000
97B222LEU0-0.0150.00334.9660.0030.0030.0000.0000.0000.000
98B223GLN0-0.0130.00135.483-0.001-0.0010.0000.0000.0000.000
99B224PRO00.013-0.00731.455-0.004-0.0040.0000.0000.0000.000
100B225GLU-1-0.873-0.94932.570-0.082-0.0820.0000.0000.0000.000
101B226LEU00.0170.00634.680-0.003-0.0030.0000.0000.0000.000
102B227VAL00.0080.00729.290-0.004-0.0040.0000.0000.0000.000
103B228MET0-0.059-0.03629.667-0.011-0.0110.0000.0000.0000.000
104B229GLU-1-0.840-0.89532.351-0.086-0.0860.0000.0000.0000.000
105B230ASP-1-0.739-0.83231.618-0.108-0.1080.0000.0000.0000.000
106B231VAL0-0.046-0.01227.594-0.013-0.0130.0000.0000.0000.000
107B232SER00.0050.00228.0920.0130.0130.0000.0000.0000.000
108B233GLN0-0.009-0.02529.960-0.001-0.0010.0000.0000.0000.000
109B234ASP-1-0.755-0.85728.909-0.152-0.1520.0000.0000.0000.000
110B235HIS0-0.060-0.04827.480-0.014-0.0140.0000.0000.0000.000
111B236ALA00.0000.00224.951-0.013-0.0130.0000.0000.0000.000
112B237ARG10.9060.95923.7340.1180.1180.0000.0000.0000.000
113B238LYS10.7800.87921.3570.2160.2160.0000.0000.0000.000
114B239THR00.0170.01823.2550.0160.0160.0000.0000.0000.000
115B240VAL0-0.007-0.00623.717-0.017-0.0170.0000.0000.0000.000
116B241THR0-0.041-0.02424.0800.0150.0150.0000.0000.0000.000
117B242ILE00.0530.01926.893-0.007-0.0070.0000.0000.0000.000
118B243GLU-1-0.797-0.86923.141-0.125-0.1250.0000.0000.0000.000
119B244ASP-1-0.818-0.90525.806-0.068-0.0680.0000.0000.0000.000
120B245HIS00.0370.02221.9480.0040.0040.0000.0000.0000.000
121B246PRO0-0.048-0.03519.3870.0140.0140.0000.0000.0000.000
122B247HIS0-0.005-0.00718.679-0.007-0.0070.0000.0000.0000.000
123B248LEU00.0410.03723.1500.0060.0060.0000.0000.0000.000
124B249PRO00.0220.00426.633-0.001-0.0010.0000.0000.0000.000
125B250GLY00.0380.03529.735-0.007-0.0070.0000.0000.0000.000
126B251LYS10.8040.88129.0880.0730.0730.0000.0000.0000.000
127B252HIS10.8190.89326.4140.1010.1010.0000.0000.0000.000
128B253ALA00.0630.05027.301-0.002-0.0020.0000.0000.0000.000
129B254SER0-0.047-0.04121.632-0.012-0.0120.0000.0000.0000.000
130B255VAL00.0470.02120.7540.0100.0100.0000.0000.0000.000
131B256HIS00.0550.02919.627-0.041-0.0410.0000.0000.0000.000
132B257PRO00.0300.00514.959-0.012-0.0120.0000.0000.0000.000
133B258CYS0-0.066-0.02715.443-0.041-0.0410.0000.0000.0000.000
134B259ARG10.9260.95116.7170.2210.2210.0000.0000.0000.000
135B260HIS00.0270.03314.014-0.030-0.0300.0000.0000.0000.000
136B261GLY00.0810.04911.043-0.055-0.0550.0000.0000.0000.000
137B262ALA0-0.021-0.01811.762-0.035-0.0350.0000.0000.0000.000
138B263VAL0-0.056-0.02314.5440.0220.0220.0000.0000.0000.000
139B264MET0-0.031-0.01011.210-0.007-0.0070.0000.0000.0000.000
140B265LYS10.9310.96011.3650.4560.4560.0000.0000.0000.000
141B266LYS10.9610.98612.3990.3170.3170.0000.0000.0000.000
142B267ILE0-0.005-0.00715.0250.0400.0400.0000.0000.0000.000
143B268ILE00.0010.00010.2050.0190.0190.0000.0000.0000.000
144B269ASP-1-0.868-0.93813.686-0.420-0.4200.0000.0000.0000.000
145B270VAL0-0.025-0.00915.8530.0490.0490.0000.0000.0000.000
146B271LEU0-0.075-0.03215.1940.0400.0400.0000.0000.0000.000
147B272MET00.0470.02212.4720.0050.0050.0000.0000.0000.000
148B273SER0-0.049-0.02816.4860.0520.0520.0000.0000.0000.000
149B274ARG10.8800.94819.7330.3110.3110.0000.0000.0000.000
150B275GLY00.0290.02119.8990.0170.0170.0000.0000.0000.000
151B276VAL0-0.072-0.03316.4770.0050.0050.0000.0000.0000.000
152B277GLU-1-0.777-0.87813.000-0.561-0.5610.0000.0000.0000.000
153B278PRO0-0.067-0.02011.6310.0020.0020.0000.0000.0000.000
154B279GLU-1-0.848-0.9188.772-0.699-0.6990.0000.0000.0000.000
155B280VAL00.011-0.0043.7290.2640.460-0.001-0.050-0.1470.000
156B281ASP-1-0.764-0.8806.973-0.558-0.5580.0000.0000.0000.000
157B282LYS10.7960.8789.6240.7940.7940.0000.0000.0000.000
158B283TYR0-0.032-0.0317.7420.2370.2370.0000.0000.0000.000
159B284LEU00.022-0.00511.0280.1060.1060.0000.0000.0000.000
160B285PHE00.0400.04213.8870.0620.0620.0000.0000.0000.000
161B286LEU0-0.008-0.00512.3410.0650.0650.0000.0000.0000.000
162B287PHE00.026-0.00613.8140.0480.0480.0000.0000.0000.000
163B288LEU00.0060.01415.8290.0510.0510.0000.0000.0000.000
164B289LYS10.9140.98017.6870.4770.4770.0000.0000.0000.000
165B290PHE0-0.047-0.01217.3550.0220.0220.0000.0000.0000.000
166B291MET00.0170.01018.9490.0310.0310.0000.0000.0000.000
167B292ALA00.0520.04521.4210.0260.0260.0000.0000.0000.000
168B293SER0-0.073-0.05022.8570.0210.0210.0000.0000.0000.000
169B294VAL0-0.060-0.03821.8900.0160.0160.0000.0000.0000.000
170B295ILE0-0.002-0.00124.0170.0160.0160.0000.0000.0000.000
171B296PRO00.0110.01527.2080.0000.0000.0000.0000.0000.000
172B297THR0-0.027-0.01129.1420.0010.0010.0000.0000.0000.000
173B298ILE0-0.0100.00927.9250.0090.0090.0000.0000.0000.000
174B299GLU-1-0.927-0.96928.192-0.134-0.1340.0000.0000.0000.000
175B300TYR0-0.028-0.03522.2790.0080.0080.0000.0000.0000.000
176B301ASP-1-0.817-0.88524.447-0.175-0.1750.0000.0000.0000.000
177B302TYR0-0.008-0.02620.367-0.035-0.0350.0000.0000.0000.000
178B303THR00.0340.01320.5300.0130.0130.0000.0000.0000.000
179B304MET0-0.011-0.00116.810-0.037-0.0370.0000.0000.0000.000