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: KGNK3

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 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 179
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2022889.919262
FMO2-HF: Nuclear repulsion 1949505.635502
FMO2-HF: Total energy -73384.28376
FMO2-MP2: Total energy -73595.026809


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.
-15.795-12.60112.174-6.648-8.722-0.043
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 : -0.007 / q_NPA : -0.029
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].
3B25MET00.0120.0083.142-2.2600.8240.048-1.464-1.6680.003
4B26ALA0-0.008-0.0052.183-1.312-0.9332.718-1.038-2.0590.000
5B27PHE00.0090.0033.522-0.1810.0810.0060.113-0.3810.000
6B28LYS10.9720.9725.7110.9430.9430.0000.0000.0000.000
7B29GLU-1-0.897-0.9356.9060.2990.2990.0000.0000.0000.000
8B30LYS10.8730.9255.413-0.478-0.4780.0000.0000.0000.000
9B31GLY00.0070.0298.1800.0420.0420.0000.0000.0000.000
10B32VAL0-0.084-0.0374.689-0.0210.065-0.001-0.006-0.0800.000
11B33LEU00.0140.0084.963-0.525-0.5250.0000.0000.0000.000
12B34SER0-0.0040.0253.0131.0771.8330.124-0.227-0.6530.001
13B35VAL00.0390.0034.972-0.069-0.066-0.001-0.0040.0020.000
14B36SER00.0180.0115.519-0.028-0.0280.0000.0000.0000.000
15B37GLU-1-0.720-0.8641.945-14.726-16.2779.281-3.981-3.750-0.047
16B38PHE0-0.040-0.0196.2120.0590.0590.0000.0000.0000.000
17B39VAL0-0.003-0.0059.1460.0730.0730.0000.0000.0000.000
18B40LEU00.0400.0258.5480.0340.0340.0000.0000.0000.000
19B41ALA0-0.002-0.0069.5130.0670.0670.0000.0000.0000.000
20B42GLY0-0.016-0.02311.1670.0790.0790.0000.0000.0000.000
21B43ASP-1-0.816-0.90413.696-0.167-0.1670.0000.0000.0000.000
22B44ASN0-0.020-0.01413.7120.1110.1110.0000.0000.0000.000
23B45LEU0-0.037-0.02015.4520.0250.0250.0000.0000.0000.000
24B46VAL00.0040.00717.3200.0280.0280.0000.0000.0000.000
25B47SER0-0.070-0.02118.7250.0190.0190.0000.0000.0000.000
26B48LYS10.8920.94418.5360.2580.2580.0000.0000.0000.000
27B49CYS0-0.034-0.00220.9380.0080.0080.0000.0000.0000.000
28B50PRO00.0540.02622.671-0.004-0.0040.0000.0000.0000.000
29B51THR0-0.0010.00924.5640.0090.0090.0000.0000.0000.000
30B52TRP0-0.071-0.03820.7010.0010.0010.0000.0000.0000.000
31B53SER0-0.0030.00422.5840.0060.0060.0000.0000.0000.000
32B54TRP0-0.018-0.02114.018-0.009-0.0090.0000.0000.0000.000
33B55GLU-1-0.886-0.94220.747-0.080-0.0800.0000.0000.0000.000
34B56SER00.0200.00821.210-0.004-0.0040.0000.0000.0000.000
35B57GLY0-0.038-0.01723.2320.0010.0010.0000.0000.0000.000
36B58ASP-1-0.865-0.92725.344-0.042-0.0420.0000.0000.0000.000
37B59ALA00.005-0.01225.5190.0000.0000.0000.0000.0000.000
38B60SER0-0.028-0.02025.7550.0020.0020.0000.0000.0000.000
39B61LYS10.8560.94024.0240.0560.0560.0000.0000.0000.000
40B62ARG10.9340.98719.8750.0100.0100.0000.0000.0000.000
41B63LYS10.9230.96616.3410.0850.0850.0000.0000.0000.000
42B64PRO0-0.016-0.00917.224-0.007-0.0070.0000.0000.0000.000
43B65TYR0-0.003-0.00912.1250.0230.0230.0000.0000.0000.000
44B66LEU0-0.019-0.01012.339-0.012-0.0120.0000.0000.0000.000
45B67PRO00.0750.03913.8270.0190.0190.0000.0000.0000.000
46B68SER0-0.026-0.00917.068-0.011-0.0110.0000.0000.0000.000
47B69ASP-1-0.915-0.96220.405-0.074-0.0740.0000.0000.0000.000
48B70LYS10.8640.93016.2030.1360.1360.0000.0000.0000.000
49B71GLN0-0.019-0.01016.656-0.016-0.0160.0000.0000.0000.000
50B72PHE0-0.053-0.04417.274-0.018-0.0180.0000.0000.0000.000
51B73LEU00.0250.02915.1470.0070.0070.0000.0000.0000.000
52B74ILE0-0.020-0.01819.4650.0010.0010.0000.0000.0000.000
53B75THR00.0140.02222.9730.0020.0020.0000.0000.0000.000
54B76ARG10.9350.95525.4270.0950.0950.0000.0000.0000.000
55B77ASN0-0.038-0.02029.1590.0010.0010.0000.0000.0000.000
56B78VAL00.0450.03627.2860.0010.0010.0000.0000.0000.000
57B79PRO00.0160.02030.7320.0040.0040.0000.0000.0000.000
58B80CYS0-0.0080.02132.341-0.006-0.0060.0000.0000.0000.000
59B81LEU00.015-0.00334.2250.0060.0060.0000.0000.0000.000
60B82ARG10.9500.98235.7070.0830.0830.0000.0000.0000.000
61B83ARG10.8820.92735.9540.0640.0640.0000.0000.0000.000
62B84ALA00.0440.02732.874-0.001-0.0010.0000.0000.0000.000
63B85ALA0-0.063-0.01334.622-0.001-0.0010.0000.0000.0000.000
64B86SER0-0.047-0.01736.6010.0030.0030.0000.0000.0000.000
65B190LEU0-0.009-0.01441.830-0.001-0.0010.0000.0000.0000.000
66B191ARG10.9971.00741.7820.0490.0490.0000.0000.0000.000
67B192THR00.0150.00438.993-0.002-0.0020.0000.0000.0000.000
68B193ARG10.8520.92435.4610.0710.0710.0000.0000.0000.000
69B194THR00.0230.01433.971-0.004-0.0040.0000.0000.0000.000
70B195TYR0-0.041-0.09229.1250.0020.0020.0000.0000.0000.000
71B196ASP-1-0.842-0.90928.390-0.091-0.0910.0000.0000.0000.000
72B197LEU0-0.032-0.02823.6860.0020.0020.0000.0000.0000.000
73B198SER00.0010.00421.750-0.006-0.0060.0000.0000.0000.000
74B199ILE00.007-0.00115.733-0.007-0.0070.0000.0000.0000.000
75B200THR0-0.0090.00617.2550.0070.0070.0000.0000.0000.000
76B201TYR0-0.002-0.0427.2120.0840.0840.0000.0000.0000.000
77B202ASP-1-0.863-0.93613.524-0.074-0.0740.0000.0000.0000.000
78B203LYS10.9450.9579.254-0.096-0.0960.0000.0000.0000.000
79B204TYR0-0.0330.00010.8920.0390.0390.0000.0000.0000.000
80B205TYR00.021-0.00411.6570.0340.0340.0000.0000.0000.000
81B206GLN0-0.062-0.0145.6680.0660.0660.0000.0000.0000.000
82B207THR00.0440.0198.405-0.175-0.1750.0000.0000.0000.000
83B208PRO00.0050.00411.0160.0710.0710.0000.0000.0000.000
84B209ARG10.9060.95213.7260.1470.1470.0000.0000.0000.000
85B210VAL00.0600.03517.4260.0000.0000.0000.0000.0000.000
86B211TRP0-0.080-0.03219.7160.0220.0220.0000.0000.0000.000
87B212LEU00.0320.01023.613-0.005-0.0050.0000.0000.0000.000
88B213THR0-0.036-0.01726.8370.0090.0090.0000.0000.0000.000
89B214GLY00.0690.03730.193-0.003-0.0030.0000.0000.0000.000
90B215TYR0-0.041-0.02832.1570.0060.0060.0000.0000.0000.000
91B216ASP-1-0.836-0.93936.274-0.051-0.0510.0000.0000.0000.000
92B217GLU-1-0.947-0.97139.529-0.049-0.0490.0000.0000.0000.000
93B218SER0-0.052-0.01941.7690.0000.0000.0000.0000.0000.000
94B219ARG10.8230.91732.8170.0730.0730.0000.0000.0000.000
95B220MET00.0470.03439.7360.0010.0010.0000.0000.0000.000
96B221LEU0-0.014-0.00834.409-0.003-0.0030.0000.0000.0000.000
97B222LEU0-0.0040.00935.3490.0030.0030.0000.0000.0000.000
98B223GLN00.0370.01036.124-0.002-0.0020.0000.0000.0000.000
99B224PRO00.0190.00132.263-0.003-0.0030.0000.0000.0000.000
100B225GLU-1-0.910-0.95933.218-0.053-0.0530.0000.0000.0000.000
101B226LEU00.0110.00335.354-0.001-0.0010.0000.0000.0000.000
102B227VAL00.0030.00930.186-0.002-0.0020.0000.0000.0000.000
103B228MET0-0.035-0.01730.401-0.007-0.0070.0000.0000.0000.000
104B229GLU-1-0.923-0.95433.168-0.058-0.0580.0000.0000.0000.000
105B230ASP-1-0.773-0.85931.881-0.079-0.0790.0000.0000.0000.000
106B231VAL0-0.061-0.01828.212-0.009-0.0090.0000.0000.0000.000
107B232SER00.0280.01429.1240.0100.0100.0000.0000.0000.000
108B233GLN0-0.043-0.04030.425-0.003-0.0030.0000.0000.0000.000
109B234ASP-1-0.782-0.87429.953-0.089-0.0890.0000.0000.0000.000
110B235HIS0-0.042-0.03928.800-0.007-0.0070.0000.0000.0000.000
111B236ALA00.0130.00726.119-0.005-0.0050.0000.0000.0000.000
112B237ARG10.9050.95624.9800.0700.0700.0000.0000.0000.000
113B238LYS10.7930.89222.3240.1170.1170.0000.0000.0000.000
114B239THR00.0040.00324.4720.0100.0100.0000.0000.0000.000
115B240VAL0-0.0030.00024.686-0.009-0.0090.0000.0000.0000.000
116B241THR0-0.010-0.00125.0660.0100.0100.0000.0000.0000.000
117B242ILE00.0210.01527.076-0.007-0.0070.0000.0000.0000.000
118B243GLU-1-0.909-0.97725.510-0.058-0.0580.0000.0000.0000.000
119B244ASP-1-0.898-0.94226.961-0.050-0.0500.0000.0000.0000.000
120B245HIS00.0300.01422.5490.0040.0040.0000.0000.0000.000
121B246PRO0-0.045-0.03719.8830.0100.0100.0000.0000.0000.000
122B247HIS0-0.022-0.02219.399-0.007-0.0070.0000.0000.0000.000
123B248LEU00.0320.02523.8530.0040.0040.0000.0000.0000.000
124B249PRO00.0670.03627.2790.0020.0020.0000.0000.0000.000
125B250GLY00.0330.01930.416-0.005-0.0050.0000.0000.0000.000
126B251LYS10.8950.95329.8090.0460.0460.0000.0000.0000.000
127B252HIS10.8640.93626.8260.0790.0790.0000.0000.0000.000
128B253ALA00.0730.05027.8270.0010.0010.0000.0000.0000.000
129B254SER0-0.049-0.04422.465-0.010-0.0100.0000.0000.0000.000
130B255VAL00.0520.02921.1840.0100.0100.0000.0000.0000.000
131B256HIS00.0600.04019.519-0.024-0.0240.0000.0000.0000.000
132B257PRO00.0520.00115.438-0.007-0.0070.0000.0000.0000.000
133B258CYS0-0.064-0.02615.989-0.019-0.0190.0000.0000.0000.000
134B259ARG10.9260.95016.6450.1080.1080.0000.0000.0000.000
135B260HIS00.0290.03414.609-0.005-0.0050.0000.0000.0000.000
136B261GLY00.0640.05311.973-0.045-0.0450.0000.0000.0000.000
137B262ALA0-0.010-0.02212.814-0.022-0.0220.0000.0000.0000.000
138B263VAL0-0.058-0.02215.3160.0030.0030.0000.0000.0000.000
139B264MET00.007-0.00411.576-0.021-0.0210.0000.0000.0000.000
140B265LYS10.9781.00011.2630.0920.0920.0000.0000.0000.000
141B266LYS10.9500.98312.9100.1740.1740.0000.0000.0000.000
142B267ILE0-0.013-0.01115.3910.0190.0190.0000.0000.0000.000
143B268ILE00.0020.00910.5150.0020.0020.0000.0000.0000.000
144B269ASP-1-0.887-0.94313.764-0.182-0.1820.0000.0000.0000.000
145B270VAL0-0.070-0.04015.5810.0210.0210.0000.0000.0000.000
146B271LEU0-0.088-0.05515.5660.0250.0250.0000.0000.0000.000
147B272MET00.0590.02911.7750.0000.0000.0000.0000.0000.000
148B273SER0-0.0130.01116.3610.0250.0250.0000.0000.0000.000
149B274ARG10.8810.94219.7100.2160.2160.0000.0000.0000.000
150B275GLY00.0420.03519.7970.0140.0140.0000.0000.0000.000
151B276VAL0-0.071-0.02716.485-0.007-0.0070.0000.0000.0000.000
152B277GLU-1-0.900-0.95713.104-0.284-0.2840.0000.0000.0000.000
153B278PRO0-0.082-0.02712.123-0.013-0.0130.0000.0000.0000.000
154B279GLU-1-0.888-0.9508.867-0.696-0.6960.0000.0000.0000.000
155B280VAL0-0.004-0.0153.8230.3140.489-0.001-0.041-0.1330.000
156B281ASP-1-0.840-0.9137.104-0.524-0.5240.0000.0000.0000.000
157B282LYS10.9370.9529.8320.6730.6730.0000.0000.0000.000
158B283TYR0-0.018-0.0147.8110.2010.2010.0000.0000.0000.000
159B284LEU00.023-0.00110.8450.1030.1030.0000.0000.0000.000
160B285PHE00.0240.03113.8300.0560.0560.0000.0000.0000.000
161B286LEU0-0.026-0.00712.2350.0600.0600.0000.0000.0000.000
162B287PHE0-0.024-0.03913.7430.0520.0520.0000.0000.0000.000
163B288LEU00.0190.00915.6640.0440.0440.0000.0000.0000.000
164B289LYS10.9901.02518.3500.3120.3120.0000.0000.0000.000
165B290PHE0-0.060-0.02518.3240.0260.0260.0000.0000.0000.000
166B291MET00.0160.01019.1690.0270.0270.0000.0000.0000.000
167B292ALA00.0570.04921.5800.0200.0200.0000.0000.0000.000
168B293SER0-0.081-0.04223.5760.0180.0180.0000.0000.0000.000
169B294VAL0-0.047-0.02623.1630.0140.0140.0000.0000.0000.000
170B295ILE0-0.024-0.01524.4120.0130.0130.0000.0000.0000.000
171B296PRO00.0150.01627.604-0.003-0.0030.0000.0000.0000.000
172B297THR0-0.044-0.02929.377-0.002-0.0020.0000.0000.0000.000
173B298ILE0-0.022-0.00427.5550.0050.0050.0000.0000.0000.000
174B299GLU-1-0.953-0.97328.185-0.106-0.1060.0000.0000.0000.000
175B300TYR0-0.038-0.04122.0230.0040.0040.0000.0000.0000.000
176B301ASP-1-0.854-0.92924.366-0.145-0.1450.0000.0000.0000.000
177B302TYR00.007-0.03220.199-0.027-0.0270.0000.0000.0000.000
178B303THR00.0100.01820.6910.0110.0110.0000.0000.0000.000
179B304MET0-0.020-0.01117.042-0.028-0.0280.0000.0000.0000.000