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: VR2R1

Calculation Name: 4EQ6-B-Xray321

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 4EQ6

Chain ID: B

ChEMBL ID:

UniProt ID: P40465

Base Structure: X-ray

Registration Date: 2021-09-07

Reference: C. Watanabe, S. Koyama, K. Kamisaka, D. Takaya, T. Honma et. al., Interaction energy analysis of Apo structure dataset on FMODB, To be pubulished.

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. 1.20200129
FMO calculation
FMO method FMO2-MP2/6-31G(d)
Fragmentation Auto
Number of fragment 219
LigandCharge
Software ABINIT-MP - Open Ver.1 Rev. 15 / 20190524
Total energy (hartree)
FMO2-HF: Electronic energy -2659728.714275
FMO2-HF: Nuclear repulsion 2571904.301794
FMO2-HF: Total energy -87824.412481
FMO2-MP2: Total energy -88080.110869


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:0:ACE )


Summations of interaction energy for fragment #1(B:0:ACE )
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.
1.5332.594-0.003-0.405-0.6520
Interaction energy analysis for fragmet #1(B:0:ACE )
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.023 / 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].
3B2GLU -1-0.793-0.8753.8160.0020.797-0.006-0.348-0.4410.000
4B3VAL 00.008-0.0027.1010.3120.3120.0000.0000.0000.000
5B4LEU 00.0210.0043.8570.0830.2240.002-0.034-0.1080.000
6B5LYS 10.8460.9094.0920.7230.8480.001-0.023-0.1030.000
7B6ASN 0-0.025-0.0177.7370.1610.1610.0000.0000.0000.000
8B7ILE 00.0150.02410.0680.0340.0340.0000.0000.0000.000
9B8ARG 10.8760.94711.9380.1630.1630.0000.0000.0000.000
10B9ILE 00.0170.00814.309-0.011-0.0110.0000.0000.0000.000
11B10TYR 0-0.013-0.01017.3400.0190.0190.0000.0000.0000.000
12B11PRO 00.0410.02420.923-0.003-0.0030.0000.0000.0000.000
13B12LEU 00.0460.01223.544-0.003-0.0030.0000.0000.0000.000
14B13SER 00.0660.02026.706-0.001-0.0010.0000.0000.0000.000
15B14ASN 0-0.008-0.01123.2540.0040.0040.0000.0000.0000.000
16B15PHE 0-0.031-0.01324.175-0.003-0.0030.0000.0000.0000.000
17B16ILE 0-0.041-0.01129.272-0.001-0.0010.0000.0000.0000.000
18B17THR 0-0.0200.01230.5530.0030.0030.0000.0000.0000.000
19B18SER 0-0.016-0.02131.790-0.002-0.0020.0000.0000.0000.000
20B19THR 00.0110.01533.6850.0020.0020.0000.0000.0000.000
21B20LYS 10.7960.88335.1580.0120.0120.0000.0000.0000.000
22B21ASN 00.0270.02037.9710.0010.0010.0000.0000.0000.000
23B22TYR 00.006-0.01435.879-0.001-0.0010.0000.0000.0000.000
24B23ILE 0-0.032-0.01042.2400.0010.0010.0000.0000.0000.000
25B24ASN 00.0240.01445.2390.0000.0000.0000.0000.0000.000
26B25LEU 0-0.0100.00247.3360.0010.0010.0000.0000.0000.000
27B26PRO 00.0320.02849.5500.0000.0000.0000.0000.0000.000
28B27ASN 00.035-0.00952.781-0.001-0.0010.0000.0000.0000.000
29B28GLU -1-0.881-0.92253.973-0.009-0.0090.0000.0000.0000.000
30B29LEU 0-0.065-0.04051.9650.0000.0000.0000.0000.0000.000
31B30ARG 10.7930.84944.6780.0140.0140.0000.0000.0000.000
32B31ASN 0-0.052-0.02849.528-0.001-0.0010.0000.0000.0000.000
33B32LEU 0-0.0180.01249.460-0.001-0.0010.0000.0000.0000.000
34B33ILE 0-0.049-0.00244.378-0.002-0.0020.0000.0000.0000.000
35B34SER 00.003-0.00540.5490.0010.0010.0000.0000.0000.000
36B35GLU -1-0.748-0.84740.694-0.016-0.0160.0000.0000.0000.000
37B36GLU -1-0.822-0.92634.987-0.026-0.0260.0000.0000.0000.000
38B37GLN 0-0.022-0.02138.7120.0020.0020.0000.0000.0000.000
39B38GLU -1-0.786-0.89840.483-0.013-0.0130.0000.0000.0000.000
40B39SER 0-0.0240.00238.2700.0020.0020.0000.0000.0000.000
41B40LYS 10.8030.90034.2120.0240.0240.0000.0000.0000.000
42B41LEU 0-0.0030.00438.8600.0000.0000.0000.0000.0000.000
43B42GLY 00.001-0.01441.4200.0020.0020.0000.0000.0000.000
44B43PHE 0-0.038-0.01740.5630.0020.0020.0000.0000.0000.000
45B44LEU 00.0280.01845.056-0.001-0.0010.0000.0000.0000.000
46B45HIS 00.0200.00548.2480.0010.0010.0000.0000.0000.000
47B46ILE 0-0.0050.00651.328-0.001-0.0010.0000.0000.0000.000
48B47ILE 0-0.020-0.00354.6340.0010.0010.0000.0000.0000.000
49B48GLU -1-0.701-0.83457.645-0.008-0.0080.0000.0000.0000.000
50B49SER 00.0580.00360.9120.0000.0000.0000.0000.0000.000
51B50ASP -1-0.890-0.90864.267-0.007-0.0070.0000.0000.0000.000
52B51PHE 00.0130.00664.1860.0000.0000.0000.0000.0000.000
53B52LYS 10.9530.96964.5630.0050.0050.0000.0000.0000.000
54B53PRO 00.0100.01660.5920.0000.0000.0000.0000.0000.000
55B54SER 00.007-0.04159.7060.0000.0000.0000.0000.0000.000
56B55VAL 00.0430.00560.3200.0000.0000.0000.0000.0000.000
57B56ALA 00.0170.01656.2320.0000.0000.0000.0000.0000.000
58B57LEU 00.0320.01755.3560.0000.0000.0000.0000.0000.000
59B58GLN 0-0.023-0.02356.2550.0010.0010.0000.0000.0000.000
60B59LYS 10.8440.90155.7320.0070.0070.0000.0000.0000.000
61B60LEU 0-0.0310.00650.6520.0000.0000.0000.0000.0000.000
62B61VAL 0-0.0040.00052.1300.0000.0000.0000.0000.0000.000
63B62ASN 0-0.044-0.01053.6230.0010.0010.0000.0000.0000.000
64B63CYS 0-0.079-0.01549.9940.0000.0000.0000.0000.0000.000
65B64THR 0-0.0310.00350.3000.0000.0000.0000.0000.0000.000
66B65THR 00.013-0.00849.0590.0000.0000.0000.0000.0000.000
67B66GLY 00.008-0.00550.5390.0000.0000.0000.0000.0000.000
68B67ASP -1-0.878-0.93647.8070.0070.0070.0000.0000.0000.000
69B68GLU -1-0.865-0.91645.6830.0010.0010.0000.0000.0000.000
70B69LYS 10.8920.94049.463-0.004-0.0040.0000.0000.0000.000
71B70ILE 0-0.033-0.00649.8910.0000.0000.0000.0000.0000.000
72B71LEU 00.0010.00951.1540.0000.0000.0000.0000.0000.000
73B72ILE 0-0.002-0.00752.999-0.001-0.0010.0000.0000.0000.000
74B73ILE 0-0.002-0.01752.7200.0010.0010.0000.0000.0000.000
75B74ASP -1-0.729-0.84256.772-0.004-0.0040.0000.0000.0000.000
76B75ILE 0-0.016-0.01157.7440.0000.0000.0000.0000.0000.000
77B76VAL 0-0.016-0.01561.5680.0000.0000.0000.0000.0000.000
78B77SER 00.0090.03263.7900.0000.0000.0000.0000.0000.000
79B78ILE 0-0.062-0.01863.9470.0000.0000.0000.0000.0000.000
80B79TRP 0-0.048-0.05758.3320.0010.0010.0000.0000.0000.000
81B80SER 0-0.049-0.04962.1660.0010.0010.0000.0000.0000.000
82B81GLN 0-0.031-0.03063.6870.0010.0010.0000.0000.0000.000
83B82GLN 00.0630.01466.6850.0000.0000.0000.0000.0000.000
84B83LYS 10.8840.95468.0520.0020.0020.0000.0000.0000.000
85B84GLN 0-0.062-0.03764.7560.0000.0000.0000.0000.0000.000
86B85ARG 10.8980.97162.575-0.001-0.0010.0000.0000.0000.000
87B86GLN 00.0430.01356.8500.0000.0000.0000.0000.0000.000
88B87HIS 00.0320.00355.3540.0010.0010.0000.0000.0000.000
89B88GLY 00.0100.01755.1590.0010.0010.0000.0000.0000.000
90B89ALA 0-0.023-0.00654.2520.0000.0000.0000.0000.0000.000
91B90ILE 00.0050.01952.8620.0010.0010.0000.0000.0000.000
92B91TYR 00.0330.00656.304-0.001-0.0010.0000.0000.0000.000
93B92MET 0-0.008-0.00456.7710.0000.0000.0000.0000.0000.000
94B93ASN 0-0.062-0.05258.7050.0000.0000.0000.0000.0000.000
95B94SER 00.0780.03661.3680.0000.0000.0000.0000.0000.000
96B95LEU 00.0540.02263.1780.0000.0000.0000.0000.0000.000
97B96SER 0-0.075-0.03160.8120.0000.0000.0000.0000.0000.000
98B97CYS 0-0.033-0.01657.5720.0000.0000.0000.0000.0000.000
99B98ILE 00.0630.04260.0650.0000.0000.0000.0000.0000.000
100B99ASN 00.0140.01860.545-0.001-0.0010.0000.0000.0000.000
101B100ILE 00.020-0.00254.0810.0000.0000.0000.0000.0000.000
102B101THR 00.003-0.00955.8860.0000.0000.0000.0000.0000.000
103B102GLY 00.0430.02556.1980.0000.0000.0000.0000.0000.000
104B103LEU 00.0040.00053.7860.0000.0000.0000.0000.0000.000
105B104ILE 0-0.053-0.03650.6430.0000.0000.0000.0000.0000.000
106B105VAL 00.0250.02151.6720.0000.0000.0000.0000.0000.000
107B106PHE 0-0.033-0.01752.6010.0010.0010.0000.0000.0000.000
108B107LEU 00.006-0.01049.1150.0010.0010.0000.0000.0000.000
109B108GLU -1-0.923-0.97947.880-0.003-0.0030.0000.0000.0000.000
110B109LEU 00.0300.02647.9630.0010.0010.0000.0000.0000.000
111B110LEU 0-0.058-0.02347.8290.0010.0010.0000.0000.0000.000
112B111TYR 0-0.042-0.04039.0150.0000.0000.0000.0000.0000.000
113B112ASP -1-0.918-0.95444.3330.0030.0030.0000.0000.0000.000
114B113SER 0-0.072-0.09445.6150.0020.0020.0000.0000.0000.000
115B114PRO 00.0500.01945.3880.0000.0000.0000.0000.0000.000
116B115MET 00.011-0.00548.5490.0000.0000.0000.0000.0000.000
117B116ASP -1-0.839-0.85950.9230.0070.0070.0000.0000.0000.000
118B117ALA 0-0.041-0.02351.371-0.001-0.0010.0000.0000.0000.000
119B118LEU 00.035-0.00349.688-0.001-0.0010.0000.0000.0000.000
120B119ARG 10.9380.97253.910-0.008-0.0080.0000.0000.0000.000
121B120ARG 10.9020.95356.321-0.002-0.0020.0000.0000.0000.000
122B121CYS 0-0.112-0.03955.945-0.001-0.0010.0000.0000.0000.000
123B122GLN 0-0.071-0.03358.3960.0000.0000.0000.0000.0000.000
124B123VAL 00.0350.05453.7670.0000.0000.0000.0000.0000.000
125B124ASP -1-0.879-0.94556.8290.0070.0070.0000.0000.0000.000
126B125ASN 0-0.052-0.03453.8750.0010.0010.0000.0000.0000.000
127B126PHE 00.040-0.00649.658-0.001-0.0010.0000.0000.0000.000
128B127ASN 0-0.045-0.00549.1670.0010.0010.0000.0000.0000.000
129B128PHE 0-0.023-0.02449.044-0.001-0.0010.0000.0000.0000.000
130B129GLN 00.0380.05442.6120.0020.0020.0000.0000.0000.000
131B130LEU 0-0.035-0.03145.977-0.001-0.0010.0000.0000.0000.000
132B131ARG 10.8870.92245.2720.0020.0020.0000.0000.0000.000
133B132GLY 00.011-0.01745.623-0.001-0.0010.0000.0000.0000.000
134B133ILE 0-0.034-0.01247.5100.0010.0010.0000.0000.0000.000
135B134VAL 00.0210.00350.030-0.001-0.0010.0000.0000.0000.000
136B135ILE 0-0.031-0.01251.5350.0010.0010.0000.0000.0000.000
137B136ASP -1-0.786-0.88054.918-0.007-0.0070.0000.0000.0000.000
138B137ASN 00.0450.02658.3040.0000.0000.0000.0000.0000.000
139B138LEU 00.007-0.01853.0130.0000.0000.0000.0000.0000.000
140B139SER 0-0.020-0.01757.7030.0000.0000.0000.0000.0000.000
141B140PHE 0-0.0060.00560.6970.0000.0000.0000.0000.0000.000
142B141LEU 0-0.0200.00656.3240.0000.0000.0000.0000.0000.000
143B142ASN 0-0.122-0.08057.251-0.001-0.0010.0000.0000.0000.000
144B143NME 00.0950.06260.9360.0000.0000.0000.0000.0000.000
145B152ACE 00.0660.03357.3310.0000.0000.0000.0000.0000.000
146B153ASN 0-0.021-0.03356.5140.0010.0010.0000.0000.0000.000
147B154LEU 00.1060.03850.6920.0000.0000.0000.0000.0000.000
148B155SER 00.0190.02750.8260.0000.0000.0000.0000.0000.000
149B156LYS 10.9060.96050.7350.0080.0080.0000.0000.0000.000
150B157PHE 00.0530.01351.7690.0000.0000.0000.0000.0000.000
151B158GLU -1-0.889-0.92644.683-0.017-0.0170.0000.0000.0000.000
152B159LYS 10.9080.95846.8030.0060.0060.0000.0000.0000.000
153B160LEU 00.0130.00247.6060.0010.0010.0000.0000.0000.000
154B161PHE 00.0560.03742.2920.0010.0010.0000.0000.0000.000
155B162LYS 10.9490.97841.1700.0120.0120.0000.0000.0000.000
156B163ILE 0-0.029-0.01643.1490.0000.0000.0000.0000.0000.000
157B164LEU 00.0480.02144.7550.0010.0010.0000.0000.0000.000
158B165ARG 10.9550.98337.5400.0180.0180.0000.0000.0000.000
159B166LYS 10.8800.95439.9190.0030.0030.0000.0000.0000.000
160B167LEU 00.0180.00940.6430.0010.0010.0000.0000.0000.000
161B168ARG 10.8500.94339.1420.0110.0110.0000.0000.0000.000
162B169GLU -1-0.927-0.95134.939-0.011-0.0110.0000.0000.0000.000
163B170PHE 0-0.055-0.01636.9470.0010.0010.0000.0000.0000.000
164B171LEU 00.0200.00039.0600.0020.0020.0000.0000.0000.000
165B172GLY 00.0360.03539.4630.0010.0010.0000.0000.0000.000
166B173CYS 0-0.0430.01140.239-0.001-0.0010.0000.0000.0000.000
167B174TRP 00.0300.01943.033-0.002-0.0020.0000.0000.0000.000
168B175ILE 0-0.015-0.02244.5820.0010.0010.0000.0000.0000.000
169B176ILE 00.0130.01147.230-0.001-0.0010.0000.0000.0000.000
170B177THR 0-0.032-0.02250.3650.0010.0010.0000.0000.0000.000
171B178LYS 10.8390.91052.9530.0070.0070.0000.0000.0000.000
172B179SER 0-0.058-0.02856.2720.0000.0000.0000.0000.0000.000
173B180PHE 00.0110.00858.4320.0000.0000.0000.0000.0000.000
174B181PRO 00.0560.02060.737-0.001-0.0010.0000.0000.0000.000
175B182THR 0-0.011-0.02762.0650.0000.0000.0000.0000.0000.000
176B183ASP -1-0.921-0.94563.595-0.009-0.0090.0000.0000.0000.000
177B184PHE 00.0320.01664.0770.0000.0000.0000.0000.0000.000
178B185TYR 0-0.045-0.02559.8470.0000.0000.0000.0000.0000.000
179B186ASN 00.0240.02165.8160.0000.0000.0000.0000.0000.000
180B187GLY 00.0170.01868.8630.0000.0000.0000.0000.0000.000
181B188ILE 00.0280.00370.8830.0000.0000.0000.0000.0000.000
182B189GLU -1-0.919-0.96274.505-0.006-0.0060.0000.0000.0000.000
183B190ASN 0-0.033-0.02072.5680.0000.0000.0000.0000.0000.000
184B191THR 0-0.028-0.00472.9420.0000.0000.0000.0000.0000.000
185B192LEU 0-0.052-0.01767.8260.0000.0000.0000.0000.0000.000
186B193VAL 0-0.078-0.03268.394-0.001-0.0010.0000.0000.0000.000
187B194NME 0-0.0150.00069.0480.0000.0000.0000.0000.0000.000
188B207ACE 00.0350.00755.3890.0000.0000.0000.0000.0000.000
189B208PRO 0-0.0350.00155.9980.0000.0000.0000.0000.0000.000
190B209THR 00.049-0.00455.9100.0010.0010.0000.0000.0000.000
191B210LYS 10.9460.99157.8090.0110.0110.0000.0000.0000.000
192B211LEU 0-0.004-0.00353.7300.0010.0010.0000.0000.0000.000
193B212PRO 0-0.010-0.02051.783-0.001-0.0010.0000.0000.0000.000
194B213ASP -1-0.794-0.90548.780-0.022-0.0220.0000.0000.0000.000
195B214SER 0-0.0290.00646.901-0.001-0.0010.0000.0000.0000.000
196B215TYR 00.023-0.02046.6420.0000.0000.0000.0000.0000.000
197B216MET 0-0.017-0.00647.6530.0000.0000.0000.0000.0000.000
198B217LYS 10.8140.90943.4640.0240.0240.0000.0000.0000.000
199B218GLY 0-0.002-0.00643.279-0.001-0.0010.0000.0000.0000.000
200B219MET 0-0.087-0.02543.4330.0010.0010.0000.0000.0000.000
201B220ASP -1-0.768-0.86041.222-0.021-0.0210.0000.0000.0000.000
202B221LEU 0-0.061-0.04243.645-0.001-0.0010.0000.0000.0000.000
203B222ILE 0-0.011-0.00246.9230.0010.0010.0000.0000.0000.000
204B223ILE 0-0.009-0.01650.401-0.001-0.0010.0000.0000.0000.000
205B224TYR 0-0.040-0.01853.3210.0010.0010.0000.0000.0000.000
206B225ARG 10.8820.93656.8400.0080.0080.0000.0000.0000.000
207B226GLU -1-0.835-0.89959.830-0.013-0.0130.0000.0000.0000.000
208B227VAL 0-0.033-0.03662.8970.0000.0000.0000.0000.0000.000
209B228VAL 0-0.0120.01265.0490.0000.0000.0000.0000.0000.000
210B229ASP -1-0.773-0.86867.570-0.010-0.0100.0000.0000.0000.000
211B230GLY 00.0030.00569.0870.0000.0000.0000.0000.0000.000
212B231ARG 10.7740.87564.5590.0110.0110.0000.0000.0000.000
213B232PRO 0-0.013-0.01062.7520.0000.0000.0000.0000.0000.000
214B233GLN 00.0260.01360.2720.0000.0000.0000.0000.0000.000
215B234TYR 00.0510.01055.9010.0000.0000.0000.0000.0000.000
216B235ARG 10.8690.92755.3030.0150.0150.0000.0000.0000.000
217B236ARG 10.9970.99744.4270.0230.0230.0000.0000.0000.000
218B237ILE 0-0.040-0.02351.3670.0000.0000.0000.0000.0000.000
219B238NME 00.0050.01348.3840.0000.0000.0000.0000.0000.000