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: 22YKR

Calculation Name: 4EQ6-B-Xray372

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: 2023-06-20

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 OptHSide
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 -2633856.195007
FMO2-HF: Nuclear repulsion 2546543.876826
FMO2-HF: Total energy -87312.31818
FMO2-MP2: Total energy -87566.399812


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.
-7.685-1.4223.483-2.842-6.9030.001
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 : 0.013 / 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].
3B3VAL00.0190.0002.270-2.7180.4022.386-1.521-3.9840.003
4B4LEU00.0160.0032.149-1.7650.0191.003-0.829-1.958-0.004
5B5LYS10.8580.9143.076-3.785-2.4260.094-0.492-0.9610.002
6B6ASN0-0.018-0.0045.9590.4650.4650.0000.0000.0000.000
7B7ILE00.0100.0277.0520.1130.1130.0000.0000.0000.000
8B8ARG10.8430.9188.900-0.007-0.0070.0000.0000.0000.000
9B9ILE00.0160.00912.1470.0160.0160.0000.0000.0000.000
10B10TYR0-0.004-0.00515.080-0.010-0.0100.0000.0000.0000.000
11B11PRO00.0380.02318.7270.0030.0030.0000.0000.0000.000
12B12LEU00.0480.01321.763-0.004-0.0040.0000.0000.0000.000
13B13SER00.0690.03024.510-0.003-0.0030.0000.0000.0000.000
14B14ASN0-0.013-0.00821.793-0.002-0.0020.0000.0000.0000.000
15B15PHE0-0.022-0.00920.877-0.003-0.0030.0000.0000.0000.000
16B16ILE0-0.041-0.01226.648-0.003-0.0030.0000.0000.0000.000
17B17THR0-0.028-0.00628.742-0.001-0.0010.0000.0000.0000.000
18B18SER0-0.013-0.01029.623-0.001-0.0010.0000.0000.0000.000
19B19THR00.0140.01131.8490.0010.0010.0000.0000.0000.000
20B20LYS10.7650.87132.396-0.010-0.0100.0000.0000.0000.000
21B21ASN00.0430.02635.8040.0010.0010.0000.0000.0000.000
22B22TYR00.003-0.01132.997-0.001-0.0010.0000.0000.0000.000
23B23ILE0-0.040-0.01539.5820.0000.0000.0000.0000.0000.000
24B24ASN00.0000.00242.2980.0000.0000.0000.0000.0000.000
25B25LEU00.0140.01144.1690.0000.0000.0000.0000.0000.000
26B26PRO00.0320.02946.4310.0000.0000.0000.0000.0000.000
27B27ASN00.036-0.00849.523-0.001-0.0010.0000.0000.0000.000
28B28GLU-1-0.862-0.92550.7000.0010.0010.0000.0000.0000.000
29B29LEU0-0.065-0.03948.652-0.001-0.0010.0000.0000.0000.000
30B30ARG10.7980.85241.439-0.004-0.0040.0000.0000.0000.000
31B31ASN0-0.067-0.04145.9150.0000.0000.0000.0000.0000.000
32B32LEU0-0.0080.01945.762-0.001-0.0010.0000.0000.0000.000
33B33ILE0-0.040-0.01340.693-0.001-0.0010.0000.0000.0000.000
34B34SER00.0150.00536.8040.0010.0010.0000.0000.0000.000
35B35GLU-1-0.761-0.85737.1420.0050.0050.0000.0000.0000.000
36B36GLU-1-0.811-0.90931.5550.0070.0070.0000.0000.0000.000
37B37GLN0-0.012-0.01435.1770.0010.0010.0000.0000.0000.000
38B38GLU-1-0.809-0.89436.9100.0030.0030.0000.0000.0000.000
39B39SER0-0.0220.00435.2070.0010.0010.0000.0000.0000.000
40B40LYS10.7960.88230.951-0.007-0.0070.0000.0000.0000.000
41B41LEU0-0.0050.01135.704-0.001-0.0010.0000.0000.0000.000
42B42GLY00.015-0.01938.5480.0010.0010.0000.0000.0000.000
43B43PHE0-0.052-0.02737.4220.0010.0010.0000.0000.0000.000
44B44LEU00.0200.01542.053-0.001-0.0010.0000.0000.0000.000
45B45HIS00.0250.01145.1000.0010.0010.0000.0000.0000.000
46B46ILE00.0100.01148.0080.0000.0000.0000.0000.0000.000
47B47ILE0-0.029-0.00951.2510.0000.0000.0000.0000.0000.000
48B48GLU-1-0.692-0.83154.0450.0000.0000.0000.0000.0000.000
49B49SER00.0530.00857.4020.0000.0000.0000.0000.0000.000
50B50ASP-1-0.865-0.89460.9130.0000.0000.0000.0000.0000.000
51B51PHE00.0460.02161.0660.0000.0000.0000.0000.0000.000
52B52LYS10.9580.97161.654-0.001-0.0010.0000.0000.0000.000
53B53PRO00.0050.01357.6620.0000.0000.0000.0000.0000.000
54B54SER00.011-0.02556.6040.0000.0000.0000.0000.0000.000
55B55VAL00.027-0.00257.4270.0000.0000.0000.0000.0000.000
56B56ALA00.0390.03053.0400.0000.0000.0000.0000.0000.000
57B57LEU00.0170.00852.2870.0000.0000.0000.0000.0000.000
58B58GLN0-0.041-0.04053.4380.0010.0010.0000.0000.0000.000
59B59LYS10.8440.91152.865-0.002-0.0020.0000.0000.0000.000
60B60LEU0-0.0240.00947.6680.0000.0000.0000.0000.0000.000
61B61VAL00.0030.00549.4780.0010.0010.0000.0000.0000.000
62B62ASN0-0.052-0.00851.2290.0010.0010.0000.0000.0000.000
63B63CYS0-0.083-0.03047.6300.0000.0000.0000.0000.0000.000
64B64THR0-0.041-0.00548.0630.0010.0010.0000.0000.0000.000
65B65THR0-0.013-0.01846.9750.0000.0000.0000.0000.0000.000
66B66GLY00.0240.00248.8470.0000.0000.0000.0000.0000.000
67B67ASP-1-0.869-0.93546.5110.0140.0140.0000.0000.0000.000
68B68GLU-1-0.813-0.87444.2200.0120.0120.0000.0000.0000.000
69B69LYS10.8400.91847.759-0.011-0.0110.0000.0000.0000.000
70B70ILE0-0.035-0.00547.9900.0000.0000.0000.0000.0000.000
71B71LEU00.0090.01349.1740.0000.0000.0000.0000.0000.000
72B72ILE00.005-0.00350.809-0.001-0.0010.0000.0000.0000.000
73B73ILE0-0.002-0.01450.7050.0000.0000.0000.0000.0000.000
74B74ASP-1-0.726-0.84654.5430.0030.0030.0000.0000.0000.000
75B75ILE0-0.021-0.01255.1920.0000.0000.0000.0000.0000.000
76B76VAL0-0.015-0.01459.1470.0000.0000.0000.0000.0000.000
77B77SER0-0.0040.02261.3860.0000.0000.0000.0000.0000.000
78B78ILE0-0.065-0.02861.3640.0000.0000.0000.0000.0000.000
79B79TRP0-0.038-0.04555.6440.0000.0000.0000.0000.0000.000
80B80SER0-0.033-0.03660.0580.0000.0000.0000.0000.0000.000
81B81GLN0-0.028-0.02661.5440.0000.0000.0000.0000.0000.000
82B82GLN00.0670.01764.5420.0000.0000.0000.0000.0000.000
83B83LYS10.8830.95266.040-0.003-0.0030.0000.0000.0000.000
84B84GLN0-0.062-0.03462.4380.0000.0000.0000.0000.0000.000
85B85ARG10.8860.96660.678-0.006-0.0060.0000.0000.0000.000
86B86GLN00.0440.01754.6470.0000.0000.0000.0000.0000.000
87B87HIS00.0620.02054.4420.0000.0000.0000.0000.0000.000
88B88GLY0-0.0010.00153.3400.0010.0010.0000.0000.0000.000
89B89ALA0-0.023-0.00652.3210.0000.0000.0000.0000.0000.000
90B90ILE00.0160.02651.0020.0000.0000.0000.0000.0000.000
91B91TYR00.029-0.00154.3650.0000.0000.0000.0000.0000.000
92B92MET0-0.0110.00054.9600.0000.0000.0000.0000.0000.000
93B93ASN0-0.051-0.04256.7950.0000.0000.0000.0000.0000.000
94B94SER00.0860.04659.5840.0000.0000.0000.0000.0000.000
95B95LEU00.0540.02261.1970.0000.0000.0000.0000.0000.000
96B96SER0-0.068-0.03459.4000.0000.0000.0000.0000.0000.000
97B97CYS0-0.055-0.03555.6830.0000.0000.0000.0000.0000.000
98B98ILE00.0620.04458.0290.0000.0000.0000.0000.0000.000
99B99ASN00.0150.01958.5860.0000.0000.0000.0000.0000.000
100B100ILE00.0290.00151.4770.0000.0000.0000.0000.0000.000
101B101THR00.0200.00053.7490.0000.0000.0000.0000.0000.000
102B102GLY00.0300.02054.4320.0000.0000.0000.0000.0000.000
103B103LEU00.0130.00751.6810.0000.0000.0000.0000.0000.000
104B104ILE0-0.048-0.03248.8710.0000.0000.0000.0000.0000.000
105B105VAL00.0240.01549.9930.0010.0010.0000.0000.0000.000
106B106PHE0-0.026-0.01551.1260.0010.0010.0000.0000.0000.000
107B107LEU00.012-0.00447.2440.0010.0010.0000.0000.0000.000
108B108GLU-1-0.827-0.91946.2940.0060.0060.0000.0000.0000.000
109B109LEU00.0260.02446.5530.0010.0010.0000.0000.0000.000
110B110LEU0-0.051-0.02246.2960.0010.0010.0000.0000.0000.000
111B111TYR0-0.017-0.03137.4670.0010.0010.0000.0000.0000.000
112B112ASP-1-0.907-0.95642.9480.0120.0120.0000.0000.0000.000
113B113SER0-0.059-0.06244.4200.0010.0010.0000.0000.0000.000
114B114PRO00.0470.01944.006-0.001-0.0010.0000.0000.0000.000
115B115MET00.006-0.00347.131-0.001-0.0010.0000.0000.0000.000
116B116ASP-1-0.835-0.88349.6280.0120.0120.0000.0000.0000.000
117B117ALA0-0.055-0.02349.842-0.001-0.0010.0000.0000.0000.000
118B118LEU00.030-0.01048.252-0.001-0.0010.0000.0000.0000.000
119B119ARG10.9460.97452.470-0.012-0.0120.0000.0000.0000.000
120B120ARG10.8920.95054.835-0.009-0.0090.0000.0000.0000.000
121B121CYS0-0.116-0.04454.449-0.001-0.0010.0000.0000.0000.000
122B122GLN0-0.064-0.03156.8940.0000.0000.0000.0000.0000.000
123B123VAL00.0340.05452.3610.0000.0000.0000.0000.0000.000
124B124ASP-1-0.885-0.94355.3990.0110.0110.0000.0000.0000.000
125B125ASN0-0.012-0.02452.9300.0010.0010.0000.0000.0000.000
126B126PHE00.0360.00348.4390.0000.0000.0000.0000.0000.000
127B127ASN0-0.072-0.02148.0270.0010.0010.0000.0000.0000.000
128B128PHE00.006-0.01347.801-0.001-0.0010.0000.0000.0000.000
129B129GLN00.0230.04840.9890.0010.0010.0000.0000.0000.000
130B130LEU0-0.041-0.03444.487-0.001-0.0010.0000.0000.0000.000
131B131ARG10.8720.90943.453-0.010-0.0100.0000.0000.0000.000
132B132GLY00.017-0.01243.4270.0000.0000.0000.0000.0000.000
133B133ILE0-0.030-0.01245.4270.0000.0000.0000.0000.0000.000
134B134VAL00.0200.00447.673-0.001-0.0010.0000.0000.0000.000
135B135ILE0-0.031-0.01149.1980.0000.0000.0000.0000.0000.000
136B136ASP-1-0.757-0.87852.3510.0010.0010.0000.0000.0000.000
137B137ASN00.0160.00755.6030.0000.0000.0000.0000.0000.000
138B138LEU00.002-0.02250.0230.0000.0000.0000.0000.0000.000
139B139SER0-0.019-0.01254.6820.0000.0000.0000.0000.0000.000
140B140PHE0-0.0090.00257.4280.0000.0000.0000.0000.0000.000
141B141LEU0-0.0310.00653.4590.0000.0000.0000.0000.0000.000
142B142ASN0-0.010-0.01253.998-0.001-0.0010.0000.0000.0000.000
143B153ASN00.044-0.00353.6520.0000.0000.0000.0000.0000.000
144B154LEU00.0720.03046.5180.0010.0010.0000.0000.0000.000
145B155SER00.0210.02747.9310.0000.0000.0000.0000.0000.000
146B156LYS10.9260.96848.0480.0010.0010.0000.0000.0000.000
147B157PHE00.0650.01748.5450.0010.0010.0000.0000.0000.000
148B158GLU-1-0.855-0.90141.595-0.003-0.0030.0000.0000.0000.000
149B159LYS10.8000.89544.074-0.004-0.0040.0000.0000.0000.000
150B160LEU00.0080.00145.2990.0010.0010.0000.0000.0000.000
151B161PHE00.0670.03638.8820.0010.0010.0000.0000.0000.000
152B162LYS10.9550.97638.952-0.001-0.0010.0000.0000.0000.000
153B163ILE0-0.016-0.00840.9560.0010.0010.0000.0000.0000.000
154B164LEU00.0480.02042.6880.0010.0010.0000.0000.0000.000
155B165ARG10.9210.97135.4770.0010.0010.0000.0000.0000.000
156B166LYS10.8530.95237.999-0.008-0.0080.0000.0000.0000.000
157B167LEU00.0090.00238.7440.0010.0010.0000.0000.0000.000
158B168ARG10.8250.92336.905-0.006-0.0060.0000.0000.0000.000
159B169GLU-1-0.892-0.93332.1900.0090.0090.0000.0000.0000.000
160B170PHE0-0.066-0.02335.1300.0010.0010.0000.0000.0000.000
161B171LEU00.0180.00137.4310.0010.0010.0000.0000.0000.000
162B172GLY00.0310.03637.4160.0010.0010.0000.0000.0000.000
163B173CYS0-0.0160.01638.2680.0000.0000.0000.0000.0000.000
164B174TRP00.0180.02040.704-0.001-0.0010.0000.0000.0000.000
165B175ILE0-0.028-0.03142.0740.0000.0000.0000.0000.0000.000
166B176ILE00.0190.01544.596-0.001-0.0010.0000.0000.0000.000
167B177THR0-0.029-0.02047.5490.0000.0000.0000.0000.0000.000
168B178LYS10.8220.91050.062-0.001-0.0010.0000.0000.0000.000
169B179SER0-0.066-0.03953.2050.0000.0000.0000.0000.0000.000
170B180PHE00.0280.02155.0940.0000.0000.0000.0000.0000.000
171B181PRO00.0660.03157.0370.0000.0000.0000.0000.0000.000
172B182THR0-0.023-0.03657.8490.0000.0000.0000.0000.0000.000
173B183ASP-1-0.903-0.93959.513-0.003-0.0030.0000.0000.0000.000
174B184PHE00.0190.01360.6320.0000.0000.0000.0000.0000.000
175B185TYR0-0.055-0.03255.7660.0000.0000.0000.0000.0000.000
176B186ASN00.0150.02261.9430.0000.0000.0000.0000.0000.000
177B187GLY00.0160.01564.7990.0000.0000.0000.0000.0000.000
178B188ILE00.0240.00267.0610.0000.0000.0000.0000.0000.000
179B189GLU-1-0.916-0.95570.737-0.002-0.0020.0000.0000.0000.000
180B190ASN0-0.040-0.02168.4500.0000.0000.0000.0000.0000.000
181B191THR0-0.013-0.00468.7960.0000.0000.0000.0000.0000.000
182B192LEU0-0.061-0.01764.4950.0000.0000.0000.0000.0000.000
183B193VAL0-0.085-0.03164.0280.0000.0000.0000.0000.0000.000
184B208PRO00.0280.02551.9180.0000.0000.0000.0000.0000.000
185B209THR00.020-0.02952.1650.0010.0010.0000.0000.0000.000
186B210LYS10.9250.97953.6960.0030.0030.0000.0000.0000.000
187B211LEU00.0060.01050.2170.0000.0000.0000.0000.0000.000
188B212PRO0-0.012-0.01848.219-0.001-0.0010.0000.0000.0000.000
189B213ASP-1-0.778-0.90344.517-0.009-0.0090.0000.0000.0000.000
190B214SER0-0.065-0.03343.1730.0000.0000.0000.0000.0000.000
191B215TYR00.029-0.00842.9240.0000.0000.0000.0000.0000.000
192B216MET0-0.009-0.00244.0680.0010.0010.0000.0000.0000.000
193B217LYS10.8050.90539.1230.0100.0100.0000.0000.0000.000
194B218GLY0-0.011-0.00139.6700.0000.0000.0000.0000.0000.000
195B219MET0-0.083-0.02739.9850.0010.0010.0000.0000.0000.000
196B220ASP-1-0.762-0.84937.536-0.001-0.0010.0000.0000.0000.000
197B221LEU0-0.036-0.02940.077-0.001-0.0010.0000.0000.0000.000
198B222ILE0-0.017-0.00543.2610.0010.0010.0000.0000.0000.000
199B223ILE0-0.006-0.01446.616-0.001-0.0010.0000.0000.0000.000
200B224TYR0-0.058-0.04049.6000.0000.0000.0000.0000.0000.000
201B225ARG10.8330.90852.9620.0000.0000.0000.0000.0000.000
202B226GLU-1-0.812-0.87356.093-0.005-0.0050.0000.0000.0000.000
203B227VAL0-0.016-0.03858.9470.0000.0000.0000.0000.0000.000
204B228VAL0-0.0170.00860.5230.0000.0000.0000.0000.0000.000
205B229ASP-1-0.771-0.86663.481-0.003-0.0030.0000.0000.0000.000
206B230GLY00.0070.00565.0730.0000.0000.0000.0000.0000.000
207B231ARG10.7750.87459.8730.0030.0030.0000.0000.0000.000
208B232PRO0-0.016-0.01059.2700.0000.0000.0000.0000.0000.000
209B233GLN00.0140.01856.4170.0000.0000.0000.0000.0000.000
210B234TYR00.039-0.00452.3410.0000.0000.0000.0000.0000.000
211B235ARG10.8630.92151.1990.0060.0060.0000.0000.0000.000
212B236ARG10.9380.96640.9850.0060.0060.0000.0000.0000.000
213B237ILE0-0.022-0.00844.8000.0000.0000.0000.0000.0000.000