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: 66M3Z

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 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 213
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2640125.041628
FMO2-HF: Nuclear repulsion 2552812.143879
FMO2-HF: Total energy -87312.897749
FMO2-MP2: Total energy -87566.908807


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.
-12.386-6.423.699-2.768-6.8980.01
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 : 0.039 / q_NPA : 0.011
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].
3B3VAL00.0410.0252.299-2.2280.5012.288-1.433-3.5850.003
4B4LEU00.0330.0162.803-1.7170.0840.312-0.516-1.597-0.002
5B5LYS10.8270.8882.674-8.528-7.0921.099-0.819-1.7160.009
6B6ASN0-0.023-0.0115.7960.2370.2370.0000.0000.0000.000
7B7ILE00.0020.0187.0830.0100.0100.0000.0000.0000.000
8B8ARG10.8420.9229.467-0.143-0.1430.0000.0000.0000.000
9B9ILE00.0180.01012.831-0.012-0.0120.0000.0000.0000.000
10B10TYR00.001-0.00515.8080.0090.0090.0000.0000.0000.000
11B11PRO00.0420.01919.482-0.007-0.0070.0000.0000.0000.000
12B12LEU00.0520.02222.484-0.004-0.0040.0000.0000.0000.000
13B13SER00.0650.02525.314-0.004-0.0040.0000.0000.0000.000
14B14ASN0-0.029-0.01421.998-0.004-0.0040.0000.0000.0000.000
15B15PHE0-0.026-0.00621.431-0.003-0.0030.0000.0000.0000.000
16B16ILE0-0.049-0.00927.315-0.005-0.0050.0000.0000.0000.000
17B17THR0-0.013-0.01129.290-0.001-0.0010.0000.0000.0000.000
18B18SER0-0.027-0.02630.4500.0000.0000.0000.0000.0000.000
19B19THR0-0.012-0.00231.8200.0010.0010.0000.0000.0000.000
20B20LYS10.7950.88432.628-0.036-0.0360.0000.0000.0000.000
21B21ASN00.0510.04636.4220.0010.0010.0000.0000.0000.000
22B22TYR0-0.002-0.00733.630-0.001-0.0010.0000.0000.0000.000
23B23ILE0-0.024-0.00940.1470.0000.0000.0000.0000.0000.000
24B24ASN0-0.010-0.00242.7510.0000.0000.0000.0000.0000.000
25B25LEU00.0160.01544.7110.0000.0000.0000.0000.0000.000
26B26PRO00.0130.02247.1600.0000.0000.0000.0000.0000.000
27B27ASN00.049-0.00650.002-0.001-0.0010.0000.0000.0000.000
28B28GLU-1-0.835-0.91551.4930.0040.0040.0000.0000.0000.000
29B29LEU0-0.042-0.02448.842-0.001-0.0010.0000.0000.0000.000
30B30ARG10.7880.84141.980-0.006-0.0060.0000.0000.0000.000
31B31ASN0-0.036-0.02745.307-0.001-0.0010.0000.0000.0000.000
32B32LEU0-0.0230.00945.729-0.002-0.0020.0000.0000.0000.000
33B33ILE0-0.057-0.02240.732-0.001-0.0010.0000.0000.0000.000
34B34SER00.0350.01836.8020.0010.0010.0000.0000.0000.000
35B35GLU-1-0.765-0.85937.1790.0070.0070.0000.0000.0000.000
36B36GLU-1-0.830-0.90231.8840.0140.0140.0000.0000.0000.000
37B37GLN0-0.025-0.01735.2950.0000.0000.0000.0000.0000.000
38B38GLU-1-0.808-0.90737.0440.0080.0080.0000.0000.0000.000
39B39SER0-0.0230.00035.5040.0020.0020.0000.0000.0000.000
40B40LYS10.8400.90131.340-0.014-0.0140.0000.0000.0000.000
41B41LEU0-0.0260.00735.9770.0000.0000.0000.0000.0000.000
42B42GLY00.014-0.02138.8260.0020.0020.0000.0000.0000.000
43B43PHE0-0.023-0.00937.1820.0020.0020.0000.0000.0000.000
44B44LEU0-0.0010.00441.973-0.002-0.0020.0000.0000.0000.000
45B45HIS00.0280.01045.0820.0020.0020.0000.0000.0000.000
46B46ILE0-0.005-0.00448.161-0.001-0.0010.0000.0000.0000.000
47B47ILE0-0.0170.00451.4070.0000.0000.0000.0000.0000.000
48B48GLU-1-0.682-0.83654.0640.0050.0050.0000.0000.0000.000
49B49SER00.009-0.03057.3160.0000.0000.0000.0000.0000.000
50B50ASP-1-0.824-0.84760.5890.0030.0030.0000.0000.0000.000
51B51PHE00.0320.00761.0210.0000.0000.0000.0000.0000.000
52B52LYS10.9650.97861.874-0.005-0.0050.0000.0000.0000.000
53B53PRO00.0010.01157.757-0.001-0.0010.0000.0000.0000.000
54B54SER00.003-0.02356.9700.0000.0000.0000.0000.0000.000
55B55VAL00.020-0.00257.6060.0010.0010.0000.0000.0000.000
56B56ALA00.0320.02553.3040.0010.0010.0000.0000.0000.000
57B57LEU00.0160.00852.4040.0010.0010.0000.0000.0000.000
58B58GLN0-0.051-0.04553.8440.0010.0010.0000.0000.0000.000
59B59LYS10.8460.90953.173-0.006-0.0060.0000.0000.0000.000
60B60LEU0-0.0250.00147.9440.0010.0010.0000.0000.0000.000
61B61VAL00.0080.01349.6310.0010.0010.0000.0000.0000.000
62B62ASN0-0.048-0.01451.7860.0010.0010.0000.0000.0000.000
63B63CYS0-0.060-0.01647.8560.0000.0000.0000.0000.0000.000
64B64THR0-0.046-0.00448.4240.0010.0010.0000.0000.0000.000
65B65THR0-0.033-0.03847.076-0.001-0.0010.0000.0000.0000.000
66B66GLY00.0200.00048.9290.0010.0010.0000.0000.0000.000
67B67ASP-1-0.841-0.92146.5940.0280.0280.0000.0000.0000.000
68B68GLU-1-0.798-0.85544.8230.0240.0240.0000.0000.0000.000
69B69LYS10.7850.89048.263-0.023-0.0230.0000.0000.0000.000
70B70ILE0-0.0200.00248.1820.0010.0010.0000.0000.0000.000
71B71LEU00.0020.00549.356-0.001-0.0010.0000.0000.0000.000
72B72ILE00.009-0.00451.174-0.001-0.0010.0000.0000.0000.000
73B73ILE00.012-0.00551.0590.0000.0000.0000.0000.0000.000
74B74ASP-1-0.704-0.83154.9740.0100.0100.0000.0000.0000.000
75B75ILE0-0.0120.00155.4810.0000.0000.0000.0000.0000.000
76B76VAL0-0.031-0.02359.4260.0000.0000.0000.0000.0000.000
77B77SER0-0.0110.01661.7140.0000.0000.0000.0000.0000.000
78B78ILE0-0.068-0.03062.0630.0000.0000.0000.0000.0000.000
79B79TRP0-0.030-0.04255.6470.0000.0000.0000.0000.0000.000
80B80SER0-0.026-0.02960.2440.0010.0010.0000.0000.0000.000
81B81GLN0-0.014-0.01361.7930.0000.0000.0000.0000.0000.000
82B82GLN00.0580.00864.8990.0000.0000.0000.0000.0000.000
83B83LYS10.8430.91965.962-0.008-0.0080.0000.0000.0000.000
84B84GLN0-0.0180.00562.969-0.001-0.0010.0000.0000.0000.000
85B85ARG10.8760.95360.917-0.014-0.0140.0000.0000.0000.000
86B86GLN00.011-0.00355.3140.0000.0000.0000.0000.0000.000
87B87HIS00.0610.02454.5700.0000.0000.0000.0000.0000.000
88B88GLY00.0400.02953.1550.0010.0010.0000.0000.0000.000
89B89ALA0-0.041-0.01352.4880.0000.0000.0000.0000.0000.000
90B90ILE00.0260.02351.0630.0000.0000.0000.0000.0000.000
91B91TYR00.000-0.01654.4080.0000.0000.0000.0000.0000.000
92B92MET0-0.022-0.00955.0280.0000.0000.0000.0000.0000.000
93B93ASN0-0.051-0.03356.868-0.001-0.0010.0000.0000.0000.000
94B94SER00.0840.03659.8590.0000.0000.0000.0000.0000.000
95B95LEU00.0500.01561.2420.0000.0000.0000.0000.0000.000
96B96SER0-0.060-0.03259.1840.0000.0000.0000.0000.0000.000
97B97CYS0-0.014-0.00555.7140.0010.0010.0000.0000.0000.000
98B98ILE00.0020.02257.4090.0000.0000.0000.0000.0000.000
99B99ASN00.0260.01658.443-0.001-0.0010.0000.0000.0000.000
100B100ILE00.0270.00951.7680.0010.0010.0000.0000.0000.000
101B101THR00.0160.00053.5530.0010.0010.0000.0000.0000.000
102B102GLY00.0280.01754.2090.0010.0010.0000.0000.0000.000
103B103LEU00.007-0.00151.7550.0010.0010.0000.0000.0000.000
104B104ILE0-0.040-0.02148.9020.0010.0010.0000.0000.0000.000
105B105VAL00.0330.01549.8100.0010.0010.0000.0000.0000.000
106B106PHE0-0.034-0.01851.0780.0010.0010.0000.0000.0000.000
107B107LEU00.015-0.00247.4260.0010.0010.0000.0000.0000.000
108B108GLU-1-0.824-0.92646.0230.0230.0230.0000.0000.0000.000
109B109LEU0-0.0040.00946.3060.0020.0020.0000.0000.0000.000
110B110LEU0-0.029-0.01746.3420.0010.0010.0000.0000.0000.000
111B111TYR0-0.006-0.01637.0530.0010.0010.0000.0000.0000.000
112B112ASP-1-0.856-0.93343.0220.0340.0340.0000.0000.0000.000
113B113SER0-0.045-0.04944.4370.0020.0020.0000.0000.0000.000
114B114PRO00.0450.02243.815-0.002-0.0020.0000.0000.0000.000
115B115MET0-0.015-0.00946.972-0.001-0.0010.0000.0000.0000.000
116B116ASP-1-0.839-0.88649.3990.0280.0280.0000.0000.0000.000
117B117ALA0-0.041-0.02349.793-0.002-0.0020.0000.0000.0000.000
118B118LEU00.042-0.00148.080-0.002-0.0020.0000.0000.0000.000
119B119ARG10.9230.95952.277-0.027-0.0270.0000.0000.0000.000
120B120ARG10.9140.96354.944-0.022-0.0220.0000.0000.0000.000
121B121CYS0-0.099-0.02954.010-0.001-0.0010.0000.0000.0000.000
122B122GLN0-0.081-0.03856.3980.0000.0000.0000.0000.0000.000
123B123VAL0-0.0070.00252.5240.0000.0000.0000.0000.0000.000
124B124ASP-1-0.815-0.90154.9350.0240.0240.0000.0000.0000.000
125B125ASN0-0.020-0.01152.8720.0020.0020.0000.0000.0000.000
126B126PHE00.025-0.00648.3750.0000.0000.0000.0000.0000.000
127B127ASN0-0.071-0.02347.9690.0030.0030.0000.0000.0000.000
128B128PHE0-0.007-0.01647.635-0.001-0.0010.0000.0000.0000.000
129B129GLN00.0290.03540.9820.0020.0020.0000.0000.0000.000
130B130LEU0-0.038-0.02544.275-0.002-0.0020.0000.0000.0000.000
131B131ARG10.8620.89743.751-0.021-0.0210.0000.0000.0000.000
132B132GLY00.013-0.01243.8660.0000.0000.0000.0000.0000.000
133B133ILE0-0.017-0.00745.3490.0000.0000.0000.0000.0000.000
134B134VAL00.0310.01147.890-0.001-0.0010.0000.0000.0000.000
135B135ILE0-0.030-0.01249.5190.0000.0000.0000.0000.0000.000
136B136ASP-1-0.719-0.86552.7180.0070.0070.0000.0000.0000.000
137B137ASN0-0.011-0.00655.9320.0000.0000.0000.0000.0000.000
138B138LEU00.001-0.01650.1860.0000.0000.0000.0000.0000.000
139B139SER0-0.017-0.01454.8190.0000.0000.0000.0000.0000.000
140B140PHE00.0140.01257.7070.0000.0000.0000.0000.0000.000
141B141LEU0-0.059-0.00653.3930.0010.0010.0000.0000.0000.000
142B142ASN00.0290.00354.1350.0000.0000.0000.0000.0000.000
143B153ASN00.0520.00953.5630.0010.0010.0000.0000.0000.000
144B154LEU00.0700.04046.4620.0010.0010.0000.0000.0000.000
145B155SER00.0140.01447.5950.0010.0010.0000.0000.0000.000
146B156LYS10.9120.96247.811-0.007-0.0070.0000.0000.0000.000
147B157PHE00.0640.02048.5700.0010.0010.0000.0000.0000.000
148B158GLU-1-0.813-0.88041.3170.0090.0090.0000.0000.0000.000
149B159LYS10.8070.89644.077-0.018-0.0180.0000.0000.0000.000
150B160LEU00.0060.00345.2790.0020.0020.0000.0000.0000.000
151B161PHE00.0780.05338.7990.0010.0010.0000.0000.0000.000
152B162LYS10.9410.96938.991-0.018-0.0180.0000.0000.0000.000
153B163ILE0-0.015-0.00341.0640.0020.0020.0000.0000.0000.000
154B164LEU00.0270.01242.8820.0020.0020.0000.0000.0000.000
155B165ARG10.8420.92736.397-0.014-0.0140.0000.0000.0000.000
156B166LYS10.8180.92038.472-0.029-0.0290.0000.0000.0000.000
157B167LEU00.008-0.00238.9080.0020.0020.0000.0000.0000.000
158B168ARG10.8500.92337.250-0.021-0.0210.0000.0000.0000.000
159B169GLU-1-0.889-0.92332.5200.0360.0360.0000.0000.0000.000
160B170PHE0-0.066-0.02434.9510.0040.0040.0000.0000.0000.000
161B171LEU00.0190.00337.2940.0020.0020.0000.0000.0000.000
162B172GLY00.0150.02737.5780.0000.0000.0000.0000.0000.000
163B173CYS0-0.0020.02238.468-0.002-0.0020.0000.0000.0000.000
164B174TRP00.0060.01441.070-0.001-0.0010.0000.0000.0000.000
165B175ILE0-0.039-0.03142.2960.0000.0000.0000.0000.0000.000
166B176ILE00.0210.01344.658-0.001-0.0010.0000.0000.0000.000
167B177THR0-0.037-0.02847.6560.0010.0010.0000.0000.0000.000
168B178LYS10.8110.91950.163-0.007-0.0070.0000.0000.0000.000
169B179SER0-0.053-0.03453.2770.0000.0000.0000.0000.0000.000
170B180PHE00.0250.02755.3570.0000.0000.0000.0000.0000.000
171B181PRO00.0700.02857.2350.0000.0000.0000.0000.0000.000
172B182THR0-0.032-0.03557.4610.0010.0010.0000.0000.0000.000
173B183ASP-1-0.864-0.92359.1800.0000.0000.0000.0000.0000.000
174B184PHE00.0130.01660.9060.0000.0000.0000.0000.0000.000
175B185TYR0-0.058-0.03855.8530.0010.0010.0000.0000.0000.000
176B186ASN00.0170.01562.136-0.001-0.0010.0000.0000.0000.000
177B187GLY00.0080.00964.9520.0000.0000.0000.0000.0000.000
178B188ILE00.0310.00867.1270.0000.0000.0000.0000.0000.000
179B189GLU-1-0.911-0.94770.8850.0000.0000.0000.0000.0000.000
180B190ASN0-0.047-0.02268.2990.0000.0000.0000.0000.0000.000
181B191THR0-0.023-0.02468.5420.0000.0000.0000.0000.0000.000
182B192LEU0-0.057-0.01664.3980.0000.0000.0000.0000.0000.000
183B193VAL0-0.067-0.02563.5670.0000.0000.0000.0000.0000.000
184B208PRO00.0370.02552.0150.0000.0000.0000.0000.0000.000
185B209THR00.020-0.01352.3390.0010.0010.0000.0000.0000.000
186B210LYS10.8980.97353.6010.0000.0000.0000.0000.0000.000
187B211LEU00.0020.00750.5990.0010.0010.0000.0000.0000.000
188B212PRO0-0.035-0.03048.436-0.001-0.0010.0000.0000.0000.000
189B213ASP-1-0.760-0.88344.449-0.005-0.0050.0000.0000.0000.000
190B214SER0-0.076-0.04742.812-0.001-0.0010.0000.0000.0000.000
191B215TYR00.024-0.00242.7930.0010.0010.0000.0000.0000.000
192B216MET0-0.0010.00044.1920.0010.0010.0000.0000.0000.000
193B217LYS10.7960.88639.2910.0050.0050.0000.0000.0000.000
194B218GLY00.0160.00039.7550.0000.0000.0000.0000.0000.000
195B219MET0-0.072-0.02640.3390.0020.0020.0000.0000.0000.000
196B220ASP-1-0.788-0.86937.5860.0080.0080.0000.0000.0000.000
197B221LEU0-0.038-0.02540.103-0.002-0.0020.0000.0000.0000.000
198B222ILE00.0010.02043.4770.0010.0010.0000.0000.0000.000
199B223ILE00.006-0.00646.602-0.001-0.0010.0000.0000.0000.000
200B224TYR0-0.071-0.05149.4450.0010.0010.0000.0000.0000.000
201B225ARG10.8110.89352.777-0.003-0.0030.0000.0000.0000.000
202B226GLU-1-0.815-0.87555.895-0.004-0.0040.0000.0000.0000.000
203B227VAL0-0.009-0.02159.0150.0000.0000.0000.0000.0000.000
204B228VAL0-0.019-0.00460.6070.0000.0000.0000.0000.0000.000
205B229ASP-1-0.771-0.86963.093-0.003-0.0030.0000.0000.0000.000
206B230GLY00.0230.01565.1100.0000.0000.0000.0000.0000.000
207B231ARG10.7650.87559.6170.0030.0030.0000.0000.0000.000
208B232PRO0-0.027-0.01359.3590.0000.0000.0000.0000.0000.000
209B233GLN00.0230.02056.5350.0000.0000.0000.0000.0000.000
210B234TYR00.038-0.01152.4960.0000.0000.0000.0000.0000.000
211B235ARG10.8590.91250.6460.0050.0050.0000.0000.0000.000
212B236ARG10.9160.95140.4510.0040.0040.0000.0000.0000.000
213B237ILE0-0.0100.00144.145-0.001-0.0010.0000.0000.0000.000