Manual

About

FMODB

FMODB: The database of quantum mechanical data based on the FMO method

Last updated: 2024-05-02

All entries: 37386

Number of unique PDB entries: 7781

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FMODB ID: 2LLRR

Calculation Name: 4I61-B-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 4I61

Chain ID: B

ChEMBL ID:

UniProt ID: F8DQ39

Base Structure: X-ray

Registration Date: 2023-09-27

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 227
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2507582.123943
FMO2-HF: Nuclear repulsion 2423025.957643
FMO2-HF: Total energy -84556.1663
FMO2-MP2: Total energy -84798.862206


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:11:VAL)


Summations of interaction energy for fragment #1(B:11:VAL)
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.
-6.005-1.3612.917-2.386-5.177-0.019
Interaction energy analysis for fragmet #1(B:11:VAL)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.006 / q_NPA : -0.017
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].
3B13GLU-1-0.879-0.9502.360-6.113-3.1412.328-1.830-3.471-0.015
4B14PHE0-0.059-0.0042.6160.2341.8510.588-0.527-1.678-0.004
5B15VAL0-0.061-0.0184.2220.2770.3320.001-0.029-0.0280.000
6B16GLY00.023-0.0067.8340.2360.2360.0000.0000.0000.000
7B17ALA0-0.018-0.0209.173-0.082-0.0820.0000.0000.0000.000
8B18SER00.0180.01510.7910.0910.0910.0000.0000.0000.000
9B19GLU-1-0.918-0.96414.537-0.279-0.2790.0000.0000.0000.000
10B20ILE00.0090.01717.0200.0270.0270.0000.0000.0000.000
11B21GLY00.0690.04317.947-0.036-0.0360.0000.0000.0000.000
12B22ASP-1-0.894-0.93615.345-0.357-0.3570.0000.0000.0000.000
13B23THR0-0.009-0.02414.323-0.023-0.0230.0000.0000.0000.000
14B24ILE0-0.032-0.0266.648-0.052-0.0520.0000.0000.0000.000
15B25GLY00.0470.0199.8070.1060.1060.0000.0000.0000.000
16B26MET0-0.057-0.0395.104-0.365-0.3650.0000.0000.0000.000
17B27VAL00.008-0.0046.2740.3970.3970.0000.0000.0000.000
18B28ILE00.0180.0296.531-0.333-0.3330.0000.0000.0000.000
19B29PRO0-0.005-0.0167.3610.2210.2210.0000.0000.0000.000
20B30ARG10.9250.96410.6870.2790.2790.0000.0000.0000.000
21B31VAL00.0240.02211.7880.0050.0050.0000.0000.0000.000
22B32ASP-1-0.852-0.92812.606-0.132-0.1320.0000.0000.0000.000
23B33GLN0-0.032-0.03114.487-0.022-0.0220.0000.0000.0000.000
24B34GLN00.000-0.00317.8180.0110.0110.0000.0000.0000.000
25B35LEU0-0.039-0.01212.402-0.001-0.0010.0000.0000.0000.000
26B36LEU0-0.006-0.00316.473-0.010-0.0100.0000.0000.0000.000
27B37ASP-1-0.863-0.93017.653-0.164-0.1640.0000.0000.0000.000
28B38LYS10.8440.92118.6410.1810.1810.0000.0000.0000.000
29B39LEU0-0.055-0.00814.569-0.012-0.0120.0000.0000.0000.000
30B40HIS00.0110.00419.1010.0280.0280.0000.0000.0000.000
31B41VAL0-0.0080.00218.425-0.016-0.0160.0000.0000.0000.000
32B42THR0-0.016-0.02321.6570.0150.0150.0000.0000.0000.000
33B43LYS10.9290.97222.7190.2050.2050.0000.0000.0000.000
34B44GLN0-0.017-0.01220.321-0.018-0.0180.0000.0000.0000.000
35B45TYR0-0.012-0.01717.9290.0250.0250.0000.0000.0000.000
36B46LYS10.8570.91116.3450.2290.2290.0000.0000.0000.000
37B47THR0-0.060-0.03912.509-0.022-0.0220.0000.0000.0000.000
38B48LEU00.0160.01111.6790.0380.0380.0000.0000.0000.000
39B49GLY00.0210.00010.857-0.144-0.1440.0000.0000.0000.000
40B50ILE0-0.033-0.0118.9960.0890.0890.0000.0000.0000.000
41B51LEU00.024-0.00710.956-0.129-0.1290.0000.0000.0000.000
42B52SER0-0.0150.00011.5120.0990.0990.0000.0000.0000.000
43B53ASP-1-0.797-0.91413.407-0.453-0.4530.0000.0000.0000.000
44B54ARG10.7970.88415.8450.3580.3580.0000.0000.0000.000
45B55THR0-0.038-0.02718.1590.0510.0510.0000.0000.0000.000
46B56GLY00.0570.02520.975-0.008-0.0080.0000.0000.0000.000
47B57ALA00.0450.03421.134-0.015-0.0150.0000.0000.0000.000
48B58GLY00.0400.01422.875-0.013-0.0130.0000.0000.0000.000
49B59PRO00.0260.01822.830-0.003-0.0030.0000.0000.0000.000
50B60GLN00.0200.01617.9850.0250.0250.0000.0000.0000.000
51B61ILE00.0080.00920.417-0.016-0.0160.0000.0000.0000.000
52B62MET0-0.035-0.01722.4930.0050.0050.0000.0000.0000.000
53B63ALA0-0.0090.00520.2580.0080.0080.0000.0000.0000.000
54B64MET0-0.011-0.01015.832-0.004-0.0040.0000.0000.0000.000
55B65ASP-1-0.752-0.87920.079-0.211-0.2110.0000.0000.0000.000
56B66GLU-1-0.924-0.96222.652-0.187-0.1870.0000.0000.0000.000
57B67GLY00.0060.00119.2770.0060.0060.0000.0000.0000.000
58B68ILE0-0.064-0.03220.0520.0010.0010.0000.0000.0000.000
59B69LYS10.8290.91922.0030.2010.2010.0000.0000.0000.000
60B70ALA0-0.065-0.01121.4190.0180.0180.0000.0000.0000.000
61B71THR0-0.128-0.06118.322-0.005-0.0050.0000.0000.0000.000
62B72ASN0-0.047-0.02220.7850.0280.0280.0000.0000.0000.000
63B73MET0-0.0550.00815.252-0.003-0.0030.0000.0000.0000.000
64B74GLU-1-0.813-0.87319.797-0.194-0.1940.0000.0000.0000.000
65B75CYS0-0.054-0.01619.731-0.035-0.0350.0000.0000.0000.000
66B76ILE0-0.0100.00417.4390.0230.0230.0000.0000.0000.000
67B77ASH0-0.021-0.07018.7020.0290.0290.0000.0000.0000.000
68B78VAL00.0220.01119.524-0.033-0.0330.0000.0000.0000.000
69B79GLU-1-0.912-0.91119.148-0.288-0.2880.0000.0000.0000.000
70B80TRP00.0320.00720.734-0.017-0.0170.0000.0000.0000.000
71B81PRO00.0160.03918.8540.0260.0260.0000.0000.0000.000
72B82ARG10.8490.94321.7400.1730.1730.0000.0000.0000.000
73B83ASP-1-0.802-0.90519.712-0.287-0.2870.0000.0000.0000.000
74B84THR0-0.0300.00822.2410.0270.0270.0000.0000.0000.000
75B85LYS10.8040.88918.7170.2890.2890.0000.0000.0000.000
76B86GLY0-0.034-0.00823.4720.0130.0130.0000.0000.0000.000
77B87GLY00.0360.03926.6390.0140.0140.0000.0000.0000.000
78B88GLY0-0.012-0.02428.304-0.002-0.0020.0000.0000.0000.000
79B89GLY00.0720.03627.2650.0070.0070.0000.0000.0000.000
80B90HIS00.0140.01823.7910.0090.0090.0000.0000.0000.000
81B91GLY00.0540.05319.9580.0010.0010.0000.0000.0000.000
82B92CYS0-0.043-0.03218.4880.0270.0270.0000.0000.0000.000
83B93LEU00.0180.02513.589-0.056-0.0560.0000.0000.0000.000
84B94ILE00.0270.01215.8700.0490.0490.0000.0000.0000.000
85B95ILE0-0.017-0.00914.337-0.082-0.0820.0000.0000.0000.000
86B96ILE0-0.016-0.00314.6740.0530.0530.0000.0000.0000.000
87B97GLY00.004-0.01315.394-0.059-0.0590.0000.0000.0000.000
88B98GLY00.0920.03216.9150.0260.0260.0000.0000.0000.000
89B99ASP-1-0.900-0.95717.556-0.220-0.2200.0000.0000.0000.000
90B100ASP-1-0.861-0.93116.570-0.234-0.2340.0000.0000.0000.000
91B101PRO0-0.012-0.01811.241-0.046-0.0460.0000.0000.0000.000
92B102ALA0-0.046-0.02412.536-0.101-0.1010.0000.0000.0000.000
93B103ASP-1-0.793-0.90314.498-0.320-0.3200.0000.0000.0000.000
94B104ALA00.0880.03012.569-0.016-0.0160.0000.0000.0000.000
95B105ARG10.9100.9478.8730.6830.6830.0000.0000.0000.000
96B106GLN00.0090.00212.253-0.044-0.0440.0000.0000.0000.000
97B107ALA00.0500.03015.7730.0130.0130.0000.0000.0000.000
98B108ILE0-0.0200.00410.6270.0100.0100.0000.0000.0000.000
99B109ARG10.9200.95911.6670.5380.5380.0000.0000.0000.000
100B110VAL00.0150.02314.9130.0380.0380.0000.0000.0000.000
101B111ALA00.0160.01616.2240.0320.0320.0000.0000.0000.000
102B112LEU0-0.013-0.02111.6300.0210.0210.0000.0000.0000.000
103B113ASP-1-0.906-0.93916.336-0.322-0.3220.0000.0000.0000.000
104B114ASN0-0.089-0.07019.0480.0710.0710.0000.0000.0000.000
105B115LEU00.0350.02516.7460.0220.0220.0000.0000.0000.000
106B116HIS0-0.009-0.00221.0490.0300.0300.0000.0000.0000.000
107B117ARG10.8770.95723.4520.2230.2230.0000.0000.0000.000
108B118THR0-0.072-0.05923.3360.0150.0150.0000.0000.0000.000
109B119PHE00.0280.00221.2000.0050.0050.0000.0000.0000.000
110B120GLY00.0210.03126.0160.0110.0110.0000.0000.0000.000
111B121ASP-1-0.808-0.87029.171-0.118-0.1180.0000.0000.0000.000
112B122VAL00.0220.01426.8250.0020.0020.0000.0000.0000.000
113B123TYR0-0.051-0.04129.9640.0040.0040.0000.0000.0000.000
114B124ASN00.009-0.00627.937-0.003-0.0030.0000.0000.0000.000
115B125ALA00.0530.02232.0010.0070.0070.0000.0000.0000.000
116B126LYS10.9150.94433.4890.0780.0780.0000.0000.0000.000
117B127ALA0-0.060-0.03134.617-0.002-0.0020.0000.0000.0000.000
118B128GLY00.0150.00533.7160.0010.0010.0000.0000.0000.000
119B129HIS0-0.038-0.02629.7480.0030.0030.0000.0000.0000.000
120B130LEU0-0.052-0.02932.9290.0060.0060.0000.0000.0000.000
121B131GLU-1-0.805-0.90027.702-0.208-0.2080.0000.0000.0000.000
122B132LEU0-0.072-0.02631.5680.0090.0090.0000.0000.0000.000
123B133GLN0-0.0080.00327.213-0.007-0.0070.0000.0000.0000.000
124B134PHE00.013-0.00631.3670.0130.0130.0000.0000.0000.000
125B135THR00.0160.00930.335-0.004-0.0040.0000.0000.0000.000
126B136ALA00.0150.00232.5280.0060.0060.0000.0000.0000.000
127B137ARG10.8770.93132.5580.1200.1200.0000.0000.0000.000
128B138ALA00.0240.02330.074-0.009-0.0090.0000.0000.0000.000
129B139ALA00.0070.00826.2380.0120.0120.0000.0000.0000.000
130B140GLY00.1020.04025.4780.0010.0010.0000.0000.0000.000
131B141ALA00.0150.00222.050-0.004-0.0040.0000.0000.0000.000
132B142ALA0-0.002-0.00823.9250.0030.0030.0000.0000.0000.000
133B143HIS0-0.087-0.04427.0750.0090.0090.0000.0000.0000.000
134B144LEU0-0.029-0.00822.7650.0070.0070.0000.0000.0000.000
135B145GLY0-0.013-0.00924.9870.0020.0020.0000.0000.0000.000
136B146LEU0-0.017-0.02525.6200.0090.0090.0000.0000.0000.000
137B147GLY00.0190.02229.0130.0120.0120.0000.0000.0000.000
138B148ALA0-0.057-0.02130.5360.0120.0120.0000.0000.0000.000
139B149VAL00.0280.01432.163-0.001-0.0010.0000.0000.0000.000
140B150GLU-1-0.886-0.95028.909-0.172-0.1720.0000.0000.0000.000
141B151GLY0-0.066-0.04532.2740.0100.0100.0000.0000.0000.000
142B152LYS10.8710.93034.1500.1080.1080.0000.0000.0000.000
143B153ALA00.0070.01634.527-0.008-0.0080.0000.0000.0000.000
144B154PHE00.0190.01530.2320.0020.0020.0000.0000.0000.000
145B155GLY00.0240.00434.224-0.001-0.0010.0000.0000.0000.000
146B156LEU0-0.0080.01329.4460.0020.0020.0000.0000.0000.000
147B157ILE0-0.004-0.02233.5970.0010.0010.0000.0000.0000.000
148B158CYS00.0300.01630.8860.0060.0060.0000.0000.0000.000
149B159GLY00.0170.00534.2760.0010.0010.0000.0000.0000.000
150B160CYS0-0.0350.01832.0550.0020.0020.0000.0000.0000.000
151B161PRO00.1050.02834.9730.0010.0010.0000.0000.0000.000
152B162SER0-0.018-0.00236.0760.0050.0050.0000.0000.0000.000
153B163GLY0-0.017-0.00537.3410.0010.0010.0000.0000.0000.000
154B164ILE0-0.012-0.01238.7170.0040.0040.0000.0000.0000.000
155B165GLY00.0820.03537.7610.0010.0010.0000.0000.0000.000
156B166VAL0-0.024-0.00438.6390.0010.0010.0000.0000.0000.000
157B167VAL0-0.035-0.01441.6440.0030.0030.0000.0000.0000.000
158B168MET0-0.062-0.01236.5460.0020.0020.0000.0000.0000.000
159B169GLY00.0550.02941.0820.0000.0000.0000.0000.0000.000
160B170ASP-1-0.819-0.89841.644-0.069-0.0690.0000.0000.0000.000
161B171LYS10.9160.95244.3580.0730.0730.0000.0000.0000.000
162B172ALA00.0010.01741.5850.0020.0020.0000.0000.0000.000
163B173LEU00.021-0.00342.9640.0020.0020.0000.0000.0000.000
164B174LYS10.7530.88045.5150.0700.0700.0000.0000.0000.000
165B175THR0-0.080-0.03845.5400.0030.0030.0000.0000.0000.000
166B176ALA0-0.034-0.03145.5720.0020.0020.0000.0000.0000.000
167B177GLY0-0.0130.01446.802-0.001-0.0010.0000.0000.0000.000
168B178VAL0-0.043-0.01842.051-0.001-0.0010.0000.0000.0000.000
169B179GLU-1-0.918-0.96641.840-0.077-0.0770.0000.0000.0000.000
170B180PRO0-0.014-0.00740.550-0.006-0.0060.0000.0000.0000.000
171B181LEU0-0.076-0.03035.1180.0020.0020.0000.0000.0000.000
172B182ASN00.0270.00234.4770.0080.0080.0000.0000.0000.000
173B183PHE0-0.016-0.00937.2940.0000.0000.0000.0000.0000.000
174B184THR0-0.0150.01532.2440.0040.0040.0000.0000.0000.000
175B185SER00.025-0.00735.0890.0040.0040.0000.0000.0000.000
176B186PRO00.0270.03433.852-0.004-0.0040.0000.0000.0000.000
177B187SER0-0.030-0.03233.975-0.002-0.0020.0000.0000.0000.000
178B188HIS0-0.035-0.02135.5710.0010.0010.0000.0000.0000.000
179B189GLY00.0660.03232.3240.0000.0000.0000.0000.0000.000
180B190THR0-0.041-0.00429.586-0.009-0.0090.0000.0000.0000.000
181B191SER0-0.022-0.04725.2500.0090.0090.0000.0000.0000.000
182B192PHE0-0.044-0.02328.3580.0000.0000.0000.0000.0000.000
183B193SER0-0.025-0.00229.0070.0030.0030.0000.0000.0000.000
184B194ASN0-0.021-0.03630.5820.0130.0130.0000.0000.0000.000
185B195GLU-1-0.806-0.91929.199-0.173-0.1730.0000.0000.0000.000
186B196GLY0-0.024-0.01433.5070.0030.0030.0000.0000.0000.000
187B197CYS0-0.016-0.00431.6840.0000.0000.0000.0000.0000.000
188B198LEU0-0.0040.00634.9590.0020.0020.0000.0000.0000.000
189B199THR00.0180.01232.707-0.004-0.0040.0000.0000.0000.000
190B200ILE0-0.031-0.00535.8120.0070.0070.0000.0000.0000.000
191B201THR00.017-0.01036.716-0.005-0.0050.0000.0000.0000.000
192B202GLY00.0600.02838.7260.0050.0050.0000.0000.0000.000
193B203ASP-1-0.905-0.95740.635-0.083-0.0830.0000.0000.0000.000
194B204SER00.007-0.01338.5710.0000.0000.0000.0000.0000.000
195B205GLY0-0.067-0.03140.199-0.002-0.0020.0000.0000.0000.000
196B206ALA00.0950.05342.8920.0000.0000.0000.0000.0000.000
197B207VAL00.0380.01437.195-0.001-0.0010.0000.0000.0000.000
198B208ARG10.9250.96838.1530.0940.0940.0000.0000.0000.000
199B209GLN0-0.010-0.01239.7410.0000.0000.0000.0000.0000.000
200B210ALA00.0310.02641.3400.0010.0010.0000.0000.0000.000
201B211VAL00.0200.00235.7210.0000.0000.0000.0000.0000.000
202B212MET0-0.047-0.02438.958-0.001-0.0010.0000.0000.0000.000
203B213ALA00.0280.02540.4990.0010.0010.0000.0000.0000.000
204B214GLY0-0.002-0.00840.2520.0020.0020.0000.0000.0000.000
205B215ARG10.9010.94235.9670.1090.1090.0000.0000.0000.000
206B216GLU-1-0.920-0.95039.171-0.071-0.0710.0000.0000.0000.000
207B217VAL0-0.050-0.04242.4310.0030.0030.0000.0000.0000.000
208B218GLY00.0790.02639.4830.0020.0020.0000.0000.0000.000
209B219LEU00.0030.00437.0540.0000.0000.0000.0000.0000.000
210B220LYS10.8830.95840.4290.0720.0720.0000.0000.0000.000
211B221LEU0-0.011-0.02142.2990.0030.0030.0000.0000.0000.000
212B222LEU00.0160.01835.6810.0030.0030.0000.0000.0000.000
213B223SER00.020-0.00840.3590.0010.0010.0000.0000.0000.000
214B224GLN0-0.092-0.02042.1740.0050.0050.0000.0000.0000.000
215B225PHE0-0.066-0.03540.4030.0030.0030.0000.0000.0000.000
216B226GLY0-0.061-0.02842.7980.0010.0010.0000.0000.0000.000
217B227GLU-1-0.899-0.93236.023-0.095-0.0950.0000.0000.0000.000
218B228GLU-1-0.975-0.99038.714-0.084-0.0840.0000.0000.0000.000
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