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: MNNRZ

Calculation Name: 4L5T-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 4L5T

Chain ID: A

ChEMBL ID:

UniProt ID: Q9R002

Base Structure: X-ray

Registration Date: 2023-09-21

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 180
LigandCharge CYM=-1
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -1924168.110108
FMO2-HF: Nuclear repulsion 1850870.646843
FMO2-HF: Total energy -73297.463265
FMO2-MP2: Total energy -73506.043664


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(A:245:LEU)


Summations of interaction energy for fragment #1(A:245:LEU)
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.
-0.5480.85-0.017-0.597-0.7840.002
Interaction energy analysis for fragmet #1(A:245:LEU)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.028 / q_NPA : -0.025
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].
3A247LYS10.9560.9773.7880.5671.965-0.017-0.597-0.7840.002
4A248GLU-1-0.886-0.9376.6140.2860.2860.0000.0000.0000.000
5A249SER0-0.040-0.0539.413-0.148-0.1480.0000.0000.0000.000
6A250PHE00.0270.02012.6750.0790.0790.0000.0000.0000.000
7A251GLU-1-0.853-0.89616.389-0.010-0.0100.0000.0000.0000.000
8A252GLY00.0050.00618.5030.0060.0060.0000.0000.0000.000
9A253ASP-1-0.876-0.92921.7070.0010.0010.0000.0000.0000.000
10A254GLY0-0.0070.00324.527-0.011-0.0110.0000.0000.0000.000
11A255TYR0-0.062-0.04226.2250.0080.0080.0000.0000.0000.000
12A256HIS10.8620.92122.712-0.008-0.0080.0000.0000.0000.000
13A257LYS10.9570.98925.829-0.002-0.0020.0000.0000.0000.000
14A258GLY0-0.025-0.00925.770-0.006-0.0060.0000.0000.0000.000
15A259PRO0-0.007-0.00123.3160.0080.0080.0000.0000.0000.000
16A260LYS10.9080.96315.374-0.073-0.0730.0000.0000.0000.000
17A261GLN0-0.002-0.01316.6220.0370.0370.0000.0000.0000.000
18A262VAL0-0.070-0.03314.058-0.020-0.0200.0000.0000.0000.000
19A263VAL00.0650.02410.879-0.024-0.0240.0000.0000.0000.000
20A264ALA00.0210.02312.3950.1050.1050.0000.0000.0000.000
21A265LEU00.0240.0218.294-0.005-0.0050.0000.0000.0000.000
22A266LYS10.8540.90711.284-0.848-0.8480.0000.0000.0000.000
23A267ALA00.0210.01414.676-0.025-0.0250.0000.0000.0000.000
24A268THR00.0330.02618.0280.0030.0030.0000.0000.0000.000
25A269LYS10.9600.99420.940-0.191-0.1910.0000.0000.0000.000
26A270LEU00.0410.03024.464-0.003-0.0030.0000.0000.0000.000
27A271PHE0-0.026-0.01124.210-0.012-0.0120.0000.0000.0000.000
28A272THR0-0.048-0.03428.672-0.008-0.0080.0000.0000.0000.000
29A273TYR00.0570.02128.665-0.002-0.0020.0000.0000.0000.000
30A274ASP-1-0.897-0.96130.5040.0660.0660.0000.0000.0000.000
31A275SER00.011-0.00834.152-0.003-0.0030.0000.0000.0000.000
32A276ILE0-0.0220.00236.683-0.004-0.0040.0000.0000.0000.000
33A277LYS10.8880.93237.840-0.055-0.0550.0000.0000.0000.000
34A278SER0-0.0030.00137.205-0.001-0.0010.0000.0000.0000.000
35A279LYS10.9621.00233.624-0.064-0.0640.0000.0000.0000.000
36A280LYS10.9360.95930.729-0.105-0.1050.0000.0000.0000.000
37A281MET0-0.0240.01024.210-0.012-0.0120.0000.0000.0000.000
38A282PHE0-0.027-0.00821.0440.0020.0020.0000.0000.0000.000
39A283HIS00.013-0.00319.3090.0010.0010.0000.0000.0000.000
40A284ALA00.0570.01517.0960.0230.0230.0000.0000.0000.000
41A285THR0-0.0180.01310.829-0.030-0.0300.0000.0000.0000.000
42A286VAL0-0.015-0.01313.1410.0650.0650.0000.0000.0000.000
43A287ALA00.013-0.0048.3720.0800.0800.0000.0000.0000.000
44A288THR00.0720.05510.201-0.050-0.0500.0000.0000.0000.000
45A289ASP-1-0.886-0.9497.2860.3980.3980.0000.0000.0000.000
46A290THR0-0.109-0.0926.691-0.353-0.3530.0000.0000.0000.000
47A291GLU-1-0.893-0.9196.969-0.930-0.9300.0000.0000.0000.000
48A292PHE0-0.038-0.0226.3560.3750.3750.0000.0000.0000.000
49A293PHE00.0460.0349.567-0.125-0.1250.0000.0000.0000.000
50A294ARG10.9600.97113.170-0.231-0.2310.0000.0000.0000.000
51A295VAL0-0.024-0.02615.403-0.063-0.0630.0000.0000.0000.000
52A296MET0-0.013-0.01818.6740.0180.0180.0000.0000.0000.000
53A297VAL0-0.0030.01521.749-0.021-0.0210.0000.0000.0000.000
54A298PHE0-0.076-0.06124.248-0.003-0.0030.0000.0000.0000.000
55A299GLU-1-0.889-0.93327.5180.0860.0860.0000.0000.0000.000
56A300GLU-1-0.913-0.97228.0610.1090.1090.0000.0000.0000.000
57A301ASN0-0.065-0.04528.9960.0120.0120.0000.0000.0000.000
58A302LEU00.0220.00025.276-0.006-0.0060.0000.0000.0000.000
59A303GLU-1-0.948-0.96923.9310.1860.1860.0000.0000.0000.000
60A304LYS10.8880.94323.443-0.109-0.1090.0000.0000.0000.000
61A305LYS10.9370.97422.804-0.109-0.1090.0000.0000.0000.000
62A306PHE0-0.0120.00118.1110.0060.0060.0000.0000.0000.000
63A307ILE0-0.0070.00818.5730.0420.0420.0000.0000.0000.000
64A308PRO0-0.031-0.02915.4560.0200.0200.0000.0000.0000.000
65A309GLY0-0.013-0.00414.337-0.021-0.0210.0000.0000.0000.000
66A310ASN0-0.0130.00315.321-0.019-0.0190.0000.0000.0000.000
67A311THR0-0.009-0.00214.6240.0200.0200.0000.0000.0000.000
68A312ILE00.0340.02516.772-0.029-0.0290.0000.0000.0000.000
69A313ALA0-0.017-0.00918.316-0.004-0.0040.0000.0000.0000.000
70A314LEU0-0.027-0.00718.3260.0040.0040.0000.0000.0000.000
71A315SER0-0.001-0.01521.613-0.021-0.0210.0000.0000.0000.000
72A316ASP-1-0.888-0.96824.8330.0420.0420.0000.0000.0000.000
73A317TYR0-0.059-0.03920.3350.0080.0080.0000.0000.0000.000
74A318PHE0-0.004-0.01624.797-0.016-0.0160.0000.0000.0000.000
75A319GLY00.0510.04722.7850.0170.0170.0000.0000.0000.000
76A320MET0-0.009-0.02323.001-0.011-0.0110.0000.0000.0000.000
77A321TYR00.0130.00022.8220.0130.0130.0000.0000.0000.000
78A322GLY00.0560.05019.0740.0080.0080.0000.0000.0000.000
79A323SER0-0.061-0.03517.7650.0380.0380.0000.0000.0000.000
80A324LEU0-0.030-0.01417.484-0.022-0.0220.0000.0000.0000.000
81A325ALA00.012-0.00720.8130.0200.0200.0000.0000.0000.000
82A326ILE0-0.0190.00120.931-0.012-0.0120.0000.0000.0000.000
83A327HIS00.0210.00624.9700.0160.0160.0000.0000.0000.000
84A328GLU-1-0.871-0.95428.6120.0560.0560.0000.0000.0000.000
85A329TYR0-0.010-0.02028.5370.0060.0060.0000.0000.0000.000
86A330SER0-0.009-0.01628.8250.0040.0040.0000.0000.0000.000
87A331SER00.0330.04726.6970.0000.0000.0000.0000.0000.000
88A332VAL0-0.0010.01922.4620.0020.0020.0000.0000.0000.000
89A333SER0-0.015-0.01224.178-0.007-0.0070.0000.0000.0000.000
90A334GLU-1-0.906-0.98822.3410.1670.1670.0000.0000.0000.000
91A335VAL0-0.070-0.00220.163-0.013-0.0130.0000.0000.0000.000
92A354LEU0-0.033-0.0349.7270.0260.0260.0000.0000.0000.000
93A355LYS10.9660.99411.137-0.253-0.2530.0000.0000.0000.000
94A356ILE00.0450.01513.340-0.024-0.0240.0000.0000.0000.000
95A357CYS0-0.0410.00415.108-0.010-0.0100.0000.0000.0000.000
96A358ASP-1-0.847-0.94311.9080.0580.0580.0000.0000.0000.000
97A359LEU0-0.039-0.02814.969-0.018-0.0180.0000.0000.0000.000
98A360HIS0-0.034-0.01417.132-0.013-0.0130.0000.0000.0000.000
99A361LEU0-0.074-0.02815.481-0.013-0.0130.0000.0000.0000.000
100A362GLN0-0.047-0.01713.855-0.014-0.0140.0000.0000.0000.000
101A363THR00.0040.00118.2760.0050.0050.0000.0000.0000.000
102A364GLU-1-0.944-0.98719.625-0.058-0.0580.0000.0000.0000.000
103A365GLU-1-0.929-0.90819.6590.0120.0120.0000.0000.0000.000
104A366ARG10.8990.94012.485-0.087-0.0870.0000.0000.0000.000
105A367LEU0-0.040-0.02917.1270.0140.0140.0000.0000.0000.000
106A368VAL0-0.090-0.04815.3750.0180.0180.0000.0000.0000.000
107A369ASP-1-0.838-0.92913.9690.3900.3900.0000.0000.0000.000
108A370GLY0-0.001-0.01114.5610.0150.0150.0000.0000.0000.000
109A371GLU-1-0.952-0.97315.4930.4140.4140.0000.0000.0000.000
110A372PHE00.0420.02815.8230.0010.0010.0000.0000.0000.000
111A373LYS10.9770.99519.926-0.163-0.1630.0000.0000.0000.000
112A374VAL00.0270.02423.127-0.008-0.0080.0000.0000.0000.000
113A375TYR0-0.006-0.01525.905-0.004-0.0040.0000.0000.0000.000
114A376ARG10.8800.93128.662-0.079-0.0790.0000.0000.0000.000
115A377LYS10.9430.97630.238-0.085-0.0850.0000.0000.0000.000
116A378SER0-0.069-0.02332.758-0.007-0.0070.0000.0000.0000.000
117A379SER00.0530.02535.0210.0030.0030.0000.0000.0000.000
118A380GLY00.0170.00336.243-0.002-0.0020.0000.0000.0000.000
119A381ASN0-0.066-0.01937.2180.0000.0000.0000.0000.0000.000
120A382ASN00.0760.00837.564-0.001-0.0010.0000.0000.0000.000
121A383CYS0-0.106-0.03633.4290.0020.0020.0000.0000.0000.000
122A384ILE00.0060.00632.190-0.003-0.0030.0000.0000.0000.000
123A385CYM-1-0.877-0.91831.0450.0770.0770.0000.0000.0000.000
124A386TYR00.022-0.02227.485-0.001-0.0010.0000.0000.0000.000
125A387GLY0-0.006-0.00426.957-0.005-0.0050.0000.0000.0000.000
126A388ILE0-0.032-0.01920.7240.0040.0040.0000.0000.0000.000
127A389TRP0-0.010-0.01721.909-0.008-0.0080.0000.0000.0000.000
128A390ASP-1-0.741-0.91316.8660.2170.2170.0000.0000.0000.000
129A391ASP-1-0.934-0.95217.5260.1420.1420.0000.0000.0000.000
130A392THR0-0.138-0.08015.874-0.024-0.0240.0000.0000.0000.000
131A393GLY00.0110.00918.468-0.015-0.0150.0000.0000.0000.000
132A394ALA0-0.006-0.01021.4420.0140.0140.0000.0000.0000.000
133A395MET0-0.0070.02021.091-0.005-0.0050.0000.0000.0000.000
134A396LYS10.9721.00323.844-0.048-0.0480.0000.0000.0000.000
135A397VAL00.0220.00723.9220.0060.0060.0000.0000.0000.000
136A398VAL0-0.0170.00926.469-0.007-0.0070.0000.0000.0000.000
137A399VAL00.0310.01327.7980.0060.0060.0000.0000.0000.000
138A400SER00.0260.00930.060-0.006-0.0060.0000.0000.0000.000
139A401GLY00.005-0.00431.7460.0060.0060.0000.0000.0000.000
140A402GLN00.0440.00832.2150.0030.0030.0000.0000.0000.000
141A403LEU00.0450.02626.2770.0020.0020.0000.0000.0000.000
142A404THR0-0.048-0.00530.6520.0040.0040.0000.0000.0000.000
143A405SER0-0.028-0.01333.250-0.003-0.0030.0000.0000.0000.000
144A406VAL0-0.066-0.00928.4160.0000.0000.0000.0000.0000.000
145A407ASN0-0.024-0.01231.664-0.001-0.0010.0000.0000.0000.000
146A408CYS00.0610.02428.5360.0130.0130.0000.0000.0000.000
147A409GLU-1-0.979-0.98430.6900.0810.0810.0000.0000.0000.000
148A410ILE0-0.004-0.00530.0790.0090.0090.0000.0000.0000.000
149A411GLY0-0.0210.00128.789-0.004-0.0040.0000.0000.0000.000
150A412ASN0-0.047-0.01527.2630.0050.0050.0000.0000.0000.000
151A413THR00.0390.00820.788-0.010-0.0100.0000.0000.0000.000
152A414ILE00.0250.01322.2260.0020.0020.0000.0000.0000.000
153A415ARG10.8850.96514.074-0.502-0.5020.0000.0000.0000.000
154A416LEU0-0.009-0.01919.020-0.027-0.0270.0000.0000.0000.000
155A417VAL0-0.024-0.01417.2220.0510.0510.0000.0000.0000.000
156A418CYS0-0.011-0.00118.465-0.039-0.0390.0000.0000.0000.000
157A419PHE00.0150.01919.769-0.026-0.0260.0000.0000.0000.000
158A420GLU-1-0.862-0.94520.3400.0750.0750.0000.0000.0000.000
159A421LEU0-0.018-0.00518.3100.0000.0000.0000.0000.0000.000
160A422THR0-0.047-0.02421.782-0.011-0.0110.0000.0000.0000.000
161A423SER00.0850.05325.159-0.002-0.0020.0000.0000.0000.000
162A424ASN0-0.117-0.09226.8570.0020.0020.0000.0000.0000.000
163A425ALA0-0.043-0.01429.041-0.003-0.0030.0000.0000.0000.000
164A426ASP-1-0.998-0.98230.5640.0280.0280.0000.0000.0000.000
165A427GLU-1-0.842-0.92626.2960.0420.0420.0000.0000.0000.000
166A428TRP00.0290.02721.9530.0030.0030.0000.0000.0000.000
167A429PHE0-0.011-0.03024.5540.0060.0060.0000.0000.0000.000
168A430LEU00.0340.01119.627-0.002-0.0020.0000.0000.0000.000
169A431ARG10.9330.98323.706-0.065-0.0650.0000.0000.0000.000
170A432ALA00.0070.00324.9620.0110.0110.0000.0000.0000.000
171A433THR0-0.042-0.00925.077-0.008-0.0080.0000.0000.0000.000
172A434ARG10.9240.94527.695-0.071-0.0710.0000.0000.0000.000
173A435TYR00.006-0.00524.986-0.003-0.0030.0000.0000.0000.000
174A436SER00.0500.04523.6860.0110.0110.0000.0000.0000.000
175A437TYR0-0.065-0.03622.403-0.022-0.0220.0000.0000.0000.000
176A438MET00.007-0.00122.9170.0120.0120.0000.0000.0000.000
177A439GLU-1-0.895-0.96222.9230.2560.2560.0000.0000.0000.000
178A440VAL0-0.0160.00323.5410.0140.0140.0000.0000.0000.000
179A441ILE00.0170.00220.4590.0000.0000.0000.0000.0000.000
180A442MET0-0.026-0.01222.468-0.013-0.0130.0000.0000.0000.000