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: 6NL7Z

Calculation Name: 3T5X-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3T5X

Chain ID: A

ChEMBL ID:

UniProt ID: Q5JVF3

Base Structure: X-ray

Registration Date: 2023-06-21

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 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 195
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2255820.961832
FMO2-HF: Nuclear repulsion 2175706.605656
FMO2-HF: Total energy -80114.356176
FMO2-MP2: Total energy -80345.768806


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:205:SER)


Summations of interaction energy for fragment #1(A:205:SER)
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.
-27.705-21.6268.891-6.168-8.8020.017
Interaction energy analysis for fragmet #1(A:205:SER)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.074 / q_NPA : 0.033
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].
3A207ALA00.0260.0122.158-9.695-7.1093.918-2.996-3.5080.032
4A208GLN00.0450.0222.317-10.928-8.2014.964-3.004-4.687-0.016
5A209ARG10.9951.0023.684-3.861-3.1490.010-0.167-0.5550.001
6A210VAL0-0.0040.0065.772-0.126-0.1260.0000.0000.0000.000
7A211THR0-0.011-0.0166.578-0.294-0.2940.0000.0000.0000.000
8A212TYR00.0150.0017.680-0.029-0.0290.0000.0000.0000.000
9A213LYS10.9160.9739.547-0.345-0.3450.0000.0000.0000.000
10A214TYR00.0140.01711.284-0.031-0.0310.0000.0000.0000.000
11A215TYR00.013-0.00511.750-0.004-0.0040.0000.0000.0000.000
12A216VAL0-0.026-0.00313.046-0.009-0.0090.0000.0000.0000.000
13A217GLY00.0430.02015.4060.0130.0130.0000.0000.0000.000
14A218ARG10.8830.94716.1500.0140.0140.0000.0000.0000.000
15A219LYS10.9430.96916.8910.1410.1410.0000.0000.0000.000
16A220ALA00.0830.04719.633-0.002-0.0020.0000.0000.0000.000
17A221MET0-0.040-0.00421.3640.0080.0080.0000.0000.0000.000
18A222PHE0-0.098-0.06122.459-0.001-0.0010.0000.0000.0000.000
19A223ASP-1-0.914-0.93424.343-0.007-0.0070.0000.0000.0000.000
20A224SER0-0.079-0.03826.0230.0040.0040.0000.0000.0000.000
21A225ASP-1-0.795-0.88923.8220.1000.1000.0000.0000.0000.000
22A226PHE00.019-0.02423.6660.0140.0140.0000.0000.0000.000
23A227LYS10.9290.95623.956-0.146-0.1460.0000.0000.0000.000
24A228GLN00.0450.04018.8370.0350.0350.0000.0000.0000.000
25A229ALA0-0.014-0.01119.3770.0230.0230.0000.0000.0000.000
26A230GLU-1-0.781-0.87819.3850.2340.2340.0000.0000.0000.000
27A231GLU-1-0.892-0.91718.0270.2920.2920.0000.0000.0000.000
28A232TYR0-0.052-0.04315.0260.0700.0700.0000.0000.0000.000
29A233LEU00.0260.00514.7210.0770.0770.0000.0000.0000.000
30A234SER0-0.003-0.02416.1550.0470.0470.0000.0000.0000.000
31A235PHE00.0010.0159.3350.1010.1010.0000.0000.0000.000
32A236ALA00.014-0.01111.4630.1620.1620.0000.0000.0000.000
33A237PHE0-0.001-0.00512.0070.1370.1370.0000.0000.0000.000
34A238GLU-1-0.936-0.97314.2410.6410.6410.0000.0000.0000.000
35A239HIS10.8280.9209.648-1.027-1.0270.0000.0000.0000.000
36A240CYS0-0.0230.0159.1430.3760.3760.0000.0000.0000.000
37A241HIS00.0280.0125.028-0.829-0.775-0.001-0.001-0.0520.000
38A242ARG10.9670.95910.337-0.805-0.8050.0000.0000.0000.000
39A243SER00.0430.03711.755-0.042-0.0420.0000.0000.0000.000
40A244SER00.0160.01611.329-0.046-0.0460.0000.0000.0000.000
41A245GLN00.0870.02013.3910.0380.0380.0000.0000.0000.000
42A246LYS10.9950.98715.586-0.062-0.0620.0000.0000.0000.000
43A247ASN00.0400.01710.203-0.145-0.1450.0000.0000.0000.000
44A248LYS10.8910.94313.685-0.744-0.7440.0000.0000.0000.000
45A249ARG10.8620.92915.440-0.139-0.1390.0000.0000.0000.000
46A250MET0-0.006-0.00515.947-0.019-0.0190.0000.0000.0000.000
47A251ILE0-0.0010.00012.202-0.022-0.0220.0000.0000.0000.000
48A252LEU0-0.0080.00316.847-0.020-0.0200.0000.0000.0000.000
49A253ILE0-0.004-0.00419.957-0.017-0.0170.0000.0000.0000.000
50A254TYR0-0.002-0.02618.968-0.027-0.0270.0000.0000.0000.000
51A255LEU0-0.006-0.01018.767-0.006-0.0060.0000.0000.0000.000
52A256LEU0-0.020-0.00521.383-0.002-0.0020.0000.0000.0000.000
53A257PRO00.0330.01624.180-0.003-0.0030.0000.0000.0000.000
54A258VAL00.0160.01322.514-0.006-0.0060.0000.0000.0000.000
55A259LYS10.8260.90122.710-0.247-0.2470.0000.0000.0000.000
56A260MET00.0090.00526.337-0.007-0.0070.0000.0000.0000.000
57A261LEU0-0.020-0.00228.086-0.006-0.0060.0000.0000.0000.000
58A262LEU0-0.066-0.02325.951-0.004-0.0040.0000.0000.0000.000
59A263GLY0-0.022-0.01730.0320.0030.0030.0000.0000.0000.000
60A264HIS0-0.076-0.02727.4260.0010.0010.0000.0000.0000.000
61A265MET00.0120.00929.1370.0010.0010.0000.0000.0000.000
62A266PRO0-0.0100.00527.0390.0120.0120.0000.0000.0000.000
63A267THR00.0610.02428.598-0.009-0.0090.0000.0000.0000.000
64A268VAL00.0580.01029.3310.0040.0040.0000.0000.0000.000
65A269GLU-1-0.789-0.90128.9920.1360.1360.0000.0000.0000.000
66A270LEU0-0.0210.00022.5360.0100.0100.0000.0000.0000.000
67A271LEU00.0270.00625.2960.0080.0080.0000.0000.0000.000
68A272LYS10.8850.93827.090-0.124-0.1240.0000.0000.0000.000
69A273LYS10.9080.97821.044-0.311-0.3110.0000.0000.0000.000
70A274TYR0-0.045-0.02418.4910.0260.0260.0000.0000.0000.000
71A275HIS00.0160.01323.314-0.020-0.0200.0000.0000.0000.000
72A276LEU0-0.019-0.00322.498-0.012-0.0120.0000.0000.0000.000
73A277MET00.0510.01726.8910.0040.0040.0000.0000.0000.000
74A278GLN00.0350.03028.8690.0060.0060.0000.0000.0000.000
75A279PHE00.0470.00925.652-0.004-0.0040.0000.0000.0000.000
76A280ALA0-0.0180.00530.6950.0030.0030.0000.0000.0000.000
77A281GLU-1-0.815-0.89533.2440.0520.0520.0000.0000.0000.000
78A282VAL00.0480.03132.526-0.001-0.0010.0000.0000.0000.000
79A283THR00.010-0.01631.6820.0030.0030.0000.0000.0000.000
80A284ARG10.8590.93233.932-0.062-0.0620.0000.0000.0000.000
81A285ALA00.0350.02237.407-0.001-0.0010.0000.0000.0000.000
82A286VAL00.0560.02034.350-0.002-0.0020.0000.0000.0000.000
83A287SER0-0.064-0.04335.8530.0020.0020.0000.0000.0000.000
84A288GLU-1-0.916-0.93037.9490.0620.0620.0000.0000.0000.000
85A289GLY0-0.014-0.01740.691-0.002-0.0020.0000.0000.0000.000
86A290ASN0-0.031-0.02741.736-0.007-0.0070.0000.0000.0000.000
87A291LEU00.0620.00741.3650.0010.0010.0000.0000.0000.000
88A292LEU00.0650.03742.3720.0000.0000.0000.0000.0000.000
89A293LEU0-0.010-0.00740.253-0.001-0.0010.0000.0000.0000.000
90A294LEU0-0.042-0.02735.6730.0010.0010.0000.0000.0000.000
91A295HIS0-0.027-0.01538.434-0.002-0.0020.0000.0000.0000.000
92A296GLU-1-0.821-0.90140.0710.0240.0240.0000.0000.0000.000
93A297ALA0-0.092-0.05136.541-0.001-0.0010.0000.0000.0000.000
94A298LEU0-0.047-0.04233.7870.0020.0020.0000.0000.0000.000
95A299ALA00.0700.04235.838-0.003-0.0030.0000.0000.0000.000
96A300LYS10.8330.90637.558-0.044-0.0440.0000.0000.0000.000
97A301HIS0-0.040-0.02432.553-0.003-0.0030.0000.0000.0000.000
98A302GLU-1-0.876-0.92532.7470.0050.0050.0000.0000.0000.000
99A303ALA00.0450.01132.531-0.002-0.0020.0000.0000.0000.000
100A304PHE0-0.064-0.03426.053-0.004-0.0040.0000.0000.0000.000
101A305PHE00.0510.01727.9990.0020.0020.0000.0000.0000.000
102A306ILE00.0360.01927.9250.0000.0000.0000.0000.0000.000
103A307ARG10.9190.96226.710-0.004-0.0040.0000.0000.0000.000
104A308CYS0-0.091-0.03823.878-0.002-0.0020.0000.0000.0000.000
105A309GLY00.0030.02523.2520.0030.0030.0000.0000.0000.000
106A310ILE0-0.035-0.03023.9910.0020.0020.0000.0000.0000.000
107A311PHE00.0460.02526.5380.0070.0070.0000.0000.0000.000
108A312LEU00.0960.03529.9610.0040.0040.0000.0000.0000.000
109A313ILE0-0.030-0.02225.7860.0040.0040.0000.0000.0000.000
110A314LEU0-0.016-0.01329.0140.0080.0080.0000.0000.0000.000
111A315GLU-1-0.761-0.85031.1800.0280.0280.0000.0000.0000.000
112A316LYS10.8930.95229.780-0.032-0.0320.0000.0000.0000.000
113A317LEU0-0.018-0.01330.9730.0050.0050.0000.0000.0000.000
114A318LYS10.8980.94634.492-0.023-0.0230.0000.0000.0000.000
115A319ILE00.0400.03735.3870.0000.0000.0000.0000.0000.000
116A320ILE00.0120.00433.5380.0000.0000.0000.0000.0000.000
117A321THR0-0.016-0.01637.5250.0030.0030.0000.0000.0000.000
118A322TYR00.0740.03239.5580.0000.0000.0000.0000.0000.000
119A323ARG10.8450.91938.777-0.078-0.0780.0000.0000.0000.000
120A324ASN0-0.068-0.05837.5280.0010.0010.0000.0000.0000.000
121A325LEU00.0130.02041.8640.0010.0010.0000.0000.0000.000
122A326PHE00.0340.00244.9730.0000.0000.0000.0000.0000.000
123A327LYS10.9470.98641.907-0.077-0.0770.0000.0000.0000.000
124A328LYS10.9160.96143.552-0.065-0.0650.0000.0000.0000.000
125A329VAL00.0440.03347.467-0.001-0.0010.0000.0000.0000.000
126A330TYR0-0.015-0.01947.9060.0000.0000.0000.0000.0000.000
127A331LEU0-0.052-0.03245.7970.0000.0000.0000.0000.0000.000
128A332LEU0-0.030-0.00950.3390.0000.0000.0000.0000.0000.000
129A333LEU00.0020.00952.950-0.001-0.0010.0000.0000.0000.000
130A334LYS10.8410.92852.685-0.053-0.0530.0000.0000.0000.000
131A335THR00.0750.03854.675-0.001-0.0010.0000.0000.0000.000
132A336HIS00.003-0.01251.7900.0030.0030.0000.0000.0000.000
133A337GLN0-0.021-0.00454.542-0.001-0.0010.0000.0000.0000.000
134A338LEU0-0.0010.01051.6630.0000.0000.0000.0000.0000.000
135A339SER00.0440.02155.724-0.001-0.0010.0000.0000.0000.000
136A340LEU00.0420.02053.5950.0010.0010.0000.0000.0000.000
137A341ASP-1-0.848-0.94154.9820.0250.0250.0000.0000.0000.000
138A342ALA0-0.024-0.00155.2600.0000.0000.0000.0000.0000.000
139A343PHE0-0.033-0.02749.5570.0020.0020.0000.0000.0000.000
140A344LEU00.0110.02551.7310.0000.0000.0000.0000.0000.000
141A345VAL00.0010.00453.7580.0000.0000.0000.0000.0000.000
142A346ALA0-0.030-0.01749.8860.0000.0000.0000.0000.0000.000
143A347LEU00.005-0.00847.2070.0010.0010.0000.0000.0000.000
144A348LYS10.9981.01250.315-0.023-0.0230.0000.0000.0000.000
145A349PHE0-0.036-0.00849.7160.0000.0000.0000.0000.0000.000
146A350MET0-0.110-0.03246.4110.0020.0020.0000.0000.0000.000
147A351GLN0-0.044-0.02748.003-0.001-0.0010.0000.0000.0000.000
148A352VAL0-0.011-0.00246.859-0.001-0.0010.0000.0000.0000.000
149A353GLU-1-0.934-0.97249.3450.0130.0130.0000.0000.0000.000
150A354ASP-1-0.926-0.96151.5260.0100.0100.0000.0000.0000.000
151A355VAL0-0.079-0.01451.0920.0000.0000.0000.0000.0000.000
152A356ASP-1-0.815-0.93353.0910.0160.0160.0000.0000.0000.000
153A357ILE0-0.057-0.05554.0860.0020.0020.0000.0000.0000.000
154A358ASP-1-0.856-0.92354.4710.0170.0170.0000.0000.0000.000
155A359GLU-1-0.881-0.93948.8950.0200.0200.0000.0000.0000.000
156A360VAL0-0.041-0.02449.7180.0020.0020.0000.0000.0000.000
157A361GLN0-0.032-0.02249.9980.0020.0020.0000.0000.0000.000
158A362CYS00.0040.01748.0040.0020.0020.0000.0000.0000.000
159A363ILE00.0190.01644.5700.0020.0020.0000.0000.0000.000
160A364LEU0-0.028-0.03145.3190.0030.0030.0000.0000.0000.000
161A365ALA0-0.0020.00746.4120.0020.0020.0000.0000.0000.000
162A366ASN0-0.022-0.02142.2970.0010.0010.0000.0000.0000.000
163A367LEU0-0.024-0.01140.9370.0030.0030.0000.0000.0000.000
164A368ILE0-0.069-0.03742.1600.0040.0040.0000.0000.0000.000
165A369TYR0-0.036-0.00539.9780.0020.0020.0000.0000.0000.000
166A370MET0-0.025-0.01137.8890.0020.0020.0000.0000.0000.000
167A371GLY00.0380.03437.9990.0050.0050.0000.0000.0000.000
168A372HIS0-0.053-0.03935.9660.0020.0020.0000.0000.0000.000
169A373VAL0-0.031-0.02040.4030.0030.0030.0000.0000.0000.000
170A374LYS10.8600.93342.713-0.067-0.0670.0000.0000.0000.000
171A375GLY00.008-0.02145.8600.0010.0010.0000.0000.0000.000
172A376TYR00.0140.01948.922-0.001-0.0010.0000.0000.0000.000
173A377ILE00.0600.03051.0930.0010.0010.0000.0000.0000.000
174A378SER0-0.034-0.00554.036-0.002-0.0020.0000.0000.0000.000
175A379HIS00.0980.02255.2680.0000.0000.0000.0000.0000.000
176A380GLN0-0.0140.01259.5290.0000.0000.0000.0000.0000.000
177A381HIS00.0240.00861.4420.0000.0000.0000.0000.0000.000
178A382GLN00.0730.04758.8700.0020.0020.0000.0000.0000.000
179A383LYS10.8320.91157.338-0.027-0.0270.0000.0000.0000.000
180A384LEU00.0180.01349.3100.0000.0000.0000.0000.0000.000
181A385VAL0-0.032-0.01253.8160.0020.0020.0000.0000.0000.000
182A386VAL00.0190.01049.3360.0010.0010.0000.0000.0000.000
183A387SER00.009-0.01948.007-0.001-0.0010.0000.0000.0000.000
184A388LYS10.9140.95350.136-0.042-0.0420.0000.0000.0000.000
185A389GLN00.0300.02447.1420.0030.0030.0000.0000.0000.000
186A390ASN0-0.018-0.02043.483-0.001-0.0010.0000.0000.0000.000
187A391PRO00.0620.03144.4930.0020.0020.0000.0000.0000.000
188A392PHE00.0550.04042.400-0.001-0.0010.0000.0000.0000.000
189A393PRO00.0110.02038.5730.0050.0050.0000.0000.0000.000
190A394PRO00.0190.01435.356-0.001-0.0010.0000.0000.0000.000
191A395LEU00.0780.03833.781-0.001-0.0010.0000.0000.0000.000
192A396SER0-0.023-0.00430.308-0.005-0.0050.0000.0000.0000.000
193A397THR0-0.066-0.05931.1830.0030.0030.0000.0000.0000.000
194A398VAL0-0.0220.00833.864-0.003-0.0030.0000.0000.0000.000
195A399CYS0-0.0050.01729.6490.0010.0010.0000.0000.0000.000