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: Z6RLN

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 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 195
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2261804.735138
FMO2-HF: Nuclear repulsion 2181690.192095
FMO2-HF: Total energy -80114.543044
FMO2-MP2: Total energy -80345.976818


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.
-31.269-22.2175.023-6.162-7.9120.007
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 : 0.080 / q_NPA : 0.036
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].
3A207ALA00.0420.0292.654-6.703-3.4610.567-1.761-2.0480.016
4A208GLN00.0520.0342.429-10.664-7.5384.213-3.048-4.291-0.024
5A209ARG10.9710.9872.940-11.323-8.6390.243-1.353-1.5730.015
6A210VAL00.0020.0065.739-0.165-0.1650.0000.0000.0000.000
7A211THR0-0.013-0.0167.034-0.207-0.2070.0000.0000.0000.000
8A212TYR00.0270.0007.8310.0080.0080.0000.0000.0000.000
9A213LYS10.8420.9409.636-0.528-0.5280.0000.0000.0000.000
10A214TYR00.0040.00411.653-0.042-0.0420.0000.0000.0000.000
11A215TYR00.006-0.00612.198-0.008-0.0080.0000.0000.0000.000
12A216VAL0-0.031-0.01312.921-0.008-0.0080.0000.0000.0000.000
13A217GLY00.0390.02215.4100.0090.0090.0000.0000.0000.000
14A218ARG10.8590.93016.2260.0250.0250.0000.0000.0000.000
15A219LYS10.9380.96917.1850.0960.0960.0000.0000.0000.000
16A220ALA00.0560.03919.625-0.005-0.0050.0000.0000.0000.000
17A221MET0-0.030-0.00221.4230.0050.0050.0000.0000.0000.000
18A222PHE0-0.073-0.04522.777-0.005-0.0050.0000.0000.0000.000
19A223ASP-1-0.917-0.95524.1860.0360.0360.0000.0000.0000.000
20A224SER0-0.034-0.00625.7170.0000.0000.0000.0000.0000.000
21A225ASP-1-0.767-0.86023.6160.1640.1640.0000.0000.0000.000
22A226PHE00.006-0.03923.4950.0170.0170.0000.0000.0000.000
23A227LYS10.8880.94924.193-0.185-0.1850.0000.0000.0000.000
24A228GLN00.0380.02818.7910.0530.0530.0000.0000.0000.000
25A229ALA0-0.008-0.00519.0320.0300.0300.0000.0000.0000.000
26A230GLU-1-0.761-0.86719.5010.2740.2740.0000.0000.0000.000
27A231GLU-1-0.884-0.91417.7320.4050.4050.0000.0000.0000.000
28A232TYR0-0.008-0.03114.9230.0910.0910.0000.0000.0000.000
29A233LEU00.0310.00814.7100.0650.0650.0000.0000.0000.000
30A234SER0-0.003-0.02216.7230.0150.0150.0000.0000.0000.000
31A235PHE00.0150.0149.1460.0910.0910.0000.0000.0000.000
32A236ALA00.023-0.00311.7640.1540.1540.0000.0000.0000.000
33A237PHE0-0.004-0.00112.3360.0890.0890.0000.0000.0000.000
34A238GLU-1-0.898-0.93914.4290.7300.7300.0000.0000.0000.000
35A239HIS10.7990.8879.453-1.107-1.1070.0000.0000.0000.000
36A240CYS0-0.0110.0159.0230.3320.3320.0000.0000.0000.000
37A241HIS00.0350.0215.238-0.353-0.3530.0000.0000.0000.000
38A242ARG10.9720.96610.277-0.779-0.7790.0000.0000.0000.000
39A243SER00.0640.04212.378-0.030-0.0300.0000.0000.0000.000
40A244SER00.0210.02311.564-0.034-0.0340.0000.0000.0000.000
41A245GLN00.0460.00513.5360.0240.0240.0000.0000.0000.000
42A246LYS11.0140.99616.0120.0290.0290.0000.0000.0000.000
43A247ASN00.0460.02510.274-0.089-0.0890.0000.0000.0000.000
44A248LYS10.8660.92713.188-0.720-0.7200.0000.0000.0000.000
45A249ARG10.8830.93515.638-0.090-0.0900.0000.0000.0000.000
46A250MET0-0.017-0.01416.126-0.015-0.0150.0000.0000.0000.000
47A251ILE0-0.0110.00012.242-0.018-0.0180.0000.0000.0000.000
48A252LEU0-0.012-0.00616.878-0.014-0.0140.0000.0000.0000.000
49A253ILE0-0.019-0.00920.065-0.009-0.0090.0000.0000.0000.000
50A254TYR00.025-0.01319.469-0.025-0.0250.0000.0000.0000.000
51A255LEU0-0.018-0.00919.0070.0010.0010.0000.0000.0000.000
52A256LEU0-0.005-0.00421.623-0.001-0.0010.0000.0000.0000.000
53A257PRO00.0180.01524.269-0.002-0.0020.0000.0000.0000.000
54A258VAL00.0180.01222.679-0.004-0.0040.0000.0000.0000.000
55A259LYS10.8020.89022.066-0.286-0.2860.0000.0000.0000.000
56A260MET00.0120.00126.495-0.006-0.0060.0000.0000.0000.000
57A261LEU0-0.0060.00028.298-0.006-0.0060.0000.0000.0000.000
58A262LEU0-0.037-0.00726.036-0.004-0.0040.0000.0000.0000.000
59A263GLY0-0.002-0.01730.1170.0030.0030.0000.0000.0000.000
60A264HIS0-0.090-0.03326.758-0.006-0.0060.0000.0000.0000.000
61A265MET0-0.0020.00928.8790.0020.0020.0000.0000.0000.000
62A266PRO0-0.0170.00227.3210.0110.0110.0000.0000.0000.000
63A267THR00.0520.02128.893-0.010-0.0100.0000.0000.0000.000
64A268VAL00.0490.00929.3730.0030.0030.0000.0000.0000.000
65A269GLU-1-0.784-0.89929.1280.1260.1260.0000.0000.0000.000
66A270LEU0-0.0250.00022.5860.0080.0080.0000.0000.0000.000
67A271LEU00.0070.00025.3330.0040.0040.0000.0000.0000.000
68A272LYS10.9010.94227.552-0.118-0.1180.0000.0000.0000.000
69A273LYS10.9040.96920.751-0.298-0.2980.0000.0000.0000.000
70A274TYR0-0.021-0.01418.4610.0180.0180.0000.0000.0000.000
71A275HIS00.0260.01823.397-0.021-0.0210.0000.0000.0000.000
72A276LEU0-0.031-0.00522.653-0.013-0.0130.0000.0000.0000.000
73A277MET00.0460.01027.0820.0060.0060.0000.0000.0000.000
74A278GLN00.0480.04329.3390.0090.0090.0000.0000.0000.000
75A279PHE00.0470.00825.796-0.002-0.0020.0000.0000.0000.000
76A280ALA0-0.0170.00330.8520.0050.0050.0000.0000.0000.000
77A281GLU-1-0.805-0.89033.3210.0470.0470.0000.0000.0000.000
78A282VAL00.0450.02832.5870.0000.0000.0000.0000.0000.000
79A283THR00.014-0.01531.8280.0050.0050.0000.0000.0000.000
80A284ARG10.8590.92934.040-0.060-0.0600.0000.0000.0000.000
81A285ALA00.0400.02237.6010.0000.0000.0000.0000.0000.000
82A286VAL00.0550.02334.592-0.001-0.0010.0000.0000.0000.000
83A287SER0-0.036-0.01936.1830.0030.0030.0000.0000.0000.000
84A288GLU-1-0.869-0.92438.4450.0630.0630.0000.0000.0000.000
85A289GLY0-0.033-0.01840.881-0.003-0.0030.0000.0000.0000.000
86A290ASN0-0.004-0.01341.968-0.007-0.0070.0000.0000.0000.000
87A291LEU00.049-0.00541.5490.0000.0000.0000.0000.0000.000
88A292LEU00.0690.04742.636-0.001-0.0010.0000.0000.0000.000
89A293LEU0-0.016-0.01440.350-0.001-0.0010.0000.0000.0000.000
90A294LEU0-0.040-0.03535.9670.0010.0010.0000.0000.0000.000
91A295HIS0-0.017-0.00538.630-0.002-0.0020.0000.0000.0000.000
92A296GLU-1-0.803-0.89440.1000.0220.0220.0000.0000.0000.000
93A297ALA0-0.096-0.04336.492-0.001-0.0010.0000.0000.0000.000
94A298LEU0-0.052-0.04033.9300.0000.0000.0000.0000.0000.000
95A299ALA00.0820.03935.968-0.004-0.0040.0000.0000.0000.000
96A300LYS10.7990.89037.966-0.040-0.0400.0000.0000.0000.000
97A301HIS0-0.038-0.02632.663-0.005-0.0050.0000.0000.0000.000
98A302GLU-1-0.858-0.90732.7660.0010.0010.0000.0000.0000.000
99A303ALA00.0560.02032.595-0.003-0.0030.0000.0000.0000.000
100A304PHE0-0.107-0.04726.148-0.008-0.0080.0000.0000.0000.000
101A305PHE00.0570.00628.412-0.001-0.0010.0000.0000.0000.000
102A306ILE00.0420.02528.3180.0000.0000.0000.0000.0000.000
103A307ARG10.8950.94226.9440.0190.0190.0000.0000.0000.000
104A308CYS0-0.074-0.03024.162-0.006-0.0060.0000.0000.0000.000
105A309GLY0-0.0010.02623.6050.0040.0040.0000.0000.0000.000
106A310ILE0-0.017-0.02224.1960.0070.0070.0000.0000.0000.000
107A311PHE00.0380.02726.7560.0090.0090.0000.0000.0000.000
108A312LEU00.0850.03030.3060.0050.0050.0000.0000.0000.000
109A313ILE0-0.050-0.03126.1150.0040.0040.0000.0000.0000.000
110A314LEU0-0.018-0.02129.0590.0090.0090.0000.0000.0000.000
111A315GLU-1-0.774-0.86031.3410.0320.0320.0000.0000.0000.000
112A316LYS10.8890.95029.577-0.047-0.0470.0000.0000.0000.000
113A317LEU0-0.012-0.00831.1680.0050.0050.0000.0000.0000.000
114A318LYS10.8910.94034.634-0.028-0.0280.0000.0000.0000.000
115A319ILE00.0430.03335.6980.0000.0000.0000.0000.0000.000
116A320ILE0-0.001-0.00333.7600.0000.0000.0000.0000.0000.000
117A321THR0-0.032-0.02137.7080.0030.0030.0000.0000.0000.000
118A322TYR00.0890.04439.8480.0000.0000.0000.0000.0000.000
119A323ARG10.8500.91738.129-0.094-0.0940.0000.0000.0000.000
120A324ASN0-0.069-0.04837.4880.0030.0030.0000.0000.0000.000
121A325LEU00.0270.02341.9000.0010.0010.0000.0000.0000.000
122A326PHE00.0370.00545.179-0.001-0.0010.0000.0000.0000.000
123A327LYS10.8840.95641.188-0.091-0.0910.0000.0000.0000.000
124A328LYS10.8630.93942.362-0.074-0.0740.0000.0000.0000.000
125A329VAL00.0340.02547.453-0.001-0.0010.0000.0000.0000.000
126A330TYR0-0.026-0.03547.5470.0010.0010.0000.0000.0000.000
127A331LEU0-0.033-0.02045.4430.0000.0000.0000.0000.0000.000
128A332LEU0-0.039-0.00550.0030.0000.0000.0000.0000.0000.000
129A333LEU00.015-0.00152.848-0.001-0.0010.0000.0000.0000.000
130A334LYS10.8420.92652.784-0.060-0.0600.0000.0000.0000.000
131A335THR00.0470.02854.5120.0000.0000.0000.0000.0000.000
132A336HIS00.019-0.01051.6120.0040.0040.0000.0000.0000.000
133A337GLN0-0.012-0.01054.553-0.001-0.0010.0000.0000.0000.000
134A338LEU00.0020.02251.321-0.001-0.0010.0000.0000.0000.000
135A339SER00.0210.01155.258-0.001-0.0010.0000.0000.0000.000
136A340LEU00.0400.02453.5520.0010.0010.0000.0000.0000.000
137A341ASP-1-0.790-0.91354.9430.0290.0290.0000.0000.0000.000
138A342ALA0-0.0180.00555.1890.0000.0000.0000.0000.0000.000
139A343PHE0-0.030-0.02649.6860.0020.0020.0000.0000.0000.000
140A344LEU00.0090.02751.7390.0000.0000.0000.0000.0000.000
141A345VAL0-0.014-0.00553.937-0.001-0.0010.0000.0000.0000.000
142A346ALA0-0.020-0.01149.8480.0000.0000.0000.0000.0000.000
143A347LEU0-0.018-0.01847.4260.0010.0010.0000.0000.0000.000
144A348LYS10.9550.98750.565-0.028-0.0280.0000.0000.0000.000
145A349PHE0-0.033-0.01149.695-0.001-0.0010.0000.0000.0000.000
146A350MET0-0.112-0.04046.5380.0010.0010.0000.0000.0000.000
147A351GLN0-0.042-0.01948.434-0.002-0.0020.0000.0000.0000.000
148A352VAL0-0.021-0.00647.281-0.001-0.0010.0000.0000.0000.000
149A353GLU-1-0.919-0.96349.7270.0140.0140.0000.0000.0000.000
150A354ASP-1-0.934-0.96651.8420.0130.0130.0000.0000.0000.000
151A355VAL0-0.065-0.01051.0150.0010.0010.0000.0000.0000.000
152A356ASP-1-0.799-0.91453.2890.0210.0210.0000.0000.0000.000
153A357ILE0-0.050-0.05354.1120.0020.0020.0000.0000.0000.000
154A358ASP-1-0.871-0.92254.5010.0240.0240.0000.0000.0000.000
155A359GLU-1-0.879-0.94349.3130.0260.0260.0000.0000.0000.000
156A360VAL0-0.038-0.02449.7530.0030.0030.0000.0000.0000.000
157A361GLN0-0.053-0.04550.0490.0030.0030.0000.0000.0000.000
158A362CYS0-0.0090.01247.9470.0030.0030.0000.0000.0000.000
159A363ILE00.0180.01344.6010.0030.0030.0000.0000.0000.000
160A364LEU0-0.031-0.02445.2080.0040.0040.0000.0000.0000.000
161A365ALA00.0120.00846.2650.0030.0030.0000.0000.0000.000
162A366ASN0-0.023-0.01942.3290.0020.0020.0000.0000.0000.000
163A367LEU0-0.035-0.02140.8850.0050.0050.0000.0000.0000.000
164A368ILE0-0.070-0.03342.1260.0050.0050.0000.0000.0000.000
165A369TYR0-0.033-0.00839.7410.0040.0040.0000.0000.0000.000
166A370MET0-0.017-0.00637.7460.0030.0030.0000.0000.0000.000
167A371GLY00.0290.02537.8870.0060.0060.0000.0000.0000.000
168A372HIS0-0.050-0.03935.8140.0020.0020.0000.0000.0000.000
169A373VAL0-0.027-0.01940.2160.0020.0020.0000.0000.0000.000
170A374LYS10.8560.92742.439-0.086-0.0860.0000.0000.0000.000
171A375GLY00.004-0.01645.6170.0000.0000.0000.0000.0000.000
172A376TYR00.0290.02948.759-0.001-0.0010.0000.0000.0000.000
173A377ILE00.0490.02351.0700.0010.0010.0000.0000.0000.000
174A378SER0-0.013-0.00154.136-0.002-0.0020.0000.0000.0000.000
175A379HIS00.0930.02955.174-0.001-0.0010.0000.0000.0000.000
176A380GLN0-0.0100.01059.3180.0000.0000.0000.0000.0000.000
177A381HIS00.0130.01061.347-0.001-0.0010.0000.0000.0000.000
178A382GLN00.0850.04958.3590.0020.0020.0000.0000.0000.000
179A383LYS10.8210.89957.087-0.033-0.0330.0000.0000.0000.000
180A384LEU00.0400.02749.0930.0000.0000.0000.0000.0000.000
181A385VAL0-0.038-0.01153.5930.0020.0020.0000.0000.0000.000
182A386VAL00.0090.01749.1890.0020.0020.0000.0000.0000.000
183A387SER00.010-0.01647.837-0.001-0.0010.0000.0000.0000.000
184A388LYS10.9060.94549.984-0.053-0.0530.0000.0000.0000.000
185A389GLN00.0520.03347.0210.0030.0030.0000.0000.0000.000
186A390ASN00.006-0.00642.779-0.002-0.0020.0000.0000.0000.000
187A391PRO00.0300.02344.0110.0040.0040.0000.0000.0000.000
188A392PHE00.0750.05242.423-0.001-0.0010.0000.0000.0000.000
189A393PRO00.0530.03138.3440.0040.0040.0000.0000.0000.000
190A394PRO00.0200.02034.969-0.003-0.0030.0000.0000.0000.000
191A395LEU00.0740.04833.5750.0010.0010.0000.0000.0000.000
192A396SER0-0.014-0.00330.153-0.004-0.0040.0000.0000.0000.000
193A397THR0-0.082-0.06830.6630.0090.0090.0000.0000.0000.000
194A398VAL0-0.0210.00833.393-0.003-0.0030.0000.0000.0000.000
195A399CYS0-0.0090.01629.6330.0040.0040.0000.0000.0000.000