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: 6NM5Z

Calculation Name: 4Y5J-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 4Y5J

Chain ID: A

ChEMBL ID:

UniProt ID: Q9VEZ3

Base Structure: X-ray

Registration Date: 2023-09-20

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 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 227
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2646911.5641
FMO2-HF: Nuclear repulsion 2559599.309496
FMO2-HF: Total energy -87312.254604
FMO2-MP2: Total energy -87568.134187


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:592:ILE)


Summations of interaction energy for fragment #1(A:592:ILE)
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.
-9.49-3.14.065-2.985-7.469-0.012
Interaction energy analysis for fragmet #1(A:592:ILE)
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 : -0.022
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].
3A594PRO00.0430.0363.604-0.6091.052-0.009-0.718-0.9350.002
4A595ALA00.056-0.0015.8960.4550.4550.0000.0000.0000.000
5A596GLU-1-0.865-0.9288.124-0.242-0.2420.0000.0000.0000.000
6A597ILE00.0110.0127.6320.1050.1050.0000.0000.0000.000
7A598LEU0-0.048-0.0244.756-0.0340.053-0.001-0.004-0.0810.000
8A599ASN0-0.005-0.0129.1580.1180.1180.0000.0000.0000.000
9A600GLY00.0460.02612.3730.0010.0010.0000.0000.0000.000
10A601LEU0-0.013-0.0208.8540.0050.0050.0000.0000.0000.000
11A602VAL0-0.082-0.04813.0550.0210.0210.0000.0000.0000.000
12A603ASP-1-0.832-0.88215.5240.0590.0590.0000.0000.0000.000
13A604SER00.0280.02218.1560.0010.0010.0000.0000.0000.000
14A605ASN00.014-0.00421.677-0.005-0.0050.0000.0000.0000.000
15A606TRP00.0500.00120.4160.0010.0010.0000.0000.0000.000
16A607LYS10.9340.96620.372-0.010-0.0100.0000.0000.0000.000
17A608ASN00.002-0.00517.802-0.033-0.0330.0000.0000.0000.000
18A609ARG10.7600.88215.739-0.170-0.1700.0000.0000.0000.000
19A610LEU0-0.032-0.01015.6050.0030.0030.0000.0000.0000.000
20A611ALA00.0400.03316.609-0.016-0.0160.0000.0000.0000.000
21A612ALA0-0.001-0.00312.096-0.039-0.0390.0000.0000.0000.000
22A613VAL0-0.031-0.02111.572-0.025-0.0250.0000.0000.0000.000
23A614GLU-1-0.888-0.95212.559-0.102-0.1020.0000.0000.0000.000
24A615GLN0-0.062-0.03010.7160.0480.0480.0000.0000.0000.000
25A616LEU0-0.016-0.0206.111-0.048-0.0480.0000.0000.0000.000
26A617LEU0-0.051-0.0379.591-0.065-0.0650.0000.0000.0000.000
27A618GLY0-0.021-0.00512.275-0.013-0.0130.0000.0000.0000.000
28A619GLU-1-0.867-0.9397.234-1.145-1.1450.0000.0000.0000.000
29A620ILE0-0.043-0.0176.873-0.133-0.1330.0000.0000.0000.000
30A621SER00.0070.0028.3710.0240.0240.0000.0000.0000.000
31A622GLY0-0.0100.0148.8950.0840.0840.0000.0000.0000.000
32A623PHE0-0.0250.0022.655-2.021-0.3370.555-0.690-1.549-0.008
33A624ASP-1-0.812-0.9205.081-0.175-0.1750.0000.0000.0000.000
34A625ALA00.014-0.0086.9460.1370.1370.0000.0000.0000.000
35A626LYS10.8640.9269.2920.2700.2700.0000.0000.0000.000
36A627GLN00.0320.0352.480-2.861-0.9320.547-0.948-1.529-0.006
37A628ALA0-0.003-0.0097.3580.0750.0750.0000.0000.0000.000
38A629GLY0-0.001-0.0037.0310.1150.1150.0000.0000.0000.000
39A630ILE00.0190.0172.4720.204-0.0161.819-0.271-1.327-0.001
40A631SER00.0840.0354.7020.1020.172-0.001-0.002-0.0670.000
41A632GLN0-0.031-0.0237.4440.0770.0770.0000.0000.0000.000
42A633ILE0-0.007-0.0022.516-0.719-0.1901.031-0.228-1.3320.001
43A634LEU00.0260.0183.102-0.3780.2570.125-0.122-0.6380.000
44A635ILE00.0230.0104.860-0.019-0.004-0.001-0.002-0.0110.000
45A636ARG10.9210.9557.525-0.840-0.8400.0000.0000.0000.000
46A637THR0-0.057-0.0145.3520.2150.2150.0000.0000.0000.000
47A638ILE0-0.016-0.0038.004-0.128-0.1280.0000.0000.0000.000
48A639SER0-0.040-0.02310.992-0.036-0.0360.0000.0000.0000.000
49A640GLY0-0.017-0.00511.665-0.052-0.0520.0000.0000.0000.000
50A641ARG10.8670.9459.067-1.027-1.0270.0000.0000.0000.000
51A642LYS10.9540.98713.956-0.413-0.4130.0000.0000.0000.000
52A643PRO00.0460.00616.6500.0210.0210.0000.0000.0000.000
53A644GLY00.0150.02215.215-0.009-0.0090.0000.0000.0000.000
54A645LEU00.0490.00415.401-0.032-0.0320.0000.0000.0000.000
55A646LYS10.8320.90618.120-0.264-0.2640.0000.0000.0000.000
56A647GLU-1-0.772-0.86418.3020.1650.1650.0000.0000.0000.000
57A648MET00.0140.02520.979-0.016-0.0160.0000.0000.0000.000
58A649ASN0-0.014-0.00421.997-0.018-0.0180.0000.0000.0000.000
59A650PHE00.0830.02222.3150.0050.0050.0000.0000.0000.000
60A651GLN00.0120.00921.7030.0030.0030.0000.0000.0000.000
61A652VAL00.014-0.00217.213-0.005-0.0050.0000.0000.0000.000
62A653LEU00.0050.00217.8930.0110.0110.0000.0000.0000.000
63A654LYS10.8590.93118.4010.0110.0110.0000.0000.0000.000
64A655PHE00.0630.01516.444-0.001-0.0010.0000.0000.0000.000
65A656LYS10.8350.91713.949-0.255-0.2550.0000.0000.0000.000
66A657LEU0-0.022-0.01414.0360.0170.0170.0000.0000.0000.000
67A658ASP-1-0.746-0.84415.719-0.012-0.0120.0000.0000.0000.000
68A659ILE0-0.0090.0139.465-0.011-0.0110.0000.0000.0000.000
69A660ILE0-0.032-0.02111.428-0.003-0.0030.0000.0000.0000.000
70A661ARG10.8140.88412.5670.0320.0320.0000.0000.0000.000
71A662SER00.008-0.00412.080-0.014-0.0140.0000.0000.0000.000
72A663VAL0-0.040-0.0097.774-0.031-0.0310.0000.0000.0000.000
73A664ALA0-0.050-0.03410.348-0.005-0.0050.0000.0000.0000.000
74A665GLU-1-0.861-0.91913.375-0.057-0.0570.0000.0000.0000.000
75A666ASN0-0.052-0.02811.070-0.035-0.0350.0000.0000.0000.000
76A667TYR0-0.061-0.0327.509-0.051-0.0510.0000.0000.0000.000
77A668PRO0-0.008-0.00210.7040.0350.0350.0000.0000.0000.000
78A669LEU00.0100.01611.5340.0520.0520.0000.0000.0000.000
79A670THR00.0100.00813.212-0.005-0.0050.0000.0000.0000.000
80A671THR00.0730.01715.2170.0170.0170.0000.0000.0000.000
81A672THR00.0120.00915.0920.0010.0010.0000.0000.0000.000
82A673THR00.001-0.00710.6880.0560.0560.0000.0000.0000.000
83A674VAL00.0050.01713.7180.0070.0070.0000.0000.0000.000
84A675ASP-1-0.798-0.88316.5720.1680.1680.0000.0000.0000.000
85A676LEU0-0.082-0.02012.9090.0060.0060.0000.0000.0000.000
86A677VAL00.0270.00013.7550.0090.0090.0000.0000.0000.000
87A678ILE00.0120.01416.952-0.021-0.0210.0000.0000.0000.000
88A679ASN00.0270.01419.730-0.014-0.0140.0000.0000.0000.000
89A680GLU-1-0.798-0.88519.0830.2360.2360.0000.0000.0000.000
90A681ILE0-0.015-0.00616.926-0.014-0.0140.0000.0000.0000.000
91A682ILE00.0240.01120.958-0.016-0.0160.0000.0000.0000.000
92A683GLU-1-0.891-0.94324.3340.1360.1360.0000.0000.0000.000
93A684LYS10.7590.87621.851-0.159-0.1590.0000.0000.0000.000
94A685LEU00.0170.01724.862-0.010-0.0100.0000.0000.0000.000
95A686ALA0-0.041-0.02127.010-0.008-0.0080.0000.0000.0000.000
96A687ASP-1-0.858-0.91325.9440.0650.0650.0000.0000.0000.000
97A688ALA00.011-0.00528.464-0.005-0.0050.0000.0000.0000.000
98A689LYS10.8660.94327.332-0.033-0.0330.0000.0000.0000.000
99A690ASN0-0.050-0.04523.085-0.012-0.0120.0000.0000.0000.000
100A691GLY00.0530.05023.9710.0040.0040.0000.0000.0000.000
101A692ALA0-0.004-0.01325.3760.0020.0020.0000.0000.0000.000
102A693ALA00.0270.01220.797-0.003-0.0030.0000.0000.0000.000
103A694ALA00.0080.00620.6840.0050.0050.0000.0000.0000.000
104A695ALA0-0.005-0.01121.6880.0060.0060.0000.0000.0000.000
105A696ASP-1-0.841-0.92921.4830.0140.0140.0000.0000.0000.000
106A697VAL0-0.048-0.01316.604-0.003-0.0030.0000.0000.0000.000
107A698LEU0-0.0150.00718.8830.0050.0050.0000.0000.0000.000
108A699SER00.0250.00721.2890.0030.0030.0000.0000.0000.000
109A700ALA00.0480.03617.108-0.005-0.0050.0000.0000.0000.000
110A701PHE00.011-0.02014.3670.0060.0060.0000.0000.0000.000
111A702ALA0-0.035-0.00818.4470.0020.0020.0000.0000.0000.000
112A703GLU-1-0.814-0.90320.210-0.009-0.0090.0000.0000.0000.000
113A704ALA0-0.0060.01815.905-0.005-0.0050.0000.0000.0000.000
114A705THR0-0.070-0.03517.4550.0120.0120.0000.0000.0000.000
115A706LYS10.9130.93019.866-0.053-0.0530.0000.0000.0000.000
116A707LEU00.0480.03823.5620.0090.0090.0000.0000.0000.000
117A708GLU-1-0.854-0.94025.8230.0580.0580.0000.0000.0000.000
118A709TYR0-0.068-0.05020.9650.0000.0000.0000.0000.0000.000
119A710VAL0-0.0120.00021.2610.0080.0080.0000.0000.0000.000
120A711VAL00.0440.01623.9980.0040.0040.0000.0000.0000.000
121A712GLY00.0280.02827.6450.0010.0010.0000.0000.0000.000
122A713LYS10.8340.90522.200-0.149-0.1490.0000.0000.0000.000
123A714VAL0-0.016-0.01624.6970.0040.0040.0000.0000.0000.000
124A715LEU0-0.002-0.00726.925-0.001-0.0010.0000.0000.0000.000
125A716SER0-0.041-0.01928.600-0.002-0.0020.0000.0000.0000.000
126A717PHE00.0230.00226.1680.0010.0010.0000.0000.0000.000
127A718ALA0-0.020-0.01628.786-0.001-0.0010.0000.0000.0000.000
128A719PHE0-0.030-0.01930.956-0.004-0.0040.0000.0000.0000.000
129A720GLU-1-0.908-0.92929.2980.1060.1060.0000.0000.0000.000
130A721GLN0-0.0090.00029.449-0.002-0.0020.0000.0000.0000.000
131A722LYS10.9060.93932.017-0.081-0.0810.0000.0000.0000.000
132A723SER00.0050.01232.741-0.007-0.0070.0000.0000.0000.000
133A724PRO00.001-0.02034.1570.0000.0000.0000.0000.0000.000
134A725LYS10.8820.93833.110-0.043-0.0430.0000.0000.0000.000
135A726VAL00.0340.02228.919-0.002-0.0020.0000.0000.0000.000
136A727GLN00.0150.01031.275-0.002-0.0020.0000.0000.0000.000
137A728SER00.0150.00133.609-0.001-0.0010.0000.0000.0000.000
138A729GLU-1-0.818-0.87730.3750.0370.0370.0000.0000.0000.000
139A730ALA00.0200.01629.447-0.001-0.0010.0000.0000.0000.000
140A731PHE0-0.007-0.00930.445-0.002-0.0020.0000.0000.0000.000
141A732ASN0-0.050-0.04632.563-0.005-0.0050.0000.0000.0000.000
142A733TRP00.0220.00024.3060.0000.0000.0000.0000.0000.000
143A734VAL00.0300.01729.417-0.003-0.0030.0000.0000.0000.000
144A735ASN00.0390.03230.764-0.005-0.0050.0000.0000.0000.000
145A736ARG10.8550.91425.999-0.021-0.0210.0000.0000.0000.000
146A737SER00.004-0.01127.703-0.004-0.0040.0000.0000.0000.000
147A738ILE00.0030.00129.494-0.002-0.0020.0000.0000.0000.000
148A739ILE0-0.037-0.01132.532-0.003-0.0030.0000.0000.0000.000
149A740GLU-1-0.864-0.92227.3020.0070.0070.0000.0000.0000.000
150A741PHE00.0280.00723.737-0.004-0.0040.0000.0000.0000.000
151A742GLY00.0120.03029.722-0.002-0.0020.0000.0000.0000.000
152A743PHE00.006-0.01532.1970.0040.0040.0000.0000.0000.000
153A744GLN0-0.089-0.04129.7450.0010.0010.0000.0000.0000.000
154A745LEU0-0.004-0.01429.8690.0050.0050.0000.0000.0000.000
155A746GLN00.0140.00632.892-0.005-0.0050.0000.0000.0000.000
156A747PRO00.0110.00535.3320.0020.0020.0000.0000.0000.000
157A748LYS10.9490.96838.392-0.032-0.0320.0000.0000.0000.000
158A749THR00.0900.04934.326-0.001-0.0010.0000.0000.0000.000
159A750LEU00.0520.03333.3920.0010.0010.0000.0000.0000.000
160A751ILE0-0.026-0.02236.4390.0000.0000.0000.0000.0000.000
161A752GLU-1-0.949-0.98038.9400.0440.0440.0000.0000.0000.000
162A753ASP-1-0.844-0.91634.1480.0600.0600.0000.0000.0000.000
163A754VAL0-0.002-0.02037.0640.0000.0000.0000.0000.0000.000
164A755ARG10.8350.91238.897-0.035-0.0350.0000.0000.0000.000
165A756LYS10.8470.92336.367-0.059-0.0590.0000.0000.0000.000
166A757GLY00.0020.00139.1500.0000.0000.0000.0000.0000.000
167A758VAL0-0.023-0.02139.886-0.002-0.0020.0000.0000.0000.000
168A759GLN0-0.082-0.06243.2140.0000.0000.0000.0000.0000.000
169A760SER00.0350.04340.6150.0010.0010.0000.0000.0000.000
170A761THR00.0290.00443.292-0.002-0.0020.0000.0000.0000.000
171A762ASN00.0180.00641.029-0.003-0.0030.0000.0000.0000.000
172A763PRO00.0400.00942.6730.0000.0000.0000.0000.0000.000
173A764THR00.0260.01438.532-0.002-0.0020.0000.0000.0000.000
174A765VAL0-0.024-0.01037.3740.0000.0000.0000.0000.0000.000
175A766ARG10.8760.95839.364-0.032-0.0320.0000.0000.0000.000
176A767ALA0-0.0010.00341.882-0.001-0.0010.0000.0000.0000.000
177A768SER00.0130.00336.6080.0000.0000.0000.0000.0000.000
178A769ALA00.0160.01138.1770.0000.0000.0000.0000.0000.000
179A770ILE0-0.022-0.02439.396-0.001-0.0010.0000.0000.0000.000
180A771GLN0-0.027-0.01939.594-0.001-0.0010.0000.0000.0000.000
181A772MET0-0.0040.01934.486-0.001-0.0010.0000.0000.0000.000
182A773VAL0-0.011-0.00638.489-0.001-0.0010.0000.0000.0000.000
183A774GLY00.0320.02141.579-0.001-0.0010.0000.0000.0000.000
184A775THR00.007-0.00736.256-0.003-0.0030.0000.0000.0000.000
185A776MET0-0.011-0.00937.7320.0000.0000.0000.0000.0000.000
186A777SER0-0.059-0.03639.762-0.002-0.0020.0000.0000.0000.000
187A778MET00.0250.02039.003-0.002-0.0020.0000.0000.0000.000
188A779TYR0-0.035-0.03236.009-0.001-0.0010.0000.0000.0000.000
189A780MET0-0.066-0.01839.2780.0010.0010.0000.0000.0000.000
190A781GLY00.0280.03142.9300.0000.0000.0000.0000.0000.000
191A782LYS10.9990.96046.403-0.008-0.0080.0000.0000.0000.000
192A783ALA00.0300.01948.0260.0010.0010.0000.0000.0000.000
193A784LEU00.0120.01542.5040.0010.0010.0000.0000.0000.000
194A785MET00.0140.01246.3360.0020.0020.0000.0000.0000.000
195A786MET00.0140.00748.9240.0000.0000.0000.0000.0000.000
196A787PHE0-0.064-0.01445.4230.0010.0010.0000.0000.0000.000
197A788PHE00.0520.00742.6680.0020.0020.0000.0000.0000.000
198A789ASP-1-0.811-0.89448.7550.0180.0180.0000.0000.0000.000
199A790SER0-0.029-0.00251.708-0.001-0.0010.0000.0000.0000.000
200A791GLU-1-0.858-0.89647.7390.0320.0320.0000.0000.0000.000
201A792LYS10.9730.96951.660-0.030-0.0300.0000.0000.0000.000
202A793PRO00.0630.02753.1960.0000.0000.0000.0000.0000.000
203A794ALA00.0040.01053.5930.0000.0000.0000.0000.0000.000
204A795LEU00.0080.00746.694-0.001-0.0010.0000.0000.0000.000
205A796LYS10.8600.91949.940-0.019-0.0190.0000.0000.0000.000
206A797SER00.0140.00551.701-0.001-0.0010.0000.0000.0000.000
207A798GLN0-0.048-0.02147.0230.0000.0000.0000.0000.0000.000
208A799ILE00.005-0.01546.168-0.001-0.0010.0000.0000.0000.000
209A800GLN0-0.027-0.02048.1180.0000.0000.0000.0000.0000.000
210A801VAL00.0280.01849.650-0.001-0.0010.0000.0000.0000.000
211A802GLU-1-0.857-0.91543.9740.0150.0150.0000.0000.0000.000
212A803PHE0-0.0010.00246.007-0.001-0.0010.0000.0000.0000.000
213A804ASP-1-0.880-0.94347.6460.0110.0110.0000.0000.0000.000
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