FMODB

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

Last updated: 2024-07-23

All entries: 37450

Number of unique PDB entries: 7783

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FMODB ID: LZ5J9

Calculation Name: 4GXZ-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 4GXZ

Chain ID: A

ChEMBL ID:

UniProt ID: H9L4C1

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 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 178
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -1893984.63276
FMO2-HF: Nuclear repulsion 1824884.746041
FMO2-HF: Total energy -69099.886719
FMO2-MP2: Total energy -69302.926164


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:9:ASP)


Summations of interaction energy for fragment #1(A:9:ASP)
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.
-25.459-24.2447.751-4.828-4.137-0.025
Interaction energy analysis for fragmet #1(A:9:ASP)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : -1 / q_Mulliken : -0.917 / q_NPA : -0.948
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].
3A11GLU-1-0.798-0.8941.96035.03736.1057.752-4.812-4.008-0.025
4A12LYS10.8780.9394.791-41.254-41.107-0.001-0.016-0.1290.000
5A13GLN0-0.040-0.0176.976-1.406-1.4060.0000.0000.0000.000
6A14ILE0-0.032-0.0236.636-2.323-2.3230.0000.0000.0000.000
7A15GLU-1-0.874-0.9508.48624.65124.6510.0000.0000.0000.000
8A16ASN0-0.015-0.01710.071-2.954-2.9540.0000.0000.0000.000
9A17LEU0-0.034-0.01111.873-1.492-1.4920.0000.0000.0000.000
10A18ILE0-0.0140.0089.320-0.913-0.9130.0000.0000.0000.000
11A19HIS00.0410.02313.596-0.536-0.5360.0000.0000.0000.000
12A20ALA00.0660.02517.258-0.549-0.5490.0000.0000.0000.000
13A21ALA00.0090.00414.900-0.664-0.6640.0000.0000.0000.000
14A22LEU0-0.022-0.00715.075-0.322-0.3220.0000.0000.0000.000
15A23PHE00.0160.00217.904-0.619-0.6190.0000.0000.0000.000
16A24ASN0-0.024-0.03320.975-0.598-0.5980.0000.0000.0000.000
17A25ASP-1-0.757-0.85119.11615.39415.3940.0000.0000.0000.000
18A26PRO0-0.010-0.00821.212-0.425-0.4250.0000.0000.0000.000
19A27ALA0-0.053-0.02121.317-0.549-0.5490.0000.0000.0000.000
20A28SER0-0.002-0.01720.5870.1040.1040.0000.0000.0000.000
21A29PRO0-0.025-0.01223.140-0.284-0.2840.0000.0000.0000.000
22A30ARG10.8190.90625.404-11.202-11.2020.0000.0000.0000.000
23A31ILE00.0180.02428.100-0.344-0.3440.0000.0000.0000.000
24A32GLY00.0850.02730.5790.1300.1300.0000.0000.0000.000
25A33ALA00.0140.01332.5790.0920.0920.0000.0000.0000.000
26A34LYS10.9590.96230.082-10.045-10.0450.0000.0000.0000.000
27A35HIS0-0.0130.00429.7800.5110.5110.0000.0000.0000.000
28A36PRO0-0.043-0.00129.111-0.297-0.2970.0000.0000.0000.000
29A37LYS10.8820.93830.603-8.803-8.8030.0000.0000.0000.000
30A38LEU0-0.0080.00426.5870.2870.2870.0000.0000.0000.000
31A39THR0-0.025-0.01924.207-0.241-0.2410.0000.0000.0000.000
32A40LEU00.0280.02124.2540.3750.3750.0000.0000.0000.000
33A41VAL0-0.011-0.00518.9410.0490.0490.0000.0000.0000.000
34A42ASN0-0.006-0.00521.2850.1010.1010.0000.0000.0000.000
35A43PHE00.0520.02915.6420.0480.0480.0000.0000.0000.000
36A44THR00.021-0.00920.397-0.566-0.5660.0000.0000.0000.000
37A45ASP-1-0.682-0.84622.59612.96012.9600.0000.0000.0000.000
38A46TYR00.037-0.01824.788-0.280-0.2800.0000.0000.0000.000
39A47ASN0-0.015-0.01527.515-0.910-0.9100.0000.0000.0000.000
40A48CYS0-0.084-0.03825.395-0.326-0.3260.0000.0000.0000.000
41A49PRO0-0.004-0.01028.111-0.125-0.1250.0000.0000.0000.000
42A50TYR00.0810.02827.610-0.128-0.1280.0000.0000.0000.000
43A51CYS0-0.0480.01825.5860.1500.1500.0000.0000.0000.000
44A52LYS10.8650.93028.077-9.806-9.8060.0000.0000.0000.000
45A53GLN0-0.061-0.01031.266-0.155-0.1550.0000.0000.0000.000
46A54LEU00.0300.00926.616-0.234-0.2340.0000.0000.0000.000
47A55ASP-1-0.828-0.90629.9729.7439.7430.0000.0000.0000.000
48A56PRO0-0.012-0.01231.133-0.095-0.0950.0000.0000.0000.000
49A57MET0-0.062-0.02432.496-0.310-0.3100.0000.0000.0000.000
50A58LEU00.0100.01027.477-0.002-0.0020.0000.0000.0000.000
51A59GLU-1-0.802-0.89331.3418.7028.7020.0000.0000.0000.000
52A60LYS10.8680.96134.150-8.050-8.0500.0000.0000.0000.000
53A61ILE0-0.019-0.01631.494-0.220-0.2200.0000.0000.0000.000
54A62VAL00.0010.01232.069-0.119-0.1190.0000.0000.0000.000
55A63GLN0-0.108-0.07334.730-0.309-0.3090.0000.0000.0000.000
56A64LYS10.7900.88837.735-7.832-7.8320.0000.0000.0000.000
57A65TYR0-0.042-0.03935.215-0.260-0.2600.0000.0000.0000.000
58A66PRO00.0660.03035.2270.2680.2680.0000.0000.0000.000
59A67ASP-1-0.915-0.95134.9338.7608.7600.0000.0000.0000.000
60A68VAL00.017-0.00529.9980.3060.3060.0000.0000.0000.000
61A69ALA0-0.036-0.01228.825-0.185-0.1850.0000.0000.0000.000
62A70VAL0-0.003-0.01026.2300.2680.2680.0000.0000.0000.000
63A71ILE0-0.0230.00121.802-0.229-0.2290.0000.0000.0000.000
64A72ILE0-0.021-0.00923.7810.1770.1770.0000.0000.0000.000
65A73LYS10.8250.91617.683-16.310-16.3100.0000.0000.0000.000
66A74PRO0-0.033-0.02420.0880.3250.3250.0000.0000.0000.000
67A75LEU00.0220.01316.0500.8610.8610.0000.0000.0000.000
68A76PRO0-0.0200.00219.243-0.437-0.4370.0000.0000.0000.000
69A77PHE00.041-0.00115.888-0.067-0.0670.0000.0000.0000.000
70A78LYS10.8530.93821.141-11.642-11.6420.0000.0000.0000.000
71A79GLY00.0800.05424.025-0.606-0.6060.0000.0000.0000.000
72A80GLU-1-0.878-0.94325.53911.47211.4720.0000.0000.0000.000
73A81SER00.0130.00926.9930.1220.1220.0000.0000.0000.000
74A82SER0-0.028-0.02624.851-0.299-0.2990.0000.0000.0000.000
75A83VAL00.0070.00022.2130.1780.1780.0000.0000.0000.000
76A84LEU00.0010.01224.7130.0870.0870.0000.0000.0000.000
77A85ALA00.0300.00828.154-0.118-0.1180.0000.0000.0000.000
78A86ALA00.0070.00323.603-0.099-0.0990.0000.0000.0000.000
79A87ARG10.8570.91724.178-13.132-13.1320.0000.0000.0000.000
80A88ILE00.0180.02326.150-0.102-0.1020.0000.0000.0000.000
81A89ALA00.0160.02127.678-0.194-0.1940.0000.0000.0000.000
82A90LEU00.008-0.00922.220-0.102-0.1020.0000.0000.0000.000
83A91THR0-0.034-0.02926.3930.1450.1450.0000.0000.0000.000
84A92THR0-0.018-0.02428.605-0.335-0.3350.0000.0000.0000.000
85A93TRP0-0.082-0.03226.380-0.548-0.5480.0000.0000.0000.000
86A94ARG10.8860.95322.439-13.183-13.1830.0000.0000.0000.000
87A95GLU-1-0.913-0.95828.93210.48410.4840.0000.0000.0000.000
88A96HIS0-0.025-0.01432.423-0.283-0.2830.0000.0000.0000.000
89A97PRO00.0420.02231.390-0.188-0.1880.0000.0000.0000.000
90A98GLN0-0.043-0.02933.092-0.073-0.0730.0000.0000.0000.000
91A99GLN00.0610.04435.9390.0100.0100.0000.0000.0000.000
92A100PHE0-0.0010.00628.356-0.028-0.0280.0000.0000.0000.000
93A101LEU00.0370.02233.1090.0890.0890.0000.0000.0000.000
94A102ALA00.0820.04534.3140.0110.0110.0000.0000.0000.000
95A103LEU00.0310.00732.497-0.104-0.1040.0000.0000.0000.000
96A104HIS00.008-0.00128.1990.2530.2530.0000.0000.0000.000
97A105GLU-1-0.797-0.90032.2248.2408.2400.0000.0000.0000.000
98A106LYS10.7490.90535.083-8.180-8.1800.0000.0000.0000.000
99A107LEU0-0.031-0.01030.381-0.081-0.0810.0000.0000.0000.000
100A108MET0-0.0010.01827.5770.0670.0670.0000.0000.0000.000
101A109GLN0-0.001-0.02433.010-0.137-0.1370.0000.0000.0000.000
102A110LYS10.9370.98935.525-8.357-8.3570.0000.0000.0000.000
103A111ARG10.8800.93934.462-8.440-8.4400.0000.0000.0000.000
104A112VAL0-0.043-0.03536.396-0.200-0.2000.0000.0000.0000.000
105A113TYR0-0.035-0.02228.3390.0300.0300.0000.0000.0000.000
106A114HIS0-0.006-0.00131.344-0.424-0.4240.0000.0000.0000.000
107A115THR00.0210.00333.1560.0410.0410.0000.0000.0000.000
108A116ASP-1-0.804-0.91334.3229.4899.4890.0000.0000.0000.000
109A117ASP-1-0.859-0.90535.4187.6907.6900.0000.0000.0000.000
110A118SER0-0.045-0.04135.253-0.131-0.1310.0000.0000.0000.000
111A119ILE00.0220.01631.214-0.040-0.0400.0000.0000.0000.000
112A120LYS10.8710.92535.083-8.287-8.2870.0000.0000.0000.000
113A121GLN0-0.028-0.02637.946-0.178-0.1780.0000.0000.0000.000
114A122ALA0-0.019-0.01035.594-0.153-0.1530.0000.0000.0000.000
115A123GLN00.0300.01035.526-0.025-0.0250.0000.0000.0000.000
116A124GLN00.0030.00037.886-0.122-0.1220.0000.0000.0000.000
117A125LYS10.8540.91940.958-7.609-7.6090.0000.0000.0000.000
118A126ALA0-0.017-0.00538.279-0.042-0.0420.0000.0000.0000.000
119A127GLY0-0.0220.00340.201-0.001-0.0010.0000.0000.0000.000
120A128ALA0-0.043-0.01136.3430.0140.0140.0000.0000.0000.000
121A129THR0-0.009-0.02637.526-0.201-0.2010.0000.0000.0000.000
122A130PRO0-0.041-0.02636.5780.2560.2560.0000.0000.0000.000
123A131VAL00.0210.01431.976-0.021-0.0210.0000.0000.0000.000
124A132THR00.0100.00131.235-0.011-0.0110.0000.0000.0000.000
125A133LEU00.0060.00728.0040.2870.2870.0000.0000.0000.000
126A134ASP-1-0.741-0.86626.11712.81312.8130.0000.0000.0000.000
127A135GLU-1-0.769-0.85920.78115.34015.3400.0000.0000.0000.000
128A136LYS10.8790.91821.359-11.713-11.7130.0000.0000.0000.000
129A137SER0-0.050-0.01721.8160.3030.3030.0000.0000.0000.000
130A138MET00.0120.00119.4620.0890.0890.0000.0000.0000.000
131A139GLU-1-0.810-0.89615.50521.03921.0390.0000.0000.0000.000
132A140THR00.0020.02816.6550.9250.9250.0000.0000.0000.000
133A141ILE0-0.0050.00417.4300.4730.4730.0000.0000.0000.000
134A142ARG10.8000.86413.597-17.661-17.6610.0000.0000.0000.000
135A143THR0-0.007-0.00312.7072.2642.2640.0000.0000.0000.000
136A144ASN0-0.021-0.02513.3091.0431.0430.0000.0000.0000.000
137A145LEU00.008-0.01012.5600.3080.3080.0000.0000.0000.000
138A146GLN0-0.066-0.0288.4543.2223.2220.0000.0000.0000.000
139A147LEU00.0180.0029.6771.0311.0310.0000.0000.0000.000
140A148ALA00.0180.00412.117-0.326-0.3260.0000.0000.0000.000
141A149ARG10.9230.9636.137-33.166-33.1660.0000.0000.0000.000
142A150LEU0-0.020-0.0165.9300.1710.1710.0000.0000.0000.000
143A151VAL0-0.0160.0078.866-0.974-0.9740.0000.0000.0000.000
144A152GLY00.0160.02111.143-1.194-1.1940.0000.0000.0000.000
145A153VAL0-0.051-0.03612.403-1.410-1.4100.0000.0000.0000.000
146A154GLN00.0040.00313.9220.5100.5100.0000.0000.0000.000
147A155GLY0-0.019-0.00216.539-0.385-0.3850.0000.0000.0000.000
148A156THR0-0.0490.00819.1700.1210.1210.0000.0000.0000.000
149A157PRO0-0.016-0.03321.912-0.392-0.3920.0000.0000.0000.000
150A158ALA00.0220.00619.190-0.014-0.0140.0000.0000.0000.000
151A159THR0-0.005-0.00521.1350.2080.2080.0000.0000.0000.000
152A160ILE00.0090.02017.020-0.144-0.1440.0000.0000.0000.000
153A161ILE0-0.011-0.02321.191-0.458-0.4580.0000.0000.0000.000
154A162GLY00.0270.01523.916-0.208-0.2080.0000.0000.0000.000
155A163ASP-1-0.870-0.92621.11712.31112.3110.0000.0000.0000.000
156A164GLU-1-0.850-0.90920.78611.51011.5100.0000.0000.0000.000
157A165LEU0-0.026-0.02716.3140.2190.2190.0000.0000.0000.000
158A166ILE00.0280.01920.360-0.064-0.0640.0000.0000.0000.000
159A167PRO0-0.014-0.00621.0380.1440.1440.0000.0000.0000.000
160A168GLY00.003-0.00322.771-0.482-0.4820.0000.0000.0000.000
161A169ALA0-0.046-0.03125.8760.0220.0220.0000.0000.0000.000
162A170VAL00.0250.01328.465-0.072-0.0720.0000.0000.0000.000
163A171PRO00.0250.00931.274-0.089-0.0890.0000.0000.0000.000
164A172TRP00.0450.00234.0570.1380.1380.0000.0000.0000.000
165A173ASP-1-0.859-0.93735.6058.2468.2460.0000.0000.0000.000
166A174THR00.0120.00431.3110.0620.0620.0000.0000.0000.000
167A175LEU00.0030.00529.5320.2140.2140.0000.0000.0000.000
168A176GLU-1-0.769-0.84831.9287.9767.9760.0000.0000.0000.000
169A177ALA0-0.026-0.01534.188-0.001-0.0010.0000.0000.0000.000
170A178VAL00.0710.03927.487-0.012-0.0120.0000.0000.0000.000
171A179VAL0-0.006-0.00929.4490.1580.1580.0000.0000.0000.000
172A180LYS10.8720.92530.966-7.955-7.9550.0000.0000.0000.000
173A181GLU-1-0.867-0.91029.5169.7579.7570.0000.0000.0000.000
174A182LYS10.7740.87525.767-10.935-10.9350.0000.0000.0000.000
175A183LEU0-0.043-0.01129.5010.0960.0960.0000.0000.0000.000
176A184ALA0-0.051-0.02732.012-0.133-0.1330.0000.0000.0000.000
177A185SER0-0.033-0.02229.725-0.123-0.1230.0000.0000.0000.000
178A186ALA0-0.053-0.00929.409-0.074-0.0740.0000.0000.0000.000