FMODB

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

Last updated: 2025-04-23

All entries: 37539

Number of unique PDB entries: 7791

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FMODB ID: JL839

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:

Apendix: None


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 178
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -1890254.301015
FMO2-HF: Nuclear repulsion 1821155.609672
FMO2-HF: Total energy -69098.691343
FMO2-MP2: Total energy -69301.864455


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.
-16.159-12.1350.232-1.427-2.8290.008
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 : -0.878 / q_NPA : -0.952
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-1-0.879-0.9552.91446.81150.6920.233-1.415-2.6990.008
4A12LYS10.9560.9724.953-40.030-39.887-0.001-0.012-0.1300.000
5A13GLN0-0.044-0.0256.199-1.897-1.8970.0000.0000.0000.000
6A14ILE0-0.049-0.0146.061-2.915-2.9150.0000.0000.0000.000
7A15GLU-1-0.905-0.9608.70923.83423.8340.0000.0000.0000.000
8A16ASN0-0.010-0.01210.373-2.865-2.8650.0000.0000.0000.000
9A17LEU0-0.053-0.02210.937-1.637-1.6370.0000.0000.0000.000
10A18ILE0-0.0080.0159.975-1.090-1.0900.0000.0000.0000.000
11A19HIS00.0480.02513.537-0.656-0.6560.0000.0000.0000.000
12A20ALA00.0740.03217.278-0.688-0.6880.0000.0000.0000.000
13A21ALA00.0010.01015.006-0.749-0.7490.0000.0000.0000.000
14A22LEU0-0.023-0.00715.572-0.661-0.6610.0000.0000.0000.000
15A23PHE0-0.005-0.00918.004-0.705-0.7050.0000.0000.0000.000
16A24ASN0-0.065-0.05320.839-0.564-0.5640.0000.0000.0000.000
17A25ASP-1-0.769-0.86619.24215.70215.7020.0000.0000.0000.000
18A26PRO0-0.039-0.01321.098-0.604-0.6040.0000.0000.0000.000
19A27ALA0-0.059-0.03121.452-0.663-0.6630.0000.0000.0000.000
20A28SER0-0.020-0.02220.8780.0990.0990.0000.0000.0000.000
21A29PRO0-0.016-0.00423.354-0.305-0.3050.0000.0000.0000.000
22A30ARG10.8860.95126.001-11.288-11.2880.0000.0000.0000.000
23A31ILE00.0080.01628.354-0.333-0.3330.0000.0000.0000.000
24A32GLY00.0870.03731.1130.1140.1140.0000.0000.0000.000
25A33ALA00.0220.01032.8370.1080.1080.0000.0000.0000.000
26A34LYS10.9730.96429.990-10.197-10.1970.0000.0000.0000.000
27A35HIS0-0.034-0.01130.0300.4830.4830.0000.0000.0000.000
28A36PRO0-0.0380.01429.080-0.331-0.3310.0000.0000.0000.000
29A37LYS10.9390.96530.631-8.899-8.8990.0000.0000.0000.000
30A38LEU00.0040.00827.2740.2930.2930.0000.0000.0000.000
31A39THR0-0.028-0.02024.555-0.289-0.2890.0000.0000.0000.000
32A40LEU00.0210.01724.6870.4140.4140.0000.0000.0000.000
33A41VAL0-0.0010.00819.305-0.006-0.0060.0000.0000.0000.000
34A42ASN0-0.006-0.00621.8920.0970.0970.0000.0000.0000.000
35A43PHE00.0340.01616.1230.0540.0540.0000.0000.0000.000
36A44THR00.036-0.01020.993-0.516-0.5160.0000.0000.0000.000
37A45ASP-1-0.722-0.86123.01912.98012.9800.0000.0000.0000.000
38A46TYR00.014-0.03125.036-0.264-0.2640.0000.0000.0000.000
39A47ASN0-0.013-0.01627.739-0.876-0.8760.0000.0000.0000.000
40A48CYS0-0.0930.00226.039-0.243-0.2430.0000.0000.0000.000
41A49PRO00.010-0.00328.197-0.134-0.1340.0000.0000.0000.000
42A50TYR00.0760.02028.263-0.187-0.1870.0000.0000.0000.000
43A51CYS0-0.0340.01225.8300.1370.1370.0000.0000.0000.000
44A52LYS10.8810.95628.473-9.815-9.8150.0000.0000.0000.000
45A53GLN0-0.095-0.04431.974-0.114-0.1140.0000.0000.0000.000
46A54LEU00.0480.01427.427-0.222-0.2220.0000.0000.0000.000
47A55ASP-1-0.853-0.90430.6659.9489.9480.0000.0000.0000.000
48A56PRO00.0110.00531.739-0.086-0.0860.0000.0000.0000.000
49A57MET0-0.062-0.02032.506-0.228-0.2280.0000.0000.0000.000
50A58LEU00.0230.01627.798-0.054-0.0540.0000.0000.0000.000
51A59GLU-1-0.813-0.90932.0608.7308.7300.0000.0000.0000.000
52A60LYS10.9250.98534.584-8.057-8.0570.0000.0000.0000.000
53A61ILE0-0.035-0.02032.240-0.208-0.2080.0000.0000.0000.000
54A62VAL0-0.0040.00332.440-0.121-0.1210.0000.0000.0000.000
55A63GLN0-0.073-0.04735.072-0.270-0.2700.0000.0000.0000.000
56A64LYS10.7740.89238.338-7.849-7.8490.0000.0000.0000.000
57A65TYR0-0.110-0.09835.541-0.245-0.2450.0000.0000.0000.000
58A66PRO00.0690.03535.5580.2880.2880.0000.0000.0000.000
59A67ASP-1-0.918-0.95734.8808.7638.7630.0000.0000.0000.000
60A68VAL0-0.021-0.01530.3240.3670.3670.0000.0000.0000.000
61A69ALA0-0.042-0.01129.052-0.201-0.2010.0000.0000.0000.000
62A70VAL00.011-0.00526.7940.3130.3130.0000.0000.0000.000
63A71ILE0-0.026-0.01022.224-0.164-0.1640.0000.0000.0000.000
64A72ILE00.0030.00324.1920.1980.1980.0000.0000.0000.000
65A73LYS10.8310.91518.111-16.334-16.3340.0000.0000.0000.000
66A74PRO0-0.033-0.02720.7840.2090.2090.0000.0000.0000.000
67A75LEU00.0220.01216.1440.9110.9110.0000.0000.0000.000
68A76PRO0-0.030-0.00819.541-0.499-0.4990.0000.0000.0000.000
69A77PHE00.0660.02316.1210.1210.1210.0000.0000.0000.000
70A78LYS10.8720.95221.364-11.688-11.6880.0000.0000.0000.000
71A79GLY00.0760.05124.014-0.611-0.6110.0000.0000.0000.000
72A80GLU-1-0.859-0.93925.56611.36711.3670.0000.0000.0000.000
73A81SER00.0110.01127.1400.2180.2180.0000.0000.0000.000
74A82SER0-0.037-0.03924.767-0.284-0.2840.0000.0000.0000.000
75A83VAL00.0130.00122.4000.2060.2060.0000.0000.0000.000
76A84LEU0-0.0010.00424.8370.1260.1260.0000.0000.0000.000
77A85ALA00.0310.00928.230-0.128-0.1280.0000.0000.0000.000
78A86ALA00.0260.01423.789-0.092-0.0920.0000.0000.0000.000
79A87ARG10.8730.92324.177-12.866-12.8660.0000.0000.0000.000
80A88ILE00.0130.03126.238-0.094-0.0940.0000.0000.0000.000
81A89ALA00.0190.01127.799-0.196-0.1960.0000.0000.0000.000
82A90LEU0-0.002-0.01322.353-0.076-0.0760.0000.0000.0000.000
83A91THR0-0.051-0.04626.6120.1170.1170.0000.0000.0000.000
84A92THR0-0.002-0.00428.728-0.338-0.3380.0000.0000.0000.000
85A93TRP0-0.080-0.01826.460-0.506-0.5060.0000.0000.0000.000
86A94ARG10.9110.95022.744-13.136-13.1360.0000.0000.0000.000
87A95GLU-1-0.942-0.96728.98710.23610.2360.0000.0000.0000.000
88A96HIS0-0.014-0.00932.520-0.224-0.2240.0000.0000.0000.000
89A97PRO00.0640.04131.662-0.129-0.1290.0000.0000.0000.000
90A98GLN0-0.046-0.04433.215-0.152-0.1520.0000.0000.0000.000
91A99GLN00.0240.02135.970-0.034-0.0340.0000.0000.0000.000
92A100PHE00.0080.01128.556-0.037-0.0370.0000.0000.0000.000
93A101LEU00.0380.02833.3550.1010.1010.0000.0000.0000.000
94A102ALA00.0900.04934.4950.0010.0010.0000.0000.0000.000
95A103LEU0-0.002-0.01532.707-0.108-0.1080.0000.0000.0000.000
96A104HIS00.006-0.00328.3480.2100.2100.0000.0000.0000.000
97A105GLU-1-0.888-0.95832.5568.5168.5160.0000.0000.0000.000
98A106LYS10.8610.95435.340-8.019-8.0190.0000.0000.0000.000
99A107LEU0-0.038-0.01630.703-0.102-0.1020.0000.0000.0000.000
100A108MET00.0110.02027.8660.0060.0060.0000.0000.0000.000
101A109GLN0-0.002-0.01233.208-0.223-0.2230.0000.0000.0000.000
102A110LYS10.8930.97435.836-8.267-8.2670.0000.0000.0000.000
103A111ARG10.9310.95634.930-8.460-8.4600.0000.0000.0000.000
104A112VAL0-0.020-0.01336.897-0.156-0.1560.0000.0000.0000.000
105A113TYR0-0.055-0.03828.3450.0170.0170.0000.0000.0000.000
106A114HIS00.0120.00931.731-0.404-0.4040.0000.0000.0000.000
107A115THR00.0230.00533.2330.0540.0540.0000.0000.0000.000
108A116ASP-1-0.805-0.91333.7989.5599.5590.0000.0000.0000.000
109A117ASP-1-0.914-0.96335.7217.8547.8540.0000.0000.0000.000
110A118SER0-0.099-0.07635.669-0.136-0.1360.0000.0000.0000.000
111A119ILE00.0210.01731.472-0.056-0.0560.0000.0000.0000.000
112A120LYS10.9951.00235.413-8.230-8.2300.0000.0000.0000.000
113A121GLN0-0.050-0.02738.193-0.260-0.2600.0000.0000.0000.000
114A122ALA0-0.032-0.01336.158-0.164-0.1640.0000.0000.0000.000
115A123GLN00.0690.02135.331-0.157-0.1570.0000.0000.0000.000
116A124GLN00.0020.00538.174-0.144-0.1440.0000.0000.0000.000
117A125LYS10.8820.93441.225-7.741-7.7410.0000.0000.0000.000
118A126ALA0-0.036-0.00838.250-0.095-0.0950.0000.0000.0000.000
119A127GLY0-0.0220.01240.140-0.021-0.0210.0000.0000.0000.000
120A128ALA0-0.034-0.01736.6760.0050.0050.0000.0000.0000.000
121A129THR0-0.039-0.02838.044-0.160-0.1600.0000.0000.0000.000
122A130PRO0-0.029-0.01236.8460.2500.2500.0000.0000.0000.000
123A131VAL00.0210.01431.9630.0220.0220.0000.0000.0000.000
124A132THR00.0220.00931.523-0.107-0.1070.0000.0000.0000.000
125A133LEU0-0.047-0.02628.0280.3130.3130.0000.0000.0000.000
126A134ASP-1-0.807-0.90025.61711.75211.7520.0000.0000.0000.000
127A135GLU-1-0.835-0.92919.58916.00816.0080.0000.0000.0000.000
128A136LYS10.9400.96421.206-11.725-11.7250.0000.0000.0000.000
129A137SER00.0180.02721.2640.6170.6170.0000.0000.0000.000
130A138MET00.0010.00019.8960.1020.1020.0000.0000.0000.000
131A139GLU-1-0.809-0.91815.77821.06021.0600.0000.0000.0000.000
132A140THR0-0.0170.01016.5110.9090.9090.0000.0000.0000.000
133A141ILE0-0.0080.00417.6220.4610.4610.0000.0000.0000.000
134A142ARG10.8340.91713.683-18.451-18.4510.0000.0000.0000.000
135A143THR00.003-0.00413.0442.0632.0630.0000.0000.0000.000
136A144ASN00.004-0.00413.3471.1731.1730.0000.0000.0000.000
137A145LEU0-0.024-0.01612.9650.3480.3480.0000.0000.0000.000
138A146GLN0-0.052-0.0269.2291.5301.5300.0000.0000.0000.000
139A147LEU00.0220.0069.6981.3001.3000.0000.0000.0000.000
140A148ALA00.0170.00312.226-0.288-0.2880.0000.0000.0000.000
141A149ARG10.9320.9646.563-32.403-32.4030.0000.0000.0000.000
142A150LEU0-0.002-0.0016.105-0.368-0.3680.0000.0000.0000.000
143A151VAL0-0.0140.0069.371-0.941-0.9410.0000.0000.0000.000
144A152GLY00.0140.01912.165-1.426-1.4260.0000.0000.0000.000
145A153VAL0-0.049-0.02513.713-1.511-1.5110.0000.0000.0000.000
146A154GLN0-0.008-0.00914.9980.8490.8490.0000.0000.0000.000
147A155GLY0-0.029-0.00717.248-0.428-0.4280.0000.0000.0000.000
148A156THR0-0.045-0.00319.8920.1390.1390.0000.0000.0000.000
149A157PRO0-0.028-0.05122.417-0.356-0.3560.0000.0000.0000.000
150A158ALA00.0230.00619.882-0.034-0.0340.0000.0000.0000.000
151A159THR00.006-0.00621.5960.2530.2530.0000.0000.0000.000
152A160ILE00.0080.01917.517-0.125-0.1250.0000.0000.0000.000
153A161ILE0-0.004-0.01121.902-0.423-0.4230.0000.0000.0000.000
154A162GLY00.0300.01125.020-0.173-0.1730.0000.0000.0000.000
155A163ASP-1-0.887-0.93422.11612.67712.6770.0000.0000.0000.000
156A164GLU-1-0.860-0.91522.25311.56411.5640.0000.0000.0000.000
157A165LEU0-0.040-0.02517.0550.1370.1370.0000.0000.0000.000
158A166ILE00.0270.00521.121-0.140-0.1400.0000.0000.0000.000
159A167PRO0-0.015-0.00722.2030.0840.0840.0000.0000.0000.000
160A168GLY0-0.002-0.00823.697-0.497-0.4970.0000.0000.0000.000
161A169ALA0-0.044-0.02026.4940.0090.0090.0000.0000.0000.000
162A170VAL00.0420.02129.008-0.079-0.0790.0000.0000.0000.000
163A171PRO00.0210.00431.741-0.121-0.1210.0000.0000.0000.000
164A172TRP00.0490.00534.6830.1360.1360.0000.0000.0000.000
165A173ASP-1-0.885-0.94336.2548.1478.1470.0000.0000.0000.000
166A174THR00.0040.00132.3190.0530.0530.0000.0000.0000.000
167A175LEU0-0.017-0.00830.2840.1780.1780.0000.0000.0000.000
168A176GLU-1-0.772-0.84732.7058.1268.1260.0000.0000.0000.000
169A177ALA0-0.031-0.01535.2180.0030.0030.0000.0000.0000.000
170A178VAL00.0640.03928.4890.0160.0160.0000.0000.0000.000
171A179VAL00.0050.00130.4360.1760.1760.0000.0000.0000.000
172A180LYS10.9340.96532.001-7.896-7.8960.0000.0000.0000.000
173A181GLU-1-0.858-0.91430.87310.00110.0010.0000.0000.0000.000
174A182LYS10.7700.87227.111-11.034-11.0340.0000.0000.0000.000
175A183LEU0-0.041-0.02530.3490.1090.1090.0000.0000.0000.000
176A184ALA0-0.080-0.04832.728-0.089-0.0890.0000.0000.0000.000
177A185SER0-0.027-0.01430.369-0.111-0.1110.0000.0000.0000.000
178A186ALA0-0.077-0.01630.117-0.012-0.0120.0000.0000.0000.000