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: 392QL

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 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 178
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -1890953.092808
FMO2-HF: Nuclear repulsion 1821853.505485
FMO2-HF: Total energy -69099.587323
FMO2-MP2: Total energy -69302.731463


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.
-28.779-23.3933.544-4.44-4.488-0.014
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 : -0.861 / q_NPA : -0.933
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-1-0.813-0.9142.12931.98037.1763.545-4.424-4.316-0.014
4A12LYS10.8820.9375.165-40.997-40.807-0.001-0.016-0.1720.000
5A13GLN0-0.053-0.0256.453-1.383-1.3830.0000.0000.0000.000
6A14ILE0-0.042-0.0216.351-2.534-2.5340.0000.0000.0000.000
7A15GLU-1-0.872-0.9449.01123.73923.7390.0000.0000.0000.000
8A16ASN0-0.022-0.01710.550-2.842-2.8420.0000.0000.0000.000
9A17LEU0-0.037-0.01611.315-1.486-1.4860.0000.0000.0000.000
10A18ILE0-0.0130.0119.602-1.008-1.0080.0000.0000.0000.000
11A19HIS00.0410.02213.772-0.537-0.5370.0000.0000.0000.000
12A20ALA00.0740.02717.454-0.651-0.6510.0000.0000.0000.000
13A21ALA00.0030.00915.281-0.684-0.6840.0000.0000.0000.000
14A22LEU0-0.017-0.00515.404-0.581-0.5810.0000.0000.0000.000
15A23PHE0-0.004-0.00618.199-0.643-0.6430.0000.0000.0000.000
16A24ASN0-0.038-0.04021.069-0.589-0.5890.0000.0000.0000.000
17A25ASP-1-0.756-0.84419.44115.27215.2720.0000.0000.0000.000
18A26PRO0-0.023-0.00721.377-0.545-0.5450.0000.0000.0000.000
19A27ALA0-0.058-0.03021.649-0.594-0.5940.0000.0000.0000.000
20A28SER0-0.009-0.02520.9610.0990.0990.0000.0000.0000.000
21A29PRO0-0.017-0.00623.452-0.296-0.2960.0000.0000.0000.000
22A30ARG10.8490.93025.766-11.113-11.1130.0000.0000.0000.000
23A31ILE00.0020.01428.495-0.316-0.3160.0000.0000.0000.000
24A32GLY00.0900.03931.2570.1010.1010.0000.0000.0000.000
25A33ALA00.0140.00833.0070.1060.1060.0000.0000.0000.000
26A34LYS10.9820.97030.327-9.990-9.9900.0000.0000.0000.000
27A35HIS0-0.031-0.00830.2790.4850.4850.0000.0000.0000.000
28A36PRO0-0.0510.00229.207-0.293-0.2930.0000.0000.0000.000
29A37LYS10.9130.95930.697-8.736-8.7360.0000.0000.0000.000
30A38LEU0-0.0120.00226.9080.2890.2890.0000.0000.0000.000
31A39THR0-0.024-0.02024.682-0.255-0.2550.0000.0000.0000.000
32A40LEU00.0320.02124.5720.3800.3800.0000.0000.0000.000
33A41VAL0-0.0120.00119.3410.0030.0030.0000.0000.0000.000
34A42ASN0-0.012-0.01421.7080.0910.0910.0000.0000.0000.000
35A43PHE00.0350.01816.0570.0460.0460.0000.0000.0000.000
36A44THR00.022-0.01220.907-0.494-0.4940.0000.0000.0000.000
37A45ASP-1-0.703-0.85223.08212.74912.7490.0000.0000.0000.000
38A46TYR00.035-0.02625.059-0.272-0.2720.0000.0000.0000.000
39A47ASN0-0.017-0.01927.753-0.880-0.8800.0000.0000.0000.000
40A48CYS0-0.072-0.01125.086-0.336-0.3360.0000.0000.0000.000
41A49PRO00.0170.00328.018-0.135-0.1350.0000.0000.0000.000
42A50TYR00.0680.02027.778-0.163-0.1630.0000.0000.0000.000
43A51CYS0-0.0490.00625.6860.1220.1220.0000.0000.0000.000
44A52LYS10.8380.92028.238-9.686-9.6860.0000.0000.0000.000
45A53GLN0-0.100-0.04931.793-0.066-0.0660.0000.0000.0000.000
46A54LEU00.0280.00826.941-0.217-0.2170.0000.0000.0000.000
47A55ASP-1-0.841-0.90730.5219.6389.6380.0000.0000.0000.000
48A56PRO00.0090.00431.598-0.080-0.0800.0000.0000.0000.000
49A57MET0-0.060-0.01732.397-0.243-0.2430.0000.0000.0000.000
50A58LEU00.0280.01927.812-0.062-0.0620.0000.0000.0000.000
51A59GLU-1-0.786-0.89231.8908.6308.6300.0000.0000.0000.000
52A60LYS10.8780.96934.535-7.962-7.9620.0000.0000.0000.000
53A61ILE0-0.024-0.01732.023-0.206-0.2060.0000.0000.0000.000
54A62VAL0-0.0050.00832.378-0.117-0.1170.0000.0000.0000.000
55A63GLN0-0.112-0.06835.015-0.305-0.3050.0000.0000.0000.000
56A64LYS10.7770.87738.182-7.745-7.7450.0000.0000.0000.000
57A65TYR0-0.065-0.06035.429-0.257-0.2570.0000.0000.0000.000
58A66PRO00.0710.03635.4680.2700.2700.0000.0000.0000.000
59A67ASP-1-0.901-0.94835.0408.7058.7050.0000.0000.0000.000
60A68VAL0-0.001-0.01130.2230.3380.3380.0000.0000.0000.000
61A69ALA0-0.037-0.00929.199-0.188-0.1880.0000.0000.0000.000
62A70VAL00.003-0.00926.8830.2930.2930.0000.0000.0000.000
63A71ILE0-0.019-0.00822.282-0.160-0.1600.0000.0000.0000.000
64A72ILE0-0.006-0.00324.2740.1730.1730.0000.0000.0000.000
65A73LYS10.8220.91318.079-15.914-15.9140.0000.0000.0000.000
66A74PRO0-0.023-0.02320.8750.1780.1780.0000.0000.0000.000
67A75LEU00.0070.00616.4020.8950.8950.0000.0000.0000.000
68A76PRO0-0.030-0.01319.565-0.476-0.4760.0000.0000.0000.000
69A77PHE00.0600.02316.1230.1590.1590.0000.0000.0000.000
70A78LYS10.8630.94921.491-11.397-11.3970.0000.0000.0000.000
71A79GLY00.0800.05124.228-0.598-0.5980.0000.0000.0000.000
72A80GLU-1-0.866-0.94025.65411.38311.3830.0000.0000.0000.000
73A81SER00.0090.00327.2480.1990.1990.0000.0000.0000.000
74A82SER0-0.029-0.02524.818-0.296-0.2960.0000.0000.0000.000
75A83VAL00.008-0.00322.3510.1890.1890.0000.0000.0000.000
76A84LEU0-0.0010.00224.7790.1010.1010.0000.0000.0000.000
77A85ALA00.0310.01128.170-0.128-0.1280.0000.0000.0000.000
78A86ALA00.0250.01223.813-0.096-0.0960.0000.0000.0000.000
79A87ARG10.8830.93324.146-12.891-12.8910.0000.0000.0000.000
80A88ILE00.0190.02726.206-0.075-0.0750.0000.0000.0000.000
81A89ALA00.0180.02127.814-0.198-0.1980.0000.0000.0000.000
82A90LEU00.003-0.01022.200-0.082-0.0820.0000.0000.0000.000
83A91THR0-0.059-0.04826.6340.1150.1150.0000.0000.0000.000
84A92THR00.000-0.01228.860-0.319-0.3190.0000.0000.0000.000
85A93TRP0-0.088-0.02326.624-0.520-0.5200.0000.0000.0000.000
86A94ARG10.9110.95522.907-12.953-12.9530.0000.0000.0000.000
87A95GLU-1-0.930-0.96429.17010.31010.3100.0000.0000.0000.000
88A96HIS0-0.017-0.01432.685-0.286-0.2860.0000.0000.0000.000
89A97PRO00.0670.03931.757-0.144-0.1440.0000.0000.0000.000
90A98GLN0-0.051-0.03833.385-0.115-0.1150.0000.0000.0000.000
91A99GLN00.0340.02536.042-0.054-0.0540.0000.0000.0000.000
92A100PHE00.0060.00928.595-0.028-0.0280.0000.0000.0000.000
93A101LEU00.0470.03033.4250.0810.0810.0000.0000.0000.000
94A102ALA00.0820.04334.5910.0010.0010.0000.0000.0000.000
95A103LEU00.012-0.00832.835-0.104-0.1040.0000.0000.0000.000
96A104HIS00.009-0.00428.5330.2510.2510.0000.0000.0000.000
97A105GLU-1-0.818-0.92032.6248.1738.1730.0000.0000.0000.000
98A106LYS10.7720.89935.422-8.112-8.1120.0000.0000.0000.000
99A107LEU0-0.030-0.00930.739-0.091-0.0910.0000.0000.0000.000
100A108MET00.0110.02027.8200.0030.0030.0000.0000.0000.000
101A109GLN0-0.012-0.00333.259-0.179-0.1790.0000.0000.0000.000
102A110LYS10.9080.98335.826-8.215-8.2150.0000.0000.0000.000
103A111ARG10.9430.96634.683-8.371-8.3710.0000.0000.0000.000
104A112VAL0-0.022-0.01836.932-0.147-0.1470.0000.0000.0000.000
105A113TYR0-0.041-0.02928.5580.0040.0040.0000.0000.0000.000
106A114HIS00.0080.00031.695-0.398-0.3980.0000.0000.0000.000
107A115THR00.0170.00333.2930.0660.0660.0000.0000.0000.000
108A116ASP-1-0.811-0.91334.0269.4729.4720.0000.0000.0000.000
109A117ASP-1-0.858-0.93035.6507.7937.7930.0000.0000.0000.000
110A118SER0-0.088-0.04835.715-0.131-0.1310.0000.0000.0000.000
111A119ILE00.0190.01431.408-0.056-0.0560.0000.0000.0000.000
112A120LYS10.9010.94635.388-8.269-8.2690.0000.0000.0000.000
113A121GLN0-0.007-0.00938.158-0.196-0.1960.0000.0000.0000.000
114A122ALA0-0.028-0.00936.138-0.161-0.1610.0000.0000.0000.000
115A123GLN00.0540.01635.404-0.109-0.1090.0000.0000.0000.000
116A124GLN0-0.008-0.00138.178-0.115-0.1150.0000.0000.0000.000
117A125LYS10.8820.93341.242-7.595-7.5950.0000.0000.0000.000
118A126ALA0-0.033-0.00338.263-0.091-0.0910.0000.0000.0000.000
119A127GLY0-0.0200.00940.183-0.022-0.0220.0000.0000.0000.000
120A128ALA0-0.044-0.02136.6830.0100.0100.0000.0000.0000.000
121A129THR0-0.032-0.02338.139-0.173-0.1730.0000.0000.0000.000
122A130PRO0-0.026-0.01536.8920.2470.2470.0000.0000.0000.000
123A131VAL00.0250.01331.9840.0240.0240.0000.0000.0000.000
124A132THR00.0090.00331.768-0.084-0.0840.0000.0000.0000.000
125A133LEU0-0.030-0.01628.0910.3080.3080.0000.0000.0000.000
126A134ASP-1-0.766-0.87926.21912.39012.3900.0000.0000.0000.000
127A135GLU-1-0.759-0.85820.33115.90415.9040.0000.0000.0000.000
128A136LYS10.8720.92121.248-11.685-11.6850.0000.0000.0000.000
129A137SER00.0170.02421.3740.5750.5750.0000.0000.0000.000
130A138MET00.001-0.00119.7630.0810.0810.0000.0000.0000.000
131A139GLU-1-0.803-0.89515.49721.42221.4220.0000.0000.0000.000
132A140THR0-0.0140.01216.6440.9180.9180.0000.0000.0000.000
133A141ILE0-0.0040.00217.6570.4150.4150.0000.0000.0000.000
134A142ARG10.7630.84413.723-17.986-17.9860.0000.0000.0000.000
135A143THR0-0.008-0.00913.0421.9211.9210.0000.0000.0000.000
136A144ASN0-0.005-0.01413.4180.9320.9320.0000.0000.0000.000
137A145LEU0-0.005-0.00912.9040.2530.2530.0000.0000.0000.000
138A146GLN0-0.049-0.0208.8772.0742.0740.0000.0000.0000.000
139A147LEU00.012-0.0019.8301.0091.0090.0000.0000.0000.000
140A148ALA00.0170.00012.303-0.346-0.3460.0000.0000.0000.000
141A149ARG10.9350.9696.227-31.573-31.5730.0000.0000.0000.000
142A150LEU0-0.014-0.0076.270-0.319-0.3190.0000.0000.0000.000
143A151VAL0-0.0160.0018.997-0.877-0.8770.0000.0000.0000.000
144A152GLY00.0220.02411.559-1.261-1.2610.0000.0000.0000.000
145A153VAL0-0.049-0.02812.947-1.337-1.3370.0000.0000.0000.000
146A154GLN00.003-0.00114.4270.8970.8970.0000.0000.0000.000
147A155GLY0-0.023-0.00416.571-0.369-0.3690.0000.0000.0000.000
148A156THR0-0.0640.00819.3940.0010.0010.0000.0000.0000.000
149A157PRO0-0.004-0.04622.072-0.311-0.3110.0000.0000.0000.000
150A158ALA00.0160.00419.496-0.031-0.0310.0000.0000.0000.000
151A159THR00.006-0.00121.2970.2270.2270.0000.0000.0000.000
152A160ILE00.0060.02017.454-0.113-0.1130.0000.0000.0000.000
153A161ILE0-0.002-0.01021.522-0.384-0.3840.0000.0000.0000.000
154A162GLY00.0310.01324.571-0.160-0.1600.0000.0000.0000.000
155A163ASP-1-0.891-0.93521.53512.17212.1720.0000.0000.0000.000
156A164GLU-1-0.843-0.90621.51911.19911.1990.0000.0000.0000.000
157A165LEU0-0.040-0.02516.4270.1360.1360.0000.0000.0000.000
158A166ILE00.0170.00320.459-0.129-0.1290.0000.0000.0000.000
159A167PRO0-0.016-0.00721.4010.0990.0990.0000.0000.0000.000
160A168GLY00.009-0.00123.033-0.468-0.4680.0000.0000.0000.000
161A169ALA0-0.043-0.02025.9060.0030.0030.0000.0000.0000.000
162A170VAL00.0380.01728.332-0.081-0.0810.0000.0000.0000.000
163A171PRO00.0160.00731.112-0.109-0.1090.0000.0000.0000.000
164A172TRP00.0760.01134.0900.1210.1210.0000.0000.0000.000
165A173ASP-1-0.877-0.94435.7328.0428.0420.0000.0000.0000.000
166A174THR0-0.002-0.00331.7380.0430.0430.0000.0000.0000.000
167A175LEU0-0.005-0.00229.7070.1700.1700.0000.0000.0000.000
168A176GLU-1-0.766-0.85032.1967.9137.9130.0000.0000.0000.000
169A177ALA0-0.022-0.01134.668-0.002-0.0020.0000.0000.0000.000
170A178VAL00.0700.03927.8660.0090.0090.0000.0000.0000.000
171A179VAL0-0.001-0.00230.0200.1570.1570.0000.0000.0000.000
172A180LYS10.8790.93931.553-7.824-7.8240.0000.0000.0000.000
173A181GLU-1-0.850-0.90329.9619.6729.6720.0000.0000.0000.000
174A182LYS10.7660.86326.212-10.713-10.7130.0000.0000.0000.000
175A183LEU0-0.051-0.02629.8660.1180.1180.0000.0000.0000.000
176A184ALA0-0.080-0.04632.373-0.086-0.0860.0000.0000.0000.000
177A185SER0-0.028-0.01629.895-0.111-0.1110.0000.0000.0000.000
178A186ALA0-0.065-0.01329.800-0.012-0.0120.0000.0000.0000.000