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: GQ9M1

Calculation Name: 4PBO-A-Xray308

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 4PBO

Chain ID: A

ChEMBL ID:

UniProt ID: G9D324

Base Structure: X-ray

Registration Date: 2021-09-06

Reference: C. Watanabe, S. Koyama, K. Kamisaka, D. Takaya, T. Honma et. al., Interaction energy analysis of Apo structure dataset on FMODB, To be pubulished.

DOI:


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. 1.20200116
FMO calculation
FMO method FMO2-MP2/6-31G(d)
Fragmentation Auto
Number of fragment 206
LigandCharge
Software ABINIT-MP - Open Ver.1 Rev. 15 / 20190524
Total energy (hartree)
FMO2-HF: Electronic energy -2559268.465147
FMO2-HF: Nuclear repulsion 2477210.009195
FMO2-HF: Total energy -82058.455952
FMO2-MP2: Total energy -82300.100753


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:1:PHE )


Summations of interaction energy for fragment #1(A:1:PHE )
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.
-5.282-1.1730.036-1.791-2.3510
Interaction energy analysis for fragmet #1(A:1:PHE )
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.009 / 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].
3A3ASN 00.0820.0653.667-4.366-0.6520.005-1.698-2.0200.000
4A4LEU 00.0630.0274.768-0.873-0.8060.000-0.008-0.0580.000
5A5SER 0-0.0060.0217.009-0.300-0.3000.0000.0000.0000.000
6A6GLY 00.0080.0056.9050.0120.0120.0000.0000.0000.000
7A7LYS 10.7640.8903.183-1.917-1.5890.031-0.085-0.2730.000
8A8VAL 00.0200.0189.0540.1000.1000.0000.0000.0000.000
9A9LEU 0-0.032-0.01511.246-0.111-0.1110.0000.0000.0000.000
10A10GLN 0-0.037-0.03513.4590.0040.0040.0000.0000.0000.000
11A11PHE 00.0290.01616.006-0.042-0.0420.0000.0000.0000.000
12A12LYS 10.9470.96417.4600.2610.2610.0000.0000.0000.000
13A13THR 0-0.002-0.00521.0350.0090.0090.0000.0000.0000.000
14A14ALA 00.0250.02323.448-0.004-0.0040.0000.0000.0000.000
15A15THR 0-0.053-0.02222.760-0.009-0.0090.0000.0000.0000.000
16A16ASP -1-0.804-0.89825.409-0.090-0.0900.0000.0000.0000.000
17A17ASN 00.0420.00221.6930.0090.0090.0000.0000.0000.000
18A18SER 0-0.050-0.01418.866-0.022-0.0220.0000.0000.0000.000
19A19TYR 0-0.001-0.00618.1110.0200.0200.0000.0000.0000.000
20A20VAL 00.0090.00613.308-0.043-0.0430.0000.0000.0000.000
21A21LYS 10.9290.98615.1220.0110.0110.0000.0000.0000.000
22A22LEU 0-0.018-0.01313.883-0.001-0.0010.0000.0000.0000.000
23A23TYR 0-0.066-0.06012.903-0.021-0.0210.0000.0000.0000.000
24A24PRO 0-0.058-0.02115.9000.0630.0630.0000.0000.0000.000
25A25GLU -1-0.841-0.92514.5410.6780.6780.0000.0000.0000.000
26A26LYS 10.7780.90018.246-0.263-0.2630.0000.0000.0000.000
27A27PRO 00.007-0.00922.013-0.014-0.0140.0000.0000.0000.000
28A28LEU 00.0270.01922.2500.0030.0030.0000.0000.0000.000
29A29SER 0-0.050-0.01826.085-0.020-0.0200.0000.0000.0000.000
30A30LEU 0-0.012-0.00926.2880.0090.0090.0000.0000.0000.000
31A31SER 00.0160.01330.439-0.009-0.0090.0000.0000.0000.000
32A32ALA 00.019-0.01231.449-0.008-0.0080.0000.0000.0000.000
33A33PHE 00.0080.01526.8280.0090.0090.0000.0000.0000.000
34A34THR 0-0.015-0.01825.612-0.018-0.0180.0000.0000.0000.000
35A35LEU 00.0160.02021.4440.0210.0210.0000.0000.0000.000
36A98CYS 0-0.097-0.04421.661-0.005-0.0050.0000.0000.0000.000
37A37MET 00.0480.02119.4050.0250.0250.0000.0000.0000.000
38A38ARG 10.7940.88515.745-0.060-0.0600.0000.0000.0000.000
39A39VAL 00.0000.00019.064-0.013-0.0130.0000.0000.0000.000
40A40ALA 00.0340.02221.1880.0050.0050.0000.0000.0000.000
41A41THR 0-0.014-0.03622.318-0.012-0.0120.0000.0000.0000.000
42A42GLU -1-0.878-0.93324.925-0.059-0.0590.0000.0000.0000.000
43A43LEU 0-0.045-0.01026.666-0.001-0.0010.0000.0000.0000.000
44A44PRO 00.0270.01429.3380.0060.0060.0000.0000.0000.000
45A45LEU 0-0.035-0.03332.4230.0030.0030.0000.0000.0000.000
46A46ASP -1-0.919-0.95034.255-0.017-0.0170.0000.0000.0000.000
47A47ARG 10.8260.91127.8860.0450.0450.0000.0000.0000.000
48A48GLU -1-0.916-0.94832.106-0.009-0.0090.0000.0000.0000.000
49A49VAL 0-0.011-0.00526.211-0.007-0.0070.0000.0000.0000.000
50A50ILE 00.0210.03424.7310.0100.0100.0000.0000.0000.000
51A51LEU 0-0.079-0.04823.843-0.006-0.0060.0000.0000.0000.000
52A52PHE 0-0.004-0.02520.6260.0070.0070.0000.0000.0000.000
53A53ALA 00.0750.04923.079-0.003-0.0030.0000.0000.0000.000
54A54TYR 0-0.069-0.05023.4730.0110.0110.0000.0000.0000.000
55A55TYR 00.0170.00725.163-0.002-0.0020.0000.0000.0000.000
56A56THR 0-0.022-0.02026.3950.0050.0050.0000.0000.0000.000
57A57PRO 0-0.019-0.02028.826-0.005-0.0050.0000.0000.0000.000
58A58ASP -1-0.886-0.93631.1080.0220.0220.0000.0000.0000.000
59A59VAL 0-0.060-0.01831.9560.0010.0010.0000.0000.0000.000
60A60ASP -1-0.793-0.90030.5110.0210.0210.0000.0000.0000.000
61A61GLU -1-0.815-0.88628.9720.0690.0690.0000.0000.0000.000
62A62LEU 0-0.043-0.03726.5990.0060.0060.0000.0000.0000.000
63A63ASN 00.0560.03527.2290.0080.0080.0000.0000.0000.000
64A64VAL 0-0.035-0.02326.2910.0040.0040.0000.0000.0000.000
65A65TRP 00.0850.04827.379-0.006-0.0060.0000.0000.0000.000
66A66ARG 10.8350.92529.3800.0150.0150.0000.0000.0000.000
67A67GLU -1-0.749-0.85331.0260.0060.0060.0000.0000.0000.000
68A68ARG 11.0221.00834.4100.0060.0060.0000.0000.0000.000
69A69ASP -1-0.858-0.90436.5800.0090.0090.0000.0000.0000.000
70A70GLY 00.0250.00235.1500.0020.0020.0000.0000.0000.000
71A71ARG 10.7610.88435.006-0.013-0.0130.0000.0000.0000.000
72A72VAL 00.0350.02430.094-0.003-0.0030.0000.0000.0000.000
73A73SER 0-0.060-0.05231.9630.0040.0040.0000.0000.0000.000
74A74LEU 0-0.011-0.00629.9770.0030.0030.0000.0000.0000.000
75A75TYR 0-0.034-0.02831.615-0.002-0.0020.0000.0000.0000.000
76A76ILE 0-0.002-0.00931.7570.0060.0060.0000.0000.0000.000
77A77GLN 0-0.055-0.03733.126-0.008-0.0080.0000.0000.0000.000
78A78SER 0-0.024-0.01934.601-0.005-0.0050.0000.0000.0000.000
79A79SER 00.1260.08734.6570.0020.0020.0000.0000.0000.000
80A80LYS 10.8750.92536.051-0.009-0.0090.0000.0000.0000.000
81A81ASP -1-0.975-0.97539.0150.0320.0320.0000.0000.0000.000
82A82ALA 00.0460.05135.8620.0040.0040.0000.0000.0000.000
83A83ALA 0-0.0150.01135.769-0.001-0.0010.0000.0000.0000.000
84A84PHE 00.008-0.00535.5880.0010.0010.0000.0000.0000.000
85A85PHE 0-0.006-0.00634.5820.0010.0010.0000.0000.0000.000
86A86ARG 10.8760.92935.875-0.016-0.0160.0000.0000.0000.000
87A87LEU 0-0.041-0.01531.4940.0010.0010.0000.0000.0000.000
88A88PRO 0-0.015-0.02133.053-0.004-0.0040.0000.0000.0000.000
89A89PRO 00.0120.00832.5320.0020.0020.0000.0000.0000.000
90A90LEU 00.0320.02726.5380.0020.0020.0000.0000.0000.000
91A91SER 0-0.017-0.01827.552-0.005-0.0050.0000.0000.0000.000
92A92THR 00.0440.00725.6120.0020.0020.0000.0000.0000.000
93A93LEU 0-0.043-0.01124.283-0.002-0.0020.0000.0000.0000.000
94A94GLN 0-0.003-0.00618.977-0.003-0.0030.0000.0000.0000.000
95A95THR 0-0.0120.00323.0180.0040.0040.0000.0000.0000.000
96A96HIS 0-0.021-0.00421.119-0.001-0.0010.0000.0000.0000.000
97A97LEU 00.0110.00323.561-0.005-0.0050.0000.0000.0000.000
98A99VAL 00.0270.01726.355-0.013-0.0130.0000.0000.0000.000
99A100ALA 0-0.016-0.00527.9390.0140.0140.0000.0000.0000.000
100A101TRP 0-0.018-0.02130.453-0.007-0.0070.0000.0000.0000.000
101A102GLU -1-0.871-0.93132.5720.0970.0970.0000.0000.0000.000
102A103SER 0-0.005-0.01535.270-0.009-0.0090.0000.0000.0000.000
103A104ALA 00.0000.00137.335-0.006-0.0060.0000.0000.0000.000
104A105THR 0-0.036-0.03139.307-0.006-0.0060.0000.0000.0000.000
105A106GLY 00.0490.01438.512-0.005-0.0050.0000.0000.0000.000
106A107LEU 0-0.067-0.00238.307-0.004-0.0040.0000.0000.0000.000
107A108THR 00.0230.00633.7290.0060.0060.0000.0000.0000.000
108A109ALA 0-0.040-0.02233.709-0.006-0.0060.0000.0000.0000.000
109A110PHE 00.0940.03928.7020.0060.0060.0000.0000.0000.000
110A111TRP 0-0.075-0.05328.700-0.001-0.0010.0000.0000.0000.000
111A112MET 00.0580.03728.3830.0010.0010.0000.0000.0000.000
112A113ASP -1-0.847-0.91726.4760.0590.0590.0000.0000.0000.000
113A114GLY 0-0.004-0.00327.9300.0000.0000.0000.0000.0000.000
114A115ARG 10.8170.89929.302-0.056-0.0560.0000.0000.0000.000
115A116ARG 10.9120.97132.447-0.068-0.0680.0000.0000.0000.000
116A117SER 00.0100.01834.143-0.004-0.0040.0000.0000.0000.000
117A118LEU 0-0.021-0.02936.2400.0040.0040.0000.0000.0000.000
118A119HIS 00.0240.00536.3440.0000.0000.0000.0000.0000.000
119A120GLN 0-0.032-0.01938.647-0.005-0.0050.0000.0000.0000.000
120A121VAL 0-0.016-0.01039.4140.0040.0040.0000.0000.0000.000
121A122TYR 0-0.014-0.04734.957-0.002-0.0020.0000.0000.0000.000
122A123ARG 10.8960.96636.927-0.038-0.0380.0000.0000.0000.000
123A124LYS 10.9730.97738.802-0.048-0.0480.0000.0000.0000.000
124A125GLY 0-0.045-0.02240.292-0.004-0.0040.0000.0000.0000.000
125A126TYR 0-0.0160.01636.954-0.001-0.0010.0000.0000.0000.000
126A127SER 0-0.026-0.01334.8380.0060.0060.0000.0000.0000.000
127A128ILE 0-0.0080.00728.570-0.006-0.0060.0000.0000.0000.000
128A129ARG 10.8940.93331.293-0.049-0.0490.0000.0000.0000.000
129A130SER 0-0.0060.01827.049-0.002-0.0020.0000.0000.0000.000
130A131GLY 00.015-0.00225.809-0.009-0.0090.0000.0000.0000.000
131A132GLY 00.0510.03125.604-0.010-0.0100.0000.0000.0000.000
132A133THR 0-0.087-0.05620.1720.0120.0120.0000.0000.0000.000
133A134VAL 0-0.0100.00219.454-0.007-0.0070.0000.0000.0000.000
134A135VAL 0-0.007-0.00719.212-0.006-0.0060.0000.0000.0000.000
135A136LEU 0-0.0100.00016.0110.0150.0150.0000.0000.0000.000
136A137GLY 00.0480.00219.391-0.029-0.0290.0000.0000.0000.000
137A138GLN 0-0.027-0.03221.3710.0040.0040.0000.0000.0000.000
138A139ASP -1-0.801-0.90324.3940.0090.0090.0000.0000.0000.000
139A140PRO 0-0.055-0.03724.212-0.007-0.0070.0000.0000.0000.000
140A141ASP -1-0.874-0.93126.604-0.001-0.0010.0000.0000.0000.000
141A142SER 0-0.042-0.01428.856-0.005-0.0050.0000.0000.0000.000
142A143TYR 0-0.066-0.01725.624-0.005-0.0050.0000.0000.0000.000
143A144VAL 0-0.018-0.01629.2760.0060.0060.0000.0000.0000.000
144A145GLY 0-0.047-0.02329.299-0.001-0.0010.0000.0000.0000.000
145A146SER 0-0.075-0.03827.065-0.008-0.0080.0000.0000.0000.000
146A147PHE 0-0.015-0.00722.7730.0070.0070.0000.0000.0000.000
147A148ASP -1-0.813-0.90927.867-0.042-0.0420.0000.0000.0000.000
148A149VAL 0-0.003-0.00427.971-0.001-0.0010.0000.0000.0000.000
149A150ASP -1-0.927-0.94929.169-0.050-0.0500.0000.0000.0000.000
150A151GLN 0-0.052-0.03929.8090.0040.0040.0000.0000.0000.000
151A152SER 0-0.048-0.02624.8260.0010.0010.0000.0000.0000.000
152A153PHE 0-0.041-0.02020.0400.0070.0070.0000.0000.0000.000
153A154VAL 0-0.014-0.00322.596-0.017-0.0170.0000.0000.0000.000
154A155GLY 0-0.0130.00321.3190.0180.0180.0000.0000.0000.000
155A156GLU -1-0.893-0.95017.182-0.146-0.1460.0000.0000.0000.000
156A157ILE 0-0.010-0.00616.5150.0310.0310.0000.0000.0000.000
157A158ALA 00.0340.01413.990-0.025-0.0250.0000.0000.0000.000
158A159ASN 0-0.014-0.01213.9030.0250.0250.0000.0000.0000.000
159A160LEU 0-0.0070.01215.328-0.010-0.0100.0000.0000.0000.000
160A161GLN 0-0.047-0.03015.4800.0530.0530.0000.0000.0000.000
161A162MET 0-0.013-0.00818.821-0.046-0.0460.0000.0000.0000.000
162A163TRP 00.009-0.00421.3630.0260.0260.0000.0000.0000.000
163A164ASP -1-0.818-0.90724.1040.1800.1800.0000.0000.0000.000
164A165TYR 0-0.009-0.00225.638-0.007-0.0070.0000.0000.0000.000
165A166VAL 00.0100.02128.4280.0050.0050.0000.0000.0000.000
166A167LEU 0-0.0170.00225.0150.0000.0000.0000.0000.0000.000
167A168SER 00.0260.01429.574-0.012-0.0120.0000.0000.0000.000
168A169SER 00.048-0.00830.4760.0030.0030.0000.0000.0000.000
169A170ALA 0-0.018-0.00330.8050.0010.0010.0000.0000.0000.000
170A171GLN 00.0460.02227.430-0.001-0.0010.0000.0000.0000.000
171A172ILE 00.0610.03026.3740.0130.0130.0000.0000.0000.000
172A173LYS 10.9230.95126.063-0.082-0.0820.0000.0000.0000.000
173A174ALA 00.0010.01625.7820.0000.0000.0000.0000.0000.000
174A175VAL 00.0010.00320.7670.0150.0150.0000.0000.0000.000
175A176TYR 0-0.038-0.00821.8620.0050.0050.0000.0000.0000.000
176A177TYR 0-0.041-0.03523.327-0.009-0.0090.0000.0000.0000.000
177A178ASN 0-0.0050.00617.5610.0210.0210.0000.0000.0000.000
178A179GLN 0-0.040-0.02621.440-0.009-0.0090.0000.0000.0000.000
179A180ASP -1-0.875-0.94321.2930.2510.2510.0000.0000.0000.000
180A181ASN 0-0.057-0.02922.2320.0220.0220.0000.0000.0000.000
181A182ARG 10.8870.96516.346-0.367-0.3670.0000.0000.0000.000
182A183VAL 0-0.020-0.00922.0320.0200.0200.0000.0000.0000.000
183A184LYS 10.9600.97015.481-0.543-0.5430.0000.0000.0000.000
184A185GLY 00.0230.01118.796-0.025-0.0250.0000.0000.0000.000
185A186ASN 0-0.047-0.03718.7020.0400.0400.0000.0000.0000.000
186A187VAL 0-0.027-0.00820.742-0.002-0.0020.0000.0000.0000.000
187A188PHE 00.0640.02116.3580.0050.0050.0000.0000.0000.000
188A189ASP -1-0.757-0.87414.4650.6350.6350.0000.0000.0000.000
189A190TRP 00.0090.00311.0990.1220.1220.0000.0000.0000.000
190A191ASP -1-0.908-0.9699.8360.9050.9050.0000.0000.0000.000
191A192THR 0-0.128-0.0838.8510.5100.5100.0000.0000.0000.000
192A193ILE 00.0080.03110.3370.0540.0540.0000.0000.0000.000
193A194GLU -1-0.923-0.9519.8830.8440.8440.0000.0000.0000.000
194A195TYR 0-0.060-0.0456.783-0.293-0.2930.0000.0000.0000.000
195A196ASP -1-0.843-0.92910.029-0.314-0.3140.0000.0000.0000.000
196A197VAL 0-0.056-0.01311.0460.0610.0610.0000.0000.0000.000
197A198THR 00.0120.01512.935-0.032-0.0320.0000.0000.0000.000
198A199GLY 00.0100.00016.0620.0220.0220.0000.0000.0000.000
199A200ASN 0-0.035-0.02615.865-0.091-0.0910.0000.0000.0000.000
200A201VAL 0-0.0060.00614.1650.0380.0380.0000.0000.0000.000
201A202LEU 0-0.026-0.00912.378-0.084-0.0840.0000.0000.0000.000
202A203VAL 00.0190.0136.9860.0950.0950.0000.0000.0000.000
203A204VAL 0-0.050-0.0238.859-0.214-0.2140.0000.0000.0000.000
204A205PRO 0-0.012-0.0248.4720.0920.0920.0000.0000.0000.000
205A206ASP -1-0.785-0.8729.8160.0350.0350.0000.0000.0000.000
206A207ASN -1-0.983-0.97112.0640.0130.0130.0000.0000.0000.000