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: Q1L9Y

Calculation Name: 4PBO-A-Xray372

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: 2023-03-14

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 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 206
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2559587.364995
FMO2-HF: Nuclear repulsion 2477528.054161
FMO2-HF: Total energy -82059.310833
FMO2-MP2: Total energy -82300.971952


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.
-5.354-1.2010.023-1.802-2.3740
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 : -0.010 / 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].
3A3ASN00.0890.0703.667-4.408-0.651-0.006-1.711-2.0390.000
4A4LEU00.0650.0284.768-0.822-0.753-0.001-0.007-0.0610.000
5A5SER0-0.0040.0257.009-0.308-0.3080.0000.0000.0000.000
6A6GLY0-0.005-0.0046.9050.0260.0260.0000.0000.0000.000
7A7LYS10.7630.8853.183-2.034-1.7070.030-0.084-0.2740.000
8A8VAL00.0110.0159.0540.0940.0940.0000.0000.0000.000
9A9LEU0-0.020-0.00911.247-0.106-0.1060.0000.0000.0000.000
10A10GLN0-0.046-0.03913.4590.0020.0020.0000.0000.0000.000
11A11PHE00.0330.01916.006-0.042-0.0420.0000.0000.0000.000
12A12LYS10.9500.96417.4600.2440.2440.0000.0000.0000.000
13A13THR0-0.002-0.00321.0350.0080.0080.0000.0000.0000.000
14A14ALA00.0270.02423.448-0.004-0.0040.0000.0000.0000.000
15A15THR0-0.053-0.02222.760-0.009-0.0090.0000.0000.0000.000
16A16ASP-1-0.803-0.89725.409-0.088-0.0880.0000.0000.0000.000
17A17ASN00.0430.00321.6930.0090.0090.0000.0000.0000.000
18A18SER0-0.051-0.01518.866-0.022-0.0220.0000.0000.0000.000
19A19TYR00.007-0.00318.1110.0200.0200.0000.0000.0000.000
20A20VAL00.0010.00213.308-0.043-0.0430.0000.0000.0000.000
21A21LYS10.9320.98815.1220.0110.0110.0000.0000.0000.000
22A22LEU0-0.021-0.01513.883-0.002-0.0020.0000.0000.0000.000
23A23TYR0-0.066-0.05912.903-0.022-0.0220.0000.0000.0000.000
24A24PRO0-0.054-0.02015.9000.0620.0620.0000.0000.0000.000
25A25GLU-1-0.847-0.92714.5410.6740.6740.0000.0000.0000.000
26A26LYS10.7810.90218.246-0.262-0.2620.0000.0000.0000.000
27A27PRO00.010-0.00822.013-0.012-0.0120.0000.0000.0000.000
28A28LEU00.0270.01922.2500.0040.0040.0000.0000.0000.000
29A29SER0-0.050-0.01926.085-0.019-0.0190.0000.0000.0000.000
30A30LEU0-0.009-0.00926.2880.0090.0090.0000.0000.0000.000
31A31SER00.0140.01330.439-0.008-0.0080.0000.0000.0000.000
32A32ALA00.019-0.01231.449-0.008-0.0080.0000.0000.0000.000
33A33PHE00.0100.01626.8280.0090.0090.0000.0000.0000.000
34A34THR0-0.016-0.01825.612-0.018-0.0180.0000.0000.0000.000
35A35LEU00.0130.01921.4430.0210.0210.0000.0000.0000.000
36A36CYS0-0.091-0.04221.661-0.005-0.0050.0000.0000.0000.000
37A37MET00.0420.02019.4050.0250.0250.0000.0000.0000.000
38A38ARG10.8110.89515.743-0.079-0.0790.0000.0000.0000.000
39A39VAL00.0020.00119.064-0.011-0.0110.0000.0000.0000.000
40A40ALA00.0320.02021.1870.0050.0050.0000.0000.0000.000
41A41THR0-0.014-0.03422.318-0.011-0.0110.0000.0000.0000.000
42A42GLU-1-0.877-0.93224.925-0.051-0.0510.0000.0000.0000.000
43A43LEU0-0.043-0.00926.666-0.002-0.0020.0000.0000.0000.000
44A44PRO00.0260.01429.3380.0060.0060.0000.0000.0000.000
45A45LEU0-0.037-0.03532.4230.0020.0020.0000.0000.0000.000
46A46ASP-1-0.917-0.94934.255-0.013-0.0130.0000.0000.0000.000
47A47ARG10.8290.91227.8860.0400.0400.0000.0000.0000.000
48A48GLU-1-0.915-0.94732.106-0.006-0.0060.0000.0000.0000.000
49A49VAL0-0.013-0.00626.211-0.007-0.0070.0000.0000.0000.000
50A50ILE00.0240.03624.7310.0100.0100.0000.0000.0000.000
51A51LEU0-0.081-0.05023.843-0.005-0.0050.0000.0000.0000.000
52A52PHE0-0.006-0.02620.6260.0070.0070.0000.0000.0000.000
53A53ALA00.0770.05023.079-0.003-0.0030.0000.0000.0000.000
54A54TYR0-0.073-0.05223.4730.0100.0100.0000.0000.0000.000
55A55TYR00.0230.01025.163-0.002-0.0020.0000.0000.0000.000
56A56THR0-0.024-0.02026.3950.0040.0040.0000.0000.0000.000
57A57PRO0-0.019-0.02128.826-0.005-0.0050.0000.0000.0000.000
58A58ASP-1-0.886-0.93631.1080.0220.0220.0000.0000.0000.000
59A59VAL0-0.061-0.01831.9550.0010.0010.0000.0000.0000.000
60A60ASP-1-0.790-0.89830.5110.0230.0230.0000.0000.0000.000
61A61GLU-1-0.819-0.88828.9720.0690.0690.0000.0000.0000.000
62A62LEU0-0.040-0.03726.5990.0050.0050.0000.0000.0000.000
63A63ASN00.0550.03427.2290.0080.0080.0000.0000.0000.000
64A64VAL0-0.039-0.02326.2910.0040.0040.0000.0000.0000.000
65A65TRP00.0880.04827.379-0.005-0.0050.0000.0000.0000.000
66A66ARG10.8300.92429.3800.0110.0110.0000.0000.0000.000
67A67GLU-1-0.748-0.85231.0260.0090.0090.0000.0000.0000.000
68A68ARG11.0231.00834.4100.0040.0040.0000.0000.0000.000
69A69ASP-1-0.854-0.90236.5800.0120.0120.0000.0000.0000.000
70A70GLY00.0210.00035.1500.0020.0020.0000.0000.0000.000
71A71ARG10.7620.88435.006-0.016-0.0160.0000.0000.0000.000
72A72VAL00.0300.02230.094-0.003-0.0030.0000.0000.0000.000
73A73SER0-0.054-0.05031.9630.0030.0030.0000.0000.0000.000
74A74LEU0-0.018-0.00929.9770.0040.0040.0000.0000.0000.000
75A75TYR0-0.026-0.02431.615-0.002-0.0020.0000.0000.0000.000
76A76ILE0-0.007-0.01031.7570.0060.0060.0000.0000.0000.000
77A77GLN0-0.052-0.03633.126-0.008-0.0080.0000.0000.0000.000
78A78SER0-0.023-0.01934.602-0.005-0.0050.0000.0000.0000.000
79A79SER00.1270.08734.6570.0020.0020.0000.0000.0000.000
80A80LYS10.8750.92536.051-0.011-0.0110.0000.0000.0000.000
81A81ASP-1-0.973-0.97439.0080.0330.0330.0000.0000.0000.000
82A82ALA00.0440.05035.8310.0040.0040.0000.0000.0000.000
83A83ALA0-0.0140.01235.769-0.001-0.0010.0000.0000.0000.000
84A84PHE00.009-0.00435.5880.0020.0020.0000.0000.0000.000
85A85PHE0-0.007-0.00634.5820.0010.0010.0000.0000.0000.000
86A86ARG10.8780.93035.875-0.019-0.0190.0000.0000.0000.000
87A87LEU0-0.042-0.01631.4940.0010.0010.0000.0000.0000.000
88A88PRO0-0.016-0.02133.053-0.004-0.0040.0000.0000.0000.000
89A89PRO00.0130.00832.5320.0020.0020.0000.0000.0000.000
90A90LEU00.0360.02726.5370.0030.0030.0000.0000.0000.000
91A91SER0-0.018-0.01827.552-0.005-0.0050.0000.0000.0000.000
92A92THR00.0440.00725.6120.0030.0030.0000.0000.0000.000
93A93LEU0-0.045-0.01224.283-0.001-0.0010.0000.0000.0000.000
94A94GLN0-0.015-0.01318.977-0.002-0.0020.0000.0000.0000.000
95A95THR0-0.0050.00723.0180.0030.0030.0000.0000.0000.000
96A96HIS0-0.028-0.00721.119-0.001-0.0010.0000.0000.0000.000
97A97LEU00.0150.00423.561-0.006-0.0060.0000.0000.0000.000
98A99VAL00.0270.01826.355-0.013-0.0130.0000.0000.0000.000
99A100ALA0-0.014-0.00527.9390.0140.0140.0000.0000.0000.000
100A101TRP0-0.024-0.02230.453-0.007-0.0070.0000.0000.0000.000
101A102GLU-1-0.865-0.92932.5720.0980.0980.0000.0000.0000.000
102A103SER0-0.006-0.01535.270-0.008-0.0080.0000.0000.0000.000
103A104ALA00.0030.00237.335-0.006-0.0060.0000.0000.0000.000
104A105THR0-0.035-0.03039.307-0.006-0.0060.0000.0000.0000.000
105A106GLY00.0490.01538.512-0.005-0.0050.0000.0000.0000.000
106A107LEU0-0.066-0.00338.307-0.003-0.0030.0000.0000.0000.000
107A108THR00.0160.00433.7290.0060.0060.0000.0000.0000.000
108A109ALA0-0.037-0.02033.709-0.006-0.0060.0000.0000.0000.000
109A110PHE00.0940.04028.7020.0060.0060.0000.0000.0000.000
110A111TRP0-0.072-0.05228.700-0.001-0.0010.0000.0000.0000.000
111A112MET00.0520.03528.3830.0020.0020.0000.0000.0000.000
112A113ASP-1-0.847-0.91826.4760.0660.0660.0000.0000.0000.000
113A114GLY0-0.004-0.00527.930-0.001-0.0010.0000.0000.0000.000
114A115ARG10.8180.90029.302-0.062-0.0620.0000.0000.0000.000
115A116ARG10.9140.97332.447-0.071-0.0710.0000.0000.0000.000
116A117SER00.0100.01834.143-0.004-0.0040.0000.0000.0000.000
117A118LEU0-0.019-0.02836.2400.0040.0040.0000.0000.0000.000
118A119HIS00.0240.00436.3440.0000.0000.0000.0000.0000.000
119A120GLN0-0.032-0.01838.647-0.005-0.0050.0000.0000.0000.000
120A121VAL0-0.013-0.00939.4140.0040.0040.0000.0000.0000.000
121A122TYR0-0.015-0.04734.957-0.002-0.0020.0000.0000.0000.000
122A123ARG10.8990.96736.927-0.039-0.0390.0000.0000.0000.000
123A124LYS10.9720.97638.802-0.049-0.0490.0000.0000.0000.000
124A125GLY0-0.043-0.02140.292-0.004-0.0040.0000.0000.0000.000
125A126TYR0-0.0160.01636.954-0.001-0.0010.0000.0000.0000.000
126A127SER0-0.028-0.01334.8380.0060.0060.0000.0000.0000.000
127A128ILE0-0.0080.00628.570-0.006-0.0060.0000.0000.0000.000
128A129ARG10.8940.93331.293-0.049-0.0490.0000.0000.0000.000
129A130SER0-0.0060.01727.049-0.002-0.0020.0000.0000.0000.000
130A131GLY00.019-0.00125.809-0.009-0.0090.0000.0000.0000.000
131A132GLY00.0510.03325.604-0.010-0.0100.0000.0000.0000.000
132A133THR0-0.088-0.05720.1650.0110.0110.0000.0000.0000.000
133A134VAL0-0.0100.00219.453-0.007-0.0070.0000.0000.0000.000
134A135VAL0-0.007-0.00719.212-0.005-0.0050.0000.0000.0000.000
135A136LEU0-0.016-0.00316.0110.0150.0150.0000.0000.0000.000
136A137GLY00.0460.00019.391-0.028-0.0280.0000.0000.0000.000
137A138GLN0-0.029-0.03121.3710.0030.0030.0000.0000.0000.000
138A139ASP-1-0.797-0.90124.3940.0110.0110.0000.0000.0000.000
139A140PRO0-0.052-0.03624.212-0.007-0.0070.0000.0000.0000.000
140A141ASP-1-0.874-0.93126.6040.0000.0000.0000.0000.0000.000
141A142SER0-0.044-0.01328.856-0.005-0.0050.0000.0000.0000.000
142A143TYR0-0.063-0.01725.624-0.005-0.0050.0000.0000.0000.000
143A144VAL0-0.019-0.01629.2760.0050.0050.0000.0000.0000.000
144A145GLY0-0.044-0.02229.299-0.001-0.0010.0000.0000.0000.000
145A146SER0-0.073-0.03827.064-0.008-0.0080.0000.0000.0000.000
146A147PHE0-0.017-0.00822.7730.0060.0060.0000.0000.0000.000
147A148ASP-1-0.813-0.90827.867-0.039-0.0390.0000.0000.0000.000
148A149VAL0-0.003-0.00527.972-0.001-0.0010.0000.0000.0000.000
149A150ASP-1-0.925-0.94929.169-0.047-0.0470.0000.0000.0000.000
150A151GLN0-0.051-0.03929.8090.0040.0040.0000.0000.0000.000
151A152SER0-0.049-0.02624.8260.0020.0020.0000.0000.0000.000
152A153PHE0-0.044-0.02120.0400.0070.0070.0000.0000.0000.000
153A154VAL0-0.013-0.00222.596-0.016-0.0160.0000.0000.0000.000
154A155GLY0-0.0090.00421.3190.0170.0170.0000.0000.0000.000
155A156GLU-1-0.898-0.95417.182-0.127-0.1270.0000.0000.0000.000
156A157ILE0-0.004-0.00316.5150.0290.0290.0000.0000.0000.000
157A158ALA00.0250.00813.990-0.023-0.0230.0000.0000.0000.000
158A159ASN0-0.020-0.01513.9020.0220.0220.0000.0000.0000.000
159A160LEU0-0.0050.01415.329-0.012-0.0120.0000.0000.0000.000
160A161GLN0-0.047-0.03015.4800.0510.0510.0000.0000.0000.000
161A162MET0-0.010-0.00718.821-0.046-0.0460.0000.0000.0000.000
162A163TRP00.009-0.00321.3630.0260.0260.0000.0000.0000.000
163A164ASP-1-0.812-0.90524.1040.1810.1810.0000.0000.0000.000
164A165TYR0-0.011-0.00225.638-0.007-0.0070.0000.0000.0000.000
165A166VAL00.0100.02128.4280.0060.0060.0000.0000.0000.000
166A167LEU0-0.0190.00225.015-0.001-0.0010.0000.0000.0000.000
167A168SER00.0290.01629.574-0.012-0.0120.0000.0000.0000.000
168A169SER00.048-0.00930.4760.0030.0030.0000.0000.0000.000
169A170ALA0-0.017-0.00330.8050.0010.0010.0000.0000.0000.000
170A171GLN00.0470.02327.430-0.001-0.0010.0000.0000.0000.000
171A172ILE00.0620.03026.3750.0130.0130.0000.0000.0000.000
172A173LYS10.9190.95126.063-0.085-0.0850.0000.0000.0000.000
173A174ALA00.0050.01725.7790.0000.0000.0000.0000.0000.000
174A175VAL00.0000.00320.7670.0150.0150.0000.0000.0000.000
175A176TYR0-0.038-0.00921.8620.0060.0060.0000.0000.0000.000
176A177TYR0-0.041-0.03423.327-0.008-0.0080.0000.0000.0000.000
177A178ASN0-0.0150.00017.5660.0210.0210.0000.0000.0000.000
178A179GLN0-0.036-0.02421.440-0.008-0.0080.0000.0000.0000.000
179A180ASP-1-0.878-0.94421.2870.2580.2580.0000.0000.0000.000
180A181ASN0-0.053-0.02622.2270.0220.0220.0000.0000.0000.000
181A182ARG10.8850.96416.339-0.378-0.3780.0000.0000.0000.000
182A183VAL0-0.016-0.00822.0260.0200.0200.0000.0000.0000.000
183A184LYS10.9560.96915.477-0.551-0.5510.0000.0000.0000.000
184A185GLY00.0230.01218.796-0.025-0.0250.0000.0000.0000.000
185A186ASN0-0.046-0.03718.7020.0400.0400.0000.0000.0000.000
186A187VAL0-0.022-0.00520.742-0.002-0.0020.0000.0000.0000.000
187A188PHE00.0600.02016.3580.0040.0040.0000.0000.0000.000
188A189ASP-1-0.757-0.87314.4650.6450.6450.0000.0000.0000.000
189A190TRP00.0100.00211.0990.1170.1170.0000.0000.0000.000
190A191ASP-1-0.914-0.9749.8360.9200.9200.0000.0000.0000.000
191A192THR0-0.119-0.0808.8510.5060.5060.0000.0000.0000.000
192A193ILE00.0080.03210.3370.0580.0580.0000.0000.0000.000
193A194GLU-1-0.923-0.9509.8830.8350.8350.0000.0000.0000.000
194A195TYR0-0.060-0.0466.783-0.283-0.2830.0000.0000.0000.000
195A196ASP-1-0.845-0.92810.029-0.318-0.3180.0000.0000.0000.000
196A197VAL0-0.060-0.01511.0460.0620.0620.0000.0000.0000.000
197A198THR00.0160.01812.935-0.035-0.0350.0000.0000.0000.000
198A199GLY00.0120.00216.0620.0230.0230.0000.0000.0000.000
199A200ASN0-0.033-0.02415.865-0.089-0.0890.0000.0000.0000.000
200A201VAL0-0.0050.00714.1650.0380.0380.0000.0000.0000.000
201A202LEU0-0.024-0.00712.378-0.081-0.0810.0000.0000.0000.000
202A203VAL00.0210.0146.9860.0960.0960.0000.0000.0000.000
203A204VAL0-0.042-0.0178.859-0.201-0.2010.0000.0000.0000.000
204A205PRO00.000-0.0168.4720.1010.1010.0000.0000.0000.000
205A206ASP-1-0.770-0.8619.8160.0570.0570.0000.0000.0000.000
206A207ASN0-0.060-0.01712.0540.0010.0010.0000.0000.0000.000