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: 43YMN

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 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 206
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2566459.960406
FMO2-HF: Nuclear repulsion 2484399.561902
FMO2-HF: Total energy -82060.398504
FMO2-MP2: Total energy -82302.161814


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.
-3.2470.7170.104-1.659-2.4090
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 : -0.023
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].
3A3ASN00.0440.0313.728-2.4351.0880.033-1.538-2.0180.000
4A4LEU00.0490.0294.980-0.799-0.748-0.001-0.007-0.0430.000
5A5SER0-0.042-0.0216.886-0.134-0.1340.0000.0000.0000.000
6A6GLY00.0190.0136.6340.1540.1540.0000.0000.0000.000
7A7LYS10.7700.8843.011-2.220-1.8300.072-0.114-0.3480.000
8A8VAL0-0.0130.0108.8530.0820.0820.0000.0000.0000.000
9A9LEU0-0.0030.00711.116-0.113-0.1130.0000.0000.0000.000
10A10GLN0-0.011-0.02013.3710.0240.0240.0000.0000.0000.000
11A11PHE00.0470.02116.018-0.045-0.0450.0000.0000.0000.000
12A12LYS10.9110.93317.0430.2130.2130.0000.0000.0000.000
13A13THR00.0030.00220.6790.0080.0080.0000.0000.0000.000
14A14ALA00.0380.03023.265-0.008-0.0080.0000.0000.0000.000
15A15THR0-0.049-0.04222.134-0.002-0.0020.0000.0000.0000.000
16A16ASP-1-0.726-0.83725.287-0.116-0.1160.0000.0000.0000.000
17A17ASN0-0.019-0.01421.573-0.019-0.0190.0000.0000.0000.000
18A18SER0-0.052-0.02018.861-0.019-0.0190.0000.0000.0000.000
19A19TYR00.0010.00117.9150.0330.0330.0000.0000.0000.000
20A20VAL0-0.006-0.00912.858-0.055-0.0550.0000.0000.0000.000
21A21LYS10.9150.97015.0370.1500.1500.0000.0000.0000.000
22A22LEU0-0.012-0.01313.542-0.023-0.0230.0000.0000.0000.000
23A23TYR0-0.064-0.05613.1480.0030.0030.0000.0000.0000.000
24A24PRO0-0.025-0.00515.4950.0640.0640.0000.0000.0000.000
25A25GLU-1-0.784-0.89314.1150.5700.5700.0000.0000.0000.000
26A26LYS10.7530.86818.082-0.226-0.2260.0000.0000.0000.000
27A27PRO00.0260.00021.910-0.013-0.0130.0000.0000.0000.000
28A28LEU00.0070.01422.0690.0050.0050.0000.0000.0000.000
29A29SER0-0.039-0.01925.982-0.016-0.0160.0000.0000.0000.000
30A30LEU0-0.018-0.00925.9170.0080.0080.0000.0000.0000.000
31A31SER00.0350.02230.321-0.006-0.0060.0000.0000.0000.000
32A32ALA0-0.001-0.01731.726-0.006-0.0060.0000.0000.0000.000
33A33PHE00.0000.00126.9750.0060.0060.0000.0000.0000.000
34A34THR0-0.018-0.03025.251-0.012-0.0120.0000.0000.0000.000
35A35LEU00.0110.01521.0980.0170.0170.0000.0000.0000.000
36A36CYS0-0.082-0.04521.4570.0030.0030.0000.0000.0000.000
37A37MET00.0270.01119.0300.0220.0220.0000.0000.0000.000
38A38ARG10.8180.90115.301-0.099-0.0990.0000.0000.0000.000
39A39VAL0-0.001-0.00618.818-0.011-0.0110.0000.0000.0000.000
40A40ALA00.0400.02221.1090.0080.0080.0000.0000.0000.000
41A41THR0-0.034-0.04922.203-0.012-0.0120.0000.0000.0000.000
42A42GLU-1-0.866-0.91524.848-0.037-0.0370.0000.0000.0000.000
43A43LEU0-0.0170.00726.826-0.002-0.0020.0000.0000.0000.000
44A44PRO00.0150.01029.4390.0060.0060.0000.0000.0000.000
45A45LEU0-0.041-0.02932.3840.0010.0010.0000.0000.0000.000
46A46ASP-1-0.894-0.94434.258-0.017-0.0170.0000.0000.0000.000
47A47ARG10.8180.90628.2770.0510.0510.0000.0000.0000.000
48A48GLU-1-0.811-0.86331.976-0.020-0.0200.0000.0000.0000.000
49A49VAL0-0.0040.00226.284-0.007-0.0070.0000.0000.0000.000
50A50ILE00.0260.04024.6230.0100.0100.0000.0000.0000.000
51A51LEU0-0.079-0.04923.799-0.004-0.0040.0000.0000.0000.000
52A52PHE00.000-0.02520.4100.0040.0040.0000.0000.0000.000
53A53ALA00.0550.03722.8180.0000.0000.0000.0000.0000.000
54A54TYR0-0.046-0.04623.1020.0060.0060.0000.0000.0000.000
55A55TYR0-0.011-0.01825.0740.0010.0010.0000.0000.0000.000
56A56THR0-0.002-0.03626.190-0.001-0.0010.0000.0000.0000.000
57A57PRO0-0.038-0.03528.818-0.004-0.0040.0000.0000.0000.000
58A58ASP-1-0.906-0.93531.231-0.011-0.0110.0000.0000.0000.000
59A59VAL0-0.051-0.01931.7690.0040.0040.0000.0000.0000.000
60A60ASP-1-0.747-0.88430.233-0.002-0.0020.0000.0000.0000.000
61A61GLU-1-0.809-0.83728.4190.0400.0400.0000.0000.0000.000
62A62LEU0-0.051-0.04926.3970.0080.0080.0000.0000.0000.000
63A63ASN00.0270.01926.9330.0040.0040.0000.0000.0000.000
64A64VAL0-0.029-0.02026.1450.0060.0060.0000.0000.0000.000
65A65TRP00.0780.04527.187-0.007-0.0070.0000.0000.0000.000
66A66ARG10.8030.90029.2170.0170.0170.0000.0000.0000.000
67A67GLU-1-0.762-0.85430.871-0.003-0.0030.0000.0000.0000.000
68A68ARG10.8790.92434.3510.0150.0150.0000.0000.0000.000
69A69ASP-1-0.817-0.86536.5910.0060.0060.0000.0000.0000.000
70A70GLY00.0620.01734.7970.0030.0030.0000.0000.0000.000
71A71ARG10.7460.85134.591-0.008-0.0080.0000.0000.0000.000
72A72VAL00.0240.01329.561-0.003-0.0030.0000.0000.0000.000
73A73SER0-0.056-0.05531.5710.0030.0030.0000.0000.0000.000
74A74LEU0-0.018-0.01329.6320.0030.0030.0000.0000.0000.000
75A75TYR0-0.021-0.01731.401-0.001-0.0010.0000.0000.0000.000
76A76ILE00.004-0.00231.4580.0040.0040.0000.0000.0000.000
77A77GLN0-0.050-0.03633.044-0.004-0.0040.0000.0000.0000.000
78A78SER00.009-0.00634.538-0.004-0.0040.0000.0000.0000.000
79A79SER00.1180.08934.1930.0030.0030.0000.0000.0000.000
80A80LYS10.8080.88235.5390.0050.0050.0000.0000.0000.000
81A81ASP-1-0.872-0.91538.0880.0220.0220.0000.0000.0000.000
82A82ALA00.0400.03035.5150.0020.0020.0000.0000.0000.000
83A83ALA0-0.0210.01835.3210.0000.0000.0000.0000.0000.000
84A84PHE00.012-0.00735.4160.0000.0000.0000.0000.0000.000
85A85PHE0-0.001-0.00234.3850.0010.0010.0000.0000.0000.000
86A86ARG10.8330.91535.506-0.014-0.0140.0000.0000.0000.000
87A87LEU0-0.026-0.01531.0930.0020.0020.0000.0000.0000.000
88A88PRO0-0.016-0.02332.397-0.004-0.0040.0000.0000.0000.000
89A89PRO00.004-0.00132.2890.0010.0010.0000.0000.0000.000
90A90LEU00.0320.02726.5380.0040.0040.0000.0000.0000.000
91A91SER0-0.027-0.01327.315-0.005-0.0050.0000.0000.0000.000
92A92THR00.038-0.01025.2030.0040.0040.0000.0000.0000.000
93A93LEU0-0.053-0.01424.1570.0020.0020.0000.0000.0000.000
94A94GLN0-0.014-0.01117.8160.0220.0220.0000.0000.0000.000
95A95THR0-0.0140.00422.7300.0060.0060.0000.0000.0000.000
96A96HIS0-0.011-0.01820.735-0.001-0.0010.0000.0000.0000.000
97A97LEU00.0040.00923.331-0.002-0.0020.0000.0000.0000.000
98A99VAL00.0170.01025.957-0.012-0.0120.0000.0000.0000.000
99A100ALA0-0.010-0.00227.5740.0130.0130.0000.0000.0000.000
100A101TRP0-0.031-0.02030.151-0.007-0.0070.0000.0000.0000.000
101A102GLU-1-0.807-0.88832.4750.0800.0800.0000.0000.0000.000
102A103SER00.0000.00535.206-0.007-0.0070.0000.0000.0000.000
103A104ALA00.0070.00437.619-0.005-0.0050.0000.0000.0000.000
104A105THR0-0.075-0.07239.054-0.005-0.0050.0000.0000.0000.000
105A106GLY00.0330.00238.925-0.005-0.0050.0000.0000.0000.000
106A107LEU0-0.061-0.01037.921-0.003-0.0030.0000.0000.0000.000
107A108THR00.0160.00533.8880.0040.0040.0000.0000.0000.000
108A109ALA0-0.034-0.01633.524-0.004-0.0040.0000.0000.0000.000
109A110PHE00.0890.03528.5980.0060.0060.0000.0000.0000.000
110A111TRP0-0.063-0.05128.3680.0010.0010.0000.0000.0000.000
111A112MET00.0540.04627.8110.0000.0000.0000.0000.0000.000
112A113ASP-1-0.779-0.86026.1750.0810.0810.0000.0000.0000.000
113A114GLY00.0290.02527.4840.0000.0000.0000.0000.0000.000
114A115ARG10.7960.90128.928-0.075-0.0750.0000.0000.0000.000
115A116ARG10.9060.95631.656-0.069-0.0690.0000.0000.0000.000
116A117SER00.0090.00733.758-0.003-0.0030.0000.0000.0000.000
117A118LEU0-0.011-0.01535.8670.0030.0030.0000.0000.0000.000
118A119HIS00.0290.01436.238-0.001-0.0010.0000.0000.0000.000
119A120GLN0-0.026-0.01738.310-0.004-0.0040.0000.0000.0000.000
120A121VAL0-0.017-0.01839.2720.0040.0040.0000.0000.0000.000
121A122TYR0-0.032-0.03534.674-0.002-0.0020.0000.0000.0000.000
122A123ARG10.8460.92536.762-0.022-0.0220.0000.0000.0000.000
123A124LYS10.9470.97038.778-0.042-0.0420.0000.0000.0000.000
124A125GLY0-0.030-0.00740.272-0.004-0.0040.0000.0000.0000.000
125A126TYR0-0.0060.02036.811-0.001-0.0010.0000.0000.0000.000
126A127SER0-0.034-0.02934.3840.0070.0070.0000.0000.0000.000
127A128ILE0-0.0170.01528.288-0.006-0.0060.0000.0000.0000.000
128A129ARG10.8830.92930.983-0.019-0.0190.0000.0000.0000.000
129A130SER00.0090.01826.9330.0010.0010.0000.0000.0000.000
130A131GLY0-0.002-0.01625.865-0.006-0.0060.0000.0000.0000.000
131A132GLY00.0510.03525.536-0.011-0.0110.0000.0000.0000.000
132A133THR0-0.096-0.05819.633-0.001-0.0010.0000.0000.0000.000
133A134VAL0-0.0130.00219.237-0.001-0.0010.0000.0000.0000.000
134A135VAL0-0.015-0.01118.984-0.018-0.0180.0000.0000.0000.000
135A136LEU0-0.0010.00715.8820.0250.0250.0000.0000.0000.000
136A137GLY00.0470.00419.082-0.033-0.0330.0000.0000.0000.000
137A138GLN0-0.018-0.02521.1460.0130.0130.0000.0000.0000.000
138A139ASP-1-0.802-0.91523.844-0.020-0.0200.0000.0000.0000.000
139A140PRO0-0.049-0.02723.988-0.007-0.0070.0000.0000.0000.000
140A141ASP-1-0.851-0.89026.490-0.025-0.0250.0000.0000.0000.000
141A142SER0-0.065-0.03428.300-0.005-0.0050.0000.0000.0000.000
142A143TYR0-0.085-0.03525.453-0.006-0.0060.0000.0000.0000.000
143A144VAL0-0.009-0.01129.0310.0050.0050.0000.0000.0000.000
144A145GLY0-0.029-0.01129.2140.0010.0010.0000.0000.0000.000
145A146SER0-0.097-0.05726.637-0.010-0.0100.0000.0000.0000.000
146A147PHE00.0040.00122.3300.0060.0060.0000.0000.0000.000
147A148ASP-1-0.811-0.91027.601-0.056-0.0560.0000.0000.0000.000
148A149VAL00.0270.01027.9290.0000.0000.0000.0000.0000.000
149A150ASP-1-0.930-0.96229.015-0.055-0.0550.0000.0000.0000.000
150A151GLN0-0.081-0.05129.7270.0040.0040.0000.0000.0000.000
151A152SER0-0.045-0.02924.7920.0020.0020.0000.0000.0000.000
152A153PHE0-0.037-0.01520.0040.0080.0080.0000.0000.0000.000
153A154VAL0-0.0010.00022.665-0.016-0.0160.0000.0000.0000.000
154A155GLY0-0.0090.01121.2940.0180.0180.0000.0000.0000.000
155A156GLU-1-0.877-0.94216.831-0.077-0.0770.0000.0000.0000.000
156A157ILE0-0.001-0.00416.4180.0240.0240.0000.0000.0000.000
157A158ALA00.0270.00713.910-0.025-0.0250.0000.0000.0000.000
158A159ASN0-0.011-0.01813.4390.0390.0390.0000.0000.0000.000
159A160LEU00.0050.02414.985-0.005-0.0050.0000.0000.0000.000
160A161GLN0-0.068-0.04515.1890.0700.0700.0000.0000.0000.000
161A162MET0-0.0020.00418.601-0.045-0.0450.0000.0000.0000.000
162A163TRP00.014-0.01121.2790.0230.0230.0000.0000.0000.000
163A164ASP-1-0.740-0.84624.1320.1610.1610.0000.0000.0000.000
164A165TYR0-0.0150.00025.676-0.006-0.0060.0000.0000.0000.000
165A166VAL00.0180.03128.4490.0050.0050.0000.0000.0000.000
166A167LEU0-0.0250.00024.7020.0010.0010.0000.0000.0000.000
167A168SER00.005-0.01729.285-0.012-0.0120.0000.0000.0000.000
168A169SER00.028-0.02030.0660.0040.0040.0000.0000.0000.000
169A170ALA00.0030.01330.5190.0010.0010.0000.0000.0000.000
170A171GLN00.0710.05826.827-0.004-0.0040.0000.0000.0000.000
171A172ILE00.0450.02125.8360.0140.0140.0000.0000.0000.000
172A173LYS10.8510.92425.694-0.094-0.0940.0000.0000.0000.000
173A174ALA00.0000.01125.3880.0030.0030.0000.0000.0000.000
174A175VAL00.001-0.00820.4510.0170.0170.0000.0000.0000.000
175A176TYR0-0.059-0.04421.3420.0110.0110.0000.0000.0000.000
176A177TYR0-0.026-0.02922.651-0.006-0.0060.0000.0000.0000.000
177A178ASN00.0140.00217.4810.0300.0300.0000.0000.0000.000
178A179GLN00.0180.00820.8930.0060.0060.0000.0000.0000.000
179A180ASP-1-0.888-0.94021.0110.2910.2910.0000.0000.0000.000
180A181ASN0-0.049-0.02021.9990.0130.0130.0000.0000.0000.000
181A182ARG10.8270.93016.901-0.387-0.3870.0000.0000.0000.000
182A183VAL0-0.017-0.01021.8030.0190.0190.0000.0000.0000.000
183A184LYS10.8280.88014.450-0.652-0.6520.0000.0000.0000.000
184A185GLY00.0040.01018.271-0.031-0.0310.0000.0000.0000.000
185A186ASN0-0.048-0.05118.6690.0270.0270.0000.0000.0000.000
186A187VAL0-0.044-0.01520.504-0.010-0.0100.0000.0000.0000.000
187A188PHE00.0880.02616.222-0.012-0.0120.0000.0000.0000.000
188A189ASP-1-0.748-0.83914.2940.6280.6280.0000.0000.0000.000
189A190TRP00.0360.01910.9150.0910.0910.0000.0000.0000.000
190A191ASP-1-0.825-0.8929.7811.0621.0620.0000.0000.0000.000
191A192THR0-0.103-0.0818.7760.5900.5900.0000.0000.0000.000
192A193ILE0-0.0400.0049.9860.0840.0840.0000.0000.0000.000
193A194GLU-1-0.841-0.9068.7940.4850.4850.0000.0000.0000.000
194A195TYR0-0.053-0.0445.509-0.036-0.0360.0000.0000.0000.000
195A196ASP-1-0.819-0.8809.871-0.472-0.4720.0000.0000.0000.000
196A197VAL0-0.021-0.00310.2220.0780.0780.0000.0000.0000.000
197A198THR0-0.024-0.01412.636-0.002-0.0020.0000.0000.0000.000
198A199GLY00.0560.03415.7920.0320.0320.0000.0000.0000.000
199A200ASN0-0.051-0.02915.876-0.078-0.0780.0000.0000.0000.000
200A201VAL0-0.0120.00014.6560.0440.0440.0000.0000.0000.000
201A202LEU0-0.0220.00112.612-0.079-0.0790.0000.0000.0000.000
202A203VAL00.0260.0147.5670.0830.0830.0000.0000.0000.000
203A204VAL0-0.028-0.0089.067-0.154-0.1540.0000.0000.0000.000
204A205PRO00.009-0.0147.6210.0910.0910.0000.0000.0000.000
205A206ASP-1-0.816-0.8799.3200.1050.1050.0000.0000.0000.000
206A207ASN0-0.061-0.01311.7790.0060.0060.0000.0000.0000.000