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: K3V13

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 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 206
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2561303.424279
FMO2-HF: Nuclear repulsion 2479243.253192
FMO2-HF: Total energy -82060.171086
FMO2-MP2: Total energy -82301.872963


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.
-4.373-0.190.016-1.823-2.3760
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 : -0.021
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].
3A3ASN00.0400.0403.670-3.6340.165-0.014-1.736-2.0490.000
4A4LEU00.0540.0314.771-0.746-0.680-0.001-0.007-0.0580.000
5A5SER0-0.042-0.0237.058-0.275-0.2750.0000.0000.0000.000
6A6GLY00.0090.0106.8940.0750.0750.0000.0000.0000.000
7A7LYS10.7610.8793.161-2.217-1.8990.031-0.080-0.2690.000
8A8VAL00.0100.0129.0570.0800.0800.0000.0000.0000.000
9A9LEU0-0.023-0.00411.291-0.101-0.1010.0000.0000.0000.000
10A10GLN0-0.023-0.02213.4740.0080.0080.0000.0000.0000.000
11A11PHE00.0420.01916.025-0.046-0.0460.0000.0000.0000.000
12A12LYS10.9150.92917.3670.2110.2110.0000.0000.0000.000
13A13THR00.0130.00521.0570.0090.0090.0000.0000.0000.000
14A14ALA00.0270.02323.463-0.005-0.0050.0000.0000.0000.000
15A15THR0-0.056-0.04121.988-0.002-0.0020.0000.0000.0000.000
16A16ASP-1-0.749-0.86725.190-0.099-0.0990.0000.0000.0000.000
17A17ASN0-0.016-0.01521.573-0.016-0.0160.0000.0000.0000.000
18A18SER0-0.047-0.01518.705-0.020-0.0200.0000.0000.0000.000
19A19TYR00.0160.00917.9690.0310.0310.0000.0000.0000.000
20A20VAL0-0.005-0.00313.200-0.047-0.0470.0000.0000.0000.000
21A21LYS10.9200.97815.1300.0520.0520.0000.0000.0000.000
22A22LEU0-0.014-0.01213.8410.0000.0000.0000.0000.0000.000
23A23TYR0-0.056-0.06613.532-0.017-0.0170.0000.0000.0000.000
24A24PRO0-0.049-0.01415.9000.0640.0640.0000.0000.0000.000
25A25GLU-1-0.814-0.92014.4000.6790.6790.0000.0000.0000.000
26A26LYS10.7380.86618.246-0.252-0.2520.0000.0000.0000.000
27A27PRO00.022-0.00322.013-0.010-0.0100.0000.0000.0000.000
28A28LEU00.0130.01422.2410.0050.0050.0000.0000.0000.000
29A29SER0-0.025-0.00826.085-0.019-0.0190.0000.0000.0000.000
30A30LEU0-0.032-0.02226.2060.0090.0090.0000.0000.0000.000
31A31SER00.0240.02030.439-0.008-0.0080.0000.0000.0000.000
32A32ALA00.008-0.01531.449-0.007-0.0070.0000.0000.0000.000
33A33PHE00.0150.01426.8530.0090.0090.0000.0000.0000.000
34A34THR0-0.020-0.02025.566-0.016-0.0160.0000.0000.0000.000
35A35LEU00.0070.01521.4830.0210.0210.0000.0000.0000.000
36A36CYS0-0.080-0.04221.678-0.004-0.0040.0000.0000.0000.000
37A37MET00.0330.02019.4050.0240.0240.0000.0000.0000.000
38A38ARG10.8210.88915.758-0.112-0.1120.0000.0000.0000.000
39A39VAL0-0.003-0.00719.068-0.009-0.0090.0000.0000.0000.000
40A40ALA00.0350.02621.1450.0050.0050.0000.0000.0000.000
41A41THR0-0.015-0.04322.330-0.012-0.0120.0000.0000.0000.000
42A42GLU-1-0.869-0.91324.937-0.035-0.0350.0000.0000.0000.000
43A43LEU0-0.032-0.00326.781-0.002-0.0020.0000.0000.0000.000
44A44PRO00.0290.01829.3530.0060.0060.0000.0000.0000.000
45A45LEU0-0.037-0.03232.3320.0020.0020.0000.0000.0000.000
46A46ASP-1-0.906-0.94834.268-0.010-0.0100.0000.0000.0000.000
47A47ARG10.8200.90828.0750.0380.0380.0000.0000.0000.000
48A48GLU-1-0.809-0.86732.120-0.006-0.0060.0000.0000.0000.000
49A49VAL00.0040.00026.260-0.007-0.0070.0000.0000.0000.000
50A50ILE00.0150.03424.7530.0100.0100.0000.0000.0000.000
51A51LEU0-0.077-0.04723.856-0.004-0.0040.0000.0000.0000.000
52A52PHE0-0.005-0.02520.6800.0080.0080.0000.0000.0000.000
53A53ALA00.0780.04923.092-0.003-0.0030.0000.0000.0000.000
54A54TYR0-0.066-0.04723.4830.0100.0100.0000.0000.0000.000
55A55TYR0-0.002-0.03025.261-0.001-0.0010.0000.0000.0000.000
56A56THR0-0.028-0.03726.5040.0020.0020.0000.0000.0000.000
57A57PRO0-0.006-0.01529.007-0.004-0.0040.0000.0000.0000.000
58A58ASP-1-0.897-0.94031.2030.0100.0100.0000.0000.0000.000
59A59VAL0-0.068-0.02732.0230.0020.0020.0000.0000.0000.000
60A60ASP-1-0.750-0.87930.5780.0180.0180.0000.0000.0000.000
61A61GLU-1-0.825-0.85129.0270.0610.0610.0000.0000.0000.000
62A62LEU0-0.034-0.03326.5780.0060.0060.0000.0000.0000.000
63A63ASN00.0260.02327.2370.0080.0080.0000.0000.0000.000
64A64VAL0-0.040-0.02226.3130.0040.0040.0000.0000.0000.000
65A65TRP00.0690.04027.389-0.005-0.0050.0000.0000.0000.000
66A66ARG10.8060.90329.4090.0050.0050.0000.0000.0000.000
67A67GLU-1-0.748-0.84531.0360.0090.0090.0000.0000.0000.000
68A68ARG10.8970.92934.4220.0060.0060.0000.0000.0000.000
69A69ASP-1-0.845-0.88436.5940.0140.0140.0000.0000.0000.000
70A70GLY00.0370.00435.1650.0020.0020.0000.0000.0000.000
71A71ARG10.7470.86635.014-0.016-0.0160.0000.0000.0000.000
72A72VAL00.0190.01530.026-0.003-0.0030.0000.0000.0000.000
73A73SER0-0.049-0.05131.9550.0030.0030.0000.0000.0000.000
74A74LEU0-0.017-0.00829.9080.0040.0040.0000.0000.0000.000
75A75TYR0-0.022-0.02331.624-0.003-0.0030.0000.0000.0000.000
76A76ILE0-0.001-0.00931.7640.0060.0060.0000.0000.0000.000
77A77GLN0-0.040-0.03433.133-0.007-0.0070.0000.0000.0000.000
78A78SER00.008-0.00734.613-0.005-0.0050.0000.0000.0000.000
79A79SER00.1440.09634.6670.0010.0010.0000.0000.0000.000
80A80LYS10.8010.88436.062-0.010-0.0100.0000.0000.0000.000
81A81ASP-1-0.909-0.93339.0870.0330.0330.0000.0000.0000.000
82A82ALA00.0410.04535.7170.0040.0040.0000.0000.0000.000
83A83ALA0-0.0110.01235.788-0.001-0.0010.0000.0000.0000.000
84A84PHE00.014-0.00535.5930.0020.0020.0000.0000.0000.000
85A85PHE00.002-0.00234.5790.0010.0010.0000.0000.0000.000
86A86ARG10.8710.92635.880-0.022-0.0220.0000.0000.0000.000
87A87LEU0-0.040-0.01731.6100.0010.0010.0000.0000.0000.000
88A88PRO0-0.016-0.02033.109-0.004-0.0040.0000.0000.0000.000
89A89PRO00.0070.00132.5370.0020.0020.0000.0000.0000.000
90A90LEU00.0380.03026.7560.0030.0030.0000.0000.0000.000
91A91SER0-0.022-0.01827.560-0.005-0.0050.0000.0000.0000.000
92A92THR00.037-0.01525.6260.0040.0040.0000.0000.0000.000
93A93LEU0-0.049-0.01124.2910.0000.0000.0000.0000.0000.000
94A94GLN00.008-0.00718.5870.0200.0200.0000.0000.0000.000
95A95THR0-0.0190.00423.0210.0020.0020.0000.0000.0000.000
96A96HIS0-0.023-0.00821.1370.0010.0010.0000.0000.0000.000
97A97LEU00.0170.00523.560-0.007-0.0070.0000.0000.0000.000
98A99VAL00.0200.01826.353-0.013-0.0130.0000.0000.0000.000
99A100ALA0-0.013-0.00627.9360.0130.0130.0000.0000.0000.000
100A101TRP0-0.015-0.01130.450-0.007-0.0070.0000.0000.0000.000
101A102GLU-1-0.813-0.88932.5680.0920.0920.0000.0000.0000.000
102A103SER0-0.003-0.01135.266-0.008-0.0080.0000.0000.0000.000
103A104ALA0-0.015-0.00337.332-0.006-0.0060.0000.0000.0000.000
104A105THR0-0.045-0.06139.371-0.006-0.0060.0000.0000.0000.000
105A106GLY00.0440.01438.510-0.005-0.0050.0000.0000.0000.000
106A107LEU0-0.076-0.00638.361-0.003-0.0030.0000.0000.0000.000
107A108THR00.0160.00533.7940.0060.0060.0000.0000.0000.000
108A109ALA0-0.033-0.01733.708-0.005-0.0050.0000.0000.0000.000
109A110PHE00.0900.03528.8150.0070.0070.0000.0000.0000.000
110A111TRP0-0.077-0.05628.756-0.001-0.0010.0000.0000.0000.000
111A112MET00.0570.04028.3720.0020.0020.0000.0000.0000.000
112A113ASP-1-0.792-0.87526.5140.0820.0820.0000.0000.0000.000
113A114GLY00.0110.01327.926-0.001-0.0010.0000.0000.0000.000
114A115ARG10.7860.88429.295-0.074-0.0740.0000.0000.0000.000
115A116ARG10.9120.96832.442-0.075-0.0750.0000.0000.0000.000
116A117SER00.0200.02434.138-0.004-0.0040.0000.0000.0000.000
117A118LEU0-0.025-0.02836.2380.0040.0040.0000.0000.0000.000
118A119HIS00.0260.00536.2760.0000.0000.0000.0000.0000.000
119A120GLN0-0.034-0.01838.635-0.004-0.0040.0000.0000.0000.000
120A121VAL0-0.014-0.01139.4120.0040.0040.0000.0000.0000.000
121A122TYR0-0.030-0.05134.902-0.002-0.0020.0000.0000.0000.000
122A123ARG10.8510.93336.990-0.035-0.0350.0000.0000.0000.000
123A124LYS10.9570.96938.803-0.048-0.0480.0000.0000.0000.000
124A125GLY0-0.040-0.01940.287-0.004-0.0040.0000.0000.0000.000
125A126TYR0-0.0110.01936.903-0.001-0.0010.0000.0000.0000.000
126A127SER0-0.031-0.01534.8130.0070.0070.0000.0000.0000.000
127A128ILE0-0.0230.00428.507-0.006-0.0060.0000.0000.0000.000
128A129ARG10.8800.91531.418-0.040-0.0400.0000.0000.0000.000
129A130SER00.0170.02227.3960.0020.0020.0000.0000.0000.000
130A131GLY0-0.013-0.01925.884-0.009-0.0090.0000.0000.0000.000
131A132GLY00.0510.03725.756-0.011-0.0110.0000.0000.0000.000
132A133THR0-0.077-0.05020.1880.0090.0090.0000.0000.0000.000
133A134VAL0-0.019-0.00119.556-0.005-0.0050.0000.0000.0000.000
134A135VAL0-0.005-0.00619.292-0.007-0.0070.0000.0000.0000.000
135A136LEU0-0.015-0.00116.1250.0170.0170.0000.0000.0000.000
136A137GLY00.046-0.00119.409-0.029-0.0290.0000.0000.0000.000
137A138GLN0-0.028-0.02921.3880.0040.0040.0000.0000.0000.000
138A139ASP-1-0.794-0.90124.3150.0060.0060.0000.0000.0000.000
139A140PRO0-0.042-0.02224.124-0.008-0.0080.0000.0000.0000.000
140A141ASP-1-0.844-0.89326.586-0.006-0.0060.0000.0000.0000.000
141A142SER0-0.062-0.03128.743-0.005-0.0050.0000.0000.0000.000
142A143TYR0-0.076-0.02725.615-0.006-0.0060.0000.0000.0000.000
143A144VAL0-0.016-0.01229.2030.0050.0050.0000.0000.0000.000
144A145GLY0-0.035-0.01329.180-0.001-0.0010.0000.0000.0000.000
145A146SER0-0.090-0.05426.937-0.009-0.0090.0000.0000.0000.000
146A147PHE00.0000.00122.4950.0060.0060.0000.0000.0000.000
147A148ASP-1-0.815-0.90727.744-0.043-0.0430.0000.0000.0000.000
148A149VAL00.0140.00127.8460.0000.0000.0000.0000.0000.000
149A150ASP-1-0.925-0.95029.114-0.045-0.0450.0000.0000.0000.000
150A151GLN0-0.063-0.04029.7960.0040.0040.0000.0000.0000.000
151A152SER0-0.045-0.02924.8590.0030.0030.0000.0000.0000.000
152A153PHE0-0.040-0.01719.8830.0080.0080.0000.0000.0000.000
153A154VAL0-0.0110.00122.610-0.017-0.0170.0000.0000.0000.000
154A155GLY0-0.0020.01221.3320.0170.0170.0000.0000.0000.000
155A156GLU-1-0.903-0.94917.199-0.090-0.0900.0000.0000.0000.000
156A157ILE0-0.010-0.00616.5510.0260.0260.0000.0000.0000.000
157A158ALA00.0200.00513.992-0.018-0.0180.0000.0000.0000.000
158A159ASN0-0.014-0.01713.8930.0260.0260.0000.0000.0000.000
159A160LEU00.0010.01715.339-0.014-0.0140.0000.0000.0000.000
160A161GLN0-0.063-0.04015.5050.0530.0530.0000.0000.0000.000
161A162MET0-0.009-0.00518.815-0.046-0.0460.0000.0000.0000.000
162A163TRP00.0120.00021.3630.0260.0260.0000.0000.0000.000
163A164ASP-1-0.755-0.85124.1040.1820.1820.0000.0000.0000.000
164A165TYR0-0.012-0.00325.593-0.008-0.0080.0000.0000.0000.000
165A166VAL00.0110.02028.4280.0060.0060.0000.0000.0000.000
166A167LEU0-0.030-0.00125.0120.0000.0000.0000.0000.0000.000
167A168SER00.015-0.01029.563-0.013-0.0130.0000.0000.0000.000
168A169SER00.040-0.01330.4640.0040.0040.0000.0000.0000.000
169A170ALA0-0.0070.00430.7940.0020.0020.0000.0000.0000.000
170A171GLN00.0730.05227.409-0.004-0.0040.0000.0000.0000.000
171A172ILE00.0510.02326.3700.0140.0140.0000.0000.0000.000
172A173LYS10.9070.95026.053-0.093-0.0930.0000.0000.0000.000
173A174ALA00.0090.02225.8260.0020.0020.0000.0000.0000.000
174A175VAL0-0.0020.00020.7230.0160.0160.0000.0000.0000.000
175A176TYR0-0.079-0.05121.8500.0080.0080.0000.0000.0000.000
176A177TYR0-0.038-0.03223.316-0.008-0.0080.0000.0000.0000.000
177A178ASN0-0.022-0.00717.9650.0280.0280.0000.0000.0000.000
178A179GLN00.005-0.00521.425-0.004-0.0040.0000.0000.0000.000
179A180ASP-1-0.876-0.93521.4010.2740.2740.0000.0000.0000.000
180A181ASN0-0.048-0.02422.2830.0170.0170.0000.0000.0000.000
181A182ARG10.8550.94516.634-0.387-0.3870.0000.0000.0000.000
182A183VAL0-0.012-0.00622.0330.0170.0170.0000.0000.0000.000
183A184LYS10.8140.87014.327-0.666-0.6660.0000.0000.0000.000
184A185GLY00.0170.01018.822-0.026-0.0260.0000.0000.0000.000
185A186ASN0-0.050-0.05618.7020.0370.0370.0000.0000.0000.000
186A187VAL0-0.0150.00220.742-0.004-0.0040.0000.0000.0000.000
187A188PHE00.0690.02016.2140.0040.0040.0000.0000.0000.000
188A189ASP-1-0.698-0.81414.6620.6360.6360.0000.0000.0000.000
189A190TRP00.0350.01911.1120.1110.1110.0000.0000.0000.000
190A191ASP-1-0.839-0.9049.8480.9810.9810.0000.0000.0000.000
191A192THR0-0.083-0.0658.8510.5820.5820.0000.0000.0000.000
192A193ILE0-0.0280.01910.3370.0500.0500.0000.0000.0000.000
193A194GLU-1-0.928-0.9559.8600.7750.7750.0000.0000.0000.000
194A195TYR0-0.052-0.0465.940-0.108-0.1080.0000.0000.0000.000
195A196ASP-1-0.826-0.88810.119-0.334-0.3340.0000.0000.0000.000
196A197VAL0-0.050-0.01910.8680.0740.0740.0000.0000.0000.000
197A198THR0-0.0070.00712.822-0.029-0.0290.0000.0000.0000.000
198A199GLY00.0390.01215.9120.0280.0280.0000.0000.0000.000
199A200ASN0-0.048-0.03215.617-0.081-0.0810.0000.0000.0000.000
200A201VAL0-0.0070.00814.3670.0420.0420.0000.0000.0000.000
201A202LEU0-0.019-0.00312.390-0.085-0.0850.0000.0000.0000.000
202A203VAL00.0320.0187.0910.1130.1130.0000.0000.0000.000
203A204VAL0-0.035-0.0168.881-0.188-0.1880.0000.0000.0000.000
204A205PRO00.003-0.0138.1740.1090.1090.0000.0000.0000.000
205A206ASP-1-0.787-0.8569.8210.0950.0950.0000.0000.0000.000
206A207ASN0-0.058-0.01712.051-0.010-0.0100.0000.0000.0000.000