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: LNR79

Calculation Name: 4H86-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 4H86

Chain ID: A

ChEMBL ID:

UniProt ID: P38013

Base Structure: X-ray

Registration Date: 2023-09-23

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 187
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -1951987.771449
FMO2-HF: Nuclear repulsion 1880686.94831
FMO2-HF: Total energy -71300.823139
FMO2-MP2: Total energy -71507.664086


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:-10:GLY)


Summations of interaction energy for fragment #1(A:-10:GLY)
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.
0.1982.236-0.008-0.991-1.0390.003
Interaction energy analysis for fragmet #1(A:-10:GLY)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.043 / q_NPA : 0.017
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].
3A-8VAL00.0200.0043.710-0.7781.000-0.006-0.970-0.8020.003
4A-7PRO0-0.0050.0184.4240.4200.633-0.001-0.019-0.1920.000
5A-6ARG11.0020.9705.1811.2321.279-0.001-0.002-0.0450.000
6A-5GLY0-0.001-0.0038.516-0.059-0.0590.0000.0000.0000.000
7A-4SER0-0.0260.0128.6780.0250.0250.0000.0000.0000.000
8A-3HIS0-0.012-0.01610.4590.0910.0910.0000.0000.0000.000
9A-2MET00.0040.0049.594-0.160-0.1600.0000.0000.0000.000
10A-1ALA00.0200.02212.8230.0960.0960.0000.0000.0000.000
11A0SER0-0.017-0.00615.700-0.029-0.0290.0000.0000.0000.000
12A1MET0-0.0180.00117.3150.0220.0220.0000.0000.0000.000
13A2SER00.0080.00220.5670.0130.0130.0000.0000.0000.000
14A3ASP-1-0.874-0.95623.001-0.111-0.1110.0000.0000.0000.000
15A4LEU0-0.018-0.01124.5580.0150.0150.0000.0000.0000.000
16A5VAL0-0.0010.00125.4280.0090.0090.0000.0000.0000.000
17A6ASN0-0.052-0.03127.2900.0110.0110.0000.0000.0000.000
18A7LYS10.8480.94527.7350.1190.1190.0000.0000.0000.000
19A8LYS10.9600.97032.3090.0580.0580.0000.0000.0000.000
20A9PHE00.0400.02234.144-0.002-0.0020.0000.0000.0000.000
21A10PRO0-0.0120.00632.7040.0080.0080.0000.0000.0000.000
22A11ALA00.000-0.00835.961-0.001-0.0010.0000.0000.0000.000
23A12GLY0-0.006-0.00238.7720.0010.0010.0000.0000.0000.000
24A13ASP-1-0.900-0.94540.632-0.054-0.0540.0000.0000.0000.000
25A14TYR0-0.043-0.01837.5300.0010.0010.0000.0000.0000.000
26A15LYS10.9170.94641.3300.0580.0580.0000.0000.0000.000
27A16PHE0-0.0050.01640.417-0.003-0.0030.0000.0000.0000.000
28A17GLN0-0.003-0.00942.4500.0020.0020.0000.0000.0000.000
29A18TYR00.0230.00943.337-0.006-0.0060.0000.0000.0000.000
30A19ILE00.0050.01545.2380.0040.0040.0000.0000.0000.000
31A20ALA00.0030.01847.165-0.004-0.0040.0000.0000.0000.000
32A21ILE0-0.025-0.03345.6070.0010.0010.0000.0000.0000.000
33A22SER00.038-0.01349.541-0.002-0.0020.0000.0000.0000.000
34A23GLN0-0.048-0.04250.5840.0020.0020.0000.0000.0000.000
35A24SER0-0.0160.00153.7560.0020.0020.0000.0000.0000.000
36A25ASP-1-0.866-0.91256.332-0.055-0.0550.0000.0000.0000.000
37A26ALA0-0.010-0.00154.519-0.001-0.0010.0000.0000.0000.000
38A27ASP-1-0.923-0.97355.513-0.059-0.0590.0000.0000.0000.000
39A28SER00.0020.02056.4650.0020.0020.0000.0000.0000.000
40A29GLU-1-0.854-0.94956.581-0.053-0.0530.0000.0000.0000.000
41A30SER0-0.052-0.02353.758-0.002-0.0020.0000.0000.0000.000
42A31CYS0-0.037-0.00851.976-0.004-0.0040.0000.0000.0000.000
43A32LYS10.8500.94052.4090.0570.0570.0000.0000.0000.000
44A33MET00.0110.00052.430-0.002-0.0020.0000.0000.0000.000
45A34PRO0-0.042-0.01048.115-0.001-0.0010.0000.0000.0000.000
46A35GLN00.0090.01148.6440.0040.0040.0000.0000.0000.000
47A36THR0-0.021-0.02946.585-0.004-0.0040.0000.0000.0000.000
48A37VAL00.0010.00544.2990.0030.0030.0000.0000.0000.000
49A38GLU-1-0.928-0.96644.281-0.061-0.0610.0000.0000.0000.000
50A39TRP00.0620.01236.872-0.002-0.0020.0000.0000.0000.000
51A40SER00.015-0.00341.388-0.003-0.0030.0000.0000.0000.000
52A41LYS10.9810.99542.8380.0570.0570.0000.0000.0000.000
53A42LEU00.0420.02839.8380.0000.0000.0000.0000.0000.000
54A43ILE0-0.0090.00337.640-0.001-0.0010.0000.0000.0000.000
55A44SER0-0.098-0.04141.2950.0020.0020.0000.0000.0000.000
56A45GLU-1-0.958-0.98344.290-0.064-0.0640.0000.0000.0000.000
57A46ASN0-0.060-0.03842.2390.0000.0000.0000.0000.0000.000
58A47LYS10.9240.96241.5810.0810.0810.0000.0000.0000.000
59A48LYS10.9010.95936.2020.1180.1180.0000.0000.0000.000
60A49VAL00.0020.00736.6760.0010.0010.0000.0000.0000.000
61A50ILE00.0070.01532.330-0.007-0.0070.0000.0000.0000.000
62A51ILE0-0.027-0.01132.8240.0080.0080.0000.0000.0000.000
63A52THR0-0.038-0.03329.402-0.016-0.0160.0000.0000.0000.000
64A53GLY00.0520.04129.9020.0130.0130.0000.0000.0000.000
65A54ALA00.015-0.02629.513-0.020-0.0200.0000.0000.0000.000
66A55PRO0-0.060-0.03228.0270.0110.0110.0000.0000.0000.000
67A56ALA00.0610.00830.9740.0090.0090.0000.0000.0000.000
68A57ALA00.0440.02334.077-0.008-0.0080.0000.0000.0000.000
69A58PHE0-0.030-0.02836.8960.0040.0040.0000.0000.0000.000
70A59SER0-0.0370.00631.902-0.006-0.0060.0000.0000.0000.000
71A60PRO00.0640.01530.315-0.003-0.0030.0000.0000.0000.000
72A61THR00.016-0.01025.8650.0040.0040.0000.0000.0000.000
73A62CYS0-0.0560.02529.101-0.008-0.0080.0000.0000.0000.000
74A63THR00.002-0.00231.3100.0050.0050.0000.0000.0000.000
75A64VAL0-0.006-0.00631.4500.0050.0050.0000.0000.0000.000
76A65SER0-0.028-0.01827.551-0.006-0.0060.0000.0000.0000.000
77A66HIS0-0.0140.02328.576-0.009-0.0090.0000.0000.0000.000
78A67ILE00.006-0.00329.8860.0020.0020.0000.0000.0000.000
79A68PRO00.0220.01432.7860.0060.0060.0000.0000.0000.000
80A69GLY00.0430.02532.0800.0060.0060.0000.0000.0000.000
81A70TYR0-0.022-0.05428.8330.0080.0080.0000.0000.0000.000
82A71ILE0-0.025-0.00734.6360.0080.0080.0000.0000.0000.000
83A72ASN0-0.054-0.02235.0990.0140.0140.0000.0000.0000.000
84A73TYR00.0110.00531.7210.0050.0050.0000.0000.0000.000
85A74LEU0-0.0040.01436.8060.0030.0030.0000.0000.0000.000
86A75ASP-1-0.895-0.95539.234-0.103-0.1030.0000.0000.0000.000
87A76GLU-1-0.935-0.96236.124-0.150-0.1500.0000.0000.0000.000
88A77LEU0-0.024-0.02934.0850.0010.0010.0000.0000.0000.000
89A78VAL0-0.022-0.00738.1260.0030.0030.0000.0000.0000.000
90A79LYS10.8930.93941.6280.1000.1000.0000.0000.0000.000
91A80GLU-1-0.918-0.95339.319-0.105-0.1050.0000.0000.0000.000
92A81LYS10.8510.94434.3900.1500.1500.0000.0000.0000.000
93A82GLU-1-0.942-0.95938.242-0.097-0.0970.0000.0000.0000.000
94A83VAL0-0.042-0.01936.4430.0000.0000.0000.0000.0000.000
95A84ASP-1-0.819-0.91139.474-0.091-0.0910.0000.0000.0000.000
96A85GLN0-0.050-0.02740.2510.0020.0020.0000.0000.0000.000
97A86VAL00.0260.02135.673-0.007-0.0070.0000.0000.0000.000
98A87ILE0-0.035-0.02736.6710.0060.0060.0000.0000.0000.000
99A88VAL00.0260.01534.513-0.010-0.0100.0000.0000.0000.000
100A89VAL0-0.007-0.00733.8060.0100.0100.0000.0000.0000.000
101A90THR00.0180.01933.859-0.008-0.0080.0000.0000.0000.000
102A91VAL00.0150.00734.5580.0060.0060.0000.0000.0000.000
103A92ASP-1-0.854-0.90837.176-0.115-0.1150.0000.0000.0000.000
104A93ASN00.0250.01739.5590.0030.0030.0000.0000.0000.000
105A94PRO00.0840.02843.039-0.003-0.0030.0000.0000.0000.000
106A95PHE00.0320.00644.664-0.001-0.0010.0000.0000.0000.000
107A96ALA0-0.033-0.01442.381-0.001-0.0010.0000.0000.0000.000
108A97ASN00.0560.01839.355-0.007-0.0070.0000.0000.0000.000
109A98GLN0-0.045-0.01541.950-0.003-0.0030.0000.0000.0000.000
110A99ALA00.000-0.00844.914-0.001-0.0010.0000.0000.0000.000
111A100TRP00.0070.00834.333-0.002-0.0020.0000.0000.0000.000
112A101ALA00.0570.04341.175-0.004-0.0040.0000.0000.0000.000
113A102LYS10.9290.96042.1440.0770.0770.0000.0000.0000.000
114A103SER0-0.134-0.07641.504-0.001-0.0010.0000.0000.0000.000
115A104LEU00.000-0.00337.097-0.003-0.0030.0000.0000.0000.000
116A105GLY0-0.025-0.00440.854-0.003-0.0030.0000.0000.0000.000
117A106VAL0-0.0050.00441.6480.0020.0020.0000.0000.0000.000
118A107LYS10.9110.94944.1520.0950.0950.0000.0000.0000.000
119A108ASP-1-0.765-0.83946.523-0.076-0.0760.0000.0000.0000.000
120A109THR00.0100.01744.788-0.003-0.0030.0000.0000.0000.000
121A110THR0-0.074-0.07745.9560.0000.0000.0000.0000.0000.000
122A111HIS0-0.003-0.01442.7150.0030.0030.0000.0000.0000.000
123A112ILE00.0110.02438.269-0.006-0.0060.0000.0000.0000.000
124A113LYS10.8240.90040.6550.0950.0950.0000.0000.0000.000
125A114PHE00.0190.00038.142-0.006-0.0060.0000.0000.0000.000
126A115ALA0-0.011-0.00138.6430.0060.0060.0000.0000.0000.000
127A116SER0-0.015-0.02338.792-0.005-0.0050.0000.0000.0000.000
128A117ASP-1-0.760-0.88635.617-0.100-0.1000.0000.0000.0000.000
129A118PRO00.0280.00338.056-0.003-0.0030.0000.0000.0000.000
130A119GLY0-0.002-0.00738.6920.0020.0020.0000.0000.0000.000
131A120CYS0-0.088-0.02232.242-0.003-0.0030.0000.0000.0000.000
132A121ALA0-0.0030.01034.606-0.003-0.0030.0000.0000.0000.000
133A122PHE00.0270.00333.8870.0000.0000.0000.0000.0000.000
134A123THR0-0.021-0.01030.321-0.005-0.0050.0000.0000.0000.000
135A124LYS10.9190.95030.6120.0800.0800.0000.0000.0000.000
136A125SER0-0.119-0.05331.0030.0010.0010.0000.0000.0000.000
137A126ILE0-0.026-0.01329.3940.0030.0030.0000.0000.0000.000
138A127GLY00.0080.01926.933-0.010-0.0100.0000.0000.0000.000
139A128PHE0-0.069-0.04624.315-0.023-0.0230.0000.0000.0000.000
140A129GLU-1-0.873-0.95027.078-0.144-0.1440.0000.0000.0000.000
141A130LEU0-0.041-0.02425.055-0.018-0.0180.0000.0000.0000.000
142A131ALA0-0.030-0.01627.0060.0120.0120.0000.0000.0000.000
143A132VAL0-0.018-0.01427.954-0.011-0.0110.0000.0000.0000.000
144A133GLY00.0140.01530.4430.0030.0030.0000.0000.0000.000
145A134ASP-1-0.912-0.96232.122-0.070-0.0700.0000.0000.0000.000
146A135GLY0-0.037-0.01633.7360.0040.0040.0000.0000.0000.000
147A136VAL0-0.0210.00234.5860.0000.0000.0000.0000.0000.000
148A137TYR0-0.007-0.01829.446-0.003-0.0030.0000.0000.0000.000
149A138TRP00.0200.01230.9400.0010.0010.0000.0000.0000.000
150A139SER00.0510.00929.9410.0000.0000.0000.0000.0000.000
151A140GLY00.0330.01926.358-0.005-0.0050.0000.0000.0000.000
152A141ARG10.7850.85924.9740.2620.2620.0000.0000.0000.000
153A142TRP0-0.008-0.00624.657-0.029-0.0290.0000.0000.0000.000
154A143ALA00.0080.02926.2090.0130.0130.0000.0000.0000.000
155A144MET0-0.031-0.01827.196-0.004-0.0040.0000.0000.0000.000
156A145VAL00.0290.02629.6730.0040.0040.0000.0000.0000.000
157A146VAL0-0.029-0.01631.8670.0020.0020.0000.0000.0000.000
158A147GLU-1-0.823-0.92333.633-0.129-0.1290.0000.0000.0000.000
159A148ASN0-0.023-0.01736.7300.0060.0060.0000.0000.0000.000
160A149GLY00.0300.01138.6910.0040.0040.0000.0000.0000.000
161A150ILE0-0.060-0.03033.0960.0030.0030.0000.0000.0000.000
162A151VAL00.0190.01529.227-0.005-0.0050.0000.0000.0000.000
163A152THR0-0.011-0.00530.168-0.002-0.0020.0000.0000.0000.000
164A153TYR0-0.023-0.03523.451-0.021-0.0210.0000.0000.0000.000
165A154ALA00.0190.00025.4810.0140.0140.0000.0000.0000.000
166A155ALA00.0270.02421.389-0.012-0.0120.0000.0000.0000.000
167A156LYS10.9930.99820.8240.2630.2630.0000.0000.0000.000
168A157GLU-1-0.740-0.82720.221-0.436-0.4360.0000.0000.0000.000
169A158THR0-0.024-0.02015.3360.0150.0150.0000.0000.0000.000
170A159ASN0-0.026-0.00415.9450.0810.0810.0000.0000.0000.000
171A160PRO00.0360.02920.0400.0020.0020.0000.0000.0000.000
172A161GLY00.0020.00123.5920.0150.0150.0000.0000.0000.000
173A162THR0-0.030-0.01220.3370.0240.0240.0000.0000.0000.000
174A163ASP-1-0.857-0.91818.224-0.538-0.5380.0000.0000.0000.000
175A164VAL0-0.029-0.03021.5870.0340.0340.0000.0000.0000.000
176A165THR00.003-0.01518.624-0.018-0.0180.0000.0000.0000.000
177A166VAL0-0.0100.00819.2770.0320.0320.0000.0000.0000.000
178A167SER0-0.039-0.03722.0540.0400.0400.0000.0000.0000.000
179A168SER00.0080.01224.2730.0330.0330.0000.0000.0000.000
180A169VAL00.0570.02926.5120.0020.0020.0000.0000.0000.000
181A170GLU-1-0.869-0.94026.125-0.252-0.2520.0000.0000.0000.000
182A171SER0-0.035-0.02222.800-0.007-0.0070.0000.0000.0000.000
183A172VAL00.0050.01425.2490.0080.0080.0000.0000.0000.000
184A173LEU00.0250.01528.3650.0120.0120.0000.0000.0000.000
185A174ALA0-0.073-0.02425.4760.0100.0100.0000.0000.0000.000
186A175HIS10.7640.86322.9200.2780.2780.0000.0000.0000.000
187A176LEU00.0250.03628.1180.0160.0160.0000.0000.0000.000