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: GYYN1

Calculation Name: 3LB9-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3LB9

Chain ID: A

ChEMBL ID:

UniProt ID: P09850

Base Structure: X-ray

Registration Date: 2023-09-27

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 182
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -1973212.666225
FMO2-HF: Nuclear repulsion 1903722.422694
FMO2-HF: Total energy -69490.243531
FMO2-MP2: Total energy -69696.605604


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:2:ALA)


Summations of interaction energy for fragment #1(A:2:ALA)
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.
-10.561-8.18611.36-5.663-8.07-0.027
Interaction energy analysis for fragmet #1(A:2:ALA)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.014 / q_NPA : 0.001
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].
3A4PHE0-0.070-0.0242.755-0.8581.2730.117-0.873-1.3750.003
4A5THR00.0180.0085.9460.1770.1770.0000.0000.0000.000
5A6GLN0-0.014-0.0079.2630.0110.0110.0000.0000.0000.000
6A7TYR0-0.039-0.04611.2410.1130.1130.0000.0000.0000.000
7A8TRP00.0250.00413.547-0.003-0.0030.0000.0000.0000.000
8A9SER0-0.023-0.01717.4490.0310.0310.0000.0000.0000.000
9A10VAL00.0050.00620.335-0.007-0.0070.0000.0000.0000.000
10A11ARG10.9771.02422.8520.1350.1350.0000.0000.0000.000
11A12GLN0-0.063-0.05026.5030.0020.0020.0000.0000.0000.000
12A13SER0-0.014-0.01228.8660.0060.0060.0000.0000.0000.000
13A14LYS10.8600.94127.7890.1050.1050.0000.0000.0000.000
14A15ARG10.8440.91027.8890.1470.1470.0000.0000.0000.000
15A16PRO0-0.013-0.01030.558-0.002-0.0020.0000.0000.0000.000
16A17THR0-0.031-0.01629.673-0.007-0.0070.0000.0000.0000.000
17A18GLY00.0560.02832.6990.0050.0050.0000.0000.0000.000
18A19SER0-0.0320.00035.1020.0040.0040.0000.0000.0000.000
19A20ASN00.016-0.00633.261-0.010-0.0100.0000.0000.0000.000
20A21ALA0-0.0150.00429.9720.0050.0050.0000.0000.0000.000
21A22THR00.026-0.01229.861-0.004-0.0040.0000.0000.0000.000
22A23ILE0-0.033-0.01823.6370.0010.0010.0000.0000.0000.000
23A24THR00.000-0.02026.257-0.008-0.0080.0000.0000.0000.000
24A25PHE00.0070.00118.082-0.001-0.0010.0000.0000.0000.000
25A26THR00.0520.02023.481-0.004-0.0040.0000.0000.0000.000
26A27ASN0-0.002-0.00625.5320.0070.0070.0000.0000.0000.000
27A28HIS00.0190.01721.750-0.004-0.0040.0000.0000.0000.000
28A29VAL00.0010.01520.070-0.006-0.0060.0000.0000.0000.000
29A30ASN00.001-0.01221.9650.0020.0020.0000.0000.0000.000
30A31ALA00.0190.02224.2980.0080.0080.0000.0000.0000.000
31A32TRP00.008-0.00917.149-0.006-0.0060.0000.0000.0000.000
32A33LYS10.9460.97621.0270.1680.1680.0000.0000.0000.000
33A34SER0-0.081-0.03322.2120.0130.0130.0000.0000.0000.000
34A35HIS10.8770.93622.1010.1350.1350.0000.0000.0000.000
35A36GLY00.0390.02320.653-0.002-0.0020.0000.0000.0000.000
36A37MET0-0.091-0.02517.044-0.007-0.0070.0000.0000.0000.000
37A38ASN00.0220.00916.4860.0080.0080.0000.0000.0000.000
38A39LEU00.0230.02214.210-0.029-0.0290.0000.0000.0000.000
39A40GLY0-0.001-0.00112.6970.0340.0340.0000.0000.0000.000
40A41SER0-0.012-0.02013.6300.0050.0050.0000.0000.0000.000
41A42ASN0-0.0200.00212.987-0.015-0.0150.0000.0000.0000.000
42A43TRP00.0630.03513.520-0.074-0.0740.0000.0000.0000.000
43A44ALA0-0.040-0.01211.9840.0180.0180.0000.0000.0000.000
44A45TYR00.0920.05211.2090.0790.0790.0000.0000.0000.000
45A46GLN00.0040.00015.461-0.012-0.0120.0000.0000.0000.000
46A47VAL0-0.0040.00717.1550.0380.0380.0000.0000.0000.000
47A48MET0-0.0100.03419.486-0.020-0.0200.0000.0000.0000.000
48A49ALA0-0.018-0.01518.1220.0150.0150.0000.0000.0000.000
49A50THR0-0.035-0.01720.2130.0230.0230.0000.0000.0000.000
50A51GLU-1-0.874-0.92714.411-0.472-0.4720.0000.0000.0000.000
51A52GLY00.0230.02017.3770.0390.0390.0000.0000.0000.000
52A53TYR0-0.011-0.02913.495-0.036-0.0360.0000.0000.0000.000
53A54GLN00.0080.00217.2920.0160.0160.0000.0000.0000.000
54A55SER0-0.058-0.02019.6370.0110.0110.0000.0000.0000.000
55A56SER00.0270.02422.597-0.002-0.0020.0000.0000.0000.000
56A57GLY0-0.032-0.00725.2980.0030.0030.0000.0000.0000.000
57A58SER0-0.034-0.00827.1660.0030.0030.0000.0000.0000.000
58A59SER0-0.007-0.00325.0010.0030.0030.0000.0000.0000.000
59A60ASN00.0180.00128.0530.0000.0000.0000.0000.0000.000
60A61VAL00.0210.01725.5700.0060.0060.0000.0000.0000.000
61A62THR00.0250.01728.2960.0020.0020.0000.0000.0000.000
62A63VAL0-0.030-0.02024.9550.0010.0010.0000.0000.0000.000
63A64TRP0-0.019-0.00228.3650.0000.0000.0000.0000.0000.000
64A65GLY00.045-0.00329.925-0.006-0.0060.0000.0000.0000.000
65A66ALA00.0040.00230.9850.0020.0020.0000.0000.0000.000
66A67SER0-0.014-0.01528.6900.0010.0010.0000.0000.0000.000
67A68THR0-0.043-0.00125.967-0.007-0.0070.0000.0000.0000.000
68A69ASP-1-0.782-0.86523.837-0.200-0.2000.0000.0000.0000.000
69A70TYR0-0.019-0.00515.8880.0060.0060.0000.0000.0000.000
70A71TRP00.032-0.00721.6840.0020.0020.0000.0000.0000.000
71A72GLN0-0.0030.01314.879-0.018-0.0180.0000.0000.0000.000
72A73ASN00.012-0.01218.3230.0130.0130.0000.0000.0000.000
73A74TRP00.0290.01510.505-0.019-0.0190.0000.0000.0000.000
74A75THR00.034-0.01115.1640.0200.0200.0000.0000.0000.000
75A76ASP-1-0.887-0.91811.966-0.252-0.2520.0000.0000.0000.000
76A77GLY0-0.0070.00213.6210.0490.0490.0000.0000.0000.000
77A78GLY00.0200.01816.9180.0330.0330.0000.0000.0000.000
78A79GLY0-0.006-0.01317.9290.0210.0210.0000.0000.0000.000
79A80ILE0-0.043-0.01321.032-0.011-0.0110.0000.0000.0000.000
80A81VAL00.031-0.00519.441-0.004-0.0040.0000.0000.0000.000
81A82ASN0-0.053-0.01722.917-0.002-0.0020.0000.0000.0000.000
82A83ALA00.0200.01422.891-0.001-0.0010.0000.0000.0000.000
83A84VAL00.0130.01224.9730.0010.0010.0000.0000.0000.000
84A85ASN00.0210.00026.100-0.008-0.0080.0000.0000.0000.000
85A86GLY00.0370.01827.5150.0090.0090.0000.0000.0000.000
86A87SER00.0100.00630.228-0.003-0.0030.0000.0000.0000.000
87A88GLY00.008-0.00531.8650.0020.0020.0000.0000.0000.000
88A89GLY00.0790.02828.298-0.008-0.0080.0000.0000.0000.000
89A90ASN0-0.082-0.05828.116-0.007-0.0070.0000.0000.0000.000
90A91TYR00.001-0.00423.264-0.006-0.0060.0000.0000.0000.000
91A92SER00.0180.01728.0590.0040.0040.0000.0000.0000.000
92A93VAL0-0.003-0.00722.734-0.008-0.0080.0000.0000.0000.000
93A94ASN0-0.006-0.00526.1050.0050.0050.0000.0000.0000.000
94A95TRP0-0.0020.01222.2690.0000.0000.0000.0000.0000.000
95A96SER0-0.002-0.02224.0520.0100.0100.0000.0000.0000.000
96A97ASN00.013-0.00622.9360.0010.0010.0000.0000.0000.000
97A98THR00.0220.03119.0590.0110.0110.0000.0000.0000.000
98A99GLY00.0100.01116.0620.0200.0200.0000.0000.0000.000
99A100ASN0-0.110-0.05911.312-0.109-0.1090.0000.0000.0000.000
100A101PHE0-0.012-0.00114.3530.0010.0010.0000.0000.0000.000
101A102VAL00.0360.02713.2910.0050.0050.0000.0000.0000.000
102A103VAL00.0100.00416.4850.0060.0060.0000.0000.0000.000
103A104GLY00.0270.01219.7660.0110.0110.0000.0000.0000.000
104A105LYS10.8270.95120.9050.1490.1490.0000.0000.0000.000
105A106GLY0-0.028-0.03021.5990.0010.0010.0000.0000.0000.000
106A107TRP0-0.051-0.03320.7330.0170.0170.0000.0000.0000.000
107A108THR0-0.008-0.03619.331-0.040-0.0400.0000.0000.0000.000
108A109THR0-0.029-0.00818.052-0.022-0.0220.0000.0000.0000.000
109A110GLY0-0.034-0.01717.7090.0220.0220.0000.0000.0000.000
110A111SER00.019-0.00118.8440.0140.0140.0000.0000.0000.000
111A112PRO00.0270.00720.473-0.006-0.0060.0000.0000.0000.000
112A113PHE00.007-0.01821.7840.0090.0090.0000.0000.0000.000
113A114ARG10.8470.94921.9610.2240.2240.0000.0000.0000.000
114A115THR00.003-0.01124.9400.0040.0040.0000.0000.0000.000
115A116ILE0-0.023-0.00123.0290.0000.0000.0000.0000.0000.000
116A117ASN00.0500.04027.3210.0040.0040.0000.0000.0000.000
117A118TYR0-0.016-0.05027.100-0.003-0.0030.0000.0000.0000.000
118A119ASN00.0130.02029.5740.0090.0090.0000.0000.0000.000
119A120ALA0-0.018-0.01228.699-0.001-0.0010.0000.0000.0000.000
120A121GLY00.0130.01830.4100.0070.0070.0000.0000.0000.000
121A122VAL0-0.003-0.00831.2770.0070.0070.0000.0000.0000.000
122A123TRP0-0.041-0.01823.046-0.011-0.0110.0000.0000.0000.000
123A124ALA00.0010.00229.3100.0060.0060.0000.0000.0000.000
124A125PRO0-0.031-0.00225.0970.0010.0010.0000.0000.0000.000
125A126ASN0-0.013-0.01926.6710.0090.0090.0000.0000.0000.000
126A127GLY00.1170.03624.2050.0060.0060.0000.0000.0000.000
127A128ASN0-0.0110.00217.8270.0090.0090.0000.0000.0000.000
128A129GLY00.0720.03120.473-0.009-0.0090.0000.0000.0000.000
129A130TYR0-0.034-0.02615.8860.0360.0360.0000.0000.0000.000
130A131LEU00.0190.02320.979-0.010-0.0100.0000.0000.0000.000
131A132THR00.005-0.02417.6220.0140.0140.0000.0000.0000.000
132A133LEU00.0080.00318.863-0.004-0.0040.0000.0000.0000.000
133A134TYR0-0.072-0.06410.5690.0000.0000.0000.0000.0000.000
134A135GLY00.0660.02914.1310.0480.0480.0000.0000.0000.000
135A136TRP00.0250.0185.051-0.015-0.0150.0000.0000.0000.000
136A137THR0-0.0060.00710.3210.1160.1160.0000.0000.0000.000
137A138ARG10.8950.9299.1430.4120.4120.0000.0000.0000.000
138A139SER00.0010.0359.5730.0470.0470.0000.0000.0000.000
139A140PRO00.0700.0399.5290.0420.0420.0000.0000.0000.000
140A141LEU00.002-0.0223.207-0.2400.0950.087-0.093-0.3280.000
141A142ILE0-0.034-0.0147.329-0.099-0.0990.0000.0000.0000.000
142A143GLU-1-0.687-0.7638.134-1.159-1.1590.0000.0000.0000.000
143A144TYR0-0.022-0.0209.9570.0930.0930.0000.0000.0000.000
144A145TYR0-0.004-0.02811.5550.0490.0490.0000.0000.0000.000
145A146VAL0-0.049-0.03016.4270.0330.0330.0000.0000.0000.000
146A147VAL00.0210.01819.2380.0070.0070.0000.0000.0000.000
147A148ASP-1-0.705-0.79021.730-0.147-0.1470.0000.0000.0000.000
148A149SER00.012-0.01224.5380.0200.0200.0000.0000.0000.000
149A150TRP00.0710.02623.210-0.022-0.0220.0000.0000.0000.000
150A151GLY00.0230.02523.9460.0130.0130.0000.0000.0000.000
151A152THR0-0.063-0.05624.4420.0070.0070.0000.0000.0000.000
152A153TYR00.0220.01518.1720.0020.0020.0000.0000.0000.000
153A154ARG10.7600.88522.4070.1140.1140.0000.0000.0000.000
154A155PRO00.0240.00117.8370.0120.0120.0000.0000.0000.000
155A156THR0-0.040-0.00819.4080.0080.0080.0000.0000.0000.000
156A157GLY00.0550.01017.743-0.029-0.0290.0000.0000.0000.000
157A158THR0-0.053-0.01517.6740.0330.0330.0000.0000.0000.000
158A159TYR00.0110.00419.711-0.021-0.0210.0000.0000.0000.000
159A160LYS10.9260.94718.1610.1720.1720.0000.0000.0000.000
160A161GLY0-0.0030.01423.0420.0090.0090.0000.0000.0000.000
161A162THR0-0.009-0.00625.275-0.007-0.0070.0000.0000.0000.000
162A163VAL0-0.019-0.01224.7590.0040.0040.0000.0000.0000.000
163A164LYS10.9050.96627.9030.0960.0960.0000.0000.0000.000
164A165SER00.017-0.02927.9910.0010.0010.0000.0000.0000.000
165A166ASP-1-0.777-0.84328.833-0.139-0.1390.0000.0000.0000.000
166A167GLY00.0200.01031.9400.0000.0000.0000.0000.0000.000
167A168GLY0-0.022-0.02230.8090.0040.0040.0000.0000.0000.000
168A169THR0-0.016-0.00129.731-0.005-0.0050.0000.0000.0000.000
169A170TYR0-0.079-0.06524.1710.0020.0020.0000.0000.0000.000
170A171ASP-1-0.752-0.86124.504-0.107-0.1070.0000.0000.0000.000
171A172ILE0-0.041-0.02120.501-0.017-0.0170.0000.0000.0000.000
172A173TYR00.0310.00418.4600.0230.0230.0000.0000.0000.000
173A174THR00.0240.01814.950-0.016-0.0160.0000.0000.0000.000
174A175THR00.003-0.00512.3200.0730.0730.0000.0000.0000.000
175A176THR00.002-0.0028.743-0.111-0.1110.0000.0000.0000.000
176A177ARG10.8930.9516.3381.2521.2520.0000.0000.0000.000
177A178TYR00.026-0.0025.288-0.871-0.868-0.001-0.0170.0150.000
178A179ASN0-0.014-0.0032.5920.1240.8112.720-1.804-1.6030.012
179A180ALA0-0.011-0.0062.485-1.616-1.8511.4000.407-1.5710.000
180A181PRO00.0100.0042.066-8.270-9.1207.035-3.168-3.016-0.041
181A182SER0-0.013-0.0203.846-0.407-0.1030.002-0.115-0.192-0.001
182A183ILE0-0.0100.0136.6300.1250.1250.0000.0000.0000.000