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: YNZ82

Calculation Name: 5LSB-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 5LSB

Chain ID: A

ChEMBL ID:

UniProt ID: Q02554

Base Structure: X-ray

Registration Date: 2023-09-26

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 179
LigandCharge DGL=-1
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -1885704.543044
FMO2-HF: Nuclear repulsion 1814169.256954
FMO2-HF: Total energy -71535.28609
FMO2-MP2: Total energy -71748.93978


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:8:GLY)


Summations of interaction energy for fragment #1(A:8: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.
-3.3480.6340.731-2.127-2.5870.001
Interaction energy analysis for fragmet #1(A:8:GLY)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.016 / q_NPA : -0.007
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].
3A10THR0-0.005-0.0032.648-2.3950.0250.248-1.255-1.4130.005
4A11VAL0-0.024-0.0163.224-2.701-1.8450.042-0.527-0.372-0.004
5A12TYR00.0150.0196.0700.3240.3240.0000.0000.0000.000
6A13VAL00.014-0.0038.942-0.122-0.1220.0000.0000.0000.000
7A14GLY00.0370.00612.3770.0590.0590.0000.0000.0000.000
8A15ASN0-0.043-0.03515.554-0.007-0.0070.0000.0000.0000.000
9A16ILE00.0180.02115.599-0.005-0.0050.0000.0000.0000.000
10A17ASP-1-0.769-0.86619.888-0.009-0.0090.0000.0000.0000.000
11A18PRO00.024-0.00423.1530.0020.0020.0000.0000.0000.000
12A19ARG10.8360.89924.1440.0220.0220.0000.0000.0000.000
13A20ILE0-0.0060.01720.639-0.002-0.0020.0000.0000.0000.000
14A21THR00.0540.02922.7920.0100.0100.0000.0000.0000.000
15A22LYS10.9210.94116.641-0.179-0.1790.0000.0000.0000.000
16A23GLU-1-0.917-0.94819.2680.0140.0140.0000.0000.0000.000
17A24GLN00.1100.05321.185-0.009-0.0090.0000.0000.0000.000
18A25LEU0-0.049-0.01616.092-0.015-0.0150.0000.0000.0000.000
19A26TYR0-0.024-0.02416.093-0.026-0.0260.0000.0000.0000.000
20A27GLU-1-0.912-0.95417.880-0.057-0.0570.0000.0000.0000.000
21A28LEU0-0.0090.00417.858-0.015-0.0150.0000.0000.0000.000
22A29PHE0-0.003-0.02812.788-0.025-0.0250.0000.0000.0000.000
23A30ILE00.0030.00415.543-0.040-0.0400.0000.0000.0000.000
24A31GLN0-0.075-0.02717.519-0.009-0.0090.0000.0000.0000.000
25A32ILE0-0.089-0.03014.244-0.019-0.0190.0000.0000.0000.000
26A33ASN00.011-0.01411.9050.0010.0010.0000.0000.0000.000
27A34PRO00.0160.02813.4700.0380.0380.0000.0000.0000.000
28A35VAL00.005-0.00312.360-0.027-0.0270.0000.0000.0000.000
29A36LEU0-0.040-0.0089.9690.0220.0220.0000.0000.0000.000
30A37ARG10.8470.90010.698-0.572-0.5720.0000.0000.0000.000
31A38ILE00.0490.03011.7350.0020.0020.0000.0000.0000.000
32A39LYS10.9100.95511.904-0.359-0.3590.0000.0000.0000.000
33A40TYR0-0.001-0.02413.454-0.009-0.0090.0000.0000.0000.000
34A41PRO0-0.054-0.01714.9560.0030.0030.0000.0000.0000.000
35A42LYS10.9260.96118.039-0.082-0.0820.0000.0000.0000.000
36A43ASP-1-0.726-0.85121.8450.0800.0800.0000.0000.0000.000
37A44LYS10.8080.88822.109-0.123-0.1230.0000.0000.0000.000
38A45VAL00.0170.01927.040-0.003-0.0030.0000.0000.0000.000
39A46LEU00.0220.00027.193-0.005-0.0050.0000.0000.0000.000
40A47GLN0-0.045-0.01327.306-0.002-0.0020.0000.0000.0000.000
41A48ALA00.0400.04026.043-0.002-0.0020.0000.0000.0000.000
42A49TYR0-0.028-0.02720.6760.0150.0150.0000.0000.0000.000
43A50GLN0-0.069-0.05519.0980.0050.0050.0000.0000.0000.000
44A51GLY00.0340.02619.933-0.004-0.0040.0000.0000.0000.000
45A52TYR0-0.086-0.03913.549-0.011-0.0110.0000.0000.0000.000
46A53ALA0-0.011-0.01513.6240.0280.0280.0000.0000.0000.000
47A54PHE0-0.014-0.0027.398-0.023-0.0230.0000.0000.0000.000
48A55ILE0-0.0050.0038.7760.0540.0540.0000.0000.0000.000
49A56GLU-1-0.786-0.8697.0480.9720.9720.0000.0000.0000.000
50A57PHE00.0200.0077.551-0.090-0.0900.0000.0000.0000.000
51A58TYR00.0550.0228.2250.1720.1720.0000.0000.0000.000
52A59ASN0-0.028-0.0166.811-0.040-0.0400.0000.0000.0000.000
53A60GLN0-0.001-0.0112.656-0.685-0.3760.442-0.281-0.4700.000
54A61GLY00.0580.0285.071-0.0320.024-0.001-0.007-0.0480.000
55A62ASP-1-0.801-0.9038.440-0.467-0.4670.0000.0000.0000.000
56A63ALA00.0300.0205.3660.1590.196-0.001-0.010-0.0260.000
57A64GLN0-0.036-0.0294.8560.5970.5970.0000.0000.0000.000
58A65TYR00.0010.0178.0000.1970.1970.0000.0000.0000.000
59A66ALA00.0560.0159.9890.0860.0860.0000.0000.0000.000
60A67ILE0-0.053-0.0376.3280.1020.1020.0000.0000.0000.000
61A68LYS10.8290.9049.8800.8340.8340.0000.0000.0000.000
62A69ILE00.0420.04713.7840.0600.0600.0000.0000.0000.000
63A70MET00.0250.02613.7900.0600.0600.0000.0000.0000.000
64A71ASN0-0.031-0.00513.3920.0580.0580.0000.0000.0000.000
65A72ASN0-0.040-0.01615.3550.0210.0210.0000.0000.0000.000
66A73THR00.0110.00118.4240.0200.0200.0000.0000.0000.000
67A74VAL00.0380.02119.2820.0170.0170.0000.0000.0000.000
68A75ARG10.7810.87720.9610.0810.0810.0000.0000.0000.000
69A76LEU00.0190.00819.7850.0050.0050.0000.0000.0000.000
70A77TYR0-0.011-0.02623.8270.0030.0030.0000.0000.0000.000
71A78ASP-1-0.876-0.94227.125-0.055-0.0550.0000.0000.0000.000
72A79ARG10.7430.85622.6790.0290.0290.0000.0000.0000.000
73A80LEU00.0270.02221.026-0.004-0.0040.0000.0000.0000.000
74A81ILE00.0100.02715.9630.0000.0000.0000.0000.0000.000
75A82LYS10.8040.88714.9370.1330.1330.0000.0000.0000.000
76A83VAL00.0220.0069.9020.0260.0260.0000.0000.0000.000
77A84ARG10.9440.9689.0720.2710.2710.0000.0000.0000.000
78A85GLN00.0690.0444.193-0.158-0.092-0.001-0.009-0.0560.000
79A86VAL00.0060.0103.6390.3410.5790.002-0.038-0.2020.000
80A106PRO0-0.024-0.03519.572-0.004-0.0040.0000.0000.0000.000
81A107ILE00.0320.03422.5630.0010.0010.0000.0000.0000.000
82A108ALA00.0850.05724.934-0.005-0.0050.0000.0000.0000.000
83A109LYS10.7660.89427.1720.0650.0650.0000.0000.0000.000
84A110LEU00.0410.02029.3180.0010.0010.0000.0000.0000.000
85A111PHE00.008-0.01532.813-0.004-0.0040.0000.0000.0000.000
86A112ILE0-0.0070.00235.3360.0030.0030.0000.0000.0000.000
87A113LYS10.8330.91438.3140.0270.0270.0000.0000.0000.000
88A114ASN00.013-0.01141.2100.0010.0010.0000.0000.0000.000
89A115LEU0-0.0070.00238.9020.0020.0020.0000.0000.0000.000
90A116ALA00.0540.03343.510-0.001-0.0010.0000.0000.0000.000
91A117ASP-1-0.840-0.93544.373-0.027-0.0270.0000.0000.0000.000
92A118SER0-0.023-0.01744.2170.0000.0000.0000.0000.0000.000
93A119ILE0-0.049-0.00740.4970.0010.0010.0000.0000.0000.000
94A120ASP-1-0.792-0.88838.236-0.030-0.0300.0000.0000.0000.000
95A121SER00.0370.00633.2630.0010.0010.0000.0000.0000.000
96A122ASP-1-0.777-0.88935.923-0.016-0.0160.0000.0000.0000.000
97A123GLN0-0.014-0.01537.3310.0030.0030.0000.0000.0000.000
98A124LEU00.0000.00536.0930.0020.0020.0000.0000.0000.000
99A125VAL00.0200.01032.9950.0010.0010.0000.0000.0000.000
100A126LYS10.8160.89635.6540.0170.0170.0000.0000.0000.000
101A127ILE0-0.064-0.02839.0680.0020.0020.0000.0000.0000.000
102A128PHE00.037-0.00635.3020.0010.0010.0000.0000.0000.000
103A129ASN00.0340.00433.7320.0000.0000.0000.0000.0000.000
104A130LYS10.8300.93735.7620.0110.0110.0000.0000.0000.000
105A131PHE0-0.0010.00536.8700.0010.0010.0000.0000.0000.000
106A132GLY00.0190.00533.5840.0020.0020.0000.0000.0000.000
107A133LYS10.8180.90026.1110.0080.0080.0000.0000.0000.000
108A134LEU00.0310.01729.188-0.001-0.0010.0000.0000.0000.000
109A135ILE0-0.0030.00921.5920.0000.0000.0000.0000.0000.000
110A136ARG10.8350.91519.3780.0580.0580.0000.0000.0000.000
111A137GLU-1-0.839-0.91926.204-0.048-0.0480.0000.0000.0000.000
112A138PRO0-0.055-0.03029.081-0.004-0.0040.0000.0000.0000.000
113A139GLU-1-0.812-0.87028.919-0.069-0.0690.0000.0000.0000.000
114A140ILE00.010-0.00731.5240.0010.0010.0000.0000.0000.000
115A141PHE0-0.035-0.01634.188-0.003-0.0030.0000.0000.0000.000
116A142TYR00.0250.01236.3940.0030.0030.0000.0000.0000.000
117A143LEU00.0400.02937.622-0.003-0.0030.0000.0000.0000.000
118A144SER0-0.021-0.01341.1650.0030.0030.0000.0000.0000.000
119A145ASN00.0420.01543.6550.0030.0030.0000.0000.0000.000
120A146GLY00.0460.02842.723-0.001-0.0010.0000.0000.0000.000
121A147LYS10.8730.92943.7780.0310.0310.0000.0000.0000.000
122A148LEU00.0300.01842.8600.0010.0010.0000.0000.0000.000
123A149LYS10.8330.93240.6410.0260.0260.0000.0000.0000.000
124A150CYS0-0.080-0.03637.9170.0020.0020.0000.0000.0000.000
125A151ALA00.0400.01235.115-0.001-0.0010.0000.0000.0000.000
126A152TYR0-0.019-0.00530.9100.0010.0010.0000.0000.0000.000
127A153VAL00.0150.01231.6480.0000.0000.0000.0000.0000.000
128A154TYR0-0.004-0.03525.240-0.004-0.0040.0000.0000.0000.000
129A155PHE00.0370.02228.2310.0010.0010.0000.0000.0000.000
130A156GLU-1-0.836-0.92424.974-0.011-0.0110.0000.0000.0000.000
131A157ASP-1-0.772-0.87326.6140.0050.0050.0000.0000.0000.000
132A158PHE00.025-0.01427.056-0.004-0.0040.0000.0000.0000.000
133A159GLU-1-0.857-0.90431.3620.0060.0060.0000.0000.0000.000
134A160LYS10.7730.87032.817-0.006-0.0060.0000.0000.0000.000
135A161ALA00.0060.01032.310-0.001-0.0010.0000.0000.0000.000
136A162ASP-1-0.818-0.88734.366-0.013-0.0130.0000.0000.0000.000
137A163LEU0-0.045-0.02037.1990.0000.0000.0000.0000.0000.000
138A164ALA0-0.0010.01636.8350.0000.0000.0000.0000.0000.000
139A165ILE00.000-0.00936.257-0.001-0.0010.0000.0000.0000.000
140A166LYS10.9220.95539.8730.0040.0040.0000.0000.0000.000
141A167SER0-0.041-0.02442.1530.0010.0010.0000.0000.0000.000
142A168LEU0-0.041-0.01839.8880.0000.0000.0000.0000.0000.000
143A169ASN00.0540.03242.247-0.002-0.0020.0000.0000.0000.000
144A170ASN0-0.025-0.01343.8250.0020.0020.0000.0000.0000.000
145A171GLN00.0420.04146.2610.0010.0010.0000.0000.0000.000
146A172LEU0-0.027-0.01347.675-0.001-0.0010.0000.0000.0000.000
147A173VAL00.0230.00844.0290.0010.0010.0000.0000.0000.000
148A174ALA00.0340.00947.386-0.001-0.0010.0000.0000.0000.000
149A175ASN0-0.006-0.01249.2640.0000.0000.0000.0000.0000.000
150A176ASN0-0.0160.00747.756-0.001-0.0010.0000.0000.0000.000
151A177ARG10.8590.92248.1920.0130.0130.0000.0000.0000.000
152A178ILE00.0220.02742.427-0.001-0.0010.0000.0000.0000.000
153A179THR0-0.090-0.05641.8250.0010.0010.0000.0000.0000.000
154A180VAL0-0.003-0.01038.021-0.002-0.0020.0000.0000.0000.000
155A181ASP-1-0.783-0.88038.190-0.026-0.0260.0000.0000.0000.000
156A182TYR0-0.012-0.04932.318-0.003-0.0030.0000.0000.0000.000
157A183ALA0-0.036-0.00530.756-0.001-0.0010.0000.0000.0000.000
158A184PHE00.016-0.00731.8290.0000.0000.0000.0000.0000.000
159A185LYS10.7100.84426.3910.0520.0520.0000.0000.0000.000
160A186DGL-1-0.804-0.86226.740-0.080-0.0800.0000.0000.0000.000
161A187ASN00.1050.05229.7380.0010.0010.0000.0000.0000.000
162A188GLY00.0770.03032.471-0.002-0.0020.0000.0000.0000.000
163A189LYS10.7940.90724.9080.0530.0530.0000.0000.0000.000
164A190GLY00.0810.04130.3210.0020.0020.0000.0000.0000.000
165A191ASN0-0.041-0.01028.1130.0020.0020.0000.0000.0000.000
166A192ALA00.0830.02230.4620.0000.0000.0000.0000.0000.000
167A193LYS10.8900.95327.2170.0340.0340.0000.0000.0000.000
168A194TYR0-0.0230.00024.375-0.001-0.0010.0000.0000.0000.000
169A195GLY00.0690.04027.3550.0020.0020.0000.0000.0000.000
170A196ASP-1-0.780-0.87921.910-0.013-0.0130.0000.0000.0000.000
171A197ASP-1-0.856-0.93623.013-0.008-0.0080.0000.0000.0000.000
172A198VAL00.0660.02725.1970.0040.0040.0000.0000.0000.000
173A199ASP-1-0.843-0.90822.0230.0620.0620.0000.0000.0000.000
174A200ARG10.8020.87619.6510.0090.0090.0000.0000.0000.000
175A201LEU0-0.0250.00721.6270.0010.0010.0000.0000.0000.000
176A202LEU0-0.0110.00324.6400.0050.0050.0000.0000.0000.000
177A203ASN0-0.048-0.04019.7900.0230.0230.0000.0000.0000.000
178A204LYS10.8540.94220.515-0.074-0.0740.0000.0000.0000.000
179A205GLU-1-0.922-0.94417.1850.0260.0260.0000.0000.0000.000