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: LNQG9

Calculation Name: 1XB4-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1XB4

Chain ID: A

ChEMBL ID:

UniProt ID: P47142

Base Structure: X-ray

Registration Date: 2023-09-22

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 184
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2102978.967511
FMO2-HF: Nuclear repulsion 2026230.635177
FMO2-HF: Total energy -76748.332334
FMO2-MP2: Total energy -76970.178602


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:MET)


Summations of interaction energy for fragment #1(A:1:MET)
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.
-5.386-2.33-0.029-1.548-1.479-0.002
Interaction energy analysis for fragmet #1(A:1:MET)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.011 / q_NPA : -0.018
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].
3A3ALA00.0090.0123.851-2.843-0.106-0.035-1.456-1.246-0.002
4A4LEU00.0270.0276.328-0.006-0.0060.0000.0000.0000.000
5A5PRO00.001-0.0039.303-0.126-0.1260.0000.0000.0000.000
6A6PRO00.0660.02411.335-0.008-0.0080.0000.0000.0000.000
7A7VAL00.011-0.00413.983-0.003-0.0030.0000.0000.0000.000
8A8TYR00.0130.00613.8810.0030.0030.0000.0000.0000.000
9A9SER00.0640.02215.8760.0020.0020.0000.0000.0000.000
10A10PHE00.0290.01418.162-0.020-0.0200.0000.0000.0000.000
11A11PRO00.0930.03820.7860.0080.0080.0000.0000.0000.000
12A12PRO0-0.056-0.02323.8250.0050.0050.0000.0000.0000.000
13A13LEU0-0.032-0.01218.529-0.004-0.0040.0000.0000.0000.000
14A14TYR0-0.016-0.04518.0690.0060.0060.0000.0000.0000.000
15A15THR0-0.0540.01124.062-0.005-0.0050.0000.0000.0000.000
16A16ARG10.8550.90727.005-0.096-0.0960.0000.0000.0000.000
17A17GLN00.0320.00527.609-0.013-0.0130.0000.0000.0000.000
18A18PRO0-0.0290.00630.0580.0020.0020.0000.0000.0000.000
19A19ASN00.078-0.00732.025-0.004-0.0040.0000.0000.0000.000
20A20SER0-0.0290.01031.3330.0080.0080.0000.0000.0000.000
21A21LEU00.0390.01130.4290.0080.0080.0000.0000.0000.000
22A22THR00.0640.02027.5900.0060.0060.0000.0000.0000.000
23A23ARG10.8640.95026.733-0.091-0.0910.0000.0000.0000.000
24A24ARG10.9130.96924.700-0.132-0.1320.0000.0000.0000.000
25A25GLN00.0290.01223.3330.0230.0230.0000.0000.0000.000
26A26GLN0-0.009-0.01122.0430.0140.0140.0000.0000.0000.000
27A27ILE00.012-0.00121.6130.0170.0170.0000.0000.0000.000
28A28SER0-0.0090.00320.1540.0240.0240.0000.0000.0000.000
29A29THR0-0.0030.00017.2760.0320.0320.0000.0000.0000.000
30A30TRP00.0320.00916.7160.0500.0500.0000.0000.0000.000
31A31ILE0-0.031-0.01517.0190.0420.0420.0000.0000.0000.000
32A32ASP-1-0.973-1.00012.9670.5980.5980.0000.0000.0000.000
33A33ILE00.0140.00312.8040.1250.1250.0000.0000.0000.000
34A34ILE0-0.0150.00012.3090.1130.1130.0000.0000.0000.000
35A35SER00.0020.00312.7270.0630.0630.0000.0000.0000.000
36A36GLN00.0480.0286.1320.3400.3400.0000.0000.0000.000
37A37TYR00.0590.0247.9950.5270.5270.0000.0000.0000.000
38A38CYS0-0.045-0.0268.9390.1010.1010.0000.0000.0000.000
39A39LYS10.9490.9826.438-1.905-1.9050.0000.0000.0000.000
40A40THR0-0.091-0.0454.111-0.2980.0210.006-0.092-0.2330.000
41A41LYS10.8950.9565.929-0.933-0.9330.0000.0000.0000.000
42A42LYS10.8450.9317.806-1.153-1.1530.0000.0000.0000.000
43A43ILE00.0120.01810.441-0.147-0.1470.0000.0000.0000.000
44A44TRP00.0470.00713.3040.0810.0810.0000.0000.0000.000
45A45TYR00.0270.00716.476-0.013-0.0130.0000.0000.0000.000
46A46MET0-0.0050.00717.1470.0290.0290.0000.0000.0000.000
47A47SER0-0.012-0.02619.721-0.015-0.0150.0000.0000.0000.000
48A48VAL00.0460.02022.6660.0130.0130.0000.0000.0000.000
49A49ASP-1-0.708-0.82424.3820.1560.1560.0000.0000.0000.000
50A50GLY0-0.030-0.02520.6780.0010.0010.0000.0000.0000.000
51A51THR0-0.093-0.05119.3750.0240.0240.0000.0000.0000.000
52A52VAL0-0.021-0.01115.0990.0120.0120.0000.0000.0000.000
53A53ILE0-0.054-0.03918.092-0.030-0.0300.0000.0000.0000.000
54A54ASN0-0.035-0.02816.2970.0580.0580.0000.0000.0000.000
55A55ASP-1-0.860-0.92016.3240.0660.0660.0000.0000.0000.000
56A73LYS10.9200.95916.777-0.162-0.1620.0000.0000.0000.000
57A74ASN0-0.003-0.01118.4460.0200.0200.0000.0000.0000.000
58A75LEU00.0570.04613.7960.0000.0000.0000.0000.0000.000
59A76PHE00.0090.01217.1990.0130.0130.0000.0000.0000.000
60A77ASN0-0.035-0.02220.236-0.020-0.0200.0000.0000.0000.000
61A78ASN0-0.031-0.00517.654-0.003-0.0030.0000.0000.0000.000
62A79GLU-1-0.817-0.92220.0160.1020.1020.0000.0000.0000.000
63A80ASP-1-0.926-0.95717.0720.1240.1240.0000.0000.0000.000
64A81ILE0-0.103-0.05019.539-0.010-0.0100.0000.0000.0000.000
65A82GLN0-0.0210.00922.110-0.010-0.0100.0000.0000.0000.000
66A83ARG10.8490.91723.222-0.106-0.1060.0000.0000.0000.000
67A84SER00.0630.02323.2200.0120.0120.0000.0000.0000.000
68A85VAL0-0.090-0.01422.087-0.011-0.0110.0000.0000.0000.000
69A86SER00.0190.00925.1150.0010.0010.0000.0000.0000.000
70A87GLN00.047-0.00126.6790.0070.0070.0000.0000.0000.000
71A88VAL00.0170.00728.7130.0040.0040.0000.0000.0000.000
72A89PHE0-0.013-0.00625.1200.0030.0030.0000.0000.0000.000
73A90ILE00.0530.02723.5410.0060.0060.0000.0000.0000.000
74A91ASP-1-0.822-0.90125.2550.1350.1350.0000.0000.0000.000
75A92GLU-1-0.798-0.87827.7360.1120.1120.0000.0000.0000.000
76A93ILE0-0.052-0.02221.1330.0040.0040.0000.0000.0000.000
77A94TRP00.0550.01119.4030.0210.0210.0000.0000.0000.000
78A95SER00.0270.02924.5030.0020.0020.0000.0000.0000.000
79A96GLN00.0130.02524.552-0.008-0.0080.0000.0000.0000.000
80A97MET00.0200.00217.147-0.006-0.0060.0000.0000.0000.000
81A98THR0-0.043-0.04322.5530.0040.0040.0000.0000.0000.000
82A99LYS10.8000.90224.937-0.129-0.1290.0000.0000.0000.000
83A100GLU-1-0.908-0.95521.6830.2010.2010.0000.0000.0000.000
84A101GLY00.0090.01522.5610.0060.0060.0000.0000.0000.000
85A102LYS10.8720.93117.702-0.264-0.2640.0000.0000.0000.000
86A103CYS0-0.0340.00518.3630.0340.0340.0000.0000.0000.000
87A104LEU00.0050.00720.781-0.028-0.0280.0000.0000.0000.000
88A105PRO00.0270.00323.6330.0040.0040.0000.0000.0000.000
89A106ILE0-0.0250.00423.441-0.010-0.0100.0000.0000.0000.000
90A107ASP-1-0.757-0.89327.5190.0870.0870.0000.0000.0000.000
91A108GLN0-0.097-0.03028.5880.0070.0070.0000.0000.0000.000
92A109SER0-0.009-0.03229.030-0.008-0.0080.0000.0000.0000.000
93A110GLY0-0.0080.01628.1870.0080.0080.0000.0000.0000.000
94A111ARG10.9580.96227.435-0.110-0.1100.0000.0000.0000.000
95A112ARG10.8940.95829.558-0.078-0.0780.0000.0000.0000.000
96A113SER00.0660.02029.7000.0050.0050.0000.0000.0000.000
97A114SER0-0.053-0.02231.497-0.002-0.0020.0000.0000.0000.000
98A115ASN00.0520.02334.683-0.003-0.0030.0000.0000.0000.000
99A116THR00.010-0.02033.6900.0030.0030.0000.0000.0000.000
100A117THR0-0.0090.01433.052-0.001-0.0010.0000.0000.0000.000
101A118THR0-0.0120.02228.3140.0030.0030.0000.0000.0000.000
102A119THR0-0.015-0.02027.5030.0020.0020.0000.0000.0000.000
103A120ARG10.8680.93823.196-0.126-0.1260.0000.0000.0000.000
104A121TYR00.002-0.00721.220-0.011-0.0110.0000.0000.0000.000
105A122PHE00.0380.03517.6310.0100.0100.0000.0000.0000.000
106A123ILE0-0.013-0.04314.937-0.004-0.0040.0000.0000.0000.000
107A124LEU0-0.020-0.01116.4890.0130.0130.0000.0000.0000.000
108A125TRP00.0050.00910.7610.1070.1070.0000.0000.0000.000
109A126LYS10.8720.93412.002-0.277-0.2770.0000.0000.0000.000
110A127SER0-0.0010.00015.216-0.031-0.0310.0000.0000.0000.000
111A128LEU00.0790.04518.829-0.001-0.0010.0000.0000.0000.000
112A129ASP-1-0.865-0.92221.3060.0940.0940.0000.0000.0000.000
113A130SER0-0.058-0.03917.123-0.002-0.0020.0000.0000.0000.000
114A131TRP00.045-0.00212.830-0.024-0.0240.0000.0000.0000.000
115A132ALA00.0240.01218.610-0.024-0.0240.0000.0000.0000.000
116A133SER0-0.059-0.02220.155-0.021-0.0210.0000.0000.0000.000
117A134LEU00.0000.00814.255-0.010-0.0100.0000.0000.0000.000
118A135ILE00.0080.01018.525-0.023-0.0230.0000.0000.0000.000
119A136LEU00.002-0.01920.717-0.015-0.0150.0000.0000.0000.000
120A137GLN0-0.042-0.02118.594-0.007-0.0070.0000.0000.0000.000
121A138TRP00.0160.02118.8630.0020.0020.0000.0000.0000.000
122A139PHE00.028-0.00921.135-0.010-0.0100.0000.0000.0000.000
123A140GLU-1-0.894-0.94224.677-0.021-0.0210.0000.0000.0000.000
124A141ASP-1-0.919-0.96020.728-0.100-0.1000.0000.0000.0000.000
125A142SER0-0.015-0.01422.057-0.023-0.0230.0000.0000.0000.000
126A143GLY0-0.036-0.00624.1700.0040.0040.0000.0000.0000.000
127A144LYS10.8870.94824.8500.0720.0720.0000.0000.0000.000
128A145LEU0-0.027-0.01628.5200.0080.0080.0000.0000.0000.000
129A146ASN0-0.061-0.03729.7270.0070.0070.0000.0000.0000.000
130A147GLN0-0.037-0.02030.6140.0000.0000.0000.0000.0000.000
131A148VAL0-0.013-0.01832.3270.0050.0050.0000.0000.0000.000
132A149ILE00.0040.03525.046-0.003-0.0030.0000.0000.0000.000
133A150THR00.040-0.00428.4430.0070.0070.0000.0000.0000.000
134A151LEU0-0.016-0.02525.714-0.002-0.0020.0000.0000.0000.000
135A152TYR0-0.029-0.02223.6580.0000.0000.0000.0000.0000.000
136A153GLU-1-0.831-0.94423.721-0.050-0.0500.0000.0000.0000.000
137A154LEU0-0.051-0.00622.038-0.010-0.0100.0000.0000.0000.000
138A155SER0-0.026-0.00719.4350.0070.0070.0000.0000.0000.000
139A156GLU-1-0.916-0.94617.931-0.003-0.0030.0000.0000.0000.000
140A157GLY00.1230.07419.485-0.018-0.0180.0000.0000.0000.000
141A158ASP-1-0.960-0.98021.403-0.073-0.0730.0000.0000.0000.000
142A159GLU-1-0.941-1.00918.968-0.163-0.1630.0000.0000.0000.000
143A160THR0-0.095-0.05018.629-0.021-0.0210.0000.0000.0000.000
144A161VAL0-0.0590.00318.351-0.011-0.0110.0000.0000.0000.000
145A162ASN00.047-0.00311.6680.0050.0050.0000.0000.0000.000
146A163TRP0-0.0050.01412.706-0.077-0.0770.0000.0000.0000.000
147A164GLU-1-0.862-0.9518.9880.6450.6450.0000.0000.0000.000
148A165PHE0-0.030-0.01612.1850.0570.0570.0000.0000.0000.000
149A166HIS00.0970.06713.7750.0410.0410.0000.0000.0000.000
150A167ARG10.8500.91815.2390.0410.0410.0000.0000.0000.000
151A168MET0-0.089-0.00416.9820.0240.0240.0000.0000.0000.000
152A169PRO00.0260.00818.433-0.020-0.0200.0000.0000.0000.000
153A170GLU-1-0.699-0.85321.7980.0370.0370.0000.0000.0000.000
154A171SER0-0.033-0.01224.7060.0050.0050.0000.0000.0000.000
155A172LEU0-0.018-0.02320.2100.0010.0010.0000.0000.0000.000
156A173LEU00.0850.04320.4040.0080.0080.0000.0000.0000.000
157A174TYR0-0.002-0.00822.801-0.005-0.0050.0000.0000.0000.000
158A175TYR0-0.042-0.02824.301-0.006-0.0060.0000.0000.0000.000
159A176CYS0-0.070-0.02720.8190.0140.0140.0000.0000.0000.000
160A177LEU00.0680.03423.115-0.007-0.0070.0000.0000.0000.000
161A178LYS10.8560.93425.848-0.063-0.0630.0000.0000.0000.000
162A179PRO00.008-0.00824.679-0.007-0.0070.0000.0000.0000.000
163A180LEU0-0.030-0.01824.781-0.004-0.0040.0000.0000.0000.000
164A181CYS0-0.072-0.01328.491-0.008-0.0080.0000.0000.0000.000
165A182ASP-1-0.803-0.87930.7920.0510.0510.0000.0000.0000.000
166A183ARG10.9070.94027.195-0.040-0.0400.0000.0000.0000.000
167A184ASN0-0.030-0.02032.159-0.002-0.0020.0000.0000.0000.000
168A185ARG10.8200.93329.064-0.004-0.0040.0000.0000.0000.000
169A186ALA00.0100.00229.869-0.005-0.0050.0000.0000.0000.000
170A187THR0-0.048-0.02232.0020.0020.0020.0000.0000.0000.000
171A188MET00.0130.01230.944-0.001-0.0010.0000.0000.0000.000
172A189LEU0-0.023-0.00733.543-0.001-0.0010.0000.0000.0000.000
173A190LYS10.8680.92034.404-0.021-0.0210.0000.0000.0000.000
174A191ASP-1-0.831-0.92236.1530.0170.0170.0000.0000.0000.000
175A192GLU-1-0.918-0.97938.2650.0130.0130.0000.0000.0000.000
176A193ASN0-0.083-0.02738.5800.0020.0020.0000.0000.0000.000
177A194ASP-1-0.894-0.95638.1780.0270.0270.0000.0000.0000.000
178A195LYS10.8730.95730.025-0.028-0.0280.0000.0000.0000.000
179A196VAL0-0.071-0.03630.557-0.004-0.0040.0000.0000.0000.000
180A197ILE00.0260.01731.3200.0030.0030.0000.0000.0000.000
181A198ALA00.0020.00830.333-0.004-0.0040.0000.0000.0000.000
182A199ILE0-0.049-0.02227.6620.0070.0070.0000.0000.0000.000
183A200LYS10.9580.99930.830-0.008-0.0080.0000.0000.0000.000
184A201VAL00.0440.02427.3580.0040.0040.0000.0000.0000.000