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: 3JKZL

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 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 184
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2104137.36421
FMO2-HF: Nuclear repulsion 2027390.848615
FMO2-HF: Total energy -76746.515595
FMO2-MP2: Total energy -76968.606892


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.
-5.502-2.672-0.033-1.426-1.371-0.002
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 : -0.006 / q_NPA : -0.014
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].
3A3ALA0-0.0100.0053.851-2.4950.100-0.034-1.371-1.189-0.002
4A4LEU00.0160.0186.3650.0090.0090.0000.0000.0000.000
5A5PRO00.0160.0089.322-0.154-0.1540.0000.0000.0000.000
6A6PRO00.0740.02611.3350.0070.0070.0000.0000.0000.000
7A7VAL00.0280.00113.9830.0090.0090.0000.0000.0000.000
8A8TYR00.0230.01814.0150.0120.0120.0000.0000.0000.000
9A9SER00.0500.02515.9030.0110.0110.0000.0000.0000.000
10A10PHE00.0210.01418.177-0.016-0.0160.0000.0000.0000.000
11A11PRO00.0870.03420.7860.0100.0100.0000.0000.0000.000
12A12PRO0-0.063-0.02523.8470.0070.0070.0000.0000.0000.000
13A13LEU0-0.0140.00718.6770.0000.0000.0000.0000.0000.000
14A14TYR0-0.017-0.05118.1260.0120.0120.0000.0000.0000.000
15A15THR0-0.0440.00724.097-0.002-0.0020.0000.0000.0000.000
16A16ARG10.8260.88627.044-0.090-0.0900.0000.0000.0000.000
17A17GLN00.0230.00027.470-0.013-0.0130.0000.0000.0000.000
18A18PRO0-0.050-0.00329.9530.0040.0040.0000.0000.0000.000
19A19ASN00.1020.00331.664-0.002-0.0020.0000.0000.0000.000
20A20SER0-0.024-0.01031.1700.0080.0080.0000.0000.0000.000
21A21LEU00.0540.02130.2680.0070.0070.0000.0000.0000.000
22A22THR00.0390.01427.4270.0060.0060.0000.0000.0000.000
23A23ARG10.9140.99826.571-0.082-0.0820.0000.0000.0000.000
24A24ARG10.9600.99025.568-0.108-0.1080.0000.0000.0000.000
25A25GLN00.0440.01723.0820.0240.0240.0000.0000.0000.000
26A26GLN0-0.045-0.04221.8820.0100.0100.0000.0000.0000.000
27A27ILE00.004-0.00721.4480.0150.0150.0000.0000.0000.000
28A28SER00.0140.02119.8150.0260.0260.0000.0000.0000.000
29A29THR0-0.0060.00516.9540.0290.0290.0000.0000.0000.000
30A30TRP00.0190.00116.5750.0450.0450.0000.0000.0000.000
31A31ILE0-0.017-0.00117.0190.0450.0450.0000.0000.0000.000
32A32ASP-1-0.975-0.99812.5920.5270.5270.0000.0000.0000.000
33A33ILE00.0320.00512.7900.1180.1180.0000.0000.0000.000
34A34ILE0-0.0150.00112.3630.1170.1170.0000.0000.0000.000
35A35SER00.002-0.00112.6920.0770.0770.0000.0000.0000.000
36A36GLN00.0050.0045.886-0.030-0.0300.0000.0000.0000.000
37A37TYR00.0380.0198.0560.5690.5690.0000.0000.0000.000
38A38CYS0-0.038-0.0178.9890.1490.1490.0000.0000.0000.000
39A39LYS10.9971.0126.573-1.801-1.8010.0000.0000.0000.000
40A40THR0-0.114-0.0533.964-0.258-0.0230.001-0.055-0.1820.000
41A41LYS10.9120.9555.983-0.910-0.9100.0000.0000.0000.000
42A42LYS10.9140.9697.416-1.721-1.7210.0000.0000.0000.000
43A43ILE00.0510.03610.482-0.174-0.1740.0000.0000.0000.000
44A44TRP00.0600.00913.3470.0710.0710.0000.0000.0000.000
45A45TYR00.010-0.00316.525-0.023-0.0230.0000.0000.0000.000
46A46MET0-0.013-0.00217.1450.0260.0260.0000.0000.0000.000
47A47SER0-0.001-0.03719.768-0.014-0.0140.0000.0000.0000.000
48A48VAL00.0630.02822.7120.0120.0120.0000.0000.0000.000
49A49ASP-1-0.761-0.81924.2490.1600.1600.0000.0000.0000.000
50A50GLY0-0.003-0.02020.721-0.002-0.0020.0000.0000.0000.000
51A51THR0-0.098-0.06419.4130.0220.0220.0000.0000.0000.000
52A52VAL0-0.017-0.01215.2060.0150.0150.0000.0000.0000.000
53A53ILE0-0.075-0.05518.126-0.034-0.0340.0000.0000.0000.000
54A54ASN0-0.046-0.03415.9110.0670.0670.0000.0000.0000.000
55A55ASP-1-0.853-0.91516.0390.1920.1920.0000.0000.0000.000
56A73LYS10.9460.97517.003-0.164-0.1640.0000.0000.0000.000
57A74ASN00.007-0.01218.4640.0160.0160.0000.0000.0000.000
58A75LEU00.0540.04713.572-0.005-0.0050.0000.0000.0000.000
59A76PHE0-0.0040.00817.2340.0080.0080.0000.0000.0000.000
60A77ASN0-0.019-0.01020.299-0.023-0.0230.0000.0000.0000.000
61A78ASN0-0.0050.00717.659-0.003-0.0030.0000.0000.0000.000
62A79GLU-1-0.839-0.94020.0600.0960.0960.0000.0000.0000.000
63A80ASP-1-0.932-0.96517.2000.0870.0870.0000.0000.0000.000
64A81ILE0-0.111-0.04519.468-0.011-0.0110.0000.0000.0000.000
65A82GLN0-0.0200.00422.119-0.008-0.0080.0000.0000.0000.000
66A83ARG10.8550.92723.289-0.083-0.0830.0000.0000.0000.000
67A84SER00.0470.01723.2440.0130.0130.0000.0000.0000.000
68A85VAL0-0.0610.00422.323-0.012-0.0120.0000.0000.0000.000
69A86SER00.0190.00925.1530.0030.0030.0000.0000.0000.000
70A87GLN00.0680.00427.1910.0070.0070.0000.0000.0000.000
71A88VAL00.0190.01228.7610.0040.0040.0000.0000.0000.000
72A89PHE0-0.007-0.01024.9790.0030.0030.0000.0000.0000.000
73A90ILE00.0190.01723.5450.0070.0070.0000.0000.0000.000
74A91ASP-1-0.837-0.90625.3090.1370.1370.0000.0000.0000.000
75A92GLU-1-0.805-0.87527.7940.1060.1060.0000.0000.0000.000
76A93ILE0-0.026-0.02021.3380.0040.0040.0000.0000.0000.000
77A94TRP00.0590.02319.4200.0220.0220.0000.0000.0000.000
78A95SER00.0190.06224.5070.0040.0040.0000.0000.0000.000
79A96GLN0-0.061-0.01523.7910.0020.0020.0000.0000.0000.000
80A97MET00.0490.00617.037-0.006-0.0060.0000.0000.0000.000
81A98THR0-0.049-0.09222.5530.0070.0070.0000.0000.0000.000
82A99LYS10.8440.93424.937-0.122-0.1220.0000.0000.0000.000
83A100GLU-1-0.943-0.97421.1590.2080.2080.0000.0000.0000.000
84A101GLY0-0.0070.00722.5040.0070.0070.0000.0000.0000.000
85A102LYS10.8670.93317.368-0.272-0.2720.0000.0000.0000.000
86A103CYS0-0.0300.00818.3630.0390.0390.0000.0000.0000.000
87A104LEU0-0.003-0.00920.781-0.032-0.0320.0000.0000.0000.000
88A105PRO00.0110.00423.6330.0050.0050.0000.0000.0000.000
89A106ILE0-0.0070.01423.682-0.009-0.0090.0000.0000.0000.000
90A107ASP-1-0.729-0.88727.5740.1070.1070.0000.0000.0000.000
91A108GLN0-0.111-0.04028.6370.0080.0080.0000.0000.0000.000
92A109SER0-0.026-0.04529.059-0.008-0.0080.0000.0000.0000.000
93A110GLY00.0360.03728.2380.0100.0100.0000.0000.0000.000
94A111ARG10.9050.93827.400-0.132-0.1320.0000.0000.0000.000
95A112ARG10.8890.95729.571-0.095-0.0950.0000.0000.0000.000
96A113SER00.0750.01729.6600.0050.0050.0000.0000.0000.000
97A114SER0-0.039-0.01431.504-0.003-0.0030.0000.0000.0000.000
98A115ASN00.0410.01734.583-0.003-0.0030.0000.0000.0000.000
99A116THR0-0.008-0.01933.8140.0040.0040.0000.0000.0000.000
100A117THR0-0.0030.01333.094-0.001-0.0010.0000.0000.0000.000
101A118THR0-0.0600.00527.7530.0030.0030.0000.0000.0000.000
102A119THR00.006-0.00227.4380.0010.0010.0000.0000.0000.000
103A120ARG10.9000.94923.089-0.156-0.1560.0000.0000.0000.000
104A121TYR00.000-0.00921.246-0.012-0.0120.0000.0000.0000.000
105A122PHE00.0170.03317.9670.0140.0140.0000.0000.0000.000
106A123ILE0-0.009-0.04514.973-0.010-0.0100.0000.0000.0000.000
107A124LEU0-0.005-0.00816.4890.0250.0250.0000.0000.0000.000
108A125TRP0-0.0230.00110.6760.1170.1170.0000.0000.0000.000
109A126LYS10.9130.96612.960-0.337-0.3370.0000.0000.0000.000
110A127SER00.0320.00515.300-0.033-0.0330.0000.0000.0000.000
111A128LEU00.0750.04218.9530.0060.0060.0000.0000.0000.000
112A129ASP-1-0.838-0.90921.4380.1240.1240.0000.0000.0000.000
113A130SER0-0.093-0.05117.0460.0080.0080.0000.0000.0000.000
114A131TRP00.035-0.00713.136-0.019-0.0190.0000.0000.0000.000
115A132ALA00.0380.01918.734-0.021-0.0210.0000.0000.0000.000
116A133SER0-0.062-0.02320.208-0.022-0.0220.0000.0000.0000.000
117A134LEU00.0040.01114.496-0.010-0.0100.0000.0000.0000.000
118A135ILE00.0190.00518.619-0.022-0.0220.0000.0000.0000.000
119A136LEU0-0.018-0.02020.829-0.018-0.0180.0000.0000.0000.000
120A137GLN0-0.043-0.02519.333-0.008-0.0080.0000.0000.0000.000
121A138TRP00.0230.02319.078-0.008-0.0080.0000.0000.0000.000
122A139PHE00.002-0.02521.363-0.013-0.0130.0000.0000.0000.000
123A140GLU-1-0.922-0.96624.8480.0110.0110.0000.0000.0000.000
124A141ASP-1-0.939-0.95920.496-0.046-0.0460.0000.0000.0000.000
125A142SER0-0.028-0.02022.174-0.019-0.0190.0000.0000.0000.000
126A143GLY0-0.032-0.00524.3820.0010.0010.0000.0000.0000.000
127A144LYS10.9450.96424.8140.0260.0260.0000.0000.0000.000
128A145LEU0-0.060-0.02228.6490.0070.0070.0000.0000.0000.000
129A146ASN0-0.048-0.03529.9520.0050.0050.0000.0000.0000.000
130A147GLN0-0.038-0.01330.5060.0000.0000.0000.0000.0000.000
131A148VAL0-0.014-0.01932.5540.0050.0050.0000.0000.0000.000
132A149ILE00.0270.03725.269-0.003-0.0030.0000.0000.0000.000
133A150THR00.024-0.01329.1650.0060.0060.0000.0000.0000.000
134A151LEU0-0.023-0.02925.8580.0010.0010.0000.0000.0000.000
135A152TYR00.0200.02224.6010.0040.0040.0000.0000.0000.000
136A153GLU-1-0.905-0.97224.1400.0000.0000.0000.0000.0000.000
137A154LEU0-0.047-0.00622.462-0.005-0.0050.0000.0000.0000.000
138A155SER0-0.0190.00419.7170.0160.0160.0000.0000.0000.000
139A156GLU-1-1.014-1.04518.5260.0600.0600.0000.0000.0000.000
140A157GLY00.1200.07619.988-0.015-0.0150.0000.0000.0000.000
141A158ASP-1-0.883-0.94421.817-0.019-0.0190.0000.0000.0000.000
142A159GLU-1-0.979-1.02519.342-0.081-0.0810.0000.0000.0000.000
143A160THR0-0.104-0.05218.894-0.018-0.0180.0000.0000.0000.000
144A161VAL0-0.0740.00518.456-0.006-0.0060.0000.0000.0000.000
145A162ASN00.049-0.00511.7100.0180.0180.0000.0000.0000.000
146A163TRP00.0180.03112.925-0.043-0.0430.0000.0000.0000.000
147A164GLU-1-0.949-1.01110.0030.6270.6270.0000.0000.0000.000
148A165PHE0-0.044-0.02012.3180.0650.0650.0000.0000.0000.000
149A166HIS00.0690.05314.3450.0100.0100.0000.0000.0000.000
150A167ARG10.8590.94415.523-0.033-0.0330.0000.0000.0000.000
151A168MET0-0.0800.00317.1420.0120.0120.0000.0000.0000.000
152A169PRO00.0230.00818.605-0.028-0.0280.0000.0000.0000.000
153A170GLU-1-0.747-0.89721.8380.0780.0780.0000.0000.0000.000
154A171SER0-0.041-0.01424.8770.0050.0050.0000.0000.0000.000
155A172LEU00.001-0.02120.178-0.002-0.0020.0000.0000.0000.000
156A173LEU00.0800.03720.6960.0070.0070.0000.0000.0000.000
157A174TYR0-0.012-0.01122.963-0.008-0.0080.0000.0000.0000.000
158A175TYR0-0.039-0.02524.394-0.009-0.0090.0000.0000.0000.000
159A176CYS0-0.041-0.00720.7930.0130.0130.0000.0000.0000.000
160A177LEU00.0610.03523.259-0.008-0.0080.0000.0000.0000.000
161A178LYS10.9320.98825.986-0.090-0.0900.0000.0000.0000.000
162A179PRO00.0140.00124.800-0.010-0.0100.0000.0000.0000.000
163A180LEU0-0.021-0.02425.212-0.007-0.0070.0000.0000.0000.000
164A181CYS0-0.089-0.02028.607-0.010-0.0100.0000.0000.0000.000
165A182ASP-1-0.878-0.92530.8560.0720.0720.0000.0000.0000.000
166A183ARG10.8810.92427.917-0.067-0.0670.0000.0000.0000.000
167A184ASN0-0.009-0.01532.258-0.001-0.0010.0000.0000.0000.000
168A185ARG10.8650.95628.980-0.036-0.0360.0000.0000.0000.000
169A186ALA00.0100.00929.983-0.003-0.0030.0000.0000.0000.000
170A187THR0-0.049-0.01932.118-0.001-0.0010.0000.0000.0000.000
171A188MET00.0240.00831.1090.0010.0010.0000.0000.0000.000
172A189LEU0-0.023-0.00933.684-0.003-0.0030.0000.0000.0000.000
173A190LYS10.8930.95734.557-0.037-0.0370.0000.0000.0000.000
174A191ASP-1-0.841-0.91936.5760.0390.0390.0000.0000.0000.000
175A192GLU-1-0.923-0.98538.4280.0290.0290.0000.0000.0000.000
176A193ASN0-0.087-0.02838.7310.0000.0000.0000.0000.0000.000
177A194ASP-1-0.897-0.97938.3500.0450.0450.0000.0000.0000.000
178A195LYS10.9711.01230.993-0.057-0.0570.0000.0000.0000.000
179A196VAL0-0.069-0.03430.410-0.004-0.0040.0000.0000.0000.000
180A197ILE00.0120.00931.5020.0040.0040.0000.0000.0000.000
181A198ALA00.0150.01030.484-0.001-0.0010.0000.0000.0000.000
182A199ILE0-0.053-0.02027.8320.0050.0050.0000.0000.0000.000
183A200LYS10.9460.99330.958-0.031-0.0310.0000.0000.0000.000
184A201VAL00.0430.02027.5080.0020.0020.0000.0000.0000.000