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: J3GL9

Calculation Name: 1XQB-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1XQB

Chain ID: A

ChEMBL ID:

UniProt ID: P44740

Base Structure: X-ray

Registration Date: 2023-06-20

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 189
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -1972255.082681
FMO2-HF: Nuclear repulsion 1896823.131295
FMO2-HF: Total energy -75431.951385
FMO2-MP2: Total energy -75651.775204


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.
-10.533-6.3351.727-2.853-3.073-0.009
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 : -0.016 / q_NPA : -0.004
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].
3A3ASP-1-0.904-0.9532.651-10.856-7.0381.722-2.777-2.763-0.009
4A4LEU00.001-0.0113.906-0.607-0.2270.005-0.076-0.3100.000
5A5THR0-0.040-0.0135.7000.3930.3930.0000.0000.0000.000
6A6LEU0-0.0100.0037.7760.1610.1610.0000.0000.0000.000
7A7SER00.0220.00710.9070.0120.0120.0000.0000.0000.000
8A8PRO0-0.020-0.01514.5670.0510.0510.0000.0000.0000.000
9A9ILE00.0290.02515.8430.0050.0050.0000.0000.0000.000
10A10ALA00.0110.00118.5480.0280.0280.0000.0000.0000.000
11A11ILE0-0.0160.01720.655-0.027-0.0270.0000.0000.0000.000
12A12ILE0-0.025-0.00123.2380.0220.0220.0000.0000.0000.000
13A13HIS0-0.027-0.00724.991-0.013-0.0130.0000.0000.0000.000
14A14THR00.003-0.02526.9580.0160.0160.0000.0000.0000.000
15A15PRO0-0.019-0.00629.955-0.009-0.0090.0000.0000.0000.000
16A16TYR0-0.016-0.02828.796-0.007-0.0070.0000.0000.0000.000
17A17LYS10.8520.93129.7300.0530.0530.0000.0000.0000.000
18A18GLU-1-0.854-0.90029.135-0.080-0.0800.0000.0000.0000.000
19A19LYS10.9810.95823.4780.0660.0660.0000.0000.0000.000
20A20PHE0-0.035-0.01328.2880.0120.0120.0000.0000.0000.000
21A21SER0-0.024-0.02931.6740.0060.0060.0000.0000.0000.000
22A22VAL0-0.0290.01027.3490.0060.0060.0000.0000.0000.000
23A23PRO0-0.0080.00730.6340.0000.0000.0000.0000.0000.000
24A24ARG10.8170.87930.051-0.024-0.0240.0000.0000.0000.000
25A25GLN0-0.019-0.01730.4170.0070.0070.0000.0000.0000.000
26A26PRO00.0590.02228.044-0.001-0.0010.0000.0000.0000.000
27A27ASN0-0.008-0.00429.1720.0030.0030.0000.0000.0000.000
28A28LEU0-0.0240.01132.5040.0010.0010.0000.0000.0000.000
29A29VAL0-0.018-0.02134.609-0.003-0.0030.0000.0000.0000.000
30A30GLU-1-0.790-0.86934.8970.0380.0380.0000.0000.0000.000
31A31ASP-1-0.801-0.89036.9980.0190.0190.0000.0000.0000.000
32A32GLY0-0.0150.01733.236-0.006-0.0060.0000.0000.0000.000
33A33VAL0-0.063-0.04631.6480.0060.0060.0000.0000.0000.000
34A34GLY00.0340.01528.948-0.010-0.0100.0000.0000.0000.000
35A35ILE0-0.0390.00129.2430.0100.0100.0000.0000.0000.000
36A36VAL0-0.011-0.00522.906-0.011-0.0110.0000.0000.0000.000
37A37GLU-1-0.836-0.90625.588-0.055-0.0550.0000.0000.0000.000
38A38LEU0-0.014-0.01021.555-0.014-0.0140.0000.0000.0000.000
39A39LEU0-0.009-0.00120.959-0.003-0.0030.0000.0000.0000.000
40A40PRO0-0.0030.01622.8780.0090.0090.0000.0000.0000.000
41A41PRO0-0.061-0.03220.964-0.025-0.0250.0000.0000.0000.000
42A42TYR00.035-0.02016.6550.0260.0260.0000.0000.0000.000
43A43ASN0-0.0340.00122.2150.0190.0190.0000.0000.0000.000
44A44SER0-0.014-0.03825.0830.0030.0030.0000.0000.0000.000
45A45PRO00.064-0.00326.4450.0100.0100.0000.0000.0000.000
46A46GLU-1-0.961-0.95226.4440.0540.0540.0000.0000.0000.000
47A47ALA0-0.022-0.00122.3070.0210.0210.0000.0000.0000.000
48A48VAL00.0090.01023.1160.0130.0130.0000.0000.0000.000
49A49ARG10.9280.96025.627-0.090-0.0900.0000.0000.0000.000
50A50GLY00.0410.02327.1910.0170.0170.0000.0000.0000.000
51A51LEU0-0.010-0.01123.0450.0130.0130.0000.0000.0000.000
52A52GLU-1-0.917-0.97026.9560.1160.1160.0000.0000.0000.000
53A53GLN0-0.091-0.02028.8450.0030.0030.0000.0000.0000.000
54A54PHE0-0.016-0.01025.0270.0080.0080.0000.0000.0000.000
55A55SER00.0650.02928.302-0.008-0.0080.0000.0000.0000.000
56A56HIS0-0.071-0.03225.784-0.002-0.0020.0000.0000.0000.000
57A57LEU00.0310.01622.5910.0150.0150.0000.0000.0000.000
58A58TRP0-0.080-0.04417.767-0.024-0.0240.0000.0000.0000.000
59A59LEU00.0080.01018.424-0.009-0.0090.0000.0000.0000.000
60A60ILE00.0090.00011.7600.0130.0130.0000.0000.0000.000
61A61PHE00.0130.00815.212-0.044-0.0440.0000.0000.0000.000
62A62GLN00.0250.01714.927-0.033-0.0330.0000.0000.0000.000
63A63MET0-0.077-0.02215.2580.0190.0190.0000.0000.0000.000
64A86VAL00.0520.02523.4320.0040.0040.0000.0000.0000.000
65A87GLY00.001-0.00320.670-0.022-0.0220.0000.0000.0000.000
66A88VAL00.0500.01015.9560.0240.0240.0000.0000.0000.000
67A89PHE0-0.008-0.02311.7830.0150.0150.0000.0000.0000.000
68A90ALA0-0.0090.02416.6630.0420.0420.0000.0000.0000.000
69A91SER0-0.0020.00619.514-0.013-0.0130.0000.0000.0000.000
70A92ARG10.9520.95518.369-0.144-0.1440.0000.0000.0000.000
71A93ALA0-0.0330.00419.635-0.019-0.0190.0000.0000.0000.000
72A94THR00.0730.01418.1820.0220.0220.0000.0000.0000.000
73A95HIS0-0.009-0.00217.060-0.042-0.0420.0000.0000.0000.000
74A96ARG10.8630.92813.211-0.005-0.0050.0000.0000.0000.000
75A97PRO0-0.012-0.01310.177-0.038-0.0380.0000.0000.0000.000
76A98ASN00.0700.0376.623-0.298-0.2980.0000.0000.0000.000
77A99PRO0-0.0270.01210.4400.1560.1560.0000.0000.0000.000
78A100LEU00.0330.0008.2710.0170.0170.0000.0000.0000.000
79A101GLY0-0.0130.00512.5810.0760.0760.0000.0000.0000.000
80A102MET0-0.006-0.00713.5870.0130.0130.0000.0000.0000.000
81A103SER0-0.055-0.04416.9830.0120.0120.0000.0000.0000.000
82A104LYS10.9861.01420.649-0.133-0.1330.0000.0000.0000.000
83A105VAL0-0.019-0.00622.815-0.014-0.0140.0000.0000.0000.000
84A106GLU-1-0.897-0.94725.6700.1190.1190.0000.0000.0000.000
85A107LEU0-0.026-0.02026.721-0.016-0.0160.0000.0000.0000.000
86A108ARG10.9250.96729.067-0.049-0.0490.0000.0000.0000.000
87A109GLN0-0.010-0.00331.5110.0030.0030.0000.0000.0000.000
88A110VAL00.0120.02428.369-0.006-0.0060.0000.0000.0000.000
89A111GLU-1-0.884-0.93930.7500.0120.0120.0000.0000.0000.000
90A112CYS0-0.0100.00431.273-0.005-0.0050.0000.0000.0000.000
91A113ILE00.0180.00133.1080.0020.0020.0000.0000.0000.000
92A114ASN0-0.031-0.02134.745-0.002-0.0020.0000.0000.0000.000
93A115GLY00.0140.00931.963-0.007-0.0070.0000.0000.0000.000
94A116ASN0-0.0190.00930.417-0.016-0.0160.0000.0000.0000.000
95A117ILE0-0.007-0.00827.1140.0100.0100.0000.0000.0000.000
96A118PHE0-0.003-0.00327.976-0.009-0.0090.0000.0000.0000.000
97A119LEU00.0040.00824.0020.0120.0120.0000.0000.0000.000
98A120HIS0-0.019-0.03028.156-0.006-0.0060.0000.0000.0000.000
99A121LEU00.023-0.00625.0000.0120.0120.0000.0000.0000.000
100A122GLY00.010-0.00429.297-0.004-0.0040.0000.0000.0000.000
101A123ALA0-0.037-0.02530.860-0.009-0.0090.0000.0000.0000.000
102A124VAL00.0020.00426.2770.0100.0100.0000.0000.0000.000
103A125ASP-1-0.869-0.93124.1510.0420.0420.0000.0000.0000.000
104A126LEU00.0020.01121.106-0.010-0.0100.0000.0000.0000.000
105A127VAL0-0.020-0.02124.2760.0030.0030.0000.0000.0000.000
106A128ASP-1-0.796-0.87925.478-0.069-0.0690.0000.0000.0000.000
107A129GLY00.0300.01825.911-0.012-0.0120.0000.0000.0000.000
108A130THR0-0.097-0.05219.987-0.023-0.0230.0000.0000.0000.000
109A131PRO00.0120.00517.8210.0190.0190.0000.0000.0000.000
110A132ILE0-0.024-0.02717.8010.0040.0040.0000.0000.0000.000
111A133PHE0-0.013-0.03912.466-0.043-0.0430.0000.0000.0000.000
112A134ASP-1-0.824-0.90913.1770.2530.2530.0000.0000.0000.000
113A135ILE00.0020.00115.324-0.002-0.0020.0000.0000.0000.000
114A136LYS10.8630.92813.021-0.394-0.3940.0000.0000.0000.000
115A137PRO00.0230.02718.681-0.026-0.0260.0000.0000.0000.000
116A138TYR0-0.041-0.03120.9010.0270.0270.0000.0000.0000.000
117A139ILE0-0.014-0.00821.384-0.023-0.0230.0000.0000.0000.000
118A140ALA00.014-0.01223.2470.0190.0190.0000.0000.0000.000
119A141TYR0-0.036-0.02123.996-0.006-0.0060.0000.0000.0000.000
120A142ALA00.011-0.00719.7780.0020.0020.0000.0000.0000.000
121A143ASP-1-0.800-0.88119.5000.4270.4270.0000.0000.0000.000
122A144SER0-0.105-0.04621.581-0.023-0.0230.0000.0000.0000.000
123A145GLU-1-0.906-0.95023.8010.3190.3190.0000.0000.0000.000
124A146PRO0-0.003-0.01725.697-0.012-0.0120.0000.0000.0000.000
125A147ASN0-0.043-0.01728.965-0.011-0.0110.0000.0000.0000.000
126A148ALA00.0160.01924.998-0.002-0.0020.0000.0000.0000.000
127A149GLN00.0220.01826.864-0.024-0.0240.0000.0000.0000.000
128A150SER0-0.049-0.04026.5520.0040.0040.0000.0000.0000.000
129A151SER0-0.0300.00728.2460.0050.0050.0000.0000.0000.000
130A159VAL00.005-0.01440.6380.0000.0000.0000.0000.0000.000
131A160LYS10.9460.99142.148-0.027-0.0270.0000.0000.0000.000
132A161MET00.0230.02241.971-0.002-0.0020.0000.0000.0000.000
133A162THR0-0.003-0.01345.2420.0010.0010.0000.0000.0000.000
134A163VAL00.0270.00644.206-0.002-0.0020.0000.0000.0000.000
135A164GLU-1-0.924-0.95047.512-0.002-0.0020.0000.0000.0000.000
136A165PHE00.0360.01346.465-0.003-0.0030.0000.0000.0000.000
137A166THR00.0500.03150.9400.0010.0010.0000.0000.0000.000
138A167GLU-1-0.795-0.90453.481-0.005-0.0050.0000.0000.0000.000
139A168GLN0-0.007-0.00252.6240.0000.0000.0000.0000.0000.000
140A169ALA00.0150.01549.687-0.001-0.0010.0000.0000.0000.000
141A170LYS10.8110.88650.7060.0040.0040.0000.0000.0000.000
142A171SER0-0.0100.00752.4570.0010.0010.0000.0000.0000.000
143A172ALA0-0.018-0.01349.2010.0000.0000.0000.0000.0000.000
144A173VAL00.010-0.00746.590-0.001-0.0010.0000.0000.0000.000
145A174LYS10.8600.92648.4180.0040.0040.0000.0000.0000.000
146A175LYS10.9981.01250.3810.0250.0250.0000.0000.0000.000
147A176ARG10.8430.92845.0510.0250.0250.0000.0000.0000.000
148A177GLU-1-0.828-0.90545.973-0.001-0.0010.0000.0000.0000.000
149A178GLU-1-0.907-0.95047.512-0.007-0.0070.0000.0000.0000.000
150A179LYS10.8750.93944.2130.0240.0240.0000.0000.0000.000
151A180ARG10.8990.94936.9810.0240.0240.0000.0000.0000.000
152A181PRO00.0460.03242.7400.0010.0010.0000.0000.0000.000
153A182HIS00.018-0.00342.1740.0010.0010.0000.0000.0000.000
154A183LEU00.0060.01341.1160.0010.0010.0000.0000.0000.000
155A184SER0-0.022-0.01743.0400.0000.0000.0000.0000.0000.000
156A185ARG10.8170.87840.740-0.024-0.0240.0000.0000.0000.000
157A186PHE00.0160.01735.2120.0020.0020.0000.0000.0000.000
158A187ILE0-0.011-0.00639.212-0.002-0.0020.0000.0000.0000.000
159A188ARG10.8180.88139.355-0.030-0.0300.0000.0000.0000.000
160A189GLN00.0320.00534.119-0.001-0.0010.0000.0000.0000.000
161A190VAL00.0330.01837.9680.0010.0010.0000.0000.0000.000
162A191LEU0-0.115-0.04040.4710.0010.0010.0000.0000.0000.000
163A192GLU-1-0.807-0.88635.2320.0320.0320.0000.0000.0000.000
164A206ASP-1-0.908-0.95150.350-0.026-0.0260.0000.0000.0000.000
165A207ARG10.8360.91543.8270.0140.0140.0000.0000.0000.000
166A208ILE00.0310.02246.5570.0030.0030.0000.0000.0000.000
167A209TYR0-0.030-0.00841.032-0.002-0.0020.0000.0000.0000.000
168A210GLY00.0460.01140.6630.0020.0020.0000.0000.0000.000
169A211MET0-0.015-0.00436.1420.0000.0000.0000.0000.0000.000
170A212SER0-0.007-0.00535.0260.0030.0030.0000.0000.0000.000
171A213LEU0-0.0250.01735.2120.0010.0010.0000.0000.0000.000
172A214TYR0-0.008-0.02835.3190.0000.0000.0000.0000.0000.000
173A215GLU-1-0.843-0.93236.576-0.042-0.0420.0000.0000.0000.000
174A216PHE0-0.0210.00038.794-0.001-0.0010.0000.0000.0000.000
175A217ASN00.0330.00839.033-0.001-0.0010.0000.0000.0000.000
176A218VAL00.0070.00440.7700.0020.0020.0000.0000.0000.000
177A219LYS10.8110.89042.1370.0420.0420.0000.0000.0000.000
178A220TRP0-0.047-0.05839.0740.0030.0030.0000.0000.0000.000
179A221ARG11.1481.14745.9280.0130.0130.0000.0000.0000.000
180A222ILE0-0.031-0.00947.3120.0020.0020.0000.0000.0000.000
181A223LYS10.9420.90942.867-0.006-0.0060.0000.0000.0000.000
182A224ALA00.009-0.00246.9520.0020.0020.0000.0000.0000.000
183A225GLY0-0.0520.03146.700-0.002-0.0020.0000.0000.0000.000
184A226THR0-0.086-0.06347.7490.0010.0010.0000.0000.0000.000
185A227VAL00.0220.00345.694-0.003-0.0030.0000.0000.0000.000
186A228ASN0-0.007-0.03247.8180.0030.0030.0000.0000.0000.000
187A229CYS0-0.011-0.01248.1760.0020.0020.0000.0000.0000.000
188A230VAL00.0380.03144.245-0.002-0.0020.0000.0000.0000.000
189A231GLU-1-0.785-0.87942.913-0.042-0.0420.0000.0000.0000.000