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: 3QR9L

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 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 189
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -1973282.802588
FMO2-HF: Nuclear repulsion 1897849.342085
FMO2-HF: Total energy -75433.460502
FMO2-MP2: Total energy -75653.193575


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.
-11.035-6.7071.939-2.941-3.328-0.012
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 : -0.024 / q_NPA : -0.008
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-1-0.894-0.9512.642-11.722-7.8891.922-2.860-2.896-0.012
4A4LEU0-0.010-0.0043.489-0.3740.1210.017-0.081-0.4320.000
5A5THR0-0.049-0.0345.4410.4350.4350.0000.0000.0000.000
6A6LEU0-0.0020.0057.5110.1170.1170.0000.0000.0000.000
7A7SER00.0250.00810.754-0.009-0.0090.0000.0000.0000.000
8A8PRO0-0.033-0.02414.3440.0440.0440.0000.0000.0000.000
9A9ILE00.0080.01515.3450.0010.0010.0000.0000.0000.000
10A10ALA00.004-0.00218.0170.0230.0230.0000.0000.0000.000
11A11ILE0-0.0240.00620.143-0.028-0.0280.0000.0000.0000.000
12A12ILE0-0.027-0.00522.7950.0240.0240.0000.0000.0000.000
13A13HIS0-0.015-0.00724.867-0.016-0.0160.0000.0000.0000.000
14A14THR0-0.004-0.03627.0130.0150.0150.0000.0000.0000.000
15A15PRO0-0.032-0.00529.968-0.009-0.0090.0000.0000.0000.000
16A16TYR0-0.034-0.03928.545-0.006-0.0060.0000.0000.0000.000
17A17LYS10.8770.94129.7650.0460.0460.0000.0000.0000.000
18A18GLU-1-0.837-0.89229.576-0.069-0.0690.0000.0000.0000.000
19A19LYS10.9720.95923.6770.0470.0470.0000.0000.0000.000
20A20PHE0-0.0250.00028.5940.0110.0110.0000.0000.0000.000
21A21SER0-0.022-0.03432.1360.0070.0070.0000.0000.0000.000
22A22VAL00.0070.01927.3680.0050.0050.0000.0000.0000.000
23A23PRO0-0.024-0.00130.7210.0000.0000.0000.0000.0000.000
24A24ARG10.8450.89530.145-0.033-0.0330.0000.0000.0000.000
25A25GLN0-0.0140.00030.2430.0070.0070.0000.0000.0000.000
26A26PRO00.0610.02428.4730.0010.0010.0000.0000.0000.000
27A27ASN00.0230.00829.2720.0020.0020.0000.0000.0000.000
28A28LEU00.0040.01732.4470.0000.0000.0000.0000.0000.000
29A29VAL0-0.053-0.02934.553-0.005-0.0050.0000.0000.0000.000
30A30GLU-1-0.761-0.85334.9760.0430.0430.0000.0000.0000.000
31A31ASP-1-0.746-0.87836.2170.0270.0270.0000.0000.0000.000
32A32GLY0-0.031-0.01233.418-0.007-0.0070.0000.0000.0000.000
33A33VAL0-0.064-0.03531.5630.0040.0040.0000.0000.0000.000
34A34GLY00.0430.02628.464-0.010-0.0100.0000.0000.0000.000
35A35ILE0-0.034-0.01628.9160.0100.0100.0000.0000.0000.000
36A36VAL0-0.0070.00122.565-0.012-0.0120.0000.0000.0000.000
37A37GLU-1-0.843-0.91025.056-0.051-0.0510.0000.0000.0000.000
38A38LEU0-0.023-0.01521.232-0.013-0.0130.0000.0000.0000.000
39A39LEU00.0020.00520.448-0.005-0.0050.0000.0000.0000.000
40A40PRO00.0090.00422.8840.0110.0110.0000.0000.0000.000
41A41PRO0-0.071-0.03520.447-0.025-0.0250.0000.0000.0000.000
42A42TYR00.0560.01517.0560.0130.0130.0000.0000.0000.000
43A43ASN0-0.025-0.00921.7930.0170.0170.0000.0000.0000.000
44A44SER0-0.007-0.01424.6830.0060.0060.0000.0000.0000.000
45A45PRO00.053-0.00625.9060.0110.0110.0000.0000.0000.000
46A46GLU-1-0.845-0.90525.5420.0650.0650.0000.0000.0000.000
47A47ALA0-0.036-0.00121.7230.0220.0220.0000.0000.0000.000
48A48VAL0-0.001-0.00622.7120.0110.0110.0000.0000.0000.000
49A49ARG10.8230.90825.423-0.083-0.0830.0000.0000.0000.000
50A50GLY00.0320.01726.9270.0160.0160.0000.0000.0000.000
51A51LEU0-0.023-0.02022.5190.0140.0140.0000.0000.0000.000
52A52GLU-1-0.826-0.92126.6020.1240.1240.0000.0000.0000.000
53A53GLN0-0.104-0.03728.8280.0000.0000.0000.0000.0000.000
54A54PHE0-0.037-0.01725.2340.0160.0160.0000.0000.0000.000
55A55SER00.0320.00828.304-0.008-0.0080.0000.0000.0000.000
56A56HIS0-0.070-0.03025.9270.0000.0000.0000.0000.0000.000
57A57LEU00.0420.02222.5370.0170.0170.0000.0000.0000.000
58A58TRP0-0.094-0.05417.810-0.023-0.0230.0000.0000.0000.000
59A59LEU00.0060.00118.454-0.016-0.0160.0000.0000.0000.000
60A60ILE00.006-0.00411.8010.0150.0150.0000.0000.0000.000
61A61PHE00.0050.00215.251-0.047-0.0470.0000.0000.0000.000
62A62GLN00.0220.02015.109-0.019-0.0190.0000.0000.0000.000
63A63MET0-0.092-0.02415.2560.0190.0190.0000.0000.0000.000
64A86VAL00.0580.02824.0960.0040.0040.0000.0000.0000.000
65A87GLY00.010-0.00120.952-0.023-0.0230.0000.0000.0000.000
66A88VAL00.0450.01716.1250.0250.0250.0000.0000.0000.000
67A89PHE0-0.002-0.01011.9980.0140.0140.0000.0000.0000.000
68A90ALA0-0.0090.01717.0340.0490.0490.0000.0000.0000.000
69A91SER0-0.013-0.00619.761-0.024-0.0240.0000.0000.0000.000
70A92ARG10.9290.95019.042-0.168-0.1680.0000.0000.0000.000
71A93ALA0-0.0180.01120.255-0.016-0.0160.0000.0000.0000.000
72A94THR00.0620.00118.5300.0260.0260.0000.0000.0000.000
73A95HIS0-0.0070.01517.329-0.030-0.0300.0000.0000.0000.000
74A96ARG10.8440.89013.346-0.021-0.0210.0000.0000.0000.000
75A97PRO0-0.002-0.00710.323-0.038-0.0380.0000.0000.0000.000
76A98ASN00.0700.0386.584-0.248-0.2480.0000.0000.0000.000
77A99PRO0-0.0230.01210.5070.1610.1610.0000.0000.0000.000
78A100LEU00.0300.0148.2950.0130.0130.0000.0000.0000.000
79A101GLY0-0.008-0.00412.6070.0760.0760.0000.0000.0000.000
80A102MET00.008-0.00613.6320.0200.0200.0000.0000.0000.000
81A103SER0-0.054-0.05216.8430.0100.0100.0000.0000.0000.000
82A104LYS10.9610.99220.406-0.130-0.1300.0000.0000.0000.000
83A105VAL0-0.043-0.02722.881-0.019-0.0190.0000.0000.0000.000
84A106GLU-1-0.852-0.91725.6920.1320.1320.0000.0000.0000.000
85A107LEU0-0.005-0.00926.492-0.015-0.0150.0000.0000.0000.000
86A108ARG10.8590.94129.052-0.056-0.0560.0000.0000.0000.000
87A109GLN0-0.039-0.02431.5760.0030.0030.0000.0000.0000.000
88A110VAL00.0170.02528.367-0.005-0.0050.0000.0000.0000.000
89A111GLU-1-0.832-0.90230.5460.0170.0170.0000.0000.0000.000
90A112CYS0-0.033-0.01930.482-0.001-0.0010.0000.0000.0000.000
91A113ILE00.0230.01632.6120.0010.0010.0000.0000.0000.000
92A114ASN0-0.015-0.01734.342-0.003-0.0030.0000.0000.0000.000
93A115GLY00.0230.01931.850-0.007-0.0070.0000.0000.0000.000
94A116ASN0-0.0310.00230.051-0.013-0.0130.0000.0000.0000.000
95A117ILE0-0.008-0.01226.9450.0100.0100.0000.0000.0000.000
96A118PHE0-0.016-0.00627.505-0.008-0.0080.0000.0000.0000.000
97A119LEU0-0.005-0.00123.7960.0130.0130.0000.0000.0000.000
98A120HIS0-0.004-0.01727.925-0.005-0.0050.0000.0000.0000.000
99A121LEU00.0150.00625.1380.0120.0120.0000.0000.0000.000
100A122GLY0-0.017-0.02129.576-0.005-0.0050.0000.0000.0000.000
101A123ALA0-0.044-0.02730.598-0.008-0.0080.0000.0000.0000.000
102A124VAL00.0110.01326.1740.0120.0120.0000.0000.0000.000
103A125ASP-1-0.872-0.91823.4990.0610.0610.0000.0000.0000.000
104A126LEU00.0070.00920.995-0.013-0.0130.0000.0000.0000.000
105A127VAL0-0.007-0.00424.2790.0020.0020.0000.0000.0000.000
106A128ASP-1-0.785-0.87025.459-0.058-0.0580.0000.0000.0000.000
107A129GLY00.0360.02625.847-0.012-0.0120.0000.0000.0000.000
108A130THR0-0.092-0.05620.163-0.023-0.0230.0000.0000.0000.000
109A131PRO00.0110.00017.8130.0160.0160.0000.0000.0000.000
110A132ILE0-0.008-0.01517.3870.0120.0120.0000.0000.0000.000
111A133PHE0-0.007-0.01712.221-0.028-0.0280.0000.0000.0000.000
112A134ASP-1-0.808-0.89612.4750.3120.3120.0000.0000.0000.000
113A135ILE00.0070.00414.839-0.008-0.0080.0000.0000.0000.000
114A136LYS10.8250.91113.036-0.392-0.3920.0000.0000.0000.000
115A137PRO00.0420.03418.815-0.024-0.0240.0000.0000.0000.000
116A138TYR0-0.029-0.02020.6870.0370.0370.0000.0000.0000.000
117A139ILE0-0.008-0.01420.840-0.025-0.0250.0000.0000.0000.000
118A140ALA00.003-0.01123.1980.0270.0270.0000.0000.0000.000
119A141TYR0-0.033-0.01524.116-0.010-0.0100.0000.0000.0000.000
120A142ALA0-0.012-0.00820.0950.0130.0130.0000.0000.0000.000
121A143ASP-1-0.811-0.88319.6250.4580.4580.0000.0000.0000.000
122A144SER0-0.080-0.04121.512-0.034-0.0340.0000.0000.0000.000
123A145GLU-1-0.855-0.92024.1960.3180.3180.0000.0000.0000.000
124A146PRO0-0.021-0.02625.912-0.014-0.0140.0000.0000.0000.000
125A147ASN0-0.050-0.02228.875-0.018-0.0180.0000.0000.0000.000
126A148ALA00.0040.00625.1070.0020.0020.0000.0000.0000.000
127A149GLN00.0100.01926.810-0.025-0.0250.0000.0000.0000.000
128A150SER0-0.040-0.02926.7070.0070.0070.0000.0000.0000.000
129A151SER0-0.037-0.00628.3580.0010.0010.0000.0000.0000.000
130A159VAL00.015-0.01040.6040.0010.0010.0000.0000.0000.000
131A160LYS10.9280.97442.403-0.034-0.0340.0000.0000.0000.000
132A161MET00.0360.04642.280-0.002-0.0020.0000.0000.0000.000
133A162THR0-0.014-0.01945.4390.0020.0020.0000.0000.0000.000
134A163VAL00.0150.00244.555-0.002-0.0020.0000.0000.0000.000
135A164GLU-1-0.893-0.94647.8590.0000.0000.0000.0000.0000.000
136A165PHE00.0270.00546.359-0.002-0.0020.0000.0000.0000.000
137A166THR00.0330.00851.2680.0000.0000.0000.0000.0000.000
138A167GLU-1-0.783-0.89253.633-0.003-0.0030.0000.0000.0000.000
139A168GLN0-0.0040.01152.4060.0000.0000.0000.0000.0000.000
140A169ALA00.0230.01449.293-0.001-0.0010.0000.0000.0000.000
141A170LYS10.8130.88350.3130.0020.0020.0000.0000.0000.000
142A171SER0-0.0020.00952.3090.0010.0010.0000.0000.0000.000
143A172ALA0-0.016-0.01249.1970.0000.0000.0000.0000.0000.000
144A173VAL00.0030.00546.270-0.002-0.0020.0000.0000.0000.000
145A174LYS10.8730.93048.0910.0000.0000.0000.0000.0000.000
146A175LYS11.0001.01150.2750.0220.0220.0000.0000.0000.000
147A176ARG10.8190.89244.8480.0210.0210.0000.0000.0000.000
148A177GLU-1-0.784-0.87345.8420.0040.0040.0000.0000.0000.000
149A178GLU-1-0.893-0.95846.964-0.005-0.0050.0000.0000.0000.000
150A179LYS10.8550.92544.3030.0190.0190.0000.0000.0000.000
151A180ARG10.8520.92236.9500.0180.0180.0000.0000.0000.000
152A181PRO00.0480.03242.7900.0010.0010.0000.0000.0000.000
153A182HIS00.0330.01541.9450.0020.0020.0000.0000.0000.000
154A183LEU00.0020.01440.9110.0010.0010.0000.0000.0000.000
155A184SER0-0.019-0.03342.896-0.001-0.0010.0000.0000.0000.000
156A185ARG10.7510.85240.922-0.030-0.0300.0000.0000.0000.000
157A186PHE00.0330.01935.1910.0030.0030.0000.0000.0000.000
158A187ILE00.0170.00139.1270.0000.0000.0000.0000.0000.000
159A188ARG10.7840.86839.233-0.037-0.0370.0000.0000.0000.000
160A189GLN00.0340.01733.728-0.002-0.0020.0000.0000.0000.000
161A190VAL0-0.0140.00238.0420.0000.0000.0000.0000.0000.000
162A191LEU0-0.055-0.01940.6140.0000.0000.0000.0000.0000.000
163A192GLU-1-0.863-0.92435.0550.0380.0380.0000.0000.0000.000
164A206ASP-1-0.890-0.94250.680-0.022-0.0220.0000.0000.0000.000
165A207ARG10.8110.89743.6540.0110.0110.0000.0000.0000.000
166A208ILE00.0190.01946.7920.0030.0030.0000.0000.0000.000
167A209TYR0-0.0090.00141.454-0.002-0.0020.0000.0000.0000.000
168A210GLY00.029-0.00641.0630.0020.0020.0000.0000.0000.000
169A211MET0-0.0320.00136.0290.0000.0000.0000.0000.0000.000
170A212SER0-0.024-0.02134.9570.0020.0020.0000.0000.0000.000
171A213LEU0-0.044-0.00535.0460.0010.0010.0000.0000.0000.000
172A214TYR0-0.005-0.01135.5560.0000.0000.0000.0000.0000.000
173A215GLU-1-0.834-0.90536.268-0.039-0.0390.0000.0000.0000.000
174A216PHE0-0.015-0.01138.798-0.001-0.0010.0000.0000.0000.000
175A217ASN00.0290.01538.6700.0000.0000.0000.0000.0000.000
176A218VAL00.0150.02640.7640.0010.0010.0000.0000.0000.000
177A219LYS10.8230.88242.0140.0350.0350.0000.0000.0000.000
178A220TRP00.006-0.00639.2030.0030.0030.0000.0000.0000.000
179A221ARG10.9380.99645.9820.0070.0070.0000.0000.0000.000
180A222ILE00.0330.02048.1180.0020.0020.0000.0000.0000.000
181A223LYS10.9250.93442.676-0.010-0.0100.0000.0000.0000.000
182A224ALA00.0140.00847.2690.0010.0010.0000.0000.0000.000
183A225GLY0-0.0160.01946.154-0.002-0.0020.0000.0000.0000.000
184A226THR0-0.033-0.03247.2100.0010.0010.0000.0000.0000.000
185A227VAL00.0210.01646.117-0.003-0.0030.0000.0000.0000.000
186A228ASN00.0130.00648.0490.0030.0030.0000.0000.0000.000
187A229CYS0-0.053-0.03748.0180.0010.0010.0000.0000.0000.000
188A230VAL00.0470.01743.8170.0000.0000.0000.0000.0000.000
189A231GLU-1-0.745-0.84342.734-0.036-0.0360.0000.0000.0000.000