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: N1Q9Q

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 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 189
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -1971142.65705
FMO2-HF: Nuclear repulsion 1895712.039502
FMO2-HF: Total energy -75430.617548
FMO2-MP2: Total energy -75650.519221


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.
-9.703-5.7371.692-2.713-2.945-0.008
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 : -0.008 / q_NPA : 0.000
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-1-0.900-0.9452.663-9.922-6.2341.691-2.670-2.709-0.008
4A4LEU0-0.007-0.0234.148-0.441-0.1630.001-0.043-0.2360.000
5A5THR0-0.037-0.0095.9240.3350.3350.0000.0000.0000.000
6A6LEU0-0.023-0.0048.1890.1450.1450.0000.0000.0000.000
7A7SER00.0210.01311.285-0.011-0.0110.0000.0000.0000.000
8A8PRO0-0.027-0.02014.9600.0490.0490.0000.0000.0000.000
9A9ILE00.0440.03416.4310.0060.0060.0000.0000.0000.000
10A10ALA00.007-0.01518.9550.0270.0270.0000.0000.0000.000
11A11ILE0-0.0170.01721.014-0.026-0.0260.0000.0000.0000.000
12A12ILE0-0.0260.00023.6090.0210.0210.0000.0000.0000.000
13A13HIS0-0.030-0.01825.310-0.011-0.0110.0000.0000.0000.000
14A14THR00.019-0.00927.3040.0160.0160.0000.0000.0000.000
15A15PRO0-0.031-0.00430.228-0.009-0.0090.0000.0000.0000.000
16A16TYR0-0.003-0.01929.466-0.005-0.0050.0000.0000.0000.000
17A17LYS10.9811.01129.9510.0540.0540.0000.0000.0000.000
18A18GLU-1-0.896-0.93229.292-0.079-0.0790.0000.0000.0000.000
19A19LYS10.9530.94523.8980.0710.0710.0000.0000.0000.000
20A20PHE0-0.028-0.01428.4190.0120.0120.0000.0000.0000.000
21A21SER0-0.031-0.03231.8450.0050.0050.0000.0000.0000.000
22A22VAL0-0.0100.02027.6350.0060.0060.0000.0000.0000.000
23A23PRO0-0.0070.00530.7830.0010.0010.0000.0000.0000.000
24A24ARG10.9590.95330.138-0.021-0.0210.0000.0000.0000.000
25A25GLN0-0.032-0.02130.5010.0050.0050.0000.0000.0000.000
26A26PRO00.0500.01728.372-0.001-0.0010.0000.0000.0000.000
27A27ASN00.0180.01229.463-0.007-0.0070.0000.0000.0000.000
28A28LEU0-0.0490.00432.6720.0010.0010.0000.0000.0000.000
29A29VAL0-0.038-0.02334.691-0.003-0.0030.0000.0000.0000.000
30A30GLU-1-0.866-0.93635.1050.0360.0360.0000.0000.0000.000
31A31ASP-1-0.768-0.88537.2300.0150.0150.0000.0000.0000.000
32A32GLY0-0.0390.00033.452-0.006-0.0060.0000.0000.0000.000
33A33VAL0-0.076-0.04631.8900.0050.0050.0000.0000.0000.000
34A34GLY00.0320.01429.239-0.009-0.0090.0000.0000.0000.000
35A35ILE0-0.0280.00829.5550.0100.0100.0000.0000.0000.000
36A36VAL0-0.019-0.01023.193-0.011-0.0110.0000.0000.0000.000
37A37GLU-1-0.829-0.90025.947-0.054-0.0540.0000.0000.0000.000
38A38LEU0-0.010-0.01121.711-0.014-0.0140.0000.0000.0000.000
39A39LEU0-0.030-0.00521.171-0.002-0.0020.0000.0000.0000.000
40A40PRO0-0.0150.01823.3010.0070.0070.0000.0000.0000.000
41A41PRO0-0.055-0.03621.439-0.023-0.0230.0000.0000.0000.000
42A42TYR00.042-0.00517.2580.0100.0100.0000.0000.0000.000
43A43ASN00.0130.03022.6480.0180.0180.0000.0000.0000.000
44A44SER00.0250.00525.5140.0040.0040.0000.0000.0000.000
45A45PRO00.049-0.01226.8680.0100.0100.0000.0000.0000.000
46A46GLU-1-1.016-1.00527.0360.0490.0490.0000.0000.0000.000
47A47ALA0-0.0090.00522.7410.0200.0200.0000.0000.0000.000
48A48VAL00.0100.01723.5180.0120.0120.0000.0000.0000.000
49A49ARG10.9460.96826.023-0.087-0.0870.0000.0000.0000.000
50A50GLY00.0400.02427.5630.0160.0160.0000.0000.0000.000
51A51LEU0-0.027-0.02624.0910.0120.0120.0000.0000.0000.000
52A52GLU-1-0.925-0.98227.3100.1070.1070.0000.0000.0000.000
53A53GLN0-0.083-0.00428.9820.0070.0070.0000.0000.0000.000
54A54PHE0-0.023-0.01625.7020.0070.0070.0000.0000.0000.000
55A55SER00.0720.03628.591-0.007-0.0070.0000.0000.0000.000
56A56HIS0-0.039-0.00525.947-0.003-0.0030.0000.0000.0000.000
57A57LEU00.0230.01222.9840.0150.0150.0000.0000.0000.000
58A58TRP0-0.079-0.04018.022-0.023-0.0230.0000.0000.0000.000
59A59LEU00.0070.01018.710-0.008-0.0080.0000.0000.0000.000
60A60ILE00.0000.00012.0180.0140.0140.0000.0000.0000.000
61A61PHE00.0180.01115.484-0.041-0.0410.0000.0000.0000.000
62A62GLN00.0210.01215.152-0.051-0.0510.0000.0000.0000.000
63A63MET0-0.085-0.02115.3400.0210.0210.0000.0000.0000.000
64A86VAL00.0570.02523.7030.0030.0030.0000.0000.0000.000
65A87GLY0-0.003-0.00420.440-0.022-0.0220.0000.0000.0000.000
66A88VAL00.0570.01315.8880.0230.0230.0000.0000.0000.000
67A89PHE0-0.020-0.03012.0410.0160.0160.0000.0000.0000.000
68A90ALA0-0.0070.03016.4870.0390.0390.0000.0000.0000.000
69A91SER0-0.0090.00719.388-0.014-0.0140.0000.0000.0000.000
70A92ARG10.9440.94918.563-0.141-0.1410.0000.0000.0000.000
71A93ALA0-0.0090.01019.538-0.019-0.0190.0000.0000.0000.000
72A94THR00.0630.00518.1770.0170.0170.0000.0000.0000.000
73A95HIS0-0.021-0.00217.078-0.048-0.0480.0000.0000.0000.000
74A96ARG10.8950.94813.166-0.008-0.0080.0000.0000.0000.000
75A97PRO0-0.020-0.01410.341-0.036-0.0360.0000.0000.0000.000
76A98ASN00.0820.0446.537-0.324-0.3240.0000.0000.0000.000
77A99PRO0-0.0210.01310.4590.1520.1520.0000.0000.0000.000
78A100LEU00.0360.0018.5490.0170.0170.0000.0000.0000.000
79A101GLY0-0.0120.00312.7320.0730.0730.0000.0000.0000.000
80A102MET0-0.020-0.01614.0280.0110.0110.0000.0000.0000.000
81A103SER0-0.055-0.03117.1540.0130.0130.0000.0000.0000.000
82A104LYS10.9951.01320.843-0.145-0.1450.0000.0000.0000.000
83A105VAL00.0030.00623.023-0.012-0.0120.0000.0000.0000.000
84A106GLU-1-0.931-0.98125.9140.1120.1120.0000.0000.0000.000
85A107LEU0-0.026-0.01827.037-0.015-0.0150.0000.0000.0000.000
86A108ARG10.9460.97629.369-0.044-0.0440.0000.0000.0000.000
87A109GLN00.010-0.00131.8590.0000.0000.0000.0000.0000.000
88A110VAL00.0060.02328.677-0.006-0.0060.0000.0000.0000.000
89A111GLU-1-0.920-0.97431.1210.0060.0060.0000.0000.0000.000
90A112CYS0-0.0130.00131.688-0.005-0.0050.0000.0000.0000.000
91A113ILE00.0090.00533.5170.0020.0020.0000.0000.0000.000
92A114ASN0-0.031-0.02635.162-0.002-0.0020.0000.0000.0000.000
93A115GLY00.0000.00132.392-0.006-0.0060.0000.0000.0000.000
94A116ASN0-0.0200.01530.845-0.014-0.0140.0000.0000.0000.000
95A117ILE0-0.002-0.01427.4110.0090.0090.0000.0000.0000.000
96A118PHE00.0030.00028.373-0.009-0.0090.0000.0000.0000.000
97A119LEU0-0.0010.00624.2380.0120.0120.0000.0000.0000.000
98A120HIS00.0010.00228.517-0.006-0.0060.0000.0000.0000.000
99A121LEU00.015-0.01025.3270.0120.0120.0000.0000.0000.000
100A122GLY0-0.007-0.00729.583-0.004-0.0040.0000.0000.0000.000
101A123ALA0-0.037-0.02531.126-0.009-0.0090.0000.0000.0000.000
102A124VAL00.0000.00226.5770.0090.0090.0000.0000.0000.000
103A125ASP-1-0.870-0.95424.4620.0390.0390.0000.0000.0000.000
104A126LEU0-0.022-0.00321.484-0.009-0.0090.0000.0000.0000.000
105A127VAL0-0.008-0.01524.4530.0030.0030.0000.0000.0000.000
106A128ASP-1-0.911-0.97525.725-0.076-0.0760.0000.0000.0000.000
107A129GLY00.0270.01726.200-0.012-0.0120.0000.0000.0000.000
108A130THR0-0.094-0.04420.363-0.023-0.0230.0000.0000.0000.000
109A131PRO00.0070.00218.1950.0170.0170.0000.0000.0000.000
110A132ILE0-0.017-0.02318.1240.0030.0030.0000.0000.0000.000
111A133PHE0-0.016-0.04312.836-0.038-0.0380.0000.0000.0000.000
112A134ASP-1-0.875-0.95813.5410.1840.1840.0000.0000.0000.000
113A135ILE00.0230.01115.6890.0010.0010.0000.0000.0000.000
114A136LYS10.9020.97313.230-0.381-0.3810.0000.0000.0000.000
115A137PRO00.0330.02318.995-0.026-0.0260.0000.0000.0000.000
116A138TYR0-0.039-0.02621.1550.0300.0300.0000.0000.0000.000
117A139ILE0-0.0080.00221.631-0.021-0.0210.0000.0000.0000.000
118A140ALA00.007-0.01823.4070.0180.0180.0000.0000.0000.000
119A141TYR0-0.036-0.01924.383-0.004-0.0040.0000.0000.0000.000
120A142ALA00.003-0.01319.8780.0020.0020.0000.0000.0000.000
121A143ASP-1-0.803-0.88719.5320.4110.4110.0000.0000.0000.000
122A144SER0-0.108-0.04321.691-0.021-0.0210.0000.0000.0000.000
123A145GLU-1-0.905-0.95223.8550.3310.3310.0000.0000.0000.000
124A146PRO0-0.021-0.02625.718-0.012-0.0120.0000.0000.0000.000
125A147ASN0-0.035-0.01728.984-0.007-0.0070.0000.0000.0000.000
126A148ALA00.0240.02324.981-0.001-0.0010.0000.0000.0000.000
127A149GLN00.0140.01426.808-0.021-0.0210.0000.0000.0000.000
128A150SER0-0.042-0.03226.4460.0040.0040.0000.0000.0000.000
129A151SER0-0.0280.00428.1210.0010.0010.0000.0000.0000.000
130A159VAL00.007-0.01140.4770.0000.0000.0000.0000.0000.000
131A160LYS10.9691.00342.209-0.027-0.0270.0000.0000.0000.000
132A161MET00.0130.02242.085-0.002-0.0020.0000.0000.0000.000
133A162THR0-0.017-0.02045.3300.0010.0010.0000.0000.0000.000
134A163VAL00.0390.01144.301-0.002-0.0020.0000.0000.0000.000
135A164GLU-1-0.933-0.95447.649-0.001-0.0010.0000.0000.0000.000
136A165PHE0-0.007-0.00646.534-0.002-0.0020.0000.0000.0000.000
137A166THR00.0140.01051.1050.0010.0010.0000.0000.0000.000
138A167GLU-1-0.811-0.92153.661-0.006-0.0060.0000.0000.0000.000
139A168GLN0-0.021-0.01552.7190.0000.0000.0000.0000.0000.000
140A169ALA00.0030.01049.737-0.001-0.0010.0000.0000.0000.000
141A170LYS10.9080.94950.9140.0020.0020.0000.0000.0000.000
142A171SER0-0.0180.00352.6800.0010.0010.0000.0000.0000.000
143A172ALA0-0.015-0.01049.4210.0000.0000.0000.0000.0000.000
144A173VAL00.030-0.00346.734-0.002-0.0020.0000.0000.0000.000
145A174LYS10.9330.96948.6660.0050.0050.0000.0000.0000.000
146A175LYS10.9781.00749.8010.0260.0260.0000.0000.0000.000
147A176ARG10.8180.91545.5450.0240.0240.0000.0000.0000.000
148A177GLU-1-0.842-0.92246.250-0.002-0.0020.0000.0000.0000.000
149A178GLU-1-0.913-0.95647.799-0.008-0.0080.0000.0000.0000.000
150A179LYS10.8820.94744.4380.0240.0240.0000.0000.0000.000
151A180ARG10.9540.97537.3860.0200.0200.0000.0000.0000.000
152A181PRO00.0340.03143.0220.0010.0010.0000.0000.0000.000
153A182HIS00.010-0.00842.3940.0010.0010.0000.0000.0000.000
154A183LEU00.0120.02441.4990.0010.0010.0000.0000.0000.000
155A184SER0-0.013-0.02243.263-0.001-0.0010.0000.0000.0000.000
156A185ARG10.8620.92541.390-0.021-0.0210.0000.0000.0000.000
157A186PHE00.0160.01935.1850.0020.0020.0000.0000.0000.000
158A187ILE00.004-0.00339.407-0.001-0.0010.0000.0000.0000.000
159A188ARG10.8020.89739.147-0.028-0.0280.0000.0000.0000.000
160A189GLN00.0450.02135.131-0.002-0.0020.0000.0000.0000.000
161A190VAL00.0290.01438.1150.0010.0010.0000.0000.0000.000
162A191LEU0-0.099-0.03040.4840.0010.0010.0000.0000.0000.000
163A192GLU-1-0.942-0.96835.4050.0310.0310.0000.0000.0000.000
164A206ASP-1-0.896-0.94450.392-0.025-0.0250.0000.0000.0000.000
165A207ARG10.7880.89843.9430.0120.0120.0000.0000.0000.000
166A208ILE00.0280.02446.4680.0030.0030.0000.0000.0000.000
167A209TYR0-0.001-0.00641.111-0.002-0.0020.0000.0000.0000.000
168A210GLY00.017-0.00140.7580.0020.0020.0000.0000.0000.000
169A211MET00.0050.01236.2220.0000.0000.0000.0000.0000.000
170A212SER00.0180.02135.3250.0030.0030.0000.0000.0000.000
171A213LEU0-0.0050.01235.4040.0000.0000.0000.0000.0000.000
172A214TYR0-0.029-0.03335.5560.0000.0000.0000.0000.0000.000
173A215GLU-1-0.915-0.97436.825-0.042-0.0420.0000.0000.0000.000
174A216PHE0-0.0200.00539.048-0.001-0.0010.0000.0000.0000.000
175A217ASN00.0310.01139.339-0.002-0.0020.0000.0000.0000.000
176A218VAL0-0.002-0.00440.9500.0020.0020.0000.0000.0000.000
177A219LYS10.9470.97642.2900.0420.0420.0000.0000.0000.000
178A220TRP0-0.081-0.07639.2110.0030.0030.0000.0000.0000.000
179A221ARG11.1401.15846.0510.0120.0120.0000.0000.0000.000
180A222ILE0-0.053-0.05348.3570.0020.0020.0000.0000.0000.000
181A223LYS10.9640.93743.270-0.008-0.0080.0000.0000.0000.000
182A224ALA00.006-0.00347.4320.0020.0020.0000.0000.0000.000
183A225GLY00.0010.04546.803-0.002-0.0020.0000.0000.0000.000
184A226THR0-0.087-0.04047.8500.0010.0010.0000.0000.0000.000
185A227VAL00.0420.00345.911-0.003-0.0030.0000.0000.0000.000
186A228ASN0-0.011-0.03647.9660.0030.0030.0000.0000.0000.000
187A229CYS0-0.005-0.01948.3200.0010.0010.0000.0000.0000.000
188A230VAL00.0470.03944.571-0.002-0.0020.0000.0000.0000.000
189A231GLU-1-0.877-0.94843.237-0.043-0.0430.0000.0000.0000.000