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: LL549

Calculation Name: 1XQB-A-Xray316

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: 2021-09-06

Reference: C. Watanabe, S. Koyama, K. Kamisaka, D. Takaya, T. Honma et. al., Interaction energy analysis of Apo structure dataset on FMODB, To be pubulished.

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. 1.20200129
FMO calculation
FMO method FMO2-MP2/6-31G(d)
Fragmentation Auto
Number of fragment 196
LigandCharge
Software ABINIT-MP - Open Ver.1 Rev. 15 / 20190524
Total energy (hartree)
FMO2-HF: Electronic energy -1996396.43153
FMO2-HF: Nuclear repulsion 1920433.83824
FMO2-HF: Total energy -75962.59329
FMO2-MP2: Total energy -76184.242522


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.
-8.816-4.9071.087-2.427-2.567-0.005
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 : -0.007 / q_NPA : -0.001
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 -1-0.902-0.9432.735-9.204-5.4791.087-2.411-2.400-0.005
4A4LEU 0-0.005-0.0224.466-0.240-0.0560.000-0.016-0.1670.000
5A5THR 0-0.037-0.0106.2810.3200.3200.0000.0000.0000.000
6A6LEU 0-0.023-0.0058.6420.1410.1410.0000.0000.0000.000
7A7SER 00.0200.01311.755-0.003-0.0030.0000.0000.0000.000
8A8PRO 0-0.027-0.02015.4360.0460.0460.0000.0000.0000.000
9A9ILE 00.0440.03416.8940.0090.0090.0000.0000.0000.000
10A10ALA 00.003-0.01619.4160.0280.0280.0000.0000.0000.000
11A11ILE 0-0.0150.01721.446-0.026-0.0260.0000.0000.0000.000
12A12ILE 0-0.0240.00023.9590.0210.0210.0000.0000.0000.000
13A13HIS 0-0.024-0.01525.697-0.010-0.0100.0000.0000.0000.000
14A14THR 00.014-0.01127.6380.0150.0150.0000.0000.0000.000
15A15PRO 0-0.030-0.00330.572-0.008-0.0080.0000.0000.0000.000
16A16TYR 0-0.005-0.02029.748-0.004-0.0040.0000.0000.0000.000
17A17LYS 10.9801.01130.2580.0590.0590.0000.0000.0000.000
18A18GLU -1-0.893-0.93129.565-0.083-0.0830.0000.0000.0000.000
19A19LYS 10.9520.94424.0770.0790.0790.0000.0000.0000.000
20A20PHE 0-0.029-0.01328.6430.0120.0120.0000.0000.0000.000
21A21SER 0-0.029-0.03132.0790.0060.0060.0000.0000.0000.000
22A22VAL 0-0.0160.01827.8760.0060.0060.0000.0000.0000.000
23A23PRO 0-0.0050.00431.0050.0020.0020.0000.0000.0000.000
24A24ARG 10.9630.95130.279-0.015-0.0150.0000.0000.0000.000
25A25GLN 0-0.031-0.02030.6270.0050.0050.0000.0000.0000.000
26A26PRO 00.0460.01528.5680.0000.0000.0000.0000.0000.000
27A27ASN 00.0210.01329.628-0.007-0.0070.0000.0000.0000.000
28A28LEU 0-0.0470.00432.8660.0010.0010.0000.0000.0000.000
29A29VAL 0-0.040-0.02334.926-0.003-0.0030.0000.0000.0000.000
30A30GLU -1-0.865-0.93535.3540.0280.0280.0000.0000.0000.000
31A31ASP -1-0.768-0.88637.4910.0080.0080.0000.0000.0000.000
32A32GLY 0-0.0390.00033.728-0.006-0.0060.0000.0000.0000.000
33A33VAL 0-0.070-0.04232.1790.0040.0040.0000.0000.0000.000
34A34GLY 00.0260.01129.582-0.009-0.0090.0000.0000.0000.000
35A35ILE 0-0.0270.00829.9280.0090.0090.0000.0000.0000.000
36A36VAL 0-0.020-0.01023.590-0.011-0.0110.0000.0000.0000.000
37A37GLU -1-0.830-0.89926.367-0.065-0.0650.0000.0000.0000.000
38A38LEU 0-0.010-0.01122.148-0.015-0.0150.0000.0000.0000.000
39A39LEU 0-0.030-0.00521.6400.0000.0000.0000.0000.0000.000
40A40PRO 0-0.0150.01823.7740.0060.0060.0000.0000.0000.000
41A41PRO 0-0.054-0.03621.784-0.023-0.0230.0000.0000.0000.000
42A42TYR 00.044-0.00417.6070.0100.0100.0000.0000.0000.000
43A43ASN 00.0120.03023.0850.0170.0170.0000.0000.0000.000
44A44SER 00.0230.00425.8590.0060.0060.0000.0000.0000.000
45A45PRO 00.049-0.01327.2980.0090.0090.0000.0000.0000.000
46A46GLU -1-1.014-1.00327.3020.0320.0320.0000.0000.0000.000
47A47ALA 0-0.0080.00623.1630.0190.0190.0000.0000.0000.000
48A48VAL 00.0080.01523.9120.0100.0100.0000.0000.0000.000
49A49ARG 10.9470.96826.413-0.068-0.0680.0000.0000.0000.000
50A50GLY 00.0400.02327.9050.0140.0140.0000.0000.0000.000
51A51LEU 0-0.026-0.02524.4260.0110.0110.0000.0000.0000.000
52A52GLU -1-0.926-0.98327.6440.0890.0890.0000.0000.0000.000
53A53GLN 0-0.081-0.00429.2620.0090.0090.0000.0000.0000.000
54A54PHE 0-0.022-0.01625.9370.0070.0070.0000.0000.0000.000
55A55SER 00.0730.03628.851-0.007-0.0070.0000.0000.0000.000
56A56HIS 0-0.043-0.00526.167-0.002-0.0020.0000.0000.0000.000
57A57LEU 00.0240.01223.2890.0130.0130.0000.0000.0000.000
58A58TRP 0-0.077-0.04018.272-0.021-0.0210.0000.0000.0000.000
59A59LEU 00.0080.01019.039-0.011-0.0110.0000.0000.0000.000
60A60ILE 00.0000.00012.3380.0130.0130.0000.0000.0000.000
61A61PHE 00.0150.01015.800-0.040-0.0400.0000.0000.0000.000
62A62GLN 00.0280.01415.472-0.054-0.0540.0000.0000.0000.000
63A63MET 0-0.103-0.03115.4700.0500.0500.0000.0000.0000.000
64A64NME 00.0130.00918.322-0.039-0.0390.0000.0000.0000.000
65A85ACE 00.011-0.00427.449-0.003-0.0030.0000.0000.0000.000
66A86VAL 0-0.003-0.00623.5550.0160.0160.0000.0000.0000.000
67A87GLY 00.0470.03020.253-0.021-0.0210.0000.0000.0000.000
68A88VAL 00.0570.01415.8350.0200.0200.0000.0000.0000.000
69A89PHE 0-0.021-0.02911.9230.0120.0120.0000.0000.0000.000
70A90ALA 0-0.0040.03116.3530.0370.0370.0000.0000.0000.000
71A91SER 0-0.0090.00719.301-0.016-0.0160.0000.0000.0000.000
72A92ARG 10.9430.94918.618-0.117-0.1170.0000.0000.0000.000
73A93ALA 0-0.0120.00919.548-0.021-0.0210.0000.0000.0000.000
74A94THR 00.0660.00318.2540.0140.0140.0000.0000.0000.000
75A95HIS 0-0.022-0.00117.205-0.050-0.0500.0000.0000.0000.000
76A96ARG 10.8920.94613.2060.0120.0120.0000.0000.0000.000
77A97PRO 0-0.018-0.01410.317-0.039-0.0390.0000.0000.0000.000
78A98ASN 00.0820.0446.593-0.298-0.2980.0000.0000.0000.000
79A99PRO 0-0.0190.01610.6050.1460.1460.0000.0000.0000.000
80A100LEU 00.0350.0008.8700.0200.0200.0000.0000.0000.000
81A101GLY 0-0.0150.00212.9710.0730.0730.0000.0000.0000.000
82A102MET 0-0.019-0.01514.1990.0060.0060.0000.0000.0000.000
83A103SER 0-0.057-0.03217.3640.0160.0160.0000.0000.0000.000
84A104LYS 10.9951.01221.069-0.125-0.1250.0000.0000.0000.000
85A105VAL 00.0050.00623.243-0.009-0.0090.0000.0000.0000.000
86A106GLU -1-0.936-0.98326.1760.0950.0950.0000.0000.0000.000
87A107LEU 0-0.023-0.01627.368-0.015-0.0150.0000.0000.0000.000
88A108ARG 10.9430.97529.676-0.032-0.0320.0000.0000.0000.000
89A109GLN 00.0130.00032.2060.0010.0010.0000.0000.0000.000
90A110VAL 00.0050.02329.044-0.007-0.0070.0000.0000.0000.000
91A111GLU -1-0.920-0.97431.501-0.004-0.0040.0000.0000.0000.000
92A112CYS 0-0.0140.00132.109-0.006-0.0060.0000.0000.0000.000
93A113ILE 00.0090.00533.9450.0030.0030.0000.0000.0000.000
94A114ASN 0-0.027-0.02535.617-0.002-0.0020.0000.0000.0000.000
95A115GLY 0-0.0020.00132.854-0.006-0.0060.0000.0000.0000.000
96A116ASN 0-0.0210.01431.305-0.015-0.0150.0000.0000.0000.000
97A117ILE 00.000-0.01427.8500.0100.0100.0000.0000.0000.000
98A118PHE 00.0060.00028.808-0.009-0.0090.0000.0000.0000.000
99A119LEU 0-0.0070.00424.6310.0120.0120.0000.0000.0000.000
100A120HIS 00.0020.00228.904-0.006-0.0060.0000.0000.0000.000
101A121LEU 00.018-0.01025.6740.0110.0110.0000.0000.0000.000
102A122GLY 0-0.008-0.00729.884-0.003-0.0030.0000.0000.0000.000
103A123ALA 0-0.042-0.02531.427-0.009-0.0090.0000.0000.0000.000
104A124VAL 00.0060.00526.8710.0080.0080.0000.0000.0000.000
105A125ASP -1-0.873-0.95624.7020.0210.0210.0000.0000.0000.000
106A126LEU 0-0.024-0.00421.804-0.009-0.0090.0000.0000.0000.000
107A127VAL 0-0.010-0.01724.7390.0040.0040.0000.0000.0000.000
108A128ASP -1-0.913-0.97426.058-0.086-0.0860.0000.0000.0000.000
109A129GLY 00.0370.02126.581-0.011-0.0110.0000.0000.0000.000
110A130THR 0-0.101-0.04720.716-0.023-0.0230.0000.0000.0000.000
111A131PRO 00.0090.00318.5940.0160.0160.0000.0000.0000.000
112A132ILE 0-0.020-0.02418.5120.0010.0010.0000.0000.0000.000
113A133PHE 0-0.017-0.04313.255-0.036-0.0360.0000.0000.0000.000
114A134ASP -1-0.873-0.95713.9310.1170.1170.0000.0000.0000.000
115A135ILE 00.0230.01116.0810.0060.0060.0000.0000.0000.000
116A136LYS 10.9020.97213.524-0.295-0.2950.0000.0000.0000.000
117A137PRO 00.0370.02419.295-0.022-0.0220.0000.0000.0000.000
118A138TYR 0-0.042-0.02621.3750.0280.0280.0000.0000.0000.000
119A139ILE 0-0.0080.00121.782-0.017-0.0170.0000.0000.0000.000
120A140ALA 00.006-0.01923.5180.0170.0170.0000.0000.0000.000
121A141TYR 0-0.034-0.01924.388-0.003-0.0030.0000.0000.0000.000
122A142ALA 00.001-0.01319.9120.0040.0040.0000.0000.0000.000
123A143ASP -1-0.802-0.88619.6310.3630.3630.0000.0000.0000.000
124A144SER 0-0.108-0.04321.757-0.021-0.0210.0000.0000.0000.000
125A145GLU -1-0.903-0.95123.7890.3130.3130.0000.0000.0000.000
126A146PRO 0-0.022-0.02725.693-0.012-0.0120.0000.0000.0000.000
127A147ASN 0-0.035-0.01728.968-0.007-0.0070.0000.0000.0000.000
128A148ALA 00.0230.02324.9060.0000.0000.0000.0000.0000.000
129A149GLN 00.0170.01526.722-0.022-0.0220.0000.0000.0000.000
130A150SER 0-0.050-0.04226.3240.0030.0030.0000.0000.0000.000
131A151SER 0-0.051-0.01327.9890.0060.0060.0000.0000.0000.000
132A152NME 00.0270.02430.3220.0000.0000.0000.0000.0000.000
133A158ACE 00.0340.00840.9400.0010.0010.0000.0000.0000.000
134A159VAL 0-0.019-0.02240.466-0.003-0.0030.0000.0000.0000.000
135A160LYS 10.9561.00542.316-0.022-0.0220.0000.0000.0000.000
136A161MET 00.0300.03542.208-0.002-0.0020.0000.0000.0000.000
137A162THR 0-0.017-0.02045.4690.0010.0010.0000.0000.0000.000
138A163VAL 00.0320.00944.505-0.002-0.0020.0000.0000.0000.000
139A164GLU -1-0.927-0.95347.845-0.003-0.0030.0000.0000.0000.000
140A165PHE 0-0.006-0.00746.789-0.002-0.0020.0000.0000.0000.000
141A166THR 00.0130.00951.3430.0010.0010.0000.0000.0000.000
142A167GLU -1-0.810-0.91953.917-0.008-0.0080.0000.0000.0000.000
143A168GLN 0-0.022-0.01552.996-0.001-0.0010.0000.0000.0000.000
144A169ALA 00.0040.01050.000-0.001-0.0010.0000.0000.0000.000
145A170LYS 10.9080.94951.2000.0050.0050.0000.0000.0000.000
146A171SER 0-0.0210.00252.9760.0000.0000.0000.0000.0000.000
147A172ALA 0-0.010-0.00949.7290.0000.0000.0000.0000.0000.000
148A173VAL 00.025-0.00247.246-0.002-0.0020.0000.0000.0000.000
149A174LYS 10.9480.97248.9860.0080.0080.0000.0000.0000.000
150A175LYS 10.9781.00750.1570.0290.0290.0000.0000.0000.000
151A176ARG 10.8110.91745.8850.0280.0280.0000.0000.0000.000
152A177GLU -1-0.841-0.92246.598-0.007-0.0070.0000.0000.0000.000
153A178GLU -1-0.915-0.95748.147-0.012-0.0120.0000.0000.0000.000
154A179LYS 10.8810.94744.8170.0280.0280.0000.0000.0000.000
155A180ARG 10.9510.97437.7610.0260.0260.0000.0000.0000.000
156A181PRO 00.0370.03343.3820.0010.0010.0000.0000.0000.000
157A182HIS 00.011-0.00942.7070.0010.0010.0000.0000.0000.000
158A183LEU 00.0140.02741.8120.0000.0000.0000.0000.0000.000
159A184SER 0-0.024-0.02843.551-0.001-0.0010.0000.0000.0000.000
160A185ARG 10.8630.92541.683-0.014-0.0140.0000.0000.0000.000
161A186PHE 00.0190.02135.4730.0020.0020.0000.0000.0000.000
162A187ILE 0-0.001-0.00439.664-0.002-0.0020.0000.0000.0000.000
163A188ARG 10.8070.89739.371-0.021-0.0210.0000.0000.0000.000
164A189GLN 00.0430.02135.381-0.002-0.0020.0000.0000.0000.000
165A190VAL 00.0280.00938.3240.0010.0010.0000.0000.0000.000
166A191LEU 0-0.099-0.03140.6530.0010.0010.0000.0000.0000.000
167A192GLU -1-0.944-0.96835.5590.0250.0250.0000.0000.0000.000
168A193NME 0-0.0020.00637.500-0.001-0.0010.0000.0000.0000.000
169A205ACE 0-0.007-0.00950.370-0.001-0.0010.0000.0000.0000.000
170A206ASP -1-0.874-0.94549.836-0.024-0.0240.0000.0000.0000.000
171A207ARG 10.7720.90844.0720.0140.0140.0000.0000.0000.000
172A208ILE 00.0350.02746.6760.0020.0020.0000.0000.0000.000
173A209TYR 0-0.007-0.00841.291-0.002-0.0020.0000.0000.0000.000
174A210GLY 00.0210.00140.9590.0020.0020.0000.0000.0000.000
175A211MET 00.0060.01136.4540.0000.0000.0000.0000.0000.000
176A212SER 00.0170.02035.6050.0030.0030.0000.0000.0000.000
177A213LEU 0-0.0030.01235.6840.0000.0000.0000.0000.0000.000
178A214TYR 0-0.030-0.03335.8740.0000.0000.0000.0000.0000.000
179A215GLU -1-0.916-0.97337.160-0.048-0.0480.0000.0000.0000.000
180A216PHE 00.007-0.00639.3950.0000.0000.0000.0000.0000.000
181A217ASN 00.0050.00139.644-0.002-0.0020.0000.0000.0000.000
182A218VAL 0-0.003-0.00541.2210.0020.0020.0000.0000.0000.000
183A219LYS 10.9500.97742.5330.0440.0440.0000.0000.0000.000
184A220TRP 0-0.086-0.07739.4020.0030.0030.0000.0000.0000.000
185A221ARG 11.1471.16346.2600.0140.0140.0000.0000.0000.000
186A222ILE 0-0.058-0.05648.4910.0020.0020.0000.0000.0000.000
187A223LYS 10.9620.93143.285-0.005-0.0050.0000.0000.0000.000
188A224ALA 0-0.003-0.00747.5510.0020.0020.0000.0000.0000.000
189A225GLY 0-0.0040.04446.974-0.002-0.0020.0000.0000.0000.000
190A226THR 0-0.077-0.03648.0210.0010.0010.0000.0000.0000.000
191A227VAL 00.0390.00146.163-0.003-0.0030.0000.0000.0000.000
192A228ASN 0-0.014-0.03748.1940.0030.0030.0000.0000.0000.000
193A229CYS 0-0.002-0.01848.5770.0010.0010.0000.0000.0000.000
194A230VAL 00.0280.02144.868-0.002-0.0020.0000.0000.0000.000
195A231GLU -1-0.906-0.99744.575-0.045-0.0450.0000.0000.0000.000
196A232NME 00.0470.08142.050-0.001-0.0010.0000.0000.0000.000