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

tag_button

FMODB ID: YNVM2

Calculation Name: 2HXO-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2HXO

Chain ID: A

ChEMBL ID:

UniProt ID: Q9K463

Base Structure: X-ray

Registration Date: 2023-09-27

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 207
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -1951885.389389
FMO2-HF: Nuclear repulsion 1876146.929659
FMO2-HF: Total energy -75738.459729
FMO2-MP2: Total energy -75963.876178


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:15:LEU)


Summations of interaction energy for fragment #1(A:15:LEU)
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.
-12.776-9.1318.966-5.969-16.645-0.023
Interaction energy analysis for fragmet #1(A:15:LEU)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.068 / q_NPA : -0.045
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].
3A17ARG11.0171.0203.804-1.2680.251-0.024-0.735-0.7610.002
4A18GLU-1-0.814-0.9326.7210.3550.3550.0000.0000.0000.000
5A19ARG10.9140.9822.408-7.189-6.0303.393-1.410-3.1420.001
6A20ILE0-0.0060.0072.194-0.525-0.5852.414-0.516-1.838-0.004
7A21VAL0-0.009-0.0145.3730.1380.194-0.001-0.001-0.0540.000
8A22GLY00.0290.0158.7960.0480.0480.0000.0000.0000.000
9A23ALA00.0150.0046.9770.0150.0150.0000.0000.0000.000
10A24ALA0-0.002-0.0179.023-0.003-0.0030.0000.0000.0000.000
11A25VAL00.0310.02011.3330.0150.0150.0000.0000.0000.000
12A26GLU-1-0.787-0.86310.9160.3210.3210.0000.0000.0000.000
13A27LEU0-0.052-0.02010.803-0.009-0.0090.0000.0000.0000.000
14A28LEU0-0.065-0.02714.577-0.009-0.0090.0000.0000.0000.000
15A29ASP-1-0.793-0.86116.9170.0450.0450.0000.0000.0000.000
16A30THR0-0.063-0.02916.6870.0000.0000.0000.0000.0000.000
17A31VAL0-0.030-0.01516.398-0.007-0.0070.0000.0000.0000.000
18A32GLY00.0440.04318.999-0.011-0.0110.0000.0000.0000.000
19A33GLU-1-0.852-0.95818.071-0.155-0.1550.0000.0000.0000.000
20A34ARG10.9200.96817.7380.0810.0810.0000.0000.0000.000
21A35GLY00.0470.03117.932-0.010-0.0100.0000.0000.0000.000
22A36LEU0-0.0090.01211.522-0.010-0.0100.0000.0000.0000.000
23A37THR0-0.013-0.02413.482-0.028-0.0280.0000.0000.0000.000
24A38PHE00.0430.0148.733-0.012-0.0120.0000.0000.0000.000
25A39ARG10.9620.9849.2780.1010.1010.0000.0000.0000.000
26A40ALA00.0760.05610.3830.0010.0010.0000.0000.0000.000
27A41LEU00.0190.0075.6890.0330.0330.0000.0000.0000.000
28A42ALA00.007-0.0135.747-0.019-0.0190.0000.0000.0000.000
29A43GLU-1-0.939-0.9846.258-0.079-0.0790.0000.0000.0000.000
30A44ARG10.8070.8848.357-0.134-0.1340.0000.0000.0000.000
31A45LEU0-0.045-0.0092.2590.089-1.2885.082-0.603-3.102-0.001
32A46ALA0-0.0100.0024.2350.1980.4150.000-0.042-0.1760.000
33A47THR0-0.054-0.0352.279-1.067-1.0474.204-1.125-3.099-0.010
34A48GLY00.0380.0204.5480.0250.086-0.001-0.021-0.0400.000
35A49PRO00.048-0.0025.638-0.125-0.1250.0000.0000.0000.000
36A50GLY0-0.022-0.0047.583-0.001-0.0010.0000.0000.0000.000
37A51ALA0-0.008-0.0055.3240.0090.0090.0000.0000.0000.000
38A52ILE00.0150.0042.350-0.861-0.4621.029-0.247-1.1810.001
39A53TYR0-0.019-0.0034.255-0.245-0.181-0.0010.000-0.0640.000
40A54TRP0-0.019-0.0074.799-0.0200.059-0.001-0.003-0.0750.000
41A55HIS0-0.016-0.0092.280-2.900-1.4732.873-1.258-3.041-0.012
42A56ILE0-0.040-0.0124.6010.0630.145-0.001-0.008-0.0720.000
43A57THR00.0230.0047.2250.0300.0300.0000.0000.0000.000
44A58GLY00.0480.03210.8650.0290.0290.0000.0000.0000.000
45A59LYS10.8010.88912.6660.1690.1690.0000.0000.0000.000
46A60ALA00.0180.00814.0800.0110.0110.0000.0000.0000.000
47A61GLU-1-0.852-0.93513.317-0.327-0.3270.0000.0000.0000.000
48A62LEU0-0.036-0.0079.197-0.013-0.0130.0000.0000.0000.000
49A63LEU0-0.003-0.00112.5300.0300.0300.0000.0000.0000.000
50A64GLY00.0220.02615.6530.0360.0360.0000.0000.0000.000
51A65ALA0-0.012-0.00612.0200.0250.0250.0000.0000.0000.000
52A66ALA00.002-0.00413.1550.0360.0360.0000.0000.0000.000
53A67THR00.022-0.01714.2660.0500.0500.0000.0000.0000.000
54A68ASP-1-0.836-0.89416.246-0.116-0.1160.0000.0000.0000.000
55A69ALA0-0.0040.01113.7920.0280.0280.0000.0000.0000.000
56A70VAL0-0.009-0.00315.8990.0410.0410.0000.0000.0000.000
57A71VAL00.0210.01118.3140.0170.0170.0000.0000.0000.000
58A72THR0-0.037-0.02518.6640.0100.0100.0000.0000.0000.000
59A73ALA0-0.032-0.00418.0950.0150.0150.0000.0000.0000.000
60A74ALA00.0080.00820.1980.0130.0130.0000.0000.0000.000
61A75VAL0-0.029-0.02323.3920.0030.0030.0000.0000.0000.000
62A76THR0-0.099-0.05922.4080.0050.0050.0000.0000.0000.000
63A77ALA0-0.0130.00623.5040.0100.0100.0000.0000.0000.000
64A78GLY0-0.0220.00124.7100.0060.0060.0000.0000.0000.000
65A79PRO0-0.020-0.00228.215-0.002-0.0020.0000.0000.0000.000
66A80THR00.0230.01030.364-0.004-0.0040.0000.0000.0000.000
67A81GLY0-0.010-0.01433.0440.0050.0050.0000.0000.0000.000
68A82ALA0-0.061-0.04536.652-0.003-0.0030.0000.0000.0000.000
69A83ALA0-0.048-0.02739.229-0.002-0.0020.0000.0000.0000.000
70A84ASP-1-0.848-0.90235.5540.0340.0340.0000.0000.0000.000
71A85SER0-0.051-0.04539.136-0.003-0.0030.0000.0000.0000.000
72A86PRO00.031-0.00538.3970.0010.0010.0000.0000.0000.000
73A87GLN00.0530.00837.941-0.001-0.0010.0000.0000.0000.000
74A88ASP-1-0.786-0.85638.1140.0200.0200.0000.0000.0000.000
75A89ALA00.0350.02934.3290.0020.0020.0000.0000.0000.000
76A90VAL0-0.024-0.01933.532-0.001-0.0010.0000.0000.0000.000
77A91ARG10.8800.92533.975-0.017-0.0170.0000.0000.0000.000
78A92ALA00.0220.02631.5480.0010.0010.0000.0000.0000.000
79A93VAL0-0.028-0.01628.8120.0010.0010.0000.0000.0000.000
80A94ALA0-0.011-0.01329.401-0.002-0.0020.0000.0000.0000.000
81A95LEU00.0250.01130.898-0.001-0.0010.0000.0000.0000.000
82A96GLY00.0290.04027.5050.0040.0040.0000.0000.0000.000
83A97LEU0-0.044-0.04925.296-0.001-0.0010.0000.0000.0000.000
84A98TRP00.0050.00227.198-0.006-0.0060.0000.0000.0000.000
85A99ASP-1-0.760-0.86627.6730.0440.0440.0000.0000.0000.000
86A100ALA0-0.042-0.01822.9380.0050.0050.0000.0000.0000.000
87A101THR0-0.094-0.07023.881-0.004-0.0040.0000.0000.0000.000
88A102GLU-1-0.837-0.89125.7790.0290.0290.0000.0000.0000.000
89A103ALA0-0.046-0.01322.9530.0040.0040.0000.0000.0000.000
90A104HIS10.7580.85118.545-0.048-0.0480.0000.0000.0000.000
91A105PRO00.1310.06122.413-0.015-0.0150.0000.0000.0000.000
92A106TRP0-0.090-0.06017.113-0.025-0.0250.0000.0000.0000.000
93A107LEU0-0.022-0.01320.190-0.017-0.0170.0000.0000.0000.000
94A108ALA00.0960.04522.589-0.010-0.0100.0000.0000.0000.000
95A109THR0-0.011-0.01124.244-0.003-0.0030.0000.0000.0000.000
96A110GLN0-0.008-0.00819.516-0.021-0.0210.0000.0000.0000.000
97A111LEU00.0430.02522.666-0.014-0.0140.0000.0000.0000.000
98A112ALA00.0500.03924.845-0.004-0.0040.0000.0000.0000.000
99A113THR0-0.032-0.02123.093-0.003-0.0030.0000.0000.0000.000
100A114GLN0-0.056-0.03019.811-0.020-0.0200.0000.0000.0000.000
101A115LEU00.005-0.00224.120-0.006-0.0060.0000.0000.0000.000
102A116SER0-0.032-0.01027.3820.0060.0060.0000.0000.0000.000
103A117ARG10.8930.93522.9590.1340.1340.0000.0000.0000.000
104A118THR0-0.053-0.01220.984-0.017-0.0170.0000.0000.0000.000
105A119PRO00.0280.01924.1140.0010.0010.0000.0000.0000.000
106A120TRP0-0.009-0.00921.7130.0040.0040.0000.0000.0000.000
107A121GLY00.0090.01320.819-0.017-0.0170.0000.0000.0000.000
108A122THR0-0.049-0.04918.4880.0010.0010.0000.0000.0000.000
109A123VAL00.0370.00720.5350.0160.0160.0000.0000.0000.000
110A124ALA00.0340.02122.1810.0140.0140.0000.0000.0000.000
111A125PRO00.0170.00624.1950.0120.0120.0000.0000.0000.000
112A126ARG10.8950.94917.8500.1320.1320.0000.0000.0000.000
113A127ILE00.0330.03625.2280.0120.0120.0000.0000.0000.000
114A128PHE00.000-0.01927.4750.0080.0080.0000.0000.0000.000
115A129GLU-1-0.844-0.88228.204-0.035-0.0350.0000.0000.0000.000
116A130SER0-0.066-0.04527.6740.0090.0090.0000.0000.0000.000
117A131LEU0-0.006-0.00830.3420.0060.0060.0000.0000.0000.000
118A132GLY00.0550.02333.1420.0030.0030.0000.0000.0000.000
119A133ARG10.8350.89629.9190.0240.0240.0000.0000.0000.000
120A134GLN00.0170.01433.6670.0050.0050.0000.0000.0000.000
121A135VAL00.0080.00137.2790.0020.0020.0000.0000.0000.000
122A136GLN0-0.055-0.03337.2600.0020.0020.0000.0000.0000.000
123A137ALA0-0.0010.00839.4920.0010.0010.0000.0000.0000.000
124A138MET0-0.085-0.03041.0550.0020.0020.0000.0000.0000.000
125A139GLY00.0020.01243.4070.0000.0000.0000.0000.0000.000
126A140VAL0-0.018-0.00642.728-0.001-0.0010.0000.0000.0000.000
127A141PRO00.006-0.00344.239-0.002-0.0020.0000.0000.0000.000
128A142GLU-1-0.853-0.94442.041-0.031-0.0310.0000.0000.0000.000
129A143ALA0-0.061-0.02642.751-0.002-0.0020.0000.0000.0000.000
130A144HIS0-0.012-0.01643.508-0.002-0.0020.0000.0000.0000.000
131A145TRP00.0350.03638.700-0.001-0.0010.0000.0000.0000.000
132A146PHE00.0430.03033.8910.0010.0010.0000.0000.0000.000
133A147THR00.0240.01437.896-0.002-0.0020.0000.0000.0000.000
134A148ALA00.0260.01139.7780.0000.0000.0000.0000.0000.000
135A149SER00.010-0.01534.6990.0020.0020.0000.0000.0000.000
136A150SER0-0.013-0.02635.014-0.002-0.0020.0000.0000.0000.000
137A151ALA0-0.041-0.00336.0730.0000.0000.0000.0000.0000.000
138A152LEU00.0160.01335.6440.0010.0010.0000.0000.0000.000
139A153MET0-0.0030.00727.8020.0030.0030.0000.0000.0000.000
140A154HIS0-0.004-0.01833.0050.0000.0000.0000.0000.0000.000
141A155TYR0-0.061-0.02635.2140.0000.0000.0000.0000.0000.000
142A156ILE00.013-0.00330.7340.0020.0020.0000.0000.0000.000
143A157LEU0-0.036-0.03028.8320.0010.0010.0000.0000.0000.000
144A158GLY0-0.0180.00831.944-0.001-0.0010.0000.0000.0000.000
145A159ALA00.0050.00835.1360.0010.0010.0000.0000.0000.000
146A160ALA00.0430.01630.0480.0020.0020.0000.0000.0000.000
147A161GLY0-0.033-0.01430.5100.0000.0000.0000.0000.0000.000
148A162GLN0-0.056-0.03431.567-0.003-0.0030.0000.0000.0000.000
149A163ASN0-0.025-0.02631.2460.0010.0010.0000.0000.0000.000
150A164ALA0-0.042-0.01928.3150.0020.0020.0000.0000.0000.000
151A165ALA0-0.105-0.03630.2040.0010.0010.0000.0000.0000.000
152A166ASN00.0150.02032.5330.0000.0000.0000.0000.0000.000
153A180ASP-1-0.946-0.98238.9320.0240.0240.0000.0000.0000.000
154A181GLU-1-0.898-0.95238.3740.0200.0200.0000.0000.0000.000
155A182PHE0-0.032-0.02340.153-0.003-0.0030.0000.0000.0000.000
156A183LEU00.0510.02041.144-0.002-0.0020.0000.0000.0000.000
157A184ASP-1-0.823-0.89644.0150.0120.0120.0000.0000.0000.000
158A185THR0-0.032-0.02245.165-0.001-0.0010.0000.0000.0000.000
159A186VAL0-0.026-0.00944.458-0.002-0.0020.0000.0000.0000.000
160A187SER00.0030.01247.496-0.001-0.0010.0000.0000.0000.000
161A188THR0-0.029-0.01449.949-0.001-0.0010.0000.0000.0000.000
162A189ALA0-0.034-0.01449.967-0.001-0.0010.0000.0000.0000.000
163A190TRP00.012-0.01547.318-0.001-0.0010.0000.0000.0000.000
164A191GLU-1-0.842-0.90752.8270.0070.0070.0000.0000.0000.000
165A192GLY0-0.038-0.01655.2910.0000.0000.0000.0000.0000.000
166A193LEU0-0.099-0.04053.026-0.001-0.0010.0000.0000.0000.000
167A194ASP-1-0.858-0.93957.346-0.002-0.0020.0000.0000.0000.000
168A195PRO00.005-0.02160.2540.0000.0000.0000.0000.0000.000
169A196ASP-1-0.933-0.95461.945-0.001-0.0010.0000.0000.0000.000
170A197ALA0-0.084-0.03160.422-0.001-0.0010.0000.0000.0000.000
171A198TYR0-0.059-0.03954.731-0.001-0.0010.0000.0000.0000.000
172A199PRO00.0310.02058.1210.0010.0010.0000.0000.0000.000
173A200PHE0-0.017-0.01251.6320.0010.0010.0000.0000.0000.000
174A201THR00.0430.00451.9320.0010.0010.0000.0000.0000.000
175A202ARG10.9210.97054.341-0.001-0.0010.0000.0000.0000.000
176A203ALA0-0.055-0.02257.0060.0010.0010.0000.0000.0000.000
177A204VAL0-0.0070.00450.9760.0010.0010.0000.0000.0000.000
178A205ALA0-0.041-0.01152.1760.0010.0010.0000.0000.0000.000
179A206ASP-1-0.865-0.93651.3120.0090.0090.0000.0000.0000.000
180A207GLN0-0.047-0.02850.1200.0000.0000.0000.0000.0000.000
181A208VAL0-0.037-0.01245.9620.0010.0010.0000.0000.0000.000
182A209ARG10.7890.86545.974-0.011-0.0110.0000.0000.0000.000
183A210GLY00.0090.01044.9120.0000.0000.0000.0000.0000.000
184A211HIS0-0.0370.01141.3190.0000.0000.0000.0000.0000.000
185A212ASP-1-0.863-0.94639.0020.0270.0270.0000.0000.0000.000
186A213ASP-1-0.868-0.94537.1160.0100.0100.0000.0000.0000.000
187A214ARG10.8690.91031.628-0.043-0.0430.0000.0000.0000.000
188A215GLU-1-0.913-0.96936.9990.0260.0260.0000.0000.0000.000
189A216GLN0-0.053-0.01640.332-0.003-0.0030.0000.0000.0000.000
190A217PHE0-0.010-0.00732.807-0.004-0.0040.0000.0000.0000.000
191A218LEU00.0490.01636.462-0.004-0.0040.0000.0000.0000.000
192A219ALA0-0.0070.01238.943-0.001-0.0010.0000.0000.0000.000
193A220GLY00.0390.01241.110-0.002-0.0020.0000.0000.0000.000
194A221ILE0-0.003-0.00336.113-0.003-0.0030.0000.0000.0000.000
195A222THR0-0.027-0.01039.481-0.001-0.0010.0000.0000.0000.000
196A223LEU00.0060.02342.384-0.001-0.0010.0000.0000.0000.000
197A224VAL0-0.004-0.00440.068-0.002-0.0020.0000.0000.0000.000
198A225LEU0-0.017-0.01938.817-0.002-0.0020.0000.0000.0000.000
199A226THR0-0.024-0.01242.5700.0000.0000.0000.0000.0000.000
200A227GLY0-0.0100.00445.7450.0000.0000.0000.0000.0000.000
201A228ILE0-0.012-0.01940.401-0.001-0.0010.0000.0000.0000.000
202A229THR0-0.016-0.01444.6540.0000.0000.0000.0000.0000.000
203A230ALA0-0.045-0.00746.5560.0000.0000.0000.0000.0000.000
204A231LEU0-0.061-0.04044.488-0.001-0.0010.0000.0000.0000.000
205A232HIS0-0.068-0.01347.7540.0000.0000.0000.0000.0000.000
206A233ARG10.8820.93849.3370.0110.0110.0000.0000.0000.000
207A234PRO00.0290.02352.931-0.001-0.0010.0000.0000.0000.000