FMODB

FMODB: The database of quantum mechanical data based on the FMO method

Last updated: 2024-07-23

All entries: 37450

Number of unique PDB entries: 7783

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FMODB ID: 2N29R

Calculation Name: 1V43-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1V43

Chain ID: A

ChEMBL ID:

UniProt ID: O57758

Base Structure: X-ray

Registration Date: 2023-09-21

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 367
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -5757506.143586
FMO2-HF: Nuclear repulsion 5612000.025906
FMO2-HF: Total energy -145506.11768
FMO2-MP2: Total energy -145928.682219


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:7:VAL)


Summations of interaction energy for fragment #1(A:7:VAL)
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.
-15.433-14.07112.964-7.197-7.127-0.062
Interaction energy analysis for fragmet #1(A:7:VAL)
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 : -0.029
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].
3A9LYS10.8570.9192.7630.1633.8180.431-1.969-2.116-0.004
4A10MET00.0090.0085.2870.1680.222-0.001-0.003-0.0490.000
5A11VAL0-0.0020.0008.2940.1270.1270.0000.0000.0000.000
6A12GLU-1-0.825-0.88911.239-0.307-0.3070.0000.0000.0000.000
7A13VAL0-0.032-0.01514.780-0.027-0.0270.0000.0000.0000.000
8A14LYS10.8710.95217.4050.3920.3920.0000.0000.0000.000
9A15LEU0-0.020-0.00921.048-0.012-0.0120.0000.0000.0000.000
10A16GLU-1-0.865-0.95324.025-0.205-0.2050.0000.0000.0000.000
11A17ASN00.000-0.02127.1110.0110.0110.0000.0000.0000.000
12A18LEU00.0140.02025.1860.0050.0050.0000.0000.0000.000
13A19THR0-0.032-0.01229.5460.0130.0130.0000.0000.0000.000
14A20LYS10.8040.90131.0630.1950.1950.0000.0000.0000.000
15A21ARG10.8920.94133.3440.1420.1420.0000.0000.0000.000
16A22PHE0-0.0130.00232.235-0.001-0.0010.0000.0000.0000.000
17A23GLY00.0220.00937.8550.0060.0060.0000.0000.0000.000
18A24ASN00.004-0.00741.203-0.002-0.0020.0000.0000.0000.000
19A25PHE00.0020.01436.9200.0010.0010.0000.0000.0000.000
20A26THR00.004-0.01036.601-0.008-0.0080.0000.0000.0000.000
21A27ALA0-0.022-0.00134.0780.0020.0020.0000.0000.0000.000
22A28VAL0-0.039-0.02629.590-0.003-0.0030.0000.0000.0000.000
23A29ASN0-0.020-0.02932.979-0.001-0.0010.0000.0000.0000.000
24A30LYS10.8500.92032.5770.1400.1400.0000.0000.0000.000
25A31LEU00.0150.01526.2970.0040.0040.0000.0000.0000.000
26A32ASN0-0.022-0.01027.533-0.013-0.0130.0000.0000.0000.000
27A33LEU0-0.003-0.01022.2970.0100.0100.0000.0000.0000.000
28A34THR00.0410.03620.051-0.015-0.0150.0000.0000.0000.000
29A35ILE0-0.043-0.03016.8430.0250.0250.0000.0000.0000.000
30A36LYS11.0040.98816.2910.1680.1680.0000.0000.0000.000
31A37ASP-1-0.898-0.94911.229-0.460-0.4600.0000.0000.0000.000
32A38GLY00.0400.01610.6710.0580.0580.0000.0000.0000.000
33A39GLU-1-0.841-0.86111.321-0.220-0.2200.0000.0000.0000.000
34A40PHE00.0030.00114.715-0.076-0.0760.0000.0000.0000.000
35A41LEU00.003-0.00816.7210.0500.0500.0000.0000.0000.000
36A42VAL00.0110.00919.700-0.023-0.0230.0000.0000.0000.000
37A43LEU0-0.040-0.02122.6490.0170.0170.0000.0000.0000.000
38A44LEU00.0220.00825.2980.0000.0000.0000.0000.0000.000
39A45GLY00.0590.01028.4520.0060.0060.0000.0000.0000.000
40A46PRO00.0590.04831.886-0.007-0.0070.0000.0000.0000.000
41A47SER00.013-0.01933.830-0.012-0.0120.0000.0000.0000.000
42A48GLY00.0130.00934.0120.0060.0060.0000.0000.0000.000
43A49CYS0-0.0840.01531.711-0.001-0.0010.0000.0000.0000.000
44A50GLY00.1190.05131.7220.0000.0000.0000.0000.0000.000
45A51LYS10.8540.92327.3120.1710.1710.0000.0000.0000.000
46A52THR00.009-0.00126.645-0.013-0.0130.0000.0000.0000.000
47A53THR0-0.034-0.01526.906-0.015-0.0150.0000.0000.0000.000
48A54THR00.0360.00324.442-0.009-0.0090.0000.0000.0000.000
49A55LEU00.0290.02120.289-0.022-0.0220.0000.0000.0000.000
50A56ARG10.8730.92322.5320.2180.2180.0000.0000.0000.000
51A57MET0-0.0230.00824.018-0.007-0.0070.0000.0000.0000.000
52A58ILE0-0.016-0.00719.018-0.017-0.0170.0000.0000.0000.000
53A59ALA0-0.032-0.02919.214-0.046-0.0460.0000.0000.0000.000
54A60GLY00.0640.00920.103-0.027-0.0270.0000.0000.0000.000
55A61LEU0-0.116-0.04822.3510.0220.0220.0000.0000.0000.000
56A62GLU-1-0.858-0.91824.770-0.186-0.1860.0000.0000.0000.000
57A63GLU-1-0.776-0.89325.693-0.307-0.3070.0000.0000.0000.000
58A64PRO00.0440.00026.8470.0160.0160.0000.0000.0000.000
59A65THR0-0.077-0.03729.8090.0060.0060.0000.0000.0000.000
60A66GLU-1-0.789-0.89132.176-0.133-0.1330.0000.0000.0000.000
61A67GLY00.0480.02029.708-0.007-0.0070.0000.0000.0000.000
62A68ARG10.8490.93224.7720.2250.2250.0000.0000.0000.000
63A69ILE0-0.007-0.00120.5790.0020.0020.0000.0000.0000.000
64A70TYR00.0190.00919.591-0.008-0.0080.0000.0000.0000.000
65A71PHE0-0.024-0.01614.112-0.022-0.0220.0000.0000.0000.000
66A72GLY00.0160.00414.764-0.019-0.0190.0000.0000.0000.000
67A73ASP-1-0.895-0.96115.444-0.293-0.2930.0000.0000.0000.000
68A74ARG10.8380.92713.9930.7260.7260.0000.0000.0000.000
69A75ASP-1-0.766-0.83918.628-0.314-0.3140.0000.0000.0000.000
70A76VAL0-0.047-0.05016.852-0.007-0.0070.0000.0000.0000.000
71A77THR0-0.034-0.04320.271-0.004-0.0040.0000.0000.0000.000
72A78TYR0-0.0030.00723.6700.0080.0080.0000.0000.0000.000
73A79LEU0-0.0240.01118.2430.0080.0080.0000.0000.0000.000
74A80PRO00.0240.00920.465-0.009-0.0090.0000.0000.0000.000
75A81PRO00.0670.03819.053-0.045-0.0450.0000.0000.0000.000
76A82LYS10.7690.86616.3920.3370.3370.0000.0000.0000.000
77A83ASP-1-0.798-0.89114.942-0.539-0.5390.0000.0000.0000.000
78A84ARG10.8540.94915.0830.4030.4030.0000.0000.0000.000
79A85ASN0-0.092-0.0329.7980.0320.0320.0000.0000.0000.000
80A86ILE00.0410.04711.452-0.156-0.1560.0000.0000.0000.000
81A87SER0-0.044-0.04612.1290.0420.0420.0000.0000.0000.000
82A88MET0-0.0250.00714.1900.0180.0180.0000.0000.0000.000
83A89VAL0-0.021-0.01516.4250.0160.0160.0000.0000.0000.000
84A90PHE0-0.012-0.02418.9600.0200.0200.0000.0000.0000.000
85A91GLN0-0.144-0.08522.7460.0180.0180.0000.0000.0000.000
86A92SER00.0670.03325.9460.0170.0170.0000.0000.0000.000
87A93TYR00.0530.05327.8340.0070.0070.0000.0000.0000.000
88A94ALA0-0.021-0.02027.739-0.010-0.0100.0000.0000.0000.000
89A95VAL00.0090.02127.7630.0090.0090.0000.0000.0000.000
90A96TRP0-0.003-0.01525.056-0.020-0.0200.0000.0000.0000.000
91A97PRO00.0190.00923.9680.0110.0110.0000.0000.0000.000
92A98HIS00.024-0.00626.5340.0040.0040.0000.0000.0000.000
93A99MET0-0.0330.00321.3130.0010.0010.0000.0000.0000.000
94A100THR00.0590.03021.2260.0010.0010.0000.0000.0000.000
95A101VAL00.0120.01218.333-0.032-0.0320.0000.0000.0000.000
96A102TYR0-0.013-0.04915.942-0.064-0.0640.0000.0000.0000.000
97A103GLU-1-0.802-0.91516.932-0.160-0.1600.0000.0000.0000.000
98A104ASN0-0.058-0.02018.453-0.062-0.0620.0000.0000.0000.000
99A105ILE00.004-0.02312.792-0.047-0.0470.0000.0000.0000.000
100A106ALA00.0480.03713.687-0.085-0.0850.0000.0000.0000.000
101A107PHE0-0.008-0.00715.019-0.036-0.0360.0000.0000.0000.000
102A108PRO0-0.042-0.01713.1320.0090.0090.0000.0000.0000.000
103A109LEU00.0030.0259.396-0.089-0.0890.0000.0000.0000.000
104A110LYS10.7680.87713.5910.2250.2250.0000.0000.0000.000
105A111ILE00.0650.02316.1500.0270.0270.0000.0000.0000.000
106A112LYS10.9110.96910.4221.0921.0920.0000.0000.0000.000
107A113LYS10.9270.94914.5750.2810.2810.0000.0000.0000.000
108A114PHE00.0150.0068.043-0.019-0.0190.0000.0000.0000.000
109A115PRO00.0800.04311.8470.0240.0240.0000.0000.0000.000
110A116LYS10.9960.98113.454-0.020-0.0200.0000.0000.0000.000
111A117ASP-1-0.852-0.92414.2070.1610.1610.0000.0000.0000.000
112A118GLU-1-0.824-0.8976.5360.5990.5990.0000.0000.0000.000
113A119ILE0-0.046-0.0379.583-0.055-0.0550.0000.0000.0000.000
114A120ASP-1-0.771-0.83511.7130.1430.1430.0000.0000.0000.000
115A121LYS10.8860.9405.349-1.767-1.7670.0000.0000.0000.000
116A122ARG10.7790.8743.9112.7642.873-0.001-0.014-0.0930.000
117A123VAL00.0050.0108.153-0.076-0.0760.0000.0000.0000.000
118A124ARG10.8570.91311.629-0.267-0.2670.0000.0000.0000.000
119A125TRP00.0140.0104.206-0.552-0.281-0.001-0.025-0.2460.000
120A126ALA00.0150.0029.319-0.035-0.0350.0000.0000.0000.000
121A127ALA0-0.014-0.02610.2190.0130.0130.0000.0000.0000.000
122A128GLU-1-0.835-0.92310.7440.2870.2870.0000.0000.0000.000
123A129LEU0-0.027-0.0047.144-0.030-0.0300.0000.0000.0000.000
124A130LEU0-0.063-0.02611.832-0.030-0.0300.0000.0000.0000.000
125A131GLN0-0.0380.00314.8550.0210.0210.0000.0000.0000.000
126A132ILE0-0.053-0.03215.967-0.013-0.0130.0000.0000.0000.000
127A133GLU-1-0.830-0.91915.6970.0830.0830.0000.0000.0000.000
128A134GLU-1-0.873-0.92117.9960.0860.0860.0000.0000.0000.000
129A135LEU0-0.074-0.05720.741-0.009-0.0090.0000.0000.0000.000
130A136LEU00.0180.02116.122-0.024-0.0240.0000.0000.0000.000
131A137ASN0-0.007-0.00420.275-0.019-0.0190.0000.0000.0000.000
132A138ARG10.8860.95923.4450.0040.0040.0000.0000.0000.000
133A139TYR00.0540.01224.167-0.018-0.0180.0000.0000.0000.000
134A140PRO00.004-0.00724.2520.0050.0050.0000.0000.0000.000
135A141ALA00.0170.01126.4880.0030.0030.0000.0000.0000.000
136A142GLN00.0220.02428.7540.0010.0010.0000.0000.0000.000
137A143LEU0-0.068-0.02522.8670.0080.0080.0000.0000.0000.000
138A144SER0-0.0260.00427.092-0.003-0.0030.0000.0000.0000.000
139A145GLY0-0.019-0.02027.1780.0010.0010.0000.0000.0000.000
140A146GLY00.0510.01323.5610.0080.0080.0000.0000.0000.000
141A147GLN00.0230.02622.326-0.010-0.0100.0000.0000.0000.000
142A148ARG10.8910.93620.4630.1980.1980.0000.0000.0000.000
143A149GLN00.0230.00921.072-0.012-0.0120.0000.0000.0000.000
144A150ARG10.8990.91418.0330.0440.0440.0000.0000.0000.000
145A151VAL0-0.0080.00516.860-0.037-0.0370.0000.0000.0000.000
146A152ALA0-0.049-0.02416.942-0.044-0.0440.0000.0000.0000.000
147A153VAL00.0390.01813.702-0.060-0.0600.0000.0000.0000.000
148A154ALA00.0610.03612.495-0.107-0.1070.0000.0000.0000.000
149A155ARG10.9050.94611.9280.2470.2470.0000.0000.0000.000
150A156ALA0-0.0170.00612.719-0.089-0.0890.0000.0000.0000.000
151A157ILE00.0470.0218.446-0.166-0.1660.0000.0000.0000.000
152A158VAL00.0060.0347.770-0.458-0.4580.0000.0000.0000.000
153A159VAL0-0.071-0.0497.402-0.160-0.1600.0000.0000.0000.000
154A160GLU-1-0.867-0.9031.858-14.839-17.56612.536-5.186-4.623-0.058
155A161PRO0-0.084-0.0215.897-0.205-0.2050.0000.0000.0000.000
156A162ASP-1-0.779-0.8878.290-2.434-2.4340.0000.0000.0000.000
157A163VAL0-0.009-0.0119.6730.2010.2010.0000.0000.0000.000
158A164LEU0-0.0320.00111.644-0.002-0.0020.0000.0000.0000.000
159A165LEU00.0170.00113.6560.1070.1070.0000.0000.0000.000
160A166MET0-0.018-0.00515.4720.0280.0280.0000.0000.0000.000
161A167ASP-1-0.823-0.92619.649-0.240-0.2400.0000.0000.0000.000
162A168GLU-1-0.739-0.85123.402-0.176-0.1760.0000.0000.0000.000
163A169PRO0-0.013-0.01020.6610.0120.0120.0000.0000.0000.000
164A170LEU0-0.010-0.01521.8880.0090.0090.0000.0000.0000.000
165A171SER0-0.0050.01025.5310.0210.0210.0000.0000.0000.000
166A172ASN0-0.035-0.01428.5960.0080.0080.0000.0000.0000.000
167A173LEU00.0350.01625.0080.0010.0010.0000.0000.0000.000
168A174ASP-1-0.841-0.91429.738-0.081-0.0810.0000.0000.0000.000
169A175ALA00.0650.01630.605-0.004-0.0040.0000.0000.0000.000
170A176LYS10.9740.98830.5710.0410.0410.0000.0000.0000.000
171A177LEU0-0.014-0.00525.6990.0000.0000.0000.0000.0000.000
172A178ARG10.8260.88926.1770.1500.1500.0000.0000.0000.000
173A179VAL00.0300.01025.527-0.012-0.0120.0000.0000.0000.000
174A180ALA0-0.011-0.00324.698-0.003-0.0030.0000.0000.0000.000
175A181MET0-0.004-0.00319.567-0.001-0.0010.0000.0000.0000.000
176A182ARG10.8290.90620.7040.1170.1170.0000.0000.0000.000
177A183ALA00.0190.00520.239-0.015-0.0150.0000.0000.0000.000
178A184GLU-1-0.911-0.94917.422-0.100-0.1000.0000.0000.0000.000
179A185ILE0-0.008-0.02516.290-0.021-0.0210.0000.0000.0000.000
180A186LYS10.8020.89515.3220.1740.1740.0000.0000.0000.000
181A187LYS10.9820.98515.1210.0390.0390.0000.0000.0000.000
182A188LEU00.0130.01310.5680.0190.0190.0000.0000.0000.000
183A189GLN0-0.028-0.03110.6550.0460.0460.0000.0000.0000.000
184A190GLN00.0120.00310.795-0.031-0.0310.0000.0000.0000.000
185A191LYS10.8610.9498.379-0.188-0.1880.0000.0000.0000.000
186A192LEU0-0.058-0.0425.7720.0990.0990.0000.0000.0000.000
187A193LYS10.9050.9516.3540.1550.1550.0000.0000.0000.000
188A194VAL00.0450.0398.067-0.116-0.1160.0000.0000.0000.000
189A195THR0-0.004-0.0158.9900.1730.1730.0000.0000.0000.000
190A196THR0-0.042-0.01812.209-0.085-0.0850.0000.0000.0000.000
191A197ILE0-0.0040.01814.9540.0740.0740.0000.0000.0000.000
192A198TYR0-0.017-0.05718.549-0.020-0.0200.0000.0000.0000.000
193A199VAL0-0.0030.01120.9010.0310.0310.0000.0000.0000.000
194A200THR00.003-0.02824.4610.0050.0050.0000.0000.0000.000
195A201HIS0-0.050-0.02727.1760.0010.0010.0000.0000.0000.000
196A202ASP-1-0.839-0.91529.190-0.117-0.1170.0000.0000.0000.000
197A203GLN00.1000.04029.124-0.009-0.0090.0000.0000.0000.000
198A204VAL00.0390.02729.544-0.002-0.0020.0000.0000.0000.000
199A205GLU-1-0.747-0.80524.960-0.186-0.1860.0000.0000.0000.000
200A206ALA00.004-0.01525.078-0.011-0.0110.0000.0000.0000.000
201A207MET0-0.037-0.00824.886-0.011-0.0110.0000.0000.0000.000
202A208THR0-0.089-0.04323.5290.0080.0080.0000.0000.0000.000
203A209MET0-0.052-0.02019.6210.0040.0040.0000.0000.0000.000
204A210GLY00.0210.02819.917-0.021-0.0210.0000.0000.0000.000
205A211ASP-1-0.860-0.91116.656-0.224-0.2240.0000.0000.0000.000
206A212ARG10.7420.81820.1630.2650.2650.0000.0000.0000.000
207A213ILE0-0.0040.00222.475-0.020-0.0200.0000.0000.0000.000
208A214ALA00.0270.00725.1470.0110.0110.0000.0000.0000.000
209A215VAL00.0100.00826.728-0.007-0.0070.0000.0000.0000.000
210A216MET0-0.020-0.01928.719-0.005-0.0050.0000.0000.0000.000
211A217ASN00.032-0.00431.8100.0030.0030.0000.0000.0000.000
212A218ARG10.9300.96335.4130.1020.1020.0000.0000.0000.000
213A219GLY00.0480.03833.5560.0030.0030.0000.0000.0000.000
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