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: 3938L

Calculation Name: 4GIW-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 4GIW

Chain ID: A

ChEMBL ID:

UniProt ID: Q9BVN2

Base Structure: X-ray

Registration Date: 2023-06-21

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 184
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -1889572.174931
FMO2-HF: Nuclear repulsion 1820438.652119
FMO2-HF: Total energy -69133.522812
FMO2-MP2: Total energy -69338.118793


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:GLN)


Summations of interaction energy for fragment #1(A:7:GLN)
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.
-14.821-9.9745.239-3.446-6.6390.027
Interaction energy analysis for fragmet #1(A:7:GLN)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.080 / q_NPA : 0.040
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].
3A9LYS10.8600.9031.963-17.123-12.7615.230-3.640-5.9520.027
4A10GLY00.0170.0203.248-1.421-1.3000.0110.219-0.3510.000
5A11LEU0-0.015-0.0135.2170.2740.487-0.001-0.019-0.1920.000
6A12LEU00.0300.0126.427-0.018-0.0180.0000.0000.0000.000
7A13ILE00.0150.0166.280-0.289-0.2890.0000.0000.0000.000
8A14ALA00.0040.0129.095-0.074-0.0740.0000.0000.0000.000
9A15VAL00.0040.01011.157-0.034-0.0340.0000.0000.0000.000
10A16SER00.0340.01111.742-0.040-0.0400.0000.0000.0000.000
11A17VAL00.0100.01013.097-0.062-0.0620.0000.0000.0000.000
12A18SER0-0.055-0.04715.196-0.053-0.0530.0000.0000.0000.000
13A19VAL0-0.012-0.00816.631-0.032-0.0320.0000.0000.0000.000
14A20ASP-1-0.879-0.92616.7100.2070.2070.0000.0000.0000.000
15A21LYS10.9100.95618.233-0.012-0.0120.0000.0000.0000.000
16A22ILE00.004-0.00120.559-0.011-0.0110.0000.0000.0000.000
17A23ILE00.012-0.00121.706-0.013-0.0130.0000.0000.0000.000
18A24SER0-0.009-0.00823.708-0.017-0.0170.0000.0000.0000.000
19A25HIS0-0.072-0.02325.630-0.016-0.0160.0000.0000.0000.000
20A26PHE00.0330.00826.850-0.006-0.0060.0000.0000.0000.000
21A27GLY0-0.058-0.02828.250-0.002-0.0020.0000.0000.0000.000
22A28ALA00.0140.02129.736-0.007-0.0070.0000.0000.0000.000
23A29ALA0-0.0250.00832.664-0.006-0.0060.0000.0000.0000.000
24A30ARG10.9910.98433.862-0.063-0.0630.0000.0000.0000.000
25A31ASN0-0.044-0.02036.4290.0070.0070.0000.0000.0000.000
26A32LEU00.1050.02433.8590.0000.0000.0000.0000.0000.000
27A33VAL00.0270.02735.8370.0040.0040.0000.0000.0000.000
28A34GLN00.030-0.00537.1890.0020.0020.0000.0000.0000.000
29A35LYS10.9180.95530.980-0.127-0.1270.0000.0000.0000.000
30A36ALA00.0000.00632.7640.0050.0050.0000.0000.0000.000
31A37GLN0-0.006-0.00534.6240.0050.0050.0000.0000.0000.000
32A38LEU0-0.026-0.00431.612-0.004-0.0040.0000.0000.0000.000
33A39GLY00.0500.01930.4880.0020.0020.0000.0000.0000.000
34A40ASP-1-0.857-0.91831.4460.1000.1000.0000.0000.0000.000
35A41SER00.007-0.00331.609-0.005-0.0050.0000.0000.0000.000
36A42ARG10.7780.84633.424-0.092-0.0920.0000.0000.0000.000
37A43LEU0-0.060-0.00836.764-0.007-0.0070.0000.0000.0000.000
38A44SER00.001-0.00132.183-0.008-0.0080.0000.0000.0000.000
39A45PRO00.0440.01932.5370.0080.0080.0000.0000.0000.000
40A46ASP-1-0.879-0.94429.8720.0400.0400.0000.0000.0000.000
41A47VAL0-0.047-0.01027.5320.0030.0030.0000.0000.0000.000
42A48GLY00.0390.01326.8960.0120.0120.0000.0000.0000.000
43A49HIS00.0240.00526.4280.0050.0050.0000.0000.0000.000
44A50LEU00.0190.03822.620-0.007-0.0070.0000.0000.0000.000
45A51VAL00.0210.02322.3310.0040.0040.0000.0000.0000.000
46A52LEU00.014-0.00221.4350.0140.0140.0000.0000.0000.000
47A53THR0-0.070-0.05020.828-0.014-0.0140.0000.0000.0000.000
48A54THR0-0.099-0.06418.025-0.021-0.0210.0000.0000.0000.000
49A55LEU00.0700.02916.7290.0020.0020.0000.0000.0000.000
50A56CYS0-0.043-0.00517.1720.0430.0430.0000.0000.0000.000
51A57PRO0-0.017-0.01615.8140.0200.0200.0000.0000.0000.000
52A58ALA00.0230.02612.880-0.026-0.0260.0000.0000.0000.000
53A59LEU00.0250.00712.6440.0800.0800.0000.0000.0000.000
54A60HIS0-0.038-0.01314.5220.0200.0200.0000.0000.0000.000
55A61ALA0-0.012-0.0179.9900.0090.0090.0000.0000.0000.000
56A62LEU0-0.0140.0029.232-0.050-0.0500.0000.0000.0000.000
57A63VAL00.0020.00510.9870.1120.1120.0000.0000.0000.000
58A64ALA00.0240.00912.2240.0030.0030.0000.0000.0000.000
59A65ASP-1-0.793-0.8446.1260.3900.3900.0000.0000.0000.000
60A66GLY00.022-0.0159.4160.2140.2140.0000.0000.0000.000
61A67LEU0-0.0340.00610.5420.0100.0100.0000.0000.0000.000
62A68LYS10.8770.94214.042-0.358-0.3580.0000.0000.0000.000
63A69PRO00.0010.00216.158-0.002-0.0020.0000.0000.0000.000
64A70PHE00.011-0.00718.035-0.012-0.0120.0000.0000.0000.000
65A71ARG10.9040.95121.528-0.125-0.1250.0000.0000.0000.000
66A72LYS10.9870.98123.928-0.121-0.1210.0000.0000.0000.000
67A73ASP-1-0.833-0.91627.5770.0870.0870.0000.0000.0000.000
68A74LEU00.0410.01730.458-0.005-0.0050.0000.0000.0000.000
69A75ILE0-0.0280.01333.240-0.005-0.0050.0000.0000.0000.000
70A76THR00.019-0.00630.302-0.008-0.0080.0000.0000.0000.000
71A77GLY00.0210.03831.134-0.004-0.0040.0000.0000.0000.000
72A78GLN0-0.082-0.06925.9220.0130.0130.0000.0000.0000.000
73A79ARG10.8960.95525.590-0.091-0.0910.0000.0000.0000.000
74A80ARG10.9120.94617.537-0.014-0.0140.0000.0000.0000.000
75A81SER00.0030.01518.8100.0080.0080.0000.0000.0000.000
76A82SER0-0.029-0.03118.046-0.025-0.0250.0000.0000.0000.000
77A83PRO00.0870.02615.6520.0160.0160.0000.0000.0000.000
78A84TRP00.005-0.00218.2300.0260.0260.0000.0000.0000.000
79A85SER0-0.039-0.01721.033-0.002-0.0020.0000.0000.0000.000
80A86VAL00.0320.02417.183-0.003-0.0030.0000.0000.0000.000
81A87VAL0-0.0090.00620.6390.0150.0150.0000.0000.0000.000
82A88GLU-1-0.848-0.91023.1440.1490.1490.0000.0000.0000.000
83A89ALA0-0.055-0.02223.037-0.009-0.0090.0000.0000.0000.000
84A90SER00.0140.00322.6480.0050.0050.0000.0000.0000.000
85A91VAL0-0.064-0.01724.7930.0020.0020.0000.0000.0000.000
86A92LYS10.9380.96627.941-0.172-0.1720.0000.0000.0000.000
87A93PRO0-0.052-0.01628.522-0.016-0.0160.0000.0000.0000.000
88A94GLY00.0990.05729.720-0.009-0.0090.0000.0000.0000.000
89A95SER0-0.065-0.04329.5930.0050.0050.0000.0000.0000.000
90A96SER00.005-0.00425.153-0.014-0.0140.0000.0000.0000.000
91A97THR00.0980.04727.942-0.008-0.0080.0000.0000.0000.000
92A98ARG11.0110.99130.332-0.167-0.1670.0000.0000.0000.000
93A99SER00.0020.00930.561-0.015-0.0150.0000.0000.0000.000
94A100LEU00.0400.02825.337-0.009-0.0090.0000.0000.0000.000
95A101GLY00.0240.00929.229-0.007-0.0070.0000.0000.0000.000
96A102THR0-0.055-0.02731.881-0.015-0.0150.0000.0000.0000.000
97A103LEU00.0330.04527.443-0.013-0.0130.0000.0000.0000.000
98A104TYR00.0400.01027.567-0.014-0.0140.0000.0000.0000.000
99A105SER0-0.060-0.04230.088-0.016-0.0160.0000.0000.0000.000
100A106GLN0-0.043-0.03932.876-0.005-0.0050.0000.0000.0000.000
101A107VAL00.0170.00427.414-0.010-0.0100.0000.0000.0000.000
102A108SER0-0.019-0.01530.835-0.013-0.0130.0000.0000.0000.000
103A109ARG10.9510.98631.744-0.119-0.1190.0000.0000.0000.000
104A110LEU0-0.054-0.00232.798-0.008-0.0080.0000.0000.0000.000
105A111ALA0-0.002-0.01730.5830.0000.0000.0000.0000.0000.000
106A112PRO0-0.0320.00032.462-0.001-0.0010.0000.0000.0000.000
107A113LEU00.0540.01532.5870.0000.0000.0000.0000.0000.000
108A114SER00.0110.02428.915-0.008-0.0080.0000.0000.0000.000
109A115SER00.0820.03623.9940.0090.0090.0000.0000.0000.000
110A116SER00.016-0.00622.7840.0080.0080.0000.0000.0000.000
111A117ARG10.8990.95716.5690.0260.0260.0000.0000.0000.000
112A118SER00.040-0.00521.8710.0110.0110.0000.0000.0000.000
113A119ARG10.8670.94725.059-0.088-0.0880.0000.0000.0000.000
114A120PHE0-0.020-0.01717.4950.0060.0060.0000.0000.0000.000
115A121HIS00.0320.00618.8290.0480.0480.0000.0000.0000.000
116A122ALA00.0500.02922.9640.0140.0140.0000.0000.0000.000
117A123PHE00.005-0.01122.9860.0020.0020.0000.0000.0000.000
118A124ILE00.0120.00819.4330.0210.0210.0000.0000.0000.000
119A125LEU00.0150.01123.2480.0140.0140.0000.0000.0000.000
120A126GLY00.0540.01326.3780.0010.0010.0000.0000.0000.000
121A127LEU0-0.058-0.02022.1340.0040.0040.0000.0000.0000.000
122A128LEU0-0.0140.00022.3220.0150.0150.0000.0000.0000.000
123A129ASN0-0.035-0.00925.768-0.001-0.0010.0000.0000.0000.000
124A130THR0-0.059-0.03428.5560.0000.0000.0000.0000.0000.000
125A131LYS10.8480.93425.725-0.232-0.2320.0000.0000.0000.000
126A132GLN0-0.022-0.03825.0600.0180.0180.0000.0000.0000.000
127A133LEU00.0250.01119.6710.0170.0170.0000.0000.0000.000
128A134GLU-1-0.864-0.93619.0910.5390.5390.0000.0000.0000.000
129A135LEU00.0090.00720.0050.0350.0350.0000.0000.0000.000
130A136TRP00.0060.00018.6730.0180.0180.0000.0000.0000.000
131A137PHE00.033-0.01016.0920.0190.0190.0000.0000.0000.000
132A138SER00.0090.01017.5380.0620.0620.0000.0000.0000.000
133A139SER0-0.027-0.02219.494-0.032-0.0320.0000.0000.0000.000
134A140LEU0-0.037-0.00916.902-0.024-0.0240.0000.0000.0000.000
135A141GLN0-0.052-0.01714.3220.1280.1280.0000.0000.0000.000
136A142GLU-1-0.902-0.95017.4670.5870.5870.0000.0000.0000.000
137A143ASP-1-0.863-0.90320.6390.2960.2960.0000.0000.0000.000
138A144ALA0-0.001-0.02320.1030.0250.0250.0000.0000.0000.000
139A145GLY00.0080.00621.011-0.003-0.0030.0000.0000.0000.000
140A146LEU0-0.0030.00119.388-0.011-0.0110.0000.0000.0000.000
141A147LEU00.007-0.00715.513-0.002-0.0020.0000.0000.0000.000
142A148SER0-0.0210.00417.531-0.002-0.0020.0000.0000.0000.000
143A149LEU0-0.033-0.01719.586-0.032-0.0320.0000.0000.0000.000
144A150MET0-0.064-0.03218.490-0.033-0.0330.0000.0000.0000.000
145A151TYR0-0.046-0.03012.589-0.011-0.0110.0000.0000.0000.000
146A152MET0-0.027-0.01511.734-0.043-0.0430.0000.0000.0000.000
147A153PRO00.0300.01012.5940.1250.1250.0000.0000.0000.000
148A154THR00.013-0.0047.7440.1220.1220.0000.0000.0000.000
149A155GLY00.0240.0087.5630.2560.2560.0000.0000.0000.000
150A156PHE00.013-0.0066.6810.3310.3310.0000.0000.0000.000
151A157PHE00.0600.0108.8940.2450.2450.0000.0000.0000.000
152A158SER0-0.0290.00711.979-0.145-0.1450.0000.0000.0000.000
153A159LEU0-0.011-0.0156.138-0.062-0.0620.0000.0000.0000.000
154A160ALA0-0.059-0.0199.5750.0740.0740.0000.0000.0000.000
155A161ARG10.8700.95510.438-0.945-0.9450.0000.0000.0000.000
156A162GLY00.0590.02312.338-0.158-0.1580.0000.0000.0000.000
157A163GLY0-0.013-0.00510.3630.3560.3560.0000.0000.0000.000
158A164CYS0-0.032-0.00411.363-0.079-0.0790.0000.0000.0000.000
159A165PRO00.0270.01310.830-0.142-0.1420.0000.0000.0000.000
160A166SER00.0340.0309.9410.3360.3360.0000.0000.0000.000
161A167LEU00.0520.0014.5470.1430.294-0.001-0.006-0.1440.000
162A168SER0-0.025-0.0098.267-0.304-0.3040.0000.0000.0000.000
163A169THR00.024-0.00511.885-0.249-0.2490.0000.0000.0000.000
164A170GLU-1-0.809-0.8877.2953.9943.9940.0000.0000.0000.000
165A171LEU0-0.011-0.00410.948-0.233-0.2330.0000.0000.0000.000
166A172LEU0-0.002-0.01112.247-0.234-0.2340.0000.0000.0000.000
167A173LEU0-0.0020.00014.216-0.137-0.1370.0000.0000.0000.000
168A174LEU0-0.036-0.02010.720-0.110-0.1100.0000.0000.0000.000
169A175LEU0-0.001-0.00515.091-0.129-0.1290.0000.0000.0000.000
170A176GLN00.0390.03417.889-0.062-0.0620.0000.0000.0000.000
171A177PRO00.0160.02319.143-0.060-0.0600.0000.0000.0000.000
172A178LEU00.0290.00419.764-0.049-0.0490.0000.0000.0000.000
173A179SER0-0.034-0.01623.101-0.039-0.0390.0000.0000.0000.000
174A180VAL0-0.0090.00025.122-0.024-0.0240.0000.0000.0000.000
175A181LEU0-0.062-0.00524.913-0.027-0.0270.0000.0000.0000.000
176A182THR0-0.037-0.03528.4250.0170.0170.0000.0000.0000.000
177A183PHE00.0270.00424.520-0.012-0.0120.0000.0000.0000.000
178A184HIS0-0.038-0.02230.1110.0100.0100.0000.0000.0000.000
179A185LEU00.0280.01527.096-0.012-0.0120.0000.0000.0000.000
180A186ASP-1-0.757-0.84231.4750.0950.0950.0000.0000.0000.000
181A187LEU0-0.020-0.02729.5340.0000.0000.0000.0000.0000.000
182A188LEU0-0.029-0.03329.9690.0000.0000.0000.0000.0000.000
183A189PHE0-0.0560.00029.119-0.007-0.0070.0000.0000.0000.000
184A190GLU-1-0.843-0.89524.8920.0470.0470.0000.0000.0000.000