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: JL679

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 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 184
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -1888113.488426
FMO2-HF: Nuclear repulsion 1818980.522578
FMO2-HF: Total energy -69132.965848
FMO2-MP2: Total energy -69337.552166


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.
-6.731-9.21914.021-3.914-7.6190.005
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 : 0.028 / q_NPA : -0.002
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].
3A9LYS10.9530.9681.593-13.377-15.55214.012-4.999-6.8380.006
4A10GLY00.0170.0222.9520.172-0.5610.0111.125-0.403-0.001
5A11LEU0-0.012-0.0105.0190.5420.768-0.001-0.021-0.2040.000
6A12LEU00.0270.0126.0320.1560.1560.0000.0000.0000.000
7A13ILE00.0160.0176.488-0.172-0.1720.0000.0000.0000.000
8A14ALA00.0070.0118.881-0.015-0.0150.0000.0000.0000.000
9A15VAL00.0030.00410.8160.0110.0110.0000.0000.0000.000
10A16SER00.0320.00911.566-0.038-0.0380.0000.0000.0000.000
11A17VAL00.0080.01012.942-0.046-0.0460.0000.0000.0000.000
12A18SER0-0.045-0.03514.960-0.037-0.0370.0000.0000.0000.000
13A19VAL0-0.011-0.00716.349-0.025-0.0250.0000.0000.0000.000
14A20ASP-1-0.877-0.92416.8100.1850.1850.0000.0000.0000.000
15A21LYS10.8980.94718.3120.0740.0740.0000.0000.0000.000
16A22ILE00.0070.00320.092-0.006-0.0060.0000.0000.0000.000
17A23ILE00.0110.00121.656-0.008-0.0080.0000.0000.0000.000
18A24SER0-0.037-0.02223.503-0.010-0.0100.0000.0000.0000.000
19A25HIS0-0.028-0.00525.401-0.017-0.0170.0000.0000.0000.000
20A26PHE00.005-0.00726.271-0.004-0.0040.0000.0000.0000.000
21A27GLY0-0.048-0.02128.0340.0000.0000.0000.0000.0000.000
22A28ALA00.0160.02229.540-0.008-0.0080.0000.0000.0000.000
23A29ALA0-0.0040.01532.468-0.006-0.0060.0000.0000.0000.000
24A30ARG10.9940.98833.661-0.070-0.0700.0000.0000.0000.000
25A31ASN0-0.057-0.03236.2340.0080.0080.0000.0000.0000.000
26A32LEU00.1000.02433.442-0.001-0.0010.0000.0000.0000.000
27A33VAL00.0210.02335.5520.0040.0040.0000.0000.0000.000
28A34GLN00.025-0.00636.9250.0000.0000.0000.0000.0000.000
29A35LYS10.9240.96030.720-0.143-0.1430.0000.0000.0000.000
30A36ALA00.0010.00432.4650.0050.0050.0000.0000.0000.000
31A37GLN0-0.009-0.00634.2920.0050.0050.0000.0000.0000.000
32A38LEU0-0.019-0.00131.320-0.005-0.0050.0000.0000.0000.000
33A39GLY00.0470.01930.1530.0010.0010.0000.0000.0000.000
34A40ASP-1-0.875-0.92331.1080.1170.1170.0000.0000.0000.000
35A41SER00.011-0.00431.359-0.007-0.0070.0000.0000.0000.000
36A42ARG10.8260.90933.146-0.108-0.1080.0000.0000.0000.000
37A43LEU0-0.057-0.00836.391-0.009-0.0090.0000.0000.0000.000
38A44SER00.0080.00531.861-0.011-0.0110.0000.0000.0000.000
39A45PRO00.0440.01632.2260.0080.0080.0000.0000.0000.000
40A46ASP-1-0.884-0.94329.6570.0260.0260.0000.0000.0000.000
41A47VAL0-0.054-0.01027.2260.0010.0010.0000.0000.0000.000
42A48GLY00.0350.00826.6560.0140.0140.0000.0000.0000.000
43A49HIS00.0330.00726.1610.0050.0050.0000.0000.0000.000
44A50LEU00.0220.04022.469-0.010-0.0100.0000.0000.0000.000
45A51VAL00.0240.04422.1110.0010.0010.0000.0000.0000.000
46A52LEU00.008-0.01321.1590.0170.0170.0000.0000.0000.000
47A53THR0-0.068-0.04320.577-0.014-0.0140.0000.0000.0000.000
48A54THR0-0.090-0.07317.847-0.029-0.0290.0000.0000.0000.000
49A55LEU00.0630.01916.3560.0010.0010.0000.0000.0000.000
50A56CYS0-0.0370.00216.8630.0540.0540.0000.0000.0000.000
51A57PRO0-0.027-0.01615.4470.0420.0420.0000.0000.0000.000
52A58ALA00.0160.02212.5770.0010.0010.0000.0000.0000.000
53A59LEU00.0230.00412.3230.1040.1040.0000.0000.0000.000
54A60HIS0-0.053-0.02114.5160.0670.0670.0000.0000.0000.000
55A61ALA0-0.003-0.0139.7820.0500.0500.0000.0000.0000.000
56A62LEU0-0.015-0.0019.3380.0690.0690.0000.0000.0000.000
57A63VAL00.0010.01011.0760.1670.1670.0000.0000.0000.000
58A64ALA00.0160.00712.6080.0090.0090.0000.0000.0000.000
59A65ASP-1-0.783-0.8487.1962.1662.1660.0000.0000.0000.000
60A66GLY00.007-0.01910.0760.1610.1610.0000.0000.0000.000
61A67LEU0-0.038-0.00311.282-0.082-0.0820.0000.0000.0000.000
62A68LYS10.8690.94314.920-0.524-0.5240.0000.0000.0000.000
63A69PRO0-0.0040.00617.305-0.018-0.0180.0000.0000.0000.000
64A70PHE00.012-0.01418.930-0.030-0.0300.0000.0000.0000.000
65A71ARG10.9590.99722.462-0.197-0.1970.0000.0000.0000.000
66A72LYS10.9830.97724.845-0.228-0.2280.0000.0000.0000.000
67A73ASP-1-0.890-0.97228.4530.1440.1440.0000.0000.0000.000
68A74LEU00.0410.01831.338-0.007-0.0070.0000.0000.0000.000
69A75ILE0-0.0250.02234.035-0.008-0.0080.0000.0000.0000.000
70A76THR00.006-0.01331.042-0.013-0.0130.0000.0000.0000.000
71A77GLY00.0100.04332.003-0.004-0.0040.0000.0000.0000.000
72A78GLN0-0.054-0.05226.8770.0220.0220.0000.0000.0000.000
73A79ARG10.9630.98926.348-0.158-0.1580.0000.0000.0000.000
74A80ARG10.9250.95618.420-0.124-0.1240.0000.0000.0000.000
75A81SER0-0.0040.01319.651-0.005-0.0050.0000.0000.0000.000
76A82SER0-0.031-0.03018.565-0.022-0.0220.0000.0000.0000.000
77A83PRO00.0960.02516.0520.0110.0110.0000.0000.0000.000
78A84TRP00.0170.01018.6270.0210.0210.0000.0000.0000.000
79A85SER0-0.029-0.01421.587-0.007-0.0070.0000.0000.0000.000
80A86VAL00.0330.02217.797-0.007-0.0070.0000.0000.0000.000
81A87VAL0-0.0160.00021.1740.0100.0100.0000.0000.0000.000
82A88GLU-1-0.961-0.99023.5700.2240.2240.0000.0000.0000.000
83A89ALA0-0.035-0.01423.366-0.013-0.0130.0000.0000.0000.000
84A90SER00.0100.01322.7300.0030.0030.0000.0000.0000.000
85A91VAL0-0.047-0.00924.880-0.002-0.0020.0000.0000.0000.000
86A92LYS10.9390.97028.112-0.232-0.2320.0000.0000.0000.000
87A93PRO0-0.047-0.01628.673-0.020-0.0200.0000.0000.0000.000
88A94GLY00.1000.05729.654-0.011-0.0110.0000.0000.0000.000
89A95SER0-0.068-0.04529.8930.0040.0040.0000.0000.0000.000
90A96SER00.000-0.00125.490-0.017-0.0170.0000.0000.0000.000
91A97THR00.1020.05827.947-0.009-0.0090.0000.0000.0000.000
92A98ARG11.0290.98830.544-0.218-0.2180.0000.0000.0000.000
93A99SER0-0.0220.00430.632-0.018-0.0180.0000.0000.0000.000
94A100LEU00.0110.01125.518-0.011-0.0110.0000.0000.0000.000
95A101GLY00.0320.01329.506-0.007-0.0070.0000.0000.0000.000
96A102THR0-0.035-0.01632.206-0.017-0.0170.0000.0000.0000.000
97A103LEU00.0210.04627.310-0.016-0.0160.0000.0000.0000.000
98A104TYR00.0440.01528.055-0.017-0.0170.0000.0000.0000.000
99A105SER0-0.069-0.05030.327-0.019-0.0190.0000.0000.0000.000
100A106GLN0-0.053-0.04032.945-0.008-0.0080.0000.0000.0000.000
101A107VAL00.0190.01027.552-0.013-0.0130.0000.0000.0000.000
102A108SER0-0.010-0.01630.986-0.014-0.0140.0000.0000.0000.000
103A109ARG10.9470.98431.987-0.152-0.1520.0000.0000.0000.000
104A110LEU0-0.061-0.00432.591-0.011-0.0110.0000.0000.0000.000
105A111ALA0-0.010-0.01530.8870.0000.0000.0000.0000.0000.000
106A112PRO0-0.0240.00132.6000.0010.0010.0000.0000.0000.000
107A113LEU00.0490.00932.8690.0010.0010.0000.0000.0000.000
108A114SER0-0.0010.01628.769-0.011-0.0110.0000.0000.0000.000
109A115SER00.0800.03424.5800.0130.0130.0000.0000.0000.000
110A116SER0-0.022-0.02223.0780.0050.0050.0000.0000.0000.000
111A117ARG10.9420.98116.441-0.039-0.0390.0000.0000.0000.000
112A118SER00.0640.03521.9310.0100.0100.0000.0000.0000.000
113A119ARG10.9240.97425.010-0.148-0.1480.0000.0000.0000.000
114A120PHE0-0.007-0.00917.6590.0070.0070.0000.0000.0000.000
115A121HIS00.0340.00918.7540.0550.0550.0000.0000.0000.000
116A122ALA00.0500.02622.8220.0120.0120.0000.0000.0000.000
117A123PHE00.006-0.01023.034-0.001-0.0010.0000.0000.0000.000
118A124ILE00.0150.00819.4160.0230.0230.0000.0000.0000.000
119A125LEU00.0080.00823.0970.0120.0120.0000.0000.0000.000
120A126GLY00.0460.01026.108-0.001-0.0010.0000.0000.0000.000
121A127LEU0-0.058-0.02822.1130.0040.0040.0000.0000.0000.000
122A128LEU0-0.0160.00021.8520.0170.0170.0000.0000.0000.000
123A129ASN0-0.0240.00325.386-0.004-0.0040.0000.0000.0000.000
124A130THR0-0.061-0.02928.3990.0020.0020.0000.0000.0000.000
125A131LYS10.8760.94825.651-0.274-0.2740.0000.0000.0000.000
126A132GLN0-0.006-0.02925.2110.0220.0220.0000.0000.0000.000
127A133LEU00.0230.00819.0670.0210.0210.0000.0000.0000.000
128A134GLU-1-0.870-0.93319.0580.6320.6320.0000.0000.0000.000
129A135LEU00.0090.00720.1110.0440.0440.0000.0000.0000.000
130A136TRP00.000-0.00918.7190.0250.0250.0000.0000.0000.000
131A137PHE00.036-0.01016.2930.0200.0200.0000.0000.0000.000
132A138SER0-0.0150.00517.7490.0530.0530.0000.0000.0000.000
133A139SER0-0.001-0.01519.630-0.027-0.0270.0000.0000.0000.000
134A140LEU0-0.031-0.00617.154-0.020-0.0200.0000.0000.0000.000
135A141GLN0-0.080-0.05914.6630.0920.0920.0000.0000.0000.000
136A142GLU-1-0.909-0.95117.6730.7100.7100.0000.0000.0000.000
137A143ASP-1-0.882-0.92020.9010.4060.4060.0000.0000.0000.000
138A144ALA0-0.007-0.02420.3820.0340.0340.0000.0000.0000.000
139A145GLY00.0070.00321.1120.0030.0030.0000.0000.0000.000
140A146LEU00.0100.01819.252-0.006-0.0060.0000.0000.0000.000
141A147LEU00.000-0.01115.7710.0100.0100.0000.0000.0000.000
142A148SER0-0.0230.00717.5060.0150.0150.0000.0000.0000.000
143A149LEU0-0.013-0.01219.563-0.030-0.0300.0000.0000.0000.000
144A150MET0-0.072-0.03818.884-0.039-0.0390.0000.0000.0000.000
145A151TYR0-0.053-0.03313.043-0.015-0.0150.0000.0000.0000.000
146A152MET0-0.022-0.01112.033-0.090-0.0900.0000.0000.0000.000
147A153PRO00.0330.01212.5450.1580.1580.0000.0000.0000.000
148A154THR00.013-0.0037.6610.1090.1090.0000.0000.0000.000
149A155GLY00.0250.0107.5410.5020.5020.0000.0000.0000.000
150A156PHE00.0220.0087.0310.2170.2170.0000.0000.0000.000
151A157PHE00.0530.0068.8720.2050.2050.0000.0000.0000.000
152A158SER0-0.0330.00711.969-0.176-0.1760.0000.0000.0000.000
153A159LEU0-0.004-0.0226.334-0.080-0.0800.0000.0000.0000.000
154A160ALA0-0.059-0.0169.6510.1150.1150.0000.0000.0000.000
155A161ARG10.8760.95810.556-1.138-1.1380.0000.0000.0000.000
156A162GLY00.0550.02112.376-0.171-0.1710.0000.0000.0000.000
157A163GLY0-0.013-0.00410.0880.4270.4270.0000.0000.0000.000
158A164CYS0-0.057-0.01311.110-0.165-0.1650.0000.0000.0000.000
159A165PRO00.0510.02110.407-0.137-0.1370.0000.0000.0000.000
160A166SER00.0380.0209.5130.4650.4650.0000.0000.0000.000
161A167LEU00.0570.0054.1670.1310.325-0.001-0.019-0.1740.000
162A168SER0-0.0040.0218.165-0.435-0.4350.0000.0000.0000.000
163A169THR00.0360.01411.851-0.293-0.2930.0000.0000.0000.000
164A170GLU-1-0.865-0.9377.2434.8344.8340.0000.0000.0000.000
165A171LEU0-0.024-0.00910.845-0.293-0.2930.0000.0000.0000.000
166A172LEU0-0.011-0.01612.219-0.257-0.2570.0000.0000.0000.000
167A173LEU00.000-0.00113.777-0.155-0.1550.0000.0000.0000.000
168A174LEU0-0.025-0.01710.382-0.137-0.1370.0000.0000.0000.000
169A175LEU0-0.006-0.00814.836-0.150-0.1500.0000.0000.0000.000
170A176GLN00.0450.03917.575-0.062-0.0620.0000.0000.0000.000
171A177PRO00.0140.02118.787-0.066-0.0660.0000.0000.0000.000
172A178LEU00.0310.00219.606-0.054-0.0540.0000.0000.0000.000
173A179SER0-0.040-0.01522.795-0.041-0.0410.0000.0000.0000.000
174A180VAL0-0.015-0.00524.891-0.025-0.0250.0000.0000.0000.000
175A181LEU0-0.070-0.01224.294-0.031-0.0310.0000.0000.0000.000
176A182THR0-0.043-0.03628.1200.0210.0210.0000.0000.0000.000
177A183PHE00.0320.00624.259-0.015-0.0150.0000.0000.0000.000
178A184HIS0-0.019-0.01829.7420.0120.0120.0000.0000.0000.000
179A185LEU00.0170.00626.758-0.014-0.0140.0000.0000.0000.000
180A186ASP-1-0.797-0.89331.1010.1150.1150.0000.0000.0000.000
181A187LEU0-0.037-0.04029.4010.0000.0000.0000.0000.0000.000
182A188LEU0-0.025-0.03429.7620.0020.0020.0000.0000.0000.000
183A189PHE0-0.0390.01028.751-0.008-0.0080.0000.0000.0000.000
184A190GLU-1-0.905-0.95424.8460.0680.0680.0000.0000.0000.000