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: VR4R1

Calculation Name: 1G62-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1G62

Chain ID: A

ChEMBL ID:

UniProt ID: Q12522

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 224
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2670026.581479
FMO2-HF: Nuclear repulsion 2584899.475135
FMO2-HF: Total energy -85127.106344
FMO2-MP2: Total energy -85374.82702


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.
-25.289-11.0165.358-7.915-11.713-0.07
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 : -0.008 / q_NPA : 0.020
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].
3A3THR0-0.004-0.0122.521-4.411-0.8721.289-2.117-2.710-0.007
4A4ARG10.7780.9025.1221.7801.843-0.001-0.003-0.0590.000
5A5THR00.002-0.0038.402-0.017-0.0170.0000.0000.0000.000
6A6GLN0-0.031-0.03511.8140.1020.1020.0000.0000.0000.000
7A7PHE00.0030.02915.452-0.006-0.0060.0000.0000.0000.000
8A8GLU-1-0.851-0.92718.491-0.353-0.3530.0000.0000.0000.000
9A9ASN0-0.015-0.00919.290-0.034-0.0340.0000.0000.0000.000
10A10SER00.0040.01119.4700.0120.0120.0000.0000.0000.000
11A11ASN00.009-0.00615.342-0.136-0.1360.0000.0000.0000.000
12A12GLU-1-0.920-0.95315.142-0.496-0.4960.0000.0000.0000.000
13A13ILE00.0300.01712.3220.0790.0790.0000.0000.0000.000
14A14GLY00.0540.03615.5690.0070.0070.0000.0000.0000.000
15A15VAL0-0.041-0.02416.4360.0760.0760.0000.0000.0000.000
16A16PHE0-0.041-0.03018.3820.0620.0620.0000.0000.0000.000
17A17SER0-0.006-0.01414.484-0.061-0.0610.0000.0000.0000.000
18A18LYS10.8300.91415.5870.4840.4840.0000.0000.0000.000
19A19LEU00.0040.0147.9260.0330.0330.0000.0000.0000.000
20A20THR00.0360.03212.6380.0730.0730.0000.0000.0000.000
21A21ASN0-0.037-0.03710.475-0.232-0.2320.0000.0000.0000.000
22A22THR0-0.050-0.02712.0350.0200.0200.0000.0000.0000.000
23A23TYR00.0110.00014.0440.0200.0200.0000.0000.0000.000
24A24CYS0-0.0020.02212.290-0.090-0.0900.0000.0000.0000.000
25A25LEU0-0.0060.00814.3140.0710.0710.0000.0000.0000.000
26A26VAL00.0510.01614.788-0.060-0.0600.0000.0000.0000.000
27A27ALA00.0380.02117.6900.0780.0780.0000.0000.0000.000
28A28VAL0-0.0060.00820.572-0.030-0.0300.0000.0000.0000.000
29A29GLY0-0.038-0.01023.1780.0060.0060.0000.0000.0000.000
30A30GLY00.0130.01219.7950.0080.0080.0000.0000.0000.000
31A31SER0-0.016-0.01418.8360.0120.0120.0000.0000.0000.000
32A32GLU-1-0.821-0.90916.634-0.743-0.7430.0000.0000.0000.000
33A33ASN0-0.028-0.01813.632-0.098-0.0980.0000.0000.0000.000
34A34PHE00.0080.00213.404-0.138-0.1380.0000.0000.0000.000
35A35TYR00.019-0.02813.377-0.111-0.1110.0000.0000.0000.000
36A36SER00.021-0.00512.251-0.109-0.1090.0000.0000.0000.000
37A37ALA0-0.0440.0019.198-0.165-0.1650.0000.0000.0000.000
38A38PHE0-0.018-0.0017.999-0.527-0.5270.0000.0000.0000.000
39A39GLU-1-0.872-0.9718.847-0.908-0.9080.0000.0000.0000.000
40A40ALA0-0.054-0.0338.7050.1310.1310.0000.0000.0000.000
41A41GLU-1-0.881-0.9422.540-14.110-11.0590.990-1.966-2.076-0.024
42A42LEU0-0.072-0.0266.0670.1610.1610.0000.0000.0000.000
43A43GLY00.0260.0168.5220.3160.3160.0000.0000.0000.000
44A44ASP-1-0.983-0.99511.278-0.411-0.4110.0000.0000.0000.000
45A45ALA0-0.082-0.02910.4850.0930.0930.0000.0000.0000.000
46A46ILE0-0.038-0.01610.6940.0950.0950.0000.0000.0000.000
47A47PRO00.007-0.00213.717-0.071-0.0710.0000.0000.0000.000
48A48ILE00.0420.03011.917-0.042-0.0420.0000.0000.0000.000
49A49VAL0-0.011-0.01015.7930.0520.0520.0000.0000.0000.000
50A50HIS10.8460.94117.4740.5710.5710.0000.0000.0000.000
51A51THR00.0410.00320.8410.0550.0550.0000.0000.0000.000
52A52THR0-0.048-0.04623.449-0.028-0.0280.0000.0000.0000.000
53A53ILE00.0190.00524.1060.0070.0070.0000.0000.0000.000
54A54ALA00.0000.00927.1440.0000.0000.0000.0000.0000.000
55A55GLY0-0.028-0.01230.0710.0100.0100.0000.0000.0000.000
56A56THR0-0.090-0.03827.553-0.014-0.0140.0000.0000.0000.000
57A57ARG10.8820.90324.0160.3840.3840.0000.0000.0000.000
58A58ILE0-0.0070.01522.906-0.041-0.0410.0000.0000.0000.000
59A59ILE00.014-0.01218.6680.0190.0190.0000.0000.0000.000
60A60GLY00.0110.04119.0410.0090.0090.0000.0000.0000.000
61A61ARG10.8480.91618.4000.4460.4460.0000.0000.0000.000
62A62MET0-0.042-0.01622.6240.0390.0390.0000.0000.0000.000
63A63THR00.0120.00821.1390.0160.0160.0000.0000.0000.000
64A64ALA00.0330.01620.560-0.026-0.0260.0000.0000.0000.000
65A65GLY00.0210.02019.6460.0200.0200.0000.0000.0000.000
66A66ASN00.0010.00316.864-0.041-0.0410.0000.0000.0000.000
67A67ARG10.9570.97614.7810.0910.0910.0000.0000.0000.000
68A68ARG10.8030.87017.4770.0820.0820.0000.0000.0000.000
69A69GLY00.0440.02621.0310.0140.0140.0000.0000.0000.000
70A70LEU0-0.040-0.01720.175-0.027-0.0270.0000.0000.0000.000
71A71LEU00.0130.00422.7290.0240.0240.0000.0000.0000.000
72A72VAL0-0.004-0.01824.699-0.026-0.0260.0000.0000.0000.000
73A73PRO00.0610.04227.0400.0210.0210.0000.0000.0000.000
74A74THR00.030-0.00830.023-0.003-0.0030.0000.0000.0000.000
75A75GLN0-0.024-0.02432.7570.0000.0000.0000.0000.0000.000
76A76THR0-0.029-0.01028.375-0.014-0.0140.0000.0000.0000.000
77A77THR0-0.009-0.02431.1160.0150.0150.0000.0000.0000.000
78A78ASP-1-0.774-0.88931.834-0.157-0.1570.0000.0000.0000.000
79A79GLN00.0120.00632.6990.0010.0010.0000.0000.0000.000
80A80GLU-1-0.717-0.81227.985-0.253-0.2530.0000.0000.0000.000
81A81LEU00.0220.01327.695-0.015-0.0150.0000.0000.0000.000
82A82GLN0-0.065-0.03728.5760.0030.0030.0000.0000.0000.000
83A83HIS0-0.034-0.02323.7780.0210.0210.0000.0000.0000.000
84A84LEU00.0090.01022.645-0.017-0.0170.0000.0000.0000.000
85A85ARG10.8560.91924.4660.1790.1790.0000.0000.0000.000
86A86ASN0-0.052-0.01126.2270.0090.0090.0000.0000.0000.000
87A87SER0-0.0050.00221.851-0.002-0.0020.0000.0000.0000.000
88A88LEU0-0.039-0.00819.891-0.022-0.0220.0000.0000.0000.000
89A89PRO00.0430.01618.8040.0270.0270.0000.0000.0000.000
90A90ASP-1-0.884-0.95622.043-0.149-0.1490.0000.0000.0000.000
91A91SER0-0.077-0.03821.4330.0070.0070.0000.0000.0000.000
92A92VAL0-0.0590.00620.6420.0080.0080.0000.0000.0000.000
93A93LYS10.8120.90323.0380.1010.1010.0000.0000.0000.000
94A94ILE00.0260.01324.315-0.015-0.0150.0000.0000.0000.000
95A95GLN0-0.040-0.01726.5970.0180.0180.0000.0000.0000.000
96A96ARG10.7740.86228.3900.1440.1440.0000.0000.0000.000
97A97VAL00.0220.00428.7190.0130.0130.0000.0000.0000.000
98A98GLU-1-0.835-0.86831.405-0.139-0.1390.0000.0000.0000.000
99A99GLU-1-0.766-0.89829.523-0.153-0.1530.0000.0000.0000.000
100A100ARG10.7800.84532.9120.1220.1220.0000.0000.0000.000
101A101LEU0-0.0010.02731.8440.0010.0010.0000.0000.0000.000
102A102SER0-0.041-0.03929.042-0.009-0.0090.0000.0000.0000.000
103A103ALA0-0.0090.01726.3920.0010.0010.0000.0000.0000.000
104A104LEU00.0980.04125.313-0.005-0.0050.0000.0000.0000.000
105A105GLY0-0.030-0.00622.1970.0040.0040.0000.0000.0000.000
106A106ASN0-0.044-0.04222.039-0.036-0.0360.0000.0000.0000.000
107A107VAL0-0.0230.00024.5730.0160.0160.0000.0000.0000.000
108A108ILE00.004-0.00222.5650.0200.0200.0000.0000.0000.000
109A109CYS0-0.0320.00319.058-0.031-0.0310.0000.0000.0000.000
110A110CYS0-0.036-0.00418.4540.0310.0310.0000.0000.0000.000
111A111ASN00.0940.06515.465-0.054-0.0540.0000.0000.0000.000
112A112ASP-1-0.811-0.92415.297-0.196-0.1960.0000.0000.0000.000
113A113TYR0-0.029-0.00416.7180.0200.0200.0000.0000.0000.000
114A114VAL00.0270.01620.2710.0040.0040.0000.0000.0000.000
115A115ALA00.014-0.01220.815-0.029-0.0290.0000.0000.0000.000
116A116LEU0-0.0090.00422.8050.0180.0180.0000.0000.0000.000
117A117VAL0-0.027-0.03024.652-0.025-0.0250.0000.0000.0000.000
118A118HIS00.0620.02727.3670.0160.0160.0000.0000.0000.000
119A119PRO00.001-0.01329.6560.0050.0050.0000.0000.0000.000
120A120ASP-1-0.921-0.96932.472-0.073-0.0730.0000.0000.0000.000
121A121ILE0-0.085-0.02830.205-0.001-0.0010.0000.0000.0000.000
122A122ASP-1-0.827-0.88533.920-0.080-0.0800.0000.0000.0000.000
123A123ARG10.7580.81235.0060.0460.0460.0000.0000.0000.000
124A124GLU-1-0.808-0.88935.464-0.057-0.0570.0000.0000.0000.000
125A125THR0-0.033-0.05531.471-0.005-0.0050.0000.0000.0000.000
126A126GLU-1-0.830-0.88930.852-0.067-0.0670.0000.0000.0000.000
127A127GLU-1-0.810-0.88230.795-0.048-0.0480.0000.0000.0000.000
128A128LEU0-0.0220.00030.872-0.001-0.0010.0000.0000.0000.000
129A129ILE0-0.014-0.00725.885-0.008-0.0080.0000.0000.0000.000
130A130SER0-0.032-0.02026.833-0.004-0.0040.0000.0000.0000.000
131A131ASP-1-0.822-0.90227.599-0.080-0.0800.0000.0000.0000.000
132A132VAL0-0.079-0.05525.6120.0000.0000.0000.0000.0000.000
133A133LEU0-0.031-0.00821.911-0.012-0.0120.0000.0000.0000.000
134A134GLY00.0170.00923.2090.0040.0040.0000.0000.0000.000
135A135VAL0-0.090-0.01521.4030.0090.0090.0000.0000.0000.000
136A136GLU-1-0.911-0.92324.7300.0170.0170.0000.0000.0000.000
137A137VAL0-0.011-0.01925.416-0.010-0.0100.0000.0000.0000.000
138A138PHE00.0170.00526.1550.0110.0110.0000.0000.0000.000
139A139ARG10.7860.89627.8010.0440.0440.0000.0000.0000.000
140A140GLN00.0390.00927.1140.0050.0050.0000.0000.0000.000
141A141THR0-0.029-0.01028.388-0.013-0.0130.0000.0000.0000.000
142A142ILE00.0180.02122.8290.0120.0120.0000.0000.0000.000
143A143SER00.001-0.01125.937-0.009-0.0090.0000.0000.0000.000
144A144GLY0-0.0090.00227.825-0.005-0.0050.0000.0000.0000.000
145A145ASN0-0.079-0.03126.811-0.011-0.0110.0000.0000.0000.000
146A146ILE00.0850.02628.5130.0020.0020.0000.0000.0000.000
147A147LEU0-0.052-0.01226.264-0.005-0.0050.0000.0000.0000.000
148A148VAL00.0780.02124.003-0.019-0.0190.0000.0000.0000.000
149A149GLY0-0.0030.02021.055-0.008-0.0080.0000.0000.0000.000
150A150SER0-0.037-0.03820.290-0.052-0.0520.0000.0000.0000.000
151A151TYR0-0.096-0.05321.319-0.026-0.0260.0000.0000.0000.000
152A152CYS00.025-0.00518.4060.0460.0460.0000.0000.0000.000
153A153SER0-0.0190.01613.469-0.057-0.0570.0000.0000.0000.000
154A154LEU0-0.008-0.01714.4950.0700.0700.0000.0000.0000.000
155A155SER00.0770.0459.739-0.039-0.0390.0000.0000.0000.000
156A156ASN0-0.049-0.05612.0500.0300.0300.0000.0000.0000.000
157A157GLN0-0.036-0.0039.1920.2110.2110.0000.0000.0000.000
158A158GLY00.0740.03212.1690.1030.1030.0000.0000.0000.000
159A159GLY00.004-0.00913.676-0.110-0.1100.0000.0000.0000.000
160A160LEU0-0.047-0.00312.8500.0540.0540.0000.0000.0000.000
161A161VAL00.0300.00515.933-0.057-0.0570.0000.0000.0000.000
162A162HIS00.0810.03819.2940.0120.0120.0000.0000.0000.000
163A163PRO0-0.0080.00819.7730.0270.0270.0000.0000.0000.000
164A164GLN0-0.053-0.03721.1940.0080.0080.0000.0000.0000.000
165A165THR0-0.029-0.01723.0450.0030.0030.0000.0000.0000.000
166A166SER00.002-0.00524.7610.0190.0190.0000.0000.0000.000
167A167VAL00.029-0.01424.7830.0000.0000.0000.0000.0000.000
168A168GLN00.0450.03226.3010.0090.0090.0000.0000.0000.000
169A169ASP-1-0.801-0.89026.5420.0020.0020.0000.0000.0000.000
170A170GLN0-0.043-0.02221.3160.0160.0160.0000.0000.0000.000
171A171GLU-1-0.936-0.95223.2200.1270.1270.0000.0000.0000.000
172A172GLU-1-0.961-0.97825.3440.0390.0390.0000.0000.0000.000
173A173LEU00.003-0.01723.055-0.004-0.0040.0000.0000.0000.000
174A174SER0-0.010-0.01721.1040.0060.0060.0000.0000.0000.000
175A175SER0-0.065-0.03822.0130.0130.0130.0000.0000.0000.000
176A176LEU0-0.057-0.01724.6310.0000.0000.0000.0000.0000.000
177A177LEU0-0.022-0.02719.674-0.013-0.0130.0000.0000.0000.000
178A178GLN0-0.050-0.01719.9030.0170.0170.0000.0000.0000.000
179A179VAL0-0.033-0.00115.6740.0340.0340.0000.0000.0000.000
180A180PRO0-0.024-0.01315.438-0.029-0.0290.0000.0000.0000.000
181A181LEU0-0.0200.01616.173-0.020-0.0200.0000.0000.0000.000
182A182VAL0-0.007-0.00315.8180.0290.0290.0000.0000.0000.000
183A183ALA0-0.0300.00017.515-0.045-0.0450.0000.0000.0000.000
184A184GLY0-0.001-0.01415.8220.0380.0380.0000.0000.0000.000
185A185THR0-0.077-0.05515.476-0.001-0.0010.0000.0000.0000.000
186A186VAL00.0210.01311.801-0.011-0.0110.0000.0000.0000.000
187A187ASN0-0.075-0.04612.970-0.024-0.0240.0000.0000.0000.000
188A188ARG10.8290.90014.2300.4470.4470.0000.0000.0000.000
189A189GLY0-0.0010.00016.0450.0280.0280.0000.0000.0000.000
190A190SER0-0.0160.01017.7480.0460.0460.0000.0000.0000.000
191A191SER00.0590.01118.093-0.010-0.0100.0000.0000.0000.000
192A192VAL0-0.0170.00220.1570.0220.0220.0000.0000.0000.000
193A193VAL00.041-0.00615.850-0.061-0.0610.0000.0000.0000.000
194A194GLY0-0.0240.01916.138-0.063-0.0630.0000.0000.0000.000
195A195ALA0-0.016-0.02117.219-0.054-0.0540.0000.0000.0000.000
196A196GLY0-0.011-0.01316.118-0.051-0.0510.0000.0000.0000.000
197A197MET0-0.035-0.00910.058-0.051-0.0510.0000.0000.0000.000
198A198VAL0-0.0180.01010.1870.1740.1740.0000.0000.0000.000
199A199VAL0-0.028-0.0247.284-0.299-0.2990.0000.0000.0000.000
200A200ASN00.0000.0006.8600.0230.0230.0000.0000.0000.000
201A201ASP-1-0.773-0.9027.260-0.076-0.0760.0000.0000.0000.000
202A202TYR0-0.059-0.0264.5510.4650.651-0.001-0.030-0.1550.000
203A203LEU00.0290.0352.451-4.932-2.7581.088-1.442-1.819-0.015
204A204ALA0-0.0010.0023.7362.0342.3660.001-0.087-0.2460.000
205A205VAL00.0050.0225.976-0.718-0.7180.0000.0000.0000.000
206A206THR00.022-0.0077.8510.5930.5930.0000.0000.0000.000
207A207GLY00.0820.03210.313-0.115-0.1150.0000.0000.0000.000
208A208LEU0-0.037-0.04311.145-0.037-0.0370.0000.0000.0000.000
209A209ASP-1-0.795-0.88612.122-0.467-0.4670.0000.0000.0000.000
210A210THR0-0.0570.0049.2460.1090.1090.0000.0000.0000.000
211A211THR0-0.012-0.03110.364-0.055-0.0550.0000.0000.0000.000
212A212ALA00.0190.0028.677-0.091-0.0910.0000.0000.0000.000
213A213PRO00.0400.0028.7640.0310.0310.0000.0000.0000.000
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