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: 39QYL

Calculation Name: 3UV1-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3UV1

Chain ID: A

ChEMBL ID:

UniProt ID: Q26456

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 190
LigandCharge DAS=-1
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -1942465.519687
FMO2-HF: Nuclear repulsion 1868304.213044
FMO2-HF: Total energy -74161.306643
FMO2-MP2: Total energy -74377.857294


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:6:ASP)


Summations of interaction energy for fragment #1(A:6:ASP)
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.
94.27286.89234.122-15.531-11.2110.13
Interaction energy analysis for fragmet #1(A:6:ASP)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : -1 / q_Mulliken : -0.829 / q_NPA : -0.915
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].
3A8ILE00.0770.0472.699-20.029-13.5950.861-3.462-3.8330.030
4A9THR0-0.028-0.0411.585-44.667-59.29033.191-11.919-6.6490.095
5A10GLU-1-0.903-0.9323.54322.27822.9820.071-0.147-0.6280.005
6A11GLU-1-0.909-0.9725.91634.77134.7710.0000.0000.0000.000
7A12ILE0-0.013-0.0065.884-6.182-6.1820.0000.0000.0000.000
8A13ASN0-0.047-0.0567.006-4.851-4.8510.0000.0000.0000.000
9A14LYS10.8230.8999.502-23.817-23.8170.0000.0000.0000.000
10A15ALA00.0220.01311.282-2.285-2.2850.0000.0000.0000.000
11A16ILE0-0.028-0.01712.024-2.065-2.0650.0000.0000.0000.000
12A17ASP-1-0.801-0.87612.65321.22021.2200.0000.0000.0000.000
13A18ASP-1-0.815-0.88315.49918.08018.0800.0000.0000.0000.000
14A19ALA0-0.0010.00316.968-1.235-1.2350.0000.0000.0000.000
15A20ILE0-0.033-0.01516.761-0.936-0.9360.0000.0000.0000.000
16A21ALA00.0470.03919.748-0.894-0.8940.0000.0000.0000.000
17A22ALA0-0.023-0.01321.469-0.847-0.8470.0000.0000.0000.000
18A23ILE0-0.040-0.02921.343-0.831-0.8310.0000.0000.0000.000
19A24GLU-1-0.846-0.93622.77513.06713.0670.0000.0000.0000.000
20A25GLN0-0.117-0.05925.392-0.770-0.7700.0000.0000.0000.000
21A26SER0-0.089-0.03927.890-0.367-0.3670.0000.0000.0000.000
22A27GLU-1-0.806-0.90629.5619.2679.2670.0000.0000.0000.000
23A28THR0-0.112-0.05732.1930.0760.0760.0000.0000.0000.000
24A29ILE0-0.011-0.00826.9390.0330.0330.0000.0000.0000.000
25A30ASP-1-0.827-0.89429.91710.25810.2580.0000.0000.0000.000
26A31PRO00.0440.01731.926-0.040-0.0400.0000.0000.0000.000
27A32MET0-0.029-0.00528.946-0.061-0.0610.0000.0000.0000.000
28A33LYS10.8070.90433.957-7.910-7.9100.0000.0000.0000.000
29A34VAL00.0220.00635.0450.1940.1940.0000.0000.0000.000
30A35PRO0-0.023-0.01837.573-0.271-0.2710.0000.0000.0000.000
31A36ASP-1-0.820-0.91940.5877.1617.1610.0000.0000.0000.000
32A37HIS00.0500.02741.7560.1150.1150.0000.0000.0000.000
33A38ALA0-0.023-0.00543.897-0.090-0.0900.0000.0000.0000.000
34A39ASP-1-0.900-0.95445.0047.1627.1620.0000.0000.0000.000
35A40LYS10.8760.94447.077-6.112-6.1120.0000.0000.0000.000
36A41PHE00.0260.01447.7410.0600.0600.0000.0000.0000.000
37A42GLU-1-0.790-0.91049.1325.7925.7920.0000.0000.0000.000
38A43ARG10.7750.88042.804-7.057-7.0570.0000.0000.0000.000
39A44HIS0-0.011-0.00650.133-0.062-0.0620.0000.0000.0000.000
40A45VAL0-0.019-0.00150.1840.1130.1130.0000.0000.0000.000
41A46GLY00.0380.00351.9440.0420.0420.0000.0000.0000.000
42A47ILE0-0.068-0.00955.097-0.063-0.0630.0000.0000.0000.000
43A48LEU0-0.012-0.01256.397-0.060-0.0600.0000.0000.0000.000
44A49ASP-1-0.841-0.92855.0475.8415.8410.0000.0000.0000.000
45A50PHE0-0.017-0.01552.455-0.093-0.0930.0000.0000.0000.000
46A51LYS10.8130.90452.775-5.650-5.6500.0000.0000.0000.000
47A52GLY0-0.006-0.01853.135-0.114-0.1140.0000.0000.0000.000
48A53GLU-1-0.924-0.95151.0756.1426.1420.0000.0000.0000.000
49A54LEU0-0.019-0.00845.315-0.069-0.0690.0000.0000.0000.000
50A55ALA00.0140.00547.6830.0510.0510.0000.0000.0000.000
51A56MET0-0.0210.00240.157-0.067-0.0670.0000.0000.0000.000
52A57ARG10.9060.94145.030-6.640-6.6400.0000.0000.0000.000
53A58ASN0-0.089-0.06043.6520.0500.0500.0000.0000.0000.000
54A59ILE0-0.0130.00138.2590.0160.0160.0000.0000.0000.000
55A60GLU-1-0.829-0.89937.6368.2388.2380.0000.0000.0000.000
56A61ALA00.000-0.01032.746-0.052-0.0520.0000.0000.0000.000
57A62ARG10.8340.88932.894-8.455-8.4550.0000.0000.0000.000
58A63GLY00.1350.06229.875-0.020-0.0200.0000.0000.0000.000
59A64LEU0-0.065-0.03426.0290.4170.4170.0000.0000.0000.000
60A65LYS10.8220.90725.587-9.872-9.8720.0000.0000.0000.000
61A66GLN0-0.0130.01124.4350.0630.0630.0000.0000.0000.000
62A67MET0-0.044-0.00621.2530.4150.4150.0000.0000.0000.000
63A68LYS10.9030.94416.134-16.126-16.1260.0000.0000.0000.000
64A69ARG10.7930.8719.960-25.397-25.3970.0000.0000.0000.000
65A70GLN0-0.042-0.03515.408-0.164-0.1640.0000.0000.0000.000
66A71GLY0-0.014-0.00912.016-0.532-0.5320.0000.0000.0000.000
67A72ASP-1-0.915-0.9406.49534.12234.1220.0000.0000.0000.000
68A73ALA00.0040.0077.009-2.363-2.3630.0000.0000.0000.000
69A74ASN0-0.060-0.0317.1825.2575.2570.0000.0000.0000.000
70A75VAL00.0340.0104.707-3.745-3.640-0.001-0.003-0.1010.000
71A76LYS10.8160.9026.726-20.762-20.7620.0000.0000.0000.000
72A77GLY00.0180.0178.350-1.054-1.0540.0000.0000.0000.000
73A78GLU-1-0.875-0.94110.15319.65519.6550.0000.0000.0000.000
74A79GLU-1-0.959-0.99213.91115.68715.6870.0000.0000.0000.000
75A80GLY0-0.015-0.00314.303-0.886-0.8860.0000.0000.0000.000
76A81ILE0-0.0130.01513.6140.3830.3830.0000.0000.0000.000
77A82VAL00.0190.0127.2551.3671.3670.0000.0000.0000.000
78A83LYS10.8200.90010.009-21.530-21.5300.0000.0000.0000.000
79A84ALA00.0260.0118.7842.9162.9160.0000.0000.0000.000
80A85HIS0-0.066-0.03710.183-3.343-3.3430.0000.0000.0000.000
81A86LEU00.0370.01410.6091.9631.9630.0000.0000.0000.000
82A87LEU00.0270.00513.408-1.652-1.6520.0000.0000.0000.000
83A88ILE0-0.0220.00015.8150.8360.8360.0000.0000.0000.000
84A89GLY00.0650.03918.255-0.712-0.7120.0000.0000.0000.000
85A90VAL0-0.0170.00021.0810.1880.1880.0000.0000.0000.000
86A91HIS0-0.023-0.00520.2420.7080.7080.0000.0000.0000.000
87A92DAS-1-0.922-0.97522.79612.10812.1080.0000.0000.0000.000
88A93ASP-1-0.881-0.94025.8249.7909.7900.0000.0000.0000.000
89A94ILE0-0.093-0.03527.5200.2730.2730.0000.0000.0000.000
90A95VAL00.0250.01827.8670.0170.0170.0000.0000.0000.000
91A96SER0-0.030-0.01530.564-0.303-0.3030.0000.0000.0000.000
92A97MET0-0.0060.01134.3430.1210.1210.0000.0000.0000.000
93A98GLU-1-0.834-0.89836.8087.4787.4780.0000.0000.0000.000
94A99TYR0-0.012-0.02640.120-0.022-0.0220.0000.0000.0000.000
95A100ASP-1-0.859-0.89543.1576.7056.7050.0000.0000.0000.000
96A101LEU0-0.006-0.00645.9140.0770.0770.0000.0000.0000.000
97A102ALA00.0040.00648.075-0.145-0.1450.0000.0000.0000.000
98A103TYR00.0270.00650.4040.0650.0650.0000.0000.0000.000
99A104LYS10.8280.89652.263-5.525-5.5250.0000.0000.0000.000
100A105LEU00.0230.01252.8200.0790.0790.0000.0000.0000.000
101A106GLY00.0320.03256.783-0.075-0.0750.0000.0000.0000.000
102A107ASP-1-0.857-0.92860.1565.1565.1560.0000.0000.0000.000
103A108LEU0-0.0020.02257.027-0.037-0.0370.0000.0000.0000.000
104A109HIS0-0.078-0.06956.7660.0510.0510.0000.0000.0000.000
105A110PRO00.0150.03054.571-0.045-0.0450.0000.0000.0000.000
106A111THR00.015-0.00652.7840.0480.0480.0000.0000.0000.000
107A112THR0-0.069-0.05248.793-0.054-0.0540.0000.0000.0000.000
108A113HIS10.8250.87743.550-7.103-7.1030.0000.0000.0000.000
109A114VAL0-0.029-0.01542.136-0.101-0.1010.0000.0000.0000.000
110A115ILE00.0100.02438.6520.0660.0660.0000.0000.0000.000
111A116SER0-0.006-0.02337.675-0.167-0.1670.0000.0000.0000.000
112A117ASP-1-0.832-0.89934.2438.7008.7000.0000.0000.0000.000
113A118ILE0-0.009-0.00729.768-0.086-0.0860.0000.0000.0000.000
114A119GLN0-0.026-0.01529.8470.3290.3290.0000.0000.0000.000
115A120ASP-1-0.928-0.96423.68312.95112.9510.0000.0000.0000.000
116A121PHE00.0110.01324.7800.0920.0920.0000.0000.0000.000
117A122VAL00.033-0.00220.2120.5220.5220.0000.0000.0000.000
118A123VAL0-0.037-0.00719.610-0.565-0.5650.0000.0000.0000.000
119A124ALA0-0.012-0.00318.0180.8470.8470.0000.0000.0000.000
120A125LEU0-0.014-0.01114.882-0.882-0.8820.0000.0000.0000.000
121A126SER0-0.009-0.00514.6091.5101.5100.0000.0000.0000.000
122A127LEU0-0.014-0.00812.342-1.164-1.1640.0000.0000.0000.000
123A128GLU-1-0.842-0.91613.17119.57819.5780.0000.0000.0000.000
124A129ILE00.012-0.0139.544-1.036-1.0360.0000.0000.0000.000
125A130PRO00.0190.02812.3771.5711.5710.0000.0000.0000.000
126A131ASP-1-0.913-0.94112.31627.06027.0600.0000.0000.0000.000
127A132GLU-1-0.959-0.98515.07717.18417.1840.0000.0000.0000.000
128A133GLY0-0.024-0.03217.641-0.856-0.8560.0000.0000.0000.000
129A134ASN0-0.058-0.01517.673-0.007-0.0070.0000.0000.0000.000
130A135ILE00.0590.03113.025-0.054-0.0540.0000.0000.0000.000
131A136THR0-0.033-0.00516.313-1.360-1.3600.0000.0000.0000.000
132A137MET0-0.033-0.01716.6981.1901.1900.0000.0000.0000.000
133A138THR0-0.035-0.01417.191-0.963-0.9630.0000.0000.0000.000
134A139SER0-0.052-0.02618.451-0.638-0.6380.0000.0000.0000.000
135A140PHE00.0600.00419.3180.6130.6130.0000.0000.0000.000
136A141GLU-1-0.883-0.91521.49712.77312.7730.0000.0000.0000.000
137A142VAL00.0690.04522.7300.4800.4800.0000.0000.0000.000
138A143ARG10.8850.93521.113-14.085-14.0850.0000.0000.0000.000
139A144GLN0-0.054-0.03725.320-0.112-0.1120.0000.0000.0000.000
140A145PHE00.0470.01927.9290.2040.2040.0000.0000.0000.000
141A146ALA00.0400.02628.052-0.277-0.2770.0000.0000.0000.000
142A147ASN0-0.035-0.03930.129-0.463-0.4630.0000.0000.0000.000
143A148VAL00.0010.00832.6710.2040.2040.0000.0000.0000.000
144A149VAL0-0.039-0.00435.293-0.269-0.2690.0000.0000.0000.000
145A150ASN00.0210.03637.8550.1200.1200.0000.0000.0000.000
146A151HIS10.8060.87438.315-8.134-8.1340.0000.0000.0000.000
147A152ILE00.0520.02443.0770.0000.0000.0000.0000.0000.000
148A153GLY00.0470.02246.212-0.115-0.1150.0000.0000.0000.000
149A154GLY0-0.030-0.01148.656-0.089-0.0890.0000.0000.0000.000
150A155LEU0-0.0300.00349.125-0.138-0.1380.0000.0000.0000.000
151A156SER0-0.010-0.00249.2710.1620.1620.0000.0000.0000.000
152A157ILE00.0390.00244.424-0.024-0.0240.0000.0000.0000.000
153A158LEU0-0.029-0.01648.2240.0160.0160.0000.0000.0000.000
154A159ASP-1-0.870-0.92751.2465.7875.7870.0000.0000.0000.000
155A160PRO00.0120.00251.3510.1260.1260.0000.0000.0000.000
156A161ILE0-0.009-0.01251.6770.0810.0810.0000.0000.0000.000
157A162PHE00.0040.00243.7180.1160.1160.0000.0000.0000.000
158A163GLY00.005-0.00146.2510.1560.1560.0000.0000.0000.000
159A164VAL00.0070.00245.9410.1560.1560.0000.0000.0000.000
160A165LEU00.0190.01546.6480.1170.1170.0000.0000.0000.000
161A166SER00.0320.03142.1380.2060.2060.0000.0000.0000.000
162A167ASP-1-0.814-0.88541.9227.7857.7850.0000.0000.0000.000
163A168VAL0-0.054-0.02041.9270.1620.1620.0000.0000.0000.000
164A169LEU00.020-0.00141.5160.1150.1150.0000.0000.0000.000
165A170THR0-0.013-0.01636.7480.2720.2720.0000.0000.0000.000
166A171ALA0-0.001-0.00437.2810.2740.2740.0000.0000.0000.000
167A172ILE0-0.005-0.00238.0830.1650.1650.0000.0000.0000.000
168A173PHE00.005-0.02735.0470.2020.2020.0000.0000.0000.000
169A174GLN0-0.001-0.01232.2020.4910.4910.0000.0000.0000.000
170A175ASP-1-0.831-0.89333.4368.9258.9250.0000.0000.0000.000
171A176THR00.0230.00434.7240.2440.2440.0000.0000.0000.000
172A177VAL00.0030.01333.4960.1340.1340.0000.0000.0000.000
173A178ARG10.8520.93127.714-10.524-10.5240.0000.0000.0000.000
174A179LYS10.7970.91430.403-8.640-8.6400.0000.0000.0000.000
175A180GLU-1-0.845-0.90231.9208.9868.9860.0000.0000.0000.000
176A181MET00.0400.01729.0730.0580.0580.0000.0000.0000.000
177A182THR0-0.045-0.03526.3540.4920.4920.0000.0000.0000.000
178A183LYS10.7790.86127.960-8.648-8.6480.0000.0000.0000.000
179A184VAL0-0.0170.00829.3380.0250.0250.0000.0000.0000.000
180A185LEU00.0200.00724.5880.2560.2560.0000.0000.0000.000
181A186ALA00.0220.02123.7250.4880.4880.0000.0000.0000.000
182A187PRO0-0.020-0.01523.7750.5220.5220.0000.0000.0000.000
183A188ALA00.0070.00625.2430.1110.1110.0000.0000.0000.000
184A189PHE00.0810.01418.4760.3160.3160.0000.0000.0000.000
185A190LYS10.8130.89820.260-13.230-13.2300.0000.0000.0000.000
186A191ARG10.8390.90121.438-12.093-12.0930.0000.0000.0000.000
187A192GLU-1-0.811-0.87919.94513.97513.9750.0000.0000.0000.000
188A193LEU0-0.0150.01314.8960.5220.5220.0000.0000.0000.000
189A194GLU-1-0.808-0.85717.30115.42515.4250.0000.0000.0000.000
190A195LYS10.7580.84919.814-15.733-15.7330.0000.0000.0000.000