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: JL3J9

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 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 190
LigandCharge DAS=-1
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -1940823.704283
FMO2-HF: Nuclear repulsion 1866663.327738
FMO2-HF: Total energy -74160.376545
FMO2-MP2: Total energy -74376.865816


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.
96.80190.84930.634-14.677-10.0030.116
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 : -0.848 / q_NPA : -0.918
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].
3A8ILE00.0930.0562.931-15.224-9.9880.399-2.672-2.9620.017
4A9THR0-0.023-0.0381.572-43.917-56.05230.187-11.667-6.3840.095
5A10GLU-1-0.884-0.9153.66921.67322.5260.049-0.334-0.5680.004
6A11GLU-1-0.956-0.9875.86732.48632.4860.0000.0000.0000.000
7A12ILE0-0.010-0.0035.866-5.691-5.6910.0000.0000.0000.000
8A13ASN0-0.026-0.0356.966-4.121-4.1210.0000.0000.0000.000
9A14LYS10.8440.9189.629-23.247-23.2470.0000.0000.0000.000
10A15ALA00.0290.01811.427-2.135-2.1350.0000.0000.0000.000
11A16ILE0-0.023-0.01412.270-1.931-1.9310.0000.0000.0000.000
12A17ASP-1-0.798-0.86512.83620.59920.5990.0000.0000.0000.000
13A18ASP-1-0.841-0.90615.64317.70517.7050.0000.0000.0000.000
14A19ALA00.0050.00517.106-1.181-1.1810.0000.0000.0000.000
15A20ILE0-0.033-0.01116.931-0.908-0.9080.0000.0000.0000.000
16A21ALA00.0210.02119.881-0.875-0.8750.0000.0000.0000.000
17A22ALA0-0.026-0.01421.609-0.762-0.7620.0000.0000.0000.000
18A23ILE0-0.036-0.02621.505-0.808-0.8080.0000.0000.0000.000
19A24GLU-1-0.827-0.92122.95412.83412.8340.0000.0000.0000.000
20A25GLN0-0.075-0.04525.769-0.551-0.5510.0000.0000.0000.000
21A26SER0-0.129-0.06828.010-0.387-0.3870.0000.0000.0000.000
22A27GLU-1-0.839-0.89929.6929.0919.0910.0000.0000.0000.000
23A28THR0-0.088-0.05932.2160.1090.1090.0000.0000.0000.000
24A29ILE0-0.025-0.01327.0100.0620.0620.0000.0000.0000.000
25A30ASP-1-0.837-0.90929.98710.15210.1520.0000.0000.0000.000
26A31PRO00.0340.00832.036-0.048-0.0480.0000.0000.0000.000
27A32MET0-0.0140.00529.116-0.061-0.0610.0000.0000.0000.000
28A33LYS10.9280.96734.057-7.775-7.7750.0000.0000.0000.000
29A34VAL00.001-0.00335.2290.2090.2090.0000.0000.0000.000
30A35PRO0-0.042-0.02937.528-0.261-0.2610.0000.0000.0000.000
31A36ASP-1-0.863-0.94440.6727.0987.0980.0000.0000.0000.000
32A37HIS00.0190.00941.8300.0980.0980.0000.0000.0000.000
33A38ALA0-0.022-0.00343.965-0.091-0.0910.0000.0000.0000.000
34A39ASP-1-0.915-0.95944.9917.1527.1520.0000.0000.0000.000
35A40LYS10.9300.96047.126-6.112-6.1120.0000.0000.0000.000
36A41PHE00.0230.01847.7500.0590.0590.0000.0000.0000.000
37A42GLU-1-0.831-0.93349.1565.7825.7820.0000.0000.0000.000
38A43ARG10.8940.95742.639-7.032-7.0320.0000.0000.0000.000
39A44HIS00.0440.03550.149-0.041-0.0410.0000.0000.0000.000
40A45VAL0-0.0160.00050.0520.1120.1120.0000.0000.0000.000
41A46GLY00.0300.00051.9330.0430.0430.0000.0000.0000.000
42A47ILE0-0.066-0.00755.088-0.067-0.0670.0000.0000.0000.000
43A48LEU0-0.020-0.02056.492-0.061-0.0610.0000.0000.0000.000
44A49ASP-1-0.871-0.96455.0055.8805.8800.0000.0000.0000.000
45A50PHE0-0.033-0.01352.448-0.095-0.0950.0000.0000.0000.000
46A51LYS10.8630.93652.800-5.612-5.6120.0000.0000.0000.000
47A52GLY0-0.009-0.02053.158-0.115-0.1150.0000.0000.0000.000
48A53GLU-1-0.984-0.97651.1206.1556.1550.0000.0000.0000.000
49A54LEU0-0.013-0.00745.398-0.069-0.0690.0000.0000.0000.000
50A55ALA00.0180.00747.7510.0500.0500.0000.0000.0000.000
51A56MET0-0.021-0.00340.145-0.068-0.0680.0000.0000.0000.000
52A57ARG10.9630.97445.225-6.503-6.5030.0000.0000.0000.000
53A58ASN0-0.122-0.06743.7560.0440.0440.0000.0000.0000.000
54A59ILE0-0.0020.00938.2970.0050.0050.0000.0000.0000.000
55A60GLU-1-0.918-0.96537.7118.0888.0880.0000.0000.0000.000
56A61ALA00.002-0.01132.911-0.042-0.0420.0000.0000.0000.000
57A62ARG10.9150.95332.860-8.454-8.4540.0000.0000.0000.000
58A63GLY00.1330.06429.838-0.007-0.0070.0000.0000.0000.000
59A64LEU0-0.062-0.03326.0270.4060.4060.0000.0000.0000.000
60A65LYS10.8420.92425.568-9.966-9.9660.0000.0000.0000.000
61A66GLN0-0.0080.01324.4250.0010.0010.0000.0000.0000.000
62A67MET0-0.050-0.00621.2680.4150.4150.0000.0000.0000.000
63A68LYS10.9690.98315.703-16.602-16.6020.0000.0000.0000.000
64A69ARG10.7840.85410.061-24.693-24.6930.0000.0000.0000.000
65A70GLN0-0.044-0.03715.374-0.709-0.7090.0000.0000.0000.000
66A71GLY0-0.021-0.01311.984-0.510-0.5100.0000.0000.0000.000
67A72ASP-1-0.921-0.9516.44334.50034.5000.0000.0000.0000.000
68A73ALA0-0.007-0.0027.085-2.309-2.3090.0000.0000.0000.000
69A74ASN0-0.058-0.0297.1955.5925.5920.0000.0000.0000.000
70A75VAL00.0350.0124.686-4.094-4.000-0.001-0.004-0.0890.000
71A76LYS10.8400.9106.650-20.992-20.9920.0000.0000.0000.000
72A77GLY00.0160.0178.282-1.264-1.2640.0000.0000.0000.000
73A78GLU-1-0.912-0.95710.09619.53919.5390.0000.0000.0000.000
74A79GLU-1-0.961-0.98913.85415.88815.8880.0000.0000.0000.000
75A80GLY0-0.013-0.00214.175-0.913-0.9130.0000.0000.0000.000
76A81ILE00.0030.02313.5800.3700.3700.0000.0000.0000.000
77A82VAL00.0120.0117.4911.5421.5420.0000.0000.0000.000
78A83LYS10.9010.9469.990-22.034-22.0340.0000.0000.0000.000
79A84ALA00.0230.0139.0253.0703.0700.0000.0000.0000.000
80A85HIS0-0.070-0.03910.212-3.417-3.4170.0000.0000.0000.000
81A86LEU00.0420.01510.8021.9631.9630.0000.0000.0000.000
82A87LEU00.0240.00513.458-1.601-1.6010.0000.0000.0000.000
83A88ILE0-0.029-0.00415.7890.8380.8380.0000.0000.0000.000
84A89GLY00.0750.04418.265-0.664-0.6640.0000.0000.0000.000
85A90VAL0-0.031-0.00721.0520.1750.1750.0000.0000.0000.000
86A91HIS0-0.082-0.04420.4730.6070.6070.0000.0000.0000.000
87A92DAS-1-0.922-0.97122.80311.95411.9540.0000.0000.0000.000
88A93ASP-1-0.880-0.93725.8349.7309.7300.0000.0000.0000.000
89A94ILE0-0.073-0.03427.4990.2770.2770.0000.0000.0000.000
90A95VAL00.0020.01027.8500.0260.0260.0000.0000.0000.000
91A96SER0-0.038-0.01230.532-0.274-0.2740.0000.0000.0000.000
92A97MET0-0.0130.00734.3110.1250.1250.0000.0000.0000.000
93A98GLU-1-0.861-0.92636.7817.5017.5010.0000.0000.0000.000
94A99TYR0-0.014-0.03639.977-0.023-0.0230.0000.0000.0000.000
95A100ASP-1-0.874-0.91343.2066.6286.6280.0000.0000.0000.000
96A101LEU0-0.001-0.00645.9660.0790.0790.0000.0000.0000.000
97A102ALA0-0.017-0.00348.144-0.148-0.1480.0000.0000.0000.000
98A103TYR00.0380.01250.5060.0700.0700.0000.0000.0000.000
99A104LYS10.9270.96352.320-5.623-5.6230.0000.0000.0000.000
100A105LEU00.0320.01052.9670.0850.0850.0000.0000.0000.000
101A106GLY00.0190.02556.826-0.069-0.0690.0000.0000.0000.000
102A107ASP-1-0.920-0.97660.2045.0825.0820.0000.0000.0000.000
103A108LEU00.0060.03357.064-0.034-0.0340.0000.0000.0000.000
104A109HIS0-0.131-0.09856.8210.0490.0490.0000.0000.0000.000
105A110PRO00.0150.02654.514-0.046-0.0460.0000.0000.0000.000
106A111THR0-0.012-0.01952.7990.0620.0620.0000.0000.0000.000
107A112THR0-0.033-0.02948.765-0.044-0.0440.0000.0000.0000.000
108A113HIS10.8480.91043.507-7.068-7.0680.0000.0000.0000.000
109A114VAL0-0.024-0.01842.309-0.095-0.0950.0000.0000.0000.000
110A115ILE00.0190.03138.6630.0600.0600.0000.0000.0000.000
111A116SER0-0.007-0.02437.599-0.171-0.1710.0000.0000.0000.000
112A117ASP-1-0.836-0.90634.2258.6988.6980.0000.0000.0000.000
113A118ILE0-0.008-0.00829.701-0.076-0.0760.0000.0000.0000.000
114A119GLN0-0.005-0.01329.8270.3560.3560.0000.0000.0000.000
115A120ASP-1-0.939-0.97123.70412.88112.8810.0000.0000.0000.000
116A121PHE00.0090.01424.8450.0870.0870.0000.0000.0000.000
117A122VAL00.0450.00520.4740.5030.5030.0000.0000.0000.000
118A123VAL0-0.026-0.00619.672-0.553-0.5530.0000.0000.0000.000
119A124ALA0-0.013-0.00218.0630.8570.8570.0000.0000.0000.000
120A125LEU0-0.009-0.00514.960-0.869-0.8690.0000.0000.0000.000
121A126SER0-0.035-0.01114.6651.5001.5000.0000.0000.0000.000
122A127LEU00.0030.00311.992-1.175-1.1750.0000.0000.0000.000
123A128GLU-1-0.904-0.95913.21019.48219.4820.0000.0000.0000.000
124A129ILE0-0.003-0.0199.510-1.019-1.0190.0000.0000.0000.000
125A130PRO00.0250.04512.4191.6301.6300.0000.0000.0000.000
126A131ASP-1-0.907-0.94112.60026.66326.6630.0000.0000.0000.000
127A132GLU-1-0.973-0.99215.15317.18017.1800.0000.0000.0000.000
128A133GLY0-0.019-0.04617.702-0.862-0.8620.0000.0000.0000.000
129A134ASN0-0.112-0.05217.755-0.113-0.1130.0000.0000.0000.000
130A135ILE00.0590.03312.9670.0320.0320.0000.0000.0000.000
131A136THR0-0.032-0.00116.402-1.319-1.3190.0000.0000.0000.000
132A137MET0-0.037-0.02216.7661.1871.1870.0000.0000.0000.000
133A138THR0-0.051-0.02217.245-0.976-0.9760.0000.0000.0000.000
134A139SER0-0.058-0.03718.513-0.837-0.8370.0000.0000.0000.000
135A140PHE00.0740.00719.3740.6070.6070.0000.0000.0000.000
136A141GLU-1-0.950-0.96121.55312.81412.8140.0000.0000.0000.000
137A142VAL00.0720.04722.7800.4790.4790.0000.0000.0000.000
138A143ARG10.9230.96021.107-14.212-14.2120.0000.0000.0000.000
139A144GLN0-0.044-0.02625.351-0.093-0.0930.0000.0000.0000.000
140A145PHE00.0340.02127.9520.2110.2110.0000.0000.0000.000
141A146ALA00.0450.03128.064-0.283-0.2830.0000.0000.0000.000
142A147ASN0-0.035-0.03230.114-0.448-0.4480.0000.0000.0000.000
143A148VAL00.0080.01232.6490.2050.2050.0000.0000.0000.000
144A149VAL0-0.045-0.01135.271-0.260-0.2600.0000.0000.0000.000
145A150ASN00.0250.04437.8310.1250.1250.0000.0000.0000.000
146A151HIS10.8150.88638.486-8.062-8.0620.0000.0000.0000.000
147A152ILE00.0500.02843.0490.0030.0030.0000.0000.0000.000
148A153GLY00.0380.01846.185-0.114-0.1140.0000.0000.0000.000
149A154GLY0-0.032-0.01048.626-0.088-0.0880.0000.0000.0000.000
150A155LEU0-0.0230.00549.161-0.137-0.1370.0000.0000.0000.000
151A156SER0-0.009-0.00549.2450.1620.1620.0000.0000.0000.000
152A157ILE00.0500.01244.501-0.024-0.0240.0000.0000.0000.000
153A158LEU0-0.042-0.02448.2010.0170.0170.0000.0000.0000.000
154A159ASP-1-0.890-0.94251.2245.7645.7640.0000.0000.0000.000
155A160PRO00.0200.00651.3310.1270.1270.0000.0000.0000.000
156A161ILE0-0.0040.00051.6590.0810.0810.0000.0000.0000.000
157A162PHE0-0.009-0.00743.5940.1070.1070.0000.0000.0000.000
158A163GLY00.0060.00046.2320.1520.1520.0000.0000.0000.000
159A164VAL00.0380.01945.9240.1430.1430.0000.0000.0000.000
160A165LEU00.0040.00446.6320.1170.1170.0000.0000.0000.000
161A166SER00.0250.03042.1160.2070.2070.0000.0000.0000.000
162A167ASP-1-0.894-0.94641.9047.5807.5800.0000.0000.0000.000
163A168VAL0-0.084-0.03641.9540.1690.1690.0000.0000.0000.000
164A169LEU00.017-0.00341.4810.1190.1190.0000.0000.0000.000
165A170THR0-0.003-0.00436.5970.2760.2760.0000.0000.0000.000
166A171ALA0-0.017-0.01237.3160.2740.2740.0000.0000.0000.000
167A172ILE00.0150.00938.1190.1650.1650.0000.0000.0000.000
168A173PHE00.003-0.02734.9160.1960.1960.0000.0000.0000.000
169A174GLN0-0.017-0.02932.3120.4740.4740.0000.0000.0000.000
170A175ASP-1-0.874-0.90533.4718.8458.8450.0000.0000.0000.000
171A176THR00.0140.00234.7720.2450.2450.0000.0000.0000.000
172A177VAL00.0120.02033.4270.1370.1370.0000.0000.0000.000
173A178ARG10.8780.94027.664-10.550-10.5500.0000.0000.0000.000
174A179LYS10.8230.91830.464-8.764-8.7640.0000.0000.0000.000
175A180GLU-1-0.883-0.94931.9888.9268.9260.0000.0000.0000.000
176A181MET00.0320.01429.1970.0690.0690.0000.0000.0000.000
177A182THR0-0.048-0.04226.4070.4770.4770.0000.0000.0000.000
178A183LYS10.8390.91728.041-8.678-8.6780.0000.0000.0000.000
179A184VAL0-0.0100.01829.1660.0320.0320.0000.0000.0000.000
180A185LEU00.0150.00424.6620.2560.2560.0000.0000.0000.000
181A186ALA00.0220.02223.8110.4760.4760.0000.0000.0000.000
182A187PRO0-0.019-0.01423.8690.5170.5170.0000.0000.0000.000
183A188ALA00.0020.00025.3540.0990.0990.0000.0000.0000.000
184A189PHE00.0730.01018.7990.2940.2940.0000.0000.0000.000
185A190LYS10.8330.91920.371-13.184-13.1840.0000.0000.0000.000
186A191ARG10.8310.89621.547-12.144-12.1440.0000.0000.0000.000
187A192GLU-1-0.858-0.90819.96914.01714.0170.0000.0000.0000.000
188A193LEU0-0.011-0.01715.0470.5330.5330.0000.0000.0000.000
189A194GLU-1-0.826-0.88117.41915.42115.4210.0000.0000.0000.000
190A195LYS10.8750.95919.926-14.838-14.8380.0000.0000.0000.000