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: LZJ89

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 OptAll
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 -1945790.424512
FMO2-HF: Nuclear repulsion 1871628.698976
FMO2-HF: Total energy -74161.725537
FMO2-MP2: Total energy -74378.199744


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.
85.27973.74143.961-18.319-14.1060.158
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 : -0.817 / q_NPA : -0.899
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].
3A8ILE00.0590.0341.984-26.058-22.2298.057-5.499-6.3870.057
4A9THR0-0.042-0.0571.607-46.229-62.53335.831-12.570-6.9570.095
5A10GLU-1-0.897-0.9263.55722.18722.9300.074-0.226-0.5920.006
6A11GLU-1-0.905-0.9666.03135.13635.1360.0000.0000.0000.000
7A12ILE0-0.012-0.0106.006-6.035-6.0350.0000.0000.0000.000
8A13ASN0-0.028-0.0387.280-4.842-4.8420.0000.0000.0000.000
9A14LYS10.8130.8949.447-24.185-24.1850.0000.0000.0000.000
10A15ALA00.0220.01011.258-2.355-2.3550.0000.0000.0000.000
11A16ILE0-0.015-0.01012.005-2.120-2.1200.0000.0000.0000.000
12A17ASP-1-0.810-0.89012.65821.73021.7300.0000.0000.0000.000
13A18ASP-1-0.826-0.89015.42318.36618.3660.0000.0000.0000.000
14A19ALA0-0.002-0.00516.767-1.247-1.2470.0000.0000.0000.000
15A20ILE0-0.033-0.01416.785-0.980-0.9800.0000.0000.0000.000
16A21ALA00.0560.03719.849-0.885-0.8850.0000.0000.0000.000
17A22ALA0-0.032-0.00221.380-0.846-0.8460.0000.0000.0000.000
18A23ILE0-0.032-0.01521.327-0.836-0.8360.0000.0000.0000.000
19A24GLU-1-0.850-0.93323.24212.95312.9530.0000.0000.0000.000
20A25GLN0-0.088-0.05525.019-0.884-0.8840.0000.0000.0000.000
21A26SER0-0.070-0.03427.421-0.303-0.3030.0000.0000.0000.000
22A27GLU-1-0.812-0.91029.2279.4849.4840.0000.0000.0000.000
23A28THR0-0.101-0.05431.5100.0510.0510.0000.0000.0000.000
24A29ILE0-0.013-0.00427.1010.0690.0690.0000.0000.0000.000
25A30ASP-1-0.842-0.90130.08210.26110.2610.0000.0000.0000.000
26A31PRO00.0330.02132.046-0.054-0.0540.0000.0000.0000.000
27A32MET0-0.0140.01228.708-0.022-0.0220.0000.0000.0000.000
28A33LYS10.7920.88633.728-7.994-7.9940.0000.0000.0000.000
29A34VAL00.0330.02234.6760.1530.1530.0000.0000.0000.000
30A35PRO0-0.017-0.01837.100-0.277-0.2770.0000.0000.0000.000
31A36ASP-1-0.789-0.87940.1217.2357.2350.0000.0000.0000.000
32A37HIS00.0510.02541.5190.1090.1090.0000.0000.0000.000
33A38ALA0-0.032-0.01843.666-0.106-0.1060.0000.0000.0000.000
34A39ASP-1-0.873-0.94444.9717.1577.1570.0000.0000.0000.000
35A40LYS10.8230.89647.022-6.211-6.2110.0000.0000.0000.000
36A41PHE00.0230.02547.5620.0390.0390.0000.0000.0000.000
37A42GLU-1-0.784-0.89949.1915.8005.8000.0000.0000.0000.000
38A43ARG10.7860.87942.792-7.078-7.0780.0000.0000.0000.000
39A44HIS0-0.016-0.01850.164-0.045-0.0450.0000.0000.0000.000
40A45VAL0-0.029-0.00550.2530.1280.1280.0000.0000.0000.000
41A46GLY00.0350.00852.1680.0430.0430.0000.0000.0000.000
42A47ILE0-0.073-0.01355.243-0.066-0.0660.0000.0000.0000.000
43A48LEU0-0.014-0.01256.229-0.065-0.0650.0000.0000.0000.000
44A49ASP-1-0.810-0.91355.0165.8605.8600.0000.0000.0000.000
45A50PHE0-0.012-0.01052.346-0.104-0.1040.0000.0000.0000.000
46A51LYS10.7990.88752.466-5.645-5.6450.0000.0000.0000.000
47A52GLY0-0.017-0.02152.942-0.117-0.1170.0000.0000.0000.000
48A53GLU-1-0.881-0.90550.9916.1206.1200.0000.0000.0000.000
49A54LEU0-0.041-0.02145.263-0.067-0.0670.0000.0000.0000.000
50A55ALA00.008-0.00447.5560.0400.0400.0000.0000.0000.000
51A56MET0-0.0250.01539.803-0.074-0.0740.0000.0000.0000.000
52A57ARG10.8520.89644.953-6.752-6.7520.0000.0000.0000.000
53A58ASN0-0.052-0.04843.9220.0600.0600.0000.0000.0000.000
54A59ILE0-0.0260.00238.0600.0450.0450.0000.0000.0000.000
55A60GLU-1-0.830-0.89437.2038.3148.3140.0000.0000.0000.000
56A61ALA00.010-0.01032.338-0.047-0.0470.0000.0000.0000.000
57A62ARG10.8340.88332.780-8.602-8.6020.0000.0000.0000.000
58A63GLY00.1020.04830.056-0.076-0.0760.0000.0000.0000.000
59A64LEU0-0.060-0.04026.2560.4320.4320.0000.0000.0000.000
60A65LYS10.7760.88426.027-9.973-9.9730.0000.0000.0000.000
61A66GLN00.0050.02024.903-0.137-0.1370.0000.0000.0000.000
62A67MET0-0.052-0.01921.1560.3430.3430.0000.0000.0000.000
63A68LYS10.8990.95216.420-16.058-16.0580.0000.0000.0000.000
64A69ARG10.7970.8729.717-26.312-26.3120.0000.0000.0000.000
65A70GLN0-0.031-0.02515.511-0.259-0.2590.0000.0000.0000.000
66A71GLY0-0.011-0.00712.422-0.598-0.5980.0000.0000.0000.000
67A72ASP-1-0.874-0.9156.69731.53631.5360.0000.0000.0000.000
68A73ALA0-0.004-0.0026.676-1.916-1.9160.0000.0000.0000.000
69A74ASN0-0.035-0.0176.8205.8465.8460.0000.0000.0000.000
70A75VAL00.0070.0004.330-4.687-4.493-0.001-0.024-0.1700.000
71A76LYS10.8000.8886.484-22.555-22.5550.0000.0000.0000.000
72A77GLY00.0330.0168.0980.8180.8180.0000.0000.0000.000
73A78GLU-1-0.862-0.9279.89219.99619.9960.0000.0000.0000.000
74A79GLU-1-0.966-0.99413.69415.84715.8470.0000.0000.0000.000
75A80GLY0-0.0140.00314.391-1.003-1.0030.0000.0000.0000.000
76A81ILE0-0.0250.00213.3730.7000.7000.0000.0000.0000.000
77A82VAL00.0450.0247.1111.2311.2310.0000.0000.0000.000
78A83LYS10.8030.8939.388-22.389-22.3890.0000.0000.0000.000
79A84ALA00.0260.0128.2403.5483.5480.0000.0000.0000.000
80A85HIS0-0.060-0.0339.852-3.333-3.3330.0000.0000.0000.000
81A86LEU00.0350.01310.2952.0712.0710.0000.0000.0000.000
82A87LEU00.0030.00213.239-1.657-1.6570.0000.0000.0000.000
83A88ILE00.0020.00115.6590.9280.9280.0000.0000.0000.000
84A89GLY00.0370.01318.104-0.706-0.7060.0000.0000.0000.000
85A90VAL0-0.0300.00721.2660.3470.3470.0000.0000.0000.000
86A91HIS0-0.034-0.02320.5990.8630.8630.0000.0000.0000.000
87A92DAS-1-0.936-0.96823.10212.20312.2030.0000.0000.0000.000
88A93ASP-1-0.874-0.92725.8699.7499.7490.0000.0000.0000.000
89A94ILE0-0.092-0.04527.3280.3290.3290.0000.0000.0000.000
90A95VAL00.0100.00128.0130.1560.1560.0000.0000.0000.000
91A96SER0-0.026-0.01130.727-0.288-0.2880.0000.0000.0000.000
92A97MET0-0.0290.00634.3110.1500.1500.0000.0000.0000.000
93A98GLU-1-0.824-0.89636.6547.5117.5110.0000.0000.0000.000
94A99TYR0-0.027-0.04040.051-0.024-0.0240.0000.0000.0000.000
95A100ASP-1-0.824-0.87842.8006.7286.7280.0000.0000.0000.000
96A101LEU0-0.008-0.01545.7420.1040.1040.0000.0000.0000.000
97A102ALA00.0130.01547.869-0.141-0.1410.0000.0000.0000.000
98A103TYR00.022-0.00650.0740.0880.0880.0000.0000.0000.000
99A104LYS10.8130.88152.109-5.544-5.5440.0000.0000.0000.000
100A105LEU00.0440.02352.6920.0800.0800.0000.0000.0000.000
101A106GLY00.0140.01756.722-0.083-0.0830.0000.0000.0000.000
102A107ASP-1-0.846-0.91659.9985.1985.1980.0000.0000.0000.000
103A108LEU0-0.0060.02657.376-0.041-0.0410.0000.0000.0000.000
104A109HIS0-0.066-0.05856.7990.0700.0700.0000.0000.0000.000
105A110PRO00.0140.02154.148-0.026-0.0260.0000.0000.0000.000
106A111THR00.006-0.00952.5630.0590.0590.0000.0000.0000.000
107A112THR0-0.063-0.04048.685-0.076-0.0760.0000.0000.0000.000
108A113HIS10.8310.88543.548-7.142-7.1420.0000.0000.0000.000
109A114VAL0-0.050-0.02142.517-0.105-0.1050.0000.0000.0000.000
110A115ILE00.0280.03138.8530.0640.0640.0000.0000.0000.000
111A116SER0-0.031-0.03837.880-0.181-0.1810.0000.0000.0000.000
112A117ASP-1-0.788-0.86934.1908.8268.8260.0000.0000.0000.000
113A118ILE0-0.015-0.00329.752-0.077-0.0770.0000.0000.0000.000
114A119GLN0-0.019-0.01329.7410.2150.2150.0000.0000.0000.000
115A120ASP-1-0.907-0.96623.72413.01813.0180.0000.0000.0000.000
116A121PHE0-0.006-0.00124.8210.0830.0830.0000.0000.0000.000
117A122VAL00.0200.00620.0210.4720.4720.0000.0000.0000.000
118A123VAL0-0.0040.00219.370-0.509-0.5090.0000.0000.0000.000
119A124ALA0-0.012-0.00818.0090.7790.7790.0000.0000.0000.000
120A125LEU0-0.015-0.00714.786-0.944-0.9440.0000.0000.0000.000
121A126SER0-0.024-0.01414.2271.4231.4230.0000.0000.0000.000
122A127LEU0-0.015-0.00411.924-1.276-1.2760.0000.0000.0000.000
123A128GLU-1-0.836-0.91612.46420.59820.5980.0000.0000.0000.000
124A129ILE00.021-0.0039.407-1.222-1.2220.0000.0000.0000.000
125A130PRO00.0090.01612.3531.4721.4720.0000.0000.0000.000
126A131ASP-1-0.886-0.94112.04727.64727.6470.0000.0000.0000.000
127A132GLU-1-0.995-0.99514.73617.48017.4800.0000.0000.0000.000
128A133GLY0-0.022-0.01416.997-0.824-0.8240.0000.0000.0000.000
129A134ASN0-0.042-0.02217.521-0.883-0.8830.0000.0000.0000.000
130A135ILE00.0320.03012.979-0.025-0.0250.0000.0000.0000.000
131A136THR0-0.038-0.02015.809-1.593-1.5930.0000.0000.0000.000
132A137MET0-0.018-0.00516.2811.2201.2200.0000.0000.0000.000
133A138THR0-0.023-0.00916.929-1.052-1.0520.0000.0000.0000.000
134A139SER0-0.031-0.01618.391-0.740-0.7400.0000.0000.0000.000
135A140PHE00.0340.00018.9220.7270.7270.0000.0000.0000.000
136A141GLU-1-0.874-0.91521.19812.83712.8370.0000.0000.0000.000
137A142VAL00.0610.04022.6150.4870.4870.0000.0000.0000.000
138A143ARG10.8970.94421.088-14.015-14.0150.0000.0000.0000.000
139A144GLN0-0.061-0.03825.194-0.129-0.1290.0000.0000.0000.000
140A145PHE00.0370.01027.6990.2260.2260.0000.0000.0000.000
141A146ALA00.0480.03127.763-0.287-0.2870.0000.0000.0000.000
142A147ASN0-0.037-0.03629.829-0.477-0.4770.0000.0000.0000.000
143A148VAL00.0040.00332.6420.2290.2290.0000.0000.0000.000
144A149VAL0-0.036-0.00435.441-0.284-0.2840.0000.0000.0000.000
145A150ASN00.0350.02737.9580.0640.0640.0000.0000.0000.000
146A151HIS10.8290.89138.399-8.184-8.1840.0000.0000.0000.000
147A152ILE00.0280.00643.068-0.031-0.0310.0000.0000.0000.000
148A153GLY00.0430.03246.116-0.096-0.0960.0000.0000.0000.000
149A154GLY0-0.030-0.01348.435-0.091-0.0910.0000.0000.0000.000
150A155LEU0-0.0360.00249.318-0.138-0.1380.0000.0000.0000.000
151A156SER00.0030.00649.5600.1530.1530.0000.0000.0000.000
152A157ILE00.0470.00544.483-0.012-0.0120.0000.0000.0000.000
153A158LEU0-0.042-0.02148.1880.0290.0290.0000.0000.0000.000
154A159ASP-1-0.873-0.92651.0945.8105.8100.0000.0000.0000.000
155A160PRO0-0.007-0.01451.1640.1260.1260.0000.0000.0000.000
156A161ILE00.017-0.00451.4950.0900.0900.0000.0000.0000.000
157A162PHE00.0220.01744.0760.1230.1230.0000.0000.0000.000
158A163GLY00.0070.00446.5570.1660.1660.0000.0000.0000.000
159A164VAL0-0.012-0.00446.1150.1580.1580.0000.0000.0000.000
160A165LEU00.0110.00646.4800.1310.1310.0000.0000.0000.000
161A166SER00.0330.02842.2610.2120.2120.0000.0000.0000.000
162A167ASP-1-0.814-0.86841.7597.8677.8670.0000.0000.0000.000
163A168VAL0-0.038-0.01741.6980.1630.1630.0000.0000.0000.000
164A169LEU00.0130.00141.4370.1180.1180.0000.0000.0000.000
165A170THR00.007-0.01636.7360.2710.2710.0000.0000.0000.000
166A171ALA0-0.015-0.00437.1760.2730.2730.0000.0000.0000.000
167A172ILE0-0.003-0.00737.7820.1950.1950.0000.0000.0000.000
168A173PHE0-0.005-0.02335.0520.2000.2000.0000.0000.0000.000
169A174GLN00.016-0.00331.9390.5120.5120.0000.0000.0000.000
170A175ASP-1-0.835-0.89233.1739.0349.0340.0000.0000.0000.000
171A176THR00.0010.00234.7310.1890.1890.0000.0000.0000.000
172A177VAL0-0.0010.00233.1900.1840.1840.0000.0000.0000.000
173A178ARG10.8440.92727.486-10.626-10.6260.0000.0000.0000.000
174A179LYS10.7770.90530.085-8.682-8.6820.0000.0000.0000.000
175A180GLU-1-0.833-0.90531.4009.1589.1580.0000.0000.0000.000
176A181MET00.0430.01829.0200.0580.0580.0000.0000.0000.000
177A182THR0-0.030-0.02626.0870.5200.5200.0000.0000.0000.000
178A183LYS10.7730.85627.608-8.746-8.7460.0000.0000.0000.000
179A184VAL0-0.0030.01628.9510.0260.0260.0000.0000.0000.000
180A185LEU00.0270.00224.3450.2970.2970.0000.0000.0000.000
181A186ALA00.0160.02223.4470.5400.5400.0000.0000.0000.000
182A187PRO0-0.032-0.02323.4560.5320.5320.0000.0000.0000.000
183A188ALA0-0.0010.00824.8420.1980.1980.0000.0000.0000.000
184A189PHE00.0840.01018.2980.3340.3340.0000.0000.0000.000
185A190LYS10.8130.89119.864-13.577-13.5770.0000.0000.0000.000
186A191ARG10.8220.89621.101-12.123-12.1230.0000.0000.0000.000
187A192GLU-1-0.816-0.88319.62814.13014.1300.0000.0000.0000.000
188A193LEU0-0.0130.00114.5370.5770.5770.0000.0000.0000.000
189A194GLU-1-0.794-0.84616.65416.02216.0220.0000.0000.0000.000
190A195LYS10.7620.86419.222-16.171-16.1710.0000.0000.0000.000