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: 1NYNZ

Calculation Name: 4UML-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 4UML

Chain ID: A

ChEMBL ID:

UniProt ID: Q9NXN4

Base Structure: X-ray

Registration Date: 2023-09-22

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 201
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2339392.399511
FMO2-HF: Nuclear repulsion 2260761.282387
FMO2-HF: Total energy -78631.117124
FMO2-MP2: Total energy -78861.38652


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:PRO)


Summations of interaction energy for fragment #1(A:7:PRO)
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.
-2.2660.4290.004-1.195-1.5040.004
Interaction energy analysis for fragmet #1(A:7:PRO)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.006 / q_NPA : 0.001
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].
3A9GLN0-0.042-0.0273.391-2.4350.2600.004-1.195-1.5040.004
4A10PHE0-0.018-0.0015.9580.1860.1860.0000.0000.0000.000
5A11VAL0-0.017-0.0137.731-0.113-0.1130.0000.0000.0000.000
6A12ASP-1-0.837-0.92410.350-0.013-0.0130.0000.0000.0000.000
7A13VAL0-0.002-0.02511.999-0.007-0.0070.0000.0000.0000.000
8A14ASP-1-0.914-0.94914.347-0.017-0.0170.0000.0000.0000.000
9A15THR0-0.128-0.06311.306-0.010-0.0100.0000.0000.0000.000
10A16LEU0-0.080-0.03114.264-0.008-0.0080.0000.0000.0000.000
11A17PRO00.0000.00616.9830.0140.0140.0000.0000.0000.000
12A18SER00.018-0.00520.292-0.001-0.0010.0000.0000.0000.000
13A19TRP0-0.056-0.07123.312-0.003-0.0030.0000.0000.0000.000
14A20GLY0-0.086-0.06226.4980.0010.0010.0000.0000.0000.000
15A21ASP-1-0.881-0.91923.223-0.046-0.0460.0000.0000.0000.000
16A22SER0-0.097-0.04524.769-0.001-0.0010.0000.0000.0000.000
17A43ARG10.9660.97142.4380.0190.0190.0000.0000.0000.000
18A44SER0-0.0210.00039.4440.0010.0010.0000.0000.0000.000
19A45PRO00.0000.00241.6040.0010.0010.0000.0000.0000.000
20A46PHE0-0.034-0.01338.8330.0010.0010.0000.0000.0000.000
21A47LEU00.0760.03940.864-0.001-0.0010.0000.0000.0000.000
22A48TYR0-0.0030.00034.3500.0000.0000.0000.0000.0000.000
23A49ASN00.0300.01135.4800.0020.0020.0000.0000.0000.000
24A50LYS10.9890.99231.4870.0190.0190.0000.0000.0000.000
25A51ASP-1-0.891-0.94231.506-0.013-0.0130.0000.0000.0000.000
26A52VAL00.0180.00130.541-0.001-0.0010.0000.0000.0000.000
27A53ASN0-0.043-0.04429.880-0.002-0.0020.0000.0000.0000.000
28A54GLY00.0160.02427.177-0.005-0.0050.0000.0000.0000.000
29A55LYS10.9170.98125.5420.0070.0070.0000.0000.0000.000
30A56VAL0-0.0220.01225.279-0.002-0.0020.0000.0000.0000.000
31A57VAL00.0460.03419.625-0.002-0.0020.0000.0000.0000.000
32A58LEU0-0.050-0.01823.0540.0030.0030.0000.0000.0000.000
33A59TRP00.0470.02213.5050.0030.0030.0000.0000.0000.000
34A60LYS10.8940.96919.3130.1380.1380.0000.0000.0000.000
35A61GLY00.000-0.00816.185-0.022-0.0220.0000.0000.0000.000
36A62ASP-1-0.851-0.92214.994-0.115-0.1150.0000.0000.0000.000
37A63VAL00.0540.00115.639-0.012-0.0120.0000.0000.0000.000
38A64ALA0-0.050-0.02216.1200.0080.0080.0000.0000.0000.000
39A65LEU0-0.011-0.00110.4610.0110.0110.0000.0000.0000.000
40A66LEU0-0.0140.00412.090-0.020-0.0200.0000.0000.0000.000
41A67ASN00.0250.02712.6770.0010.0010.0000.0000.0000.000
42A68CYS0-0.0270.00314.7380.0150.0150.0000.0000.0000.000
43A69THR0-0.0120.00418.4320.0130.0130.0000.0000.0000.000
44A70ALA00.005-0.01120.7120.0100.0100.0000.0000.0000.000
45A71ILE00.0310.04217.971-0.008-0.0080.0000.0000.0000.000
46A72VAL00.0040.00421.3410.0100.0100.0000.0000.0000.000
47A73ASN00.0510.05623.610-0.014-0.0140.0000.0000.0000.000
48A74THR0-0.036-0.03825.2030.0060.0060.0000.0000.0000.000
49A75SER00.0450.02028.056-0.001-0.0010.0000.0000.0000.000
50A76ASN0-0.016-0.01830.5130.0010.0010.0000.0000.0000.000
51A77GLU-1-0.770-0.89133.904-0.011-0.0110.0000.0000.0000.000
52A78SER0-0.036-0.02435.8350.0020.0020.0000.0000.0000.000
53A79LEU0-0.022-0.00230.5140.0020.0020.0000.0000.0000.000
54A80THR0-0.002-0.01330.6470.0000.0000.0000.0000.0000.000
55A81ASP-1-0.886-0.92630.203-0.030-0.0300.0000.0000.0000.000
56A82LYS10.9040.97325.9580.0470.0470.0000.0000.0000.000
57A83ASN0-0.072-0.06226.342-0.005-0.0050.0000.0000.0000.000
58A84PRO00.1100.03023.5380.0020.0020.0000.0000.0000.000
59A85VAL00.0390.03322.017-0.006-0.0060.0000.0000.0000.000
60A86SER0-0.004-0.04321.711-0.001-0.0010.0000.0000.0000.000
61A87GLU-1-0.920-0.96222.327-0.053-0.0530.0000.0000.0000.000
62A88SER00.0210.01617.3430.0100.0100.0000.0000.0000.000
63A89ILE00.0140.01318.0880.0040.0040.0000.0000.0000.000
64A90PHE0-0.065-0.04619.5420.0130.0130.0000.0000.0000.000
65A91MET0-0.034-0.00316.3980.0070.0070.0000.0000.0000.000
66A92LEU0-0.003-0.00913.1180.0140.0140.0000.0000.0000.000
67A93ALA00.0000.01215.7960.0240.0240.0000.0000.0000.000
68A94GLY00.0780.04418.4270.0230.0230.0000.0000.0000.000
69A95PRO0-0.043-0.05619.329-0.009-0.0090.0000.0000.0000.000
70A96ASP-1-0.791-0.88521.9400.0840.0840.0000.0000.0000.000
71A97LEU0-0.051-0.01322.678-0.005-0.0050.0000.0000.0000.000
72A98LYS10.8540.92723.103-0.021-0.0210.0000.0000.0000.000
73A99GLU-1-0.862-0.93327.3430.0390.0390.0000.0000.0000.000
74A100ASP-1-0.892-0.97926.8800.0400.0400.0000.0000.0000.000
75A101LEU0-0.005-0.01126.956-0.003-0.0030.0000.0000.0000.000
76A102GLN00.0020.00530.025-0.004-0.0040.0000.0000.0000.000
77A103LYS10.8550.95030.344-0.035-0.0350.0000.0000.0000.000
78A104LEU0-0.021-0.00730.285-0.001-0.0010.0000.0000.0000.000
79A105LYS10.9280.96734.590-0.016-0.0160.0000.0000.0000.000
80A106GLY00.0110.00635.503-0.001-0.0010.0000.0000.0000.000
81A107CYS0-0.0250.00733.7870.0020.0020.0000.0000.0000.000
82A108ARG10.8860.94535.849-0.001-0.0010.0000.0000.0000.000
83A109THR00.014-0.01537.0260.0000.0000.0000.0000.0000.000
84A110GLY00.0050.00336.5580.0010.0010.0000.0000.0000.000
85A111GLU-1-0.881-0.93135.7690.0020.0020.0000.0000.0000.000
86A112ALA00.007-0.00931.142-0.002-0.0020.0000.0000.0000.000
87A113LYS10.8730.93031.145-0.004-0.0040.0000.0000.0000.000
88A114LEU00.0120.02126.560-0.003-0.0030.0000.0000.0000.000
89A115THR00.0020.01524.734-0.001-0.0010.0000.0000.0000.000
90A116LYS10.9220.96922.534-0.067-0.0670.0000.0000.0000.000
91A117GLY00.0330.01219.662-0.008-0.0080.0000.0000.0000.000
92A118PHE0-0.041-0.02319.053-0.009-0.0090.0000.0000.0000.000
93A119ASN0-0.0140.00012.2320.0630.0630.0000.0000.0000.000
94A120LEU0-0.042-0.00914.040-0.008-0.0080.0000.0000.0000.000
95A121ALA00.0410.01711.7750.0280.0280.0000.0000.0000.000
96A122ALA0-0.0090.02213.6110.0180.0180.0000.0000.0000.000
97A123ARG10.9430.98017.217-0.047-0.0470.0000.0000.0000.000
98A124PHE0-0.030-0.04919.7190.0100.0100.0000.0000.0000.000
99A125ILE00.0410.02821.230-0.009-0.0090.0000.0000.0000.000
100A126ILE0-0.034-0.01223.5050.0060.0060.0000.0000.0000.000
101A127HIS00.016-0.00725.375-0.012-0.0120.0000.0000.0000.000
102A128THR00.021-0.00428.4610.0030.0030.0000.0000.0000.000
103A129VAL0-0.024-0.00130.908-0.003-0.0030.0000.0000.0000.000
104A130GLY00.1090.05733.1830.0010.0010.0000.0000.0000.000
105A131PRO0-0.018-0.00134.7550.0010.0010.0000.0000.0000.000
106A132LYS10.9270.95137.3640.0140.0140.0000.0000.0000.000
107A133TYR00.0120.02038.9330.0020.0020.0000.0000.0000.000
108A134LYS10.9480.96740.6830.0160.0160.0000.0000.0000.000
109A135SER00.0790.03344.3310.0000.0000.0000.0000.0000.000
110A136ARG10.9670.98746.4420.0140.0140.0000.0000.0000.000
111A137TYR0-0.028-0.02145.4380.0010.0010.0000.0000.0000.000
112A138ARG10.8980.95943.0690.0200.0200.0000.0000.0000.000
113A139THR00.0940.04544.2380.0000.0000.0000.0000.0000.000
114A140ALA00.0200.00944.7730.0000.0000.0000.0000.0000.000
115A141ALA0-0.033-0.01640.5950.0000.0000.0000.0000.0000.000
116A142GLU-1-0.833-0.92239.961-0.018-0.0180.0000.0000.0000.000
117A143SER0-0.014-0.00240.2240.0000.0000.0000.0000.0000.000
118A144SER00.012-0.00738.8510.0010.0010.0000.0000.0000.000
119A145LEU00.011-0.00133.4240.0000.0000.0000.0000.0000.000
120A146TYR0-0.021-0.00835.513-0.001-0.0010.0000.0000.0000.000
121A147SER0-0.017-0.00936.5890.0010.0010.0000.0000.0000.000
122A148CYS0-0.0480.01132.6460.0010.0010.0000.0000.0000.000
123A149TYR00.0340.01229.1690.0010.0010.0000.0000.0000.000
124A150ARG10.9120.95832.5380.0040.0040.0000.0000.0000.000
125A151ASN00.019-0.00934.5610.0030.0030.0000.0000.0000.000
126A152VAL0-0.0180.01527.8670.0030.0030.0000.0000.0000.000
127A153LEU00.0140.00329.2970.0020.0020.0000.0000.0000.000
128A154GLN0-0.050-0.01631.3750.0000.0000.0000.0000.0000.000
129A155LEU00.0290.00630.1040.0020.0020.0000.0000.0000.000
130A156ALA00.0250.00027.7700.0040.0040.0000.0000.0000.000
131A157LYS10.9250.97829.094-0.002-0.0020.0000.0000.0000.000
132A158GLU-1-0.950-0.98931.7570.0130.0130.0000.0000.0000.000
133A159GLN0-0.073-0.03127.7720.0070.0070.0000.0000.0000.000
134A160SER0-0.030-0.00427.9610.0040.0040.0000.0000.0000.000
135A161MET0-0.092-0.03624.5880.0010.0010.0000.0000.0000.000
136A162SER00.0950.06421.331-0.003-0.0030.0000.0000.0000.000
137A163SER00.0600.02619.662-0.006-0.0060.0000.0000.0000.000
138A164VAL0-0.021-0.01722.7200.0050.0050.0000.0000.0000.000
139A165GLY00.0360.01520.395-0.007-0.0070.0000.0000.0000.000
140A166PHE0-0.026-0.04121.3880.0060.0060.0000.0000.0000.000
141A167CYS0-0.0010.01222.949-0.007-0.0070.0000.0000.0000.000
142A168VAL00.0400.01424.0300.0070.0070.0000.0000.0000.000
143A169ILE0-0.015-0.00527.0390.0010.0010.0000.0000.0000.000
144A170ASN0-0.0250.00029.3960.0030.0030.0000.0000.0000.000
145A171SER00.0790.03629.675-0.003-0.0030.0000.0000.0000.000
146A172ALA00.0850.02930.0970.0030.0030.0000.0000.0000.000
147A173LYS10.8130.90831.2400.0330.0330.0000.0000.0000.000
148A174ARG10.7560.87333.8860.0230.0230.0000.0000.0000.000
149A175GLY00.0290.01335.4210.0020.0020.0000.0000.0000.000
150A176TYR0-0.003-0.01235.4930.0020.0020.0000.0000.0000.000
151A177PRO0-0.0060.00435.962-0.002-0.0020.0000.0000.0000.000
152A178LEU00.0740.04030.7230.0020.0020.0000.0000.0000.000
153A179GLU-1-0.795-0.88234.351-0.036-0.0360.0000.0000.0000.000
154A180ASP-1-0.869-0.94436.221-0.025-0.0250.0000.0000.0000.000
155A181ALA0-0.028-0.02234.0330.0010.0010.0000.0000.0000.000
156A182THR00.0160.00331.2190.0000.0000.0000.0000.0000.000
157A183HIS00.0550.07033.4440.0010.0010.0000.0000.0000.000
158A184ILE0-0.075-0.02235.8990.0020.0020.0000.0000.0000.000
159A185ALA00.0160.03130.7390.0020.0020.0000.0000.0000.000
160A186LEU00.0220.01129.7610.0010.0010.0000.0000.0000.000
161A187ARG10.9670.99532.8830.0210.0210.0000.0000.0000.000
162A188THR0-0.079-0.06134.3350.0030.0030.0000.0000.0000.000
163A189VAL00.0200.01029.2470.0020.0020.0000.0000.0000.000
164A190ARG10.7580.87432.5270.0220.0220.0000.0000.0000.000
165A191ARG10.9470.96234.4350.0160.0160.0000.0000.0000.000
166A192PHE00.0130.00931.2790.0020.0020.0000.0000.0000.000
167A193LEU00.005-0.00729.2580.0020.0020.0000.0000.0000.000
168A194GLU-1-0.873-0.92233.451-0.013-0.0130.0000.0000.0000.000
169A195ILE0-0.035-0.00536.7790.0010.0010.0000.0000.0000.000
170A196HIS0-0.028-0.02634.4830.0030.0030.0000.0000.0000.000
171A197GLY00.0420.02031.8010.0010.0010.0000.0000.0000.000
172A198GLU-1-0.988-0.98630.6590.0030.0030.0000.0000.0000.000
173A199THR0-0.018-0.01228.9790.0020.0020.0000.0000.0000.000
174A200ILE0-0.070-0.01826.2160.0020.0020.0000.0000.0000.000
175A201GLU-1-0.896-0.95021.9380.0060.0060.0000.0000.0000.000
176A202LYS10.9100.94220.6920.0330.0330.0000.0000.0000.000
177A203VAL0-0.027-0.01623.7150.0040.0040.0000.0000.0000.000
178A204VAL00.0170.00818.914-0.003-0.0030.0000.0000.0000.000
179A205PHE0-0.037-0.02722.1800.0050.0050.0000.0000.0000.000
180A206ALA00.0430.02419.655-0.006-0.0060.0000.0000.0000.000
181A207VAL0-0.078-0.03321.1560.0100.0100.0000.0000.0000.000
182A208SER0-0.001-0.03421.097-0.012-0.0120.0000.0000.0000.000
183A209ASP-1-0.842-0.95522.623-0.108-0.1080.0000.0000.0000.000
184A210LEU0-0.088-0.02324.7220.0070.0070.0000.0000.0000.000
185A211GLU-1-0.834-0.91225.757-0.066-0.0660.0000.0000.0000.000
186A212GLU-1-0.859-0.93223.111-0.094-0.0940.0000.0000.0000.000
187A213GLY00.0510.02726.4090.0040.0040.0000.0000.0000.000
188A214THR0-0.009-0.00829.6580.0040.0040.0000.0000.0000.000
189A215TYR00.0400.01027.5950.0040.0040.0000.0000.0000.000
190A216GLN0-0.017-0.00825.5490.0070.0070.0000.0000.0000.000
191A217LYS10.8410.91029.7290.0400.0400.0000.0000.0000.000
192A218LEU0-0.035-0.02832.8230.0030.0030.0000.0000.0000.000
193A219LEU00.0300.02227.3730.0030.0030.0000.0000.0000.000
194A220PRO0-0.015-0.00831.9830.0030.0030.0000.0000.0000.000
195A221LEU0-0.033-0.00634.5010.0030.0030.0000.0000.0000.000
196A222TYR0-0.046-0.08334.1960.0040.0040.0000.0000.0000.000
197A223PHE00.0180.00931.6890.0020.0020.0000.0000.0000.000
198A224PRO00.0240.04533.484-0.003-0.0030.0000.0000.0000.000
199A225ARG10.9530.97228.3790.0480.0480.0000.0000.0000.000
200A226SER00.0160.01434.5080.0010.0010.0000.0000.0000.000
201A227LEU00.0180.01037.7190.0010.0010.0000.0000.0000.000