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

tag_button

FMODB ID: G5R51

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 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 201
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2340538.906992
FMO2-HF: Nuclear repulsion 2261907.082011
FMO2-HF: Total energy -78631.824982
FMO2-MP2: Total energy -78862.14583


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.
-2.4960.2120.061-1.215-1.5540.004
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 : -0.001 / q_NPA : -0.004
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].
3A9GLN0-0.052-0.0372.985-2.6590.0490.061-1.215-1.5540.004
4A10PHE0-0.020-0.0026.0120.1980.1980.0000.0000.0000.000
5A11VAL0-0.011-0.0117.670-0.121-0.1210.0000.0000.0000.000
6A12ASP-1-0.832-0.91710.326-0.010-0.0100.0000.0000.0000.000
7A13VAL00.016-0.01611.896-0.008-0.0080.0000.0000.0000.000
8A14ASP-1-0.876-0.94914.909-0.021-0.0210.0000.0000.0000.000
9A15THR0-0.117-0.04711.168-0.010-0.0100.0000.0000.0000.000
10A16LEU0-0.080-0.03014.228-0.010-0.0100.0000.0000.0000.000
11A17PRO0-0.0010.00816.8590.0150.0150.0000.0000.0000.000
12A18SER00.035-0.00720.160-0.003-0.0030.0000.0000.0000.000
13A19TRP0-0.032-0.05323.186-0.004-0.0040.0000.0000.0000.000
14A20GLY0-0.085-0.05926.3790.0010.0010.0000.0000.0000.000
15A21ASP-1-0.865-0.90522.937-0.053-0.0530.0000.0000.0000.000
16A22SER0-0.113-0.05624.7010.0000.0000.0000.0000.0000.000
17A43ARG11.0001.00341.5860.0230.0230.0000.0000.0000.000
18A44SER0-0.040-0.02339.1940.0010.0010.0000.0000.0000.000
19A45PRO0-0.013-0.00641.6910.0010.0010.0000.0000.0000.000
20A46PHE0-0.045-0.01738.7210.0010.0010.0000.0000.0000.000
21A47LEU00.0740.04140.755-0.001-0.0010.0000.0000.0000.000
22A48TYR00.0080.00834.5970.0000.0000.0000.0000.0000.000
23A49ASN00.0370.01135.5610.0020.0020.0000.0000.0000.000
24A50LYS10.9870.99131.4190.0210.0210.0000.0000.0000.000
25A51ASP-1-0.800-0.88931.374-0.015-0.0150.0000.0000.0000.000
26A52VAL00.0150.00630.479-0.002-0.0020.0000.0000.0000.000
27A53ASN0-0.050-0.05229.767-0.003-0.0030.0000.0000.0000.000
28A54GLY00.0290.02727.048-0.005-0.0050.0000.0000.0000.000
29A55LYS10.8570.95425.4170.0090.0090.0000.0000.0000.000
30A56VAL0-0.0310.00625.176-0.003-0.0030.0000.0000.0000.000
31A57VAL00.0430.03419.479-0.002-0.0020.0000.0000.0000.000
32A58LEU0-0.052-0.01922.9540.0030.0030.0000.0000.0000.000
33A59TRP00.0480.01713.4090.0010.0010.0000.0000.0000.000
34A60LYS10.8330.91519.3890.1540.1540.0000.0000.0000.000
35A61GLY00.0120.00216.154-0.025-0.0250.0000.0000.0000.000
36A62ASP-1-0.844-0.89315.053-0.141-0.1410.0000.0000.0000.000
37A63VAL00.0580.00115.634-0.014-0.0140.0000.0000.0000.000
38A64ALA0-0.053-0.02616.1440.0100.0100.0000.0000.0000.000
39A65LEU0-0.015-0.00310.4820.0110.0110.0000.0000.0000.000
40A66LEU0-0.0110.00812.069-0.022-0.0220.0000.0000.0000.000
41A67ASN0-0.0010.00412.4460.0050.0050.0000.0000.0000.000
42A68CYS0-0.0020.01714.6910.0170.0170.0000.0000.0000.000
43A69THR0-0.022-0.00718.3770.0110.0110.0000.0000.0000.000
44A70ALA00.013-0.00620.7050.0100.0100.0000.0000.0000.000
45A71ILE00.0370.05017.905-0.008-0.0080.0000.0000.0000.000
46A72VAL00.0000.00421.3280.0110.0110.0000.0000.0000.000
47A73ASN00.0400.03723.616-0.016-0.0160.0000.0000.0000.000
48A74THR0-0.034-0.03125.2250.0080.0080.0000.0000.0000.000
49A75SER00.0510.01428.094-0.001-0.0010.0000.0000.0000.000
50A76ASN0-0.021-0.01530.5540.0010.0010.0000.0000.0000.000
51A77GLU-1-0.702-0.84133.951-0.018-0.0180.0000.0000.0000.000
52A78SER0-0.002-0.00835.8420.0020.0020.0000.0000.0000.000
53A79LEU0-0.032-0.00330.5350.0020.0020.0000.0000.0000.000
54A80THR00.016-0.00730.5420.0000.0000.0000.0000.0000.000
55A81ASP-1-0.892-0.91730.292-0.040-0.0400.0000.0000.0000.000
56A82LYS10.9230.98326.1660.0600.0600.0000.0000.0000.000
57A83ASN0-0.062-0.04626.464-0.005-0.0050.0000.0000.0000.000
58A84PRO00.1160.03423.4500.0010.0010.0000.0000.0000.000
59A85VAL00.0310.03122.069-0.008-0.0080.0000.0000.0000.000
60A86SER00.007-0.02721.759-0.003-0.0030.0000.0000.0000.000
61A87GLU-1-0.913-0.96222.323-0.068-0.0680.0000.0000.0000.000
62A88SER0-0.002-0.01917.4660.0080.0080.0000.0000.0000.000
63A89ILE00.0190.01418.1610.0040.0040.0000.0000.0000.000
64A90PHE0-0.069-0.05119.4930.0130.0130.0000.0000.0000.000
65A91MET0-0.0290.00016.4720.0080.0080.0000.0000.0000.000
66A92LEU00.0060.00012.8800.0140.0140.0000.0000.0000.000
67A93ALA0-0.0020.01615.6390.0260.0260.0000.0000.0000.000
68A94GLY00.0990.05018.2660.0250.0250.0000.0000.0000.000
69A95PRO0-0.048-0.05519.223-0.009-0.0090.0000.0000.0000.000
70A96ASP-1-0.803-0.89221.4790.0800.0800.0000.0000.0000.000
71A97LEU0-0.033-0.00622.540-0.005-0.0050.0000.0000.0000.000
72A98LYS10.8330.91622.772-0.009-0.0090.0000.0000.0000.000
73A99GLU-1-0.842-0.92427.3080.0320.0320.0000.0000.0000.000
74A100ASP-1-0.841-0.93926.7800.0330.0330.0000.0000.0000.000
75A101LEU00.0100.00027.362-0.003-0.0030.0000.0000.0000.000
76A102GLN0-0.014-0.00729.868-0.003-0.0030.0000.0000.0000.000
77A103LYS10.8210.91930.352-0.030-0.0300.0000.0000.0000.000
78A104LEU0-0.024-0.00430.430-0.001-0.0010.0000.0000.0000.000
79A105LYS10.9110.96334.474-0.013-0.0130.0000.0000.0000.000
80A106GLY00.0050.00135.420-0.001-0.0010.0000.0000.0000.000
81A107CYS0-0.0200.01233.8060.0020.0020.0000.0000.0000.000
82A108ARG10.8620.93135.8830.0030.0030.0000.0000.0000.000
83A109THR00.007-0.01837.0450.0000.0000.0000.0000.0000.000
84A110GLY00.0140.00736.5620.0010.0010.0000.0000.0000.000
85A111GLU-1-0.845-0.89835.646-0.002-0.0020.0000.0000.0000.000
86A112ALA0-0.001-0.00331.176-0.003-0.0030.0000.0000.0000.000
87A113LYS10.8730.92831.1470.0010.0010.0000.0000.0000.000
88A114LEU00.0120.02126.615-0.004-0.0040.0000.0000.0000.000
89A115THR0-0.0020.00924.701-0.001-0.0010.0000.0000.0000.000
90A116LYS10.8940.95222.713-0.060-0.0600.0000.0000.0000.000
91A117GLY00.0320.01619.664-0.009-0.0090.0000.0000.0000.000
92A118PHE0-0.038-0.02818.969-0.011-0.0110.0000.0000.0000.000
93A119ASN0-0.037-0.01912.4350.0690.0690.0000.0000.0000.000
94A120LEU0-0.035-0.00213.876-0.012-0.0120.0000.0000.0000.000
95A121ALA00.0360.01411.7870.0310.0310.0000.0000.0000.000
96A122ALA0-0.0090.02113.6110.0230.0230.0000.0000.0000.000
97A123ARG10.9450.97617.217-0.045-0.0450.0000.0000.0000.000
98A124PHE0-0.020-0.04119.7040.0110.0110.0000.0000.0000.000
99A125ILE00.0420.03221.364-0.011-0.0110.0000.0000.0000.000
100A126ILE0-0.035-0.01423.5190.0070.0070.0000.0000.0000.000
101A127HIS00.0210.01125.479-0.014-0.0140.0000.0000.0000.000
102A128THR00.029-0.01228.4820.0030.0030.0000.0000.0000.000
103A129VAL0-0.034-0.00530.930-0.003-0.0030.0000.0000.0000.000
104A130GLY00.1150.06133.1990.0020.0020.0000.0000.0000.000
105A131PRO0-0.027-0.00834.7660.0010.0010.0000.0000.0000.000
106A132LYS10.8290.90237.3800.0180.0180.0000.0000.0000.000
107A133TYR00.0140.01638.9570.0030.0030.0000.0000.0000.000
108A134LYS10.9570.97140.6950.0210.0210.0000.0000.0000.000
109A135SER00.0760.03044.3450.0000.0000.0000.0000.0000.000
110A136ARG10.9440.97146.4460.0170.0170.0000.0000.0000.000
111A137TYR0-0.015-0.00645.4980.0010.0010.0000.0000.0000.000
112A138ARG10.8160.89042.6680.0260.0260.0000.0000.0000.000
113A139THR00.0890.04544.2250.0000.0000.0000.0000.0000.000
114A140ALA00.0180.00844.7570.0000.0000.0000.0000.0000.000
115A141ALA0-0.025-0.00640.6450.0000.0000.0000.0000.0000.000
116A142GLU-1-0.784-0.90239.951-0.023-0.0230.0000.0000.0000.000
117A143SER0-0.0060.00340.2000.0000.0000.0000.0000.0000.000
118A144SER0-0.016-0.02139.0550.0010.0010.0000.0000.0000.000
119A145LEU00.0130.00033.2940.0000.0000.0000.0000.0000.000
120A146TYR0-0.008-0.00435.491-0.001-0.0010.0000.0000.0000.000
121A147SER0-0.032-0.02136.5570.0010.0010.0000.0000.0000.000
122A148CYS0-0.0580.00432.6100.0010.0010.0000.0000.0000.000
123A149TYR00.0390.01428.7110.0010.0010.0000.0000.0000.000
124A150ARG10.8890.94032.5000.0080.0080.0000.0000.0000.000
125A151ASN00.016-0.01534.5360.0040.0040.0000.0000.0000.000
126A152VAL0-0.0190.00727.8020.0030.0030.0000.0000.0000.000
127A153LEU00.0160.00929.3540.0020.0020.0000.0000.0000.000
128A154GLN0-0.060-0.02831.3290.0010.0010.0000.0000.0000.000
129A155LEU00.0110.00230.1980.0030.0030.0000.0000.0000.000
130A156ALA00.0310.00027.7610.0040.0040.0000.0000.0000.000
131A157LYS10.9320.97829.0910.0010.0010.0000.0000.0000.000
132A158GLU-1-0.909-0.95531.7530.0090.0090.0000.0000.0000.000
133A159GLN0-0.082-0.03427.8280.0070.0070.0000.0000.0000.000
134A160SER0-0.025-0.00227.9440.0040.0040.0000.0000.0000.000
135A161MET0-0.096-0.03724.6760.0010.0010.0000.0000.0000.000
136A162SER00.0300.01121.652-0.003-0.0030.0000.0000.0000.000
137A163SER00.0680.02420.374-0.009-0.0090.0000.0000.0000.000
138A164VAL0-0.049-0.02722.6960.0050.0050.0000.0000.0000.000
139A165GLY00.0630.03120.354-0.007-0.0070.0000.0000.0000.000
140A166PHE0-0.044-0.04921.3440.0060.0060.0000.0000.0000.000
141A167CYS00.0000.00822.917-0.008-0.0080.0000.0000.0000.000
142A168VAL00.0420.01024.0170.0080.0080.0000.0000.0000.000
143A169ILE0-0.013-0.00527.0240.0010.0010.0000.0000.0000.000
144A170ASN0-0.032-0.00529.3910.0040.0040.0000.0000.0000.000
145A171SER00.0720.03129.709-0.003-0.0030.0000.0000.0000.000
146A172ALA00.0800.02830.1200.0030.0030.0000.0000.0000.000
147A173LYS10.7960.87531.1780.0440.0440.0000.0000.0000.000
148A174ARG10.7560.86133.9160.0310.0310.0000.0000.0000.000
149A175GLY00.0370.01735.4300.0030.0030.0000.0000.0000.000
150A176TYR0-0.007-0.01135.4830.0020.0020.0000.0000.0000.000
151A177PRO00.0050.01035.959-0.003-0.0030.0000.0000.0000.000
152A178LEU00.0790.04330.6380.0020.0020.0000.0000.0000.000
153A179GLU-1-0.797-0.87134.322-0.043-0.0430.0000.0000.0000.000
154A180ASP-1-0.819-0.89136.186-0.030-0.0300.0000.0000.0000.000
155A181ALA0-0.024-0.01734.0920.0020.0020.0000.0000.0000.000
156A182THR00.000-0.00731.1180.0000.0000.0000.0000.0000.000
157A183HIS00.0490.03833.4010.0010.0010.0000.0000.0000.000
158A184ILE0-0.067-0.02135.8730.0020.0020.0000.0000.0000.000
159A185ALA00.0210.03330.7050.0020.0020.0000.0000.0000.000
160A186LEU00.0200.01229.6980.0020.0020.0000.0000.0000.000
161A187ARG10.9610.99232.8170.0270.0270.0000.0000.0000.000
162A188THR0-0.074-0.05834.2800.0030.0030.0000.0000.0000.000
163A189VAL00.0170.00829.1200.0030.0030.0000.0000.0000.000
164A190ARG10.7400.86732.4570.0260.0260.0000.0000.0000.000
165A191ARG10.9530.96834.3500.0200.0200.0000.0000.0000.000
166A192PHE0-0.009-0.00331.4370.0020.0020.0000.0000.0000.000
167A193LEU00.0200.00329.1530.0020.0020.0000.0000.0000.000
168A194GLU-1-0.858-0.92933.360-0.017-0.0170.0000.0000.0000.000
169A195ILE0-0.044-0.01336.6810.0010.0010.0000.0000.0000.000
170A196HIS0-0.031-0.02534.4410.0030.0030.0000.0000.0000.000
171A197GLY00.0240.01431.8140.0010.0010.0000.0000.0000.000
172A198GLU-1-0.965-0.97730.6730.0020.0020.0000.0000.0000.000
173A199THR0-0.030-0.01329.0930.0020.0020.0000.0000.0000.000
174A200ILE0-0.084-0.03326.1350.0020.0020.0000.0000.0000.000
175A201GLU-1-0.855-0.90321.9090.0060.0060.0000.0000.0000.000
176A202LYS10.8730.92919.4540.0380.0380.0000.0000.0000.000
177A203VAL0-0.034-0.02123.6170.0040.0040.0000.0000.0000.000
178A204VAL00.0230.00918.777-0.004-0.0040.0000.0000.0000.000
179A205PHE0-0.033-0.02222.1060.0060.0060.0000.0000.0000.000
180A206ALA00.0390.02219.562-0.006-0.0060.0000.0000.0000.000
181A207VAL0-0.078-0.03721.1150.0110.0110.0000.0000.0000.000
182A208SER00.011-0.02321.071-0.015-0.0150.0000.0000.0000.000
183A209ASP-1-0.817-0.91622.171-0.131-0.1310.0000.0000.0000.000
184A210LEU0-0.073-0.01424.7040.0080.0080.0000.0000.0000.000
185A211GLU-1-0.831-0.91925.714-0.081-0.0810.0000.0000.0000.000
186A212GLU-1-0.844-0.92722.985-0.111-0.1110.0000.0000.0000.000
187A213GLY00.0490.02526.3610.0040.0040.0000.0000.0000.000
188A214THR0-0.010-0.00829.6030.0040.0040.0000.0000.0000.000
189A215TYR00.0350.00427.5460.0050.0050.0000.0000.0000.000
190A216GLN0-0.033-0.00825.2180.0090.0090.0000.0000.0000.000
191A217LYS10.8380.89429.6510.0480.0480.0000.0000.0000.000
192A218LEU0-0.029-0.02132.7380.0040.0040.0000.0000.0000.000
193A219LEU00.0320.02027.3440.0040.0040.0000.0000.0000.000
194A220PRO0-0.008-0.00331.8960.0040.0040.0000.0000.0000.000
195A221LEU0-0.044-0.01234.4010.0030.0030.0000.0000.0000.000
196A222TYR0-0.029-0.05234.1320.0040.0040.0000.0000.0000.000
197A223PHE00.0260.01831.6650.0030.0030.0000.0000.0000.000
198A224PRO00.0150.03733.374-0.003-0.0030.0000.0000.0000.000
199A225ARG10.9360.96728.6280.0570.0570.0000.0000.0000.000
200A226SER0-0.0020.00234.3830.0020.0020.0000.0000.0000.000
201A227LEU00.0240.01737.5880.0010.0010.0000.0000.0000.000