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: 8979Y

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 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 201
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2346326.284724
FMO2-HF: Nuclear repulsion 2267694.054316
FMO2-HF: Total energy -78632.230408
FMO2-MP2: Total energy -78862.567445


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.
-1.711.1140.161-1.158-1.8270.003
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 : 0.003 / q_NPA : -0.002
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].
3A9GLN0-0.059-0.0352.833-2.0920.7320.161-1.158-1.8270.003
4A10PHE0-0.027-0.0165.4960.3660.3660.0000.0000.0000.000
5A11VAL0-0.006-0.0037.646-0.104-0.1040.0000.0000.0000.000
6A12ASP-1-0.788-0.89510.1590.0430.0430.0000.0000.0000.000
7A13VAL00.001-0.00911.845-0.012-0.0120.0000.0000.0000.000
8A14ASP-1-0.853-0.92614.5410.0140.0140.0000.0000.0000.000
9A15THR0-0.125-0.06410.620-0.019-0.0190.0000.0000.0000.000
10A16LEU0-0.059-0.01714.072-0.014-0.0140.0000.0000.0000.000
11A17PRO00.0070.01316.9350.0170.0170.0000.0000.0000.000
12A18SER00.023-0.01120.251-0.005-0.0050.0000.0000.0000.000
13A19TRP0-0.039-0.04023.481-0.005-0.0050.0000.0000.0000.000
14A20GLY0-0.039-0.03326.5500.0010.0010.0000.0000.0000.000
15A21ASP-1-0.855-0.90323.030-0.033-0.0330.0000.0000.0000.000
16A22SER0-0.142-0.08324.606-0.003-0.0030.0000.0000.0000.000
17A43ARG11.0011.00841.7680.0200.0200.0000.0000.0000.000
18A44SER0-0.041-0.02739.1360.0010.0010.0000.0000.0000.000
19A45PRO0-0.009-0.00541.5500.0010.0010.0000.0000.0000.000
20A46PHE0-0.031-0.01238.7070.0010.0010.0000.0000.0000.000
21A47LEU00.0590.02940.348-0.001-0.0010.0000.0000.0000.000
22A48TYR00.0230.01734.5990.0000.0000.0000.0000.0000.000
23A49ASN00.0370.01134.9530.0020.0020.0000.0000.0000.000
24A50LYS10.9890.99430.7290.0100.0100.0000.0000.0000.000
25A51ASP-1-0.801-0.87530.864-0.002-0.0020.0000.0000.0000.000
26A52VAL00.014-0.00229.915-0.002-0.0020.0000.0000.0000.000
27A53ASN0-0.047-0.05030.020-0.003-0.0030.0000.0000.0000.000
28A54GLY00.0220.01527.199-0.005-0.0050.0000.0000.0000.000
29A55LYS10.8080.92325.419-0.005-0.0050.0000.0000.0000.000
30A56VAL0-0.030-0.00425.471-0.002-0.0020.0000.0000.0000.000
31A57VAL00.0420.02319.568-0.001-0.0010.0000.0000.0000.000
32A58LEU0-0.064-0.02522.9590.0030.0030.0000.0000.0000.000
33A59TRP00.0400.00913.3790.0010.0010.0000.0000.0000.000
34A60LYS10.8250.91119.6280.1430.1430.0000.0000.0000.000
35A61GLY00.0080.00516.013-0.023-0.0230.0000.0000.0000.000
36A62ASP-1-0.838-0.89214.796-0.156-0.1560.0000.0000.0000.000
37A63VAL00.0480.00115.306-0.016-0.0160.0000.0000.0000.000
38A64ALA0-0.045-0.02315.7940.0120.0120.0000.0000.0000.000
39A65LEU0-0.012-0.00310.0800.0020.0020.0000.0000.0000.000
40A66LEU0-0.0100.00711.887-0.019-0.0190.0000.0000.0000.000
41A67ASN0-0.004-0.00812.186-0.005-0.0050.0000.0000.0000.000
42A68CYS0-0.0310.01014.3570.0240.0240.0000.0000.0000.000
43A69THR0-0.020-0.01618.1000.0150.0150.0000.0000.0000.000
44A70ALA00.002-0.01620.6870.0070.0070.0000.0000.0000.000
45A71ILE00.0320.04017.561-0.007-0.0070.0000.0000.0000.000
46A72VAL0-0.0050.00321.2030.0080.0080.0000.0000.0000.000
47A73ASN00.0410.03223.278-0.018-0.0180.0000.0000.0000.000
48A74THR0-0.062-0.03325.0900.0090.0090.0000.0000.0000.000
49A75SER00.0690.02627.665-0.003-0.0030.0000.0000.0000.000
50A76ASN0-0.051-0.03829.9190.0030.0030.0000.0000.0000.000
51A77GLU-1-0.672-0.81433.515-0.024-0.0240.0000.0000.0000.000
52A78SER0-0.026-0.00535.2450.0020.0020.0000.0000.0000.000
53A79LEU0-0.024-0.00429.8200.0020.0020.0000.0000.0000.000
54A80THR00.0310.00529.958-0.002-0.0020.0000.0000.0000.000
55A81ASP-1-0.871-0.91229.538-0.049-0.0490.0000.0000.0000.000
56A82LYS10.9480.99225.8730.0760.0760.0000.0000.0000.000
57A83ASN0-0.073-0.05926.150-0.003-0.0030.0000.0000.0000.000
58A84PRO00.1060.03922.5420.0020.0020.0000.0000.0000.000
59A85VAL00.0350.03421.494-0.009-0.0090.0000.0000.0000.000
60A86SER00.017-0.01521.6120.0000.0000.0000.0000.0000.000
61A87GLU-1-0.923-0.96921.857-0.088-0.0880.0000.0000.0000.000
62A88SER00.006-0.01817.1250.0040.0040.0000.0000.0000.000
63A89ILE00.0050.00417.703-0.002-0.0020.0000.0000.0000.000
64A90PHE0-0.057-0.04619.4620.0120.0120.0000.0000.0000.000
65A91MET0-0.0130.00616.8930.0060.0060.0000.0000.0000.000
66A92LEU00.0250.00712.7500.0110.0110.0000.0000.0000.000
67A93ALA00.0050.02315.4430.0170.0170.0000.0000.0000.000
68A94GLY00.0670.03618.1550.0240.0240.0000.0000.0000.000
69A95PRO0-0.038-0.03018.730-0.007-0.0070.0000.0000.0000.000
70A96ASP-1-0.814-0.91620.6170.0510.0510.0000.0000.0000.000
71A97LEU0-0.034-0.00622.129-0.001-0.0010.0000.0000.0000.000
72A98LYS10.8180.90322.2780.0220.0220.0000.0000.0000.000
73A99GLU-1-0.848-0.92926.8470.0120.0120.0000.0000.0000.000
74A100ASP-1-0.819-0.90526.4480.0260.0260.0000.0000.0000.000
75A101LEU00.0030.00227.057-0.001-0.0010.0000.0000.0000.000
76A102GLN00.010-0.00329.3700.0000.0000.0000.0000.0000.000
77A103LYS10.8260.90929.971-0.021-0.0210.0000.0000.0000.000
78A104LEU0-0.027-0.00729.9440.0000.0000.0000.0000.0000.000
79A105LYS10.8680.93934.273-0.005-0.0050.0000.0000.0000.000
80A106GLY00.0390.03234.241-0.001-0.0010.0000.0000.0000.000
81A107CYS0-0.0250.01533.0780.0030.0030.0000.0000.0000.000
82A108ARG10.8190.88835.1700.0060.0060.0000.0000.0000.000
83A109THR0-0.005-0.01536.7280.0000.0000.0000.0000.0000.000
84A110GLY00.0180.01636.2840.0020.0020.0000.0000.0000.000
85A111GLU-1-0.808-0.87935.399-0.005-0.0050.0000.0000.0000.000
86A112ALA00.005-0.00131.108-0.004-0.0040.0000.0000.0000.000
87A113LYS10.8280.91031.0400.0060.0060.0000.0000.0000.000
88A114LEU00.0130.01126.515-0.005-0.0050.0000.0000.0000.000
89A115THR00.0080.02024.214-0.001-0.0010.0000.0000.0000.000
90A116LYS10.8630.92822.277-0.057-0.0570.0000.0000.0000.000
91A117GLY00.0440.02519.160-0.011-0.0110.0000.0000.0000.000
92A118PHE0-0.038-0.03018.575-0.014-0.0140.0000.0000.0000.000
93A119ASN0-0.030-0.01012.4240.0660.0660.0000.0000.0000.000
94A120LEU0-0.036-0.00713.556-0.019-0.0190.0000.0000.0000.000
95A121ALA00.0370.01611.5730.0360.0360.0000.0000.0000.000
96A122ALA00.0180.03413.4780.0300.0300.0000.0000.0000.000
97A123ARG10.9250.97117.113-0.064-0.0640.0000.0000.0000.000
98A124PHE0-0.007-0.02819.5460.0110.0110.0000.0000.0000.000
99A125ILE00.0220.02220.946-0.012-0.0120.0000.0000.0000.000
100A126ILE0-0.016-0.00323.2800.0070.0070.0000.0000.0000.000
101A127HIS00.0260.01224.829-0.014-0.0140.0000.0000.0000.000
102A128THR00.038-0.02128.1660.0040.0040.0000.0000.0000.000
103A129VAL0-0.034-0.01130.658-0.004-0.0040.0000.0000.0000.000
104A130GLY00.1110.05932.5470.0030.0030.0000.0000.0000.000
105A131PRO0-0.032-0.01634.2250.0000.0000.0000.0000.0000.000
106A132LYS10.8420.90937.0690.0240.0240.0000.0000.0000.000
107A133TYR00.0170.02138.4990.0030.0030.0000.0000.0000.000
108A134LYS10.9750.97740.3860.0250.0250.0000.0000.0000.000
109A135SER00.0570.01943.9740.0010.0010.0000.0000.0000.000
110A136ARG10.9320.96746.2170.0200.0200.0000.0000.0000.000
111A137TYR00.0220.01445.3780.0010.0010.0000.0000.0000.000
112A138ARG10.7810.87242.2980.0260.0260.0000.0000.0000.000
113A139THR00.0840.04043.671-0.001-0.0010.0000.0000.0000.000
114A140ALA00.0140.01444.5540.0010.0010.0000.0000.0000.000
115A141ALA0-0.025-0.00140.2270.0000.0000.0000.0000.0000.000
116A142GLU-1-0.788-0.90939.618-0.023-0.0230.0000.0000.0000.000
117A143SER00.0050.00639.8850.0000.0000.0000.0000.0000.000
118A144SER0-0.011-0.01338.7580.0010.0010.0000.0000.0000.000
119A145LEU00.008-0.00532.8820.0000.0000.0000.0000.0000.000
120A146TYR00.0020.00035.066-0.001-0.0010.0000.0000.0000.000
121A147SER0-0.030-0.02236.1920.0010.0010.0000.0000.0000.000
122A148CYS0-0.055-0.00232.2780.0010.0010.0000.0000.0000.000
123A149TYR00.0400.01628.2020.0020.0020.0000.0000.0000.000
124A150ARG10.8770.93132.2090.0070.0070.0000.0000.0000.000
125A151ASN0-0.007-0.01334.2470.0050.0050.0000.0000.0000.000
126A152VAL0-0.0020.00827.4260.0030.0030.0000.0000.0000.000
127A153LEU00.0080.00929.3940.0030.0030.0000.0000.0000.000
128A154GLN0-0.051-0.02931.3270.0020.0020.0000.0000.0000.000
129A155LEU00.0250.00630.2730.0040.0040.0000.0000.0000.000
130A156ALA00.028-0.00127.6280.0040.0040.0000.0000.0000.000
131A157LYS10.8670.93828.815-0.004-0.0040.0000.0000.0000.000
132A158GLU-1-0.842-0.91431.5160.0120.0120.0000.0000.0000.000
133A159GLN0-0.087-0.04027.5770.0070.0070.0000.0000.0000.000
134A160SER0-0.028-0.00527.5000.0050.0050.0000.0000.0000.000
135A161MET0-0.095-0.03124.6580.0020.0020.0000.0000.0000.000
136A162SER00.0130.00621.668-0.005-0.0050.0000.0000.0000.000
137A163SER00.0750.03120.097-0.008-0.0080.0000.0000.0000.000
138A164VAL0-0.043-0.02722.2050.0040.0040.0000.0000.0000.000
139A165GLY00.0740.03720.072-0.006-0.0060.0000.0000.0000.000
140A166PHE0-0.026-0.03221.0540.0030.0030.0000.0000.0000.000
141A167CYS0-0.0070.00422.783-0.006-0.0060.0000.0000.0000.000
142A168VAL00.0460.01423.8640.0100.0100.0000.0000.0000.000
143A169ILE00.0030.00526.8470.0000.0000.0000.0000.0000.000
144A170ASN0-0.0230.00029.1510.0040.0040.0000.0000.0000.000
145A171SER00.0580.02629.086-0.002-0.0020.0000.0000.0000.000
146A172ALA00.0800.03329.8890.0040.0040.0000.0000.0000.000
147A173LYS10.8040.88230.5970.0530.0530.0000.0000.0000.000
148A174ARG10.7390.85133.5230.0370.0370.0000.0000.0000.000
149A175GLY00.0220.00435.4600.0030.0030.0000.0000.0000.000
150A176TYR00.003-0.01535.1480.0020.0020.0000.0000.0000.000
151A177PRO0-0.0010.00635.651-0.003-0.0030.0000.0000.0000.000
152A178LEU00.0820.04430.3150.0020.0020.0000.0000.0000.000
153A179GLU-1-0.790-0.86433.861-0.042-0.0420.0000.0000.0000.000
154A180ASP-1-0.819-0.88335.904-0.029-0.0290.0000.0000.0000.000
155A181ALA0-0.024-0.02033.4750.0020.0020.0000.0000.0000.000
156A182THR0-0.008-0.00530.9470.0000.0000.0000.0000.0000.000
157A183HIS00.0480.02533.0300.0020.0020.0000.0000.0000.000
158A184ILE0-0.073-0.02835.4120.0020.0020.0000.0000.0000.000
159A185ALA00.0170.03030.4130.0030.0030.0000.0000.0000.000
160A186LEU00.0140.01229.6840.0030.0030.0000.0000.0000.000
161A187ARG10.9330.97632.7070.0260.0260.0000.0000.0000.000
162A188THR0-0.074-0.05334.0250.0040.0040.0000.0000.0000.000
163A189VAL00.0190.00729.0010.0030.0030.0000.0000.0000.000
164A190ARG10.7260.86232.2650.0200.0200.0000.0000.0000.000
165A191ARG10.9610.97134.2960.0170.0170.0000.0000.0000.000
166A192PHE0-0.0120.00731.3890.0020.0020.0000.0000.0000.000
167A193LEU00.0350.00528.9710.0030.0030.0000.0000.0000.000
168A194GLU-1-0.842-0.92733.129-0.011-0.0110.0000.0000.0000.000
169A195ILE0-0.059-0.01636.5340.0010.0010.0000.0000.0000.000
170A196HIS0-0.007-0.01134.0430.0040.0040.0000.0000.0000.000
171A197GLY00.0180.00631.1880.0020.0020.0000.0000.0000.000
172A198GLU-1-0.941-0.95530.3680.0130.0130.0000.0000.0000.000
173A199THR0-0.068-0.02528.9400.0040.0040.0000.0000.0000.000
174A200ILE0-0.065-0.03325.7130.0020.0020.0000.0000.0000.000
175A201GLU-1-0.836-0.89021.5800.0330.0330.0000.0000.0000.000
176A202LYS10.8400.90718.8370.0180.0180.0000.0000.0000.000
177A203VAL0-0.030-0.01622.9830.0020.0020.0000.0000.0000.000
178A204VAL00.0240.01018.554-0.003-0.0030.0000.0000.0000.000
179A205PHE0-0.025-0.02221.8840.0020.0020.0000.0000.0000.000
180A206ALA00.0460.02619.412-0.007-0.0070.0000.0000.0000.000
181A207VAL0-0.062-0.03420.8800.0110.0110.0000.0000.0000.000
182A208SER00.010-0.02820.822-0.016-0.0160.0000.0000.0000.000
183A209ASP-1-0.807-0.90922.093-0.128-0.1280.0000.0000.0000.000
184A210LEU0-0.068-0.01224.7010.0080.0080.0000.0000.0000.000
185A211GLU-1-0.818-0.91125.523-0.083-0.0830.0000.0000.0000.000
186A212GLU-1-0.869-0.93622.858-0.105-0.1050.0000.0000.0000.000
187A213GLY00.0510.02426.1740.0050.0050.0000.0000.0000.000
188A214THR0-0.016-0.01429.5130.0040.0040.0000.0000.0000.000
189A215TYR00.032-0.00227.4760.0060.0060.0000.0000.0000.000
190A216GLN0-0.017-0.00525.1910.0090.0090.0000.0000.0000.000
191A217LYS10.8260.89729.6810.0460.0460.0000.0000.0000.000
192A218LEU0-0.028-0.01832.6120.0040.0040.0000.0000.0000.000
193A219LEU00.0470.02727.4050.0040.0040.0000.0000.0000.000
194A220PRO00.004-0.00431.9380.0040.0040.0000.0000.0000.000
195A221LEU0-0.063-0.02534.8190.0030.0030.0000.0000.0000.000
196A222TYR0-0.029-0.04134.1820.0040.0040.0000.0000.0000.000
197A223PHE00.0400.02831.6340.0020.0020.0000.0000.0000.000
198A224PRO00.0230.04333.371-0.003-0.0030.0000.0000.0000.000
199A225ARG10.9200.95428.8350.0490.0490.0000.0000.0000.000
200A226SER0-0.013-0.00634.4910.0010.0010.0000.0000.0000.000
201A227LEU00.0180.01937.7940.0000.0000.0000.0000.0000.000