Manual

About

FMODB

FMODB: The database of quantum mechanical data based on the FMO method

Last updated: 2024-05-02

All entries: 37386

Number of unique PDB entries: 7781

tag_button

FMODB ID: M3MZZ

Calculation Name: 4UY3-A-Xray323

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 4UY3

Chain ID: A

ChEMBL ID:

UniProt ID: A7X3E7

Base Structure: X-ray

Registration Date: 2021-09-07

Reference: C. Watanabe, S. Koyama, K. Kamisaka, D. Takaya, T. Honma et. al., Interaction energy analysis of Apo structure dataset on FMODB, To be pubulished.

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. 1.20200129
FMO calculation
FMO method FMO2-MP2/6-31G(d)
Fragmentation Auto
Number of fragment 195
LigandCharge
Software ABINIT-MP - Open Ver.1 Rev. 15 / 20190524
Total energy (hartree)
FMO2-HF: Electronic energy -1923278.984351
FMO2-HF: Nuclear repulsion 1842812.514435
FMO2-HF: Total energy -80466.469917
FMO2-MP2: Total energy -80699.692329


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:23:MET )


Summations of interaction energy for fragment #1(A:23:MET )
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.
-7.694-3.4769.873-4.814-9.28-0.012
Interaction energy analysis for fragmet #1(A:23:MET )
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.020 / q_NPA : 0.006
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].
3A25SER 0-0.026-0.0113.169-3.981-1.6660.015-1.058-1.2730.003
4A26ASN 00.0070.0012.432-3.074-2.8384.447-1.619-3.065-0.018
5A27LYS 10.9960.9951.8081.1871.0505.007-1.591-3.2800.007
6A28ARG 10.9960.9934.5600.6490.8530.001-0.028-0.1770.000
7A29GLN 00.0710.0397.164-0.029-0.0290.0000.0000.0000.000
8A30ILE 0-0.049-0.0156.2710.1930.1930.0000.0000.0000.000
9A31ILE 00.0150.0029.2140.1730.1730.0000.0000.0000.000
10A32GLU -1-0.931-0.96311.290-0.553-0.5530.0000.0000.0000.000
11A33LYS 10.9901.00012.4600.6180.6180.0000.0000.0000.000
12A34ALA 0-0.0040.00113.7110.0820.0820.0000.0000.0000.000
13A35ILE 00.0070.00115.3520.0640.0640.0000.0000.0000.000
14A36GLU -1-0.978-0.99216.787-0.424-0.4240.0000.0000.0000.000
15A37ARG 10.8210.89718.2130.2950.2950.0000.0000.0000.000
16A38LYS 10.9470.96919.7430.2000.2000.0000.0000.0000.000
17A39ASN 0-0.026-0.02021.5690.0360.0360.0000.0000.0000.000
18A40GLU -1-0.938-0.95722.281-0.232-0.2320.0000.0000.0000.000
19A41ILE 00.0110.02823.3970.0220.0220.0000.0000.0000.000
20A42GLU -1-0.932-0.98025.656-0.138-0.1380.0000.0000.0000.000
21A43THR 0-0.149-0.08827.9700.0150.0150.0000.0000.0000.000
22A44LEU 00.0080.01627.8590.0050.0050.0000.0000.0000.000
23A45PRO 00.0010.01731.2040.0080.0080.0000.0000.0000.000
24A46PHE 00.036-0.00631.0530.0070.0070.0000.0000.0000.000
25A47ASP -1-0.935-0.96836.117-0.072-0.0720.0000.0000.0000.000
26A48GLN 00.017-0.00736.6370.0050.0050.0000.0000.0000.000
27A49ASN 00.0010.01038.0620.0050.0050.0000.0000.0000.000
28A50LEU 00.0600.01940.0680.0050.0050.0000.0000.0000.000
29A51ALA 0-0.053-0.02442.3140.0050.0050.0000.0000.0000.000
30A52GLN 0-0.042-0.00142.0780.0050.0050.0000.0000.0000.000
31A53LEU 00.0510.02045.1790.0030.0030.0000.0000.0000.000
32A54SER 0-0.116-0.08947.5600.0030.0030.0000.0000.0000.000
33A55LYS 10.8880.95248.3460.0560.0560.0000.0000.0000.000
34A56LEU 00.0140.02849.5020.0010.0010.0000.0000.0000.000
35A57ASN 0-0.014-0.01152.8620.0010.0010.0000.0000.0000.000
36A58LEU 00.0110.02248.7950.0000.0000.0000.0000.0000.000
37A59LYS 10.8620.91552.9010.0350.0350.0000.0000.0000.000
38A60GLY 00.0930.05954.376-0.001-0.0010.0000.0000.0000.000
39A61GLU -1-0.777-0.90952.559-0.036-0.0360.0000.0000.0000.000
40A62THR 00.0120.00050.236-0.002-0.0020.0000.0000.0000.000
41A63LYS 10.8590.93449.2270.0390.0390.0000.0000.0000.000
42A64THR 0-0.016-0.00649.027-0.001-0.0010.0000.0000.0000.000
43A65LYS 10.8820.93942.1130.0580.0580.0000.0000.0000.000
44A66TYR 0-0.005-0.01944.906-0.003-0.0030.0000.0000.0000.000
45A67ASP -1-0.879-0.95444.269-0.046-0.0460.0000.0000.0000.000
46A68ALA 0-0.059-0.02944.062-0.001-0.0010.0000.0000.0000.000
47A69MET 00.0350.04540.139-0.001-0.0010.0000.0000.0000.000
48A70LYS 10.9070.96939.4590.0590.0590.0000.0000.0000.000
49A71LYS 10.8870.94139.3450.0460.0460.0000.0000.0000.000
50A72ASP -1-0.828-0.90037.232-0.063-0.0630.0000.0000.0000.000
51A73ASN 00.0220.01335.104-0.006-0.0060.0000.0000.0000.000
52A74VAL 0-0.0240.02434.389-0.005-0.0050.0000.0000.0000.000
53A75GLU -1-0.929-0.97934.429-0.057-0.0570.0000.0000.0000.000
54A76SER 0-0.017-0.02431.622-0.003-0.0030.0000.0000.0000.000
55A77THR 0-0.020-0.03030.304-0.009-0.0090.0000.0000.0000.000
56A78ASN 0-0.033-0.02929.651-0.007-0.0070.0000.0000.0000.000
57A79LYS 10.8900.97029.7380.0750.0750.0000.0000.0000.000
58A80TYR 00.004-0.02526.5480.0010.0010.0000.0000.0000.000
59A81LEU 00.0330.03024.727-0.012-0.0120.0000.0000.0000.000
60A82ALA 0-0.018-0.01325.093-0.008-0.0080.0000.0000.0000.000
61A83PRO 0-0.005-0.00424.128-0.003-0.0030.0000.0000.0000.000
62A84VAL 00.0090.01319.614-0.008-0.0080.0000.0000.0000.000
63A85GLU -1-0.952-0.97519.890-0.134-0.1340.0000.0000.0000.000
64A86GLU -1-0.931-0.95819.948-0.078-0.0780.0000.0000.0000.000
65A87LYS 10.8520.94117.6450.1310.1310.0000.0000.0000.000
66A88ILE 00.0140.00015.029-0.035-0.0350.0000.0000.0000.000
67A89HIS 00.0170.01915.198-0.005-0.0050.0000.0000.0000.000
68A90ASN 0-0.008-0.02415.8300.0300.0300.0000.0000.0000.000
69A91ALA 00.0100.00711.7550.0140.0140.0000.0000.0000.000
70A92GLU -1-0.921-0.96010.981-0.332-0.3320.0000.0000.0000.000
71A93ALA 0-0.021-0.00211.4970.0860.0860.0000.0000.0000.000
72A94LEU 0-0.009-0.01811.5080.0880.0880.0000.0000.0000.000
73A95LEU 0-0.055-0.0124.681-0.122-0.0120.000-0.020-0.0900.000
74A96ASP -1-0.937-0.9607.7390.7620.7620.0000.0000.0000.000
75A97LYS 10.9230.9649.414-0.013-0.0130.0000.0000.0000.000
76A98PHE 0-0.072-0.0495.4450.2020.2020.0000.0000.0000.000
77A99SER 0-0.028-0.0017.690-0.047-0.0470.0000.0000.0000.000
78A100PHE 0-0.015-0.0272.902-1.852-0.3620.403-0.498-1.395-0.004
79A101ASN 00.0210.0057.060-0.076-0.0760.0000.0000.0000.000
80A102ALA 00.0450.02810.008-0.034-0.0340.0000.0000.0000.000
81A103SER 0-0.031-0.0288.670-0.080-0.0800.0000.0000.0000.000
82A104GLN 0-0.027-0.0158.051-0.184-0.1840.0000.0000.0000.000
83A105SER 00.0170.00810.0450.0280.0280.0000.0000.0000.000
84A106GLU -1-0.878-0.93113.490-0.135-0.1350.0000.0000.0000.000
85A107ILE 0-0.025-0.02010.908-0.009-0.0090.0000.0000.0000.000
86A108ASP -1-0.902-0.95513.356-0.329-0.3290.0000.0000.0000.000
87A109ASP -1-0.832-0.91315.137-0.134-0.1340.0000.0000.0000.000
88A110ALA 0-0.034-0.02316.4690.0150.0150.0000.0000.0000.000
89A111ASN 0-0.019-0.02414.5520.0260.0260.0000.0000.0000.000
90A112GLU -1-0.894-0.92118.319-0.124-0.1240.0000.0000.0000.000
91A113LEU 0-0.053-0.02920.9240.0190.0190.0000.0000.0000.000
92A114MET 0-0.028-0.01818.1590.0140.0140.0000.0000.0000.000
93A115ASP -1-0.826-0.88521.400-0.209-0.2090.0000.0000.0000.000
94A116SER 0-0.053-0.01423.8340.0180.0180.0000.0000.0000.000
95A117TYR 0-0.031-0.01326.1810.0100.0100.0000.0000.0000.000
96A118GLU -1-0.861-0.94524.059-0.192-0.1920.0000.0000.0000.000
97A119GLN 0-0.009-0.00227.6970.0040.0040.0000.0000.0000.000
98A120SER 0-0.093-0.05729.7480.0110.0110.0000.0000.0000.000
99A121TYR 00.0410.01131.0250.0090.0090.0000.0000.0000.000
100A122GLN 0-0.005-0.00630.3010.0130.0130.0000.0000.0000.000
101A123GLN 0-0.0040.00533.4600.0020.0020.0000.0000.0000.000
102A124GLN 00.045-0.00335.7310.0060.0060.0000.0000.0000.000
103A125LEU 0-0.037-0.01434.7620.0050.0050.0000.0000.0000.000
104A126GLU -1-0.973-0.97037.889-0.073-0.0730.0000.0000.0000.000
105A127ASP -1-0.781-0.90339.625-0.062-0.0620.0000.0000.0000.000
106A128VAL 0-0.078-0.03941.3670.0050.0050.0000.0000.0000.000
107A129ASN 00.014-0.00140.2280.0050.0050.0000.0000.0000.000
108A130GLU -1-0.952-0.95543.801-0.051-0.0510.0000.0000.0000.000
109A131ILE 0-0.022-0.01645.7140.0030.0030.0000.0000.0000.000
110A132ILE 0-0.030-0.02445.0750.0030.0030.0000.0000.0000.000
111A133ALA 0-0.0070.00047.6770.0020.0020.0000.0000.0000.000
112A134LEU 00.0510.01749.5130.0030.0030.0000.0000.0000.000
113A135TYR 0-0.066-0.04551.7270.0030.0030.0000.0000.0000.000
114A136LYS 10.9130.96551.3650.0480.0480.0000.0000.0000.000
115A137ASP -1-0.877-0.93953.358-0.043-0.0430.0000.0000.0000.000
116A138ASN 0-0.057-0.04155.2400.0020.0020.0000.0000.0000.000
117A139ASP -1-0.806-0.89357.287-0.035-0.0350.0000.0000.0000.000
118A140GLU -1-0.919-0.94456.045-0.040-0.0400.0000.0000.0000.000
119A141LEU 0-0.054-0.03258.5100.0020.0020.0000.0000.0000.000
120A142TYR 00.0280.01261.3630.0020.0020.0000.0000.0000.000
121A143ASP -1-0.919-0.95862.385-0.032-0.0320.0000.0000.0000.000
122A144LYS 10.8600.93863.8990.0300.0300.0000.0000.0000.000
123A145CYS 0-0.006-0.00764.8650.0010.0010.0000.0000.0000.000
124A146LYS 10.9460.97066.4920.0300.0300.0000.0000.0000.000
125A147VAL 0-0.063-0.02968.2850.0010.0010.0000.0000.0000.000
126A148ASP -1-0.808-0.91068.469-0.026-0.0260.0000.0000.0000.000
127A149TYR 0-0.017-0.01071.4580.0010.0010.0000.0000.0000.000
128A150ARG 10.9280.95871.3910.0260.0260.0000.0000.0000.000
129A151GLU -1-0.951-0.97572.907-0.024-0.0240.0000.0000.0000.000
130A152MET 00.0080.01173.9850.0000.0000.0000.0000.0000.000
131A153LYS 10.9730.99877.2290.0200.0200.0000.0000.0000.000
132A154ARG 10.9380.96479.1490.0200.0200.0000.0000.0000.000
133A155ASP -1-0.903-0.95579.511-0.019-0.0190.0000.0000.0000.000
134A156VAL 00.0390.01681.4080.0010.0010.0000.0000.0000.000
135A157LEU 0-0.068-0.03282.8850.0010.0010.0000.0000.0000.000
136A158ALA 0-0.076-0.03584.7930.0000.0000.0000.0000.0000.000
137A159ASN 0-0.078-0.03583.7600.0010.0010.0000.0000.0000.000
138A160ARG 10.9831.00186.7280.0160.0160.0000.0000.0000.000
139A161HIS 00.007-0.00888.2900.0000.0000.0000.0000.0000.000
140A162GLN 0-0.049-0.01283.9540.0000.0000.0000.0000.0000.000
141A163PHE 00.0180.01781.6320.0000.0000.0000.0000.0000.000
142A164GLY 0-0.050-0.01786.8220.0000.0000.0000.0000.0000.000
143A165GLU -1-0.935-0.98489.744-0.013-0.0130.0000.0000.0000.000
144A166ALA 0-0.045-0.01384.4250.0000.0000.0000.0000.0000.000
145A167ALA 00.0570.02984.7200.0000.0000.0000.0000.0000.000
146A168SER 00.017-0.01885.3500.0000.0000.0000.0000.0000.000
147A169LEU 0-0.017-0.00283.2630.0000.0000.0000.0000.0000.000
148A170LEU 00.0480.02280.2460.0000.0000.0000.0000.0000.000
149A171GLU -1-0.894-0.94980.703-0.017-0.0170.0000.0000.0000.000
150A172THR 0-0.050-0.02381.6550.0000.0000.0000.0000.0000.000
151A173GLU -1-0.948-0.98877.184-0.019-0.0190.0000.0000.0000.000
152A174ILE 0-0.018-0.00976.490-0.001-0.0010.0000.0000.0000.000
153A175GLU -1-0.867-0.92676.443-0.020-0.0200.0000.0000.0000.000
154A176LYS 10.8800.93375.3950.0180.0180.0000.0000.0000.000
155A177PHE 0-0.019-0.02472.080-0.001-0.0010.0000.0000.0000.000
156A178GLU -1-0.931-0.95171.885-0.022-0.0220.0000.0000.0000.000
157A179PRO 00.0240.01572.378-0.001-0.0010.0000.0000.0000.000
158A180ARG 10.8440.91567.5100.0230.0230.0000.0000.0000.000
159A181LEU 00.0340.01967.701-0.001-0.0010.0000.0000.0000.000
160A182GLU -1-0.878-0.93967.418-0.023-0.0230.0000.0000.0000.000
161A183GLN 0-0.038-0.03966.866-0.001-0.0010.0000.0000.0000.000
162A184TYR 0-0.024-0.03059.725-0.001-0.0010.0000.0000.0000.000
163A185GLU -1-0.934-0.97162.967-0.030-0.0300.0000.0000.0000.000
164A186VAL 0-0.022-0.00563.426-0.001-0.0010.0000.0000.0000.000
165A187LEU 00.0270.01760.677-0.001-0.0010.0000.0000.0000.000
166A188LYS 10.9140.96458.1140.0350.0350.0000.0000.0000.000
167A189ALA 0-0.0270.00458.504-0.001-0.0010.0000.0000.0000.000
168A190ASP -1-0.967-0.99059.732-0.030-0.0300.0000.0000.0000.000
169A191GLY 0-0.023-0.01755.592-0.001-0.0010.0000.0000.0000.000
170A192ASN 0-0.0080.02054.730-0.002-0.0020.0000.0000.0000.000
171A193TYR 00.0670.02448.5740.0010.0010.0000.0000.0000.000
172A194VAL 00.0540.03351.8710.0000.0000.0000.0000.0000.000
173A195GLN 0-0.082-0.04454.7550.0020.0020.0000.0000.0000.000
174A196ALA 00.0100.00957.6620.0010.0010.0000.0000.0000.000
175A197HIS 00.0040.00955.5760.0010.0010.0000.0000.0000.000
176A198ASN 0-0.010-0.02356.0360.0010.0010.0000.0000.0000.000
177A199HIS 0-0.101-0.03359.1640.0010.0010.0000.0000.0000.000
178A200ILE 00.008-0.00660.0090.0010.0010.0000.0000.0000.000
179A201ALA 00.0220.01859.2090.0010.0010.0000.0000.0000.000
180A202ALA 0-0.0050.00061.3450.0010.0010.0000.0000.0000.000
181A203LEU 0-0.007-0.00464.1110.0010.0010.0000.0000.0000.000
182A204ASN 00.0480.00562.7240.0010.0010.0000.0000.0000.000
183A205GLU -1-0.927-0.94064.062-0.026-0.0260.0000.0000.0000.000
184A206GLN 00.0210.00665.9980.0010.0010.0000.0000.0000.000
185A207MET 0-0.0220.01469.0380.0010.0010.0000.0000.0000.000
186A208LYS 10.9090.96063.8670.0290.0290.0000.0000.0000.000
187A209GLN 0-0.061-0.04567.5080.0010.0010.0000.0000.0000.000
188A210LEU 00.0150.01071.4470.0010.0010.0000.0000.0000.000
189A211ARG 10.9430.96168.8980.0250.0250.0000.0000.0000.000
190A212SER 0-0.054-0.02771.7680.0000.0000.0000.0000.0000.000
191A213TYR 0-0.026-0.01174.3040.0010.0010.0000.0000.0000.000
192A214MET 0-0.052-0.01577.1220.0000.0000.0000.0000.0000.000
193A215HIS 0-0.056-0.00875.8000.0000.0000.0000.0000.0000.000
194A216GLY 00.016-0.00979.5690.0000.0000.0000.0000.0000.000
195A1NME 0-0.0190.01482.9120.0000.0000.0000.0000.0000.000