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: YZ652

Calculation Name: 4P4H-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 4P4H

Chain ID: A

ChEMBL ID:

UniProt ID: O95786

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 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 188
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2216907.906434
FMO2-HF: Nuclear repulsion 2138534.619075
FMO2-HF: Total energy -78373.287359
FMO2-MP2: Total energy -78599.937151


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:1:MET)


Summations of interaction energy for fragment #1(A:1: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.
-8.767-12.65918.919-5.226-9.801-0.009
Interaction energy analysis for fragmet #1(A:1:MET)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.014 / q_NPA : 0.035
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].
3A3THR00.048-0.0122.242-4.300-9.64516.814-5.154-6.315-0.001
4A4GLU-1-0.950-0.9942.177-4.413-3.7812.0990.111-2.843-0.007
5A5GLN00.0690.0413.8900.5171.3380.006-0.183-0.643-0.001
6A6ARG10.8980.9625.653-0.596-0.5960.0000.0000.0000.000
7A7ARG10.9270.9636.138-1.614-1.6140.0000.0000.0000.000
8A8SER00.0050.0167.2910.1510.1510.0000.0000.0000.000
9A9LEU0-0.011-0.0149.4180.0870.0870.0000.0000.0000.000
10A10GLN0-0.044-0.03711.2530.1820.1820.0000.0000.0000.000
11A11ALA0-0.057-0.00712.7460.0260.0260.0000.0000.0000.000
12A12PHE00.0070.00012.6560.0290.0290.0000.0000.0000.000
13A13GLN00.0530.02416.0810.0220.0220.0000.0000.0000.000
14A14ASP-1-0.902-0.94917.3930.0090.0090.0000.0000.0000.000
15A15TYR0-0.072-0.06418.5200.0040.0040.0000.0000.0000.000
16A16ILE00.0230.02614.9170.0040.0040.0000.0000.0000.000
17A17ARG10.8860.94419.564-0.009-0.0090.0000.0000.0000.000
18A18LYS10.7860.89722.4930.0500.0500.0000.0000.0000.000
19A19THR0-0.043-0.02121.9330.0000.0000.0000.0000.0000.000
20A20LEU0-0.004-0.00919.5030.0040.0040.0000.0000.0000.000
21A21ASP-1-0.763-0.83323.2070.0180.0180.0000.0000.0000.000
22A22PRO0-0.007-0.01122.519-0.004-0.0040.0000.0000.0000.000
23A23THR0-0.058-0.06223.8810.0000.0000.0000.0000.0000.000
24A24TYR0-0.055-0.05026.0310.0010.0010.0000.0000.0000.000
25A25ILE00.0240.01218.993-0.003-0.0030.0000.0000.0000.000
26A26LEU0-0.004-0.01921.654-0.001-0.0010.0000.0000.0000.000
27A27SER0-0.0320.00223.3920.0070.0070.0000.0000.0000.000
28A28TYR00.0180.00421.3580.0030.0030.0000.0000.0000.000
29A29MET0-0.0460.00215.859-0.008-0.0080.0000.0000.0000.000
30A30ALA0-0.0040.00319.9400.0160.0160.0000.0000.0000.000
31A31PRO0-0.032-0.02218.1660.0080.0080.0000.0000.0000.000
32A32TRP00.0100.03013.525-0.017-0.0170.0000.0000.0000.000
33A33PHE0-0.028-0.01217.9740.0250.0250.0000.0000.0000.000
34A34ARG10.7920.87620.809-0.155-0.1550.0000.0000.0000.000
35A35GLU-1-0.874-0.94623.6690.0530.0530.0000.0000.0000.000
36A36GLU-1-0.898-0.94525.9630.1090.1090.0000.0000.0000.000
37A37GLU-1-0.779-0.88821.2550.1600.1600.0000.0000.0000.000
38A38VAL00.0330.02024.251-0.007-0.0070.0000.0000.0000.000
39A39GLN00.0460.02425.946-0.009-0.0090.0000.0000.0000.000
40A40TYR0-0.052-0.03226.543-0.005-0.0050.0000.0000.0000.000
41A41ILE0-0.032-0.01822.310-0.004-0.0040.0000.0000.0000.000
42A42GLN0-0.009-0.01026.786-0.009-0.0090.0000.0000.0000.000
43A43ALA0-0.032-0.00629.706-0.005-0.0050.0000.0000.0000.000
44A44GLU-1-0.758-0.86728.0030.0530.0530.0000.0000.0000.000
45A45LYS10.7760.90529.347-0.014-0.0140.0000.0000.0000.000
46A46ASN0-0.037-0.02530.881-0.005-0.0050.0000.0000.0000.000
47A47ASN0-0.090-0.03733.574-0.004-0.0040.0000.0000.0000.000
48A48LYS10.8070.87630.819-0.056-0.0560.0000.0000.0000.000
49A49GLY00.0160.02932.148-0.002-0.0020.0000.0000.0000.000
50A50PRO00.042-0.00228.6160.0040.0040.0000.0000.0000.000
51A51MET00.0120.01826.1490.0020.0020.0000.0000.0000.000
52A52ALA00.0130.01225.7650.0040.0040.0000.0000.0000.000
53A53ALA00.0360.02726.2620.0090.0090.0000.0000.0000.000
54A54ALA00.0410.02222.3480.0070.0070.0000.0000.0000.000
55A55THR0-0.080-0.06021.4470.0040.0040.0000.0000.0000.000
56A56LEU0-0.031-0.00321.4710.0170.0170.0000.0000.0000.000
57A57PHE00.004-0.00817.3460.0210.0210.0000.0000.0000.000
58A58LEU00.0290.00116.0070.0110.0110.0000.0000.0000.000
59A59LYS10.7600.89316.727-0.168-0.1680.0000.0000.0000.000
60A60PHE00.050-0.00716.8750.0430.0430.0000.0000.0000.000
61A61LEU00.0060.03213.3850.0310.0310.0000.0000.0000.000
62A62LEU0-0.034-0.01911.4660.0670.0670.0000.0000.0000.000
63A63GLU-1-0.840-0.90412.1710.4330.4330.0000.0000.0000.000
64A64LEU0-0.0150.00813.5120.0330.0330.0000.0000.0000.000
65A65GLN0-0.036-0.0219.3290.1350.1350.0000.0000.0000.000
66A66GLU-1-0.965-0.97311.0450.3050.3050.0000.0000.0000.000
67A67GLU-1-0.905-0.9628.1550.7730.7730.0000.0000.0000.000
68A68GLY0-0.032-0.0268.440-0.080-0.0800.0000.0000.0000.000
69A69TRP00.0440.0167.335-0.297-0.2970.0000.0000.0000.000
70A70PHE0-0.009-0.0087.043-0.143-0.1430.0000.0000.0000.000
71A71ARG10.7350.8219.3050.2890.2890.0000.0000.0000.000
72A72GLY00.0860.02910.6770.0400.0400.0000.0000.0000.000
73A73PHE0-0.021-0.02312.5420.0370.0370.0000.0000.0000.000
74A74LEU0-0.022-0.01510.1990.0180.0180.0000.0000.0000.000
75A75ASP-1-0.786-0.89214.026-0.140-0.1400.0000.0000.0000.000
76A76ALA0-0.0070.00416.1600.0230.0230.0000.0000.0000.000
77A77LEU0-0.026-0.02615.9760.0120.0120.0000.0000.0000.000
78A78ASP-1-0.927-0.95518.068-0.079-0.0790.0000.0000.0000.000
79A79HIS0-0.052-0.03219.6270.0210.0210.0000.0000.0000.000
80A80ALA0-0.051-0.02321.7940.0090.0090.0000.0000.0000.000
81A81GLY00.0210.02523.1220.0070.0070.0000.0000.0000.000
82A82TYR0-0.008-0.01021.0130.0050.0050.0000.0000.0000.000
83A83SER00.0710.02820.316-0.011-0.0110.0000.0000.0000.000
84A84GLY00.0570.02920.1420.0110.0110.0000.0000.0000.000
85A85LEU0-0.009-0.02517.768-0.007-0.0070.0000.0000.0000.000
86A86TYR0-0.102-0.04214.302-0.019-0.0190.0000.0000.0000.000
87A87GLU-1-0.907-0.96315.418-0.130-0.1300.0000.0000.0000.000
88A88ALA0-0.0250.02016.357-0.016-0.0160.0000.0000.0000.000
89A89ILE0-0.022-0.02711.388-0.027-0.0270.0000.0000.0000.000
90A90GLU-1-0.782-0.84110.975-0.410-0.4100.0000.0000.0000.000
91A91SER0-0.064-0.04911.255-0.027-0.0270.0000.0000.0000.000
92A92TRP0-0.038-0.0237.1220.0370.0370.0000.0000.0000.000
93A93ASP-1-0.804-0.87212.909-0.093-0.0930.0000.0000.0000.000
94A94PHE00.0800.01814.8350.0140.0140.0000.0000.0000.000
95A95LYS10.7960.87819.0750.1320.1320.0000.0000.0000.000
96A96LYS10.8020.88621.7530.0900.0900.0000.0000.0000.000
97A97ILE00.0590.02920.2560.0100.0100.0000.0000.0000.000
98A98GLU-1-0.839-0.89723.229-0.049-0.0490.0000.0000.0000.000
99A99LYS10.9210.96524.9720.0510.0510.0000.0000.0000.000
100A100LEU00.0250.01526.5310.0060.0060.0000.0000.0000.000
101A101GLU-1-0.815-0.87827.583-0.023-0.0230.0000.0000.0000.000
102A102GLU-1-0.903-0.93529.467-0.023-0.0230.0000.0000.0000.000
103A103TYR0-0.014-0.02732.1760.0040.0040.0000.0000.0000.000
104A104ARG10.8540.91028.2400.0300.0300.0000.0000.0000.000
105A105LEU0-0.018-0.02631.9660.0050.0050.0000.0000.0000.000
106A106LEU0-0.0200.01434.7660.0030.0030.0000.0000.0000.000
107A107LEU00.0610.02135.2720.0020.0020.0000.0000.0000.000
108A108LYS10.9250.96632.4230.0120.0120.0000.0000.0000.000
109A109ARG10.8400.90936.7890.0110.0110.0000.0000.0000.000
110A110LEU00.0130.01740.5790.0010.0010.0000.0000.0000.000
111A111GLN00.0120.01538.6810.0000.0000.0000.0000.0000.000
112A112PRO0-0.011-0.01441.7710.0000.0000.0000.0000.0000.000
113A113GLU-1-0.807-0.89545.375-0.004-0.0040.0000.0000.0000.000
114A114PHE00.001-0.00240.1710.0000.0000.0000.0000.0000.000
115A115LYS10.7910.88144.071-0.002-0.0020.0000.0000.0000.000
116A116THR0-0.045-0.03445.1420.0000.0000.0000.0000.0000.000
117A117ARG10.7950.89047.8520.0040.0040.0000.0000.0000.000
118A118ILE00.0040.02242.937-0.001-0.0010.0000.0000.0000.000
119A119ILE00.0230.01146.3440.0010.0010.0000.0000.0000.000
120A120PRO0-0.0120.00042.352-0.001-0.0010.0000.0000.0000.000
121A121THR0-0.008-0.03443.304-0.001-0.0010.0000.0000.0000.000
122A122ASP-1-0.932-0.94545.032-0.005-0.0050.0000.0000.0000.000
123A123ILE00.0230.00541.237-0.001-0.0010.0000.0000.0000.000
124A124ILE0-0.023-0.01238.202-0.001-0.0010.0000.0000.0000.000
125A125SER00.007-0.01038.473-0.001-0.0010.0000.0000.0000.000
126A126ASP-1-0.874-0.91138.811-0.013-0.0130.0000.0000.0000.000
127A127LEU00.0210.00835.870-0.002-0.0020.0000.0000.0000.000
128A128SER0-0.034-0.03334.668-0.002-0.0020.0000.0000.0000.000
129A129GLU-1-0.872-0.92731.860-0.030-0.0300.0000.0000.0000.000
130A130CYS0-0.093-0.02430.222-0.005-0.0050.0000.0000.0000.000
131A131LEU0-0.0230.01329.760-0.002-0.0020.0000.0000.0000.000
132A132ILE00.0500.03525.5700.0000.0000.0000.0000.0000.000
133A133ASN00.0380.00729.4300.0040.0040.0000.0000.0000.000
134A134GLN00.0660.02830.1610.0010.0010.0000.0000.0000.000
135A135GLU-1-0.772-0.89229.987-0.013-0.0130.0000.0000.0000.000
136A136CYS0-0.047-0.02333.2700.0010.0010.0000.0000.0000.000
137A137GLU-1-0.926-0.96135.8910.0020.0020.0000.0000.0000.000
138A138GLU-1-0.822-0.89633.6240.0060.0060.0000.0000.0000.000
139A139ILE00.0090.00436.0250.0010.0010.0000.0000.0000.000
140A140LEU00.0440.03039.5240.0010.0010.0000.0000.0000.000
141A141GLN00.0090.01141.2130.0010.0010.0000.0000.0000.000
142A142ILE0-0.026-0.02140.3490.0010.0010.0000.0000.0000.000
143A143CYS0-0.079-0.03942.9480.0000.0000.0000.0000.0000.000
144A144SER0-0.058-0.01245.4810.0000.0000.0000.0000.0000.000
145A145THR0-0.038-0.01845.5390.0010.0010.0000.0000.0000.000
146A146LYS10.9270.95444.546-0.009-0.0090.0000.0000.0000.000
147A147GLY00.0310.03448.0590.0000.0000.0000.0000.0000.000
148A148MET00.004-0.01247.0890.0000.0000.0000.0000.0000.000
149A149MET00.0090.02145.8950.0000.0000.0000.0000.0000.000
150A150ALA00.0230.00544.7450.0000.0000.0000.0000.0000.000
151A151GLY00.0440.01642.3290.0000.0000.0000.0000.0000.000
152A152ALA00.009-0.00741.207-0.001-0.0010.0000.0000.0000.000
153A153GLU-1-0.832-0.91440.6750.0020.0020.0000.0000.0000.000
154A154LYS10.8160.91533.984-0.003-0.0030.0000.0000.0000.000
155A155LEU00.0210.00236.549-0.001-0.0010.0000.0000.0000.000
156A156VAL00.0070.00936.159-0.002-0.0020.0000.0000.0000.000
157A157GLU-1-0.870-0.91832.918-0.001-0.0010.0000.0000.0000.000
158A158CYS0-0.009-0.01031.713-0.001-0.0010.0000.0000.0000.000
159A159LEU00.0610.03731.033-0.004-0.0040.0000.0000.0000.000
160A160LEU0-0.094-0.03831.219-0.003-0.0030.0000.0000.0000.000
161A161ARG10.7460.86627.4270.0070.0070.0000.0000.0000.000
162A162SER0-0.004-0.00926.547-0.007-0.0070.0000.0000.0000.000
163A163ASP-1-0.795-0.92023.034-0.064-0.0640.0000.0000.0000.000
164A164LYS10.7860.90424.2110.0510.0510.0000.0000.0000.000
165A165GLU-1-0.785-0.89824.796-0.065-0.0650.0000.0000.0000.000
166A166ASN00.007-0.01927.4180.0040.0040.0000.0000.0000.000
167A167TRP00.0710.04729.2400.0070.0070.0000.0000.0000.000
168A168PRO00.0030.00431.5070.0030.0030.0000.0000.0000.000
169A169LYS10.9440.97234.2100.0300.0300.0000.0000.0000.000
170A170THR0-0.003-0.03233.8580.0020.0020.0000.0000.0000.000
171A171LEU0-0.0070.01036.3830.0020.0020.0000.0000.0000.000
172A172LYS10.8380.91038.0930.0160.0160.0000.0000.0000.000
173A173LEU0-0.011-0.00338.3450.0010.0010.0000.0000.0000.000
174A174ALA00.0470.02440.1220.0010.0010.0000.0000.0000.000
175A175LEU0-0.076-0.06241.3680.0020.0020.0000.0000.0000.000
176A176GLU-1-0.864-0.90544.075-0.011-0.0110.0000.0000.0000.000
177A177LYS10.7140.86044.3370.0110.0110.0000.0000.0000.000
178A178GLU-1-0.811-0.88846.305-0.008-0.0080.0000.0000.0000.000
179A179ARG10.9330.95148.6820.0070.0070.0000.0000.0000.000
180A180ASN00.1210.08545.4420.0010.0010.0000.0000.0000.000
181A181LYS10.8550.93649.3400.0050.0050.0000.0000.0000.000
182A182PHE00.0320.00541.8190.0000.0000.0000.0000.0000.000
183A183SER0-0.013-0.04645.195-0.001-0.0010.0000.0000.0000.000
184A184GLU-1-0.987-0.99845.136-0.012-0.0120.0000.0000.0000.000
185A185LEU0-0.0430.01344.6390.0010.0010.0000.0000.0000.000
186A186TRP0-0.066-0.04135.9400.0000.0000.0000.0000.0000.000
187A187ILE00.0270.01441.0860.0000.0000.0000.0000.0000.000
188A188VAL0-0.0150.00136.298-0.002-0.0020.0000.0000.0000.000