FMODB

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

Last updated: 2024-07-23

All entries: 37450

Number of unique PDB entries: 7783

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FMODB ID: R5J98

Calculation Name: 4PVC-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 4PVC

Chain ID: A

ChEMBL ID:

UniProt ID: Q12068

Base Structure: X-ray

Registration Date: 2023-06-20

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 342
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -5434031.878411
FMO2-HF: Nuclear repulsion 5300491.733874
FMO2-HF: Total energy -133540.144537
FMO2-MP2: Total energy -133931.622363


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.
-21.759-11.58711.127-6.298-15.005-0.008
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 : 0.013 / q_NPA : 0.003
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].
3A3VAL00.0180.0183.109-4.435-2.3130.108-0.824-1.407-0.001
4A4PHE00.012-0.0025.0670.4090.469-0.001-0.004-0.0540.000
5A5VAL00.0140.0018.6240.0300.0300.0000.0000.0000.000
6A6SER00.026-0.00611.4290.0320.0320.0000.0000.0000.000
7A7GLY00.0140.01014.8290.0210.0210.0000.0000.0000.000
8A8ALA00.0220.00914.2810.0150.0150.0000.0000.0000.000
9A9ASN0-0.007-0.00115.9070.0220.0220.0000.0000.0000.000
10A10GLY00.007-0.00118.875-0.016-0.0160.0000.0000.0000.000
11A11PHE0-0.021-0.02019.1990.0390.0390.0000.0000.0000.000
12A12ILE00.0550.01016.3310.0230.0230.0000.0000.0000.000
13A13ALA00.0040.01615.0530.0570.0570.0000.0000.0000.000
14A14GLN00.005-0.00614.5690.1020.1020.0000.0000.0000.000
15A15HIS00.021-0.00615.2840.1060.1060.0000.0000.0000.000
16A16ILE0-0.030-0.00310.5250.0650.0650.0000.0000.0000.000
17A17VAL0-0.0040.00210.7310.1640.1640.0000.0000.0000.000
18A18ASP-1-0.777-0.88210.8900.8260.8260.0000.0000.0000.000
19A19LEU0-0.031-0.01211.8500.0660.0660.0000.0000.0000.000
20A20LEU0-0.009-0.0045.6000.1260.1260.0000.0000.0000.000
21A21LEU0-0.035-0.0147.1850.3500.3500.0000.0000.0000.000
22A22LYS10.7940.8749.395-0.666-0.6660.0000.0000.0000.000
23A23GLU-1-0.869-0.9108.0731.0821.0820.0000.0000.0000.000
24A24ASP-1-0.839-0.9096.7201.6881.6880.0000.0000.0000.000
25A25TYR0-0.0090.0101.945-2.763-1.5154.565-1.689-4.125-0.008
26A26LYS10.8090.8962.854-6.970-4.9230.475-1.083-1.4390.015
27A27VAL00.004-0.0074.433-0.321-0.271-0.001-0.029-0.0210.000
28A28ILE00.0080.0137.251-0.205-0.2050.0000.0000.0000.000
29A29GLY00.0440.01010.207-0.119-0.1190.0000.0000.0000.000
30A30SER00.009-0.00613.109-0.056-0.0560.0000.0000.0000.000
31A31ALA00.0450.01416.5040.0210.0210.0000.0000.0000.000
32A32ARG10.8500.93920.048-0.088-0.0880.0000.0000.0000.000
33A33SER0-0.017-0.05823.384-0.020-0.0200.0000.0000.0000.000
34A34GLN00.002-0.00622.6380.0060.0060.0000.0000.0000.000
35A35GLU-1-0.691-0.78423.5040.1610.1610.0000.0000.0000.000
36A36LYS10.7810.86423.267-0.112-0.1120.0000.0000.0000.000
37A37ALA00.0160.00819.3950.0260.0260.0000.0000.0000.000
38A38GLU-1-0.830-0.90819.6290.2410.2410.0000.0000.0000.000
39A39ASN0-0.037-0.03121.6120.0220.0220.0000.0000.0000.000
40A40LEU0-0.021-0.00116.4130.0130.0130.0000.0000.0000.000
41A41THR00.014-0.00816.0250.0430.0430.0000.0000.0000.000
42A42GLU-1-0.960-0.96717.9260.3120.3120.0000.0000.0000.000
43A43ALA0-0.040-0.01320.0040.0070.0070.0000.0000.0000.000
44A44PHE0-0.040-0.02015.1020.0220.0220.0000.0000.0000.000
45A45GLY0-0.003-0.00616.5500.0720.0720.0000.0000.0000.000
46A46ASN0-0.050-0.04017.598-0.004-0.0040.0000.0000.0000.000
47A47ASN00.0340.02812.4020.0900.0900.0000.0000.0000.000
48A48PRO00.0460.01713.1540.0750.0750.0000.0000.0000.000
49A49LYS10.7530.8746.101-2.667-2.6670.0000.0000.0000.000
50A50PHE0-0.026-0.0178.4060.4330.4330.0000.0000.0000.000
51A51SER0-0.0040.00810.775-0.213-0.2130.0000.0000.0000.000
52A52MET0-0.0220.00712.9830.0130.0130.0000.0000.0000.000
53A53GLU-1-0.785-0.85914.7670.0370.0370.0000.0000.0000.000
54A54VAL0-0.002-0.00517.3390.0050.0050.0000.0000.0000.000
55A55VAL00.000-0.00317.780-0.027-0.0270.0000.0000.0000.000
56A56PRO0-0.021-0.01121.0280.0080.0080.0000.0000.0000.000
57A57ASP-1-0.838-0.89124.008-0.015-0.0150.0000.0000.0000.000
58A58ILE0-0.0160.00220.122-0.010-0.0100.0000.0000.0000.000
59A59SER0-0.016-0.02022.506-0.021-0.0210.0000.0000.0000.000
60A60LYS10.8880.94325.0000.0240.0240.0000.0000.0000.000
61A61LEU00.0290.00423.233-0.007-0.0070.0000.0000.0000.000
62A62ASP-1-0.862-0.92421.817-0.131-0.1310.0000.0000.0000.000
63A63ALA0-0.037-0.01121.132-0.005-0.0050.0000.0000.0000.000
64A64PHE00.023-0.01415.5370.0330.0330.0000.0000.0000.000
65A65ASP-1-0.779-0.87516.490-0.298-0.2980.0000.0000.0000.000
66A66HIS0-0.028-0.00417.921-0.004-0.0040.0000.0000.0000.000
67A67VAL00.0020.01412.5920.0090.0090.0000.0000.0000.000
68A68PHE00.050-0.0019.885-0.031-0.0310.0000.0000.0000.000
69A69GLN00.0030.02413.898-0.083-0.0830.0000.0000.0000.000
70A70LYS10.7700.87014.750-0.034-0.0340.0000.0000.0000.000
71A71HIS0-0.021-0.02310.3530.0190.0190.0000.0000.0000.000
72A72GLY00.0400.0399.952-0.232-0.2320.0000.0000.0000.000
73A73LYS10.9540.9869.8330.2720.2720.0000.0000.0000.000
74A74ASP-1-0.823-0.8775.135-1.030-0.974-0.001-0.008-0.0470.000
75A75ILE00.0010.0165.411-1.225-1.2250.0000.0000.0000.000
76A76LYS10.8470.9142.3343.4685.2672.039-0.890-2.948-0.004
77A77ILE0-0.0020.0092.612-1.011-0.4453.096-0.681-2.982-0.002
78A78VAL00.0020.0025.1700.2130.215-0.001-0.0050.0040.000
79A79LEU00.0050.0057.8810.0780.0780.0000.0000.0000.000
80A80HIS00.0070.00710.8930.0220.0220.0000.0000.0000.000
81A81THR0-0.014-0.02813.8430.0210.0210.0000.0000.0000.000
82A82ALA0-0.0280.00316.5120.0050.0050.0000.0000.0000.000
83A83SER0-0.022-0.03419.095-0.024-0.0240.0000.0000.0000.000
84A84PRO00.0090.01422.5120.0120.0120.0000.0000.0000.000
85A85PHE00.004-0.00425.6810.0160.0160.0000.0000.0000.000
86A86CYS0-0.067-0.03727.562-0.008-0.0080.0000.0000.0000.000
87A87PHE00.0220.01230.502-0.003-0.0030.0000.0000.0000.000
88A88ASP-1-0.762-0.86233.1790.0080.0080.0000.0000.0000.000
89A89ILE0-0.030-0.03236.195-0.002-0.0020.0000.0000.0000.000
90A90THR0-0.076-0.04138.696-0.002-0.0020.0000.0000.0000.000
91A91ASP-1-0.847-0.91838.824-0.028-0.0280.0000.0000.0000.000
92A92SER00.021-0.00136.2480.0000.0000.0000.0000.0000.000
93A93GLU-1-0.824-0.88634.779-0.049-0.0490.0000.0000.0000.000
94A94ARG10.7570.83833.9720.0110.0110.0000.0000.0000.000
95A95ASP-1-0.807-0.87833.401-0.014-0.0140.0000.0000.0000.000
96A96LEU0-0.044-0.02830.4220.0070.0070.0000.0000.0000.000
97A97LEU0-0.023-0.01830.043-0.002-0.0020.0000.0000.0000.000
98A98ILE00.0100.01129.309-0.008-0.0080.0000.0000.0000.000
99A99PRO0-0.013-0.00728.017-0.011-0.0110.0000.0000.0000.000
100A100ALA0-0.007-0.00325.355-0.004-0.0040.0000.0000.0000.000
101A101VAL0-0.0060.00324.187-0.011-0.0110.0000.0000.0000.000
102A102ASN0-0.004-0.00623.823-0.028-0.0280.0000.0000.0000.000
103A103GLY0-0.010-0.00322.261-0.019-0.0190.0000.0000.0000.000
104A104VAL0-0.032-0.00618.4770.0050.0050.0000.0000.0000.000
105A105LYS10.8360.89619.0070.1770.1770.0000.0000.0000.000
106A106GLY00.0210.01420.472-0.027-0.0270.0000.0000.0000.000
107A107ILE0-0.015-0.00713.463-0.031-0.0310.0000.0000.0000.000
108A108LEU0-0.0030.01014.458-0.072-0.0720.0000.0000.0000.000
109A109HIS00.0430.02516.436-0.082-0.0820.0000.0000.0000.000
110A110SER0-0.020-0.03216.422-0.019-0.0190.0000.0000.0000.000
111A111ILE0-0.055-0.02311.417-0.045-0.0450.0000.0000.0000.000
112A112LYS10.8730.92213.9770.3200.3200.0000.0000.0000.000
113A113LYS10.8160.91116.1650.2490.2490.0000.0000.0000.000
114A114TYR0-0.050-0.04215.3250.0500.0500.0000.0000.0000.000
115A115ALA0-0.018-0.01310.440-0.034-0.0340.0000.0000.0000.000
116A116ALA00.0180.02710.660-0.200-0.2000.0000.0000.0000.000
117A117ASP-1-0.883-0.93811.415-1.101-1.1010.0000.0000.0000.000
118A118SER0-0.029-0.0327.803-0.178-0.1780.0000.0000.0000.000
119A119VAL0-0.019-0.0116.085-0.902-0.9020.0000.0000.0000.000
120A120GLU-1-0.876-0.9383.015-8.886-7.2960.452-0.859-1.184-0.009
121A121ARG10.7710.8825.6411.1381.1380.0000.0000.0000.000
122A122VAL00.0150.0157.220-0.016-0.0160.0000.0000.0000.000
123A123VAL0-0.004-0.0019.6460.0660.0660.0000.0000.0000.000
124A124LEU0-0.0060.00812.1890.0210.0210.0000.0000.0000.000
125A125THR00.009-0.01215.7640.0210.0210.0000.0000.0000.000
126A126SER0-0.030-0.02918.196-0.011-0.0110.0000.0000.0000.000
127A127SER0-0.021-0.02721.4480.0220.0220.0000.0000.0000.000
128A128TYR00.004-0.02724.247-0.017-0.0170.0000.0000.0000.000
129A129ALA00.0350.01826.826-0.009-0.0090.0000.0000.0000.000
130A130ALA00.0280.01425.391-0.007-0.0070.0000.0000.0000.000
131A131VAL0-0.088-0.03925.609-0.011-0.0110.0000.0000.0000.000
132A132PHE0-0.0040.00928.431-0.004-0.0040.0000.0000.0000.000
133A133ASP-1-0.746-0.87931.947-0.016-0.0160.0000.0000.0000.000
134A134MET00.0140.01335.4140.0040.0040.0000.0000.0000.000
135A135ALA0-0.023-0.00736.6060.0040.0040.0000.0000.0000.000
136A136LYS10.8180.88638.5440.0120.0120.0000.0000.0000.000
137A137GLU-1-0.695-0.80033.9610.0350.0350.0000.0000.0000.000
138A138ASN00.003-0.00137.3410.0060.0060.0000.0000.0000.000
139A139ASP-1-0.848-0.90840.2380.0040.0040.0000.0000.0000.000
140A140LYS10.8820.93240.105-0.026-0.0260.0000.0000.0000.000
141A141SER0-0.101-0.05341.026-0.001-0.0010.0000.0000.0000.000
142A142LEU00.0080.01537.965-0.004-0.0040.0000.0000.0000.000
143A143THR0-0.051-0.05232.7620.0060.0060.0000.0000.0000.000
144A144PHE00.0120.02330.815-0.006-0.0060.0000.0000.0000.000
145A145ASN0-0.009-0.02427.5430.0080.0080.0000.0000.0000.000
146A146GLU-1-0.754-0.86422.2150.0050.0050.0000.0000.0000.000
147A147GLU-1-0.903-0.93224.490-0.078-0.0780.0000.0000.0000.000
148A148SER0-0.0180.00526.599-0.003-0.0030.0000.0000.0000.000
149A149TRP0-0.005-0.00423.4790.0040.0040.0000.0000.0000.000
150A150ASN00.0000.02229.520-0.002-0.0020.0000.0000.0000.000
151A151PRO00.0350.01531.796-0.009-0.0090.0000.0000.0000.000
152A152ALA0-0.0200.00434.696-0.005-0.0050.0000.0000.0000.000
153A153THR0-0.007-0.00734.074-0.004-0.0040.0000.0000.0000.000
154A154TRP0-0.007-0.01830.3360.0020.0020.0000.0000.0000.000
155A155GLU-1-0.772-0.86835.304-0.044-0.0440.0000.0000.0000.000
156A156SER0-0.039-0.04338.7960.0050.0050.0000.0000.0000.000
157A157CYS0-0.086-0.02435.0850.0040.0040.0000.0000.0000.000
158A158GLN0-0.042-0.05837.0770.0080.0080.0000.0000.0000.000
159A159SER0-0.036-0.01938.9670.0010.0010.0000.0000.0000.000
160A160ASP-1-0.793-0.86539.3030.0090.0090.0000.0000.0000.000
161A161PRO00.0420.00637.490-0.002-0.0020.0000.0000.0000.000
162A162VAL0-0.0170.01035.1920.0020.0020.0000.0000.0000.000
163A163ASN0-0.015-0.03834.506-0.001-0.0010.0000.0000.0000.000
164A164ALA00.0500.04834.417-0.005-0.0050.0000.0000.0000.000
165A165TYR00.0010.00527.199-0.004-0.0040.0000.0000.0000.000
166A166CYS0-0.051-0.03130.0830.0000.0000.0000.0000.0000.000
167A167GLY00.0430.02129.770-0.006-0.0060.0000.0000.0000.000
168A168SER0-0.062-0.04029.026-0.008-0.0080.0000.0000.0000.000
169A169LYS10.8720.93021.916-0.036-0.0360.0000.0000.0000.000
170A170LYS10.7950.88625.0610.0400.0400.0000.0000.0000.000
171A171PHE00.005-0.02125.963-0.015-0.0150.0000.0000.0000.000
172A172ALA00.0170.01723.057-0.017-0.0170.0000.0000.0000.000
173A173GLU-1-0.714-0.80120.489-0.082-0.0820.0000.0000.0000.000
174A174LYS10.7870.87821.3910.0960.0960.0000.0000.0000.000
175A175ALA00.0420.02423.084-0.021-0.0210.0000.0000.0000.000
176A176ALA0-0.003-0.00617.497-0.028-0.0280.0000.0000.0000.000
177A177TRP0-0.063-0.04416.649-0.056-0.0560.0000.0000.0000.000
178A178GLU-1-0.733-0.85120.206-0.168-0.1680.0000.0000.0000.000
179A179PHE0-0.0060.00516.556-0.016-0.0160.0000.0000.0000.000
180A180LEU00.0270.00714.379-0.019-0.0190.0000.0000.0000.000
181A181GLU-1-1.004-0.99517.989-0.253-0.2530.0000.0000.0000.000
182A182GLU-1-0.826-0.91221.411-0.234-0.2340.0000.0000.0000.000
183A183ASN0-0.028-0.00118.7180.0050.0050.0000.0000.0000.000
184A184ARG10.9500.98516.8280.3530.3530.0000.0000.0000.000
185A185ASP-1-0.907-0.94717.068-0.453-0.4530.0000.0000.0000.000
186A186SER0-0.139-0.08718.1290.0090.0090.0000.0000.0000.000
187A187VAL0-0.042-0.03313.423-0.013-0.0130.0000.0000.0000.000
188A188LYS10.7960.9156.5782.8812.8810.0000.0000.0000.000
189A189PHE0-0.056-0.0149.015-0.067-0.0670.0000.0000.0000.000
190A190GLU-1-0.846-0.9459.275-0.427-0.4270.0000.0000.0000.000
191A191LEU0-0.055-0.01810.325-0.014-0.0140.0000.0000.0000.000
192A192THR0-0.039-0.02912.5780.0150.0150.0000.0000.0000.000
193A193ALA00.0030.01614.2530.0120.0120.0000.0000.0000.000
194A194VAL0-0.002-0.00715.0040.0210.0210.0000.0000.0000.000
195A195ASN0-0.060-0.05818.091-0.009-0.0090.0000.0000.0000.000
196A196PRO0-0.025-0.00920.3950.0010.0010.0000.0000.0000.000
197A197VAL0-0.0160.01823.026-0.019-0.0190.0000.0000.0000.000
198A198TYR0-0.0130.00426.1950.0070.0070.0000.0000.0000.000
199A199VAL0-0.017-0.00722.2470.0070.0070.0000.0000.0000.000
200A200PHE00.0470.01925.543-0.002-0.0020.0000.0000.0000.000
201A201GLY00.0690.02825.0360.0190.0190.0000.0000.0000.000
202A202PRO0-0.0140.00823.761-0.011-0.0110.0000.0000.0000.000
203A203GLN00.014-0.02523.6290.0140.0140.0000.0000.0000.000
204A204MET0-0.0270.01017.4520.0010.0010.0000.0000.0000.000
205A205PHE00.0300.00718.420-0.001-0.0010.0000.0000.0000.000
206A206ASP-1-0.775-0.87823.8110.2130.2130.0000.0000.0000.000
207A207LYS10.8450.91523.256-0.305-0.3050.0000.0000.0000.000
208A208ASP-1-0.784-0.87723.8300.2520.2520.0000.0000.0000.000
209A209VAL00.0140.00627.362-0.015-0.0150.0000.0000.0000.000
210A210LYS10.8420.94330.137-0.145-0.1450.0000.0000.0000.000
211A211LYS10.9240.94730.075-0.144-0.1440.0000.0000.0000.000
212A212HIS00.0170.00825.999-0.004-0.0040.0000.0000.0000.000
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