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: MVZVZ

Calculation Name: 1PKQ-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1PKQ

Chain ID: A

ChEMBL ID:

UniProt ID: Q63345

Base Structure: X-ray

Registration Date: 2023-06-26

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 217
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2203002.252093
FMO2-HF: Nuclear repulsion 2119471.055911
FMO2-HF: Total energy -83531.196183
FMO2-MP2: Total energy -83775.583771


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:ASP)


Summations of interaction energy for fragment #1(A:1:ASP)
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.
7.50214.2722.94-3.795-5.9170.034
Interaction energy analysis for fragmet #1(A:1:ASP)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : -1 / q_Mulliken : -0.917 / q_NPA : -0.966
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].
3A3GLU-1-0.923-0.9433.77634.32136.774-0.018-1.107-1.3290.007
4A4LEU0-0.006-0.0325.641-3.325-3.3250.0000.0000.0000.000
5A5THR00.0090.0059.102-0.591-0.5910.0000.0000.0000.000
6A6GLN0-0.005-0.02312.2100.1430.1430.0000.0000.0000.000
7A7SER00.0020.01715.293-0.458-0.4580.0000.0000.0000.000
8A8PRO00.0580.00618.760-0.087-0.0870.0000.0000.0000.000
9A9SER00.0490.05019.0990.3170.3170.0000.0000.0000.000
10A10SER00.005-0.01420.1070.2250.2250.0000.0000.0000.000
11A11LEU0-0.062-0.01723.303-0.224-0.2240.0000.0000.0000.000
12A12ALA00.0380.02426.5120.0350.0350.0000.0000.0000.000
13A13VAL0-0.017-0.01029.513-0.132-0.1320.0000.0000.0000.000
14A14SER0-0.012-0.02632.209-0.078-0.0780.0000.0000.0000.000
15A15ALA0-0.023-0.01634.7540.1480.1480.0000.0000.0000.000
16A16GLY00.0280.01135.290-0.219-0.2190.0000.0000.0000.000
17A17GLU-1-0.812-0.87133.5208.7458.7450.0000.0000.0000.000
18A18LYS10.9781.00329.548-9.735-9.7350.0000.0000.0000.000
19A19VAL0-0.034-0.01526.0350.0120.0120.0000.0000.0000.000
20A20THR0-0.021-0.03123.865-0.052-0.0520.0000.0000.0000.000
21A21MET0-0.040-0.00420.1940.1480.1480.0000.0000.0000.000
22A22SER00.001-0.00518.1780.3390.3390.0000.0000.0000.000
23A23CYS0-0.042-0.01013.0940.3960.3960.0000.0000.0000.000
24A24LYS10.8060.90713.665-15.949-15.9490.0000.0000.0000.000
25A25SER00.014-0.0089.2121.8151.8150.0000.0000.0000.000
26A26SER00.0510.0305.816-1.044-1.0440.0000.0000.0000.000
27A27GLN00.0040.0063.550-5.599-4.8470.029-0.367-0.4150.003
28A28SER00.0070.0198.643-1.754-1.7540.0000.0000.0000.000
29A29LEU00.0520.0207.9981.4951.4950.0000.0000.0000.000
30A30LEU0-0.065-0.00911.230-1.375-1.3750.0000.0000.0000.000
31A30ASN00.0390.03013.854-0.044-0.0440.0000.0000.0000.000
32A30SER00.057-0.00615.350-0.528-0.5280.0000.0000.0000.000
33A30GLY00.0150.01818.159-0.764-0.7640.0000.0000.0000.000
34A30ASN0-0.063-0.02218.6010.0190.0190.0000.0000.0000.000
35A30GLN0-0.0020.00419.375-0.671-0.6710.0000.0000.0000.000
36A30LYS10.9830.98318.297-13.796-13.7960.0000.0000.0000.000
37A31ASN00.012-0.00514.459-0.036-0.0360.0000.0000.0000.000
38A32TYR0-0.027-0.03112.826-0.871-0.8710.0000.0000.0000.000
39A33LEU00.0070.01711.8971.6571.6570.0000.0000.0000.000
40A34ALA00.0170.01113.713-1.465-1.4650.0000.0000.0000.000
41A35TRP00.0340.00915.1620.8700.8700.0000.0000.0000.000
42A36TYR00.006-0.02614.908-1.361-1.3610.0000.0000.0000.000
43A37GLN0-0.006-0.00818.887-0.125-0.1250.0000.0000.0000.000
44A38GLN00.001-0.01219.5820.5550.5550.0000.0000.0000.000
45A39LYS10.8410.92722.179-10.839-10.8390.0000.0000.0000.000
46A40PRO00.0580.00025.0190.3170.3170.0000.0000.0000.000
47A41GLY00.0000.01025.743-0.402-0.4020.0000.0000.0000.000
48A42LEU0-0.0340.00825.436-0.045-0.0450.0000.0000.0000.000
49A43PRO00.0330.00321.7720.4020.4020.0000.0000.0000.000
50A44PRO00.0020.00117.860-0.483-0.4830.0000.0000.0000.000
51A45LYS10.8980.95620.700-11.726-11.7260.0000.0000.0000.000
52A46LEU00.0250.03218.3490.4240.4240.0000.0000.0000.000
53A47LEU0-0.065-0.03220.969-0.729-0.7290.0000.0000.0000.000
54A48ILE0-0.016-0.01619.764-0.612-0.6120.0000.0000.0000.000
55A49TYR00.0810.04017.8650.9160.9160.0000.0000.0000.000
56A50GLY00.000-0.00116.979-0.683-0.6830.0000.0000.0000.000
57A51ALA0-0.023-0.00916.647-0.543-0.5430.0000.0000.0000.000
58A52SER0-0.048-0.02718.101-0.330-0.3300.0000.0000.0000.000
59A53THR0-0.061-0.02921.784-0.614-0.6140.0000.0000.0000.000
60A54ARG10.8710.96022.726-10.054-10.0540.0000.0000.0000.000
61A55GLU-1-0.821-0.87723.52312.26312.2630.0000.0000.0000.000
62A56SER0-0.007-0.04225.379-0.552-0.5520.0000.0000.0000.000
63A57GLY0-0.044-0.01628.5440.1700.1700.0000.0000.0000.000
64A58VAL0-0.073-0.02825.557-0.235-0.2350.0000.0000.0000.000
65A59PRO00.012-0.00328.948-0.102-0.1020.0000.0000.0000.000
66A60ASP-1-0.854-0.94429.7789.4559.4550.0000.0000.0000.000
67A61ARG10.7290.84230.372-9.534-9.5340.0000.0000.0000.000
68A62PHE0-0.0210.00225.3040.2100.2100.0000.0000.0000.000
69A63THR0-0.028-0.02025.929-0.151-0.1510.0000.0000.0000.000
70A64GLY00.0400.01221.7340.1430.1430.0000.0000.0000.000
71A65SER0-0.0240.00022.186-0.212-0.2120.0000.0000.0000.000
72A66GLY00.0590.01219.3830.4960.4960.0000.0000.0000.000
73A67SER0-0.027-0.01817.525-0.327-0.3270.0000.0000.0000.000
74A68GLY0-0.0140.01116.342-0.197-0.1970.0000.0000.0000.000
75A69THR00.000-0.01811.7940.6780.6780.0000.0000.0000.000
76A70ASP-1-0.847-0.89813.82517.46317.4630.0000.0000.0000.000
77A71PHE00.007-0.00113.453-0.774-0.7740.0000.0000.0000.000
78A72THR0-0.012-0.01717.923-0.001-0.0010.0000.0000.0000.000
79A73LEU0-0.0310.00920.426-0.282-0.2820.0000.0000.0000.000
80A74THR0-0.037-0.03422.035-0.153-0.1530.0000.0000.0000.000
81A75ILE0-0.0080.00525.756-0.077-0.0770.0000.0000.0000.000
82A76SER0-0.018-0.02228.328-0.193-0.1930.0000.0000.0000.000
83A77SER0-0.014-0.01431.730-0.210-0.2100.0000.0000.0000.000
84A78VAL00.008-0.00229.6540.0240.0240.0000.0000.0000.000
85A79GLN0-0.0080.00831.840-0.579-0.5790.0000.0000.0000.000
86A80ALA00.0580.03532.3750.2310.2310.0000.0000.0000.000
87A81GLU-1-0.803-0.90331.8979.3879.3870.0000.0000.0000.000
88A82ASP-1-0.794-0.87328.47510.55210.5520.0000.0000.0000.000
89A83LEU0-0.0060.03627.4850.4820.4820.0000.0000.0000.000
90A84ALA0-0.061-0.04024.277-0.041-0.0410.0000.0000.0000.000
91A85VAL00.0050.00918.881-0.110-0.1100.0000.0000.0000.000
92A86TYR0-0.003-0.02119.5760.0660.0660.0000.0000.0000.000
93A87TYR00.0390.04614.3070.2950.2950.0000.0000.0000.000
94A89GLN0-0.007-0.03110.329-0.457-0.4570.0000.0000.0000.000
95A90ASN00.0540.0245.221-5.557-5.5570.0000.0000.0000.000
96A91ASP-1-0.898-0.9508.88723.18923.1890.0000.0000.0000.000
97A92HIS0-0.028-0.0049.080-0.347-0.3470.0000.0000.0000.000
98A93SER0-0.015-0.0045.385-1.150-1.1500.0000.0000.0000.000
99A94TYR0-0.068-0.0135.7101.2931.2930.0000.0000.0000.000
100A95PRO00.0210.0152.471-7.528-4.4652.922-2.261-3.7250.024
101A96LEU00.022-0.0034.4602.1532.281-0.001-0.011-0.1150.000
102A97THR00.002-0.0113.4700.6230.9970.008-0.049-0.3330.000
103A98PHE0-0.010-0.0106.777-3.205-3.2050.0000.0000.0000.000
104A99GLY00.0220.0168.9391.5181.5180.0000.0000.0000.000
105A100ALA0-0.039-0.02711.099-0.261-0.2610.0000.0000.0000.000
106A101GLY0-0.008-0.00513.283-0.937-0.9370.0000.0000.0000.000
107A102THR0-0.060-0.03216.2390.0210.0210.0000.0000.0000.000
108A103LYS10.7500.85919.536-11.636-11.6360.0000.0000.0000.000
109A104LEU0-0.020-0.01222.574-0.204-0.2040.0000.0000.0000.000
110A105GLU-1-0.778-0.88525.72510.82610.8260.0000.0000.0000.000
111A106ILE0-0.029-0.01629.029-0.065-0.0650.0000.0000.0000.000
112A107LYS10.8300.93632.369-8.966-8.9660.0000.0000.0000.000
113A108ARG10.8590.91635.047-7.722-7.7220.0000.0000.0000.000
114A109THR0-0.0070.00238.735-0.009-0.0090.0000.0000.0000.000
115A110VAL0-0.010-0.00341.6530.1120.1120.0000.0000.0000.000
116A111ALA0-0.013-0.00842.998-0.122-0.1220.0000.0000.0000.000
117A112ALA00.0200.01144.1350.1370.1370.0000.0000.0000.000
118A113PRO0-0.0070.00344.076-0.030-0.0300.0000.0000.0000.000
119A114SER0-0.0020.02246.018-0.221-0.2210.0000.0000.0000.000
120A115VAL0-0.019-0.01047.3120.0940.0940.0000.0000.0000.000
121A116PHE0-0.0020.00147.605-0.203-0.2030.0000.0000.0000.000
122A117ILE0-0.0180.00748.6110.1300.1300.0000.0000.0000.000
123A118PHE0-0.014-0.00947.357-0.090-0.0900.0000.0000.0000.000
124A119PRO00.0100.00550.7160.0750.0750.0000.0000.0000.000
125A120PRO0-0.019-0.00650.8170.0460.0460.0000.0000.0000.000
126A121SER00.0180.02050.613-0.087-0.0870.0000.0000.0000.000
127A122ASP-1-0.832-0.93252.6105.5895.5890.0000.0000.0000.000
128A123GLU-1-0.891-0.95051.8085.8255.8250.0000.0000.0000.000
129A124GLN00.0250.00446.880-0.051-0.0510.0000.0000.0000.000
130A125LEU00.0530.03651.0100.0090.0090.0000.0000.0000.000
131A126LYS10.7420.86453.929-5.754-5.7540.0000.0000.0000.000
132A127SER0-0.003-0.00550.217-0.031-0.0310.0000.0000.0000.000
133A128GLY0-0.0170.00450.6940.1170.1170.0000.0000.0000.000
134A129THR0-0.033-0.01847.194-0.010-0.0100.0000.0000.0000.000
135A130ALA0-0.001-0.00649.811-0.068-0.0680.0000.0000.0000.000
136A131SER00.0120.02745.7010.1070.1070.0000.0000.0000.000
137A132VAL0-0.035-0.01247.873-0.100-0.1000.0000.0000.0000.000
138A133VAL00.0230.01944.3150.1490.1490.0000.0000.0000.000
139A134CYS0-0.0450.00545.936-0.117-0.1170.0000.0000.0000.000
140A135LEU0-0.009-0.01742.5700.1660.1660.0000.0000.0000.000
141A136LEU0-0.034-0.01442.638-0.188-0.1880.0000.0000.0000.000
142A137ASN0-0.011-0.03342.4180.2440.2440.0000.0000.0000.000
143A138ASN00.011-0.01641.024-0.139-0.1390.0000.0000.0000.000
144A139PHE0-0.030-0.01339.618-0.145-0.1450.0000.0000.0000.000
145A140TYR00.1030.03535.2330.2130.2130.0000.0000.0000.000
146A141PRO0-0.015-0.02137.800-0.238-0.2380.0000.0000.0000.000
147A142ARG11.0241.02432.370-9.424-9.4240.0000.0000.0000.000
148A143GLU-1-0.931-0.97435.5328.5868.5860.0000.0000.0000.000
149A144ALA00.012-0.00438.572-0.217-0.2170.0000.0000.0000.000
150A145LYS10.9250.97941.400-6.807-6.8070.0000.0000.0000.000
151A146VAL00.0490.01543.024-0.149-0.1490.0000.0000.0000.000
152A147GLN0-0.015-0.00345.0830.1130.1130.0000.0000.0000.000
153A148TRP00.0340.02045.578-0.233-0.2330.0000.0000.0000.000
154A149LYS10.7970.87549.827-5.829-5.8290.0000.0000.0000.000
155A150VAL00.0080.00553.022-0.032-0.0320.0000.0000.0000.000
156A151ASP-1-0.786-0.88255.6405.2845.2840.0000.0000.0000.000
157A152ASN0-0.063-0.04457.3540.0020.0020.0000.0000.0000.000
158A153ALA00.0200.01756.0690.0000.0000.0000.0000.0000.000
159A154LEU0-0.0030.00451.2500.0840.0840.0000.0000.0000.000
160A155GLN0-0.0120.00549.097-0.005-0.0050.0000.0000.0000.000
161A156SER0-0.007-0.02546.3330.0660.0660.0000.0000.0000.000
162A157GLY0-0.0190.00142.995-0.037-0.0370.0000.0000.0000.000
163A158ASN00.0160.00043.9910.0950.0950.0000.0000.0000.000
164A159SER00.0370.01243.832-0.140-0.1400.0000.0000.0000.000
165A160GLN0-0.058-0.00637.1770.0960.0960.0000.0000.0000.000
166A161GLU-1-0.816-0.91938.2767.6357.6350.0000.0000.0000.000
167A162SER0-0.042-0.00335.0520.3450.3450.0000.0000.0000.000
168A163VAL0-0.019-0.03033.795-0.236-0.2360.0000.0000.0000.000
169A164THR00.0090.02333.2510.1570.1570.0000.0000.0000.000
170A165GLU-1-0.842-0.91027.65210.82010.8200.0000.0000.0000.000
171A166GLN0-0.040-0.06131.254-0.014-0.0140.0000.0000.0000.000
172A167ASP-1-0.777-0.88332.7718.6178.6170.0000.0000.0000.000
173A168SER0-0.104-0.05232.8330.0650.0650.0000.0000.0000.000
174A169LYS10.9310.95034.164-8.158-8.1580.0000.0000.0000.000
175A170ASP-1-0.779-0.85937.6837.7097.7090.0000.0000.0000.000
176A171SER0-0.017-0.00934.860-0.126-0.1260.0000.0000.0000.000
177A172THR0-0.109-0.06336.2850.0340.0340.0000.0000.0000.000
178A173TYR00.002-0.00732.2960.1970.1970.0000.0000.0000.000
179A174SER00.0690.05137.461-0.362-0.3620.0000.0000.0000.000
180A175LEU0-0.0570.00037.9630.2140.2140.0000.0000.0000.000
181A176SER00.0130.00039.295-0.184-0.1840.0000.0000.0000.000
182A177SER00.002-0.00640.4190.1420.1420.0000.0000.0000.000
183A178THR0-0.005-0.01141.626-0.234-0.2340.0000.0000.0000.000
184A179LEU0-0.028-0.01743.6790.0950.0950.0000.0000.0000.000
185A180THR0-0.0070.00044.299-0.078-0.0780.0000.0000.0000.000
186A181LEU0-0.021-0.01446.723-0.052-0.0520.0000.0000.0000.000
187A182SER00.0690.04949.7860.0290.0290.0000.0000.0000.000
188A183LYS10.9580.97252.018-5.561-5.5610.0000.0000.0000.000
189A184ALA0-0.019-0.01454.832-0.095-0.0950.0000.0000.0000.000
190A185ASP-1-0.803-0.92353.8475.6795.6790.0000.0000.0000.000
191A186TYR00.0060.02754.023-0.048-0.0480.0000.0000.0000.000
192A187GLU-1-0.826-0.95255.7525.4105.4100.0000.0000.0000.000
193A188LYS10.7690.90357.212-5.702-5.7020.0000.0000.0000.000
194A189HIS10.8620.92856.590-5.631-5.6310.0000.0000.0000.000
195A190LYS10.8870.93359.980-5.035-5.0350.0000.0000.0000.000
196A191VAL00.0070.00258.4480.0200.0200.0000.0000.0000.000
197A192TYR00.0050.00853.4510.0930.0930.0000.0000.0000.000
198A193ALA00.034-0.00453.678-0.048-0.0480.0000.0000.0000.000
199A195GLU-1-0.789-0.88150.2065.8025.8020.0000.0000.0000.000
200A196VAL00.0240.01445.9080.1530.1530.0000.0000.0000.000
201A197THR0-0.057-0.03246.552-0.165-0.1650.0000.0000.0000.000
202A198HIS00.0570.01641.715-0.022-0.0220.0000.0000.0000.000
203A199GLN00.0520.02242.549-0.003-0.0030.0000.0000.0000.000
204A200GLY0-0.002-0.01345.752-0.087-0.0870.0000.0000.0000.000
205A201LEU0-0.081-0.03347.467-0.124-0.1240.0000.0000.0000.000
206A202SER00.0010.00150.184-0.002-0.0020.0000.0000.0000.000
207A203SER00.0210.00453.119-0.056-0.0560.0000.0000.0000.000
208A204PRO0-0.046-0.01851.2700.0420.0420.0000.0000.0000.000
209A205VAL00.0340.03450.998-0.127-0.1270.0000.0000.0000.000
210A206THR0-0.021-0.03351.8500.1000.1000.0000.0000.0000.000
211A207LYS10.8690.93852.151-6.098-6.0980.0000.0000.0000.000
212A208SER0-0.028-0.02553.5140.0860.0860.0000.0000.0000.000
213A209PHE00.0400.02553.359-0.018-0.0180.0000.0000.0000.000
214A210ASN0-0.063-0.04558.237-0.017-0.0170.0000.0000.0000.000
215A211ARG10.8700.95358.447-5.291-5.2910.0000.0000.0000.000
216A212GLY0-0.042-0.00959.571-0.086-0.0860.0000.0000.0000.000
217A213GLU-1-0.832-0.90459.8505.1265.1260.0000.0000.0000.000