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: 4JZGN

Calculation Name: 3PKV-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3PKV

Chain ID: A

ChEMBL ID:

UniProt ID: E3SET7

Base Structure: X-ray

Registration Date: 2023-09-23

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 221
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2699627.948859
FMO2-HF: Nuclear repulsion 2614446.241585
FMO2-HF: Total energy -85181.707275
FMO2-MP2: Total energy -85433.725116


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:2:THR)


Summations of interaction energy for fragment #1(A:2:THR)
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.
-34.527-36.13925.531-12.744-11.173-0.056
Interaction energy analysis for fragmet #1(A:2:THR)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.068 / q_NPA : -0.045
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].
3A4ILE00.0330.0053.706-0.4732.162-0.012-1.421-1.2020.005
4A5LYS10.8090.9066.0780.0760.0760.0000.0000.0000.000
5A6GLN0-0.041-0.0347.5670.1210.1210.0000.0000.0000.000
6A7LEU00.0140.00810.0490.1750.1750.0000.0000.0000.000
7A8THR0-0.019-0.00912.634-0.057-0.0570.0000.0000.0000.000
8A9LEU00.0110.01515.1530.0510.0510.0000.0000.0000.000
9A10TYR0-0.003-0.01118.441-0.003-0.0030.0000.0000.0000.000
10A11THR00.034-0.01322.200-0.008-0.0080.0000.0000.0000.000
11A12ALA0-0.017-0.00425.1410.0090.0090.0000.0000.0000.000
12A13GLU-1-0.803-0.87627.876-0.082-0.0820.0000.0000.0000.000
13A14LEU00.0180.00925.431-0.012-0.0120.0000.0000.0000.000
14A15ASP-1-0.872-0.92528.395-0.106-0.1060.0000.0000.0000.000
15A16ARG10.8090.87430.4650.1050.1050.0000.0000.0000.000
16A17MET0-0.0400.03922.606-0.012-0.0120.0000.0000.0000.000
17A18LEU00.0390.03326.294-0.021-0.0210.0000.0000.0000.000
18A19ALA0-0.0080.00527.328-0.015-0.0150.0000.0000.0000.000
19A20PHE00.0190.00023.982-0.007-0.0070.0000.0000.0000.000
20A21TYR00.032-0.03120.764-0.025-0.0250.0000.0000.0000.000
21A22THR0-0.043-0.03324.907-0.022-0.0220.0000.0000.0000.000
22A23ASN0-0.104-0.05126.9500.0000.0000.0000.0000.0000.000
23A24MET0-0.0010.01323.330-0.016-0.0160.0000.0000.0000.000
24A25LEU0-0.023-0.02420.297-0.021-0.0210.0000.0000.0000.000
25A26GLY00.0240.02224.035-0.009-0.0090.0000.0000.0000.000
26A27ALA00.008-0.02424.887-0.014-0.0140.0000.0000.0000.000
27A28GLN0-0.072-0.02623.3860.0300.0300.0000.0000.0000.000
28A29HIS0-0.082-0.03820.173-0.038-0.0380.0000.0000.0000.000
29A30VAL0-0.011-0.00820.527-0.024-0.0240.0000.0000.0000.000
30A31HIS0-0.0190.00522.0090.0110.0110.0000.0000.0000.000
31A32GLU-1-0.907-0.95423.347-0.129-0.1290.0000.0000.0000.000
32A33GLN0-0.083-0.05421.929-0.012-0.0120.0000.0000.0000.000
33A34ALA0-0.007-0.00826.7380.0010.0010.0000.0000.0000.000
34A35ASP-1-0.816-0.89225.121-0.055-0.0550.0000.0000.0000.000
35A36ALA0-0.013-0.01422.6720.0070.0070.0000.0000.0000.000
36A37PHE0-0.0060.00922.9360.0010.0010.0000.0000.0000.000
37A38THR0-0.031-0.01618.492-0.004-0.0040.0000.0000.0000.000
38A39ILE00.0280.01217.5560.0110.0110.0000.0000.0000.000
39A40GLN0-0.014-0.00512.8730.0730.0730.0000.0000.0000.000
40A41LEU0-0.006-0.01814.1600.0560.0560.0000.0000.0000.000
41A42GLY00.0640.04713.172-0.156-0.1560.0000.0000.0000.000
42A43VAL0-0.059-0.0447.5540.1710.1710.0000.0000.0000.000
43A44SER0-0.023-0.0058.659-0.065-0.0650.0000.0000.0000.000
44A45GLN0-0.055-0.01510.6560.2120.2120.0000.0000.0000.000
45A46ILE00.0150.00112.7170.0200.0200.0000.0000.0000.000
46A47GLN00.0080.01215.4860.0390.0390.0000.0000.0000.000
47A48PHE00.0260.00918.1660.0230.0230.0000.0000.0000.000
48A49ARG10.8160.87820.5050.0450.0450.0000.0000.0000.000
49A50ALA00.0480.01823.466-0.003-0.0030.0000.0000.0000.000
50A51ALA0-0.038-0.01425.7970.0130.0130.0000.0000.0000.000
51A52ALA00.0010.00926.7280.0020.0020.0000.0000.0000.000
52A53ASP-1-0.862-0.93029.405-0.028-0.0280.0000.0000.0000.000
53A54GLY0-0.065-0.03432.4800.0060.0060.0000.0000.0000.000
54A55THR0-0.086-0.04627.9120.0000.0000.0000.0000.0000.000
55A56LYS10.8760.90428.0200.0600.0600.0000.0000.0000.000
56A57PRO0-0.016-0.00522.658-0.003-0.0030.0000.0000.0000.000
57A58PHE0-0.048-0.01722.109-0.007-0.0070.0000.0000.0000.000
58A59TYR0-0.018-0.02716.8060.0210.0210.0000.0000.0000.000
59A60HIS0-0.0280.00114.7450.0330.0330.0000.0000.0000.000
60A61ILE00.007-0.01914.309-0.010-0.0100.0000.0000.0000.000
61A62ALA00.0280.03813.5550.0150.0150.0000.0000.0000.000
62A63ILE0-0.011-0.01413.013-0.139-0.1390.0000.0000.0000.000
63A64ASN0-0.041-0.0239.6130.3330.3330.0000.0000.0000.000
64A65ILE00.0050.00213.4690.0230.0230.0000.0000.0000.000
65A66ALA00.0250.00815.397-0.043-0.0430.0000.0000.0000.000
66A67ALA0-0.0060.01516.6640.0520.0520.0000.0000.0000.000
67A68ASN00.013-0.00517.9980.0090.0090.0000.0000.0000.000
68A69HIS0-0.001-0.01019.629-0.014-0.0140.0000.0000.0000.000
69A70PHE0-0.0130.01020.7900.0200.0200.0000.0000.0000.000
70A71GLN00.033-0.00322.1200.0120.0120.0000.0000.0000.000
71A72GLU-1-0.864-0.92924.423-0.321-0.3210.0000.0000.0000.000
72A73GLY00.0270.01322.2590.0080.0080.0000.0000.0000.000
73A74LYS10.8250.88023.2510.2400.2400.0000.0000.0000.000
74A75ALA0-0.020-0.00625.4870.0170.0170.0000.0000.0000.000
75A76TRP0-0.021-0.01022.0090.0060.0060.0000.0000.0000.000
76A77LEU00.0100.00422.6440.0090.0090.0000.0000.0000.000
77A78SER0-0.036-0.03025.9870.0190.0190.0000.0000.0000.000
78A79GLY0-0.042-0.01029.3000.0180.0180.0000.0000.0000.000
79A80PHE0-0.054-0.03226.8220.0110.0110.0000.0000.0000.000
80A81GLY0-0.025-0.02229.5480.0090.0090.0000.0000.0000.000
81A82GLU-1-0.932-0.95430.039-0.165-0.1650.0000.0000.0000.000
82A83LEU0-0.044-0.01726.950-0.010-0.0100.0000.0000.0000.000
83A84LEU0-0.035-0.00724.8700.0140.0140.0000.0000.0000.000
84A85THR0-0.020-0.02227.901-0.011-0.0110.0000.0000.0000.000
85A86GLU-1-0.774-0.86126.576-0.126-0.1260.0000.0000.0000.000
86A87ASN0-0.101-0.06429.0080.0040.0040.0000.0000.0000.000
87A88ASP-1-0.945-0.96732.023-0.108-0.1080.0000.0000.0000.000
88A89GLU-1-0.942-0.94629.255-0.163-0.1630.0000.0000.0000.000
89A90ASP-1-0.803-0.90429.229-0.206-0.2060.0000.0000.0000.000
90A91GLN00.0090.00525.434-0.036-0.0360.0000.0000.0000.000
91A92ALA00.0240.01522.4540.0220.0220.0000.0000.0000.000
92A93TYR0-0.036-0.04620.954-0.009-0.0090.0000.0000.0000.000
93A94PHE00.0030.00918.0710.0440.0440.0000.0000.0000.000
94A95PRO00.0200.00018.514-0.035-0.0350.0000.0000.0000.000
95A96PHE0-0.079-0.03213.8370.0030.0030.0000.0000.0000.000
96A97PHE00.0330.01612.211-0.030-0.0300.0000.0000.0000.000
97A98ASN0-0.050-0.01715.014-0.048-0.0480.0000.0000.0000.000
98A99ALA00.0240.02315.642-0.038-0.0380.0000.0000.0000.000
99A100TYR0-0.0450.00217.7470.0660.0660.0000.0000.0000.000
100A101SER0-0.004-0.02618.123-0.068-0.0680.0000.0000.0000.000
101A102CYS0-0.061-0.01820.5540.0480.0480.0000.0000.0000.000
102A103TYR00.010-0.02119.075-0.026-0.0260.0000.0000.0000.000
103A104VAL00.0410.02923.3530.0200.0200.0000.0000.0000.000
104A105GLU-1-0.840-0.90323.734-0.159-0.1590.0000.0000.0000.000
105A106ASP-1-0.736-0.82422.659-0.206-0.2060.0000.0000.0000.000
106A107PRO0-0.015-0.02325.5060.0200.0200.0000.0000.0000.000
107A108SER0-0.022-0.03424.3390.0230.0230.0000.0000.0000.000
108A109GLY0-0.0040.00126.1500.0170.0170.0000.0000.0000.000
109A110ASN0-0.080-0.05820.4160.0220.0220.0000.0000.0000.000
110A111ILE00.0430.02320.323-0.005-0.0050.0000.0000.0000.000
111A112ILE0-0.033-0.00719.203-0.031-0.0310.0000.0000.0000.000
112A113GLU-1-0.727-0.84617.494-0.436-0.4360.0000.0000.0000.000
113A114LEU0-0.053-0.01317.625-0.068-0.0680.0000.0000.0000.000
114A115ILE00.0210.00114.0370.0480.0480.0000.0000.0000.000
115A116SER0-0.036-0.02815.667-0.079-0.0790.0000.0000.0000.000
116A117ARG10.8760.92210.2831.2361.2360.0000.0000.0000.000
117A118GLN0-0.065-0.04814.771-0.003-0.0030.0000.0000.0000.000
118A119GLN0-0.068-0.03415.3220.0550.0550.0000.0000.0000.000
119A120ALA0-0.025-0.00510.1980.0320.0320.0000.0000.0000.000
120A121ALA00.0650.04310.462-0.261-0.2610.0000.0000.0000.000
121A122PRO0-0.032-0.00411.7150.1330.1330.0000.0000.0000.000
122A123VAL00.0150.00814.3720.0310.0310.0000.0000.0000.000
123A124LEU0-0.062-0.04415.906-0.003-0.0030.0000.0000.0000.000
124A125ASP-1-0.934-0.95419.613-0.267-0.2670.0000.0000.0000.000
125A126LYS10.8730.92218.5650.5400.5400.0000.0000.0000.000
126A127PRO0-0.0010.00523.675-0.019-0.0190.0000.0000.0000.000
127A128PHE00.0200.01719.249-0.018-0.0180.0000.0000.0000.000
128A129SER0-0.048-0.05922.3330.0270.0270.0000.0000.0000.000
129A130ALA00.0850.04921.485-0.041-0.0410.0000.0000.0000.000
130A131ASP-1-0.826-0.87719.777-0.436-0.4360.0000.0000.0000.000
131A132GLN0-0.078-0.02818.189-0.058-0.0580.0000.0000.0000.000
132A133LEU0-0.0090.00716.372-0.049-0.0490.0000.0000.0000.000
133A134LEU0-0.051-0.02411.753-0.019-0.0190.0000.0000.0000.000
134A135SER00.023-0.0058.4520.0110.0110.0000.0000.0000.000
135A136ILE0-0.0060.0009.6920.2370.2370.0000.0000.0000.000
136A137GLY00.0230.0088.643-0.348-0.3480.0000.0000.0000.000
137A138GLU-1-0.861-0.9469.334-0.670-0.6700.0000.0000.0000.000
138A139ILE00.0190.0139.3420.0490.0490.0000.0000.0000.000
139A140ASN00.0030.01111.8370.0190.0190.0000.0000.0000.000
140A141ILE0-0.012-0.01410.4840.0420.0420.0000.0000.0000.000
141A142THR00.0060.00614.1090.0090.0090.0000.0000.0000.000
142A143THR0-0.023-0.02316.9330.0200.0200.0000.0000.0000.000
143A144SER0-0.037-0.05318.975-0.015-0.0150.0000.0000.0000.000
144A145ASP-1-0.895-0.94220.0890.2100.2100.0000.0000.0000.000
145A146VAL00.0190.00917.1080.0360.0360.0000.0000.0000.000
146A147GLU-1-0.908-0.94216.7480.2440.2440.0000.0000.0000.000
147A148GLN0-0.039-0.03017.1600.0760.0760.0000.0000.0000.000
148A149ALA00.0190.01014.4940.0670.0670.0000.0000.0000.000
149A150ALA00.0490.01712.5790.0990.0990.0000.0000.0000.000
150A151THR0-0.053-0.04012.3200.1000.1000.0000.0000.0000.000
151A152ARG10.7790.86613.069-0.305-0.3050.0000.0000.0000.000
152A153LEU00.0200.0107.8280.1450.1450.0000.0000.0000.000
153A154LYS10.8690.9368.187-0.472-0.4720.0000.0000.0000.000
154A155GLN0-0.066-0.04810.2100.0760.0760.0000.0000.0000.000
155A156ALA0-0.0260.0047.758-0.038-0.0380.0000.0000.0000.000
156A157GLU-1-0.961-0.9846.2852.3202.3200.0000.0000.0000.000
157A158LEU0-0.0030.0143.6800.0150.2770.002-0.033-0.2310.000
158A159PRO0-0.034-0.0164.579-0.334-0.249-0.001-0.005-0.0780.000
159A160VAL00.0210.0137.507-0.242-0.2420.0000.0000.0000.000
160A161LYS10.8820.94610.842-0.110-0.1100.0000.0000.0000.000
161A162LEU00.0450.01514.399-0.037-0.0370.0000.0000.0000.000
162A163ASP-1-0.889-0.94116.7390.2220.2220.0000.0000.0000.000
163A164GLN0-0.077-0.05816.851-0.051-0.0510.0000.0000.0000.000
164A165ILE0-0.0200.01114.085-0.018-0.0180.0000.0000.0000.000
165A166GLU-1-0.876-0.94918.1370.0630.0630.0000.0000.0000.000
166A167PRO00.001-0.00720.372-0.012-0.0120.0000.0000.0000.000
167A168ALA0-0.0090.00421.726-0.005-0.0050.0000.0000.0000.000
168A169GLY0-0.049-0.03821.451-0.020-0.0200.0000.0000.0000.000
169A170LEU0-0.035-0.01516.3860.0170.0170.0000.0000.0000.000
170A171ASN0-0.035-0.02114.864-0.002-0.0020.0000.0000.0000.000
171A172PHE00.0160.00912.1180.0150.0150.0000.0000.0000.000
172A173ILE0-0.036-0.0137.5070.0660.0660.0000.0000.0000.000
173A174GLY00.016-0.0045.520-0.017-0.0170.0000.0000.0000.000
174A175ASP-1-0.872-0.9495.0500.0930.0930.0000.0000.0000.000
175A176GLN0-0.104-0.0495.606-1.263-1.2630.0000.0000.0000.000
176A177ASP-1-0.818-0.8995.670-3.621-3.6210.0000.0000.0000.000
177A178LEU00.0130.0372.8210.0960.6040.104-0.152-0.4600.000
178A179PHE0-0.045-0.0276.4390.2130.2130.0000.0000.0000.000
179A180LEU00.0230.0126.3910.0870.0870.0000.0000.0000.000
180A181LEU0-0.004-0.0019.1420.0520.0520.0000.0000.0000.000
181A182LEU0-0.0120.01112.5310.0280.0280.0000.0000.0000.000
182A183GLY00.0430.01114.229-0.016-0.0160.0000.0000.0000.000
183A184PRO00.0040.02718.0870.0110.0110.0000.0000.0000.000
184A185PRO0-0.004-0.00921.494-0.021-0.0210.0000.0000.0000.000
185A186GLY0-0.047-0.02423.6080.0050.0050.0000.0000.0000.000
186A187ARG10.9100.95123.7190.0240.0240.0000.0000.0000.000
187A188ARG10.7780.86624.8540.1100.1100.0000.0000.0000.000
188A189TRP00.0300.01116.613-0.001-0.0010.0000.0000.0000.000
189A190LEU0-0.027-0.01722.2010.0060.0060.0000.0000.0000.000
190A191PHE0-0.021-0.01223.337-0.017-0.0170.0000.0000.0000.000
191A192SER00.0350.00625.1380.0060.0060.0000.0000.0000.000
192A193GLU-1-0.933-0.96926.818-0.081-0.0810.0000.0000.0000.000
193A194ARG10.8310.94025.4890.1120.1120.0000.0000.0000.000
194A195VAL0-0.002-0.00825.683-0.006-0.0060.0000.0000.0000.000
195A196ALA00.0090.00821.579-0.002-0.0020.0000.0000.0000.000
196A197VAL0-0.034-0.02322.6910.0160.0160.0000.0000.0000.000
197A198ILE00.0000.01421.214-0.006-0.0060.0000.0000.0000.000
198A199TYR00.0210.00820.611-0.010-0.0100.0000.0000.0000.000
199A200PRO0-0.0140.01719.4670.0100.0100.0000.0000.0000.000
200A201LEU0-0.0050.00513.411-0.037-0.0370.0000.0000.0000.000
201A202GLN0-0.027-0.02314.1720.0210.0210.0000.0000.0000.000
202A203MET00.0200.0206.512-0.239-0.2390.0000.0000.0000.000
203A204GLU-1-0.776-0.8647.6380.0340.0340.0000.0000.0000.000
204A205LEU00.0260.0212.584-3.952-1.9811.415-1.085-2.3010.011
205A206ASP-1-0.784-0.8571.586-24.842-34.75623.393-8.594-4.884-0.077
206A207ASN0-0.009-0.0032.342-1.9080.8270.628-1.411-1.9510.005
207A208GLY0-0.018-0.0034.0310.0020.1080.002-0.043-0.0660.000
208A209VAL0-0.031-0.0095.548-0.514-0.5140.0000.0000.0000.000
209A210SER0-0.0140.0066.9470.0140.0140.0000.0000.0000.000
210A211LEU0-0.017-0.0078.4160.0200.0200.0000.0000.0000.000
211A212ALA0-0.001-0.00111.854-0.106-0.1060.0000.0000.0000.000
212A213ILE00.0010.01714.5350.0500.0500.0000.0000.0000.000
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