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: 6N61Z

Calculation Name: 3QKS-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3QKS

Chain ID: A

ChEMBL ID:

UniProt ID: Q8U1N9

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 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 199
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2086520.421666
FMO2-HF: Nuclear repulsion 2007144.251261
FMO2-HF: Total energy -79376.170405
FMO2-MP2: Total energy -79612.035533


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.
-17.636-10.66117.893-7.143-17.726-0.032
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 : -0.015 / q_NPA : 0.004
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].
3A3LEU00.015-0.0032.547-0.9731.5000.591-1.053-2.0120.003
4A4GLU-1-0.826-0.8904.918-1.675-1.588-0.001-0.009-0.0770.000
5A5ARG10.8350.8808.0921.0521.0520.0000.0000.0000.000
6A6VAL00.0000.0198.381-0.113-0.1130.0000.0000.0000.000
7A7THR0-0.023-0.02310.1180.0980.0980.0000.0000.0000.000
8A8VAL0-0.013-0.00512.6220.0130.0130.0000.0000.0000.000
9A9LYS10.8090.88715.1270.3140.3140.0000.0000.0000.000
10A10ASN00.0100.00718.7640.0190.0190.0000.0000.0000.000
11A11PHE00.0050.01515.3470.0180.0180.0000.0000.0000.000
12A12ARG10.7820.83616.7940.0060.0060.0000.0000.0000.000
13A13SER00.0780.04219.8550.0060.0060.0000.0000.0000.000
14A14HIS0-0.0330.01016.406-0.017-0.0170.0000.0000.0000.000
15A15SER00.0470.01919.8940.0020.0020.0000.0000.0000.000
16A16ASP-1-0.819-0.91319.612-0.291-0.2910.0000.0000.0000.000
17A17THR00.0090.00815.6870.0060.0060.0000.0000.0000.000
18A18VAL0-0.001-0.01014.693-0.027-0.0270.0000.0000.0000.000
19A19VAL0-0.011-0.00612.3750.0390.0390.0000.0000.0000.000
20A20GLU-1-0.770-0.83911.709-0.937-0.9370.0000.0000.0000.000
21A21PHE0-0.008-0.0068.1330.1100.1100.0000.0000.0000.000
22A22LYS10.8780.92810.7990.9200.9200.0000.0000.0000.000
23A23GLU-1-0.817-0.9038.938-1.951-1.9510.0000.0000.0000.000
24A24GLY00.0280.02210.4560.2940.2940.0000.0000.0000.000
25A25ILE00.001-0.00411.558-0.162-0.1620.0000.0000.0000.000
26A26ASN0-0.033-0.02810.6370.1570.1570.0000.0000.0000.000
27A27LEU00.0360.01713.2840.0510.0510.0000.0000.0000.000
28A28ILE0-0.019-0.00312.5560.0360.0360.0000.0000.0000.000
29A29ILE00.0130.00515.8640.0600.0600.0000.0000.0000.000
30A30GLY00.0610.02319.579-0.005-0.0050.0000.0000.0000.000
31A31GLN00.0490.03821.7580.0150.0150.0000.0000.0000.000
32A32ASN00.0340.02122.449-0.016-0.0160.0000.0000.0000.000
33A33GLY00.0210.01422.996-0.003-0.0030.0000.0000.0000.000
34A34SER0-0.074-0.06321.551-0.014-0.0140.0000.0000.0000.000
35A35GLY00.0870.05219.222-0.015-0.0150.0000.0000.0000.000
36A36LYS10.8940.94116.0150.1870.1870.0000.0000.0000.000
37A37SER00.0260.00514.717-0.007-0.0070.0000.0000.0000.000
38A38SER0-0.004-0.00814.8630.0230.0230.0000.0000.0000.000
39A39LEU00.0090.01611.6700.0100.0100.0000.0000.0000.000
40A40LEU00.0390.01510.148-0.051-0.0510.0000.0000.0000.000
41A41ASP-1-0.763-0.8549.8820.0680.0680.0000.0000.0000.000
42A42ALA00.0010.00011.1550.0430.0430.0000.0000.0000.000
43A43ILE00.0170.0115.654-0.037-0.0370.0000.0000.0000.000
44A44LEU00.0130.0126.578-0.052-0.0520.0000.0000.0000.000
45A45VAL0-0.010-0.0107.7440.1000.1000.0000.0000.0000.000
46A46GLY0-0.007-0.0058.6990.0550.0550.0000.0000.0000.000
47A47LEU00.0020.0112.509-0.594-0.4401.604-0.251-1.507-0.002
48A48TYR0-0.009-0.0324.5070.0030.229-0.001-0.016-0.2090.000
49A49TRP0-0.0240.0248.4960.0470.0470.0000.0000.0000.000
50A50PRO0-0.042-0.03411.9470.0050.0050.0000.0000.0000.000
51A51LEU00.0080.00710.802-0.044-0.0440.0000.0000.0000.000
52A52ARG10.8430.92413.776-0.326-0.3260.0000.0000.0000.000
53A53ILE00.0750.0499.6560.0820.0820.0000.0000.0000.000
54A54LYS10.8840.92113.436-0.132-0.1320.0000.0000.0000.000
55A55ASP-1-0.805-0.89916.3550.1590.1590.0000.0000.0000.000
56A56ILE0-0.060-0.00814.190-0.022-0.0220.0000.0000.0000.000
57A57LYS10.8940.93817.946-0.101-0.1010.0000.0000.0000.000
58A58LYS10.8570.90017.787-0.145-0.1450.0000.0000.0000.000
59A59ASP-1-0.814-0.89619.4340.0560.0560.0000.0000.0000.000
60A60GLU-1-0.794-0.86618.845-0.011-0.0110.0000.0000.0000.000
61A61PHE0-0.006-0.01013.947-0.017-0.0170.0000.0000.0000.000
62A62THR0-0.039-0.04719.285-0.011-0.0110.0000.0000.0000.000
63A63LYS10.8670.92721.949-0.054-0.0540.0000.0000.0000.000
64A64VAL00.0090.02823.451-0.005-0.0050.0000.0000.0000.000
65A65GLY00.0290.01924.143-0.011-0.0110.0000.0000.0000.000
66A66ALA00.0230.00726.4000.0040.0040.0000.0000.0000.000
67A67ARG10.9000.93424.1610.1390.1390.0000.0000.0000.000
68A68ASP-1-0.777-0.88221.463-0.090-0.0900.0000.0000.0000.000
69A69THR0-0.0480.00616.996-0.011-0.0110.0000.0000.0000.000
70A70TYR0-0.085-0.06215.6950.0340.0340.0000.0000.0000.000
71A71ILE0-0.004-0.00210.567-0.021-0.0210.0000.0000.0000.000
72A72ASP-1-0.772-0.82611.543-0.476-0.4760.0000.0000.0000.000
73A73LEU0-0.0050.0145.824-0.039-0.0390.0000.0000.0000.000
74A74ILE00.001-0.0087.7990.1150.1150.0000.0000.0000.000
75A75PHE00.013-0.0012.627-2.608-1.1602.003-0.724-2.728-0.008
76A76GLU-1-0.838-0.9104.329-1.444-1.124-0.001-0.069-0.2500.000
77A77LYS10.8440.8962.405-11.754-8.6013.482-2.912-3.723-0.023
78A78ASP-1-0.808-0.8893.5262.8643.0780.025-0.002-0.2360.000
79A79GLY00.0270.0226.640-0.224-0.2240.0000.0000.0000.000
80A80THR0-0.058-0.0177.214-0.125-0.1250.0000.0000.0000.000
81A81LYS10.8080.8846.9441.3761.3760.0000.0000.0000.000
82A82TYR00.027-0.0045.7300.4070.4070.0000.0000.0000.000
83A83ARG10.8320.8837.4050.1820.1820.0000.0000.0000.000
84A84ILE0-0.017-0.0035.7500.2160.2160.0000.0000.0000.000
85A85THR0-0.036-0.0269.084-0.087-0.0870.0000.0000.0000.000
86A86ARG10.7600.8698.8520.0380.0380.0000.0000.0000.000
87A87ARG10.8900.93214.3320.1040.1040.0000.0000.0000.000
88A88PHE0-0.030-0.01214.5620.0280.0280.0000.0000.0000.000
89A89LEU00.0370.01820.048-0.012-0.0120.0000.0000.0000.000
90A90LYS10.8020.88921.7960.0730.0730.0000.0000.0000.000
91A91GLY00.0350.01226.456-0.004-0.0040.0000.0000.0000.000
92A92TYR0-0.004-0.00630.2450.0040.0040.0000.0000.0000.000
93A93SER00.0130.01129.8160.0070.0070.0000.0000.0000.000
94A94SER0-0.0330.00624.478-0.004-0.0040.0000.0000.0000.000
95A95GLY00.0200.00724.1160.0110.0110.0000.0000.0000.000
96A96GLU-1-0.781-0.87518.2090.0770.0770.0000.0000.0000.000
97A97ILE00.0050.00918.6380.0100.0100.0000.0000.0000.000
98A98HIS0-0.002-0.01114.177-0.034-0.0340.0000.0000.0000.000
99A99ALA00.005-0.00613.9570.0360.0360.0000.0000.0000.000
100A100MET00.0010.0186.637-0.036-0.0360.0000.0000.0000.000
101A101LYS10.8500.91110.4260.2270.2270.0000.0000.0000.000
102A102ARG10.9870.99010.004-0.369-0.3690.0000.0000.0000.000
103A103LEU0-0.0170.00211.8790.0160.0160.0000.0000.0000.000
104A104VAL0-0.021-0.01913.9950.0540.0540.0000.0000.0000.000
105A105GLY00.0510.02817.1470.0080.0080.0000.0000.0000.000
106A106ASN00.0050.00317.815-0.038-0.0380.0000.0000.0000.000
107A107GLU-1-0.807-0.88518.919-0.123-0.1230.0000.0000.0000.000
108A108TRP00.0160.00910.1670.0130.0130.0000.0000.0000.000
109A109LYS10.8480.91615.7100.1150.1150.0000.0000.0000.000
110A110HIS00.017-0.00314.642-0.037-0.0370.0000.0000.0000.000
111A111VAL0-0.046-0.01010.7390.0100.0100.0000.0000.0000.000
112A112THR0-0.025-0.00813.2390.0650.0650.0000.0000.0000.000
113A113GLU-1-0.804-0.87015.8130.1330.1330.0000.0000.0000.000
114A114PRO0-0.031-0.01416.4630.0130.0130.0000.0000.0000.000
115A115SER00.008-0.04016.788-0.006-0.0060.0000.0000.0000.000
116A116SER00.0460.00514.7300.0180.0180.0000.0000.0000.000
117A117LYS10.9650.99114.662-0.203-0.2030.0000.0000.0000.000
118A118ALA00.0160.00815.6730.0720.0720.0000.0000.0000.000
119A119ILE00.0130.01410.3990.0660.0660.0000.0000.0000.000
120A120SER00.0360.02211.0480.1010.1010.0000.0000.0000.000
121A121ALA0-0.045-0.02211.7980.1510.1510.0000.0000.0000.000
122A122PHE0-0.010-0.0069.0630.0640.0640.0000.0000.0000.000
123A123MET00.0380.0073.9660.0190.158-0.001-0.017-0.1220.000
124A124GLU-1-0.844-0.9118.2982.0252.0250.0000.0000.0000.000
125A125LYS10.8680.92710.609-0.762-0.7620.0000.0000.0000.000
126A126LEU0-0.0380.0075.3660.0330.0330.0000.0000.0000.000
127A127ILE00.016-0.0262.6040.635-1.0766.655-1.089-3.855-0.001
128A128PRO00.0310.0476.069-0.427-0.401-0.001-0.005-0.0190.000
129A129TYR00.023-0.0308.1600.3240.3240.0000.0000.0000.000
130A130ASN00.0050.0059.125-0.008-0.0080.0000.0000.0000.000
131A131ILE00.0180.0166.752-0.121-0.1210.0000.0000.0000.000
132A132PHE00.0380.0022.755-2.212-2.3453.487-0.860-2.494-0.001
133A133LEU0-0.041-0.0486.815-0.518-0.5180.0000.0000.0000.000
134A134ASN0-0.045-0.00910.016-0.296-0.2960.0000.0000.0000.000
135A135ALA0-0.0080.0069.238-0.163-0.1630.0000.0000.0000.000
136A136ILE0-0.060-0.0083.290-0.4190.1600.051-0.136-0.4940.000
137A137TYR0-0.064-0.0457.496-0.488-0.4880.0000.0000.0000.000
138A138ILE00.0450.0329.959-0.022-0.0220.0000.0000.0000.000
139A139ARG10.8090.88513.217-0.435-0.4350.0000.0000.0000.000
140A140GLN00.001-0.01215.596-0.044-0.0440.0000.0000.0000.000
141A141GLY00.0100.00718.7650.0270.0270.0000.0000.0000.000
142A142GLN0-0.011-0.00315.8600.0020.0020.0000.0000.0000.000
143A143ILE00.0250.00217.1670.0120.0120.0000.0000.0000.000
144A144ASP-1-0.874-0.94020.7020.0180.0180.0000.0000.0000.000
145A145ALA00.0450.01823.1780.0000.0000.0000.0000.0000.000
146A146ILE0-0.050-0.02719.7600.0100.0100.0000.0000.0000.000
147A147LEU0-0.046-0.03024.199-0.004-0.0040.0000.0000.0000.000
148A148GLU-1-0.978-0.96527.1540.0830.0830.0000.0000.0000.000
149A149SER0-0.004-0.03728.913-0.004-0.0040.0000.0000.0000.000
150A150ASP-1-0.794-0.88128.8780.1110.1110.0000.0000.0000.000
151A151GLU-1-0.862-0.90729.1260.1190.1190.0000.0000.0000.000
152A152ALA0-0.0190.00827.1080.0200.0200.0000.0000.0000.000
153A153ARG10.8130.87924.646-0.089-0.0890.0000.0000.0000.000
154A154GLU-1-0.793-0.85524.2740.2490.2490.0000.0000.0000.000
155A155LYS10.9160.95822.168-0.201-0.2010.0000.0000.0000.000
156A156VAL0-0.026-0.01619.5040.0380.0380.0000.0000.0000.000
157A157VAL00.0080.00320.0330.0530.0530.0000.0000.0000.000
158A158ARG10.7830.84820.564-0.191-0.1910.0000.0000.0000.000
159A159GLU-1-0.835-0.88917.9800.3450.3450.0000.0000.0000.000
160A160VAL00.008-0.00114.9060.0690.0690.0000.0000.0000.000
161A161LEU0-0.064-0.02816.0000.1180.1180.0000.0000.0000.000
162A162ASN0-0.069-0.02516.3630.0140.0140.0000.0000.0000.000
163A163LEU00.0010.00417.043-0.051-0.0510.0000.0000.0000.000
164A164ASP-1-0.756-0.88018.4130.5530.5530.0000.0000.0000.000
165A165LYS10.9210.97220.232-0.487-0.4870.0000.0000.0000.000
166A166PHE0-0.001-0.01922.376-0.038-0.0380.0000.0000.0000.000
167A167GLU-1-0.886-0.93723.0930.3530.3530.0000.0000.0000.000
168A168THR00.000-0.01321.912-0.027-0.0270.0000.0000.0000.000
169A169ALA0-0.052-0.02724.496-0.028-0.0280.0000.0000.0000.000
170A170TYR00.0170.00827.782-0.030-0.0300.0000.0000.0000.000
171A171LYS10.9230.95426.388-0.283-0.2830.0000.0000.0000.000
172A172LYS10.9400.95824.241-0.395-0.3950.0000.0000.0000.000
173A173LEU00.0290.01829.850-0.020-0.0200.0000.0000.0000.000
174A174SER00.0360.02532.622-0.022-0.0220.0000.0000.0000.000
175A175GLU-1-0.813-0.87730.6170.2000.2000.0000.0000.0000.000
176A176LEU0-0.0010.01833.900-0.013-0.0130.0000.0000.0000.000
177A177LYS11.0020.99935.692-0.163-0.1630.0000.0000.0000.000
178A178LYS10.8450.90034.246-0.191-0.1910.0000.0000.0000.000
179A179THR0-0.025-0.02036.364-0.009-0.0090.0000.0000.0000.000
180A180ILE0-0.007-0.00439.059-0.008-0.0080.0000.0000.0000.000
181A181ASN00.016-0.00441.685-0.010-0.0100.0000.0000.0000.000
182A182ASN00.0240.01840.437-0.012-0.0120.0000.0000.0000.000
183A183ARG10.9610.99740.189-0.143-0.1430.0000.0000.0000.000
184A184ILE00.001-0.00544.865-0.005-0.0050.0000.0000.0000.000
185A185LYS10.8300.91144.588-0.116-0.1160.0000.0000.0000.000
186A186GLU-1-0.861-0.92846.6830.0930.0930.0000.0000.0000.000
187A187TYR00.016-0.01445.7030.0000.0000.0000.0000.0000.000
188A188ARG10.9300.97850.634-0.094-0.0940.0000.0000.0000.000
189A189ASP-1-0.815-0.87551.9810.0750.0750.0000.0000.0000.000
190A190ILE00.0020.00050.255-0.003-0.0030.0000.0000.0000.000
191A191LEU0-0.015-0.00854.298-0.003-0.0030.0000.0000.0000.000
192A192ALA00.0300.02156.658-0.003-0.0030.0000.0000.0000.000
193A193ARG10.7710.85454.265-0.075-0.0750.0000.0000.0000.000
194A194THR0-0.065-0.04057.866-0.001-0.0010.0000.0000.0000.000
195A195GLU-1-0.909-0.93360.5470.0630.0630.0000.0000.0000.000
196A196GLY0-0.032-0.00263.130-0.001-0.0010.0000.0000.0000.000
197A197GLY0-0.026-0.01866.9390.0000.0000.0000.0000.0000.000
198A198HIS0-0.046-0.03463.994-0.003-0.0030.0000.0000.0000.000
199A199HIS0-0.0030.00467.7980.0000.0000.0000.0000.0000.000