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: 7MMGK

Calculation Name: 3K5R-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3K5R

Chain ID: A

ChEMBL ID:

UniProt ID: Q9WTR5

Base Structure: X-ray

Registration Date: 2023-09-27

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 OptH
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 218
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2374239.903358
FMO2-HF: Nuclear repulsion 2290497.037604
FMO2-HF: Total energy -83742.865754
FMO2-MP2: Total energy -83988.108521


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:0:SER)


Summations of interaction energy for fragment #1(A:0:SER)
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.
-41.296-33.1618.272-8.633-7.776-0.026
Interaction energy analysis for fragmet #1(A:0:SER)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.102 / q_NPA : -0.105
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].
3A2ILE00.0110.0073.396-1.5290.4220.008-1.146-0.813-0.002
4A3VAL0-0.049-0.0224.8090.8340.8340.0000.0000.0000.000
5A4VAL0-0.010-0.0127.456-0.075-0.0750.0000.0000.0000.000
6A5SER00.009-0.00411.1280.1770.1770.0000.0000.0000.000
7A6PRO0-0.0160.00114.360-0.064-0.0640.0000.0000.0000.000
8A7ILE00.0180.01616.3790.0220.0220.0000.0000.0000.000
9A8LEU00.0210.01519.519-0.019-0.0190.0000.0000.0000.000
10A9ILE0-0.047-0.03622.8520.0010.0010.0000.0000.0000.000
11A10PRO00.0130.01825.452-0.005-0.0050.0000.0000.0000.000
12A11GLU-1-0.786-0.89328.9900.0320.0320.0000.0000.0000.000
13A12ASN0-0.045-0.04631.569-0.002-0.0020.0000.0000.0000.000
14A13GLN0-0.0140.00426.308-0.008-0.0080.0000.0000.0000.000
15A14ARG10.9881.00131.868-0.047-0.0470.0000.0000.0000.000
16A15GLN00.0260.02932.3990.0020.0020.0000.0000.0000.000
17A16PRO0-0.049-0.03831.5940.0060.0060.0000.0000.0000.000
18A17PHE0-0.0260.00428.2610.0050.0050.0000.0000.0000.000
19A18PRO00.010-0.02024.900-0.004-0.0040.0000.0000.0000.000
20A19ARG10.8660.94425.180-0.021-0.0210.0000.0000.0000.000
21A20ASP-1-0.855-0.92020.034-0.009-0.0090.0000.0000.0000.000
22A21VAL0-0.105-0.06919.9580.0150.0150.0000.0000.0000.000
23A22GLY00.0790.03817.1110.0270.0270.0000.0000.0000.000
24A23LYS10.8930.97211.446-0.603-0.6030.0000.0000.0000.000
25A24VAL0-0.0070.0058.9270.0670.0670.0000.0000.0000.000
26A25VAL0-0.036-0.0194.9050.0470.0470.0000.0000.0000.000
27A26ASP-1-0.797-0.9213.627-7.721-7.3500.008-0.272-0.108-0.002
28A27SER0-0.114-0.0521.948-6.755-7.3606.031-2.621-2.8060.028
29A28ASP-1-0.863-0.9382.614-23.912-17.6082.226-4.583-3.946-0.050
30A29ARG10.8770.9624.3100.8650.979-0.001-0.011-0.1030.000
31A30PRO0-0.021-0.0026.5890.6420.6420.0000.0000.0000.000
32A31GLU-1-0.937-0.9779.826-0.500-0.5000.0000.0000.0000.000
33A32GLY00.000-0.00513.044-0.029-0.0290.0000.0000.0000.000
34A33SER0-0.032-0.0089.4680.1590.1590.0000.0000.0000.000
35A34LYS10.8860.95512.4800.6880.6880.0000.0000.0000.000
36A35PHE0-0.005-0.0027.956-0.086-0.0860.0000.0000.0000.000
37A36ARG10.8320.92613.0560.6080.6080.0000.0000.0000.000
38A37LEU00.0200.01415.286-0.030-0.0300.0000.0000.0000.000
39A38THR0-0.019-0.01917.3830.0220.0220.0000.0000.0000.000
40A39GLY00.0780.03420.0800.0130.0130.0000.0000.0000.000
41A40LYS10.9020.97122.7570.0350.0350.0000.0000.0000.000
42A41GLY00.0360.01224.7340.0080.0080.0000.0000.0000.000
43A42VAL0-0.039-0.00420.7990.0010.0010.0000.0000.0000.000
44A43ASP-1-0.798-0.90023.723-0.191-0.1910.0000.0000.0000.000
45A44GLN0-0.055-0.03925.050-0.004-0.0040.0000.0000.0000.000
46A45ASP-1-0.895-0.95027.910-0.071-0.0710.0000.0000.0000.000
47A46PRO0-0.063-0.01128.8290.0040.0040.0000.0000.0000.000
48A47LYS10.9720.99028.0830.1070.1070.0000.0000.0000.000
49A48GLY0-0.0110.00026.2070.0070.0070.0000.0000.0000.000
50A49THR0-0.0220.00326.3350.0100.0100.0000.0000.0000.000
51A50PHE00.0330.01621.4220.0140.0140.0000.0000.0000.000
52A51ARG10.9300.96321.1710.1400.1400.0000.0000.0000.000
53A52ILE00.0360.03013.2120.0240.0240.0000.0000.0000.000
54A53ASN0-0.048-0.01416.225-0.070-0.0700.0000.0000.0000.000
55A54GLU-1-0.873-0.95015.016-0.428-0.4280.0000.0000.0000.000
56A55ASN00.0340.01913.911-0.180-0.1800.0000.0000.0000.000
57A56THR0-0.034-0.03612.438-0.072-0.0720.0000.0000.0000.000
58A57GLY00.0770.04911.5990.0520.0520.0000.0000.0000.000
59A58SER0-0.034-0.00912.6620.0680.0680.0000.0000.0000.000
60A59VAL00.0330.00315.201-0.058-0.0580.0000.0000.0000.000
61A60SER00.0000.00617.6990.0360.0360.0000.0000.0000.000
62A61VAL00.0130.00621.424-0.018-0.0180.0000.0000.0000.000
63A62THR0-0.058-0.07124.6230.0090.0090.0000.0000.0000.000
64A63ARG10.8680.93827.5820.0330.0330.0000.0000.0000.000
65A64THR00.010-0.02129.4900.0050.0050.0000.0000.0000.000
66A65LEU0-0.066-0.03526.728-0.008-0.0080.0000.0000.0000.000
67A66ASP-1-0.794-0.89231.4390.0220.0220.0000.0000.0000.000
68A67ARG10.9060.93429.665-0.069-0.0690.0000.0000.0000.000
69A68GLU-1-0.920-0.96032.9150.0350.0350.0000.0000.0000.000
70A69THR0-0.133-0.04134.030-0.006-0.0060.0000.0000.0000.000
71A70ILE0-0.091-0.05728.945-0.006-0.0060.0000.0000.0000.000
72A71ALA00.0650.04330.2460.0020.0020.0000.0000.0000.000
73A72THR0-0.032-0.00525.3420.0050.0050.0000.0000.0000.000
74A73TYR0-0.004-0.03823.718-0.020-0.0200.0000.0000.0000.000
75A74GLN0-0.013-0.01219.709-0.004-0.0040.0000.0000.0000.000
76A75LEU0-0.017-0.00918.361-0.020-0.0200.0000.0000.0000.000
77A76TYR00.004-0.00216.4060.0360.0360.0000.0000.0000.000
78A77VAL0-0.0010.00211.4850.0030.0030.0000.0000.0000.000
79A78GLU-1-0.849-0.93111.751-0.566-0.5660.0000.0000.0000.000
80A79THR00.0890.0428.2360.2160.2160.0000.0000.0000.000
81A80THR0-0.029-0.01511.4100.1030.1030.0000.0000.0000.000
82A81ASP-1-0.891-0.96113.906-0.917-0.9170.0000.0000.0000.000
83A82ALA00.0590.02015.9630.0520.0520.0000.0000.0000.000
84A83SER0-0.047-0.03618.6030.0450.0450.0000.0000.0000.000
85A84GLY00.0290.01918.8020.0520.0520.0000.0000.0000.000
86A85LYS10.8870.95614.7540.9040.9040.0000.0000.0000.000
87A86THR0-0.0080.00713.695-0.049-0.0490.0000.0000.0000.000
88A87LEU0-0.103-0.05610.2180.0800.0800.0000.0000.0000.000
89A88GLU-1-0.904-0.9395.981-3.053-3.0530.0000.0000.0000.000
90A89GLY0-0.025-0.0279.6800.2310.2310.0000.0000.0000.000
91A90PRO0-0.029-0.02011.956-0.063-0.0630.0000.0000.0000.000
92A91VAL00.0140.0279.8860.1050.1050.0000.0000.0000.000
93A92PRO0-0.026-0.02413.298-0.010-0.0100.0000.0000.0000.000
94A93LEU00.0260.01614.6340.0330.0330.0000.0000.0000.000
95A94GLU-1-0.915-0.95916.3940.0630.0630.0000.0000.0000.000
96A95VAL0-0.001-0.00419.6930.0210.0210.0000.0000.0000.000
97A96ILE0-0.019-0.00521.903-0.008-0.0080.0000.0000.0000.000
98A97VAL0-0.012-0.00524.7770.0050.0050.0000.0000.0000.000
99A98ILE0-0.029-0.01226.3120.0030.0030.0000.0000.0000.000
100A99ASP-1-0.827-0.93329.2550.0520.0520.0000.0000.0000.000
101A100GLN00.0260.01432.8620.0050.0050.0000.0000.0000.000
102A101ASN0-0.077-0.03034.5300.0010.0010.0000.0000.0000.000
103A102ASP-1-0.876-0.91830.3810.1210.1210.0000.0000.0000.000
104A103ASN0-0.028-0.02131.7330.0000.0000.0000.0000.0000.000
105A104ARG10.8100.89528.757-0.132-0.1320.0000.0000.0000.000
106A105PRO00.0160.00526.6980.0000.0000.0000.0000.0000.000
107A106ILE0-0.032-0.01922.4970.0100.0100.0000.0000.0000.000
108A107PHE0-0.009-0.00119.289-0.004-0.0040.0000.0000.0000.000
109A108ARG10.9450.96019.693-0.129-0.1290.0000.0000.0000.000
110A109GLU-1-0.923-0.94516.7650.2320.2320.0000.0000.0000.000
111A110GLY0-0.0210.00313.8020.0780.0780.0000.0000.0000.000
112A111PRO0-0.015-0.0339.619-0.073-0.0730.0000.0000.0000.000
113A112TYR00.0220.02011.1900.0750.0750.0000.0000.0000.000
114A113ILE0-0.007-0.0055.9850.0670.0670.0000.0000.0000.000
115A114GLY00.002-0.0049.707-0.072-0.0720.0000.0000.0000.000
116A115HIS10.8030.8585.416-1.906-1.9060.0000.0000.0000.000
117A116VAL00.0170.00910.658-0.124-0.1240.0000.0000.0000.000
118A117MET0-0.0290.01413.0780.0300.0300.0000.0000.0000.000
119A118GLU-1-0.804-0.89014.8660.3330.3330.0000.0000.0000.000
120A119GLY0-0.033-0.02316.829-0.036-0.0360.0000.0000.0000.000
121A120SER0-0.095-0.06817.631-0.030-0.0300.0000.0000.0000.000
122A121PRO0-0.023-0.01820.251-0.003-0.0030.0000.0000.0000.000
123A122THR0-0.018-0.00722.7000.0160.0160.0000.0000.0000.000
124A123GLY0-0.021-0.01123.806-0.021-0.0210.0000.0000.0000.000
125A124THR0-0.055-0.03518.433-0.013-0.0130.0000.0000.0000.000
126A125THR00.020-0.00119.2280.0140.0140.0000.0000.0000.000
127A126VAL0-0.045-0.02513.9900.0160.0160.0000.0000.0000.000
128A127MET0-0.033-0.00812.9910.0720.0720.0000.0000.0000.000
129A128ARG10.8690.93716.638-0.318-0.3180.0000.0000.0000.000
130A129MET0-0.085-0.02416.9710.0520.0520.0000.0000.0000.000
131A130THR00.0360.00019.494-0.013-0.0130.0000.0000.0000.000
132A131ALA0-0.048-0.02921.7850.0120.0120.0000.0000.0000.000
133A132PHE0-0.027-0.01724.226-0.008-0.0080.0000.0000.0000.000
134A133ASP-1-0.961-0.95924.5190.1410.1410.0000.0000.0000.000
135A134ALA0-0.019-0.01425.4410.0160.0160.0000.0000.0000.000
136A135ASP-1-0.924-0.96027.4070.1260.1260.0000.0000.0000.000
137A136ASP-1-0.859-0.92129.5330.1080.1080.0000.0000.0000.000
138A137PRO0-0.111-0.09431.224-0.002-0.0020.0000.0000.0000.000
139A138ALA0-0.0150.01133.5940.0030.0030.0000.0000.0000.000
140A139THR00.0750.02828.4740.0010.0010.0000.0000.0000.000
141A140ASP-1-0.948-0.97731.8360.1200.1200.0000.0000.0000.000
142A141ASN0-0.078-0.05134.1810.0010.0010.0000.0000.0000.000
143A142ALA00.0280.03732.181-0.004-0.0040.0000.0000.0000.000
144A143LEU0-0.039-0.01933.9030.0050.0050.0000.0000.0000.000
145A144LEU00.0290.02027.3670.0050.0050.0000.0000.0000.000
146A145ARG10.8550.93129.693-0.167-0.1670.0000.0000.0000.000
147A146TYR00.0100.01824.4850.0080.0080.0000.0000.0000.000
148A147ASN00.037-0.00425.326-0.001-0.0010.0000.0000.0000.000
149A148ILE00.0060.00920.5700.0170.0170.0000.0000.0000.000
150A149ARG10.8200.92222.689-0.274-0.2740.0000.0000.0000.000
151A150GLN0-0.023-0.02520.877-0.023-0.0230.0000.0000.0000.000
152A151GLN00.0060.00918.2950.0290.0290.0000.0000.0000.000
153A152THR0-0.0320.01316.893-0.069-0.0690.0000.0000.0000.000
154A153PRO00.0310.00615.4720.0770.0770.0000.0000.0000.000
155A154ASP-1-0.910-0.95418.4580.3500.3500.0000.0000.0000.000
156A155LYS10.9460.98620.494-0.411-0.4110.0000.0000.0000.000
157A156PRO00.0370.02719.8200.0470.0470.0000.0000.0000.000
158A157SER00.0180.00422.517-0.036-0.0360.0000.0000.0000.000
159A158PRO00.0350.02022.4360.0340.0340.0000.0000.0000.000
160A159ASN0-0.029-0.01623.1370.0080.0080.0000.0000.0000.000
161A160MET00.0130.00818.642-0.041-0.0410.0000.0000.0000.000
162A161PHE00.023-0.00215.7640.0010.0010.0000.0000.0000.000
163A162TYR0-0.020-0.00421.200-0.025-0.0250.0000.0000.0000.000
164A163ILE0-0.0130.01421.0690.0200.0200.0000.0000.0000.000
165A164ASP-1-0.853-0.93123.6230.2020.2020.0000.0000.0000.000
166A165PRO0-0.026-0.01326.4100.0020.0020.0000.0000.0000.000
167A166GLU-1-0.970-0.98028.7530.1590.1590.0000.0000.0000.000
168A167LYS10.9530.96125.955-0.195-0.1950.0000.0000.0000.000
169A168GLY00.0680.03123.3600.0080.0080.0000.0000.0000.000
170A169ASP-1-0.855-0.90321.4310.3480.3480.0000.0000.0000.000
171A170ILE00.009-0.00317.523-0.020-0.0200.0000.0000.0000.000
172A171VAL00.0010.00819.4520.0220.0220.0000.0000.0000.000
173A172THR00.0210.01318.5710.0030.0030.0000.0000.0000.000
174A173VAL0-0.015-0.01121.068-0.034-0.0340.0000.0000.0000.000
175A174VAL0-0.0160.00821.257-0.025-0.0250.0000.0000.0000.000
176A175SER00.0060.01124.0780.0000.0000.0000.0000.0000.000
177A176PRO00.0660.02222.3970.0190.0190.0000.0000.0000.000
178A177ALA0-0.038-0.03022.0950.0130.0130.0000.0000.0000.000
179A178LEU0-0.034-0.01122.297-0.002-0.0020.0000.0000.0000.000
180A179LEU0-0.062-0.02417.3840.0350.0350.0000.0000.0000.000
181A180ASP-1-0.777-0.88618.1430.2880.2880.0000.0000.0000.000
182A181ARG10.9300.9558.318-0.658-0.6580.0000.0000.0000.000
183A182GLU-1-0.955-0.97015.7380.2510.2510.0000.0000.0000.000
184A183THR0-0.072-0.02518.100-0.024-0.0240.0000.0000.0000.000
185A184LEU0-0.082-0.03615.430-0.004-0.0040.0000.0000.0000.000
186A185GLU-1-1.021-0.99817.0490.4460.4460.0000.0000.0000.000
187A186ASN00.030-0.01212.6090.1440.1440.0000.0000.0000.000
188A187PRO00.0280.03410.951-0.015-0.0150.0000.0000.0000.000
189A188LYS10.9210.9546.113-2.787-2.7870.0000.0000.0000.000
190A189TYR0-0.025-0.04311.143-0.088-0.0880.0000.0000.0000.000
191A190GLU-1-0.926-0.96812.3340.8920.8920.0000.0000.0000.000
192A191LEU0-0.042-0.03613.966-0.107-0.1070.0000.0000.0000.000
193A192ILE00.0050.01116.5180.0150.0150.0000.0000.0000.000
194A193ILE0-0.009-0.00818.367-0.026-0.0260.0000.0000.0000.000
195A194GLU-1-0.892-0.95820.9290.2160.2160.0000.0000.0000.000
196A195ALA00.0010.00324.3360.0050.0050.0000.0000.0000.000
197A196GLN0-0.020-0.02026.564-0.019-0.0190.0000.0000.0000.000
198A197ASP-1-0.792-0.90130.2750.1460.1460.0000.0000.0000.000
199A198MET0-0.071-0.01933.051-0.004-0.0040.0000.0000.0000.000
200A199ALA0-0.057-0.03635.657-0.008-0.0080.0000.0000.0000.000
201A200GLY00.0510.02337.0360.0030.0030.0000.0000.0000.000
202A201LEU0-0.040-0.04539.1770.0000.0000.0000.0000.0000.000
203A202ASP-1-0.840-0.89335.0850.0930.0930.0000.0000.0000.000
204A203VAL0-0.035-0.02035.5490.0080.0080.0000.0000.0000.000
205A204GLY0-0.025-0.01535.342-0.005-0.0050.0000.0000.0000.000
206A205LEU0-0.058-0.01532.1240.0080.0080.0000.0000.0000.000
207A206THR0-0.004-0.01228.4660.0060.0060.0000.0000.0000.000
208A207GLY00.0300.02125.780-0.011-0.0110.0000.0000.0000.000
209A208THR0-0.059-0.03921.7190.0160.0160.0000.0000.0000.000
210A209ALA00.0240.01917.484-0.015-0.0150.0000.0000.0000.000
211A210THR0-0.011-0.01214.155-0.010-0.0100.0000.0000.0000.000
212A211ALA00.0200.00813.0590.0140.0140.0000.0000.0000.000
213A212THR0-0.042-0.0118.7300.1160.1160.0000.0000.0000.000
214A213ILE0-0.0010.00511.0870.0350.0350.0000.0000.0000.000
215A214VAL0-0.036-0.0087.0400.0240.0240.0000.0000.0000.000
216A215ILE0-0.0080.0059.995-0.097-0.0970.0000.0000.0000.000
217A216ASP-1-0.865-0.9288.2701.1981.1980.0000.0000.0000.000
218A217ASP-1-0.875-0.95011.0430.2640.2640.0000.0000.0000.000