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

tag_button

FMODB ID: VQMM1

Calculation Name: 3GKU-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3GKU

Chain ID: A

ChEMBL ID:

UniProt ID: D0VX24

Base Structure: X-ray

Registration Date: 2023-09-24

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 208
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2078524.30994
FMO2-HF: Nuclear repulsion 1995139.513562
FMO2-HF: Total energy -83384.796378
FMO2-MP2: Total energy -83627.526356


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.
-26.166-33.04429.747-12.232-10.6360.083
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 : 0.059 / q_NPA : 0.057
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].
3A3MET0-0.061-0.0512.386-8.124-5.1664.102-2.914-4.146-0.033
4A4VAL00.0400.0534.2020.5070.6530.000-0.036-0.1090.000
5A5THR00.002-0.0078.0040.2040.2040.0000.0000.0000.000
6A6VAL0-0.0260.00010.1380.1250.1250.0000.0000.0000.000
7A7THR0-0.015-0.00713.1120.0460.0460.0000.0000.0000.000
8A8ALA0-0.021-0.02016.4110.0230.0230.0000.0000.0000.000
9A9LYS10.9710.99919.5280.1420.1420.0000.0000.0000.000
10A10THR00.0380.02221.1020.0030.0030.0000.0000.0000.000
11A11VAL00.0580.01015.462-0.021-0.0210.0000.0000.0000.000
12A12GLU-1-0.942-0.96917.077-0.017-0.0170.0000.0000.0000.000
13A13GLU-1-0.805-0.91018.762-0.134-0.1340.0000.0000.0000.000
14A14ALA0-0.0040.00815.020-0.015-0.0150.0000.0000.0000.000
15A15VAL00.0470.01813.695-0.039-0.0390.0000.0000.0000.000
16A16THR0-0.041-0.01714.862-0.004-0.0040.0000.0000.0000.000
17A17LYS10.8770.92316.4610.3420.3420.0000.0000.0000.000
18A18ALA00.0380.02111.201-0.037-0.0370.0000.0000.0000.000
19A19LEU00.004-0.00912.895-0.006-0.0060.0000.0000.0000.000
20A20ILE0-0.040-0.01314.5250.0110.0110.0000.0000.0000.000
21A21GLU-1-0.919-0.96212.364-0.712-0.7120.0000.0000.0000.000
22A22LEU0-0.030-0.0138.179-0.027-0.0270.0000.0000.0000.000
23A23GLN0-0.060-0.02712.0640.1110.1110.0000.0000.0000.000
24A24THR0-0.023-0.00111.1770.0680.0680.0000.0000.0000.000
25A25THR0-0.005-0.02313.782-0.046-0.0460.0000.0000.0000.000
26A26SER00.0480.01714.7360.0610.0610.0000.0000.0000.000
27A27ASP-1-0.840-0.88414.9830.4820.4820.0000.0000.0000.000
28A28LYS10.8180.88812.287-0.380-0.3800.0000.0000.0000.000
29A29LEU00.0130.0329.5850.0640.0640.0000.0000.0000.000
30A30THR0-0.048-0.0206.2150.4130.4130.0000.0000.0000.000
31A31TYR00.008-0.0137.502-0.349-0.3490.0000.0000.0000.000
32A32GLU-1-0.822-0.8806.300-0.793-0.7930.0000.0000.0000.000
33A33ILE0-0.026-0.0319.102-0.165-0.1650.0000.0000.0000.000
34A34VAL0-0.047-0.02310.8810.0000.0000.0000.0000.0000.000
35A35GLU-1-0.837-0.93313.159-0.172-0.1720.0000.0000.0000.000
36A36LYS10.9170.97716.8270.0610.0610.0000.0000.0000.000
37A37GLY00.0310.00219.172-0.011-0.0110.0000.0000.0000.000
38A38SER0-0.008-0.01721.9760.0240.0240.0000.0000.0000.000
39A39ALA00.005-0.00325.718-0.016-0.0160.0000.0000.0000.000
40A40GLY00.0270.01328.9660.0080.0080.0000.0000.0000.000
41A41PHE0-0.0200.00432.503-0.003-0.0030.0000.0000.0000.000
42A42LEU00.0010.02235.5620.0040.0040.0000.0000.0000.000
43A43GLY00.0610.01836.5580.0040.0040.0000.0000.0000.000
44A44ILE00.003-0.02731.0760.0000.0000.0000.0000.0000.000
45A45GLY00.0240.02030.969-0.012-0.0120.0000.0000.0000.000
46A46SER0-0.081-0.02927.115-0.003-0.0030.0000.0000.0000.000
47A47LYS10.9030.92823.2180.2080.2080.0000.0000.0000.000
48A48PRO0-0.0220.04019.7220.0200.0200.0000.0000.0000.000
49A49ALA00.0500.02518.016-0.003-0.0030.0000.0000.0000.000
50A50ILE0-0.071-0.04413.124-0.036-0.0360.0000.0000.0000.000
51A51ILE0-0.024-0.00711.0990.0750.0750.0000.0000.0000.000
52A52ARG10.8890.9356.4451.4391.4390.0000.0000.0000.000
53A53ALA00.016-0.0076.7740.3740.3740.0000.0000.0000.000
54A54LYS10.8680.9212.125-22.779-32.83025.646-9.278-6.3170.116
55A55ARG10.9100.9555.2720.3350.404-0.001-0.004-0.0640.000
56A56LYS10.9050.9416.304-0.433-0.4330.0000.0000.0000.000
57A57GLU-1-0.951-0.9885.4333.7103.7100.0000.0000.0000.000
58A58THR0-0.076-0.0457.002-0.371-0.3710.0000.0000.0000.000
59A59LEU0-0.003-0.0089.5800.1430.1430.0000.0000.0000.000
60A60GLN00.0820.02011.6830.0360.0360.0000.0000.0000.000
61A61ASP-1-0.795-0.8846.6591.1401.1400.0000.0000.0000.000
62A62LYS10.9170.9668.770-1.891-1.8910.0000.0000.0000.000
63A63ALA0-0.036-0.0119.995-0.105-0.1050.0000.0000.0000.000
64A64ILE00.002-0.0079.732-0.064-0.0640.0000.0000.0000.000
65A65GLU-1-0.830-0.8936.9300.2860.2860.0000.0000.0000.000
66A66PHE0-0.019-0.0169.332-0.123-0.1230.0000.0000.0000.000
67A67LEU0-0.009-0.02112.676-0.085-0.0850.0000.0000.0000.000
68A68GLU-1-0.935-0.9608.8840.3710.3710.0000.0000.0000.000
69A69GLN0-0.038-0.0239.681-0.115-0.1150.0000.0000.0000.000
70A70VAL0-0.021-0.02012.283-0.046-0.0460.0000.0000.0000.000
71A71PHE0-0.005-0.04615.559-0.032-0.0320.0000.0000.0000.000
72A72ASP-1-0.901-0.91913.239-0.025-0.0250.0000.0000.0000.000
73A73ALA00.0040.00215.288-0.028-0.0280.0000.0000.0000.000
74A74MET0-0.176-0.09117.397-0.003-0.0030.0000.0000.0000.000
75A75ASN0-0.086-0.03418.613-0.020-0.0200.0000.0000.0000.000
76A76MET0-0.089-0.04018.601-0.003-0.0030.0000.0000.0000.000
77A77ALA00.0560.03317.0440.0150.0150.0000.0000.0000.000
78A78VAL0-0.088-0.06416.331-0.001-0.0010.0000.0000.0000.000
79A79ASP-1-0.864-0.91915.6330.1690.1690.0000.0000.0000.000
80A80ILE0-0.030-0.01813.089-0.005-0.0050.0000.0000.0000.000
81A81SER0-0.038-0.01015.0610.0030.0030.0000.0000.0000.000
82A82VAL0-0.011-0.04314.3120.0030.0030.0000.0000.0000.000
83A83GLU-1-0.931-0.93517.1360.2030.2030.0000.0000.0000.000
84A84TYR0-0.083-0.07816.4780.0130.0130.0000.0000.0000.000
85A85ASN00.0010.00419.041-0.010-0.0100.0000.0000.0000.000
86A86GLU-1-0.793-0.89818.5430.4590.4590.0000.0000.0000.000
87A87THR0-0.070-0.04821.2780.0070.0070.0000.0000.0000.000
88A88GLU-1-0.886-0.92724.9080.2000.2000.0000.0000.0000.000
89A89LYS10.7910.92220.792-0.395-0.3950.0000.0000.0000.000
90A90GLU-1-0.827-0.89722.5850.2320.2320.0000.0000.0000.000
91A91MET0-0.026-0.00915.0320.0010.0010.0000.0000.0000.000
92A92ASN0-0.054-0.03620.005-0.010-0.0100.0000.0000.0000.000
93A93VAL00.0290.00317.1250.0030.0030.0000.0000.0000.000
94A94ASN0-0.015-0.01419.576-0.025-0.0250.0000.0000.0000.000
95A95LEU00.0260.02018.2510.0150.0150.0000.0000.0000.000
96A96LYS10.8630.92620.264-0.151-0.1510.0000.0000.0000.000
97A97GLY00.1030.03320.2830.0110.0110.0000.0000.0000.000
98A98ASP-1-0.903-0.95721.9580.0480.0480.0000.0000.0000.000
99A99ASP-1-0.787-0.88821.5430.0600.0600.0000.0000.0000.000
100A100MET0-0.074-0.02421.2400.0060.0060.0000.0000.0000.000
101A101GLY0-0.008-0.00724.1670.0020.0020.0000.0000.0000.000
102A102ILE00.0220.01425.732-0.002-0.0020.0000.0000.0000.000
103A103LEU0-0.0130.00125.125-0.004-0.0040.0000.0000.0000.000
104A104ILE00.022-0.00729.0580.0070.0070.0000.0000.0000.000
105A105GLY0-0.019-0.00831.9640.0050.0050.0000.0000.0000.000
106A106LYS10.9370.94829.732-0.084-0.0840.0000.0000.0000.000
107A107ARG10.9591.02127.053-0.091-0.0910.0000.0000.0000.000
108A108GLY0-0.0310.01428.1230.0110.0110.0000.0000.0000.000
109A109GLN00.0460.00928.8870.0030.0030.0000.0000.0000.000
110A110THR0-0.009-0.00625.0670.0110.0110.0000.0000.0000.000
111A111LEU00.0680.02923.7840.0160.0160.0000.0000.0000.000
112A112ASP-1-0.919-0.95024.9020.1910.1910.0000.0000.0000.000
113A113SER0-0.063-0.04025.3110.0140.0140.0000.0000.0000.000
114A114LEU00.0500.02919.5880.0210.0210.0000.0000.0000.000
115A115GLN00.0300.02621.1340.0340.0340.0000.0000.0000.000
116A116TYR0-0.045-0.02622.0650.0300.0300.0000.0000.0000.000
117A117LEU00.009-0.00620.1340.0210.0210.0000.0000.0000.000
118A118VAL00.0670.03115.9580.0460.0460.0000.0000.0000.000
119A119SER0-0.0020.01017.6370.0560.0560.0000.0000.0000.000
120A120LEU0-0.041-0.01019.7270.0330.0330.0000.0000.0000.000
121A121VAL0-0.0090.00113.9790.0470.0470.0000.0000.0000.000
122A122VAL00.029-0.00914.7650.0820.0820.0000.0000.0000.000
123A123ASN0-0.051-0.04216.1050.0370.0370.0000.0000.0000.000
124A124LYS10.9310.99515.472-0.777-0.7770.0000.0000.0000.000
125A125SER0-0.103-0.05113.4740.1300.1300.0000.0000.0000.000
126A126SER0-0.019-0.03115.3870.0780.0780.0000.0000.0000.000
127A127SER0-0.017-0.00218.058-0.027-0.0270.0000.0000.0000.000
128A128ASP-1-0.838-0.88420.9880.3540.3540.0000.0000.0000.000
129A129TYR0-0.008-0.00321.6430.0250.0250.0000.0000.0000.000
130A130ILE00.0100.00218.681-0.012-0.0120.0000.0000.0000.000
131A131ARG10.8760.94322.012-0.282-0.2820.0000.0000.0000.000
132A132VAL00.0190.01918.7600.0050.0050.0000.0000.0000.000
133A133LYS10.7630.85921.732-0.250-0.2500.0000.0000.0000.000
134A134LEU00.0170.02319.7080.0140.0140.0000.0000.0000.000
135A135ASP-1-0.842-0.94622.8720.1380.1380.0000.0000.0000.000
136A136THR00.006-0.00323.2480.0080.0080.0000.0000.0000.000
137A137GLU-1-0.775-0.85624.9150.1140.1140.0000.0000.0000.000
138A138ASN00.021-0.00927.159-0.007-0.0070.0000.0000.0000.000
139A139TYR00.0040.00128.739-0.013-0.0130.0000.0000.0000.000
140A140ARG10.8140.89526.718-0.188-0.1880.0000.0000.0000.000
141A141GLU-1-0.850-0.89531.5600.1010.1010.0000.0000.0000.000
142A142ARG10.8490.92129.438-0.110-0.1100.0000.0000.0000.000
143A143ARG10.8480.88533.484-0.100-0.1000.0000.0000.0000.000
144A144LYS10.8330.89635.525-0.101-0.1010.0000.0000.0000.000
145A145GLU-1-0.876-0.92537.7270.0700.0700.0000.0000.0000.000
146A146THR0-0.0020.00137.952-0.006-0.0060.0000.0000.0000.000
147A147LEU00.0120.00337.704-0.005-0.0050.0000.0000.0000.000
148A148GLU-1-0.780-0.87741.2870.0830.0830.0000.0000.0000.000
149A149THR0-0.085-0.04943.327-0.005-0.0050.0000.0000.0000.000
150A150LEU00.0020.00642.377-0.004-0.0040.0000.0000.0000.000
151A151ALA0-0.0070.00245.318-0.003-0.0030.0000.0000.0000.000
152A152LYS10.9260.95346.041-0.069-0.0690.0000.0000.0000.000
153A153ASN0-0.030-0.01347.608-0.003-0.0030.0000.0000.0000.000
154A154ILE0-0.019-0.03448.316-0.004-0.0040.0000.0000.0000.000
155A155ALA00.0400.02950.958-0.002-0.0020.0000.0000.0000.000
156A156TYR00.0070.00853.168-0.003-0.0030.0000.0000.0000.000
157A157LYS11.0231.01050.032-0.046-0.0460.0000.0000.0000.000
158A158VAL0-0.0100.04454.025-0.002-0.0020.0000.0000.0000.000
159A159LYS10.8790.94756.044-0.049-0.0490.0000.0000.0000.000
160A160ARG10.9260.95658.372-0.034-0.0340.0000.0000.0000.000
161A161THR0-0.047-0.04857.847-0.001-0.0010.0000.0000.0000.000
162A162LYS10.8640.93660.321-0.037-0.0370.0000.0000.0000.000
163A163ARG10.9520.98855.273-0.039-0.0390.0000.0000.0000.000
164A164SER0-0.055-0.03654.7390.0010.0010.0000.0000.0000.000
165A165VAL0-0.004-0.01950.118-0.002-0.0020.0000.0000.0000.000
166A166SER00.0130.02248.5360.0010.0010.0000.0000.0000.000
167A167LEU0-0.052-0.02244.212-0.002-0.0020.0000.0000.0000.000
168A168GLU-1-0.843-0.92840.5360.0660.0660.0000.0000.0000.000
169A169PRO0-0.050-0.03539.7720.0020.0020.0000.0000.0000.000
170A170MET0-0.0200.00537.9050.0020.0020.0000.0000.0000.000
171A171ASN00.0770.05334.0940.0030.0030.0000.0000.0000.000
172A172PRO00.0420.00235.730-0.003-0.0030.0000.0000.0000.000
173A173TYR00.0310.01931.952-0.006-0.0060.0000.0000.0000.000
174A174GLU-1-0.812-0.87734.7750.1010.1010.0000.0000.0000.000
175A175ARG10.8440.90638.006-0.100-0.1000.0000.0000.0000.000
176A176ARG10.9540.98339.490-0.113-0.1130.0000.0000.0000.000
177A177ILE00.0020.00136.919-0.004-0.0040.0000.0000.0000.000
178A178ILE00.0260.01441.453-0.005-0.0050.0000.0000.0000.000
179A179HIS0-0.024-0.02544.167-0.001-0.0010.0000.0000.0000.000
180A180ALA0-0.024-0.00343.920-0.003-0.0030.0000.0000.0000.000
181A181ALA0-0.018-0.00245.114-0.003-0.0030.0000.0000.0000.000
182A182LEU0-0.040-0.02746.819-0.004-0.0040.0000.0000.0000.000
183A183GLN0-0.0350.00047.654-0.001-0.0010.0000.0000.0000.000
184A184ASN0-0.011-0.00850.621-0.002-0.0020.0000.0000.0000.000
185A185ASP-1-0.769-0.88553.7180.0480.0480.0000.0000.0000.000
186A186LYS10.9010.93355.388-0.053-0.0530.0000.0000.0000.000
187A187TYR00.008-0.00358.140-0.001-0.0010.0000.0000.0000.000
188A188VAL0-0.0350.00053.613-0.001-0.0010.0000.0000.0000.000
189A189VAL0-0.002-0.00154.2040.0010.0010.0000.0000.0000.000
190A190THR0-0.0090.00049.2240.0000.0000.0000.0000.0000.000
191A191ARG10.9510.95049.740-0.057-0.0570.0000.0000.0000.000
192A192SER0-0.026-0.00145.3360.0000.0000.0000.0000.0000.000
193A193ASP-1-0.847-0.91646.9410.0620.0620.0000.0000.0000.000
194A194GLY00.0410.03145.6630.0020.0020.0000.0000.0000.000
195A195GLU-1-0.880-0.92843.3810.0800.0800.0000.0000.0000.000
196A196GLU-1-0.813-0.89337.4240.0990.0990.0000.0000.0000.000
197A197PRO0-0.012-0.01636.367-0.001-0.0010.0000.0000.0000.000
198A198PHE0-0.002-0.02838.475-0.001-0.0010.0000.0000.0000.000
199A199ARG10.8810.95541.056-0.085-0.0850.0000.0000.0000.000
200A200HIS00.016-0.00141.7500.0010.0010.0000.0000.0000.000
201A201VAL00.0100.00643.9940.0000.0000.0000.0000.0000.000
202A202ILE0-0.067-0.02946.440-0.003-0.0030.0000.0000.0000.000
203A203ILE00.0280.00648.3820.0010.0010.0000.0000.0000.000
204A204SER00.0110.00152.052-0.002-0.0020.0000.0000.0000.000
205A205LEU0-0.013-0.00955.8680.0010.0010.0000.0000.0000.000
206A206LYS10.8840.94456.591-0.053-0.0530.0000.0000.0000.000
207A207ARG10.9390.95859.932-0.046-0.0460.0000.0000.0000.000
208A208GLU-1-0.928-0.94663.2070.0450.0450.0000.0000.0000.000