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: YV332

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 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 208
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2078228.639632
FMO2-HF: Nuclear repulsion 1994846.626015
FMO2-HF: Total energy -83382.013618
FMO2-MP2: Total energy -83625.05509


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.
-21.456-21.57416.711-7.017-9.5750.024
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 : 0.008 / q_NPA : 0.010
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].
3A3MET0-0.062-0.0502.378-7.565-4.7904.269-2.853-4.190-0.031
4A4VAL00.0600.0604.1480.4800.6290.001-0.037-0.1130.000
5A5THR0-0.039-0.0227.8990.2610.2610.0000.0000.0000.000
6A6VAL00.0080.01510.0230.1140.1140.0000.0000.0000.000
7A7THR0-0.017-0.01212.9400.0480.0480.0000.0000.0000.000
8A8ALA0-0.030-0.03816.2390.0230.0230.0000.0000.0000.000
9A9LYS10.9941.01119.3240.1480.1480.0000.0000.0000.000
10A10THR00.0480.03820.8600.0040.0040.0000.0000.0000.000
11A11VAL00.0500.00815.223-0.019-0.0190.0000.0000.0000.000
12A12GLU-1-0.926-0.96816.806-0.031-0.0310.0000.0000.0000.000
13A13GLU-1-0.855-0.94218.474-0.121-0.1210.0000.0000.0000.000
14A14ALA0-0.024-0.00114.765-0.019-0.0190.0000.0000.0000.000
15A15VAL00.0450.01613.518-0.043-0.0430.0000.0000.0000.000
16A16THR00.0020.00414.578-0.003-0.0030.0000.0000.0000.000
17A17LYS10.8980.94215.9460.3310.3310.0000.0000.0000.000
18A18ALA00.0240.01311.003-0.039-0.0390.0000.0000.0000.000
19A19LEU0-0.002-0.00612.650-0.012-0.0120.0000.0000.0000.000
20A20ILE0-0.040-0.00914.2530.0090.0090.0000.0000.0000.000
21A21GLU-1-0.950-0.98712.307-0.747-0.7470.0000.0000.0000.000
22A22LEU0-0.064-0.0307.895-0.028-0.0280.0000.0000.0000.000
23A23GLN0-0.081-0.03011.9160.0860.0860.0000.0000.0000.000
24A24THR0-0.0180.00110.9120.0670.0670.0000.0000.0000.000
25A25THR0-0.017-0.02913.572-0.043-0.0430.0000.0000.0000.000
26A26SER00.0550.01514.4470.0600.0600.0000.0000.0000.000
27A27ASP-1-0.882-0.92514.6760.4610.4610.0000.0000.0000.000
28A28LYS10.8570.93212.067-0.358-0.3580.0000.0000.0000.000
29A29LEU00.0280.0339.1980.0650.0650.0000.0000.0000.000
30A30THR0-0.047-0.0185.7540.4420.4420.0000.0000.0000.000
31A31TYR0-0.021-0.0267.189-0.325-0.3250.0000.0000.0000.000
32A32GLU-1-0.878-0.9285.873-0.482-0.4820.0000.0000.0000.000
33A33ILE0-0.031-0.0368.722-0.162-0.1620.0000.0000.0000.000
34A34VAL0-0.049-0.01510.709-0.005-0.0050.0000.0000.0000.000
35A35GLU-1-0.878-0.95912.924-0.178-0.1780.0000.0000.0000.000
36A36LYS10.9410.98316.5690.0220.0220.0000.0000.0000.000
37A37GLY00.0460.01618.849-0.009-0.0090.0000.0000.0000.000
38A38SER0-0.003-0.01521.6750.0240.0240.0000.0000.0000.000
39A39ALA0-0.005-0.00725.419-0.016-0.0160.0000.0000.0000.000
40A40GLY00.0320.01628.7320.0080.0080.0000.0000.0000.000
41A41PHE0-0.0290.00232.218-0.003-0.0030.0000.0000.0000.000
42A42LEU00.0010.02335.3830.0040.0040.0000.0000.0000.000
43A43GLY00.0650.01836.4220.0040.0040.0000.0000.0000.000
44A44ILE0-0.010-0.03330.937-0.001-0.0010.0000.0000.0000.000
45A45GLY00.0320.02230.767-0.012-0.0120.0000.0000.0000.000
46A46SER0-0.097-0.03227.375-0.003-0.0030.0000.0000.0000.000
47A47LYS10.9280.93322.9970.2170.2170.0000.0000.0000.000
48A48PRO0-0.0230.04419.4770.0210.0210.0000.0000.0000.000
49A49ALA00.0550.02017.778-0.001-0.0010.0000.0000.0000.000
50A50ILE0-0.065-0.03412.993-0.034-0.0340.0000.0000.0000.000
51A51ILE0-0.036-0.01310.7820.0760.0760.0000.0000.0000.000
52A52ARG10.9490.9816.3461.3601.3600.0000.0000.0000.000
53A53ALA00.036-0.0016.4840.3560.3560.0000.0000.0000.000
54A54LYS10.9250.9762.446-19.041-22.16512.442-4.122-5.1960.055
55A55ARG11.0191.0035.0020.5310.613-0.001-0.005-0.0760.000
56A56LYS10.8880.9386.040-0.421-0.4210.0000.0000.0000.000
57A57GLU-1-0.951-0.9905.3203.1393.1390.0000.0000.0000.000
58A58THR0-0.069-0.0166.891-0.364-0.3640.0000.0000.0000.000
59A59LEU0-0.002-0.0159.5380.1360.1360.0000.0000.0000.000
60A60GLN00.0810.01811.9750.0510.0510.0000.0000.0000.000
61A61ASP-1-0.794-0.9016.8401.1661.1660.0000.0000.0000.000
62A62LYS10.9300.9688.758-1.745-1.7450.0000.0000.0000.000
63A63ALA0-0.055-0.0189.992-0.096-0.0960.0000.0000.0000.000
64A64ILE00.001-0.00910.003-0.070-0.0700.0000.0000.0000.000
65A65GLU-1-0.847-0.9046.9430.5080.5080.0000.0000.0000.000
66A66PHE0-0.058-0.0309.367-0.130-0.1300.0000.0000.0000.000
67A67LEU0-0.008-0.02612.642-0.084-0.0840.0000.0000.0000.000
68A68GLU-1-0.918-0.9489.2300.5470.5470.0000.0000.0000.000
69A69GLN00.0240.01111.002-0.118-0.1180.0000.0000.0000.000
70A70VAL0-0.041-0.02612.339-0.057-0.0570.0000.0000.0000.000
71A71PHE00.001-0.04415.679-0.039-0.0390.0000.0000.0000.000
72A72ASP-1-0.915-0.92313.4370.0520.0520.0000.0000.0000.000
73A73ALA00.0080.00215.478-0.035-0.0350.0000.0000.0000.000
74A74MET0-0.179-0.09317.488-0.009-0.0090.0000.0000.0000.000
75A75ASN0-0.056-0.01518.809-0.021-0.0210.0000.0000.0000.000
76A76MET0-0.096-0.04818.860-0.006-0.0060.0000.0000.0000.000
77A77ALA00.0510.04117.4140.0200.0200.0000.0000.0000.000
78A78VAL0-0.091-0.06316.678-0.009-0.0090.0000.0000.0000.000
79A79ASP-1-0.856-0.91715.9980.2080.2080.0000.0000.0000.000
80A80ILE0-0.037-0.02313.575-0.016-0.0160.0000.0000.0000.000
81A81SER0-0.024-0.00515.2290.0020.0020.0000.0000.0000.000
82A82VAL0-0.010-0.04414.5240.0020.0020.0000.0000.0000.000
83A83GLU-1-0.949-0.94217.2230.1970.1970.0000.0000.0000.000
84A84TYR0-0.021-0.02216.7250.0070.0070.0000.0000.0000.000
85A85ASN00.0050.01519.069-0.008-0.0080.0000.0000.0000.000
86A86GLU-1-0.857-0.95718.6070.4210.4210.0000.0000.0000.000
87A87THR0-0.043-0.02721.2500.0050.0050.0000.0000.0000.000
88A88GLU-1-0.902-0.95324.8710.1980.1980.0000.0000.0000.000
89A89LYS10.7830.92921.852-0.347-0.3470.0000.0000.0000.000
90A90GLU-1-0.950-0.99422.5810.2330.2330.0000.0000.0000.000
91A91MET0-0.044-0.01214.9590.0020.0020.0000.0000.0000.000
92A92ASN0-0.032-0.03220.101-0.022-0.0220.0000.0000.0000.000
93A93VAL0-0.010-0.00617.1540.0030.0030.0000.0000.0000.000
94A94ASN00.010-0.01519.678-0.022-0.0220.0000.0000.0000.000
95A95LEU00.0030.01118.6470.0180.0180.0000.0000.0000.000
96A96LYS10.9590.97320.609-0.155-0.1550.0000.0000.0000.000
97A97GLY00.0660.01420.6580.0140.0140.0000.0000.0000.000
98A98ASP-1-0.912-0.96022.3550.0590.0590.0000.0000.0000.000
99A99ASP-1-0.790-0.89921.9410.0820.0820.0000.0000.0000.000
100A100MET0-0.093-0.03721.3730.0040.0040.0000.0000.0000.000
101A101GLY0-0.047-0.02224.4740.0000.0000.0000.0000.0000.000
102A102ILE0-0.0080.00626.058-0.004-0.0040.0000.0000.0000.000
103A103LEU00.0210.01025.011-0.005-0.0050.0000.0000.0000.000
104A104ILE00.0320.00629.3150.0070.0070.0000.0000.0000.000
105A105GLY0-0.022-0.01132.2340.0050.0050.0000.0000.0000.000
106A106LYS10.9110.93830.031-0.095-0.0950.0000.0000.0000.000
107A107ARG11.0291.03327.626-0.099-0.0990.0000.0000.0000.000
108A108GLY0-0.0190.01528.2990.0110.0110.0000.0000.0000.000
109A109GLN00.0660.00629.0180.0000.0000.0000.0000.0000.000
110A110THR0-0.0420.00825.5650.0110.0110.0000.0000.0000.000
111A111LEU00.0940.04524.1860.0160.0160.0000.0000.0000.000
112A112ASP-1-0.927-0.96524.9960.1950.1950.0000.0000.0000.000
113A113SER0-0.072-0.04225.2630.0130.0130.0000.0000.0000.000
114A114LEU00.0530.03019.4210.0190.0190.0000.0000.0000.000
115A115GLN00.0410.03221.1790.0330.0330.0000.0000.0000.000
116A116TYR0-0.063-0.03222.0890.0260.0260.0000.0000.0000.000
117A117LEU00.012-0.00420.0830.0190.0190.0000.0000.0000.000
118A118VAL00.0830.03416.1490.0400.0400.0000.0000.0000.000
119A119SER00.010-0.00317.6340.0570.0570.0000.0000.0000.000
120A120LEU0-0.056-0.01219.6910.0270.0270.0000.0000.0000.000
121A121VAL0-0.008-0.00414.0610.0430.0430.0000.0000.0000.000
122A122VAL00.031-0.00414.8760.0760.0760.0000.0000.0000.000
123A123ASN0-0.045-0.03916.0640.0460.0460.0000.0000.0000.000
124A124LYS10.9301.00314.586-0.808-0.8080.0000.0000.0000.000
125A125SER0-0.120-0.06013.3690.1300.1300.0000.0000.0000.000
126A126SER0-0.014-0.02415.2690.0800.0800.0000.0000.0000.000
127A127SER0-0.018-0.00117.948-0.025-0.0250.0000.0000.0000.000
128A128ASP-1-0.840-0.88820.8780.3370.3370.0000.0000.0000.000
129A129TYR0-0.014-0.01821.5570.0220.0220.0000.0000.0000.000
130A130ILE0-0.0010.00018.722-0.014-0.0140.0000.0000.0000.000
131A131ARG10.9310.97221.970-0.260-0.2600.0000.0000.0000.000
132A132VAL00.0140.02718.4210.0060.0060.0000.0000.0000.000
133A133LYS10.8500.93021.749-0.242-0.2420.0000.0000.0000.000
134A134LEU00.0270.01719.8720.0140.0140.0000.0000.0000.000
135A135ASP-1-0.865-0.95022.9470.1450.1450.0000.0000.0000.000
136A136THR00.0440.02623.4230.0090.0090.0000.0000.0000.000
137A137GLU-1-0.823-0.89124.8730.1240.1240.0000.0000.0000.000
138A138ASN00.0550.01927.313-0.006-0.0060.0000.0000.0000.000
139A139TYR0-0.024-0.01528.944-0.013-0.0130.0000.0000.0000.000
140A140ARG10.8150.90526.477-0.198-0.1980.0000.0000.0000.000
141A141GLU-1-0.877-0.92131.6900.1030.1030.0000.0000.0000.000
142A142ARG10.8560.92229.958-0.115-0.1150.0000.0000.0000.000
143A143ARG10.8420.90233.704-0.103-0.1030.0000.0000.0000.000
144A144LYS10.9200.94935.761-0.108-0.1080.0000.0000.0000.000
145A145GLU-1-0.864-0.92337.8890.0720.0720.0000.0000.0000.000
146A146THR0-0.052-0.01738.141-0.006-0.0060.0000.0000.0000.000
147A147LEU00.012-0.00137.644-0.005-0.0050.0000.0000.0000.000
148A148GLU-1-0.832-0.92741.4990.0840.0840.0000.0000.0000.000
149A149THR0-0.086-0.04843.563-0.006-0.0060.0000.0000.0000.000
150A150LEU0-0.0170.00343.180-0.005-0.0050.0000.0000.0000.000
151A151ALA00.0030.00545.526-0.003-0.0030.0000.0000.0000.000
152A152LYS10.9590.97446.349-0.069-0.0690.0000.0000.0000.000
153A153ASN0-0.018-0.00347.672-0.004-0.0040.0000.0000.0000.000
154A154ILE0-0.021-0.03648.512-0.004-0.0040.0000.0000.0000.000
155A155ALA00.0490.03051.177-0.002-0.0020.0000.0000.0000.000
156A156TYR0-0.036-0.01153.367-0.003-0.0030.0000.0000.0000.000
157A157LYS11.0411.00950.898-0.047-0.0470.0000.0000.0000.000
158A158VAL0-0.0190.04554.081-0.002-0.0020.0000.0000.0000.000
159A159LYS10.9030.94856.349-0.049-0.0490.0000.0000.0000.000
160A160ARG10.9280.95758.596-0.035-0.0350.0000.0000.0000.000
161A161THR0-0.043-0.03758.089-0.001-0.0010.0000.0000.0000.000
162A162LYS10.8980.95360.522-0.038-0.0380.0000.0000.0000.000
163A163ARG10.9711.00055.880-0.040-0.0400.0000.0000.0000.000
164A164SER0-0.024-0.02655.0070.0010.0010.0000.0000.0000.000
165A165VAL0-0.026-0.01750.180-0.001-0.0010.0000.0000.0000.000
166A166SER0-0.0030.00748.7700.0020.0020.0000.0000.0000.000
167A167LEU0-0.037-0.01544.484-0.002-0.0020.0000.0000.0000.000
168A168GLU-1-0.857-0.93040.6750.0670.0670.0000.0000.0000.000
169A169PRO0-0.049-0.03539.8970.0020.0020.0000.0000.0000.000
170A170MET00.0010.01138.1030.0010.0010.0000.0000.0000.000
171A171ASN00.0910.06934.0300.0020.0020.0000.0000.0000.000
172A172PRO00.049-0.00335.669-0.004-0.0040.0000.0000.0000.000
173A173TYR00.0180.00832.409-0.005-0.0050.0000.0000.0000.000
174A174GLU-1-0.828-0.90335.5770.1030.1030.0000.0000.0000.000
175A175ARG10.8770.94038.129-0.102-0.1020.0000.0000.0000.000
176A176ARG10.9400.97939.255-0.115-0.1150.0000.0000.0000.000
177A177ILE0-0.0030.00137.219-0.004-0.0040.0000.0000.0000.000
178A178ILE00.0410.02041.519-0.005-0.0050.0000.0000.0000.000
179A179HIS0-0.046-0.03044.373-0.002-0.0020.0000.0000.0000.000
180A180ALA0-0.017-0.00344.049-0.003-0.0030.0000.0000.0000.000
181A181ALA0-0.0280.00045.296-0.003-0.0030.0000.0000.0000.000
182A182LEU0-0.037-0.02846.889-0.004-0.0040.0000.0000.0000.000
183A183GLN0-0.035-0.00547.367-0.001-0.0010.0000.0000.0000.000
184A184ASN0-0.027-0.02250.673-0.001-0.0010.0000.0000.0000.000
185A185ASP-1-0.814-0.89553.8660.0490.0490.0000.0000.0000.000
186A186LYS10.9210.94855.456-0.052-0.0520.0000.0000.0000.000
187A187TYR0-0.012-0.02158.246-0.002-0.0020.0000.0000.0000.000
188A188VAL0-0.051-0.01453.799-0.001-0.0010.0000.0000.0000.000
189A189VAL0-0.0030.00254.3200.0010.0010.0000.0000.0000.000
190A190THR0-0.0070.00049.2440.0010.0010.0000.0000.0000.000
191A191ARG10.9660.95649.845-0.058-0.0580.0000.0000.0000.000
192A192SER0-0.053-0.01645.4120.0000.0000.0000.0000.0000.000
193A193ASP-1-0.857-0.91347.0130.0630.0630.0000.0000.0000.000
194A194GLY00.0540.02445.7230.0020.0020.0000.0000.0000.000
195A195GLU-1-0.878-0.92943.2600.0810.0810.0000.0000.0000.000
196A196GLU-1-0.851-0.92237.5310.1020.1020.0000.0000.0000.000
197A197PRO00.006-0.00936.472-0.001-0.0010.0000.0000.0000.000
198A198PHE0-0.016-0.03438.528-0.001-0.0010.0000.0000.0000.000
199A199ARG10.8750.95341.124-0.088-0.0880.0000.0000.0000.000
200A200HIS00.009-0.00241.8390.0010.0010.0000.0000.0000.000
201A201VAL00.0270.01144.3770.0000.0000.0000.0000.0000.000
202A202ILE0-0.083-0.03746.550-0.003-0.0030.0000.0000.0000.000
203A203ILE00.0230.00648.6790.0010.0010.0000.0000.0000.000
204A204SER00.000-0.00852.195-0.002-0.0020.0000.0000.0000.000
205A205LEU0-0.022-0.00656.0080.0010.0010.0000.0000.0000.000
206A206LYS10.9500.98557.693-0.052-0.0520.0000.0000.0000.000
207A207ARG10.9430.96160.051-0.047-0.0470.0000.0000.0000.000
208A208GLU-1-0.939-0.95663.3110.0450.0450.0000.0000.0000.000