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: 435GN

Calculation Name: 3GKU-B-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3GKU

Chain ID: B

ChEMBL ID:

UniProt ID: D0VX24

Base Structure: X-ray

Registration Date: 2023-06-19

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 193
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -1904694.366545
FMO2-HF: Nuclear repulsion 1826759.710162
FMO2-HF: Total energy -77934.656383
FMO2-MP2: Total energy -78162.180932


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(B:2:ASP)


Summations of interaction energy for fragment #1(B:2:ASP)
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.
-123.158-124.45821.68-10.993-9.3890.127
Interaction energy analysis for fragmet #1(B:2:ASP)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : -1 / q_Mulliken : -0.804 / q_NPA : -0.890
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].
3B4VAL00.0270.0133.4109.25212.1530.147-1.435-1.6130.005
4B5THR0-0.0050.0006.173-1.772-1.7720.0000.0000.0000.000
5B6VAL0-0.017-0.0108.904-1.956-1.9560.0000.0000.0000.000
6B7THR00.011-0.00112.566-0.080-0.0800.0000.0000.0000.000
7B8ALA0-0.022-0.01515.746-0.590-0.5900.0000.0000.0000.000
8B9LYS10.8050.88919.291-12.805-12.8050.0000.0000.0000.000
9B10THR0-0.046-0.03221.280-0.095-0.0950.0000.0000.0000.000
10B11VAL00.0620.02616.2040.7750.7750.0000.0000.0000.000
11B12GLU-1-0.780-0.88917.52816.12216.1220.0000.0000.0000.000
12B13GLU-1-0.814-0.87919.95513.54113.5410.0000.0000.0000.000
13B14ALA0-0.009-0.01015.9400.1960.1960.0000.0000.0000.000
14B15VAL00.0570.02214.9541.0731.0730.0000.0000.0000.000
15B16THR0-0.068-0.04216.1980.3870.3870.0000.0000.0000.000
16B17LYS10.8010.88416.316-17.847-17.8470.0000.0000.0000.000
17B18ALA00.0310.01412.791-0.571-0.5710.0000.0000.0000.000
18B19LEU0-0.0180.00414.1320.9180.9180.0000.0000.0000.000
19B20ILE00.0280.01615.757-0.338-0.3380.0000.0000.0000.000
20B21GLU-1-0.823-0.89614.88918.86818.8680.0000.0000.0000.000
21B22LEU0-0.032-0.0089.8240.3990.3990.0000.0000.0000.000
22B23GLN0-0.020-0.02213.805-0.368-0.3680.0000.0000.0000.000
23B24THR0-0.039-0.00112.573-0.364-0.3640.0000.0000.0000.000
24B25THR00.012-0.00915.574-0.805-0.8050.0000.0000.0000.000
25B26SER00.007-0.01315.5480.8760.8760.0000.0000.0000.000
26B27ASP-1-0.874-0.91915.84416.68916.6890.0000.0000.0000.000
27B28LYS10.8590.92512.089-21.162-21.1620.0000.0000.0000.000
28B29LEU0-0.021-0.00810.5242.0752.0750.0000.0000.0000.000
29B30THR0-0.023-0.0147.156-0.963-0.9630.0000.0000.0000.000
30B31TYR0-0.021-0.0279.2001.6511.6510.0000.0000.0000.000
31B32GLU-1-0.898-0.9417.13534.79334.7930.0000.0000.0000.000
32B33ILE0-0.007-0.02210.327-0.445-0.4450.0000.0000.0000.000
33B34VAL0-0.0260.00510.622-0.971-0.9710.0000.0000.0000.000
34B47LYS10.9730.97124.175-12.466-12.4660.0000.0000.0000.000
35B48PRO0-0.042-0.00918.894-0.002-0.0020.0000.0000.0000.000
36B49ALA00.0670.01817.806-0.350-0.3500.0000.0000.0000.000
37B50ILE0-0.037-0.00311.0550.1980.1980.0000.0000.0000.000
38B51ILE00.0330.02911.447-0.063-0.0630.0000.0000.0000.000
39B52ARG10.8680.9231.794-97.702-98.2889.227-4.734-3.9080.067
40B53ALA00.0780.0287.603-2.274-2.2740.0000.0000.0000.000
41B54LYS10.8870.9291.958-75.538-79.15312.306-4.824-3.8680.055
42B55ARG10.8850.9406.793-26.000-26.0000.0000.0000.0000.000
43B56LYS10.9220.9648.342-23.761-23.7610.0000.0000.0000.000
44B57GLU-1-0.814-0.8939.16522.23322.2330.0000.0000.0000.000
45B58THR0-0.049-0.03810.267-1.456-1.4560.0000.0000.0000.000
46B59LEU00.0410.03413.6060.2050.2050.0000.0000.0000.000
47B60GLN00.0660.02616.620-0.036-0.0360.0000.0000.0000.000
48B61ASP-1-0.792-0.88211.46521.71921.7190.0000.0000.0000.000
49B62LYS10.8460.91211.853-20.577-20.5770.0000.0000.0000.000
50B63ALA0-0.038-0.01514.941-0.621-0.6210.0000.0000.0000.000
51B64ILE0-0.032-0.03815.992-0.556-0.5560.0000.0000.0000.000
52B65GLU-1-0.866-0.91712.86718.45218.4520.0000.0000.0000.000
53B66PHE00.0100.00015.167-0.761-0.7610.0000.0000.0000.000
54B67LEU0-0.024-0.02618.014-0.560-0.5600.0000.0000.0000.000
55B68GLU-1-0.917-0.95216.56015.17215.1720.0000.0000.0000.000
56B69GLN0-0.0110.00015.144-0.764-0.7640.0000.0000.0000.000
57B70VAL0-0.052-0.03119.072-0.617-0.6170.0000.0000.0000.000
58B71PHE0-0.043-0.05522.469-0.669-0.6690.0000.0000.0000.000
59B72ASP-1-0.881-0.91320.50312.85312.8530.0000.0000.0000.000
60B73ALA0-0.015-0.00722.559-0.422-0.4220.0000.0000.0000.000
61B74MET0-0.149-0.08024.455-0.469-0.4690.0000.0000.0000.000
62B75ASN0-0.084-0.03626.136-0.297-0.2970.0000.0000.0000.000
63B76MET0-0.069-0.02526.263-0.373-0.3730.0000.0000.0000.000
64B77ALA00.0410.01624.4260.4430.4430.0000.0000.0000.000
65B78VAL0-0.079-0.04724.523-0.390-0.3900.0000.0000.0000.000
66B79ASP-1-0.891-0.93923.23511.94611.9460.0000.0000.0000.000
67B80ILE0-0.019-0.01520.244-0.477-0.4770.0000.0000.0000.000
68B81SER0-0.054-0.01621.6260.2310.2310.0000.0000.0000.000
69B82VAL00.007-0.02419.503-0.333-0.3330.0000.0000.0000.000
70B83GLU-1-0.899-0.91721.69711.38711.3870.0000.0000.0000.000
71B84TYR0-0.031-0.05820.537-0.191-0.1910.0000.0000.0000.000
72B85ASN00.0390.03723.4640.3730.3730.0000.0000.0000.000
73B86GLU-1-0.756-0.89020.53713.76513.7650.0000.0000.0000.000
74B87THR0-0.058-0.01424.141-0.084-0.0840.0000.0000.0000.000
75B88GLU-1-0.881-0.94527.4229.2079.2070.0000.0000.0000.000
76B89LYS10.8010.92523.236-12.566-12.5660.0000.0000.0000.000
77B90GLU-1-0.780-0.87625.9449.3939.3930.0000.0000.0000.000
78B91MET0-0.045-0.00119.7180.1970.1970.0000.0000.0000.000
79B92ASN0-0.052-0.03824.955-0.610-0.6100.0000.0000.0000.000
80B93VAL00.0230.00123.1170.3180.3180.0000.0000.0000.000
81B94ASN0-0.024-0.02325.464-0.591-0.5910.0000.0000.0000.000
82B95LEU00.0040.01725.5920.3640.3640.0000.0000.0000.000
83B96LYS10.8410.88526.988-10.444-10.4440.0000.0000.0000.000
84B97GLY00.1340.07028.3640.2390.2390.0000.0000.0000.000
85B98ASP-1-0.918-0.95830.0208.8678.8670.0000.0000.0000.000
86B99ASP-1-0.770-0.88429.0329.6009.6000.0000.0000.0000.000
87B100MET0-0.0260.00328.580-0.105-0.1050.0000.0000.0000.000
88B101GLY0-0.036-0.02332.298-0.271-0.2710.0000.0000.0000.000
89B102ILE00.0230.01333.391-0.358-0.3580.0000.0000.0000.000
90B103LEU00.0070.00030.714-0.172-0.1720.0000.0000.0000.000
91B104ILE0-0.0120.01135.359-0.130-0.1300.0000.0000.0000.000
92B105GLY0-0.023-0.01538.822-0.047-0.0470.0000.0000.0000.000
93B106LYS10.8660.93935.984-8.099-8.0990.0000.0000.0000.000
94B107ARG10.9650.96034.750-7.880-7.8800.0000.0000.0000.000
95B108GLY00.0640.05834.7000.2100.2100.0000.0000.0000.000
96B109GLN00.0510.03335.4790.2210.2210.0000.0000.0000.000
97B110THR0-0.015-0.01432.0180.1700.1700.0000.0000.0000.000
98B111LEU00.0080.00330.2780.2350.2350.0000.0000.0000.000
99B112ASP-1-0.818-0.89930.6608.8278.8270.0000.0000.0000.000
100B113SER0-0.067-0.04131.2730.1020.1020.0000.0000.0000.000
101B114LEU00.0140.00925.8200.2110.2110.0000.0000.0000.000
102B115GLN00.0400.02426.6120.3590.3590.0000.0000.0000.000
103B116TYR0-0.036-0.00527.3150.2950.2950.0000.0000.0000.000
104B117LEU00.0440.01324.8620.2510.2510.0000.0000.0000.000
105B118VAL00.0320.01721.2950.4500.4500.0000.0000.0000.000
106B119SER00.0250.01622.5820.5690.5690.0000.0000.0000.000
107B120LEU0-0.050-0.02223.9490.3030.3030.0000.0000.0000.000
108B121VAL0-0.027-0.01918.3440.2970.2970.0000.0000.0000.000
109B122VAL0-0.011-0.02019.4400.5460.5460.0000.0000.0000.000
110B123ASN0-0.033-0.02520.2430.2520.2520.0000.0000.0000.000
111B124LYS10.9450.98320.012-13.428-13.4280.0000.0000.0000.000
112B125SER0-0.083-0.03216.0770.6430.6430.0000.0000.0000.000
113B126SER0-0.006-0.02117.8820.8020.8020.0000.0000.0000.000
114B127SER0-0.0020.01020.495-0.136-0.1360.0000.0000.0000.000
115B128ASP-1-0.902-0.94922.85512.07112.0710.0000.0000.0000.000
116B129TYR0-0.031-0.00724.3860.2150.2150.0000.0000.0000.000
117B130ILE00.0280.01422.026-0.184-0.1840.0000.0000.0000.000
118B131ARG10.7430.86725.548-9.818-9.8180.0000.0000.0000.000
119B132VAL00.0240.00723.5760.0310.0310.0000.0000.0000.000
120B133LYS10.7710.87326.797-9.960-9.9600.0000.0000.0000.000
121B134LEU0-0.0110.00225.6600.2480.2480.0000.0000.0000.000
122B135ASP-1-0.842-0.95128.6458.4198.4190.0000.0000.0000.000
123B136THR00.0390.04530.0070.1450.1450.0000.0000.0000.000
124B137GLU-1-0.732-0.85831.4019.1019.1010.0000.0000.0000.000
125B138ASN00.0240.00233.393-0.260-0.2600.0000.0000.0000.000
126B139TYR0-0.034-0.01935.339-0.355-0.3550.0000.0000.0000.000
127B140ARG10.7780.87232.159-9.141-9.1410.0000.0000.0000.000
128B141GLU-1-0.815-0.89737.0827.0657.0650.0000.0000.0000.000
129B142ARG10.8890.94036.763-8.108-8.1080.0000.0000.0000.000
130B143ARG10.8530.92940.207-7.161-7.1610.0000.0000.0000.000
131B144LYS10.8320.89441.688-7.180-7.1800.0000.0000.0000.000
132B145GLU-1-0.887-0.93343.4466.5456.5450.0000.0000.0000.000
133B146THR0-0.033-0.02544.903-0.206-0.2060.0000.0000.0000.000
134B147LEU0-0.0030.00044.307-0.167-0.1670.0000.0000.0000.000
135B148GLU-1-0.851-0.92846.4156.3856.3850.0000.0000.0000.000
136B149THR0-0.106-0.05749.647-0.208-0.2080.0000.0000.0000.000
137B150LEU00.0100.00849.835-0.162-0.1620.0000.0000.0000.000
138B151ALA00.0150.00451.730-0.140-0.1400.0000.0000.0000.000
139B152LYS10.9830.98451.659-6.064-6.0640.0000.0000.0000.000
140B153ASN00.0120.01955.290-0.171-0.1710.0000.0000.0000.000
141B154ILE0-0.036-0.01655.648-0.148-0.1480.0000.0000.0000.000
142B155ALA00.0450.03757.606-0.113-0.1130.0000.0000.0000.000
143B156TYR00.0470.00759.431-0.151-0.1510.0000.0000.0000.000
144B157LYS10.9960.99459.745-5.271-5.2710.0000.0000.0000.000
145B158VAL0-0.030-0.00260.704-0.104-0.1040.0000.0000.0000.000
146B159LYS10.8750.94563.440-4.901-4.9010.0000.0000.0000.000
147B160ARG10.8750.94165.539-4.639-4.6390.0000.0000.0000.000
148B161THR0-0.012-0.01165.456-0.065-0.0650.0000.0000.0000.000
149B162LYS10.9000.95967.626-4.477-4.4770.0000.0000.0000.000
150B163ARG11.0131.00565.429-4.689-4.6890.0000.0000.0000.000
151B164SER0-0.061-0.05261.5910.0260.0260.0000.0000.0000.000
152B165VAL0-0.016-0.01457.841-0.045-0.0450.0000.0000.0000.000
153B166SER00.0080.00956.1760.0600.0600.0000.0000.0000.000
154B167LEU0-0.041-0.01351.761-0.031-0.0310.0000.0000.0000.000
155B168GLU-1-0.886-0.94848.1946.2156.2150.0000.0000.0000.000
156B169PRO0-0.035-0.01947.632-0.007-0.0070.0000.0000.0000.000
157B170MET0-0.0100.00745.0560.0670.0670.0000.0000.0000.000
158B171ASN00.0490.03440.156-0.029-0.0290.0000.0000.0000.000
159B172PRO00.0470.00341.408-0.117-0.1170.0000.0000.0000.000
160B173TYR00.0190.01436.153-0.183-0.1830.0000.0000.0000.000
161B174GLU-1-0.779-0.88041.6697.0767.0760.0000.0000.0000.000
162B175ARG10.8170.89144.016-6.736-6.7360.0000.0000.0000.000
163B176ARG10.9430.97141.744-7.165-7.1650.0000.0000.0000.000
164B177ILE00.0330.02541.891-0.120-0.1200.0000.0000.0000.000
165B178ILE0-0.008-0.00346.300-0.140-0.1400.0000.0000.0000.000
166B179HIS0-0.022-0.01749.005-0.036-0.0360.0000.0000.0000.000
167B180ALA00.021-0.00447.927-0.109-0.1090.0000.0000.0000.000
168B181ALA00.0100.02549.960-0.091-0.0910.0000.0000.0000.000
169B182LEU0-0.104-0.05651.620-0.110-0.1100.0000.0000.0000.000
170B183GLN0-0.0280.00351.225-0.016-0.0160.0000.0000.0000.000
171B184ASN00.0240.00154.601-0.026-0.0260.0000.0000.0000.000
172B185ASP-1-0.774-0.87557.2805.0955.0950.0000.0000.0000.000
173B186LYS10.8860.93359.192-5.151-5.1510.0000.0000.0000.000
174B187TYR0-0.108-0.06760.224-0.131-0.1310.0000.0000.0000.000
175B188VAL0-0.050-0.02059.357-0.077-0.0770.0000.0000.0000.000
176B189VAL00.0070.00959.3930.0650.0650.0000.0000.0000.000
177B190THR00.0330.01954.1620.0450.0450.0000.0000.0000.000
178B191ARG10.8950.94455.556-5.262-5.2620.0000.0000.0000.000
179B192SER00.009-0.02950.4360.0480.0480.0000.0000.0000.000
180B193ASP-1-0.860-0.92152.5905.4185.4180.0000.0000.0000.000
181B194GLY0-0.0040.02552.3450.0760.0760.0000.0000.0000.000
182B195GLU-1-0.866-0.94049.6056.0206.0200.0000.0000.0000.000
183B196GLU-1-0.793-0.86143.6496.7716.7710.0000.0000.0000.000
184B197PRO0-0.015-0.00243.988-0.024-0.0240.0000.0000.0000.000
185B198PHE00.022-0.03845.826-0.010-0.0100.0000.0000.0000.000
186B199ARG10.8660.94647.642-6.234-6.2340.0000.0000.0000.000
187B200HIS10.8610.93448.703-5.636-5.6360.0000.0000.0000.000
188B201VAL00.0440.01850.246-0.051-0.0510.0000.0000.0000.000
189B202ILE0-0.054-0.03452.823-0.054-0.0540.0000.0000.0000.000
190B203ILE00.0330.03454.846-0.013-0.0130.0000.0000.0000.000
191B204SER00.0210.00458.321-0.053-0.0530.0000.0000.0000.000
192B205LEU00.0040.01361.9620.0110.0110.0000.0000.0000.000
193B206LYS10.9760.99863.017-4.618-4.6180.0000.0000.0000.000