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: K3JQ3

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 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 193
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -1904802.057327
FMO2-HF: Nuclear repulsion 1826869.84293
FMO2-HF: Total energy -77932.214397
FMO2-MP2: Total energy -78159.956478


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.
-29.892-26.6180.003-1.659-1.6170.009
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 : -0.901 / q_NPA : -0.948
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].
3B4VAL00.0140.0063.8511.7204.452-0.016-1.520-1.1960.008
4B5THR0-0.024-0.0116.999-1.155-1.1550.0000.0000.0000.000
5B6VAL0-0.0070.0029.916-1.044-1.0440.0000.0000.0000.000
6B7THR00.002-0.00813.485-0.154-0.1540.0000.0000.0000.000
7B8ALA0-0.022-0.01216.727-0.408-0.4080.0000.0000.0000.000
8B9LYS10.8080.89820.197-11.752-11.7520.0000.0000.0000.000
9B10THR0-0.0040.00222.0040.0990.0990.0000.0000.0000.000
10B11VAL00.0610.02816.4580.5750.5750.0000.0000.0000.000
11B12GLU-1-0.831-0.93317.73514.91214.9120.0000.0000.0000.000
12B13GLU-1-0.808-0.88219.98312.39812.3980.0000.0000.0000.000
13B14ALA0-0.008-0.01916.7200.1900.1900.0000.0000.0000.000
14B15VAL00.0610.02415.2880.9080.9080.0000.0000.0000.000
15B16THR0-0.074-0.04416.2030.3780.3780.0000.0000.0000.000
16B17LYS10.8190.91316.342-16.474-16.4740.0000.0000.0000.000
17B18ALA00.0240.00613.147-0.379-0.3790.0000.0000.0000.000
18B19LEU0-0.0210.00313.8430.9460.9460.0000.0000.0000.000
19B20ILE00.0250.01215.529-0.160-0.1600.0000.0000.0000.000
20B21GLU-1-0.851-0.91214.80017.53017.5300.0000.0000.0000.000
21B22LEU0-0.033-0.0159.2320.5850.5850.0000.0000.0000.000
22B23GLN0-0.035-0.03513.168-0.238-0.2380.0000.0000.0000.000
23B24THR0-0.081-0.00712.009-0.085-0.0850.0000.0000.0000.000
24B25THR00.0510.01714.679-0.773-0.7730.0000.0000.0000.000
25B26SER00.025-0.01315.2640.7480.7480.0000.0000.0000.000
26B27ASP-1-0.893-0.93015.86416.23216.2320.0000.0000.0000.000
27B28LYS10.8790.94611.440-20.866-20.8660.0000.0000.0000.000
28B29LEU0-0.031-0.01910.7002.1362.1360.0000.0000.0000.000
29B30THR0-0.021-0.0137.138-0.621-0.6210.0000.0000.0000.000
30B31TYR0-0.022-0.0299.2101.1341.1340.0000.0000.0000.000
31B32GLU-1-0.913-0.9467.20828.84928.8490.0000.0000.0000.000
32B33ILE00.005-0.01810.317-0.532-0.5320.0000.0000.0000.000
33B34VAL0-0.0290.00211.455-0.762-0.7620.0000.0000.0000.000
34B47LYS10.9750.97625.129-11.497-11.4970.0000.0000.0000.000
35B48PRO0-0.036-0.01319.9710.0230.0230.0000.0000.0000.000
36B49ALA00.0580.01418.729-0.289-0.2890.0000.0000.0000.000
37B50ILE0-0.0190.00311.6670.2410.2410.0000.0000.0000.000
38B51ILE00.0290.02912.167-0.069-0.0690.0000.0000.0000.000
39B52ARG10.9150.9574.237-41.345-41.230-0.001-0.010-0.1030.000
40B53ALA00.0770.0237.826-1.161-1.1610.0000.0000.0000.000
41B54LYS10.9550.9873.203-40.972-40.5450.020-0.129-0.3180.001
42B55ARG10.9630.9676.654-25.079-25.0790.0000.0000.0000.000
43B56LYS10.9050.9547.732-22.447-22.4470.0000.0000.0000.000
44B57GLU-1-0.938-0.9748.82725.82425.8240.0000.0000.0000.000
45B58THR0-0.0330.0169.762-1.719-1.7190.0000.0000.0000.000
46B59LEU00.0410.02812.9740.3790.3790.0000.0000.0000.000
47B60GLN00.0920.02816.0150.1850.1850.0000.0000.0000.000
48B61ASP-1-0.843-0.93810.59623.07823.0780.0000.0000.0000.000
49B62LYS10.9480.97611.757-21.345-21.3450.0000.0000.0000.000
50B63ALA0-0.046-0.02014.631-0.619-0.6190.0000.0000.0000.000
51B64ILE0-0.038-0.04215.625-0.637-0.6370.0000.0000.0000.000
52B65GLU-1-0.869-0.91112.90121.21221.2120.0000.0000.0000.000
53B66PHE0-0.010-0.01015.240-0.867-0.8670.0000.0000.0000.000
54B67LEU0-0.020-0.03218.261-0.621-0.6210.0000.0000.0000.000
55B68GLU-1-0.899-0.94316.37316.65316.6530.0000.0000.0000.000
56B69GLN00.0390.02217.044-0.142-0.1420.0000.0000.0000.000
57B70VAL0-0.068-0.03519.569-0.700-0.7000.0000.0000.0000.000
58B71PHE0-0.050-0.05522.840-0.758-0.7580.0000.0000.0000.000
59B72ASP-1-0.904-0.92220.89014.12014.1200.0000.0000.0000.000
60B73ALA0-0.014-0.01123.000-0.473-0.4730.0000.0000.0000.000
61B74MET0-0.156-0.07825.044-0.544-0.5440.0000.0000.0000.000
62B75ASN0-0.045-0.01826.662-0.115-0.1150.0000.0000.0000.000
63B76MET0-0.080-0.03726.651-0.434-0.4340.0000.0000.0000.000
64B77ALA00.0430.01424.5910.5090.5090.0000.0000.0000.000
65B78VAL0-0.056-0.03524.402-0.474-0.4740.0000.0000.0000.000
66B79ASP-1-0.903-0.94723.09012.89812.8980.0000.0000.0000.000
67B80ILE0-0.016-0.01320.029-0.620-0.6200.0000.0000.0000.000
68B81SER0-0.048-0.02021.1880.2070.2070.0000.0000.0000.000
69B82VAL0-0.008-0.02519.045-0.398-0.3980.0000.0000.0000.000
70B83GLU-1-0.928-0.94121.05611.45411.4540.0000.0000.0000.000
71B84TYR0-0.002-0.03419.730-0.265-0.2650.0000.0000.0000.000
72B85ASN00.0460.03822.7450.4030.4030.0000.0000.0000.000
73B86GLU-1-0.857-0.95120.55613.71813.7180.0000.0000.0000.000
74B87THR0-0.061-0.02323.391-0.120-0.1200.0000.0000.0000.000
75B88GLU-1-0.952-0.98626.6649.3109.3100.0000.0000.0000.000
76B89LYS10.8490.95522.935-12.093-12.0930.0000.0000.0000.000
77B90GLU-1-0.923-0.97125.3289.6959.6950.0000.0000.0000.000
78B91MET0-0.068-0.00619.2230.2310.2310.0000.0000.0000.000
79B92ASN0-0.014-0.01824.345-0.494-0.4940.0000.0000.0000.000
80B93VAL00.0340.00622.1740.3190.3190.0000.0000.0000.000
81B94ASN0-0.0020.00124.950-0.770-0.7700.0000.0000.0000.000
82B95LEU0-0.0110.01425.1870.4180.4180.0000.0000.0000.000
83B96LYS10.9060.93426.645-10.977-10.9770.0000.0000.0000.000
84B97GLY00.1240.06428.2050.2840.2840.0000.0000.0000.000
85B98ASP-1-0.901-0.95029.9199.4339.4330.0000.0000.0000.000
86B99ASP-1-0.749-0.86528.96310.29210.2920.0000.0000.0000.000
87B100MET0-0.065-0.01528.656-0.136-0.1360.0000.0000.0000.000
88B101GLY0-0.038-0.02732.301-0.312-0.3120.0000.0000.0000.000
89B102ILE00.0170.00633.706-0.384-0.3840.0000.0000.0000.000
90B103LEU00.031-0.00431.110-0.189-0.1890.0000.0000.0000.000
91B104ILE0-0.042-0.00135.514-0.168-0.1680.0000.0000.0000.000
92B105GLY0-0.068-0.04738.888-0.050-0.0500.0000.0000.0000.000
93B106LYS10.8870.97536.762-8.254-8.2540.0000.0000.0000.000
94B107ARG10.9930.97034.634-8.267-8.2670.0000.0000.0000.000
95B108GLY00.0690.03934.6940.2020.2020.0000.0000.0000.000
96B109GLN00.0410.02935.4230.2210.2210.0000.0000.0000.000
97B110THR00.0260.03431.3770.1500.1500.0000.0000.0000.000
98B111LEU0-0.013-0.00629.8730.2540.2540.0000.0000.0000.000
99B112ASP-1-0.843-0.91530.5709.1039.1030.0000.0000.0000.000
100B113SER0-0.073-0.05031.3400.0970.0970.0000.0000.0000.000
101B114LEU00.0210.01525.9790.2040.2040.0000.0000.0000.000
102B115GLN00.0110.01626.6270.2980.2980.0000.0000.0000.000
103B116TYR0-0.0260.00027.1800.2350.2350.0000.0000.0000.000
104B117LEU00.0460.01325.2330.2360.2360.0000.0000.0000.000
105B118VAL00.0410.02221.3540.4550.4550.0000.0000.0000.000
106B119SER0-0.0010.01022.4440.5470.5470.0000.0000.0000.000
107B120LEU0-0.038-0.01423.7580.2650.2650.0000.0000.0000.000
108B121VAL0-0.019-0.01218.3930.2380.2380.0000.0000.0000.000
109B122VAL0-0.029-0.02719.0460.5440.5440.0000.0000.0000.000
110B123ASN0-0.030-0.02719.9650.2290.2290.0000.0000.0000.000
111B124LYS10.9700.99519.671-13.837-13.8370.0000.0000.0000.000
112B125SER0-0.094-0.03915.9660.7050.7050.0000.0000.0000.000
113B126SER0-0.002-0.02217.5790.7450.7450.0000.0000.0000.000
114B127SER00.0090.02520.265-0.158-0.1580.0000.0000.0000.000
115B128ASP-1-0.942-0.97222.87012.00112.0010.0000.0000.0000.000
116B129TYR0-0.023-0.00123.9780.2690.2690.0000.0000.0000.000
117B130ILE00.0270.01721.601-0.213-0.2130.0000.0000.0000.000
118B131ARG10.9050.95525.089-9.746-9.7460.0000.0000.0000.000
119B132VAL00.0220.01023.6470.0130.0130.0000.0000.0000.000
120B133LYS10.8880.94326.343-9.751-9.7510.0000.0000.0000.000
121B134LEU0-0.007-0.00125.4210.2760.2760.0000.0000.0000.000
122B135ASP-1-0.861-0.97228.2378.7848.7840.0000.0000.0000.000
123B136THR00.0680.05129.5380.1400.1400.0000.0000.0000.000
124B137GLU-1-0.840-0.93930.9979.3259.3250.0000.0000.0000.000
125B138ASN00.0360.00032.986-0.256-0.2560.0000.0000.0000.000
126B139TYR0-0.055-0.04234.877-0.391-0.3910.0000.0000.0000.000
127B140ARG10.7930.89331.901-9.488-9.4880.0000.0000.0000.000
128B141GLU-1-0.853-0.92636.6357.1867.1860.0000.0000.0000.000
129B142ARG10.9500.99536.560-8.360-8.3600.0000.0000.0000.000
130B143ARG10.8580.94439.766-7.428-7.4280.0000.0000.0000.000
131B144LYS10.8820.93040.445-7.603-7.6030.0000.0000.0000.000
132B145GLU-1-0.871-0.92043.0026.6346.6340.0000.0000.0000.000
133B146THR0-0.044-0.03544.615-0.199-0.1990.0000.0000.0000.000
134B147LEU00.0030.00343.849-0.173-0.1730.0000.0000.0000.000
135B148GLU-1-0.904-0.95746.1996.5416.5410.0000.0000.0000.000
136B149THR0-0.077-0.02949.202-0.228-0.2280.0000.0000.0000.000
137B150LEU0-0.0010.00449.977-0.171-0.1710.0000.0000.0000.000
138B151ALA00.0170.00251.354-0.149-0.1490.0000.0000.0000.000
139B152LYS10.9940.98752.243-6.075-6.0750.0000.0000.0000.000
140B153ASN00.0300.02855.047-0.160-0.1600.0000.0000.0000.000
141B154ILE0-0.052-0.03255.411-0.155-0.1550.0000.0000.0000.000
142B155ALA00.0470.03957.257-0.119-0.1190.0000.0000.0000.000
143B156TYR00.020-0.00359.058-0.147-0.1470.0000.0000.0000.000
144B157LYS10.9760.97759.296-5.413-5.4130.0000.0000.0000.000
145B158VAL0-0.040-0.00560.724-0.107-0.1070.0000.0000.0000.000
146B159LYS10.9400.98463.178-4.919-4.9190.0000.0000.0000.000
147B160ARG10.8650.93165.205-4.721-4.7210.0000.0000.0000.000
148B161THR0-0.018-0.00565.220-0.062-0.0620.0000.0000.0000.000
149B162LYS10.8980.95667.320-4.560-4.5600.0000.0000.0000.000
150B163ARG11.0031.00665.351-4.800-4.8000.0000.0000.0000.000
151B164SER0-0.071-0.07361.5770.0280.0280.0000.0000.0000.000
152B165VAL00.000-0.00257.805-0.046-0.0460.0000.0000.0000.000
153B166SER0-0.0100.00256.2580.0540.0540.0000.0000.0000.000
154B167LEU0-0.033-0.00751.495-0.032-0.0320.0000.0000.0000.000
155B168GLU-1-0.861-0.94848.6976.3656.3650.0000.0000.0000.000
156B169PRO0-0.063-0.02347.7530.0010.0010.0000.0000.0000.000
157B170MET00.0050.01445.0210.0720.0720.0000.0000.0000.000
158B171ASN00.0720.06440.129-0.116-0.1160.0000.0000.0000.000
159B172PRO00.046-0.00541.416-0.119-0.1190.0000.0000.0000.000
160B173TYR00.0260.02037.078-0.129-0.1290.0000.0000.0000.000
161B174GLU-1-0.829-0.92441.4917.2997.2990.0000.0000.0000.000
162B175ARG10.7910.88843.825-6.905-6.9050.0000.0000.0000.000
163B176ARG10.9480.97141.468-7.293-7.2930.0000.0000.0000.000
164B177ILE00.0400.02941.672-0.125-0.1250.0000.0000.0000.000
165B178ILE0-0.0120.00145.921-0.147-0.1470.0000.0000.0000.000
166B179HIS0-0.045-0.05448.846-0.048-0.0480.0000.0000.0000.000
167B180ALA00.006-0.00447.479-0.113-0.1130.0000.0000.0000.000
168B181ALA00.0280.03049.546-0.098-0.0980.0000.0000.0000.000
169B182LEU0-0.071-0.05051.178-0.117-0.1170.0000.0000.0000.000
170B183GLN0-0.0250.01350.876-0.026-0.0260.0000.0000.0000.000
171B184ASN00.007-0.01354.180-0.032-0.0320.0000.0000.0000.000
172B185ASP-1-0.791-0.88756.8395.1885.1880.0000.0000.0000.000
173B186LYS10.8890.93858.738-5.217-5.2170.0000.0000.0000.000
174B187TYR0-0.119-0.06959.695-0.136-0.1360.0000.0000.0000.000
175B188VAL0-0.041-0.02059.054-0.078-0.0780.0000.0000.0000.000
176B189VAL00.0220.02459.0830.0690.0690.0000.0000.0000.000
177B190THR00.0080.00853.4570.0490.0490.0000.0000.0000.000
178B191ARG10.9670.98055.372-5.390-5.3900.0000.0000.0000.000
179B192SER00.001-0.00450.1890.0550.0550.0000.0000.0000.000
180B193ASP-1-0.893-0.95252.6165.5675.5670.0000.0000.0000.000
181B194GLY00.0160.03352.4660.0860.0860.0000.0000.0000.000
182B195GLU-1-0.845-0.93950.1496.0836.0830.0000.0000.0000.000
183B196GLU-1-0.843-0.89043.9786.9526.9520.0000.0000.0000.000
184B197PRO0-0.0020.00444.377-0.017-0.0170.0000.0000.0000.000
185B198PHE00.016-0.04246.167-0.005-0.0050.0000.0000.0000.000
186B199ARG10.8930.95747.810-6.416-6.4160.0000.0000.0000.000
187B200HIS10.8650.93848.810-5.793-5.7930.0000.0000.0000.000
188B201VAL00.0270.00450.148-0.057-0.0570.0000.0000.0000.000
189B202ILE0-0.047-0.03052.749-0.056-0.0560.0000.0000.0000.000
190B203ILE00.0280.03554.745-0.014-0.0140.0000.0000.0000.000
191B204SER00.0190.00458.127-0.080-0.0800.0000.0000.0000.000
192B205LEU00.0070.01661.7740.0060.0060.0000.0000.0000.000
193B206LYS10.9650.99862.796-4.688-4.6880.0000.0000.0000.000