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: 1NRRZ

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 OptAll
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 -2077219.715356
FMO2-HF: Nuclear repulsion 1993833.327264
FMO2-HF: Total energy -83386.388092
FMO2-MP2: Total energy -83628.937386


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.
-16.541-20.95923.069-8.635-10.0160.029
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 : 0.016 / q_NPA : 0.020
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].
3A3MET0-0.030-0.0322.375-7.548-4.0333.361-2.708-4.168-0.031
4A4VAL00.0390.0534.2350.6530.8180.000-0.039-0.1270.000
5A5THR00.000-0.0118.0010.0340.0340.0000.0000.0000.000
6A6VAL0-0.0360.00110.4110.1590.1590.0000.0000.0000.000
7A7THR0-0.028-0.02013.3430.0450.0450.0000.0000.0000.000
8A8ALA0-0.009-0.00316.7980.0280.0280.0000.0000.0000.000
9A9LYS10.9500.96720.0690.2010.2010.0000.0000.0000.000
10A10THR00.002-0.01821.245-0.001-0.0010.0000.0000.0000.000
11A11VAL00.0700.00815.646-0.031-0.0310.0000.0000.0000.000
12A12GLU-1-0.926-0.94517.138-0.124-0.1240.0000.0000.0000.000
13A13GLU-1-0.767-0.86219.065-0.229-0.2290.0000.0000.0000.000
14A14ALA0-0.028-0.00715.214-0.016-0.0160.0000.0000.0000.000
15A15VAL00.0330.01013.653-0.057-0.0570.0000.0000.0000.000
16A16THR0-0.031-0.03315.1130.0020.0020.0000.0000.0000.000
17A17LYS10.8710.93816.8090.4630.4630.0000.0000.0000.000
18A18ALA00.0310.01211.449-0.020-0.0200.0000.0000.0000.000
19A19LEU0-0.024-0.01113.010-0.011-0.0110.0000.0000.0000.000
20A20ILE0-0.0180.00514.9240.0290.0290.0000.0000.0000.000
21A21GLU-1-0.895-0.96212.814-0.697-0.6970.0000.0000.0000.000
22A22LEU0-0.0050.0018.073-0.009-0.0090.0000.0000.0000.000
23A23GLN0-0.069-0.02511.8330.1440.1440.0000.0000.0000.000
24A24THR0-0.037-0.01911.3970.0900.0900.0000.0000.0000.000
25A25THR00.011-0.01814.086-0.033-0.0330.0000.0000.0000.000
26A26SER00.0230.00314.6260.0170.0170.0000.0000.0000.000
27A27ASP-1-0.836-0.88715.1290.3050.3050.0000.0000.0000.000
28A28LYS10.8560.91512.558-0.254-0.2540.0000.0000.0000.000
29A29LEU00.0450.0489.712-0.027-0.0270.0000.0000.0000.000
30A30THR0-0.036-0.0326.5730.4600.4600.0000.0000.0000.000
31A31TYR0-0.022-0.0107.147-0.346-0.3460.0000.0000.0000.000
32A32GLU-1-0.794-0.8697.024-1.249-1.2490.0000.0000.0000.000
33A33ILE0-0.021-0.0279.676-0.114-0.1140.0000.0000.0000.000
34A34VAL0-0.024-0.00510.9370.0230.0230.0000.0000.0000.000
35A35GLU-1-0.796-0.89113.366-0.253-0.2530.0000.0000.0000.000
36A36LYS10.8460.91017.0310.2500.2500.0000.0000.0000.000
37A37GLY00.0320.02719.476-0.007-0.0070.0000.0000.0000.000
38A38SER0-0.041-0.02722.2850.0280.0280.0000.0000.0000.000
39A39ALA00.000-0.02226.041-0.012-0.0120.0000.0000.0000.000
40A40GLY00.0480.03129.3950.0090.0090.0000.0000.0000.000
41A41PHE0-0.059-0.02033.087-0.008-0.0080.0000.0000.0000.000
42A42LEU00.0190.02836.1150.0040.0040.0000.0000.0000.000
43A43GLY00.0680.02336.9720.0050.0050.0000.0000.0000.000
44A44ILE00.015-0.01131.3850.0000.0000.0000.0000.0000.000
45A45GLY00.0440.03931.630-0.012-0.0120.0000.0000.0000.000
46A46SER0-0.096-0.05427.447-0.012-0.0120.0000.0000.0000.000
47A47LYS10.8700.92923.3630.2370.2370.0000.0000.0000.000
48A48PRO00.0100.02420.4180.0240.0240.0000.0000.0000.000
49A49ALA00.0310.02018.009-0.010-0.0100.0000.0000.0000.000
50A50ILE0-0.046-0.02513.491-0.026-0.0260.0000.0000.0000.000
51A51ILE0-0.025-0.00711.3050.0530.0530.0000.0000.0000.000
52A52ARG10.8730.9276.6491.6691.6690.0000.0000.0000.000
53A53ALA00.009-0.0147.0070.3270.3270.0000.0000.0000.000
54A54LYS10.8460.9132.240-17.299-25.68619.707-5.845-5.4740.060
55A55ARG10.8900.9325.5280.6480.6480.0000.0000.0000.000
56A56LYS10.8260.9226.287-0.423-0.4230.0000.0000.0000.000
57A57GLU-1-0.880-0.9405.0625.8266.1150.001-0.043-0.2470.000
58A58THR0-0.049-0.0447.473-0.438-0.4380.0000.0000.0000.000
59A59LEU0-0.021-0.0139.9770.1630.1630.0000.0000.0000.000
60A60GLN00.0860.01911.5810.0570.0570.0000.0000.0000.000
61A61ASP-1-0.778-0.8706.6931.2951.2950.0000.0000.0000.000
62A62LYS10.9270.9758.640-1.693-1.6930.0000.0000.0000.000
63A63ALA0-0.022-0.01110.044-0.110-0.1100.0000.0000.0000.000
64A64ILE0-0.006-0.0039.571-0.082-0.0820.0000.0000.0000.000
65A65GLU-1-0.832-0.9007.5870.9020.9020.0000.0000.0000.000
66A66PHE0-0.011-0.0179.647-0.152-0.1520.0000.0000.0000.000
67A67LEU0-0.018-0.02113.055-0.104-0.1040.0000.0000.0000.000
68A68GLU-1-0.897-0.9499.4440.6580.6580.0000.0000.0000.000
69A69GLN0-0.073-0.0409.818-0.190-0.1900.0000.0000.0000.000
70A70VAL0-0.037-0.02712.627-0.077-0.0770.0000.0000.0000.000
71A71PHE0-0.007-0.03415.681-0.055-0.0550.0000.0000.0000.000
72A72ASP-1-0.884-0.92913.3530.1580.1580.0000.0000.0000.000
73A73ALA0-0.0080.00015.448-0.042-0.0420.0000.0000.0000.000
74A74MET0-0.144-0.07117.712-0.018-0.0180.0000.0000.0000.000
75A75ASN0-0.093-0.04418.973-0.031-0.0310.0000.0000.0000.000
76A76MET0-0.079-0.03218.667-0.014-0.0140.0000.0000.0000.000
77A77ALA00.0400.02316.8630.0270.0270.0000.0000.0000.000
78A78VAL0-0.070-0.04916.616-0.021-0.0210.0000.0000.0000.000
79A79ASP-1-0.873-0.93615.9840.3240.3240.0000.0000.0000.000
80A80ILE0-0.035-0.02413.125-0.027-0.0270.0000.0000.0000.000
81A81SER0-0.060-0.02114.7480.0170.0170.0000.0000.0000.000
82A82VAL00.003-0.03114.020-0.005-0.0050.0000.0000.0000.000
83A83GLU-1-0.933-0.94016.8140.2590.2590.0000.0000.0000.000
84A84TYR0-0.076-0.09716.3420.0270.0270.0000.0000.0000.000
85A85ASN0-0.0010.00718.833-0.018-0.0180.0000.0000.0000.000
86A86GLU-1-0.786-0.88318.1460.4360.4360.0000.0000.0000.000
87A87THR0-0.066-0.05021.4110.0020.0020.0000.0000.0000.000
88A88GLU-1-0.904-0.93025.2620.1940.1940.0000.0000.0000.000
89A89LYS10.7870.90120.644-0.361-0.3610.0000.0000.0000.000
90A90GLU-1-0.810-0.87222.8220.2660.2660.0000.0000.0000.000
91A91MET0-0.029-0.00915.2830.0220.0220.0000.0000.0000.000
92A92ASN0-0.0240.00120.285-0.009-0.0090.0000.0000.0000.000
93A93VAL00.0330.01316.9500.0100.0100.0000.0000.0000.000
94A94ASN0-0.030-0.02519.555-0.030-0.0300.0000.0000.0000.000
95A95LEU00.0250.02918.2810.0240.0240.0000.0000.0000.000
96A96LYS10.8450.90920.339-0.253-0.2530.0000.0000.0000.000
97A97GLY00.1390.07520.5760.0190.0190.0000.0000.0000.000
98A98ASP-1-0.917-0.96822.1560.1350.1350.0000.0000.0000.000
99A99ASP-1-0.794-0.88521.4690.1610.1610.0000.0000.0000.000
100A100MET0-0.036-0.01921.6880.0000.0000.0000.0000.0000.000
101A101GLY00.0080.00724.423-0.006-0.0060.0000.0000.0000.000
102A102ILE00.0270.01226.223-0.008-0.0080.0000.0000.0000.000
103A103LEU0-0.0080.02125.435-0.012-0.0120.0000.0000.0000.000
104A104ILE0-0.034-0.04029.2810.0040.0040.0000.0000.0000.000
105A105GLY00.0210.01032.1310.0020.0020.0000.0000.0000.000
106A106LYS10.9650.96229.972-0.129-0.1290.0000.0000.0000.000
107A107ARG10.8730.97327.097-0.149-0.1490.0000.0000.0000.000
108A108GLY00.0010.01828.2310.0120.0120.0000.0000.0000.000
109A109GLN00.0190.00229.3610.0020.0020.0000.0000.0000.000
110A110THR0-0.012-0.01625.2520.0120.0120.0000.0000.0000.000
111A111LEU00.0550.04423.7760.0200.0200.0000.0000.0000.000
112A112ASP-1-0.836-0.91124.6160.2350.2350.0000.0000.0000.000
113A113SER0-0.077-0.05525.5850.0090.0090.0000.0000.0000.000
114A114LEU00.0370.02019.7860.0170.0170.0000.0000.0000.000
115A115GLN00.0130.02020.6910.0400.0400.0000.0000.0000.000
116A116TYR0-0.022-0.01522.0400.0260.0260.0000.0000.0000.000
117A117LEU00.0120.00320.0580.0190.0190.0000.0000.0000.000
118A118VAL00.0600.03315.6800.0440.0440.0000.0000.0000.000
119A119SER0-0.011-0.00217.7150.0410.0410.0000.0000.0000.000
120A120LEU0-0.033-0.01119.9660.0180.0180.0000.0000.0000.000
121A121VAL0-0.0110.00013.7460.0260.0260.0000.0000.0000.000
122A122VAL00.0210.01214.6420.0940.0940.0000.0000.0000.000
123A123ASN0-0.026-0.02316.180-0.004-0.0040.0000.0000.0000.000
124A124LYS10.8940.96115.650-0.720-0.7200.0000.0000.0000.000
125A125SER0-0.088-0.05613.4900.1290.1290.0000.0000.0000.000
126A126SER0-0.028-0.03015.3230.0630.0630.0000.0000.0000.000
127A127SER0-0.016-0.00718.061-0.024-0.0240.0000.0000.0000.000
128A128ASP-1-0.843-0.89221.0050.3070.3070.0000.0000.0000.000
129A129TYR0-0.0030.00421.4420.0330.0330.0000.0000.0000.000
130A130ILE00.0170.01018.380-0.010-0.0100.0000.0000.0000.000
131A131ARG10.8610.91721.644-0.294-0.2940.0000.0000.0000.000
132A132VAL00.0030.01318.728-0.008-0.0080.0000.0000.0000.000
133A133LYS10.7670.85321.646-0.284-0.2840.0000.0000.0000.000
134A134LEU00.0020.01519.7440.0180.0180.0000.0000.0000.000
135A135ASP-1-0.829-0.93922.9620.1810.1810.0000.0000.0000.000
136A136THR00.0040.00023.3430.0160.0160.0000.0000.0000.000
137A137GLU-1-0.795-0.88624.8570.1840.1840.0000.0000.0000.000
138A138ASN00.019-0.00927.002-0.011-0.0110.0000.0000.0000.000
139A139TYR0-0.008-0.00428.749-0.017-0.0170.0000.0000.0000.000
140A140ARG10.7820.86426.986-0.231-0.2310.0000.0000.0000.000
141A141GLU-1-0.875-0.90431.5590.1290.1290.0000.0000.0000.000
142A142ARG10.9330.96329.560-0.160-0.1600.0000.0000.0000.000
143A143ARG10.8410.91633.884-0.132-0.1320.0000.0000.0000.000
144A144LYS10.8470.90835.891-0.123-0.1230.0000.0000.0000.000
145A145GLU-1-0.885-0.93337.8680.0970.0970.0000.0000.0000.000
146A146THR0-0.020-0.03038.110-0.007-0.0070.0000.0000.0000.000
147A147LEU0-0.009-0.00138.128-0.007-0.0070.0000.0000.0000.000
148A148GLU-1-0.806-0.90241.5940.1010.1010.0000.0000.0000.000
149A149THR0-0.058-0.02443.517-0.007-0.0070.0000.0000.0000.000
150A150LEU0-0.023-0.00642.431-0.006-0.0060.0000.0000.0000.000
151A151ALA00.0150.00645.656-0.004-0.0040.0000.0000.0000.000
152A152LYS10.9350.95146.335-0.087-0.0870.0000.0000.0000.000
153A153ASN00.0140.01048.044-0.004-0.0040.0000.0000.0000.000
154A154ILE0-0.035-0.02848.759-0.004-0.0040.0000.0000.0000.000
155A155ALA00.0530.03651.396-0.003-0.0030.0000.0000.0000.000
156A156TYR00.0150.01353.436-0.004-0.0040.0000.0000.0000.000
157A157LYS10.9810.98750.636-0.066-0.0660.0000.0000.0000.000
158A158VAL0-0.0080.03054.389-0.003-0.0030.0000.0000.0000.000
159A159LYS10.8260.90756.144-0.062-0.0620.0000.0000.0000.000
160A160ARG10.9220.96659.072-0.048-0.0480.0000.0000.0000.000
161A161THR0-0.021-0.04158.386-0.002-0.0020.0000.0000.0000.000
162A162LYS10.8690.94060.775-0.047-0.0470.0000.0000.0000.000
163A163ARG10.9290.97155.283-0.054-0.0540.0000.0000.0000.000
164A164SER0-0.039-0.03855.0530.0020.0020.0000.0000.0000.000
165A165VAL0-0.014-0.01850.411-0.002-0.0020.0000.0000.0000.000
166A166SER00.0080.01248.5190.0000.0000.0000.0000.0000.000
167A167LEU0-0.053-0.02944.596-0.002-0.0020.0000.0000.0000.000
168A168GLU-1-0.819-0.92740.4050.0940.0940.0000.0000.0000.000
169A169PRO0-0.043-0.03040.0250.0020.0020.0000.0000.0000.000
170A170MET0-0.0400.00738.1170.0030.0030.0000.0000.0000.000
171A171ASN00.0810.05534.367-0.001-0.0010.0000.0000.0000.000
172A172PRO00.0560.00135.734-0.005-0.0050.0000.0000.0000.000
173A173TYR00.0100.01331.822-0.010-0.0100.0000.0000.0000.000
174A174GLU-1-0.805-0.88335.0780.1330.1330.0000.0000.0000.000
175A175ARG10.8310.89038.205-0.123-0.1230.0000.0000.0000.000
176A176ARG10.9530.97739.334-0.127-0.1270.0000.0000.0000.000
177A177ILE0-0.0010.01136.793-0.005-0.0050.0000.0000.0000.000
178A178ILE0-0.0020.00541.313-0.006-0.0060.0000.0000.0000.000
179A179HIS0-0.040-0.04444.125-0.002-0.0020.0000.0000.0000.000
180A180ALA0-0.0060.00143.680-0.004-0.0040.0000.0000.0000.000
181A181ALA0-0.018-0.00544.935-0.004-0.0040.0000.0000.0000.000
182A182LEU0-0.026-0.01946.678-0.004-0.0040.0000.0000.0000.000
183A183GLN0-0.0240.00747.639-0.001-0.0010.0000.0000.0000.000
184A184ASN00.0060.00450.632-0.004-0.0040.0000.0000.0000.000
185A185ASP-1-0.754-0.86353.6900.0590.0590.0000.0000.0000.000
186A186LYS10.9040.93655.436-0.062-0.0620.0000.0000.0000.000
187A187TYR00.0090.00458.375-0.001-0.0010.0000.0000.0000.000
188A188VAL0-0.031-0.00653.654-0.001-0.0010.0000.0000.0000.000
189A189VAL0-0.011-0.00554.3170.0010.0010.0000.0000.0000.000
190A190THR00.0060.00349.4500.0010.0010.0000.0000.0000.000
191A191ARG10.8860.93149.604-0.070-0.0700.0000.0000.0000.000
192A192SER0-0.005-0.00445.0820.0010.0010.0000.0000.0000.000
193A193ASP-1-0.803-0.88946.9280.0720.0720.0000.0000.0000.000
194A194GLY00.0630.04146.3610.0020.0020.0000.0000.0000.000
195A195GLU-1-0.863-0.93843.9260.0950.0950.0000.0000.0000.000
196A196GLU-1-0.808-0.88437.7010.1220.1220.0000.0000.0000.000
197A197PRO0-0.029-0.01036.558-0.001-0.0010.0000.0000.0000.000
198A198PHE0-0.003-0.02138.6500.0000.0000.0000.0000.0000.000
199A199ARG10.8290.93341.512-0.099-0.0990.0000.0000.0000.000
200A200HIS00.0410.02241.8710.0010.0010.0000.0000.0000.000
201A201VAL00.003-0.00544.2350.0000.0000.0000.0000.0000.000
202A202ILE0-0.0140.00746.783-0.002-0.0020.0000.0000.0000.000
203A203ILE00.0140.00348.5760.0000.0000.0000.0000.0000.000
204A204SER00.0010.00652.565-0.002-0.0020.0000.0000.0000.000
205A205LEU00.0140.00656.3880.0010.0010.0000.0000.0000.000
206A206LYS10.8340.92556.302-0.062-0.0620.0000.0000.0000.000
207A207ARG10.9490.96360.337-0.054-0.0540.0000.0000.0000.000
208A208GLU-1-0.916-0.94263.5040.0510.0510.0000.0000.0000.000