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: 72G1K

Calculation Name: 3QKS-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3QKS

Chain ID: A

ChEMBL ID:

UniProt ID: Q8U1N9

Base Structure: X-ray

Registration Date: 2023-06-21

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 199
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2084596.560456
FMO2-HF: Nuclear repulsion 2005222.161322
FMO2-HF: Total energy -79374.399134
FMO2-MP2: Total energy -79610.253966


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.
-18.126-11.35518.985-7.65-18.108-0.031
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 : -0.015 / q_NPA : 0.006
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].
3A3LEU00.002-0.0032.585-1.7951.4700.367-1.460-2.1720.006
4A4GLU-1-0.867-0.9375.132-1.605-1.521-0.001-0.005-0.0780.000
5A5ARG10.9831.0058.4200.9990.9990.0000.0000.0000.000
6A6VAL0-0.0210.0108.957-0.050-0.0500.0000.0000.0000.000
7A7THR0-0.024-0.01410.5040.0980.0980.0000.0000.0000.000
8A8VAL0-0.019-0.01513.2140.0170.0170.0000.0000.0000.000
9A9LYS10.9000.95915.6030.2970.2970.0000.0000.0000.000
10A10ASN0-0.032-0.03719.1940.0180.0180.0000.0000.0000.000
11A11PHE00.0020.00815.8000.0160.0160.0000.0000.0000.000
12A12ARG10.7900.86417.5610.0450.0450.0000.0000.0000.000
13A13SER00.0100.00621.677-0.002-0.0020.0000.0000.0000.000
14A14HIS0-0.0150.04317.321-0.024-0.0240.0000.0000.0000.000
15A15SER00.0310.01020.4510.0060.0060.0000.0000.0000.000
16A16ASP-1-0.903-0.98220.109-0.312-0.3120.0000.0000.0000.000
17A17THR00.005-0.01415.7390.0000.0000.0000.0000.0000.000
18A18VAL00.012-0.00314.995-0.031-0.0310.0000.0000.0000.000
19A19VAL0-0.021-0.00512.4510.0370.0370.0000.0000.0000.000
20A20GLU-1-0.898-0.96412.137-1.004-1.0040.0000.0000.0000.000
21A21PHE0-0.062-0.0338.7370.1010.1010.0000.0000.0000.000
22A22LYS10.9570.96210.5950.7250.7250.0000.0000.0000.000
23A23GLU-1-0.895-0.9458.614-1.901-1.9010.0000.0000.0000.000
24A24GLY00.0030.0159.9640.2790.2790.0000.0000.0000.000
25A25ILE00.008-0.00511.006-0.173-0.1730.0000.0000.0000.000
26A26ASN0-0.031-0.01711.1170.1620.1620.0000.0000.0000.000
27A27LEU00.0260.01513.8620.0410.0410.0000.0000.0000.000
28A28ILE0-0.014-0.00513.4670.0120.0120.0000.0000.0000.000
29A29ILE00.0350.01116.6520.0510.0510.0000.0000.0000.000
30A30GLY00.0530.01820.295-0.002-0.0020.0000.0000.0000.000
31A31GLN00.0750.03722.4840.0130.0130.0000.0000.0000.000
32A32ASN0-0.041-0.02723.335-0.017-0.0170.0000.0000.0000.000
33A33GLY00.0710.03423.0750.0030.0030.0000.0000.0000.000
34A34SER0-0.045-0.02621.590-0.014-0.0140.0000.0000.0000.000
35A35GLY00.0700.04019.801-0.010-0.0100.0000.0000.0000.000
36A36LYS10.8950.94416.8810.1810.1810.0000.0000.0000.000
37A37SER0-0.015-0.00215.502-0.018-0.0180.0000.0000.0000.000
38A38SER00.0520.01615.2480.0090.0090.0000.0000.0000.000
39A39LEU00.0260.02612.2070.0110.0110.0000.0000.0000.000
40A40LEU00.0490.01710.311-0.054-0.0540.0000.0000.0000.000
41A41ASP-1-0.801-0.89010.3400.0020.0020.0000.0000.0000.000
42A42ALA0-0.008-0.00411.4810.0350.0350.0000.0000.0000.000
43A43ILE00.0290.0156.093-0.037-0.0370.0000.0000.0000.000
44A44LEU00.0210.0126.927-0.058-0.0580.0000.0000.0000.000
45A45VAL0-0.027-0.0118.1710.0820.0820.0000.0000.0000.000
46A46GLY0-0.009-0.0108.7940.0490.0490.0000.0000.0000.000
47A47LEU0-0.0060.0022.733-0.758-0.1930.675-0.178-1.062-0.002
48A48TYR0-0.021-0.0364.9730.0200.192-0.001-0.007-0.1650.000
49A49TRP0-0.0200.0468.6830.0550.0550.0000.0000.0000.000
50A50PRO0-0.073-0.05711.9440.0200.0200.0000.0000.0000.000
51A51LEU00.009-0.00610.862-0.036-0.0360.0000.0000.0000.000
52A52ARG10.8600.93113.760-0.267-0.2670.0000.0000.0000.000
53A53ILE00.0860.06610.0600.0680.0680.0000.0000.0000.000
54A54LYS10.9040.94714.034-0.103-0.1030.0000.0000.0000.000
55A55ASP-1-0.874-0.92816.7920.1400.1400.0000.0000.0000.000
56A56ILE0-0.029-0.01114.450-0.026-0.0260.0000.0000.0000.000
57A57LYS10.9550.97918.355-0.085-0.0850.0000.0000.0000.000
58A58LYS10.9760.97918.050-0.149-0.1490.0000.0000.0000.000
59A59ASP-1-0.876-0.94219.4790.0370.0370.0000.0000.0000.000
60A60GLU-1-0.820-0.89219.784-0.047-0.0470.0000.0000.0000.000
61A61PHE0-0.009-0.01414.885-0.015-0.0150.0000.0000.0000.000
62A62THR0-0.035-0.02719.518-0.013-0.0130.0000.0000.0000.000
63A63LYS10.9270.94722.151-0.023-0.0230.0000.0000.0000.000
64A64VAL00.0240.04323.663-0.002-0.0020.0000.0000.0000.000
65A65GLY00.0140.01724.337-0.013-0.0130.0000.0000.0000.000
66A66ALA00.0300.01426.6470.0070.0070.0000.0000.0000.000
67A67ARG10.9360.97125.0850.1470.1470.0000.0000.0000.000
68A68ASP-1-0.834-0.92321.988-0.110-0.1100.0000.0000.0000.000
69A69THR0-0.0240.01517.339-0.007-0.0070.0000.0000.0000.000
70A70TYR0-0.066-0.03316.1650.0030.0030.0000.0000.0000.000
71A71ILE00.0240.01110.809-0.015-0.0150.0000.0000.0000.000
72A72ASP-1-0.817-0.87111.915-0.565-0.5650.0000.0000.0000.000
73A73LEU0-0.0030.0055.914-0.049-0.0490.0000.0000.0000.000
74A74ILE00.0040.0037.8620.0810.0810.0000.0000.0000.000
75A75PHE0-0.001-0.0072.581-1.833-1.4823.804-0.809-3.347-0.006
76A76GLU-1-0.904-0.9504.246-1.772-1.358-0.001-0.101-0.3120.000
77A77LYS10.8830.9252.341-11.780-8.6604.329-3.315-4.134-0.029
78A78ASP-1-0.857-0.9163.4762.9273.1390.0210.024-0.2570.000
79A79GLY00.0390.0286.065-0.229-0.2290.0000.0000.0000.000
80A80THR0-0.044-0.0107.179-0.142-0.1420.0000.0000.0000.000
81A81LYS10.9120.9656.8321.0111.0110.0000.0000.0000.000
82A82TYR00.001-0.0245.5140.3830.3830.0000.0000.0000.000
83A83ARG10.8470.8997.6220.2560.2560.0000.0000.0000.000
84A84ILE0-0.012-0.0016.2450.2090.2090.0000.0000.0000.000
85A85THR0-0.058-0.0429.417-0.058-0.0580.0000.0000.0000.000
86A86ARG10.8140.8909.0940.1450.1450.0000.0000.0000.000
87A87ARG10.9390.96914.6620.1480.1480.0000.0000.0000.000
88A88PHE0-0.018-0.00815.3240.0270.0270.0000.0000.0000.000
89A89LEU00.0260.00120.379-0.012-0.0120.0000.0000.0000.000
90A90LYS10.8190.89022.0550.0980.0980.0000.0000.0000.000
91A91GLY00.0450.02126.580-0.002-0.0020.0000.0000.0000.000
92A92TYR0-0.017-0.01630.3620.0050.0050.0000.0000.0000.000
93A93SER0-0.0100.00530.2590.0080.0080.0000.0000.0000.000
94A94SER00.0090.01824.730-0.004-0.0040.0000.0000.0000.000
95A95GLY00.0220.01324.4390.0110.0110.0000.0000.0000.000
96A96GLU-1-0.903-0.94918.9930.0260.0260.0000.0000.0000.000
97A97ILE00.0020.00618.7070.0100.0100.0000.0000.0000.000
98A98HIS0-0.003-0.00514.317-0.045-0.0450.0000.0000.0000.000
99A99ALA0-0.019-0.01714.0630.0330.0330.0000.0000.0000.000
100A100MET00.0190.0306.505-0.040-0.0400.0000.0000.0000.000
101A101LYS10.9140.95210.8220.2830.2830.0000.0000.0000.000
102A102ARG11.0221.00810.130-0.321-0.3210.0000.0000.0000.000
103A103LEU0-0.037-0.01811.6340.0240.0240.0000.0000.0000.000
104A104VAL0-0.005-0.00713.6670.0410.0410.0000.0000.0000.000
105A105GLY00.0470.03216.6760.0090.0090.0000.0000.0000.000
106A106ASN00.010-0.00517.423-0.038-0.0380.0000.0000.0000.000
107A107GLU-1-0.855-0.91718.768-0.147-0.1470.0000.0000.0000.000
108A108TRP0-0.018-0.01310.5110.0140.0140.0000.0000.0000.000
109A109LYS10.8750.93015.2540.1480.1480.0000.0000.0000.000
110A110HIS0-0.009-0.00314.470-0.023-0.0230.0000.0000.0000.000
111A111VAL0-0.045-0.01110.5740.0170.0170.0000.0000.0000.000
112A112THR00.000-0.00613.4060.0600.0600.0000.0000.0000.000
113A113GLU-1-0.844-0.91115.5750.0810.0810.0000.0000.0000.000
114A114PRO0-0.028-0.01216.4180.0080.0080.0000.0000.0000.000
115A115SER00.016-0.01016.696-0.005-0.0050.0000.0000.0000.000
116A116SER00.012-0.00515.1220.0280.0280.0000.0000.0000.000
117A117LYS10.9930.98614.738-0.200-0.2000.0000.0000.0000.000
118A118ALA00.0150.02215.8790.0610.0610.0000.0000.0000.000
119A119ILE00.0030.00410.2240.0680.0680.0000.0000.0000.000
120A120SER00.0150.00910.8100.1190.1190.0000.0000.0000.000
121A121ALA0-0.013-0.00411.7300.1250.1250.0000.0000.0000.000
122A122PHE0-0.025-0.0258.6200.1150.1150.0000.0000.0000.000
123A123MET00.0290.0063.851-0.0400.1230.001-0.025-0.1380.000
124A124GLU-1-0.844-0.9057.9981.7971.7970.0000.0000.0000.000
125A125LYS10.8840.93710.623-0.646-0.6460.0000.0000.0000.000
126A126LEU0-0.066-0.0094.8490.0950.0950.0000.0000.0000.000
127A127ILE0-0.018-0.0432.4821.364-1.7228.102-1.101-3.9150.000
128A128PRO00.0750.0666.146-0.415-0.392-0.001-0.004-0.0180.000
129A129TYR00.023-0.0338.0750.3530.3530.0000.0000.0000.000
130A130ASN00.0160.0009.050-0.114-0.1140.0000.0000.0000.000
131A131ILE00.0230.0166.460-0.139-0.1390.0000.0000.0000.000
132A132PHE00.0230.0002.753-2.278-1.4331.495-0.504-1.8360.000
133A133LEU0-0.050-0.0536.914-0.465-0.4650.0000.0000.0000.000
134A134ASN0-0.025-0.00110.002-0.301-0.3010.0000.0000.0000.000
135A135ALA0-0.0240.0038.594-0.136-0.1360.0000.0000.0000.000
136A136ILE0-0.062-0.0213.441-0.5910.0520.195-0.165-0.6740.000
137A137TYR0-0.057-0.0327.370-0.543-0.5430.0000.0000.0000.000
138A138ILE00.0570.03710.0120.0080.0080.0000.0000.0000.000
139A139ARG10.8450.92113.453-0.379-0.3790.0000.0000.0000.000
140A140GLN00.004-0.00315.618-0.041-0.0410.0000.0000.0000.000
141A141GLY00.0220.00218.7590.0250.0250.0000.0000.0000.000
142A142GLN0-0.020-0.00516.2620.0100.0100.0000.0000.0000.000
143A143ILE00.0310.00517.6800.0100.0100.0000.0000.0000.000
144A144ASP-1-0.879-0.93921.1600.0040.0040.0000.0000.0000.000
145A145ALA0-0.003-0.00323.2370.0030.0030.0000.0000.0000.000
146A146ILE0-0.043-0.01819.7360.0060.0060.0000.0000.0000.000
147A147LEU0-0.025-0.02724.2610.0000.0000.0000.0000.0000.000
148A148GLU-1-0.983-0.95927.0810.0760.0760.0000.0000.0000.000
149A149SER00.0440.01329.001-0.004-0.0040.0000.0000.0000.000
150A150ASP-1-0.821-0.91229.1010.1110.1110.0000.0000.0000.000
151A151GLU-1-0.932-0.97029.5510.1180.1180.0000.0000.0000.000
152A152ALA0-0.019-0.00527.2710.0180.0180.0000.0000.0000.000
153A153ARG10.8330.91224.795-0.094-0.0940.0000.0000.0000.000
154A154GLU-1-0.807-0.89724.4550.2540.2540.0000.0000.0000.000
155A155LYS10.9500.98423.786-0.166-0.1660.0000.0000.0000.000
156A156VAL0-0.029-0.01319.7970.0290.0290.0000.0000.0000.000
157A157VAL00.000-0.00120.3320.0500.0500.0000.0000.0000.000
158A158ARG10.8310.90020.896-0.189-0.1890.0000.0000.0000.000
159A159GLU-1-0.924-0.96117.0380.3910.3910.0000.0000.0000.000
160A160VAL00.0400.01815.0610.0610.0610.0000.0000.0000.000
161A161LEU0-0.091-0.03516.1590.1140.1140.0000.0000.0000.000
162A162ASN0-0.0380.00115.9120.0430.0430.0000.0000.0000.000
163A163LEU0-0.002-0.00417.106-0.055-0.0550.0000.0000.0000.000
164A164ASP-1-0.747-0.86918.4850.5420.5420.0000.0000.0000.000
165A165LYS10.8930.95320.151-0.472-0.4720.0000.0000.0000.000
166A166PHE0-0.025-0.03422.578-0.037-0.0370.0000.0000.0000.000
167A167GLU-1-0.896-0.94223.1340.3310.3310.0000.0000.0000.000
168A168THR00.004-0.01521.524-0.027-0.0270.0000.0000.0000.000
169A169ALA0-0.059-0.02624.274-0.025-0.0250.0000.0000.0000.000
170A170TYR00.0260.01227.604-0.027-0.0270.0000.0000.0000.000
171A171LYS11.0030.99825.889-0.287-0.2870.0000.0000.0000.000
172A172LYS10.9520.96825.184-0.346-0.3460.0000.0000.0000.000
173A173LEU00.0390.02829.726-0.019-0.0190.0000.0000.0000.000
174A174SER00.0240.01232.533-0.020-0.0200.0000.0000.0000.000
175A175GLU-1-0.886-0.93830.8470.1740.1740.0000.0000.0000.000
176A176LEU00.0040.01833.834-0.012-0.0120.0000.0000.0000.000
177A177LYS10.9960.99235.472-0.153-0.1530.0000.0000.0000.000
178A178LYS10.8550.91833.989-0.179-0.1790.0000.0000.0000.000
179A179THR0-0.0140.00136.272-0.009-0.0090.0000.0000.0000.000
180A180ILE0-0.010-0.00938.973-0.008-0.0080.0000.0000.0000.000
181A181ASN0-0.033-0.02541.477-0.011-0.0110.0000.0000.0000.000
182A182ASN00.0350.00540.129-0.010-0.0100.0000.0000.0000.000
183A183ARG10.9610.99939.906-0.137-0.1370.0000.0000.0000.000
184A184ILE0-0.017-0.00344.742-0.005-0.0050.0000.0000.0000.000
185A185LYS10.8970.94746.270-0.102-0.1020.0000.0000.0000.000
186A186GLU-1-0.850-0.92246.8630.0850.0850.0000.0000.0000.000
187A187TYR0-0.014-0.02045.8300.0000.0000.0000.0000.0000.000
188A188ARG10.9430.96950.634-0.090-0.0900.0000.0000.0000.000
189A189ASP-1-0.836-0.89852.1060.0700.0700.0000.0000.0000.000
190A190ILE0-0.026-0.01050.515-0.003-0.0030.0000.0000.0000.000
191A191LEU0-0.006-0.01654.355-0.002-0.0020.0000.0000.0000.000
192A192ALA00.0240.02556.600-0.003-0.0030.0000.0000.0000.000
193A193ARG10.7820.86754.658-0.070-0.0700.0000.0000.0000.000
194A194THR0-0.048-0.02258.014-0.002-0.0020.0000.0000.0000.000
195A195GLU-1-0.971-0.97260.2210.0610.0610.0000.0000.0000.000
196A196GLY0-0.039-0.00162.965-0.001-0.0010.0000.0000.0000.000
197A197GLY0-0.024-0.01366.7190.0010.0010.0000.0000.0000.000
198A198HIS00.022-0.00364.518-0.002-0.0020.0000.0000.0000.000
199A199HIS00.0110.01867.8350.0010.0010.0000.0000.0000.000