Manual

About

FMODB

FMODB: The database of quantum mechanical data based on the FMO method

Last updated: 2024-05-02

All entries: 37386

Number of unique PDB entries: 7781

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FMODB ID: K96R3

Calculation Name: 2QHT-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2QHT

Chain ID: A

ChEMBL ID:

UniProt ID: Q5SLQ3

Base Structure: X-ray

Registration Date: 2023-09-20

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 210
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2468188.620129
FMO2-HF: Nuclear repulsion 2388111.482993
FMO2-HF: Total energy -80077.137137
FMO2-MP2: Total energy -80315.286612


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.
-6.251-1.0391.82-2.549-4.484-0.003
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 : 0.000 / q_NPA : -0.022
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].
3A3PHE0-0.043-0.0233.817-1.1420.888-0.029-1.096-0.906-0.001
4A4LEU00.0210.0226.5750.1080.1080.0000.0000.0000.000
5A5VAL0-0.008-0.0029.981-0.029-0.0290.0000.0000.0000.000
6A6GLU-1-0.761-0.84013.146-0.106-0.1060.0000.0000.0000.000
7A7ASP-1-0.815-0.89416.425-0.182-0.1820.0000.0000.0000.000
8A8LEU0-0.020-0.02319.5520.0180.0180.0000.0000.0000.000
9A9GLY00.0090.01822.2040.0150.0150.0000.0000.0000.000
10A10LEU0-0.020-0.01524.977-0.007-0.0070.0000.0000.0000.000
11A11VAL00.0280.01124.3370.0060.0060.0000.0000.0000.000
12A12PRO00.0740.02827.679-0.006-0.0060.0000.0000.0000.000
13A13TYR00.0280.01825.903-0.003-0.0030.0000.0000.0000.000
14A14GLY00.0330.01227.410-0.005-0.0050.0000.0000.0000.000
15A15GLU-1-0.866-0.94427.851-0.083-0.0830.0000.0000.0000.000
16A16ALA00.0420.01923.864-0.004-0.0040.0000.0000.0000.000
17A17TRP0-0.012-0.00623.014-0.011-0.0110.0000.0000.0000.000
18A18ALA00.016-0.00623.510-0.005-0.0050.0000.0000.0000.000
19A19TYR0-0.092-0.08818.1770.0120.0120.0000.0000.0000.000
20A20GLN00.0650.02819.101-0.021-0.0210.0000.0000.0000.000
21A21LYS10.8520.94018.8110.1180.1180.0000.0000.0000.000
22A22ARG10.9210.95620.1180.0760.0760.0000.0000.0000.000
23A23VAL00.0860.05014.5900.0090.0090.0000.0000.0000.000
24A24HIS0-0.066-0.04315.2350.0150.0150.0000.0000.0000.000
25A25ARG10.9360.96215.8580.0880.0880.0000.0000.0000.000
26A26GLU-1-0.855-0.91314.852-0.051-0.0510.0000.0000.0000.000
27A27VAL0-0.033-0.01010.1470.0200.0200.0000.0000.0000.000
28A28VAL0-0.056-0.02812.1500.0040.0040.0000.0000.0000.000
29A29ALA0-0.064-0.02814.6860.0070.0070.0000.0000.0000.000
30A30GLY0-0.0180.00411.1150.0170.0170.0000.0000.0000.000
31A31ASN0-0.049-0.02811.6570.0820.0820.0000.0000.0000.000
32A32ARG10.8030.89211.2310.1330.1330.0000.0000.0000.000
33A33PRO00.0110.0206.3830.0080.0080.0000.0000.0000.000
34A34PRO00.0330.0094.823-0.071-0.0710.0000.0000.0000.000
35A35THR00.0190.0097.890-0.026-0.0260.0000.0000.0000.000
36A36LEU0-0.058-0.02410.872-0.002-0.0020.0000.0000.0000.000
37A37LEU0-0.0130.00613.0080.0320.0320.0000.0000.0000.000
38A38LEU0-0.002-0.00516.557-0.009-0.0090.0000.0000.0000.000
39A39LEU0-0.0190.00019.0110.0180.0180.0000.0000.0000.000
40A40GLU-1-0.834-0.91722.680-0.125-0.1250.0000.0000.0000.000
41A41HIS0-0.0080.01125.098-0.007-0.0070.0000.0000.0000.000
42A42PRO00.0530.02528.6600.0020.0020.0000.0000.0000.000
43A43ARG10.7970.89632.0100.0660.0660.0000.0000.0000.000
44A44VAL0-0.0210.00329.9700.0030.0030.0000.0000.0000.000
45A45ILE00.0140.01632.615-0.005-0.0050.0000.0000.0000.000
46A46THR0-0.029-0.00728.715-0.003-0.0030.0000.0000.0000.000
47A47LEU00.0130.00131.543-0.003-0.0030.0000.0000.0000.000
48A48GLY00.0080.00929.5590.0000.0000.0000.0000.0000.000
49A49ARG10.9160.94024.0680.1500.1500.0000.0000.0000.000
50A50LYS10.8660.92830.6230.1030.1030.0000.0000.0000.000
51A51ALA00.0110.02233.2850.0020.0020.0000.0000.0000.000
52A52THR00.0200.00635.1200.0020.0020.0000.0000.0000.000
53A53GLY00.0430.00838.824-0.002-0.0020.0000.0000.0000.000
54A54GLU-1-0.919-0.95741.612-0.059-0.0590.0000.0000.0000.000
55A55ASN0-0.051-0.02837.184-0.001-0.0010.0000.0000.0000.000
56A56LEU0-0.030-0.00537.828-0.004-0.0040.0000.0000.0000.000
57A57LEU00.0070.02540.9520.0020.0020.0000.0000.0000.000
58A58PHE0-0.002-0.00143.6610.0030.0030.0000.0000.0000.000
59A59PRO00.0650.01844.168-0.002-0.0020.0000.0000.0000.000
60A60GLU-1-0.858-0.95340.330-0.063-0.0630.0000.0000.0000.000
61A61SER0-0.045-0.03042.604-0.002-0.0020.0000.0000.0000.000
62A62TRP00.0930.05241.972-0.001-0.0010.0000.0000.0000.000
63A63TYR0-0.006-0.02639.7390.0000.0000.0000.0000.0000.000
64A64ARG10.9030.95437.9940.0610.0610.0000.0000.0000.000
65A65GLU-1-0.967-0.96441.922-0.044-0.0440.0000.0000.0000.000
66A66ASN0-0.060-0.02943.6100.0020.0020.0000.0000.0000.000
67A67GLY00.0060.00740.776-0.002-0.0020.0000.0000.0000.000
68A68PHE0-0.049-0.02336.250-0.004-0.0040.0000.0000.0000.000
69A69GLU-1-0.920-0.96033.264-0.077-0.0770.0000.0000.0000.000
70A70LEU0-0.003-0.02035.097-0.003-0.0030.0000.0000.0000.000
71A71TYR0-0.034-0.02231.4360.0030.0030.0000.0000.0000.000
72A72TRP00.0350.03132.693-0.006-0.0060.0000.0000.0000.000
73A73VAL0-0.057-0.03227.231-0.002-0.0020.0000.0000.0000.000
74A74GLU-1-0.911-0.96226.215-0.103-0.1030.0000.0000.0000.000
75A75ARG10.7520.87624.1050.1240.1240.0000.0000.0000.000
76A76GLY0-0.037-0.02224.4390.0120.0120.0000.0000.0000.000
77A77GLY00.0240.01026.244-0.005-0.0050.0000.0000.0000.000
78A78ASP-1-0.792-0.89029.047-0.095-0.0950.0000.0000.0000.000
79A79VAL00.0410.02631.350-0.005-0.0050.0000.0000.0000.000
80A80THR0-0.090-0.05227.936-0.003-0.0030.0000.0000.0000.000
81A81TYR00.045-0.00631.3000.0020.0020.0000.0000.0000.000
82A82HIS10.7980.88826.1810.1320.1320.0000.0000.0000.000
83A83GLY00.0780.04230.0100.0080.0080.0000.0000.0000.000
84A84PRO00.0220.01330.167-0.008-0.0080.0000.0000.0000.000
85A85GLY00.0240.01829.9930.0040.0040.0000.0000.0000.000
86A86GLN0-0.006-0.00226.576-0.010-0.0100.0000.0000.0000.000
87A87LEU00.0020.00020.681-0.001-0.0010.0000.0000.0000.000
88A88VAL0-0.027-0.01421.942-0.010-0.0100.0000.0000.0000.000
89A89GLY00.0410.01318.413-0.006-0.0060.0000.0000.0000.000
90A90TYR0-0.060-0.06817.4680.0100.0100.0000.0000.0000.000
91A91PRO00.0020.01412.997-0.008-0.0080.0000.0000.0000.000
92A92ILE0-0.0360.01312.9780.0250.0250.0000.0000.0000.000
93A93PHE00.0450.0059.522-0.052-0.0520.0000.0000.0000.000
94A94PRO00.0460.0257.6310.0810.0810.0000.0000.0000.000
95A95VAL0-0.0130.0009.836-0.080-0.0800.0000.0000.0000.000
96A96GLY00.0040.00812.1020.0260.0260.0000.0000.0000.000
97A97ARG10.9660.95014.3920.1780.1780.0000.0000.0000.000
98A98GLU-1-0.898-0.93614.718-0.300-0.3000.0000.0000.0000.000
99A99VAL00.0460.01715.844-0.038-0.0380.0000.0000.0000.000
100A100ARG10.9640.97017.9550.1430.1430.0000.0000.0000.000
101A101ARG10.9160.95711.8270.4850.4850.0000.0000.0000.000
102A102PHE00.0660.03912.3310.0040.0040.0000.0000.0000.000
103A103LEU0-0.015-0.01815.137-0.011-0.0110.0000.0000.0000.000
104A104ARG10.9750.99718.2140.2430.2430.0000.0000.0000.000
105A105GLN00.0210.02010.8420.0440.0440.0000.0000.0000.000
106A106ILE00.0050.00815.485-0.007-0.0070.0000.0000.0000.000
107A107GLU-1-0.927-0.98516.692-0.205-0.2050.0000.0000.0000.000
108A108GLU-1-0.917-0.95416.449-0.238-0.2380.0000.0000.0000.000
109A109ALA0-0.0020.00414.8810.0160.0160.0000.0000.0000.000
110A110ILE00.008-0.02016.7400.0310.0310.0000.0000.0000.000
111A111VAL0-0.002-0.00120.2660.0250.0250.0000.0000.0000.000
112A112ARG10.9590.98415.9650.3020.3020.0000.0000.0000.000
113A113VAL0-0.020-0.00218.7660.0200.0200.0000.0000.0000.000
114A114ALA0-0.025-0.01521.0630.0210.0210.0000.0000.0000.000
115A115ALA00.0450.02422.7150.0160.0160.0000.0000.0000.000
116A116GLY0-0.0020.00622.9910.0150.0150.0000.0000.0000.000
117A117TYR0-0.140-0.10223.8050.0050.0050.0000.0000.0000.000
118A118GLY0-0.0140.00126.9570.0100.0100.0000.0000.0000.000
119A119ILE0-0.052-0.01827.7080.0080.0080.0000.0000.0000.000
120A120SER0-0.012-0.00527.141-0.013-0.0130.0000.0000.0000.000
121A121ALA00.0160.00025.4140.0050.0050.0000.0000.0000.000
122A122TYR0-0.029-0.02325.728-0.002-0.0020.0000.0000.0000.000
123A123PRO00.0610.03023.0840.0050.0050.0000.0000.0000.000
124A124THR0-0.0180.01025.7730.0120.0120.0000.0000.0000.000
125A125PRO00.002-0.02528.097-0.007-0.0070.0000.0000.0000.000
126A126GLY0-0.015-0.00129.990-0.001-0.0010.0000.0000.0000.000
127A127TYR0-0.025-0.00130.3720.0050.0050.0000.0000.0000.000
128A128ALA00.0270.02026.580-0.008-0.0080.0000.0000.0000.000
129A129GLY0-0.025-0.01124.9720.0090.0090.0000.0000.0000.000
130A130VAL00.0120.00722.7260.0010.0010.0000.0000.0000.000
131A131TRP0-0.031-0.01326.0440.0110.0110.0000.0000.0000.000
132A132VAL00.0420.01128.926-0.005-0.0050.0000.0000.0000.000
133A133GLY00.0210.01631.2010.0060.0060.0000.0000.0000.000
134A134GLU-1-0.931-0.97333.652-0.073-0.0730.0000.0000.0000.000
135A135ASP-1-0.841-0.92534.355-0.083-0.0830.0000.0000.0000.000
136A136LYS10.9090.94528.4740.1210.1210.0000.0000.0000.000
137A137LEU0-0.0020.01126.2920.0040.0040.0000.0000.0000.000
138A138CYS0-0.024-0.00122.297-0.006-0.0060.0000.0000.0000.000
139A139ALA0-0.0290.00525.9530.0030.0030.0000.0000.0000.000
140A140ILE00.0400.00420.605-0.013-0.0130.0000.0000.0000.000
141A141GLY0-0.016-0.00722.4390.0160.0160.0000.0000.0000.000
142A142VAL00.0070.01618.235-0.001-0.0010.0000.0000.0000.000
143A143ALA0-0.011-0.01920.0520.0250.0250.0000.0000.0000.000
144A144VAL0-0.004-0.00316.731-0.024-0.0240.0000.0000.0000.000
145A145LYS10.9090.96318.3360.1330.1330.0000.0000.0000.000
146A146GLU-1-0.867-0.94817.916-0.121-0.1210.0000.0000.0000.000
147A147GLY0-0.0140.00815.592-0.003-0.0030.0000.0000.0000.000
148A148VAL00.0380.02812.580-0.058-0.0580.0000.0000.0000.000
149A149SER0-0.030-0.03113.8290.0280.0280.0000.0000.0000.000
150A150PHE00.037-0.00215.6170.0140.0140.0000.0000.0000.000
151A151HIS0-0.021-0.00317.937-0.003-0.0030.0000.0000.0000.000
152A152GLY00.013-0.00818.431-0.028-0.0280.0000.0000.0000.000
153A153PHE0-0.017-0.00116.5450.0150.0150.0000.0000.0000.000
154A154ALA0-0.003-0.00321.2950.0030.0030.0000.0000.0000.000
155A155LEU00.0540.01922.3320.0090.0090.0000.0000.0000.000
156A156ASN00.0060.02224.7880.0060.0060.0000.0000.0000.000
157A157VAL00.0140.01125.5880.0000.0000.0000.0000.0000.000
158A158ASN00.006-0.03028.5980.0090.0090.0000.0000.0000.000
159A159THR0-0.052-0.02430.1920.0030.0030.0000.0000.0000.000
160A160ASP-1-0.804-0.88432.593-0.074-0.0740.0000.0000.0000.000
161A161LEU0-0.059-0.04933.0110.0000.0000.0000.0000.0000.000
162A162ASN00.011-0.00136.2750.0010.0010.0000.0000.0000.000
163A163ASP-1-0.730-0.83136.366-0.073-0.0730.0000.0000.0000.000
164A164PHE0-0.063-0.04330.883-0.002-0.0020.0000.0000.0000.000
165A165THR0-0.034-0.01036.9010.0000.0000.0000.0000.0000.000
166A166VAL0-0.0110.01439.2380.0020.0020.0000.0000.0000.000
167A167ILE0-0.0380.00034.3510.0000.0000.0000.0000.0000.000
168A168VAL00.0250.00838.636-0.001-0.0010.0000.0000.0000.000
169A169PRO00.0280.02134.4260.0000.0000.0000.0000.0000.000
170A170CYS0-0.037-0.01635.9610.0060.0060.0000.0000.0000.000
171A171GLY0-0.016-0.00835.466-0.005-0.0050.0000.0000.0000.000
172A172LEU0-0.043-0.03034.5780.0020.0020.0000.0000.0000.000
173A173LYS10.8790.94434.1220.0730.0730.0000.0000.0000.000
174A174GLY00.0230.02134.5980.0050.0050.0000.0000.0000.000
175A175LYS10.8920.94036.3250.0640.0640.0000.0000.0000.000
176A176GLY00.0760.04637.0590.0030.0030.0000.0000.0000.000
177A177VAL0-0.059-0.01233.234-0.006-0.0060.0000.0000.0000.000
178A178THR00.018-0.00431.4940.0070.0070.0000.0000.0000.000
179A179SER00.0420.00530.490-0.006-0.0060.0000.0000.0000.000
180A180LEU00.0120.00125.5830.0050.0050.0000.0000.0000.000
181A181GLU-1-0.825-0.90430.218-0.077-0.0770.0000.0000.0000.000
182A182LYS10.9090.95833.3270.0830.0830.0000.0000.0000.000
183A183LEU0-0.076-0.04430.6980.0050.0050.0000.0000.0000.000
184A184LEU0-0.031-0.01529.7850.0040.0040.0000.0000.0000.000
185A185GLY0-0.0030.01534.3930.0050.0050.0000.0000.0000.000
186A186ARG10.9270.96231.3300.0870.0870.0000.0000.0000.000
187A187LYS10.8930.94633.4520.0740.0740.0000.0000.0000.000
188A188VAL0-0.0260.00227.3070.0030.0030.0000.0000.0000.000
189A189PRO00.0430.02227.658-0.003-0.0030.0000.0000.0000.000
190A190MET00.0380.01925.044-0.016-0.0160.0000.0000.0000.000
191A191GLU-1-0.928-0.95823.446-0.135-0.1350.0000.0000.0000.000
192A192GLU-1-0.850-0.91522.458-0.141-0.1410.0000.0000.0000.000
193A193ALA00.0160.00622.054-0.019-0.0190.0000.0000.0000.000
194A194LYS10.8560.90419.7860.1420.1420.0000.0000.0000.000
195A195ALA00.0360.02818.080-0.043-0.0430.0000.0000.0000.000
196A196ARG10.8930.94617.2530.1160.1160.0000.0000.0000.000
197A197VAL00.0120.00716.265-0.030-0.0300.0000.0000.0000.000
198A198VAL0-0.0030.00312.590-0.070-0.0700.0000.0000.0000.000
199A199ALA00.0100.00312.601-0.113-0.1130.0000.0000.0000.000
200A200ALA0-0.0190.00013.099-0.045-0.0450.0000.0000.0000.000
201A201PHE00.003-0.01911.190-0.013-0.0130.0000.0000.0000.000
202A202ALA0-0.0110.0018.540-0.159-0.1590.0000.0000.0000.000
203A203GLU-1-0.967-0.9808.507-0.497-0.4970.0000.0000.0000.000
204A204VAL0-0.055-0.02510.595-0.007-0.0070.0000.0000.0000.000
205A205PHE0-0.085-0.0617.4440.0840.0840.0000.0000.0000.000
206A206GLY00.0200.0366.579-0.246-0.2460.0000.0000.0000.000
207A207LEU0-0.099-0.0422.441-1.921-1.1061.206-0.519-1.502-0.005
208A208ARG10.9420.9522.513-3.097-0.7300.643-0.934-2.0760.003
209A209PRO00.0020.0156.131-0.197-0.1970.0000.0000.0000.000
210A210VAL00.0180.0048.2020.1680.1680.0000.0000.0000.000