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: 4943N

Calculation Name: 2QM4-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2QM4

Chain ID: A

ChEMBL ID:

UniProt ID: Q9H9Q4

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 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 232
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2582343.10211
FMO2-HF: Nuclear repulsion 2488474.394101
FMO2-HF: Total energy -93868.70801
FMO2-MP2: Total energy -94135.095933


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:SER)


Summations of interaction energy for fragment #1(A:-1:SER)
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.
-56.136-58.40331.852-17.55-12.038-0.104
Interaction energy analysis for fragmet #1(A:-1:SER)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.033 / q_NPA : -0.054
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].
3A1MET0-0.014-0.0063.000-5.600-1.5380.157-2.149-2.0710.012
4A2GLU-1-0.821-0.8761.642-48.528-56.02531.684-14.935-9.253-0.114
5A3GLU-1-0.931-0.9723.489-3.279-2.1110.011-0.466-0.714-0.002
6A4LEU0-0.095-0.0395.7210.6600.6600.0000.0000.0000.000
7A5GLU-1-0.775-0.8807.617-0.184-0.1840.0000.0000.0000.000
8A6GLN0-0.016-0.0067.0160.3860.3860.0000.0000.0000.000
9A7GLY00.0110.0029.6080.2360.2360.0000.0000.0000.000
10A8LEU0-0.050-0.02111.6480.1460.1460.0000.0000.0000.000
11A9LEU0-0.025-0.01113.0840.1140.1140.0000.0000.0000.000
12A10MET0-0.021-0.01112.2470.0850.0850.0000.0000.0000.000
13A11GLN0-0.039-0.00216.0600.1070.1070.0000.0000.0000.000
14A12PRO00.0270.00818.250-0.007-0.0070.0000.0000.0000.000
15A13TRP0-0.055-0.03621.1910.0090.0090.0000.0000.0000.000
16A14ALA00.0210.01623.8100.0080.0080.0000.0000.0000.000
17A15TRP0-0.023-0.02925.8820.0030.0030.0000.0000.0000.000
18A16LEU0-0.0020.00125.0680.0040.0040.0000.0000.0000.000
19A17GLN00.0440.01928.763-0.002-0.0020.0000.0000.0000.000
20A18LEU0-0.055-0.03827.8800.0070.0070.0000.0000.0000.000
21A19ALA0-0.069-0.04032.024-0.001-0.0010.0000.0000.0000.000
22A20GLU-1-0.948-0.95234.390-0.012-0.0120.0000.0000.0000.000
23A21ASN00.0120.00031.820-0.002-0.0020.0000.0000.0000.000
24A22SER0-0.032-0.01331.2060.0020.0020.0000.0000.0000.000
25A23LEU0-0.014-0.01125.4180.0010.0010.0000.0000.0000.000
26A24LEU00.0140.01725.289-0.002-0.0020.0000.0000.0000.000
27A25ALA00.002-0.01522.2230.0050.0050.0000.0000.0000.000
28A26LYS10.8360.94517.5380.3790.3790.0000.0000.0000.000
29A27VAL00.028-0.00416.6240.0170.0170.0000.0000.0000.000
30A28PHE00.0130.01810.124-0.037-0.0370.0000.0000.0000.000
31A29ILE00.0130.00313.4070.0570.0570.0000.0000.0000.000
32A30THR00.0400.0259.7690.0340.0340.0000.0000.0000.000
33A31LYS10.9070.9289.855-0.277-0.2770.0000.0000.0000.000
34A32GLN00.0120.0016.352-0.058-0.0580.0000.0000.0000.000
35A33GLY00.0530.0209.2580.2570.2570.0000.0000.0000.000
36A34TYR0-0.053-0.05311.271-0.127-0.1270.0000.0000.0000.000
37A35ALA00.0360.02810.4530.1240.1240.0000.0000.0000.000
38A36LEU0-0.039-0.02112.486-0.060-0.0600.0000.0000.0000.000
39A37LEU0-0.007-0.00916.0590.0060.0060.0000.0000.0000.000
40A38VAL00.0170.00718.104-0.001-0.0010.0000.0000.0000.000
41A39SER0-0.013-0.02621.728-0.009-0.0090.0000.0000.0000.000
42A40ASP-1-0.749-0.87024.702-0.068-0.0680.0000.0000.0000.000
43A41LEU0-0.049-0.02527.4920.0020.0020.0000.0000.0000.000
44A42GLN0-0.089-0.03328.9330.0000.0000.0000.0000.0000.000
45A43GLN0-0.027-0.01825.6400.0000.0000.0000.0000.0000.000
46A44VAL00.0000.00920.197-0.005-0.0050.0000.0000.0000.000
47A45TRP00.014-0.00220.3670.0020.0020.0000.0000.0000.000
48A46HIS0-0.051-0.04111.4320.0080.0080.0000.0000.0000.000
49A47GLU-1-0.686-0.81014.7060.2330.2330.0000.0000.0000.000
50A48GLN0-0.036-0.0277.3710.4150.4150.0000.0000.0000.000
51A49VAL0-0.038-0.01111.3950.0830.0830.0000.0000.0000.000
52A50ASP-1-0.690-0.8458.2911.0321.0320.0000.0000.0000.000
53A51THR00.009-0.0049.863-0.166-0.1660.0000.0000.0000.000
54A52SER0-0.067-0.05311.072-0.157-0.1570.0000.0000.0000.000
55A53VAL00.0180.01312.913-0.110-0.1100.0000.0000.0000.000
56A54VAL0-0.0240.00214.283-0.082-0.0820.0000.0000.0000.000
57A55SER0-0.056-0.04415.879-0.064-0.0640.0000.0000.0000.000
58A56GLN0-0.081-0.04817.491-0.033-0.0330.0000.0000.0000.000
59A57ARG10.8640.91117.260-0.265-0.2650.0000.0000.0000.000
60A58ALA00.0070.00720.159-0.034-0.0340.0000.0000.0000.000
61A59LYS10.9280.94822.034-0.210-0.2100.0000.0000.0000.000
62A60GLU-1-0.901-0.93622.6410.1950.1950.0000.0000.0000.000
63A61LEU0-0.047-0.01223.407-0.021-0.0210.0000.0000.0000.000
64A62ASN0-0.033-0.00824.707-0.030-0.0300.0000.0000.0000.000
65A63LYS10.8950.94027.585-0.119-0.1190.0000.0000.0000.000
66A64ARG10.9380.96830.345-0.067-0.0670.0000.0000.0000.000
67A65LEU00.0500.03827.225-0.004-0.0040.0000.0000.0000.000
68A66THR0-0.024-0.01724.3930.0120.0120.0000.0000.0000.000
69A67ALA00.0250.02123.200-0.013-0.0130.0000.0000.0000.000
70A68PRO00.0220.00619.2740.0190.0190.0000.0000.0000.000
71A69PRO00.0680.03315.000-0.027-0.0270.0000.0000.0000.000
72A70ALA00.0480.01515.479-0.024-0.0240.0000.0000.0000.000
73A71ALA0-0.0160.00316.680-0.038-0.0380.0000.0000.0000.000
74A72PHE00.0160.00019.113-0.026-0.0260.0000.0000.0000.000
75A73LEU0-0.035-0.00513.471-0.015-0.0150.0000.0000.0000.000
76A74CYS0-0.013-0.00517.615-0.039-0.0390.0000.0000.0000.000
77A75HIS00.0250.02119.949-0.026-0.0260.0000.0000.0000.000
78A76LEU00.0260.00218.486-0.016-0.0160.0000.0000.0000.000
79A77ASP-1-0.864-0.90918.759-0.117-0.1170.0000.0000.0000.000
80A78ASN0-0.046-0.05220.720-0.025-0.0250.0000.0000.0000.000
81A79LEU0-0.049-0.01024.138-0.005-0.0050.0000.0000.0000.000
82A80LEU0-0.025-0.02220.230-0.007-0.0070.0000.0000.0000.000
83A81ARG10.8410.92319.2820.1440.1440.0000.0000.0000.000
84A82PRO0-0.003-0.01224.039-0.011-0.0110.0000.0000.0000.000
85A83LEU0-0.003-0.00327.489-0.003-0.0030.0000.0000.0000.000
86A84LEU0-0.021-0.00322.427-0.004-0.0040.0000.0000.0000.000
87A85LYS10.8460.93626.5450.0750.0750.0000.0000.0000.000
88A86ASP-1-0.806-0.89428.424-0.069-0.0690.0000.0000.0000.000
89A87ALA00.0120.00931.6890.0040.0040.0000.0000.0000.000
90A88ALA0-0.049-0.01733.3310.0060.0060.0000.0000.0000.000
91A89HIS0-0.054-0.04732.1810.0020.0020.0000.0000.0000.000
92A90PRO0-0.023-0.01534.4090.0020.0020.0000.0000.0000.000
93A91SER00.0190.01731.5150.0040.0040.0000.0000.0000.000
94A92GLU-1-0.909-0.95333.0050.0090.0090.0000.0000.0000.000
95A93ALA0-0.089-0.03729.3350.0080.0080.0000.0000.0000.000
96A94THR0-0.027-0.02631.241-0.004-0.0040.0000.0000.0000.000
97A95PHE00.0320.00625.2850.0080.0080.0000.0000.0000.000
98A96SER0-0.009-0.00329.081-0.003-0.0030.0000.0000.0000.000
99A97CYS00.0310.00327.2200.0020.0020.0000.0000.0000.000
100A98ASP-1-0.823-0.85628.1450.0370.0370.0000.0000.0000.000
101A99CYS00.0130.00327.6690.0050.0050.0000.0000.0000.000
102A100VAL0-0.012-0.00427.3940.0020.0020.0000.0000.0000.000
103A101ALA0-0.022-0.01627.0470.0060.0060.0000.0000.0000.000
104A102ASP-1-0.883-0.92923.643-0.027-0.0270.0000.0000.0000.000
105A103ALA0-0.021-0.02622.891-0.002-0.0020.0000.0000.0000.000
106A104LEU0-0.0050.00122.891-0.007-0.0070.0000.0000.0000.000
107A105ILE0-0.015-0.01722.8230.0140.0140.0000.0000.0000.000
108A106LEU00.0120.01722.459-0.010-0.0100.0000.0000.0000.000
109A107ARG10.7680.84824.053-0.041-0.0410.0000.0000.0000.000
110A108VAL00.0340.00924.369-0.012-0.0120.0000.0000.0000.000
111A109ARG10.9170.97927.143-0.025-0.0250.0000.0000.0000.000
112A110SER00.012-0.00127.692-0.008-0.0080.0000.0000.0000.000
113A111GLU-1-0.925-0.97630.2360.0390.0390.0000.0000.0000.000
114A112LEU00.0160.00924.700-0.001-0.0010.0000.0000.0000.000
115A113SER0-0.025-0.02229.2670.0030.0030.0000.0000.0000.000
116A114GLY00.0370.03531.3570.0010.0010.0000.0000.0000.000
117A115LEU0-0.071-0.02931.7590.0000.0000.0000.0000.0000.000
118A116PRO0-0.022-0.01231.906-0.002-0.0020.0000.0000.0000.000
119A117PHE0-0.009-0.00422.4240.0100.0100.0000.0000.0000.000
120A118TYR0-0.006-0.01627.169-0.014-0.0140.0000.0000.0000.000
121A119TRP00.0090.00617.5800.0280.0280.0000.0000.0000.000
122A120ASN00.0250.01322.622-0.031-0.0310.0000.0000.0000.000
123A121PHE00.0170.02117.9690.0260.0260.0000.0000.0000.000
124A122HIS0-0.041-0.03419.046-0.029-0.0290.0000.0000.0000.000
125A123CYS0-0.0340.00018.2900.0180.0180.0000.0000.0000.000
126A124MET00.0240.02617.8640.0050.0050.0000.0000.0000.000
127A125LEU00.0160.01019.102-0.022-0.0220.0000.0000.0000.000
128A126ALA0-0.0290.00017.4480.0000.0000.0000.0000.0000.000
129A127SER00.0420.01414.412-0.006-0.0060.0000.0000.0000.000
130A128PRO00.0800.01317.468-0.022-0.0220.0000.0000.0000.000
131A129SER0-0.013-0.00515.0410.0090.0090.0000.0000.0000.000
132A130LEU00.0380.03412.284-0.052-0.0520.0000.0000.0000.000
133A131VAL00.0410.02116.060-0.002-0.0020.0000.0000.0000.000
134A132SER0-0.025-0.01919.0220.0140.0140.0000.0000.0000.000
135A133GLN0-0.031-0.02413.0370.0040.0040.0000.0000.0000.000
136A134HIS00.0890.05613.5950.0440.0440.0000.0000.0000.000
137A135LEU00.0000.02018.7910.0290.0290.0000.0000.0000.000
138A136ILE00.0130.00322.4380.0070.0070.0000.0000.0000.000
139A137ARG10.8780.92220.0320.4280.4280.0000.0000.0000.000
140A138PRO00.0350.02120.6970.0200.0200.0000.0000.0000.000
141A139LEU00.0590.02923.5020.0190.0190.0000.0000.0000.000
142A140MET0-0.0280.00326.3750.0160.0160.0000.0000.0000.000
143A141GLY00.017-0.00926.0080.0120.0120.0000.0000.0000.000
144A142MET0-0.0250.00926.2530.0070.0070.0000.0000.0000.000
145A143SER00.004-0.00428.6470.0180.0180.0000.0000.0000.000
146A144LEU0-0.031-0.00929.1270.0130.0130.0000.0000.0000.000
147A145ALA00.0250.01729.3660.0110.0110.0000.0000.0000.000
148A146LEU00.0240.00731.4980.0100.0100.0000.0000.0000.000
149A147GLN0-0.022-0.00634.1230.0150.0150.0000.0000.0000.000
150A148CYS0-0.037-0.03233.9880.0070.0070.0000.0000.0000.000
151A149GLN00.0350.01832.4110.0130.0130.0000.0000.0000.000
152A150VAL00.0240.01336.9040.0080.0080.0000.0000.0000.000
153A151ARG10.9140.96639.3990.1130.1130.0000.0000.0000.000
154A152GLU-1-0.911-0.94936.577-0.129-0.1290.0000.0000.0000.000
155A153LEU0-0.016-0.01540.0110.0060.0060.0000.0000.0000.000
156A154ALA0-0.0080.00242.8260.0050.0050.0000.0000.0000.000
157A155THR0-0.052-0.03743.5090.0050.0050.0000.0000.0000.000
158A156LEU0-0.022-0.01642.2900.0040.0040.0000.0000.0000.000
159A157LEU0-0.017-0.00446.2870.0040.0040.0000.0000.0000.000
160A158HIS10.8290.90448.5370.0790.0790.0000.0000.0000.000
161A159MET00.0080.01548.6110.0030.0030.0000.0000.0000.000
162A160LYS10.8860.93349.3090.0700.0700.0000.0000.0000.000
163A161ASP-1-0.819-0.90852.385-0.061-0.0610.0000.0000.0000.000
164A162LEU0-0.015-0.00354.0260.0020.0020.0000.0000.0000.000
165A163GLU-1-0.858-0.91853.588-0.059-0.0590.0000.0000.0000.000
166A164ILE0-0.037-0.03055.7230.0030.0030.0000.0000.0000.000
167A165GLN0-0.105-0.05958.5390.0010.0010.0000.0000.0000.000
168A166ASP-1-0.873-0.93858.615-0.051-0.0510.0000.0000.0000.000
169A167TYR0-0.051-0.01358.3840.0030.0030.0000.0000.0000.000
170A168GLN0-0.095-0.05362.2390.0020.0020.0000.0000.0000.000
171A169GLU-1-0.873-0.92663.638-0.043-0.0430.0000.0000.0000.000
172A170SER0-0.095-0.05364.7170.0010.0010.0000.0000.0000.000
173A171GLY0-0.026-0.01267.4270.0010.0010.0000.0000.0000.000
174A172ALA0-0.036-0.00265.6250.0010.0010.0000.0000.0000.000
175A173THR0-0.049-0.02765.9860.0010.0010.0000.0000.0000.000
176A174LEU00.0100.00468.6610.0000.0000.0000.0000.0000.000
177A175ILE0-0.007-0.00271.5320.0000.0000.0000.0000.0000.000
178A176ARG10.8650.92363.1250.0420.0420.0000.0000.0000.000
179A177ASP-1-0.781-0.87267.395-0.037-0.0370.0000.0000.0000.000
180A178ARG10.8420.89563.9980.0380.0380.0000.0000.0000.000
181A179LEU0-0.031-0.01061.2510.0000.0000.0000.0000.0000.000
182A180LYS10.8990.94960.2920.0410.0410.0000.0000.0000.000
183A181THR00.0240.00754.5470.0010.0010.0000.0000.0000.000
184A182GLU-1-0.862-0.92057.067-0.047-0.0470.0000.0000.0000.000
185A183PRO00.0140.01055.768-0.002-0.0020.0000.0000.0000.000
186A184PHE0-0.012-0.01147.022-0.001-0.0010.0000.0000.0000.000
187A185GLU-1-0.764-0.85752.426-0.069-0.0690.0000.0000.0000.000
188A186GLU-1-0.836-0.90047.320-0.080-0.0800.0000.0000.0000.000
189A187ASN0-0.086-0.06548.740-0.004-0.0040.0000.0000.0000.000
190A188SER00.004-0.01550.6540.0000.0000.0000.0000.0000.000
191A189PHE0-0.016-0.00744.4220.0000.0000.0000.0000.0000.000
192A190LEU0-0.028-0.02243.951-0.001-0.0010.0000.0000.0000.000
193A191GLU-1-0.885-0.93547.633-0.060-0.0600.0000.0000.0000.000
194A192GLN0-0.019-0.02650.2690.0010.0010.0000.0000.0000.000
195A193PHE0-0.014-0.00342.3150.0010.0010.0000.0000.0000.000
196A194MET0-0.023-0.01842.472-0.001-0.0010.0000.0000.0000.000
197A195ILE0-0.0270.00547.0080.0010.0010.0000.0000.0000.000
198A196GLU-1-0.928-0.96550.106-0.057-0.0570.0000.0000.0000.000
199A197LYS10.8440.91045.7030.0650.0650.0000.0000.0000.000
200A198LEU0-0.0160.00141.190-0.002-0.0020.0000.0000.0000.000
201A199PRO00.0070.00342.660-0.003-0.0030.0000.0000.0000.000
202A200GLU-1-0.939-0.97142.795-0.062-0.0620.0000.0000.0000.000
203A201ALA0-0.020-0.00741.079-0.003-0.0030.0000.0000.0000.000
204A202CYS0-0.100-0.04938.035-0.005-0.0050.0000.0000.0000.000
205A203SER0-0.0220.00037.365-0.003-0.0030.0000.0000.0000.000
206A204ILE00.0210.00932.665-0.002-0.0020.0000.0000.0000.000
207A205GLY00.0090.00234.9870.0000.0000.0000.0000.0000.000
208A206ASP-1-0.812-0.91634.275-0.075-0.0750.0000.0000.0000.000
209A207GLY00.0310.01831.016-0.002-0.0020.0000.0000.0000.000
210A208LYS10.8620.93231.2760.0650.0650.0000.0000.0000.000
211A209PRO00.0440.01733.045-0.006-0.0060.0000.0000.0000.000
212A210PHE00.0410.02525.493-0.006-0.0060.0000.0000.0000.000
213A211VAL0-0.032-0.01527.503-0.010-0.0100.0000.0000.0000.000
214A212MET0-0.050-0.02129.5250.0010.0010.0000.0000.0000.000
215A213ASN00.0020.00932.3950.0030.0030.0000.0000.0000.000
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