FMODB

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

Last updated: 2024-07-23

All entries: 37450

Number of unique PDB entries: 7783

tag_button

FMODB ID: 4JQMN

Calculation Name: 2H56-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2H56

Chain ID: A

ChEMBL ID:

UniProt ID: Q9KC25

Base Structure: X-ray

Registration Date: 2023-09-22

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 218
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2506927.366926
FMO2-HF: Nuclear repulsion 2421709.371605
FMO2-HF: Total energy -85217.995322
FMO2-MP2: Total energy -85468.428707


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:0:HIS)


Summations of interaction energy for fragment #1(A:0:HIS)
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.
-14.765-9.4967.437-5.574-7.131-0.031
Interaction energy analysis for fragmet #1(A:0:HIS)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.055 / q_NPA : 0.030
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].
3A2ARG10.8380.9283.668-0.2803.2130.134-1.512-2.1150.003
4A3TYR00.0310.0014.9540.4100.601-0.001-0.019-0.1710.000
5A4PHE0-0.032-0.0207.933-0.575-0.5750.0000.0000.0000.000
6A5SER00.0560.01810.9350.1420.1420.0000.0000.0000.000
7A6THR0-0.007-0.02513.778-0.059-0.0590.0000.0000.0000.000
8A7ASP-1-0.885-0.92415.990-0.698-0.6980.0000.0000.0000.000
9A8SER00.0080.00312.070-0.127-0.1270.0000.0000.0000.000
10A9PRO00.0080.00512.5800.1080.1080.0000.0000.0000.000
11A10GLU-1-0.761-0.85910.817-1.713-1.7130.0000.0000.0000.000
12A11VAL0-0.0090.00714.1830.0980.0980.0000.0000.0000.000
13A12LYS10.8340.89616.7160.6250.6250.0000.0000.0000.000
14A13THR0-0.031-0.02018.1720.0700.0700.0000.0000.0000.000
15A14ILE0-0.044-0.00917.3550.0680.0680.0000.0000.0000.000
16A15VAL00.0010.00120.6430.0550.0550.0000.0000.0000.000
17A16ALA0-0.0270.00223.0070.0440.0440.0000.0000.0000.000
18A17GLN0-0.051-0.02924.9170.0310.0310.0000.0000.0000.000
19A18ASP-1-0.775-0.86225.132-0.318-0.3180.0000.0000.0000.000
20A19SER00.0400.00926.218-0.009-0.0090.0000.0000.0000.000
21A20ARG10.8260.89328.4900.2130.2130.0000.0000.0000.000
22A21LEU00.0050.00421.0850.0080.0080.0000.0000.0000.000
23A22PHE0-0.018-0.01323.662-0.002-0.0020.0000.0000.0000.000
24A23GLN0-0.028-0.02824.8290.0000.0000.0000.0000.0000.000
25A24PHE00.0020.01321.8480.0130.0130.0000.0000.0000.000
26A25ILE00.0120.00118.9250.0080.0080.0000.0000.0000.000
27A26GLU-1-0.839-0.91721.081-0.439-0.4390.0000.0000.0000.000
28A27ILE0-0.059-0.01423.0050.0230.0230.0000.0000.0000.000
29A28ALA0-0.022-0.00220.9460.0190.0190.0000.0000.0000.000
30A29GLY00.0420.03618.6200.0190.0190.0000.0000.0000.000
31A30GLU-1-0.916-0.95011.918-0.499-0.4990.0000.0000.0000.000
32A31VAL0-0.032-0.00512.9670.1080.1080.0000.0000.0000.000
33A32GLN0-0.031-0.0588.817-0.142-0.1420.0000.0000.0000.000
34A33LEU00.0010.0067.3670.0890.0890.0000.0000.0000.000
35A34PRO0-0.023-0.0185.302-0.223-0.2230.0000.0000.0000.000
36A35THR0-0.003-0.0062.452-0.7540.7980.460-0.646-1.365-0.002
37A36LYS10.8780.9351.949-6.933-8.0206.535-2.944-2.503-0.035
38A37PRO00.0440.0212.701-1.330-0.2550.310-0.440-0.9450.003
39A38ASN00.0060.0144.467-0.525-0.480-0.001-0.013-0.0320.000
40A39PRO00.0900.0578.224-0.163-0.1630.0000.0000.0000.000
41A40PHE00.0550.02210.304-0.083-0.0830.0000.0000.0000.000
42A41GLN00.010-0.0069.204-0.114-0.1140.0000.0000.0000.000
43A42SER00.000-0.0178.316-0.147-0.1470.0000.0000.0000.000
44A43LEU0-0.0080.02310.577-0.066-0.0660.0000.0000.0000.000
45A44VAL0-0.009-0.00614.225-0.016-0.0160.0000.0000.0000.000
46A45SER0-0.062-0.04111.9560.0090.0090.0000.0000.0000.000
47A46SER00.019-0.01712.803-0.041-0.0410.0000.0000.0000.000
48A47ILE0-0.046-0.01014.971-0.012-0.0120.0000.0000.0000.000
49A48VAL0-0.040-0.02717.165-0.003-0.0030.0000.0000.0000.000
50A49GLU-1-0.825-0.90413.098-0.048-0.0480.0000.0000.0000.000
51A50GLN0-0.047-0.00617.8410.0030.0030.0000.0000.0000.000
52A51GLN0-0.047-0.03220.7830.0340.0340.0000.0000.0000.000
53A52LEU0-0.0100.01521.2080.0140.0140.0000.0000.0000.000
54A53SER00.0340.02020.980-0.006-0.0060.0000.0000.0000.000
55A54ILE00.1070.03613.6730.0160.0160.0000.0000.0000.000
56A55LYS10.9740.99017.571-0.125-0.1250.0000.0000.0000.000
57A56ALA0-0.004-0.00319.9130.0250.0250.0000.0000.0000.000
58A57ALA00.0320.02217.5590.0140.0140.0000.0000.0000.000
59A58SER00.0130.01315.5370.0280.0280.0000.0000.0000.000
60A59ALA0-0.009-0.01217.1670.0350.0350.0000.0000.0000.000
61A60ILE0-0.054-0.02020.5850.0070.0070.0000.0000.0000.000
62A61TYR0-0.017-0.03513.149-0.034-0.0340.0000.0000.0000.000
63A62GLY00.0390.01917.3480.0370.0370.0000.0000.0000.000
64A63ARG10.8620.92218.195-0.215-0.2150.0000.0000.0000.000
65A64VAL0-0.017-0.01118.726-0.012-0.0120.0000.0000.0000.000
66A65GLU-1-0.784-0.86614.0320.7970.7970.0000.0000.0000.000
67A66GLN0-0.035-0.02518.153-0.010-0.0100.0000.0000.0000.000
68A67LEU0-0.064-0.02721.428-0.012-0.0120.0000.0000.0000.000
69A68VAL0-0.054-0.01918.268-0.027-0.0270.0000.0000.0000.000
70A69GLY0-0.039-0.00620.9960.0190.0190.0000.0000.0000.000
71A70GLY0-0.033-0.02517.6780.0280.0280.0000.0000.0000.000
72A71ALA00.0320.03012.473-0.045-0.0450.0000.0000.0000.000
73A72LEU0-0.043-0.01314.274-0.075-0.0750.0000.0000.0000.000
74A73GLU-1-0.941-0.98311.9711.3441.3440.0000.0000.0000.000
75A74LYS10.8880.91913.886-0.399-0.3990.0000.0000.0000.000
76A75PRO00.0280.01516.960-0.003-0.0030.0000.0000.0000.000
77A76GLU-1-0.773-0.86019.6090.3470.3470.0000.0000.0000.000
78A77GLN0-0.010-0.01117.316-0.002-0.0020.0000.0000.0000.000
79A78LEU00.0570.01219.265-0.017-0.0170.0000.0000.0000.000
80A79TYR0-0.0470.00822.744-0.029-0.0290.0000.0000.0000.000
81A80ARG10.8410.90622.880-0.342-0.3420.0000.0000.0000.000
82A81VAL00.0110.03423.636-0.001-0.0010.0000.0000.0000.000
83A82SER00.0240.01626.702-0.013-0.0130.0000.0000.0000.000
84A83ASP-1-0.774-0.89828.0740.1240.1240.0000.0000.0000.000
85A84GLU-1-0.820-0.88229.0880.1150.1150.0000.0000.0000.000
86A85ALA00.0270.01927.9220.0010.0010.0000.0000.0000.000
87A86LEU00.0470.02022.9450.0080.0080.0000.0000.0000.000
88A87ARG10.8320.89226.172-0.103-0.1030.0000.0000.0000.000
89A88GLN0-0.079-0.04328.8730.0050.0050.0000.0000.0000.000
90A89ALA00.0090.02623.7150.0060.0060.0000.0000.0000.000
91A90GLY00.0220.00824.6460.0100.0100.0000.0000.0000.000
92A91VAL0-0.026-0.00222.407-0.016-0.0160.0000.0000.0000.000
93A92SER00.0250.00224.990-0.006-0.0060.0000.0000.0000.000
94A93LYS11.0250.99026.734-0.053-0.0530.0000.0000.0000.000
95A94ARG10.9690.99027.3760.0000.0000.0000.0000.0000.000
96A95LYS10.8570.92821.411-0.062-0.0620.0000.0000.0000.000
97A96ILE0-0.0030.00823.1350.0050.0050.0000.0000.0000.000
98A97GLU-1-0.873-0.91924.8710.0170.0170.0000.0000.0000.000
99A98TYR00.0090.00122.328-0.006-0.0060.0000.0000.0000.000
100A99ILE00.0380.02719.310-0.005-0.0050.0000.0000.0000.000
101A100ARG10.7930.85421.426-0.141-0.1410.0000.0000.0000.000
102A101HIS0-0.0020.01423.839-0.005-0.0050.0000.0000.0000.000
103A102VAL00.0350.01817.100-0.011-0.0110.0000.0000.0000.000
104A103CYS0-0.068-0.03520.2610.0150.0150.0000.0000.0000.000
105A104GLU-1-0.831-0.89421.5940.0050.0050.0000.0000.0000.000
106A105HIS00.0080.00321.459-0.006-0.0060.0000.0000.0000.000
107A106VAL0-0.0030.00717.292-0.008-0.0080.0000.0000.0000.000
108A107GLU-1-0.900-0.96720.2750.2010.2010.0000.0000.0000.000
109A108SER0-0.065-0.03922.896-0.009-0.0090.0000.0000.0000.000
110A109GLY00.000-0.00222.401-0.013-0.0130.0000.0000.0000.000
111A110ARG10.7550.85722.915-0.006-0.0060.0000.0000.0000.000
112A111LEU0-0.011-0.00417.340-0.032-0.0320.0000.0000.0000.000
113A112ASP-1-0.767-0.85717.419-0.088-0.0880.0000.0000.0000.000
114A113PHE00.019-0.02412.953-0.029-0.0290.0000.0000.0000.000
115A114THR0-0.055-0.04614.128-0.086-0.0860.0000.0000.0000.000
116A115GLU-1-0.868-0.91615.276-0.298-0.2980.0000.0000.0000.000
117A116LEU0-0.013-0.00715.157-0.041-0.0410.0000.0000.0000.000
118A117GLU-1-0.848-0.91210.556-1.182-1.1820.0000.0000.0000.000
119A118GLY0-0.012-0.01813.636-0.030-0.0300.0000.0000.0000.000
120A119ALA0-0.061-0.00816.6380.0260.0260.0000.0000.0000.000
121A120GLU-1-0.841-0.93517.852-0.564-0.5640.0000.0000.0000.000
122A121ALA00.0140.01318.3420.0290.0290.0000.0000.0000.000
123A122THR0-0.089-0.05919.2770.0220.0220.0000.0000.0000.000
124A123THR00.014-0.00522.1870.0170.0170.0000.0000.0000.000
125A124VAL0-0.0160.00215.5410.0370.0370.0000.0000.0000.000
126A125ILE00.014-0.00318.9770.0350.0350.0000.0000.0000.000
127A126GLU-1-0.859-0.89220.619-0.225-0.2250.0000.0000.0000.000
128A127LYS10.7980.87720.6480.2170.2170.0000.0000.0000.000
129A128LEU0-0.032-0.00815.7100.0370.0370.0000.0000.0000.000
130A129THR0-0.064-0.06019.7350.0360.0360.0000.0000.0000.000
131A130ALA0-0.0140.01522.8570.0230.0230.0000.0000.0000.000
132A131ILE0-0.0410.00419.1030.0320.0320.0000.0000.0000.000
133A132LYS10.8430.88923.128-0.011-0.0110.0000.0000.0000.000
134A133GLY00.014-0.01422.9400.0160.0160.0000.0000.0000.000
135A134ILE0-0.034-0.00717.786-0.006-0.0060.0000.0000.0000.000
136A135GLY00.0450.02421.0820.0020.0020.0000.0000.0000.000
137A136GLN0-0.018-0.03320.7710.0010.0010.0000.0000.0000.000
138A137TRP0-0.021-0.01818.018-0.019-0.0190.0000.0000.0000.000
139A138THR0-0.006-0.00317.134-0.032-0.0320.0000.0000.0000.000
140A139ALA00.0430.02516.043-0.032-0.0320.0000.0000.0000.000
141A140GLU-1-0.768-0.85615.762-0.419-0.4190.0000.0000.0000.000
142A141MET00.004-0.00114.235-0.111-0.1110.0000.0000.0000.000
143A142PHE0-0.029-0.00911.730-0.125-0.1250.0000.0000.0000.000
144A143MET00.0070.00010.892-0.099-0.0990.0000.0000.0000.000
145A144MET0-0.044-0.00310.703-0.157-0.1570.0000.0000.0000.000
146A145PHE0-0.015-0.0188.042-0.236-0.2360.0000.0000.0000.000
147A146SER0-0.100-0.0406.557-0.143-0.1430.0000.0000.0000.000
148A147LEU00.009-0.0046.643-0.138-0.1380.0000.0000.0000.000
149A148GLY00.0200.0336.714-0.279-0.2790.0000.0000.0000.000
150A149ARG10.7320.8337.5490.7860.7860.0000.0000.0000.000
151A150LEU0-0.003-0.0129.3470.0470.0470.0000.0000.0000.000
152A151ASP-1-0.772-0.84312.829-0.811-0.8110.0000.0000.0000.000
153A152VAL0-0.021-0.01114.3550.0950.0950.0000.0000.0000.000
154A153LEU00.0360.00617.183-0.001-0.0010.0000.0000.0000.000
155A154SER0-0.017-0.02018.7900.0550.0550.0000.0000.0000.000
156A155VAL00.010-0.01820.7230.0340.0340.0000.0000.0000.000
157A156GLY0-0.037-0.02823.5120.0290.0290.0000.0000.0000.000
158A157ASP-1-0.743-0.85319.948-0.260-0.2600.0000.0000.0000.000
159A158VAL00.014-0.00822.654-0.003-0.0030.0000.0000.0000.000
160A159GLY00.0220.02122.0630.0140.0140.0000.0000.0000.000
161A160LEU00.0130.01118.9710.0030.0030.0000.0000.0000.000
162A161GLN0-0.072-0.03022.8760.0230.0230.0000.0000.0000.000
163A162ARG10.7950.89325.7980.1420.1420.0000.0000.0000.000
164A163GLY00.0760.04124.4920.0100.0100.0000.0000.0000.000
165A164ALA00.001-0.00725.5430.0030.0030.0000.0000.0000.000
166A165LYS10.8280.90327.4910.1510.1510.0000.0000.0000.000
167A166TRP0-0.0100.01427.172-0.003-0.0030.0000.0000.0000.000
168A167LEU00.0220.02824.7060.0070.0070.0000.0000.0000.000
169A168TYR0-0.125-0.09625.561-0.001-0.0010.0000.0000.0000.000
170A169GLY0-0.0180.01231.1650.0070.0070.0000.0000.0000.000
171A170ASN0-0.020-0.01933.8640.0070.0070.0000.0000.0000.000
172A171GLY00.1290.07132.7260.0100.0100.0000.0000.0000.000
173A172GLU-1-0.941-0.96033.794-0.102-0.1020.0000.0000.0000.000
174A173GLY00.0460.01534.351-0.011-0.0110.0000.0000.0000.000
175A174ASP-1-0.836-0.91233.099-0.164-0.1640.0000.0000.0000.000
176A175GLY00.1010.03829.983-0.009-0.0090.0000.0000.0000.000
177A176LYS10.9681.00228.3010.1740.1740.0000.0000.0000.000
178A177LYS10.8700.91529.4670.1410.1410.0000.0000.0000.000
179A178LEU0-0.0200.00530.278-0.011-0.0110.0000.0000.0000.000
180A179LEU00.0540.04223.057-0.011-0.0110.0000.0000.0000.000
181A180ILE0-0.022-0.01326.676-0.020-0.0200.0000.0000.0000.000
182A181TYR0-0.091-0.04728.411-0.010-0.0100.0000.0000.0000.000
183A182HIS10.8800.91927.0440.2660.2660.0000.0000.0000.000
184A183GLY00.0690.04223.699-0.015-0.0150.0000.0000.0000.000
185A184LYS10.8940.94223.5570.2400.2400.0000.0000.0000.000
186A185ALA0-0.0080.01125.536-0.004-0.0040.0000.0000.0000.000
187A186TRP0-0.047-0.02820.268-0.010-0.0100.0000.0000.0000.000
188A187ALA00.0270.04819.614-0.064-0.0640.0000.0000.0000.000
189A188PRO0-0.069-0.02317.1240.0260.0260.0000.0000.0000.000
190A189TYR00.040-0.01514.271-0.137-0.1370.0000.0000.0000.000
191A190GLU-1-0.782-0.91416.304-0.630-0.6300.0000.0000.0000.000
192A191THR00.004-0.01111.8860.1080.1080.0000.0000.0000.000
193A192VAL00.0100.00512.4930.0250.0250.0000.0000.0000.000
194A193ALA00.0270.01614.8080.0700.0700.0000.0000.0000.000
195A194CYS0-0.086-0.05116.4450.0860.0860.0000.0000.0000.000
196A195LEU0-0.0080.00011.5390.0720.0720.0000.0000.0000.000
197A196TYR0-0.007-0.02215.9600.0580.0580.0000.0000.0000.000
198A197LEU0-0.033-0.00919.2290.0650.0650.0000.0000.0000.000
199A198TRP0-0.011-0.04315.0290.0320.0320.0000.0000.0000.000
200A199LYS10.8140.90116.7710.3560.3560.0000.0000.0000.000
201A200ALA0-0.014-0.00820.1000.0370.0370.0000.0000.0000.000
202A201ALA0-0.034-0.02822.4950.0290.0290.0000.0000.0000.000
203A202GLY00.0070.02722.2330.0240.0240.0000.0000.0000.000
204A203THR00.0860.02522.575-0.005-0.0050.0000.0000.0000.000
205A204PHE00.0570.03122.3780.0080.0080.0000.0000.0000.000
206A205ALA0-0.0090.00726.5630.0070.0070.0000.0000.0000.000
207A206GLU-1-1.020-1.02325.268-0.065-0.0650.0000.0000.0000.000
208A207GLU-1-0.908-0.93227.628-0.076-0.0760.0000.0000.0000.000
209A208TYR0-0.060-0.04828.5220.0010.0010.0000.0000.0000.000
210A209ARG10.7650.87031.8130.1060.1060.0000.0000.0000.000
211A210SER0-0.021-0.05231.975-0.007-0.0070.0000.0000.0000.000
212A211LEU00.0190.02228.1880.0060.0060.0000.0000.0000.000
213A212GLU-1-0.778-0.86631.112-0.165-0.1650.0000.0000.0000.000
214A213GLU-1-0.891-0.94334.388-0.107-0.1070.0000.0000.0000.000
215A214LEU00.0180.03327.1710.0060.0060.0000.0000.0000.000
216A215LEU0-0.032-0.00430.4580.0020.0020.0000.0000.0000.000
217A216HIS10.7430.85133.3650.1250.1250.0000.0000.0000.000
218A217HIS00.0150.02932.1260.0120.0120.0000.0000.0000.000