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

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FMODB ID: KGK13

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 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 218
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2498020.296916
FMO2-HF: Nuclear repulsion 2412802.713245
FMO2-HF: Total energy -85217.583671
FMO2-MP2: Total energy -85467.908892


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.
-13.04-7.6845.8-4.828-6.327-0.029
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 : 0.042 / 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].
3A2ARG10.9170.9693.4070.7854.2400.285-1.589-2.1510.003
4A3TYR00.025-0.0015.2350.2460.425-0.001-0.012-0.1650.000
5A4PHE0-0.031-0.0127.980-0.478-0.4780.0000.0000.0000.000
6A5SER00.0350.00111.0500.1500.1500.0000.0000.0000.000
7A6THR00.000-0.00813.592-0.047-0.0470.0000.0000.0000.000
8A7ASP-1-0.896-0.93915.870-0.704-0.7040.0000.0000.0000.000
9A8SER00.0220.01712.308-0.124-0.1240.0000.0000.0000.000
10A9PRO00.0240.01112.7270.1250.1250.0000.0000.0000.000
11A10GLU-1-0.797-0.90410.578-1.760-1.7600.0000.0000.0000.000
12A11VAL00.0060.01214.4990.0990.0990.0000.0000.0000.000
13A12LYS10.8670.92516.8240.6610.6610.0000.0000.0000.000
14A13THR0-0.027-0.02017.9200.0740.0740.0000.0000.0000.000
15A14ILE0-0.053-0.00817.3570.0660.0660.0000.0000.0000.000
16A15VAL0-0.023-0.01220.4510.0570.0570.0000.0000.0000.000
17A16ALA0-0.0230.00722.7910.0460.0460.0000.0000.0000.000
18A17GLN0-0.049-0.03124.7760.0290.0290.0000.0000.0000.000
19A18ASP-1-0.768-0.87125.321-0.327-0.3270.0000.0000.0000.000
20A19SER00.0330.00326.240-0.009-0.0090.0000.0000.0000.000
21A20ARG10.8180.89928.3140.2210.2210.0000.0000.0000.000
22A21LEU00.0000.00221.2340.0070.0070.0000.0000.0000.000
23A22PHE0-0.001-0.00323.352-0.007-0.0070.0000.0000.0000.000
24A23GLN0-0.016-0.02124.629-0.001-0.0010.0000.0000.0000.000
25A24PHE0-0.0180.00121.8990.0110.0110.0000.0000.0000.000
26A25ILE0-0.001-0.00518.9240.0070.0070.0000.0000.0000.000
27A26GLU-1-0.897-0.95120.983-0.412-0.4120.0000.0000.0000.000
28A27ILE0-0.049-0.01222.9370.0190.0190.0000.0000.0000.000
29A28ALA0-0.049-0.01820.5320.0170.0170.0000.0000.0000.000
30A29GLY00.0540.03518.3490.0180.0180.0000.0000.0000.000
31A30GLU-1-0.925-0.95011.802-0.515-0.5150.0000.0000.0000.000
32A31VAL0-0.027-0.00513.0590.1130.1130.0000.0000.0000.000
33A32GLN0-0.025-0.0439.061-0.087-0.0870.0000.0000.0000.000
34A33LEU0-0.007-0.0017.7650.0710.0710.0000.0000.0000.000
35A34PRO0-0.019-0.0195.428-0.196-0.1960.0000.0000.0000.000
36A35THR0-0.011-0.0022.512-0.6650.7990.347-0.563-1.248-0.002
37A36LYS10.9180.9632.010-6.919-7.3725.069-2.449-2.167-0.031
38A37PRO00.0250.0182.898-0.956-0.2590.101-0.212-0.5860.001
39A38ASN00.008-0.0044.919-0.793-0.779-0.001-0.003-0.0100.000
40A39PRO00.0880.0518.580-0.113-0.1130.0000.0000.0000.000
41A40PHE00.0620.01610.754-0.070-0.0700.0000.0000.0000.000
42A41GLN0-0.003-0.0109.779-0.095-0.0950.0000.0000.0000.000
43A42SER00.011-0.0168.5530.0250.0250.0000.0000.0000.000
44A43LEU00.0160.04211.182-0.044-0.0440.0000.0000.0000.000
45A44VAL0-0.022-0.00514.692-0.012-0.0120.0000.0000.0000.000
46A45SER0-0.058-0.04512.6300.0110.0110.0000.0000.0000.000
47A46SER00.001-0.01513.504-0.047-0.0470.0000.0000.0000.000
48A47ILE0-0.050-0.02415.574-0.005-0.0050.0000.0000.0000.000
49A48VAL0-0.058-0.03417.683-0.001-0.0010.0000.0000.0000.000
50A49GLU-1-0.828-0.90313.863-0.037-0.0370.0000.0000.0000.000
51A50GLN0-0.0240.00618.7120.0090.0090.0000.0000.0000.000
52A51GLN0-0.044-0.02921.5170.0330.0330.0000.0000.0000.000
53A52LEU0-0.0250.00321.7300.0150.0150.0000.0000.0000.000
54A53SER00.0250.01321.290-0.004-0.0040.0000.0000.0000.000
55A54ILE00.1240.04714.1830.0130.0130.0000.0000.0000.000
56A55LYS10.9580.97718.044-0.104-0.1040.0000.0000.0000.000
57A56ALA0-0.017-0.01520.4110.0240.0240.0000.0000.0000.000
58A57ALA00.0390.02118.2800.0170.0170.0000.0000.0000.000
59A58SER00.0060.02216.1230.0290.0290.0000.0000.0000.000
60A59ALA00.003-0.00617.7810.0360.0360.0000.0000.0000.000
61A60ILE0-0.054-0.02621.0760.0150.0150.0000.0000.0000.000
62A61TYR0-0.010-0.03313.751-0.042-0.0420.0000.0000.0000.000
63A62GLY00.0300.02017.7850.0390.0390.0000.0000.0000.000
64A63ARG10.8620.92218.693-0.199-0.1990.0000.0000.0000.000
65A64VAL0-0.013-0.01019.378-0.008-0.0080.0000.0000.0000.000
66A65GLU-1-0.794-0.87514.2310.7590.7590.0000.0000.0000.000
67A66GLN0-0.042-0.02118.6470.0020.0020.0000.0000.0000.000
68A67LEU0-0.078-0.02821.819-0.010-0.0100.0000.0000.0000.000
69A68VAL0-0.033-0.02018.574-0.020-0.0200.0000.0000.0000.000
70A69GLY0-0.0350.00321.4060.0150.0150.0000.0000.0000.000
71A70GLY0-0.026-0.02117.8060.0320.0320.0000.0000.0000.000
72A71ALA00.0200.02012.791-0.038-0.0380.0000.0000.0000.000
73A72LEU0-0.030-0.00414.586-0.081-0.0810.0000.0000.0000.000
74A73GLU-1-0.952-0.99012.4201.2011.2010.0000.0000.0000.000
75A74LYS10.8820.91914.222-0.401-0.4010.0000.0000.0000.000
76A75PRO00.0390.02117.189-0.001-0.0010.0000.0000.0000.000
77A76GLU-1-0.730-0.83519.8930.3240.3240.0000.0000.0000.000
78A77GLN0-0.024-0.01917.615-0.005-0.0050.0000.0000.0000.000
79A78LEU00.0360.00919.630-0.010-0.0100.0000.0000.0000.000
80A79TYR0-0.0470.00723.125-0.026-0.0260.0000.0000.0000.000
81A80ARG10.8550.89523.367-0.317-0.3170.0000.0000.0000.000
82A81VAL00.0080.03824.072-0.003-0.0030.0000.0000.0000.000
83A82SER00.0350.02227.109-0.013-0.0130.0000.0000.0000.000
84A83ASP-1-0.760-0.89828.6070.1110.1110.0000.0000.0000.000
85A84GLU-1-0.869-0.92129.9050.1090.1090.0000.0000.0000.000
86A85ALA00.0070.01528.5690.0020.0020.0000.0000.0000.000
87A86LEU00.0590.01523.5030.0060.0060.0000.0000.0000.000
88A87ARG10.8780.93226.771-0.092-0.0920.0000.0000.0000.000
89A88GLN0-0.073-0.03329.3780.0060.0060.0000.0000.0000.000
90A89ALA0-0.0060.01924.7000.0050.0050.0000.0000.0000.000
91A90GLY00.0090.00125.6140.0090.0090.0000.0000.0000.000
92A91VAL0-0.0300.00222.879-0.014-0.0140.0000.0000.0000.000
93A92SER00.009-0.00525.419-0.006-0.0060.0000.0000.0000.000
94A93LYS11.0641.00227.339-0.043-0.0430.0000.0000.0000.000
95A94ARG10.9580.98128.0960.0080.0080.0000.0000.0000.000
96A95LYS10.8280.90822.131-0.050-0.0500.0000.0000.0000.000
97A96ILE00.0090.01623.9530.0020.0020.0000.0000.0000.000
98A97GLU-1-0.850-0.89825.6670.0060.0060.0000.0000.0000.000
99A98TYR0-0.005-0.00722.939-0.005-0.0050.0000.0000.0000.000
100A99ILE00.0580.03420.029-0.006-0.0060.0000.0000.0000.000
101A100ARG10.8140.87822.088-0.128-0.1280.0000.0000.0000.000
102A101HIS00.0070.02624.586-0.006-0.0060.0000.0000.0000.000
103A102VAL00.0410.01617.770-0.011-0.0110.0000.0000.0000.000
104A103CYS0-0.085-0.03920.9370.0120.0120.0000.0000.0000.000
105A104GLU-1-0.801-0.88421.993-0.003-0.0030.0000.0000.0000.000
106A105HIS00.0200.01722.038-0.009-0.0090.0000.0000.0000.000
107A106VAL0-0.0140.00017.637-0.010-0.0100.0000.0000.0000.000
108A107GLU-1-0.950-0.99120.5760.1640.1640.0000.0000.0000.000
109A108SER0-0.089-0.05123.277-0.009-0.0090.0000.0000.0000.000
110A109GLY00.0090.00522.820-0.008-0.0080.0000.0000.0000.000
111A110ARG10.7590.87223.3630.0100.0100.0000.0000.0000.000
112A111LEU0-0.010-0.01417.577-0.033-0.0330.0000.0000.0000.000
113A112ASP-1-0.781-0.89117.801-0.113-0.1130.0000.0000.0000.000
114A113PHE00.002-0.03213.060-0.030-0.0300.0000.0000.0000.000
115A114THR0-0.039-0.01613.891-0.083-0.0830.0000.0000.0000.000
116A115GLU-1-0.854-0.90114.956-0.319-0.3190.0000.0000.0000.000
117A116LEU0-0.044-0.03315.606-0.042-0.0420.0000.0000.0000.000
118A117GLU-1-0.877-0.93210.204-1.240-1.2400.0000.0000.0000.000
119A118GLY00.011-0.00513.4430.0210.0210.0000.0000.0000.000
120A119ALA0-0.068-0.00816.2610.0340.0340.0000.0000.0000.000
121A120GLU-1-0.825-0.92817.750-0.593-0.5930.0000.0000.0000.000
122A121ALA00.0260.00218.2000.0320.0320.0000.0000.0000.000
123A122THR0-0.042-0.02819.2340.0300.0300.0000.0000.0000.000
124A123THR00.0050.01621.7020.0240.0240.0000.0000.0000.000
125A124VAL00.0150.01415.9450.0430.0430.0000.0000.0000.000
126A125ILE0-0.003-0.01119.3740.0420.0420.0000.0000.0000.000
127A126GLU-1-0.912-0.94220.975-0.228-0.2280.0000.0000.0000.000
128A127LYS10.7890.87920.7280.2420.2420.0000.0000.0000.000
129A128LEU0-0.009-0.01016.3090.0360.0360.0000.0000.0000.000
130A129THR0-0.085-0.06520.3880.0360.0360.0000.0000.0000.000
131A130ALA0-0.0220.00823.3150.0230.0230.0000.0000.0000.000
132A131ILE0-0.072-0.01719.8950.0300.0300.0000.0000.0000.000
133A132LYS10.8860.90323.9600.0020.0020.0000.0000.0000.000
134A133GLY0-0.034-0.03423.7760.0110.0110.0000.0000.0000.000
135A134ILE0-0.042-0.01618.562-0.007-0.0070.0000.0000.0000.000
136A135GLY00.0640.03921.8780.0000.0000.0000.0000.0000.000
137A136GLN0-0.001-0.02421.3640.0000.0000.0000.0000.0000.000
138A137TRP0-0.025-0.01718.632-0.016-0.0160.0000.0000.0000.000
139A138THR0-0.004-0.00317.696-0.030-0.0300.0000.0000.0000.000
140A139ALA00.0270.01316.744-0.035-0.0350.0000.0000.0000.000
141A140GLU-1-0.784-0.86416.385-0.427-0.4270.0000.0000.0000.000
142A141MET0-0.011-0.01114.720-0.106-0.1060.0000.0000.0000.000
143A142PHE0-0.031-0.01112.152-0.120-0.1200.0000.0000.0000.000
144A143MET00.0140.00411.558-0.081-0.0810.0000.0000.0000.000
145A144MET0-0.045-0.00211.160-0.153-0.1530.0000.0000.0000.000
146A145PHE0-0.018-0.0168.707-0.233-0.2330.0000.0000.0000.000
147A146SER0-0.032-0.0207.157-0.072-0.0720.0000.0000.0000.000
148A147LEU0-0.023-0.0047.426-0.040-0.0400.0000.0000.0000.000
149A148GLY00.0080.0316.966-0.195-0.1950.0000.0000.0000.000
150A149ARG10.7370.8577.9870.7470.7470.0000.0000.0000.000
151A150LEU00.002-0.0209.1360.0650.0650.0000.0000.0000.000
152A151ASP-1-0.769-0.83912.661-0.818-0.8180.0000.0000.0000.000
153A152VAL0-0.0040.00214.9350.1060.1060.0000.0000.0000.000
154A153LEU00.0420.00817.460-0.005-0.0050.0000.0000.0000.000
155A154SER0-0.035-0.03419.4250.0540.0540.0000.0000.0000.000
156A155VAL00.011-0.01421.2350.0330.0330.0000.0000.0000.000
157A156GLY0-0.037-0.02324.1490.0250.0250.0000.0000.0000.000
158A157ASP-1-0.705-0.83220.356-0.278-0.2780.0000.0000.0000.000
159A158VAL00.004-0.01522.992-0.002-0.0020.0000.0000.0000.000
160A159GLY00.0110.02121.9690.0150.0150.0000.0000.0000.000
161A160LEU00.0170.00419.1380.0070.0070.0000.0000.0000.000
162A161GLN0-0.092-0.05922.9670.0250.0250.0000.0000.0000.000
163A162ARG10.8350.91925.8610.1510.1510.0000.0000.0000.000
164A163GLY00.0730.04124.7470.0110.0110.0000.0000.0000.000
165A164ALA0-0.005-0.00225.7880.0020.0020.0000.0000.0000.000
166A165LYS10.8640.90827.6260.1610.1610.0000.0000.0000.000
167A166TRP0-0.0280.00427.269-0.003-0.0030.0000.0000.0000.000
168A167LEU00.0560.03524.9790.0090.0090.0000.0000.0000.000
169A168TYR0-0.131-0.09625.901-0.001-0.0010.0000.0000.0000.000
170A169GLY0-0.0210.01031.5750.0080.0080.0000.0000.0000.000
171A170ASN0-0.019-0.00534.2890.0060.0060.0000.0000.0000.000
172A171GLY00.1070.05132.9280.0100.0100.0000.0000.0000.000
173A172GLU-1-0.934-0.94934.005-0.105-0.1050.0000.0000.0000.000
174A173GLY00.0430.01934.838-0.012-0.0120.0000.0000.0000.000
175A174ASP-1-0.848-0.92233.350-0.172-0.1720.0000.0000.0000.000
176A175GLY00.1020.04029.961-0.010-0.0100.0000.0000.0000.000
177A176LYS10.9971.01128.9490.1810.1810.0000.0000.0000.000
178A177LYS10.8870.92329.6320.1480.1480.0000.0000.0000.000
179A178LEU0-0.047-0.01030.463-0.011-0.0110.0000.0000.0000.000
180A179LEU00.0620.03923.387-0.012-0.0120.0000.0000.0000.000
181A180ILE0-0.024-0.00926.677-0.020-0.0200.0000.0000.0000.000
182A181TYR0-0.071-0.03428.473-0.014-0.0140.0000.0000.0000.000
183A182HIS10.8950.92027.5520.2700.2700.0000.0000.0000.000
184A183GLY00.0710.04424.257-0.015-0.0150.0000.0000.0000.000
185A184LYS10.8820.94123.9870.2480.2480.0000.0000.0000.000
186A185ALA0-0.026-0.00325.721-0.008-0.0080.0000.0000.0000.000
187A186TRP0-0.037-0.01020.476-0.012-0.0120.0000.0000.0000.000
188A187ALA00.0080.06720.021-0.065-0.0650.0000.0000.0000.000
189A188PRO0-0.040-0.02417.3410.0300.0300.0000.0000.0000.000
190A189TYR00.026-0.02713.738-0.137-0.1370.0000.0000.0000.000
191A190GLU-1-0.776-0.91416.570-0.655-0.6550.0000.0000.0000.000
192A191THR0-0.007-0.01212.4090.0990.0990.0000.0000.0000.000
193A192VAL00.0250.01012.5230.0230.0230.0000.0000.0000.000
194A193ALA00.0210.01115.0280.0730.0730.0000.0000.0000.000
195A194CYS0-0.065-0.03916.9050.0870.0870.0000.0000.0000.000
196A195LEU00.0020.01211.9700.0680.0680.0000.0000.0000.000
197A196TYR0-0.010-0.02516.2280.0560.0560.0000.0000.0000.000
198A197LEU0-0.043-0.01119.4360.0680.0680.0000.0000.0000.000
199A198TRP0-0.017-0.04315.2980.0380.0380.0000.0000.0000.000
200A199LYS10.8390.92116.6930.3770.3770.0000.0000.0000.000
201A200ALA0-0.015-0.00920.4390.0390.0390.0000.0000.0000.000
202A201ALA0-0.037-0.02922.6620.0310.0310.0000.0000.0000.000
203A202GLY00.0230.02522.3090.0260.0260.0000.0000.0000.000
204A203THR00.0780.02622.0080.0040.0040.0000.0000.0000.000
205A204PHE0-0.001-0.00522.3250.0100.0100.0000.0000.0000.000
206A205ALA0-0.013-0.00826.6070.0100.0100.0000.0000.0000.000
207A206GLU-1-1.033-1.01125.442-0.071-0.0710.0000.0000.0000.000
208A207GLU-1-0.917-0.93628.650-0.078-0.0780.0000.0000.0000.000
209A208TYR0-0.064-0.04628.7490.0010.0010.0000.0000.0000.000
210A209ARG10.7990.89432.1480.1120.1120.0000.0000.0000.000
211A210SER0-0.019-0.04332.558-0.008-0.0080.0000.0000.0000.000
212A211LEU00.0140.01428.2210.0040.0040.0000.0000.0000.000
213A212GLU-1-0.798-0.88831.257-0.175-0.1750.0000.0000.0000.000
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