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: N973Q

Calculation Name: 4HH8-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 4HH8

Chain ID: A

ChEMBL ID:

UniProt ID: P18892

Base Structure: X-ray

Registration Date: 2023-06-26

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 209
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2191788.125955
FMO2-HF: Nuclear repulsion 2107885.336957
FMO2-HF: Total energy -83902.788998
FMO2-MP2: Total energy -84144.302259


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:ALA)


Summations of interaction energy for fragment #1(A:1:ALA)
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.
-10.324-2.8732.049-4.111-5.388-0.022
Interaction energy analysis for fragmet #1(A:1:ALA)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.010 / q_NPA : -0.001
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].
3A3PHE0-0.045-0.0312.928-1.2842.1380.125-1.649-1.898-0.002
4A4ASP-1-0.831-0.9113.229-4.111-3.4800.100-0.344-0.388-0.003
5A5VAL0-0.030-0.0015.7490.4100.4100.0000.0000.0000.000
6A6ILE0-0.045-0.0188.4410.0490.0490.0000.0000.0000.000
7A7GLY00.0660.02411.7320.0570.0570.0000.0000.0000.000
8A8PRO0-0.040-0.02814.8430.0000.0000.0000.0000.0000.000
9A9PRO0-0.044-0.02518.381-0.005-0.0050.0000.0000.0000.000
10A10GLU-1-0.958-0.97920.167-0.200-0.2000.0000.0000.0000.000
11A11PRO0-0.039-0.02722.127-0.012-0.0120.0000.0000.0000.000
12A12ILE00.0060.01421.9130.0050.0050.0000.0000.0000.000
13A13LEU0-0.022-0.00425.0090.0070.0070.0000.0000.0000.000
14A14ALA00.0210.00428.4740.0000.0000.0000.0000.0000.000
15A15VAL0-0.001-0.00130.3770.0030.0030.0000.0000.0000.000
16A16VAL0-0.007-0.01433.761-0.002-0.0020.0000.0000.0000.000
17A17GLY0-0.042-0.02434.8450.0040.0040.0000.0000.0000.000
18A18GLU-1-0.955-0.96733.208-0.095-0.0950.0000.0000.0000.000
19A19ASP-1-0.816-0.90229.142-0.121-0.1210.0000.0000.0000.000
20A20ALA0-0.052-0.02426.565-0.002-0.0020.0000.0000.0000.000
21A21GLU-1-0.903-0.96023.153-0.182-0.1820.0000.0000.0000.000
22A22LEU0-0.033-0.01419.753-0.007-0.0070.0000.0000.0000.000
23A23PRO00.002-0.00618.266-0.016-0.0160.0000.0000.0000.000
24A24CYS0-0.078-0.02512.864-0.004-0.0040.0000.0000.0000.000
25A25ARG10.9500.98012.9100.5370.5370.0000.0000.0000.000
26A26LEU00.0000.0126.969-0.092-0.0920.0000.0000.0000.000
27A27SER0-0.124-0.0388.4990.3100.3100.0000.0000.0000.000
28A28PRO00.0540.0067.726-0.341-0.3410.0000.0000.0000.000
29A29ASN0-0.037-0.01510.367-0.066-0.0660.0000.0000.0000.000
30A30VAL0-0.037-0.0228.9160.1130.1130.0000.0000.0000.000
31A31SER0-0.019-0.01912.019-0.016-0.0160.0000.0000.0000.000
32A32ALA00.0930.03511.171-0.032-0.0320.0000.0000.0000.000
33A33LYS10.8810.94112.1730.1830.1830.0000.0000.0000.000
34A34GLY0-0.022-0.01114.1150.0120.0120.0000.0000.0000.000
35A35MET0-0.0180.0246.7060.0280.0280.0000.0000.0000.000
36A36GLU-1-0.837-0.90110.886-0.141-0.1410.0000.0000.0000.000
37A37LEU0-0.033-0.00110.919-0.082-0.0820.0000.0000.0000.000
38A38ARG10.7550.86012.9670.2420.2420.0000.0000.0000.000
39A39TRP00.0430.02514.351-0.060-0.0600.0000.0000.0000.000
40A40PHE0-0.037-0.02813.3540.0480.0480.0000.0000.0000.000
41A41ARG10.9190.96218.6080.1380.1380.0000.0000.0000.000
42A42GLU-1-0.872-0.92219.587-0.174-0.1740.0000.0000.0000.000
43A43LYS10.9060.94719.9000.0920.0920.0000.0000.0000.000
44A44VAL00.0360.02314.3970.0020.0020.0000.0000.0000.000
45A45SER00.0140.02117.214-0.001-0.0010.0000.0000.0000.000
46A46PRO0-0.063-0.05119.9710.0100.0100.0000.0000.0000.000
47A47ALA0-0.0010.01518.693-0.007-0.0070.0000.0000.0000.000
48A48VAL0-0.028-0.01520.2890.0170.0170.0000.0000.0000.000
49A49PHE00.0120.00417.5580.0070.0070.0000.0000.0000.000
50A50LEU0-0.047-0.02015.943-0.027-0.0270.0000.0000.0000.000
51A51SER00.0090.02816.6360.0290.0290.0000.0000.0000.000
52A52ARG10.8480.87315.2690.0660.0660.0000.0000.0000.000
53A53GLU-1-0.908-0.95015.656-0.031-0.0310.0000.0000.0000.000
54A54GLY0-0.051-0.03017.1050.0090.0090.0000.0000.0000.000
55A55GLN0-0.059-0.03018.9780.0080.0080.0000.0000.0000.000
56A56GLU-1-0.824-0.90820.306-0.128-0.1280.0000.0000.0000.000
57A57GLN0-0.086-0.06019.6510.0280.0280.0000.0000.0000.000
58A58GLU-1-0.837-0.92122.413-0.080-0.0800.0000.0000.0000.000
59A59GLY0-0.099-0.05225.4620.0000.0000.0000.0000.0000.000
60A60GLU-1-0.823-0.90218.687-0.089-0.0890.0000.0000.0000.000
61A61GLU-1-0.775-0.87221.942-0.145-0.1450.0000.0000.0000.000
62A62MET0-0.053-0.04222.5640.0190.0190.0000.0000.0000.000
63A63ALA0-0.011-0.01526.042-0.001-0.0010.0000.0000.0000.000
64A64GLU-1-0.913-0.95128.627-0.104-0.1040.0000.0000.0000.000
65A65TYR0-0.005-0.03925.530-0.007-0.0070.0000.0000.0000.000
66A66ARG10.9000.95526.8680.0790.0790.0000.0000.0000.000
67A67GLY00.0180.01128.3710.0050.0050.0000.0000.0000.000
68A68ARG10.7230.85528.6980.1200.1200.0000.0000.0000.000
69A69VAL0-0.028-0.00223.682-0.009-0.0090.0000.0000.0000.000
70A70SER00.0340.01723.9970.0100.0100.0000.0000.0000.000
71A71LEU0-0.0370.00317.212-0.015-0.0150.0000.0000.0000.000
72A72VAL00.0090.01020.8720.0160.0160.0000.0000.0000.000
73A73GLU-1-0.905-0.99219.484-0.194-0.1940.0000.0000.0000.000
74A74ASP-1-0.887-0.94720.422-0.176-0.1760.0000.0000.0000.000
75A75HIS0-0.048-0.01819.2970.0030.0030.0000.0000.0000.000
76A76ILE00.0560.03615.395-0.031-0.0310.0000.0000.0000.000
77A77ALA0-0.094-0.05615.283-0.029-0.0290.0000.0000.0000.000
78A78GLU-1-0.932-0.95915.528-0.293-0.2930.0000.0000.0000.000
79A79GLY00.0300.01412.529-0.048-0.0480.0000.0000.0000.000
80A80SER0-0.066-0.03512.952-0.071-0.0710.0000.0000.0000.000
81A81VAL00.0040.00414.2480.0390.0390.0000.0000.0000.000
82A82ALA00.0350.00917.099-0.027-0.0270.0000.0000.0000.000
83A83VAL00.0100.03818.4320.0170.0170.0000.0000.0000.000
84A84ARG10.8300.90120.8630.1250.1250.0000.0000.0000.000
85A85ILE0-0.048-0.02723.4120.0060.0060.0000.0000.0000.000
86A86GLN00.0090.00426.6000.0000.0000.0000.0000.0000.000
87A87GLU-1-0.891-0.94830.260-0.089-0.0890.0000.0000.0000.000
88A88VAL0-0.048-0.01228.9920.0010.0010.0000.0000.0000.000
89A89LYS10.8820.92630.7030.1170.1170.0000.0000.0000.000
90A90ALA00.0700.02631.721-0.008-0.0080.0000.0000.0000.000
91A91SER0-0.001-0.00131.022-0.004-0.0040.0000.0000.0000.000
92A92ASP-1-0.719-0.80427.717-0.131-0.1310.0000.0000.0000.000
93A93ASP-1-0.782-0.85226.738-0.163-0.1630.0000.0000.0000.000
94A94GLY00.0200.01025.4040.0060.0060.0000.0000.0000.000
95A95GLU-1-0.866-0.92418.719-0.306-0.3060.0000.0000.0000.000
96A96TYR0-0.055-0.05819.0910.0150.0150.0000.0000.0000.000
97A97ARG10.8050.88913.8070.3770.3770.0000.0000.0000.000
98A99PHE00.028-0.0048.797-0.108-0.1080.0000.0000.0000.000
99A100PHE00.0350.0117.4310.0940.0940.0000.0000.0000.000
100A101ARG10.8910.9406.705-0.027-0.0270.0000.0000.0000.000
101A102GLN00.0000.0076.348-0.068-0.0680.0000.0000.0000.000
102A103ASP-1-0.912-0.9736.9540.4570.4570.0000.0000.0000.000
103A104GLU-1-0.981-0.9885.6551.2421.2420.0000.0000.0000.000
104A105ASN0-0.051-0.0202.544-0.9431.1281.710-1.619-2.161-0.014
105A106TYR00.000-0.0223.142-0.509-0.1780.033-0.079-0.2850.000
106A107GLU-1-0.864-0.9153.302-4.198-3.2020.082-0.420-0.658-0.003
107A108GLU-1-0.930-0.9795.388-0.168-0.168-0.0010.0000.0020.000
108A109ALA00.0110.0148.928-0.074-0.0740.0000.0000.0000.000
109A110ILE0-0.016-0.01211.7790.0610.0610.0000.0000.0000.000
110A111VAL00.0220.00815.505-0.009-0.0090.0000.0000.0000.000
111A112HIS0-0.024-0.00418.4840.0330.0330.0000.0000.0000.000
112A113LEU00.0140.02021.9700.0000.0000.0000.0000.0000.000
113A114LYS10.7550.85224.7980.1650.1650.0000.0000.0000.000
114A115VAL00.0290.01428.1550.0020.0020.0000.0000.0000.000
115A116ALA0-0.020-0.01531.1360.0040.0040.0000.0000.0000.000
116A117ALA00.0170.01534.5890.0010.0010.0000.0000.0000.000
117A118LEU0-0.003-0.00638.0630.0010.0010.0000.0000.0000.000
118A119GLY00.0870.05241.0960.0010.0010.0000.0000.0000.000
119A120SER0-0.016-0.01044.2970.0000.0000.0000.0000.0000.000
120A121ASP-1-0.863-0.93047.993-0.058-0.0580.0000.0000.0000.000
121A122PRO0-0.042-0.00149.4090.0010.0010.0000.0000.0000.000
122A123HIS00.0270.01151.6830.0010.0010.0000.0000.0000.000
123A124ILE00.0160.00355.1890.0000.0000.0000.0000.0000.000
124A125SER0-0.061-0.01657.6020.0020.0020.0000.0000.0000.000
125A126MET00.0100.00160.322-0.001-0.0010.0000.0000.0000.000
126A127LYS10.8810.94060.3960.0370.0370.0000.0000.0000.000
127A128VAL00.0050.01065.5690.0000.0000.0000.0000.0000.000
128A129GLN0-0.014-0.01367.2600.0000.0000.0000.0000.0000.000
129A130GLU-1-0.927-0.98069.484-0.027-0.0270.0000.0000.0000.000
130A131SER0-0.0290.00471.2060.0000.0000.0000.0000.0000.000
131A132GLY0-0.011-0.00971.7930.0000.0000.0000.0000.0000.000
132A133GLU-1-0.768-0.85066.277-0.032-0.0320.0000.0000.0000.000
133A134ILE0-0.004-0.00363.9710.0000.0000.0000.0000.0000.000
134A135GLN0-0.038-0.00361.781-0.001-0.0010.0000.0000.0000.000
135A136LEU0-0.004-0.00258.6680.0010.0010.0000.0000.0000.000
136A137GLU-1-0.881-0.94555.862-0.042-0.0420.0000.0000.0000.000
137A138CYS0-0.037-0.00751.9240.0000.0000.0000.0000.0000.000
138A139THR0-0.003-0.01251.685-0.001-0.0010.0000.0000.0000.000
139A140SER0-0.002-0.00247.887-0.001-0.0010.0000.0000.0000.000
140A141VAL00.0260.01346.7460.0000.0000.0000.0000.0000.000
141A142GLY00.0730.04043.2480.0000.0000.0000.0000.0000.000
142A143TRP0-0.040-0.03241.072-0.004-0.0040.0000.0000.0000.000
143A144TYR00.0200.03032.2590.0030.0030.0000.0000.0000.000
144A145PRO00.0350.02534.278-0.002-0.0020.0000.0000.0000.000
145A146GLU-1-0.869-0.96536.557-0.086-0.0860.0000.0000.0000.000
146A147PRO0-0.0250.01839.209-0.002-0.0020.0000.0000.0000.000
147A148GLN0-0.001-0.01141.5810.0020.0020.0000.0000.0000.000
148A149VAL00.022-0.00143.5400.0000.0000.0000.0000.0000.000
149A150GLN0-0.043-0.01047.3140.0000.0000.0000.0000.0000.000
150A151TRP00.004-0.01449.2730.0020.0020.0000.0000.0000.000
151A152GLN00.0490.02150.5080.0010.0010.0000.0000.0000.000
152A153THR0-0.015-0.01354.8510.0020.0020.0000.0000.0000.000
153A154HIS0-0.028-0.03557.3990.0000.0000.0000.0000.0000.000
154A155ARG10.8960.93958.9480.0360.0360.0000.0000.0000.000
155A156GLY00.0630.05855.1270.0000.0000.0000.0000.0000.000
156A157GLU-1-1.011-1.00454.036-0.045-0.0450.0000.0000.0000.000
157A158GLU-1-0.868-0.93048.661-0.060-0.0600.0000.0000.0000.000
158A159PHE0-0.088-0.04153.1510.0020.0020.0000.0000.0000.000
159A160PRO00.0210.00851.303-0.001-0.0010.0000.0000.0000.000
160A161SER0-0.009-0.03350.4250.0020.0020.0000.0000.0000.000
161A162MET0-0.066-0.04053.0830.0010.0010.0000.0000.0000.000
162A163SER0-0.033-0.02352.6860.0010.0010.0000.0000.0000.000
163A164GLU-1-0.770-0.85047.226-0.060-0.0600.0000.0000.0000.000
164A165SER0-0.073-0.03748.2040.0010.0010.0000.0000.0000.000
165A166ARG10.7830.86942.4910.0670.0670.0000.0000.0000.000
166A167ASN0-0.019-0.00344.8570.0020.0020.0000.0000.0000.000
167A168PRO0-0.0200.00540.5490.0010.0010.0000.0000.0000.000
168A169ASP-1-0.823-0.92342.032-0.066-0.0660.0000.0000.0000.000
169A170GLU-1-0.977-0.99542.007-0.057-0.0570.0000.0000.0000.000
170A171GLU-1-0.957-0.97238.888-0.069-0.0690.0000.0000.0000.000
171A172GLY0-0.050-0.02737.758-0.006-0.0060.0000.0000.0000.000
172A173LEU0-0.031-0.01838.009-0.004-0.0040.0000.0000.0000.000
173A174PHE0-0.020-0.00137.6610.0060.0060.0000.0000.0000.000
174A175THR0-0.041-0.00942.6270.0010.0010.0000.0000.0000.000
175A176VAL0-0.021-0.02245.6570.0000.0000.0000.0000.0000.000
176A177ARG10.8780.92747.5140.0470.0470.0000.0000.0000.000
177A178ALA00.0180.01850.373-0.001-0.0010.0000.0000.0000.000
178A179SER00.0060.00952.2770.0010.0010.0000.0000.0000.000
179A180VAL00.0340.03055.418-0.001-0.0010.0000.0000.0000.000
180A181ILE0-0.028-0.02157.6400.0010.0010.0000.0000.0000.000
181A182ILE00.008-0.00159.8900.0000.0000.0000.0000.0000.000
182A183ARG10.7840.86361.7840.0350.0350.0000.0000.0000.000
183A184ASP-1-0.757-0.88765.319-0.033-0.0330.0000.0000.0000.000
184A185SER0-0.069-0.03167.3620.0010.0010.0000.0000.0000.000
185A186SER0-0.081-0.05367.2790.0000.0000.0000.0000.0000.000
186A187MET0-0.0420.00461.419-0.001-0.0010.0000.0000.0000.000
187A188LYS10.8770.93564.6560.0340.0340.0000.0000.0000.000
188A189ASN0-0.015-0.00661.0540.0020.0020.0000.0000.0000.000
189A190VAL00.0100.00357.4420.0000.0000.0000.0000.0000.000
190A191SER0-0.016-0.00553.9170.0010.0010.0000.0000.0000.000
191A193ALA00.0740.03548.2300.0000.0000.0000.0000.0000.000
192A194ILE0-0.028-0.02244.7360.0000.0000.0000.0000.0000.000
193A195ARG10.8810.92239.8740.0820.0820.0000.0000.0000.000
194A196ASN00.003-0.00437.008-0.005-0.0050.0000.0000.0000.000
195A197LEU0-0.022-0.03837.126-0.002-0.0020.0000.0000.0000.000
196A198LEU0-0.0090.01530.507-0.003-0.0030.0000.0000.0000.000
197A199LEU00.0020.00233.809-0.005-0.0050.0000.0000.0000.000
198A200GLY0-0.021-0.00336.0230.0010.0010.0000.0000.0000.000
199A201GLN0-0.048-0.02738.1690.0060.0060.0000.0000.0000.000
200A202GLU-1-0.837-0.91041.260-0.072-0.0720.0000.0000.0000.000
201A203LYS10.7840.89144.5660.0660.0660.0000.0000.0000.000
202A204GLU-1-0.866-0.93247.885-0.054-0.0540.0000.0000.0000.000
203A205VAL0-0.037-0.00551.1780.0010.0010.0000.0000.0000.000
204A206GLU-1-0.810-0.89954.684-0.042-0.0420.0000.0000.0000.000
205A207VAL0-0.026-0.01457.8070.0010.0010.0000.0000.0000.000
206A208SER0-0.030-0.04660.9170.0010.0010.0000.0000.0000.000
207A209ILE00.0130.01562.4150.0000.0000.0000.0000.0000.000
208A210PRO0-0.059-0.02066.4620.0010.0010.0000.0000.0000.000
209A211ALA00.0150.00870.2090.0000.0000.0000.0000.0000.000