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: 148ZZ

Calculation Name: 2HLY-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2HLY

Chain ID: A

ChEMBL ID:

UniProt ID: A9CI22

Base Structure: X-ray

Registration Date: 2023-06-19

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 207
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2328991.822748
FMO2-HF: Nuclear repulsion 2248275.69367
FMO2-HF: Total energy -80716.129078
FMO2-MP2: Total energy -80948.697416


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:GLY)


Summations of interaction energy for fragment #1(A:0:GLY)
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.
-0.9941.498-0.029-1.206-1.257-0.002
Interaction energy analysis for fragmet #1(A:0:GLY)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.012 / q_NPA : -0.003
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].
3A2PHE00.0110.0053.806-2.0150.408-0.028-1.199-1.197-0.002
4A3GLU-1-0.951-0.9764.8281.8061.875-0.001-0.007-0.0600.000
5A4GLY00.0030.0017.083-0.167-0.1670.0000.0000.0000.000
6A5MET0-0.094-0.0398.692-0.277-0.2770.0000.0000.0000.000
7A6LEU00.0290.04111.042-0.033-0.0330.0000.0000.0000.000
8A7ILE00.0080.00213.644-0.062-0.0620.0000.0000.0000.000
9A8LYS10.9931.0009.049-0.096-0.0960.0000.0000.0000.000
10A9GLN00.0730.02610.366-0.119-0.1190.0000.0000.0000.000
11A10THR0-0.016-0.01111.836-0.053-0.0530.0000.0000.0000.000
12A11ASP-1-0.772-0.89713.7000.1290.1290.0000.0000.0000.000
13A12TYR00.023-0.01414.978-0.020-0.0200.0000.0000.0000.000
14A13PHE00.012-0.00215.216-0.018-0.0180.0000.0000.0000.000
15A14ARG10.7890.89517.717-0.077-0.0770.0000.0000.0000.000
16A15ILE0-0.0060.00418.944-0.014-0.0140.0000.0000.0000.000
17A16TYR00.0730.04120.968-0.009-0.0090.0000.0000.0000.000
18A17ARG10.8320.90720.879-0.068-0.0680.0000.0000.0000.000
19A18VAL0-0.0330.00224.009-0.009-0.0090.0000.0000.0000.000
20A19ILE0-0.003-0.00124.962-0.006-0.0060.0000.0000.0000.000
21A20ASN00.0550.01526.799-0.005-0.0050.0000.0000.0000.000
22A21SER0-0.055-0.04627.675-0.008-0.0080.0000.0000.0000.000
23A22LEU0-0.065-0.03229.820-0.005-0.0050.0000.0000.0000.000
24A23LEU0-0.007-0.00730.344-0.003-0.0030.0000.0000.0000.000
25A24ILE00.0050.03332.367-0.003-0.0030.0000.0000.0000.000
26A25SER0-0.071-0.04134.155-0.003-0.0030.0000.0000.0000.000
27A26GLN0-0.022-0.01836.837-0.001-0.0010.0000.0000.0000.000
28A27ASN0-0.036-0.01237.4030.0010.0010.0000.0000.0000.000
29A28ALA0-0.022-0.00235.227-0.001-0.0010.0000.0000.0000.000
30A29ASP-1-0.716-0.83236.3400.0580.0580.0000.0000.0000.000
31A30PRO00.0640.01533.6080.0040.0040.0000.0000.0000.000
32A31ALA0-0.0060.01833.1780.0060.0060.0000.0000.0000.000
33A32SER0-0.002-0.02934.2500.0060.0060.0000.0000.0000.000
34A33ALA00.0100.00531.5420.0030.0030.0000.0000.0000.000
35A34SER0-0.035-0.03229.6380.0070.0070.0000.0000.0000.000
36A35MET0-0.028-0.00529.8920.0070.0070.0000.0000.0000.000
37A36TYR00.0350.02431.3210.0030.0030.0000.0000.0000.000
38A37PHE0-0.013-0.01225.7140.0060.0060.0000.0000.0000.000
39A38SER0-0.019-0.00626.3190.0130.0130.0000.0000.0000.000
40A39THR0-0.014-0.03127.2700.0060.0060.0000.0000.0000.000
41A40PHE00.0030.00028.0580.0010.0010.0000.0000.0000.000
42A41GLY00.0370.02024.1410.0020.0020.0000.0000.0000.000
43A42ALA0-0.001-0.00323.8140.0110.0110.0000.0000.0000.000
44A43PHE0-0.0130.00125.5010.0040.0040.0000.0000.0000.000
45A44ILE00.0350.00821.830-0.001-0.0010.0000.0000.0000.000
46A45LEU0-0.003-0.00819.0750.0040.0040.0000.0000.0000.000
47A46GLN0-0.062-0.03522.240-0.003-0.0030.0000.0000.0000.000
48A47GLN0-0.066-0.03525.046-0.004-0.0040.0000.0000.0000.000
49A48HIS0-0.091-0.04820.820-0.002-0.0020.0000.0000.0000.000
50A49TYR0-0.034-0.03715.162-0.015-0.0150.0000.0000.0000.000
51A50LYS10.8980.97420.095-0.095-0.0950.0000.0000.0000.000
52A51VAL00.0620.05219.2890.0000.0000.0000.0000.0000.000
53A52LYS10.9300.95222.589-0.144-0.1440.0000.0000.0000.000
54A53ALA00.0170.01223.4040.0180.0180.0000.0000.0000.000
55A54VAL0-0.008-0.01225.020-0.016-0.0160.0000.0000.0000.000
56A55PRO00.0090.01727.1220.0090.0090.0000.0000.0000.000
57A56LYS10.8370.91628.253-0.143-0.1430.0000.0000.0000.000
58A57GLY00.1010.04230.0140.0020.0020.0000.0000.0000.000
59A58GLY0-0.014-0.00532.192-0.002-0.0020.0000.0000.0000.000
60A59LEU0-0.0320.01031.491-0.002-0.0020.0000.0000.0000.000
61A60ALA0-0.028-0.01827.8500.0080.0080.0000.0000.0000.000
62A61ALA00.0170.01527.981-0.009-0.0090.0000.0000.0000.000
63A62TYR0-0.002-0.02322.5890.0170.0170.0000.0000.0000.000
64A63ASN00.0140.01523.530-0.011-0.0110.0000.0000.0000.000
65A64LEU0-0.001-0.01921.9670.0170.0170.0000.0000.0000.000
66A65GLY00.006-0.01121.928-0.010-0.0100.0000.0000.0000.000
67A66GLY0-0.026-0.00922.906-0.010-0.0100.0000.0000.0000.000
68A67THR0-0.0230.00925.856-0.005-0.0050.0000.0000.0000.000
69A68VAL00.013-0.00426.8760.0090.0090.0000.0000.0000.000
70A69LEU0-0.0060.02027.257-0.006-0.0060.0000.0000.0000.000
71A70LEU0-0.005-0.02229.1790.0080.0080.0000.0000.0000.000
72A71PHE0-0.033-0.01028.050-0.005-0.0050.0000.0000.0000.000
73A72ALA0-0.003-0.02732.9570.0030.0030.0000.0000.0000.000
74A73ASP-1-0.797-0.88936.1180.0530.0530.0000.0000.0000.000
75A74HIS0-0.032-0.01239.8330.0000.0000.0000.0000.0000.000
76A75ARG10.9050.93941.514-0.050-0.0500.0000.0000.0000.000
77A76GLU-1-0.941-0.97244.1650.0440.0440.0000.0000.0000.000
78A77ASP-1-0.890-0.93844.6670.0400.0400.0000.0000.0000.000
79A78GLY0-0.0100.01640.9900.0020.0020.0000.0000.0000.000
80A79TYR0-0.001-0.02137.1390.0000.0000.0000.0000.0000.000
81A80VAL0-0.044-0.02538.9140.0020.0020.0000.0000.0000.000
82A81THR0-0.012-0.02236.1760.0030.0030.0000.0000.0000.000
83A82GLY00.0300.04037.078-0.003-0.0030.0000.0000.0000.000
84A83ALA0-0.012-0.02038.8320.0010.0010.0000.0000.0000.000
85A84GLY0-0.005-0.01040.994-0.002-0.0020.0000.0000.0000.000
86A85GLU-1-0.892-0.96638.4470.0530.0530.0000.0000.0000.000
87A86ASN0-0.0040.00536.0020.0030.0030.0000.0000.0000.000
88A87PHE0-0.075-0.02934.8720.0050.0050.0000.0000.0000.000
89A88HIS10.8490.90726.956-0.109-0.1090.0000.0000.0000.000
90A89CYS0-0.012-0.00830.160-0.001-0.0010.0000.0000.0000.000
91A90TRP0-0.019-0.01424.777-0.001-0.0010.0000.0000.0000.000
92A91VAL0-0.014-0.01423.097-0.009-0.0090.0000.0000.0000.000
93A92GLU-1-0.803-0.88522.9300.1760.1760.0000.0000.0000.000
94A93ALA0-0.006-0.02720.643-0.019-0.0190.0000.0000.0000.000
95A94ASP-1-0.898-0.93918.5150.3290.3290.0000.0000.0000.000
96A95GLY0-0.0080.00418.7760.0340.0340.0000.0000.0000.000
97A96TRP0-0.005-0.00411.6830.0160.0160.0000.0000.0000.000
98A97ALA00.0340.02818.528-0.035-0.0350.0000.0000.0000.000
99A98ILE0-0.028-0.03017.8670.0310.0310.0000.0000.0000.000
100A99ASP-1-0.689-0.79320.3300.1150.1150.0000.0000.0000.000
101A100PHE0-0.015-0.00919.2390.0050.0050.0000.0000.0000.000
102A101MET00.0250.03622.663-0.007-0.0070.0000.0000.0000.000
103A102ALA00.0170.01421.275-0.008-0.0080.0000.0000.0000.000
104A103PRO0-0.079-0.05220.659-0.007-0.0070.0000.0000.0000.000
105A104ALA00.0690.03023.217-0.008-0.0080.0000.0000.0000.000
106A105PHE0-0.050-0.02924.470-0.004-0.0040.0000.0000.0000.000
107A106SER00.007-0.01126.785-0.002-0.0020.0000.0000.0000.000
108A107GLU-1-0.995-0.98028.8380.0520.0520.0000.0000.0000.000
109A108GLY0-0.022-0.01631.9910.0030.0030.0000.0000.0000.000
110A109THR0-0.012-0.01230.161-0.001-0.0010.0000.0000.0000.000
111A110ASP-1-0.865-0.90833.0390.0440.0440.0000.0000.0000.000
112A111ALA0-0.040-0.04433.5210.0000.0000.0000.0000.0000.000
113A112LEU0-0.057-0.03230.2410.0000.0000.0000.0000.0000.000
114A113ALA0-0.0300.00129.4790.0030.0030.0000.0000.0000.000
115A114VAL00.0240.01925.1510.0030.0030.0000.0000.0000.000
116A115PRO0-0.035-0.01222.154-0.001-0.0010.0000.0000.0000.000
117A116ALA00.0860.05922.6880.0090.0090.0000.0000.0000.000
118A117LYS10.8530.93017.424-0.118-0.1180.0000.0000.0000.000
119A118MET0-0.0050.00512.0100.0050.0050.0000.0000.0000.000
120A119PHE0-0.0070.00417.0920.0150.0150.0000.0000.0000.000
121A120GLN00.014-0.03313.3420.0130.0130.0000.0000.0000.000
122A121ARG10.8780.94014.540-0.221-0.2210.0000.0000.0000.000
123A122PRO00.0310.02314.294-0.024-0.0240.0000.0000.0000.000
124A123LEU00.0650.01817.039-0.026-0.0260.0000.0000.0000.000
125A124SER0-0.060-0.03018.167-0.014-0.0140.0000.0000.0000.000
126A125ALA0-0.042-0.02417.421-0.008-0.0080.0000.0000.0000.000
127A126MET0-0.0890.00119.584-0.013-0.0130.0000.0000.0000.000
128A127ALA00.0370.02922.857-0.004-0.0040.0000.0000.0000.000
129A128ALA0-0.003-0.02125.158-0.002-0.0020.0000.0000.0000.000
130A129SER0-0.043-0.02828.695-0.009-0.0090.0000.0000.0000.000
131A130ILE00.019-0.00529.2860.0050.0050.0000.0000.0000.000
132A131ASN0-0.014-0.01231.153-0.003-0.0030.0000.0000.0000.000
133A132ASP-1-0.910-0.93526.8410.1120.1120.0000.0000.0000.000
134A133LEU0-0.0010.00825.4250.0110.0110.0000.0000.0000.000
135A134GLY00.0440.03425.728-0.006-0.0060.0000.0000.0000.000
136A135GLN0-0.045-0.02018.800-0.015-0.0150.0000.0000.0000.000
137A136SER00.0050.00519.2730.0030.0030.0000.0000.0000.000
138A137GLY0-0.023-0.02318.2760.0160.0160.0000.0000.0000.000
139A138ASP-1-0.860-0.91019.3120.1750.1750.0000.0000.0000.000
140A139PHE0-0.032-0.02719.597-0.005-0.0050.0000.0000.0000.000
141A140PHE0-0.0020.00823.7560.0010.0010.0000.0000.0000.000
142A141TYR0-0.007-0.03823.4930.0030.0030.0000.0000.0000.000
143A142ARG10.8990.94628.387-0.080-0.0800.0000.0000.0000.000
144A143SER00.004-0.01031.004-0.002-0.0020.0000.0000.0000.000
145A144GLU-1-0.844-0.92132.5470.0710.0710.0000.0000.0000.000
146A145PRO00.0050.01035.390-0.001-0.0010.0000.0000.0000.000
147A146GLU-1-0.873-0.94336.8070.0680.0680.0000.0000.0000.000
148A147ALA0-0.017-0.01038.281-0.003-0.0030.0000.0000.0000.000
149A148THR00.024-0.00233.9640.0000.0000.0000.0000.0000.000
150A149ALA0-0.018-0.00737.035-0.001-0.0010.0000.0000.0000.000
151A150ARG10.9440.95439.431-0.055-0.0550.0000.0000.0000.000
152A151ARG10.8670.95637.989-0.065-0.0650.0000.0000.0000.000
153A152PHE00.0080.00533.127-0.001-0.0010.0000.0000.0000.000
154A153ALA0-0.0060.01439.089-0.001-0.0010.0000.0000.0000.000
155A154ASP-1-0.862-0.94842.5960.0430.0430.0000.0000.0000.000
156A155TRP00.008-0.01134.049-0.001-0.0010.0000.0000.0000.000
157A156HIS0-0.037-0.01640.501-0.003-0.0030.0000.0000.0000.000
158A157LYS10.8920.96141.603-0.043-0.0430.0000.0000.0000.000
159A158GLN0-0.023-0.01141.332-0.003-0.0030.0000.0000.0000.000
160A159ALA00.0250.00640.8600.0020.0020.0000.0000.0000.000
161A160MET00.0190.00937.2540.0010.0010.0000.0000.0000.000
162A161ILE00.0440.02735.6730.0010.0010.0000.0000.0000.000
163A162GLY00.0190.00635.5080.0040.0040.0000.0000.0000.000
164A163ASP-1-0.793-0.86535.4590.0430.0430.0000.0000.0000.000
165A164MET0-0.037-0.01333.364-0.001-0.0010.0000.0000.0000.000
166A165ALA00.0440.03031.2670.0030.0030.0000.0000.0000.000
167A166SER0-0.026-0.01030.5810.0050.0050.0000.0000.0000.000
168A167VAL00.0090.00631.2100.0000.0000.0000.0000.0000.000
169A168ALA00.0310.00627.7600.0000.0000.0000.0000.0000.000
170A169ALA0-0.032-0.01526.4980.0040.0040.0000.0000.0000.000
171A170ASN0-0.035-0.01926.6360.0000.0000.0000.0000.0000.000
172A171TRP0-0.075-0.03327.000-0.003-0.0030.0000.0000.0000.000
173A172PHE0-0.008-0.01418.195-0.004-0.0040.0000.0000.0000.000
174A173ARG10.9200.95821.619-0.038-0.0380.0000.0000.0000.000
175A174LYS10.9440.99616.186-0.168-0.1680.0000.0000.0000.000
176A175SER0-0.023-0.00614.140-0.037-0.0370.0000.0000.0000.000
177A176PRO0-0.005-0.00615.0660.0080.0080.0000.0000.0000.000
178A177LYS10.9370.95516.983-0.043-0.0430.0000.0000.0000.000
179A178GLN00.0470.06220.4630.0160.0160.0000.0000.0000.000
180A179MET0-0.050-0.04322.2290.0050.0050.0000.0000.0000.000
181A180ALA00.0210.02124.767-0.005-0.0050.0000.0000.0000.000
182A181ALA00.0670.03627.8390.0050.0050.0000.0000.0000.000
183A182SER0-0.034-0.01229.1110.0020.0020.0000.0000.0000.000
184A183LEU00.0090.00830.461-0.002-0.0020.0000.0000.0000.000
185A184SER00.0120.01833.7080.0000.0000.0000.0000.0000.000
186A185VAL0-0.006-0.01335.1220.0020.0020.0000.0000.0000.000
187A186THR0-0.002-0.00137.879-0.002-0.0020.0000.0000.0000.000
188A187ASP-1-0.844-0.93040.8500.0300.0300.0000.0000.0000.000
189A188ARG10.8280.85141.202-0.039-0.0390.0000.0000.0000.000
190A189ASP-1-0.853-0.88545.3060.0250.0250.0000.0000.0000.000
191A190GLY0-0.034-0.01146.200-0.002-0.0020.0000.0000.0000.000
192A191LYS10.7940.88645.954-0.026-0.0260.0000.0000.0000.000
193A192ALA0-0.0040.00241.4850.0020.0020.0000.0000.0000.000
194A193ARG10.9600.98437.093-0.037-0.0370.0000.0000.0000.000
195A194THR00.003-0.00136.2030.0010.0010.0000.0000.0000.000
196A195VAL0-0.020-0.01232.6380.0000.0000.0000.0000.0000.000
197A196PRO00.0190.00632.1750.0000.0000.0000.0000.0000.000
198A197LEU0-0.009-0.01325.1460.0040.0040.0000.0000.0000.000
199A198THR0-0.0030.00027.742-0.003-0.0030.0000.0000.0000.000
200A199GLY00.028-0.00326.7970.0020.0020.0000.0000.0000.000
201A200GLU-1-0.906-0.92424.3090.0590.0590.0000.0000.0000.000
202A201MET0-0.007-0.00420.8090.0020.0020.0000.0000.0000.000
203A202LEU00.0090.00319.2680.0040.0040.0000.0000.0000.000
204A203THR0-0.031-0.01416.078-0.001-0.0010.0000.0000.0000.000
205A204GLY00.0670.03314.773-0.004-0.0040.0000.0000.0000.000
206A205ALA0-0.031-0.03112.6770.0170.0170.0000.0000.0000.000
207A206TRP00.0400.02714.714-0.012-0.0120.0000.0000.0000.000