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: G51N1

Calculation Name: 1Z9S-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1Z9S

Chain ID: A

ChEMBL ID:

UniProt ID: P26926

Base Structure: X-ray

Registration Date: 2023-09-24

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 205
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2216494.685703
FMO2-HF: Nuclear repulsion 2137057.14866
FMO2-HF: Total energy -79437.537043
FMO2-MP2: Total energy -79672.653544


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:9:SER)


Summations of interaction energy for fragment #1(A:9: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.
-26.272-27.85113.237-6.964-4.693-0.06
Interaction energy analysis for fragmet #1(A:9:SER)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.006 / q_NPA : -0.013
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].
3A11GLU-1-0.814-0.8701.691-29.725-31.34613.238-6.961-4.656-0.060
4A12TYR0-0.026-0.0314.9531.2371.279-0.001-0.003-0.0370.000
5A13GLY00.0120.0078.656-0.060-0.0600.0000.0000.0000.000
6A14VAL00.0000.00511.5810.0840.0840.0000.0000.0000.000
7A15THR0-0.0220.00115.3950.0050.0050.0000.0000.0000.000
8A16ILE0-0.005-0.00917.8790.0240.0240.0000.0000.0000.000
9A17GLY0-0.013-0.00121.686-0.005-0.0050.0000.0000.0000.000
10A18GLU-1-0.866-0.92924.413-0.229-0.2290.0000.0000.0000.000
11A19SER0-0.023-0.01824.194-0.010-0.0100.0000.0000.0000.000
12A20ARG10.7490.86925.2630.2410.2410.0000.0000.0000.000
13A21ILE00.0640.03828.360-0.007-0.0070.0000.0000.0000.000
14A22ILE0-0.012-0.00531.1490.0080.0080.0000.0000.0000.000
15A23TYR00.0150.00234.711-0.001-0.0010.0000.0000.0000.000
16A24PRO00.0030.00136.6120.0060.0060.0000.0000.0000.000
17A25LEU0-0.020-0.00740.347-0.002-0.0020.0000.0000.0000.000
18A26ASP-1-0.787-0.87342.487-0.103-0.1030.0000.0000.0000.000
19A27ALA0-0.0010.02240.2870.0030.0030.0000.0000.0000.000
20A28ALA00.0380.02141.167-0.004-0.0040.0000.0000.0000.000
21A29GLY0-0.011-0.00337.551-0.003-0.0030.0000.0000.0000.000
22A30VAL0-0.040-0.00832.8290.0050.0050.0000.0000.0000.000
23A31MET0-0.016-0.00731.278-0.001-0.0010.0000.0000.0000.000
24A32VAL00.0490.03625.969-0.001-0.0010.0000.0000.0000.000
25A33SER0-0.002-0.00324.444-0.007-0.0070.0000.0000.0000.000
26A34VAL00.012-0.00520.613-0.017-0.0170.0000.0000.0000.000
27A35LYS10.8770.93617.6690.5370.5370.0000.0000.0000.000
28A36ASN00.0050.00514.140-0.164-0.1640.0000.0000.0000.000
29A37THR0-0.013-0.02511.7470.1040.1040.0000.0000.0000.000
30A38GLN00.0050.0277.9420.1530.1530.0000.0000.0000.000
31A39ASP-1-0.831-0.9189.302-0.971-0.9710.0000.0000.0000.000
32A40TYR0-0.010-0.0258.3800.2820.2820.0000.0000.0000.000
33A41PRO0-0.021-0.00213.447-0.034-0.0340.0000.0000.0000.000
34A42VAL00.004-0.00114.269-0.053-0.0530.0000.0000.0000.000
35A43LEU0-0.003-0.00817.0690.0690.0690.0000.0000.0000.000
36A44ILE00.0100.01318.395-0.045-0.0450.0000.0000.0000.000
37A45GLN0-0.030-0.02821.0280.0490.0490.0000.0000.0000.000
38A46SER0-0.0060.00022.978-0.032-0.0320.0000.0000.0000.000
39A47ARG10.9070.95625.4300.3030.3030.0000.0000.0000.000
40A48ILE00.0310.02427.515-0.016-0.0160.0000.0000.0000.000
41A49TYR00.003-0.00625.919-0.006-0.0060.0000.0000.0000.000
42A50ASP-1-0.727-0.85930.695-0.160-0.1600.0000.0000.0000.000
43A51GLU-1-0.791-0.85231.507-0.161-0.1610.0000.0000.0000.000
44A52ASN0-0.043-0.04531.556-0.007-0.0070.0000.0000.0000.000
45A53LYS10.7810.89426.2130.2120.2120.0000.0000.0000.000
46A54GLU-1-0.892-0.93729.521-0.147-0.1470.0000.0000.0000.000
47A55LYS10.7020.81729.8040.1810.1810.0000.0000.0000.000
48A56GLU-1-0.756-0.85632.910-0.173-0.1730.0000.0000.0000.000
49A57SER0-0.063-0.03436.6430.0070.0070.0000.0000.0000.000
50A58GLU-1-0.814-0.87239.041-0.131-0.1310.0000.0000.0000.000
51A59ASP-1-0.886-0.94238.629-0.147-0.1470.0000.0000.0000.000
52A60PRO0-0.057-0.01435.8730.0020.0020.0000.0000.0000.000
53A61PHE00.010-0.01934.4880.0010.0010.0000.0000.0000.000
54A62VAL00.0410.04434.336-0.010-0.0100.0000.0000.0000.000
55A63VAL00.003-0.01028.440-0.005-0.0050.0000.0000.0000.000
56A64THR0-0.075-0.02031.2900.0090.0090.0000.0000.0000.000
57A65PRO00.0620.01927.7760.0000.0000.0000.0000.0000.000
58A66PRO00.0430.01827.843-0.018-0.0180.0000.0000.0000.000
59A67LEU0-0.006-0.02023.951-0.020-0.0200.0000.0000.0000.000
60A68PHE0-0.008-0.00123.6660.0220.0220.0000.0000.0000.000
61A69ARG10.8550.89421.0940.3160.3160.0000.0000.0000.000
62A70LEU0-0.028-0.00319.3880.0290.0290.0000.0000.0000.000
63A71ASP-1-0.724-0.84118.295-0.448-0.4480.0000.0000.0000.000
64A72ALA00.0270.02814.765-0.026-0.0260.0000.0000.0000.000
65A73LYS10.8040.89310.4931.1201.1200.0000.0000.0000.000
66A74GLN0-0.029-0.00416.2280.0700.0700.0000.0000.0000.000
67A75GLN0-0.008-0.02719.225-0.066-0.0660.0000.0000.0000.000
68A76ASN00.0230.02121.9810.0400.0400.0000.0000.0000.000
69A77SER0-0.023-0.02324.991-0.011-0.0110.0000.0000.0000.000
70A78LEU0-0.0140.01525.1470.0090.0090.0000.0000.0000.000
71A79ARG10.9230.94728.5220.1700.1700.0000.0000.0000.000
72A80ILE0-0.017-0.01429.039-0.007-0.0070.0000.0000.0000.000
73A81ALA00.006-0.01533.2070.0070.0070.0000.0000.0000.000
74A82GLN00.0210.00536.947-0.007-0.0070.0000.0000.0000.000
75A83ALA0-0.0150.00639.2930.0050.0050.0000.0000.0000.000
76A84GLY00.003-0.00341.0160.0060.0060.0000.0000.0000.000
77A85GLY00.0130.00342.939-0.002-0.0020.0000.0000.0000.000
78A86VAL0-0.011-0.01043.9560.0050.0050.0000.0000.0000.000
79A87PHE00.0160.01039.404-0.004-0.0040.0000.0000.0000.000
80A88PRO0-0.026-0.00543.0140.0050.0050.0000.0000.0000.000
81A89ARG10.8610.86945.0600.0960.0960.0000.0000.0000.000
82A90ASP-1-0.794-0.87147.399-0.091-0.0910.0000.0000.0000.000
83A91LYS10.8340.89742.9750.0990.0990.0000.0000.0000.000
84A92GLU-1-0.712-0.83638.133-0.146-0.1460.0000.0000.0000.000
85A93SER0-0.055-0.03738.9440.0070.0070.0000.0000.0000.000
86A94LEU0-0.060-0.00731.395-0.007-0.0070.0000.0000.0000.000
87A95LYS10.8660.92333.0920.1580.1580.0000.0000.0000.000
88A96TRP0-0.033-0.02425.532-0.014-0.0140.0000.0000.0000.000
89A97LEU00.0440.03525.8460.0070.0070.0000.0000.0000.000
90A98CYS0-0.070-0.03019.0370.0250.0250.0000.0000.0000.000
91A99VAL00.032-0.00220.7940.0230.0230.0000.0000.0000.000
92A100LYS10.9520.98517.5520.4310.4310.0000.0000.0000.000
93A101GLY00.0290.01616.1270.0420.0420.0000.0000.0000.000
94A102ILE0-0.063-0.04015.373-0.086-0.0860.0000.0000.0000.000
95A103PRO00.0140.00712.0030.0470.0470.0000.0000.0000.000
96A104PRO0-0.0010.01513.6110.0470.0470.0000.0000.0000.000
97A125ASP-1-0.890-0.95717.3010.3920.3920.0000.0000.0000.000
98A126VAL0-0.047-0.02016.932-0.035-0.0350.0000.0000.0000.000
99A127GLY00.0320.01414.5420.0520.0520.0000.0000.0000.000
100A128VAL0-0.046-0.01811.436-0.082-0.0820.0000.0000.0000.000
101A129PHE00.0370.0139.240-0.003-0.0030.0000.0000.0000.000
102A130VAL00.0110.0118.670-0.016-0.0160.0000.0000.0000.000
103A131GLN00.0420.0339.042-0.363-0.3630.0000.0000.0000.000
104A132PHE00.0130.0147.7290.1420.1420.0000.0000.0000.000
105A133ALA00.022-0.01311.524-0.050-0.0500.0000.0000.0000.000
106A134ILE0-0.0020.01710.6590.0960.0960.0000.0000.0000.000
107A135ASN00.0330.00014.3790.0620.0620.0000.0000.0000.000
108A136ASN0-0.0070.00117.4070.0670.0670.0000.0000.0000.000
109A138ILE00.0040.01022.648-0.003-0.0030.0000.0000.0000.000
110A139LYS10.8630.94125.5530.2370.2370.0000.0000.0000.000
111A140LEU00.0210.01629.222-0.002-0.0020.0000.0000.0000.000
112A141LEU0-0.015-0.01031.9100.0090.0090.0000.0000.0000.000
113A142VAL00.0230.02034.8430.0010.0010.0000.0000.0000.000
114A143ARG10.7690.82336.9080.1500.1500.0000.0000.0000.000
115A144PRO00.0080.01640.5120.0010.0010.0000.0000.0000.000
116A145ASN0-0.0010.00644.308-0.003-0.0030.0000.0000.0000.000
117A146GLU-1-0.774-0.88346.024-0.095-0.0950.0000.0000.0000.000
118A147LEU0-0.0360.00142.6740.0040.0040.0000.0000.0000.000
119A148LYS10.8150.88646.5290.0910.0910.0000.0000.0000.000
120A149GLY00.0230.01744.5820.0010.0010.0000.0000.0000.000
121A150THR0-0.011-0.01439.102-0.005-0.0050.0000.0000.0000.000
122A151PRO00.0440.01936.6190.0060.0060.0000.0000.0000.000
123A152ILE00.032-0.00636.6300.0030.0030.0000.0000.0000.000
124A153GLN0-0.0290.00839.2600.0010.0010.0000.0000.0000.000
125A154PHE00.0030.00041.8990.0060.0060.0000.0000.0000.000
126A155ALA00.0230.01738.4840.0010.0010.0000.0000.0000.000
127A156GLU-1-0.909-0.94740.327-0.080-0.0800.0000.0000.0000.000
128A157ASN0-0.063-0.05742.9620.0050.0050.0000.0000.0000.000
129A158LEU0-0.0350.00938.2010.0020.0020.0000.0000.0000.000
130A159SER0-0.043-0.02442.8620.0050.0050.0000.0000.0000.000
131A160TRP00.0670.00636.680-0.005-0.0050.0000.0000.0000.000
132A161LYS10.9020.95243.3800.0680.0680.0000.0000.0000.000
133A162VAL0-0.001-0.00641.854-0.004-0.0040.0000.0000.0000.000
134A163ASP-1-0.812-0.89443.137-0.053-0.0530.0000.0000.0000.000
135A164GLY00.0390.02042.812-0.004-0.0040.0000.0000.0000.000
136A165GLY0-0.030-0.00641.528-0.001-0.0010.0000.0000.0000.000
137A166LYS10.8240.90135.7640.0810.0810.0000.0000.0000.000
138A167LEU00.0000.00436.5260.0040.0040.0000.0000.0000.000
139A168ILE0-0.042-0.02738.414-0.007-0.0070.0000.0000.0000.000
140A169ALA00.0120.01538.4800.0030.0030.0000.0000.0000.000
141A170GLU-1-0.862-0.92940.496-0.073-0.0730.0000.0000.0000.000
142A171ASN00.000-0.00239.9510.0030.0030.0000.0000.0000.000
143A172PRO00.0340.02142.755-0.001-0.0010.0000.0000.0000.000
144A173SER0-0.011-0.01242.1250.0000.0000.0000.0000.0000.000
145A174PRO00.018-0.00343.760-0.001-0.0010.0000.0000.0000.000
146A175PHE00.0310.00639.159-0.004-0.0040.0000.0000.0000.000
147A176TYR0-0.034-0.04535.2610.0040.0040.0000.0000.0000.000
148A177MET00.0070.03236.071-0.011-0.0110.0000.0000.0000.000
149A178ASN00.000-0.01431.355-0.013-0.0130.0000.0000.0000.000
150A179ILE0-0.0190.00031.423-0.006-0.0060.0000.0000.0000.000
151A180GLY0-0.018-0.01128.715-0.014-0.0140.0000.0000.0000.000
152A181GLU-1-0.867-0.91828.206-0.152-0.1520.0000.0000.0000.000
153A182LEU00.0310.01430.5440.0090.0090.0000.0000.0000.000
154A183THR0-0.011-0.00231.850-0.002-0.0020.0000.0000.0000.000
155A184PHE00.0230.01434.3160.0030.0030.0000.0000.0000.000
156A185GLY00.009-0.00436.7900.0020.0020.0000.0000.0000.000
157A186GLY0-0.0010.00536.5160.0050.0050.0000.0000.0000.000
158A187LYS10.8390.91932.9800.0450.0450.0000.0000.0000.000
159A188SER00.0560.03029.018-0.001-0.0010.0000.0000.0000.000
160A189ILE0-0.045-0.02530.4630.0040.0040.0000.0000.0000.000
161A190PRO0-0.0080.00026.746-0.008-0.0080.0000.0000.0000.000
162A191SER0-0.001-0.00927.4570.0120.0120.0000.0000.0000.000
163A192HIS10.8890.94528.2390.1450.1450.0000.0000.0000.000
164A193TYR0-0.078-0.06730.7420.0010.0010.0000.0000.0000.000
165A194ILE00.0050.01133.2010.0050.0050.0000.0000.0000.000
166A195PRO00.0180.01236.760-0.003-0.0030.0000.0000.0000.000
167A196PRO0-0.018-0.00138.5980.0050.0050.0000.0000.0000.000
168A197LYS10.7810.88241.6940.0920.0920.0000.0000.0000.000
169A198SER00.0210.03041.6400.0040.0040.0000.0000.0000.000
170A199THR00.0160.00141.3430.0010.0010.0000.0000.0000.000
171A200TRP00.020-0.00532.721-0.007-0.0070.0000.0000.0000.000
172A201ALA00.0060.01037.2750.0040.0040.0000.0000.0000.000
173A202PHE0-0.021-0.00431.955-0.003-0.0030.0000.0000.0000.000
174A203ASP-1-0.826-0.91932.709-0.079-0.0790.0000.0000.0000.000
175A204LEU00.0200.00733.985-0.004-0.0040.0000.0000.0000.000
176A205PRO00.0070.00434.8520.0010.0010.0000.0000.0000.000
177A206LYS10.9190.97228.4840.1080.1080.0000.0000.0000.000
178A207GLY00.0100.00333.7450.0010.0010.0000.0000.0000.000
179A208LEU00.012-0.00736.1680.0050.0050.0000.0000.0000.000
180A209ALA00.0230.00639.636-0.002-0.0020.0000.0000.0000.000
181A210GLY00.0500.03642.6530.0020.0020.0000.0000.0000.000
182A211ALA0-0.065-0.00741.1930.0000.0000.0000.0000.0000.000
183A212ARG10.9180.93643.1530.0480.0480.0000.0000.0000.000
184A213ASN00.0150.01840.274-0.002-0.0020.0000.0000.0000.000
185A214VAL0-0.014-0.00538.132-0.001-0.0010.0000.0000.0000.000
186A215SER0-0.002-0.01936.9650.0040.0040.0000.0000.0000.000
187A216TRP0-0.017-0.01934.890-0.003-0.0030.0000.0000.0000.000
188A217ARG10.9000.94431.5930.1400.1400.0000.0000.0000.000
189A218ILE00.005-0.00333.179-0.004-0.0040.0000.0000.0000.000
190A219ILE0-0.0090.00127.369-0.001-0.0010.0000.0000.0000.000
191A220ASN00.0520.02330.977-0.006-0.0060.0000.0000.0000.000
192A221ASP-1-0.708-0.85231.830-0.167-0.1670.0000.0000.0000.000
193A222GLN00.0100.00031.222-0.008-0.0080.0000.0000.0000.000
194A223GLY0-0.0040.00927.642-0.016-0.0160.0000.0000.0000.000
195A224GLY00.004-0.00527.012-0.018-0.0180.0000.0000.0000.000
196A225LEU0-0.047-0.02327.5330.0100.0100.0000.0000.0000.000
197A226ASP-1-0.766-0.84930.656-0.119-0.1190.0000.0000.0000.000
198A227ARG10.8680.91834.0480.1080.1080.0000.0000.0000.000
199A228LEU0-0.042-0.00935.098-0.003-0.0030.0000.0000.0000.000
200A229TYR00.018-0.00337.1820.0080.0080.0000.0000.0000.000
201A230SER0-0.010-0.01939.236-0.001-0.0010.0000.0000.0000.000
202A231LYS10.8630.94641.7090.0800.0800.0000.0000.0000.000
203A232ASN0-0.009-0.01043.4150.0000.0000.0000.0000.0000.000
204A233VAL0-0.0060.01343.0390.0000.0000.0000.0000.0000.000
205A234THR00.007-0.00145.7950.0050.0050.0000.0000.0000.000