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: G5N71

Calculation Name: 1P32-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1P32

Chain ID: A

ChEMBL ID:

UniProt ID: Q07021

Base Structure: X-ray

Registration Date: 2023-09-21

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 188
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -1909901.746984
FMO2-HF: Nuclear repulsion 1834737.287804
FMO2-HF: Total energy -75164.45918
FMO2-MP2: Total energy -75384.78194


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:74:MET)


Summations of interaction energy for fragment #1(A:74:MET)
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.
-14.637-10.1783.306-2.849-4.914-0.008
Interaction energy analysis for fragmet #1(A:74:MET)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.024 / q_NPA : -0.008
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].
3A76THR0-0.084-0.0732.2421.6684.2232.577-1.725-3.4060.001
4A77ASP-1-0.847-0.9314.291-0.839-0.7030.000-0.029-0.1070.000
5A78GLY00.0060.0056.8130.0480.0480.0000.0000.0000.000
6A79ASP-1-0.752-0.8533.783-8.098-7.6390.006-0.218-0.246-0.001
7A80LYS10.8370.9107.0911.6601.6600.0000.0000.0000.000
8A81ALA00.0120.01210.0300.2070.2070.0000.0000.0000.000
9A82PHE00.0120.0158.4530.1690.1690.0000.0000.0000.000
10A83VAL00.015-0.01010.5740.1880.1880.0000.0000.0000.000
11A84ASP-1-1.001-0.99112.876-0.639-0.6390.0000.0000.0000.000
12A85PHE00.0140.00714.7750.0870.0870.0000.0000.0000.000
13A86LEU00.0630.03113.1670.0770.0770.0000.0000.0000.000
14A87SER0-0.108-0.05816.8050.0880.0880.0000.0000.0000.000
15A88ASP-1-0.803-0.89418.927-0.542-0.5420.0000.0000.0000.000
16A89GLU-1-0.874-0.91319.056-0.536-0.5360.0000.0000.0000.000
17A90ILE0-0.0080.00218.0900.0580.0580.0000.0000.0000.000
18A91LYS10.7200.84522.2350.6610.6610.0000.0000.0000.000
19A92GLU-1-0.917-0.96324.616-0.348-0.3480.0000.0000.0000.000
20A93GLU-1-0.865-0.93723.713-0.409-0.4090.0000.0000.0000.000
21A94ARG10.7530.83223.6570.5560.5560.0000.0000.0000.000
22A95LYS10.8660.93228.1390.3800.3800.0000.0000.0000.000
23A96ILE00.0660.03628.7180.0320.0320.0000.0000.0000.000
24A97GLN00.0460.03730.3290.0450.0450.0000.0000.0000.000
25A98LYS10.9390.98931.9250.3170.3170.0000.0000.0000.000
26A99HIS0-0.076-0.06633.6970.0230.0230.0000.0000.0000.000
27A100LYS10.9500.98234.4870.2650.2650.0000.0000.0000.000
28A101THR0-0.080-0.03037.7440.0080.0080.0000.0000.0000.000
29A102LEU0-0.005-0.00533.4720.0070.0070.0000.0000.0000.000
30A103PRO00.0620.05836.9480.0100.0100.0000.0000.0000.000
31A104LYS10.8120.90639.4930.1960.1960.0000.0000.0000.000
32A105MET00.0450.04141.627-0.002-0.0020.0000.0000.0000.000
33A106SER0-0.104-0.05844.5960.0050.0050.0000.0000.0000.000
34A107GLY00.0550.01447.8440.0000.0000.0000.0000.0000.000
35A108GLY0-0.093-0.05747.7500.0050.0050.0000.0000.0000.000
36A109TRP0-0.0010.00743.4330.0010.0010.0000.0000.0000.000
37A110GLU-1-0.970-0.97340.423-0.156-0.1560.0000.0000.0000.000
38A111LEU0-0.016-0.01234.7120.0010.0010.0000.0000.0000.000
39A112GLU-1-0.971-0.98536.258-0.159-0.1590.0000.0000.0000.000
40A113LEU0-0.022-0.01729.9940.0050.0050.0000.0000.0000.000
41A114ASN0-0.052-0.03328.688-0.012-0.0120.0000.0000.0000.000
42A115GLY0-0.024-0.00126.0380.0010.0010.0000.0000.0000.000
43A116THR00.0440.00325.4030.0030.0030.0000.0000.0000.000
44A117GLU-1-0.933-0.95028.170-0.177-0.1770.0000.0000.0000.000
45A118ALA00.0190.00931.345-0.001-0.0010.0000.0000.0000.000
46A119LYS10.8720.91834.2540.1810.1810.0000.0000.0000.000
47A120LEU00.0160.02737.689-0.003-0.0030.0000.0000.0000.000
48A121VAL0-0.012-0.00940.7650.0110.0110.0000.0000.0000.000
49A122ARG10.9360.96943.3800.1090.1090.0000.0000.0000.000
50A123LYS10.9210.96547.0320.1080.1080.0000.0000.0000.000
51A124VAL00.0310.02050.1690.0000.0000.0000.0000.0000.000
52A125ALA0-0.027-0.02053.8450.0010.0010.0000.0000.0000.000
53A126GLY0-0.007-0.00756.2140.0010.0010.0000.0000.0000.000
54A127GLU-1-0.782-0.86352.316-0.080-0.0800.0000.0000.0000.000
55A128LYS10.8410.92342.5340.1210.1210.0000.0000.0000.000
56A129ILE0-0.016-0.00946.8820.0030.0030.0000.0000.0000.000
57A130THR00.016-0.00941.022-0.005-0.0050.0000.0000.0000.000
58A131VAL00.0310.02740.7520.0040.0040.0000.0000.0000.000
59A132THR0-0.021-0.00836.142-0.009-0.0090.0000.0000.0000.000
60A133PHE00.0510.03234.4070.0070.0070.0000.0000.0000.000
61A134ASN00.0370.02528.934-0.026-0.0260.0000.0000.0000.000
62A135ILE00.0150.01627.4480.0090.0090.0000.0000.0000.000
63A136ASN0-0.018-0.00324.934-0.037-0.0370.0000.0000.0000.000
64A137ASN0-0.087-0.05226.9310.0110.0110.0000.0000.0000.000
65A138SER00.0400.02328.4750.0150.0150.0000.0000.0000.000
66A139ILE0-0.020-0.00327.8340.0120.0120.0000.0000.0000.000
67A140PRO0-0.0090.01030.751-0.007-0.0070.0000.0000.0000.000
68A162LEU0-0.038-0.03529.9850.0040.0040.0000.0000.0000.000
69A163THR00.0330.01631.786-0.008-0.0080.0000.0000.0000.000
70A164SER0-0.0010.02332.0390.0020.0020.0000.0000.0000.000
71A165THR00.0510.01633.8790.0060.0060.0000.0000.0000.000
72A166PRO0-0.0170.00233.7040.0040.0040.0000.0000.0000.000
73A167ASN00.0400.01735.4210.0040.0040.0000.0000.0000.000
74A168PHE0-0.045-0.03136.822-0.009-0.0090.0000.0000.0000.000
75A169VAL00.0170.01638.8580.0090.0090.0000.0000.0000.000
76A170VAL00.0040.00741.217-0.004-0.0040.0000.0000.0000.000
77A171GLU-1-0.884-0.92643.586-0.110-0.1100.0000.0000.0000.000
78A172VAL0-0.002-0.00645.685-0.001-0.0010.0000.0000.0000.000
79A173ILE0-0.014-0.00845.6850.0050.0050.0000.0000.0000.000
80A174LYS10.8850.92850.1870.0730.0730.0000.0000.0000.000
81A175ASN00.040-0.01152.426-0.001-0.0010.0000.0000.0000.000
82A176ASP-1-1.015-0.99853.943-0.063-0.0630.0000.0000.0000.000
83A177ASP-1-0.889-0.96354.446-0.058-0.0580.0000.0000.0000.000
84A178GLY00.0380.03750.678-0.002-0.0020.0000.0000.0000.000
85A179LYS10.8190.91249.0120.0560.0560.0000.0000.0000.000
86A180LYS10.9130.97548.8380.0620.0620.0000.0000.0000.000
87A181ALA00.0130.01047.028-0.001-0.0010.0000.0000.0000.000
88A182LEU0-0.048-0.01049.0160.0030.0030.0000.0000.0000.000
89A183VAL0-0.004-0.02243.274-0.004-0.0040.0000.0000.0000.000
90A184LEU00.005-0.01245.8100.0050.0050.0000.0000.0000.000
91A185ASP-1-0.878-0.92440.219-0.137-0.1370.0000.0000.0000.000
92A186CYS0-0.036-0.01842.1170.0090.0090.0000.0000.0000.000
93A187HIS00.0280.01639.674-0.001-0.0010.0000.0000.0000.000
94A188TYR00.006-0.02138.9830.0040.0040.0000.0000.0000.000
95A189PRO0-0.037-0.01140.692-0.004-0.0040.0000.0000.0000.000
96A190GLU-1-0.926-0.96238.409-0.141-0.1410.0000.0000.0000.000
97A191ASP-1-0.893-0.93140.190-0.148-0.1480.0000.0000.0000.000
98A192GLU-1-0.983-0.99541.753-0.116-0.1160.0000.0000.0000.000
99A193VAL0-0.072-0.02243.6810.0040.0040.0000.0000.0000.000
100A194GLY0-0.081-0.05446.6800.0060.0060.0000.0000.0000.000
101A195GLN0-0.068-0.05144.7610.0050.0050.0000.0000.0000.000
102A196GLU-1-0.914-0.95049.138-0.110-0.1100.0000.0000.0000.000
103A197ASP-1-0.965-0.97749.965-0.109-0.1090.0000.0000.0000.000
104A198GLU-1-0.974-0.97351.971-0.080-0.0800.0000.0000.0000.000
105A199ALA0-0.053-0.04354.186-0.002-0.0020.0000.0000.0000.000
106A200GLU-1-1.029-1.01354.854-0.075-0.0750.0000.0000.0000.000
107A201SER00.0050.00350.363-0.001-0.0010.0000.0000.0000.000
108A202ASP-1-0.866-0.90849.450-0.098-0.0980.0000.0000.0000.000
109A203ILE0-0.037-0.02944.472-0.003-0.0030.0000.0000.0000.000
110A204PHE0-0.032-0.03144.263-0.007-0.0070.0000.0000.0000.000
111A205SER00.0180.01445.0380.0070.0070.0000.0000.0000.000
112A206ILE00.025-0.00245.271-0.005-0.0050.0000.0000.0000.000
113A207ARG10.9060.96642.8060.1080.1080.0000.0000.0000.000
114A208GLU-1-0.883-0.94843.470-0.085-0.0850.0000.0000.0000.000
115A209VAL0-0.0090.00646.284-0.004-0.0040.0000.0000.0000.000
116A210SER00.0110.01746.0990.0040.0040.0000.0000.0000.000
117A211PHE0-0.043-0.01948.547-0.002-0.0020.0000.0000.0000.000
118A212GLN00.0460.02344.1160.0040.0040.0000.0000.0000.000
119A213SER0-0.045-0.05445.7470.0030.0030.0000.0000.0000.000
120A214THR0-0.038-0.04644.560-0.004-0.0040.0000.0000.0000.000
121A215GLY0-0.021-0.00640.8490.0020.0020.0000.0000.0000.000
122A216GLU-1-0.872-0.91541.401-0.071-0.0710.0000.0000.0000.000
123A217SER0-0.064-0.03638.207-0.004-0.0040.0000.0000.0000.000
124A218GLU-1-0.925-0.97734.484-0.123-0.1230.0000.0000.0000.000
125A219TRP00.0140.01738.4450.0040.0040.0000.0000.0000.000
126A220LYS10.8790.93840.4210.0630.0630.0000.0000.0000.000
127A221ASP-1-0.852-0.93140.641-0.075-0.0750.0000.0000.0000.000
128A222THR0-0.121-0.05943.5750.0030.0030.0000.0000.0000.000
129A223ASN0-0.048-0.00146.5380.0090.0090.0000.0000.0000.000
130A224TYR0-0.023-0.02347.724-0.002-0.0020.0000.0000.0000.000
131A225THR00.0120.00444.987-0.003-0.0030.0000.0000.0000.000
132A226LEU0-0.064-0.02248.3000.0030.0030.0000.0000.0000.000
133A227ASN00.017-0.00145.552-0.002-0.0020.0000.0000.0000.000
134A228THR0-0.038-0.06448.3780.0040.0040.0000.0000.0000.000
135A229ASP-1-0.851-0.90847.143-0.084-0.0840.0000.0000.0000.000
136A230SER0-0.112-0.05750.2840.0030.0030.0000.0000.0000.000
137A231LEU0-0.041-0.00852.8260.0040.0040.0000.0000.0000.000
138A232ASP-1-0.898-0.95755.052-0.057-0.0570.0000.0000.0000.000
139A233TRP00.045-0.00556.391-0.001-0.0010.0000.0000.0000.000
140A234ALA00.0490.04758.227-0.002-0.0020.0000.0000.0000.000
141A235LEU0-0.075-0.04156.404-0.001-0.0010.0000.0000.0000.000
142A236TYR00.0420.01350.085-0.002-0.0020.0000.0000.0000.000
143A237ASP-1-0.851-0.93154.804-0.075-0.0750.0000.0000.0000.000
144A238HIS0-0.038-0.02156.881-0.002-0.0020.0000.0000.0000.000
145A239LEU0-0.077-0.02752.223-0.001-0.0010.0000.0000.0000.000
146A240MET00.0270.02149.841-0.004-0.0040.0000.0000.0000.000
147A241ASP-1-0.879-0.92753.373-0.080-0.0800.0000.0000.0000.000
148A242PHE0-0.082-0.04452.444-0.001-0.0010.0000.0000.0000.000
149A243LEU00.0100.00248.429-0.002-0.0020.0000.0000.0000.000
150A244ALA00.0700.04451.775-0.003-0.0030.0000.0000.0000.000
151A245ASP-1-0.961-0.96853.433-0.080-0.0800.0000.0000.0000.000
152A246ARG10.6700.80951.1200.0850.0850.0000.0000.0000.000
153A247GLY0-0.084-0.04950.550-0.005-0.0050.0000.0000.0000.000
154A248VAL0-0.015-0.00146.297-0.005-0.0050.0000.0000.0000.000
155A249ASP-1-0.749-0.87148.861-0.110-0.1100.0000.0000.0000.000
156A250ASN00.025-0.00948.118-0.009-0.0090.0000.0000.0000.000
157A251THR0-0.031-0.01747.535-0.005-0.0050.0000.0000.0000.000
158A252PHE0-0.006-0.00443.054-0.008-0.0080.0000.0000.0000.000
159A253ALA00.0110.00243.643-0.009-0.0090.0000.0000.0000.000
160A254ASP-1-0.876-0.92242.658-0.157-0.1570.0000.0000.0000.000
161A255GLU-1-0.787-0.90042.364-0.153-0.1530.0000.0000.0000.000
162A256LEU0-0.069-0.02738.324-0.012-0.0120.0000.0000.0000.000
163A257VAL00.0450.03937.918-0.015-0.0150.0000.0000.0000.000
164A258GLU-1-0.896-0.93437.206-0.206-0.2060.0000.0000.0000.000
165A259LEU0-0.072-0.05736.298-0.018-0.0180.0000.0000.0000.000
166A260SER00.020-0.00833.648-0.019-0.0190.0000.0000.0000.000
167A261THR00.008-0.00632.658-0.024-0.0240.0000.0000.0000.000
168A262ALA0-0.076-0.03931.971-0.022-0.0220.0000.0000.0000.000
169A263LEU0-0.043-0.03331.179-0.022-0.0220.0000.0000.0000.000
170A264GLU-1-0.850-0.91926.750-0.400-0.4000.0000.0000.0000.000
171A265HIS0-0.011-0.01527.125-0.054-0.0540.0000.0000.0000.000
172A266GLN0-0.092-0.05426.682-0.038-0.0380.0000.0000.0000.000
173A267GLU-1-0.825-0.93425.046-0.403-0.4030.0000.0000.0000.000
174A268TYR00.0110.03120.594-0.083-0.0830.0000.0000.0000.000
175A269ILE0-0.031-0.03221.788-0.073-0.0730.0000.0000.0000.000
176A270THR0-0.012-0.01121.199-0.047-0.0470.0000.0000.0000.000
177A271PHE00.0440.03515.996-0.099-0.0990.0000.0000.0000.000
178A272LEU0-0.004-0.00117.281-0.153-0.1530.0000.0000.0000.000
179A273GLU-1-0.845-0.90316.558-0.764-0.7640.0000.0000.0000.000
180A274ASP-1-0.891-0.94415.614-0.936-0.9360.0000.0000.0000.000
181A275LEU0-0.042-0.00711.791-0.248-0.2480.0000.0000.0000.000
182A276LYS10.9000.93111.7400.6770.6770.0000.0000.0000.000
183A277SER0-0.075-0.04411.660-0.324-0.3240.0000.0000.0000.000
184A278PHE0-0.020-0.0087.668-0.303-0.3030.0000.0000.0000.000
185A279VAL0-0.0120.0017.243-0.717-0.7170.0000.0000.0000.000
186A280LYS10.9160.9587.1540.5640.5640.0000.0000.0000.000
187A281SER0-0.105-0.0336.9660.1460.1460.0000.0000.0000.000
188A282GLN00.0340.0052.446-4.361-3.0520.723-0.877-1.155-0.008