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: 892KY

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 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 188
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -1912766.841107
FMO2-HF: Nuclear repulsion 1837601.661224
FMO2-HF: Total energy -75165.179883
FMO2-MP2: Total energy -75385.456363


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.
-17.782-13.7376.629-4.513-6.162-0.022
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 : -0.028 / q_NPA : -0.015
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].
3A76THR0-0.044-0.0532.4061.4884.9101.075-1.657-2.8410.002
4A77ASP-1-0.845-0.9364.482-1.175-1.088-0.001-0.016-0.0710.000
5A78GLY00.0230.0226.7150.2010.2010.0000.0000.0000.000
6A79ASP-1-0.765-0.8543.269-10.400-9.0580.055-0.714-0.683-0.006
7A80LYS10.7960.8886.5921.9861.9860.0000.0000.0000.000
8A81ALA00.0170.0079.6430.2350.2350.0000.0000.0000.000
9A82PHE00.0030.0098.1450.2100.2100.0000.0000.0000.000
10A83VAL00.0200.00210.0940.2160.2160.0000.0000.0000.000
11A84ASP-1-0.985-0.97312.420-0.715-0.7150.0000.0000.0000.000
12A85PHE00.0340.01814.3880.0880.0880.0000.0000.0000.000
13A86LEU00.0520.01612.7280.1050.1050.0000.0000.0000.000
14A87SER0-0.128-0.07716.3470.0880.0880.0000.0000.0000.000
15A88ASP-1-0.841-0.91018.409-0.588-0.5880.0000.0000.0000.000
16A89GLU-1-0.855-0.91518.478-0.605-0.6050.0000.0000.0000.000
17A90ILE0-0.0070.00617.7380.0620.0620.0000.0000.0000.000
18A91LYS10.7070.84421.9590.6950.6950.0000.0000.0000.000
19A92GLU-1-0.881-0.95624.593-0.376-0.3760.0000.0000.0000.000
20A93GLU-1-0.839-0.91523.726-0.423-0.4230.0000.0000.0000.000
21A94ARG10.8060.87223.3940.5730.5730.0000.0000.0000.000
22A95LYS10.8170.91727.9360.4040.4040.0000.0000.0000.000
23A96ILE00.0240.01028.3010.0340.0340.0000.0000.0000.000
24A97GLN00.0870.04329.7550.0500.0500.0000.0000.0000.000
25A98LYS10.9440.97431.7170.3290.3290.0000.0000.0000.000
26A99HIS0-0.076-0.04633.4530.0270.0270.0000.0000.0000.000
27A100LYS10.9660.98434.3830.2720.2720.0000.0000.0000.000
28A101THR0-0.092-0.02737.1950.0110.0110.0000.0000.0000.000
29A102LEU00.003-0.00232.9560.0070.0070.0000.0000.0000.000
30A103PRO00.0720.06636.5610.0120.0120.0000.0000.0000.000
31A104LYS10.7670.87039.2090.2020.2020.0000.0000.0000.000
32A105MET00.0480.04141.499-0.003-0.0030.0000.0000.0000.000
33A106SER0-0.069-0.05244.2830.0060.0060.0000.0000.0000.000
34A107GLY00.024-0.00547.342-0.001-0.0010.0000.0000.0000.000
35A108GLY0-0.069-0.04047.5720.0050.0050.0000.0000.0000.000
36A109TRP0-0.0040.00443.1310.0020.0020.0000.0000.0000.000
37A110GLU-1-0.967-0.97240.381-0.153-0.1530.0000.0000.0000.000
38A111LEU0-0.017-0.01635.0770.0010.0010.0000.0000.0000.000
39A112GLU-1-0.942-0.96136.211-0.157-0.1570.0000.0000.0000.000
40A113LEU0-0.007-0.01430.021-0.001-0.0010.0000.0000.0000.000
41A114ASN0-0.077-0.04528.803-0.004-0.0040.0000.0000.0000.000
42A115GLY0-0.0080.00525.998-0.004-0.0040.0000.0000.0000.000
43A116THR00.0620.02624.7820.0110.0110.0000.0000.0000.000
44A117GLU-1-0.910-0.92227.716-0.178-0.1780.0000.0000.0000.000
45A118ALA00.0150.00931.019-0.001-0.0010.0000.0000.0000.000
46A119LYS10.8460.89334.0580.1780.1780.0000.0000.0000.000
47A120LEU00.0310.03737.5300.0000.0000.0000.0000.0000.000
48A121VAL0-0.016-0.00740.4520.0100.0100.0000.0000.0000.000
49A122ARG10.8720.93342.9830.1090.1090.0000.0000.0000.000
50A123LYS10.9220.95446.7360.1070.1070.0000.0000.0000.000
51A124VAL00.0400.02750.003-0.001-0.0010.0000.0000.0000.000
52A125ALA0-0.038-0.02753.7420.0020.0020.0000.0000.0000.000
53A126GLY00.0020.00656.2020.0010.0010.0000.0000.0000.000
54A127GLU-1-0.783-0.85852.107-0.079-0.0790.0000.0000.0000.000
55A128LYS10.7910.89242.5820.1150.1150.0000.0000.0000.000
56A129ILE0-0.0140.00146.5330.0030.0030.0000.0000.0000.000
57A130THR0-0.009-0.03740.534-0.005-0.0050.0000.0000.0000.000
58A131VAL00.0410.03240.1300.0060.0060.0000.0000.0000.000
59A132THR0-0.017-0.00135.705-0.010-0.0100.0000.0000.0000.000
60A133PHE00.0380.01933.9870.0060.0060.0000.0000.0000.000
61A134ASN00.014-0.00828.694-0.028-0.0280.0000.0000.0000.000
62A135ILE00.0320.03826.6140.0070.0070.0000.0000.0000.000
63A136ASN0-0.041-0.01624.353-0.040-0.0400.0000.0000.0000.000
64A137ASN0-0.066-0.04626.3490.0120.0120.0000.0000.0000.000
65A138SER00.0340.04427.9020.0220.0220.0000.0000.0000.000
66A139ILE0-0.0270.00327.6600.0130.0130.0000.0000.0000.000
67A140PRO0-0.0120.01030.535-0.010-0.0100.0000.0000.0000.000
68A162LEU00.0150.00129.429-0.005-0.0050.0000.0000.0000.000
69A163THR0-0.017-0.02131.397-0.006-0.0060.0000.0000.0000.000
70A164SER0-0.022-0.01531.6480.0050.0050.0000.0000.0000.000
71A165THR00.0530.00733.3780.0060.0060.0000.0000.0000.000
72A166PRO0-0.029-0.00433.1830.0050.0050.0000.0000.0000.000
73A167ASN00.003-0.01034.9700.0030.0030.0000.0000.0000.000
74A168PHE0-0.048-0.03636.314-0.009-0.0090.0000.0000.0000.000
75A169VAL00.0110.01238.2660.0100.0100.0000.0000.0000.000
76A170VAL00.0010.00040.571-0.003-0.0030.0000.0000.0000.000
77A171GLU-1-0.833-0.89043.213-0.107-0.1070.0000.0000.0000.000
78A172VAL00.025-0.00345.145-0.001-0.0010.0000.0000.0000.000
79A173ILE0-0.027-0.00145.5520.0060.0060.0000.0000.0000.000
80A174LYS10.8810.91749.9020.0710.0710.0000.0000.0000.000
81A175ASN00.000-0.02552.368-0.001-0.0010.0000.0000.0000.000
82A176ASP-1-0.948-0.97753.730-0.060-0.0600.0000.0000.0000.000
83A177ASP-1-0.890-0.93854.430-0.053-0.0530.0000.0000.0000.000
84A178GLY00.0740.04550.647-0.001-0.0010.0000.0000.0000.000
85A179LYS10.8120.90949.0190.0520.0520.0000.0000.0000.000
86A180LYS10.8620.93748.5080.0590.0590.0000.0000.0000.000
87A181ALA00.0180.01246.534-0.001-0.0010.0000.0000.0000.000
88A182LEU0-0.034-0.00348.5560.0030.0030.0000.0000.0000.000
89A183VAL0-0.013-0.01842.958-0.005-0.0050.0000.0000.0000.000
90A184LEU00.021-0.00345.0120.0050.0050.0000.0000.0000.000
91A185ASP-1-0.848-0.90939.645-0.139-0.1390.0000.0000.0000.000
92A186CYS0-0.046-0.00941.4920.0100.0100.0000.0000.0000.000
93A187HIS00.0480.03839.324-0.001-0.0010.0000.0000.0000.000
94A188TYR00.027-0.01238.5340.0040.0040.0000.0000.0000.000
95A189PRO0-0.027-0.00940.562-0.003-0.0030.0000.0000.0000.000
96A190GLU-1-0.943-0.96138.119-0.147-0.1470.0000.0000.0000.000
97A191ASP-1-0.891-0.93239.325-0.158-0.1580.0000.0000.0000.000
98A192GLU-1-0.965-0.98741.421-0.123-0.1230.0000.0000.0000.000
99A193VAL0-0.068-0.02043.2720.0040.0040.0000.0000.0000.000
100A194GLY0-0.081-0.05446.2270.0060.0060.0000.0000.0000.000
101A195GLN0-0.080-0.06244.3850.0060.0060.0000.0000.0000.000
102A196GLU-1-0.906-0.95148.649-0.116-0.1160.0000.0000.0000.000
103A197ASP-1-0.960-0.97349.817-0.114-0.1140.0000.0000.0000.000
104A198GLU-1-0.961-0.97151.711-0.083-0.0830.0000.0000.0000.000
105A199ALA0-0.062-0.04553.804-0.002-0.0020.0000.0000.0000.000
106A200GLU-1-1.010-0.99854.185-0.077-0.0770.0000.0000.0000.000
107A201SER0-0.023-0.01449.764-0.001-0.0010.0000.0000.0000.000
108A202ASP-1-0.870-0.90848.976-0.101-0.1010.0000.0000.0000.000
109A203ILE0-0.038-0.03044.168-0.003-0.0030.0000.0000.0000.000
110A204PHE0-0.038-0.03843.917-0.007-0.0070.0000.0000.0000.000
111A205SER00.0280.02144.6080.0080.0080.0000.0000.0000.000
112A206ILE00.0330.00644.692-0.005-0.0050.0000.0000.0000.000
113A207ARG10.8550.93142.4040.1080.1080.0000.0000.0000.000
114A208GLU-1-0.866-0.93443.442-0.080-0.0800.0000.0000.0000.000
115A209VAL0-0.0110.00345.627-0.004-0.0040.0000.0000.0000.000
116A210SER00.0090.01845.4570.0050.0050.0000.0000.0000.000
117A211PHE0-0.041-0.02448.193-0.001-0.0010.0000.0000.0000.000
118A212GLN00.0480.02643.5760.0040.0040.0000.0000.0000.000
119A213SER0-0.034-0.04645.4920.0020.0020.0000.0000.0000.000
120A214THR0-0.051-0.05144.499-0.004-0.0040.0000.0000.0000.000
121A215GLY0-0.020-0.00840.7120.0030.0030.0000.0000.0000.000
122A216GLU-1-0.860-0.91640.914-0.063-0.0630.0000.0000.0000.000
123A217SER0-0.058-0.03437.728-0.003-0.0030.0000.0000.0000.000
124A218GLU-1-0.922-0.96434.364-0.111-0.1110.0000.0000.0000.000
125A219TRP00.0050.00837.9390.0030.0030.0000.0000.0000.000
126A220LYS10.8790.93840.1480.0570.0570.0000.0000.0000.000
127A221ASP-1-0.857-0.93340.560-0.065-0.0650.0000.0000.0000.000
128A222THR0-0.087-0.04743.4050.0020.0020.0000.0000.0000.000
129A223ASN0-0.074-0.01445.6620.0090.0090.0000.0000.0000.000
130A224TYR0-0.021-0.01747.463-0.002-0.0020.0000.0000.0000.000
131A225THR00.014-0.00444.849-0.004-0.0040.0000.0000.0000.000
132A226LEU0-0.076-0.02848.2140.0040.0040.0000.0000.0000.000
133A227ASN00.006-0.01245.307-0.002-0.0020.0000.0000.0000.000
134A228THR0-0.008-0.03647.9420.0050.0050.0000.0000.0000.000
135A229ASP-1-0.839-0.89546.301-0.086-0.0860.0000.0000.0000.000
136A230SER0-0.138-0.08249.6720.0040.0040.0000.0000.0000.000
137A231LEU0-0.0430.00152.4960.0040.0040.0000.0000.0000.000
138A232ASP-1-0.891-0.96154.673-0.058-0.0580.0000.0000.0000.000
139A233TRP00.0170.01056.148-0.002-0.0020.0000.0000.0000.000
140A234ALA00.0540.04457.429-0.002-0.0020.0000.0000.0000.000
141A235LEU0-0.061-0.04355.930-0.001-0.0010.0000.0000.0000.000
142A236TYR00.0230.00749.525-0.002-0.0020.0000.0000.0000.000
143A237ASP-1-0.846-0.92954.114-0.076-0.0760.0000.0000.0000.000
144A238HIS0-0.054-0.03556.066-0.002-0.0020.0000.0000.0000.000
145A239LEU0-0.062-0.03051.899-0.001-0.0010.0000.0000.0000.000
146A240MET00.0080.02548.914-0.004-0.0040.0000.0000.0000.000
147A241ASP-1-0.882-0.94152.757-0.081-0.0810.0000.0000.0000.000
148A242PHE0-0.093-0.05051.933-0.001-0.0010.0000.0000.0000.000
149A243LEU00.0180.00647.660-0.001-0.0010.0000.0000.0000.000
150A244ALA00.0510.02951.109-0.003-0.0030.0000.0000.0000.000
151A245ASP-1-0.908-0.94852.834-0.080-0.0800.0000.0000.0000.000
152A246ARG10.6700.81750.4920.0840.0840.0000.0000.0000.000
153A247GLY0-0.056-0.02150.101-0.004-0.0040.0000.0000.0000.000
154A248VAL0-0.039-0.01645.604-0.006-0.0060.0000.0000.0000.000
155A249ASP-1-0.735-0.85948.142-0.113-0.1130.0000.0000.0000.000
156A250ASN00.021-0.00547.528-0.009-0.0090.0000.0000.0000.000
157A251THR0-0.040-0.03547.007-0.005-0.0050.0000.0000.0000.000
158A252PHE0-0.015-0.01642.560-0.008-0.0080.0000.0000.0000.000
159A253ALA00.0250.01343.241-0.009-0.0090.0000.0000.0000.000
160A254ASP-1-0.869-0.92042.191-0.164-0.1640.0000.0000.0000.000
161A255GLU-1-0.815-0.89541.800-0.156-0.1560.0000.0000.0000.000
162A256LEU0-0.046-0.01637.881-0.013-0.0130.0000.0000.0000.000
163A257VAL00.0560.05037.535-0.014-0.0140.0000.0000.0000.000
164A258GLU-1-0.924-0.94036.636-0.234-0.2340.0000.0000.0000.000
165A259LEU0-0.054-0.04835.963-0.018-0.0180.0000.0000.0000.000
166A260SER00.021-0.01033.161-0.018-0.0180.0000.0000.0000.000
167A261THR0-0.008-0.01432.202-0.025-0.0250.0000.0000.0000.000
168A262ALA0-0.067-0.04531.595-0.023-0.0230.0000.0000.0000.000
169A263LEU0-0.045-0.02230.728-0.022-0.0220.0000.0000.0000.000
170A264GLU-1-0.833-0.91826.510-0.407-0.4070.0000.0000.0000.000
171A265HIS0-0.024-0.02126.607-0.060-0.0600.0000.0000.0000.000
172A266GLN0-0.087-0.05026.476-0.046-0.0460.0000.0000.0000.000
173A267GLU-1-0.858-0.94724.673-0.415-0.4150.0000.0000.0000.000
174A268TYR00.0030.02020.353-0.087-0.0870.0000.0000.0000.000
175A269ILE0-0.017-0.02121.407-0.077-0.0770.0000.0000.0000.000
176A270THR0-0.021-0.03120.708-0.048-0.0480.0000.0000.0000.000
177A271PHE00.0240.02315.632-0.104-0.1040.0000.0000.0000.000
178A272LEU0-0.003-0.00117.015-0.162-0.1620.0000.0000.0000.000
179A273GLU-1-0.834-0.88616.326-0.787-0.7870.0000.0000.0000.000
180A274ASP-1-0.884-0.94415.132-0.983-0.9830.0000.0000.0000.000
181A275LEU0-0.048-0.00811.379-0.268-0.2680.0000.0000.0000.000
182A276LYS10.8980.93511.4610.7110.7110.0000.0000.0000.000
183A277SER0-0.073-0.04111.419-0.322-0.3220.0000.0000.0000.000
184A278PHE0-0.006-0.0047.106-0.316-0.3160.0000.0000.0000.000
185A279VAL00.0030.0236.776-0.771-0.7710.0000.0000.0000.000
186A280LYS10.9210.9616.9380.5420.5420.0000.0000.0000.000
187A281SER0-0.097-0.0426.2610.2530.2530.0000.0000.0000.000
188A282GLN00.002-0.0012.077-5.034-5.8405.500-2.126-2.567-0.018