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: 1N4VZ

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 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 188
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -1910337.385564
FMO2-HF: Nuclear repulsion 1835174.310269
FMO2-HF: Total energy -75163.075295
FMO2-MP2: Total energy -75383.483501


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.
-13.549-9.5993.349-2.681-4.619-0.006
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 : -0.031 / 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].
3A76THR0-0.073-0.0352.3321.4623.9342.206-1.616-3.0630.001
4A77ASP-1-0.912-0.9704.360-0.823-0.6620.000-0.034-0.1270.000
5A78GLY0-0.007-0.0076.8320.0990.0990.0000.0000.0000.000
6A79ASP-1-0.759-0.8804.305-7.974-7.8510.000-0.066-0.0560.000
7A80LYS10.9130.9577.4181.8561.8560.0000.0000.0000.000
8A81ALA00.0130.01610.2310.2170.2170.0000.0000.0000.000
9A82PHE00.0100.0149.0850.1650.1650.0000.0000.0000.000
10A83VAL00.005-0.01510.6980.2020.2020.0000.0000.0000.000
11A84ASP-1-1.010-1.00113.275-0.653-0.6530.0000.0000.0000.000
12A85PHE00.0450.02315.1730.0860.0860.0000.0000.0000.000
13A86LEU00.0450.02913.6160.0760.0760.0000.0000.0000.000
14A87SER0-0.133-0.07316.9930.0910.0910.0000.0000.0000.000
15A88ASP-1-0.883-0.95519.124-0.559-0.5590.0000.0000.0000.000
16A89GLU-1-0.874-0.91819.817-0.520-0.5200.0000.0000.0000.000
17A90ILE0-0.0040.01318.2820.0590.0590.0000.0000.0000.000
18A91LYS10.8160.90622.1700.6620.6620.0000.0000.0000.000
19A92GLU-1-0.903-0.95325.046-0.351-0.3510.0000.0000.0000.000
20A93GLU-1-0.871-0.94123.994-0.422-0.4220.0000.0000.0000.000
21A94ARG10.7900.87923.9630.5350.5350.0000.0000.0000.000
22A95LYS10.8440.92228.1580.3870.3870.0000.0000.0000.000
23A96ILE00.0690.04229.2480.0310.0310.0000.0000.0000.000
24A97GLN00.0430.01630.6010.0440.0440.0000.0000.0000.000
25A98LYS10.9450.99831.8460.3170.3170.0000.0000.0000.000
26A99HIS0-0.065-0.05833.7150.0180.0180.0000.0000.0000.000
27A100LYS10.9080.96834.7800.2650.2650.0000.0000.0000.000
28A101THR0-0.086-0.03037.7730.0080.0080.0000.0000.0000.000
29A102LEU0-0.031-0.01133.6230.0060.0060.0000.0000.0000.000
30A103PRO00.0560.05236.8830.0100.0100.0000.0000.0000.000
31A104LYS10.8770.93739.6350.1870.1870.0000.0000.0000.000
32A105MET00.0700.04841.7970.0000.0000.0000.0000.0000.000
33A106SER0-0.098-0.03844.6090.0050.0050.0000.0000.0000.000
34A107GLY00.0600.01947.8550.0000.0000.0000.0000.0000.000
35A108GLY0-0.091-0.05347.7640.0050.0050.0000.0000.0000.000
36A109TRP00.0090.01043.4150.0010.0010.0000.0000.0000.000
37A110GLU-1-0.975-0.97840.356-0.151-0.1510.0000.0000.0000.000
38A111LEU0-0.022-0.01334.5760.0020.0020.0000.0000.0000.000
39A112GLU-1-0.980-0.98736.254-0.151-0.1510.0000.0000.0000.000
40A113LEU0-0.021-0.01930.2900.0050.0050.0000.0000.0000.000
41A114ASN0-0.042-0.02428.433-0.018-0.0180.0000.0000.0000.000
42A115GLY0-0.025-0.00326.0480.0010.0010.0000.0000.0000.000
43A116THR00.0480.01625.4820.0030.0030.0000.0000.0000.000
44A117GLU-1-1.011-0.99328.177-0.170-0.1700.0000.0000.0000.000
45A118ALA00.0310.00931.351-0.001-0.0010.0000.0000.0000.000
46A119LYS10.9150.94334.2620.1610.1610.0000.0000.0000.000
47A120LEU00.0190.03037.697-0.003-0.0030.0000.0000.0000.000
48A121VAL0-0.003-0.00140.7750.0100.0100.0000.0000.0000.000
49A122ARG10.9540.97243.3890.1040.1040.0000.0000.0000.000
50A123LYS10.9070.95747.0800.1010.1010.0000.0000.0000.000
51A124VAL00.0410.02750.1790.0000.0000.0000.0000.0000.000
52A125ALA0-0.033-0.02353.8550.0010.0010.0000.0000.0000.000
53A126GLY0-0.009-0.00856.2220.0010.0010.0000.0000.0000.000
54A127GLU-1-0.794-0.89052.331-0.076-0.0760.0000.0000.0000.000
55A128LYS10.9170.96643.1420.1080.1080.0000.0000.0000.000
56A129ILE0-0.0070.00046.7410.0030.0030.0000.0000.0000.000
57A130THR00.004-0.01041.148-0.005-0.0050.0000.0000.0000.000
58A131VAL00.0330.03140.7330.0040.0040.0000.0000.0000.000
59A132THR0-0.010-0.00136.204-0.007-0.0070.0000.0000.0000.000
60A133PHE00.0480.03434.4080.0070.0070.0000.0000.0000.000
61A134ASN00.0400.02729.045-0.025-0.0250.0000.0000.0000.000
62A135ILE00.0510.03327.5250.0080.0080.0000.0000.0000.000
63A136ASN0-0.0020.02025.328-0.032-0.0320.0000.0000.0000.000
64A137ASN0-0.078-0.04327.1430.0110.0110.0000.0000.0000.000
65A138SER00.0350.00828.6890.0180.0180.0000.0000.0000.000
66A139ILE0-0.028-0.00228.2740.0100.0100.0000.0000.0000.000
67A140PRO00.0050.01431.037-0.008-0.0080.0000.0000.0000.000
68A162LEU0-0.040-0.03630.5770.0040.0040.0000.0000.0000.000
69A163THR00.0200.00932.227-0.006-0.0060.0000.0000.0000.000
70A164SER0-0.0310.00132.3870.0020.0020.0000.0000.0000.000
71A165THR00.0480.01534.1870.0060.0060.0000.0000.0000.000
72A166PRO0-0.031-0.00733.9790.0040.0040.0000.0000.0000.000
73A167ASN00.0510.02135.6460.0110.0110.0000.0000.0000.000
74A168PHE0-0.047-0.03237.053-0.009-0.0090.0000.0000.0000.000
75A169VAL00.0300.02539.1000.0090.0090.0000.0000.0000.000
76A170VAL0-0.0060.00341.451-0.004-0.0040.0000.0000.0000.000
77A171GLU-1-0.941-0.97043.750-0.099-0.0990.0000.0000.0000.000
78A172VAL0-0.011-0.00945.689-0.001-0.0010.0000.0000.0000.000
79A173ILE00.0170.00145.9820.0050.0050.0000.0000.0000.000
80A174LYS10.8810.93550.1920.0690.0690.0000.0000.0000.000
81A175ASN00.039-0.01052.360-0.001-0.0010.0000.0000.0000.000
82A176ASP-1-1.009-0.99353.949-0.057-0.0570.0000.0000.0000.000
83A177ASP-1-0.925-0.99954.534-0.054-0.0540.0000.0000.0000.000
84A178GLY00.0180.03050.683-0.002-0.0020.0000.0000.0000.000
85A179LYS10.8700.95449.0160.0510.0510.0000.0000.0000.000
86A180LYS10.9150.97248.8390.0580.0580.0000.0000.0000.000
87A181ALA00.0160.00847.0930.0000.0000.0000.0000.0000.000
88A182LEU0-0.058-0.01049.0980.0030.0030.0000.0000.0000.000
89A183VAL00.007-0.01843.481-0.004-0.0040.0000.0000.0000.000
90A184LEU00.001-0.01746.0460.0050.0050.0000.0000.0000.000
91A185ASP-1-0.896-0.92740.737-0.129-0.1290.0000.0000.0000.000
92A186CYS0-0.029-0.01842.3060.0080.0080.0000.0000.0000.000
93A187HIS00.0270.02339.9880.0010.0010.0000.0000.0000.000
94A188TYR00.024-0.00739.3890.0040.0040.0000.0000.0000.000
95A189PRO0-0.060-0.03040.901-0.004-0.0040.0000.0000.0000.000
96A190GLU-1-0.920-0.95839.065-0.137-0.1370.0000.0000.0000.000
97A191ASP-1-0.880-0.92040.706-0.145-0.1450.0000.0000.0000.000
98A192GLU-1-0.981-0.99642.150-0.117-0.1170.0000.0000.0000.000
99A193VAL0-0.065-0.02044.0360.0040.0040.0000.0000.0000.000
100A194GLY0-0.085-0.05447.0660.0050.0050.0000.0000.0000.000
101A195GLN0-0.079-0.05645.2430.0060.0060.0000.0000.0000.000
102A196GLU-1-0.906-0.94749.450-0.110-0.1100.0000.0000.0000.000
103A197ASP-1-0.965-0.97650.621-0.108-0.1080.0000.0000.0000.000
104A198GLU-1-0.959-0.97252.392-0.079-0.0790.0000.0000.0000.000
105A199ALA0-0.057-0.04454.547-0.001-0.0010.0000.0000.0000.000
106A200GLU-1-1.023-1.01055.002-0.075-0.0750.0000.0000.0000.000
107A201SER0-0.022-0.00550.704-0.001-0.0010.0000.0000.0000.000
108A202ASP-1-0.899-0.93549.855-0.094-0.0940.0000.0000.0000.000
109A203ILE0-0.031-0.01944.614-0.002-0.0020.0000.0000.0000.000
110A204PHE0-0.038-0.03744.467-0.006-0.0060.0000.0000.0000.000
111A205SER00.010-0.00845.2510.0050.0050.0000.0000.0000.000
112A206ILE00.0340.00545.490-0.004-0.0040.0000.0000.0000.000
113A207ARG10.9050.98743.0670.1090.1090.0000.0000.0000.000
114A208GLU-1-0.906-0.96243.068-0.084-0.0840.0000.0000.0000.000
115A209VAL0-0.0080.00746.498-0.003-0.0030.0000.0000.0000.000
116A210SER00.0020.00646.2700.0050.0050.0000.0000.0000.000
117A211PHE0-0.040-0.01348.773-0.002-0.0020.0000.0000.0000.000
118A212GLN00.0440.02044.2360.0030.0030.0000.0000.0000.000
119A213SER0-0.041-0.01845.5190.0000.0000.0000.0000.0000.000
120A214THR00.009-0.03144.561-0.004-0.0040.0000.0000.0000.000
121A215GLY0-0.028-0.01140.8510.0030.0030.0000.0000.0000.000
122A216GLU-1-0.891-0.94241.403-0.067-0.0670.0000.0000.0000.000
123A217SER0-0.080-0.04838.254-0.003-0.0030.0000.0000.0000.000
124A218GLU-1-0.941-0.98834.782-0.110-0.1100.0000.0000.0000.000
125A219TRP00.0360.03638.5740.0040.0040.0000.0000.0000.000
126A220LYS10.8690.94340.6360.0570.0570.0000.0000.0000.000
127A221ASP-1-0.860-0.94040.728-0.069-0.0690.0000.0000.0000.000
128A222THR0-0.142-0.06543.7720.0030.0030.0000.0000.0000.000
129A223ASN0-0.0210.00346.7420.0090.0090.0000.0000.0000.000
130A224TYR0-0.044-0.03047.928-0.001-0.0010.0000.0000.0000.000
131A225THR00.0340.01445.291-0.003-0.0030.0000.0000.0000.000
132A226LEU0-0.070-0.03148.5080.0030.0030.0000.0000.0000.000
133A227ASN00.0610.02946.005-0.004-0.0040.0000.0000.0000.000
134A228THR0-0.043-0.07348.6120.0040.0040.0000.0000.0000.000
135A229ASP-1-0.873-0.91847.745-0.079-0.0790.0000.0000.0000.000
136A230SER0-0.117-0.06150.5320.0020.0020.0000.0000.0000.000
137A231LEU0-0.044-0.01253.0870.0040.0040.0000.0000.0000.000
138A232ASP-1-0.910-0.96055.254-0.055-0.0550.0000.0000.0000.000
139A233TRP00.056-0.00356.483-0.001-0.0010.0000.0000.0000.000
140A234ALA00.0460.04858.441-0.002-0.0020.0000.0000.0000.000
141A235LEU0-0.089-0.04356.449-0.001-0.0010.0000.0000.0000.000
142A236TYR00.0550.01950.085-0.002-0.0020.0000.0000.0000.000
143A237ASP-1-0.846-0.93055.025-0.073-0.0730.0000.0000.0000.000
144A238HIS0-0.031-0.01557.107-0.002-0.0020.0000.0000.0000.000
145A239LEU0-0.081-0.02952.445-0.001-0.0010.0000.0000.0000.000
146A240MET00.0530.02550.125-0.004-0.0040.0000.0000.0000.000
147A241ASP-1-0.877-0.92453.602-0.077-0.0770.0000.0000.0000.000
148A242PHE0-0.092-0.04852.7820.0000.0000.0000.0000.0000.000
149A243LEU0-0.009-0.00348.595-0.001-0.0010.0000.0000.0000.000
150A244ALA00.0720.05051.940-0.003-0.0030.0000.0000.0000.000
151A245ASP-1-0.964-0.97153.671-0.078-0.0780.0000.0000.0000.000
152A246ARG10.6820.80951.0890.0820.0820.0000.0000.0000.000
153A247GLY0-0.088-0.04950.560-0.004-0.0040.0000.0000.0000.000
154A248VAL0-0.024-0.00146.643-0.005-0.0050.0000.0000.0000.000
155A249ASP-1-0.816-0.91849.056-0.106-0.1060.0000.0000.0000.000
156A250ASN00.042-0.00148.352-0.009-0.0090.0000.0000.0000.000
157A251THR00.0000.01447.764-0.004-0.0040.0000.0000.0000.000
158A252PHE00.0120.01743.139-0.008-0.0080.0000.0000.0000.000
159A253ALA00.003-0.00443.875-0.008-0.0080.0000.0000.0000.000
160A254ASP-1-0.890-0.93242.887-0.154-0.1540.0000.0000.0000.000
161A255GLU-1-0.761-0.90642.677-0.148-0.1480.0000.0000.0000.000
162A256LEU0-0.065-0.03338.495-0.012-0.0120.0000.0000.0000.000
163A257VAL00.0390.03338.308-0.015-0.0150.0000.0000.0000.000
164A258GLU-1-0.887-0.91937.536-0.194-0.1940.0000.0000.0000.000
165A259LEU0-0.083-0.05936.340-0.017-0.0170.0000.0000.0000.000
166A260SER00.016-0.02133.838-0.019-0.0190.0000.0000.0000.000
167A261THR0-0.003-0.01932.900-0.022-0.0220.0000.0000.0000.000
168A262ALA0-0.078-0.04232.382-0.021-0.0210.0000.0000.0000.000
169A263LEU0-0.042-0.03631.150-0.022-0.0220.0000.0000.0000.000
170A264GLU-1-0.844-0.91026.756-0.400-0.4000.0000.0000.0000.000
171A265HIS0-0.017-0.01627.442-0.050-0.0500.0000.0000.0000.000
172A266GLN0-0.073-0.05126.835-0.034-0.0340.0000.0000.0000.000
173A267GLU-1-0.828-0.94025.057-0.393-0.3930.0000.0000.0000.000
174A268TYR00.0210.03721.221-0.078-0.0780.0000.0000.0000.000
175A269ILE0-0.037-0.03721.957-0.071-0.0710.0000.0000.0000.000
176A270THR0-0.016-0.00821.093-0.055-0.0550.0000.0000.0000.000
177A271PHE00.0380.03316.253-0.095-0.0950.0000.0000.0000.000
178A272LEU0-0.006-0.00517.293-0.148-0.1480.0000.0000.0000.000
179A273GLU-1-0.897-0.95616.575-0.759-0.7590.0000.0000.0000.000
180A274ASP-1-0.892-0.94715.647-0.889-0.8890.0000.0000.0000.000
181A275LEU0-0.032-0.00212.213-0.238-0.2380.0000.0000.0000.000
182A276LYS10.9160.94311.7550.6880.6880.0000.0000.0000.000
183A277SER0-0.094-0.05211.681-0.331-0.3310.0000.0000.0000.000
184A278PHE0-0.008-0.0037.960-0.317-0.3170.0000.0000.0000.000
185A279VAL0-0.0040.0057.382-0.688-0.6880.0000.0000.0000.000
186A280LYS10.9090.9597.1750.5710.5710.0000.0000.0000.000
187A281SER0-0.100-0.0367.0730.1470.1470.0000.0000.0000.000
188A282GLN00.026-0.0052.215-3.614-2.4201.143-0.965-1.373-0.007