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: 39G9L

Calculation Name: 1PQZ-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1PQZ

Chain ID: A

ChEMBL ID:

UniProt ID: P01887

Base Structure: X-ray

Registration Date: 2023-06-26

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 235
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2661544.704697
FMO2-HF: Nuclear repulsion 2568047.033768
FMO2-HF: Total energy -93497.670929
FMO2-MP2: Total energy -93769.119973


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:5:GLY)


Summations of interaction energy for fragment #1(A:5: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.
-6.895-3.162.902-3.401-3.235-0.024
Interaction energy analysis for fragmet #1(A:5:GLY)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.035 / q_NPA : 0.017
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].
3A7GLU-1-0.856-0.8963.792-3.326-2.217-0.005-0.684-0.4200.004
4A8SER0-0.067-0.0504.4550.5420.692-0.001-0.027-0.1220.000
5A9GLY0-0.020-0.0145.7720.5890.5890.0000.0000.0000.000
6A10LEU0-0.047-0.0158.633-0.247-0.2470.0000.0000.0000.000
7A11ARG10.7770.8659.9520.8490.8490.0000.0000.0000.000
8A12TYR0-0.061-0.06512.847-0.056-0.0560.0000.0000.0000.000
9A13ALA0-0.0060.00815.2020.0300.0300.0000.0000.0000.000
10A14TYR0-0.011-0.02317.0250.0130.0130.0000.0000.0000.000
11A15THR00.0030.00020.8300.0120.0120.0000.0000.0000.000
12A16LEU0-0.006-0.01323.2280.0010.0010.0000.0000.0000.000
13A17VAL0-0.0100.00426.9570.0060.0060.0000.0000.0000.000
14A18VAL00.027-0.00329.2590.0030.0030.0000.0000.0000.000
15A19ASP-1-0.849-0.91732.793-0.080-0.0800.0000.0000.0000.000
16A20GLY00.0430.00535.4550.0030.0030.0000.0000.0000.000
17A21THR0-0.070-0.01638.0990.0040.0040.0000.0000.0000.000
18A22ALA0-0.056-0.01839.4950.0030.0030.0000.0000.0000.000
19A23ASN00.007-0.00838.080-0.002-0.0020.0000.0000.0000.000
20A24THR0-0.096-0.06933.238-0.005-0.0050.0000.0000.0000.000
21A25ALA00.0480.03332.519-0.005-0.0050.0000.0000.0000.000
22A26ARG10.9490.98829.8510.1070.1070.0000.0000.0000.000
23A27CYS0-0.019-0.00825.872-0.004-0.0040.0000.0000.0000.000
24A28PHE0-0.038-0.02521.9210.0010.0010.0000.0000.0000.000
25A29GLY00.0660.03220.2320.0010.0010.0000.0000.0000.000
26A30THR0-0.039-0.01415.878-0.023-0.0230.0000.0000.0000.000
27A31GLY00.0360.02015.270-0.001-0.0010.0000.0000.0000.000
28A32HIS10.8320.9089.7330.8890.8890.0000.0000.0000.000
29A33VAL00.0520.0238.6470.1290.1290.0000.0000.0000.000
30A34ASP-1-0.770-0.8504.093-2.052-1.924-0.001-0.016-0.1110.000
31A35GLY00.0560.0304.650-0.966-0.913-0.001-0.007-0.0450.000
32A36GLU-1-0.844-0.8906.631-0.598-0.5980.0000.0000.0000.000
33A37ALA0-0.028-0.0158.7520.1100.1100.0000.0000.0000.000
34A38PHE0-0.012-0.01812.4310.0290.0290.0000.0000.0000.000
35A39VAL0-0.007-0.00814.9100.0790.0790.0000.0000.0000.000
36A40GLY00.0410.02917.501-0.034-0.0340.0000.0000.0000.000
37A41TYR0-0.009-0.00219.9300.0330.0330.0000.0000.0000.000
38A42SER00.0610.01422.9890.0060.0060.0000.0000.0000.000
39A43ASN0-0.033-0.02425.8460.0120.0120.0000.0000.0000.000
40A44ASN0-0.014-0.00628.5210.0110.0110.0000.0000.0000.000
41A45LYS10.9520.99127.8960.1490.1490.0000.0000.0000.000
42A46THR00.018-0.01122.179-0.014-0.0140.0000.0000.0000.000
43A47HIS0-0.048-0.02020.8430.0230.0230.0000.0000.0000.000
44A48GLY00.0400.01520.027-0.024-0.0240.0000.0000.0000.000
45A49ILE0-0.050-0.01815.5620.0260.0260.0000.0000.0000.000
46A50GLY00.0630.03715.280-0.045-0.0450.0000.0000.0000.000
47A51ARG10.8970.95115.3090.4040.4040.0000.0000.0000.000
48A52TRP00.0280.01712.5990.0710.0710.0000.0000.0000.000
49A53VAL0-0.0620.01017.2520.0360.0360.0000.0000.0000.000
50A54ASN00.0670.03118.7890.0320.0320.0000.0000.0000.000
51A55ALA00.054-0.00622.576-0.009-0.0090.0000.0000.0000.000
52A56SER00.0100.01224.7280.0060.0060.0000.0000.0000.000
53A57HIS00.0290.01919.842-0.004-0.0040.0000.0000.0000.000
54A58VAL0-0.0070.01021.579-0.003-0.0030.0000.0000.0000.000
55A59GLU-1-0.874-0.93322.985-0.158-0.1580.0000.0000.0000.000
56A60GLU-1-0.847-0.91623.237-0.171-0.1710.0000.0000.0000.000
57A61GLU-1-0.740-0.81818.553-0.367-0.3670.0000.0000.0000.000
58A62ASN00.0000.01722.382-0.001-0.0010.0000.0000.0000.000
59A63LYS10.7730.87625.2270.1720.1720.0000.0000.0000.000
60A64GLU-1-0.724-0.82321.890-0.167-0.1670.0000.0000.0000.000
61A65PHE00.0410.02918.7460.0040.0040.0000.0000.0000.000
62A66VAL0-0.0090.00124.2220.0140.0140.0000.0000.0000.000
63A67ARG10.7220.82724.7070.1650.1650.0000.0000.0000.000
64A68GLN0-0.018-0.03122.5910.0060.0060.0000.0000.0000.000
65A70LYS10.9520.98927.1800.1180.1180.0000.0000.0000.000
66A71GLU-1-0.838-0.90526.829-0.121-0.1210.0000.0000.0000.000
67A72LEU0-0.0050.00624.7020.0060.0060.0000.0000.0000.000
68A73GLN0-0.030-0.03028.4800.0060.0060.0000.0000.0000.000
69A74ALA00.0030.01731.6320.0080.0080.0000.0000.0000.000
70A75GLU-1-0.873-0.92129.721-0.071-0.0710.0000.0000.0000.000
71A76LEU00.0110.02130.7430.0040.0040.0000.0000.0000.000
72A77ASP-1-0.846-0.93032.732-0.068-0.0680.0000.0000.0000.000
73A78LYS10.7680.85934.0540.0760.0760.0000.0000.0000.000
74A79MET00.0350.02031.2520.0070.0070.0000.0000.0000.000
75A80GLN00.0430.02335.4640.0060.0060.0000.0000.0000.000
76A81ASN0-0.130-0.06837.7530.0060.0060.0000.0000.0000.000
77A82ASN0-0.057-0.02638.0320.0070.0070.0000.0000.0000.000
78A83SER0-0.055-0.01238.2870.0040.0040.0000.0000.0000.000
79A84ALA00.0270.02334.079-0.003-0.0030.0000.0000.0000.000
80A85VAL0-0.023-0.03031.288-0.002-0.0020.0000.0000.0000.000
81A86ILE00.0210.01234.186-0.001-0.0010.0000.0000.0000.000
82A87GLY0-0.044-0.01936.0110.0010.0010.0000.0000.0000.000
83A88VAL00.0000.00829.985-0.002-0.0020.0000.0000.0000.000
84A89LYS10.9070.95031.5130.0720.0720.0000.0000.0000.000
85A90THR0-0.050-0.01825.385-0.010-0.0100.0000.0000.0000.000
86A91VAL00.0160.01325.9440.0050.0050.0000.0000.0000.000
87A92GLN0-0.052-0.02320.323-0.003-0.0030.0000.0000.0000.000
88A93LEU00.0080.00120.7550.0170.0170.0000.0000.0000.000
89A94ASP-1-0.828-0.88314.606-0.493-0.4930.0000.0000.0000.000
90A95VAL0-0.012-0.01917.5580.0310.0310.0000.0000.0000.000
91A96GLY00.0450.03013.976-0.054-0.0540.0000.0000.0000.000
92A97CYS00.013-0.01413.1040.0590.0590.0000.0000.0000.000
93A98THR00.0300.0039.056-0.046-0.0460.0000.0000.0000.000
94A99SER0-0.0480.00411.5970.0680.0680.0000.0000.0000.000
95A100LYS10.8920.92913.2420.0160.0160.0000.0000.0000.000
96A101ILE00.008-0.00915.196-0.043-0.0430.0000.0000.0000.000
97A102GLU-1-0.851-0.89814.848-0.085-0.0850.0000.0000.0000.000
98A103LYS10.9270.96517.5200.0870.0870.0000.0000.0000.000
99A104HIS10.8760.94716.1900.1430.1430.0000.0000.0000.000
100A105TYR00.0820.03620.109-0.031-0.0310.0000.0000.0000.000
101A106ALA00.0500.01921.7380.0090.0090.0000.0000.0000.000
102A107TYR00.0000.00423.737-0.014-0.0140.0000.0000.0000.000
103A108ASP-1-0.774-0.90527.103-0.082-0.0820.0000.0000.0000.000
104A109GLY0-0.025-0.01123.1930.0070.0070.0000.0000.0000.000
105A110ASN0-0.068-0.02323.2020.0090.0090.0000.0000.0000.000
106A111GLU-1-0.908-0.95819.346-0.107-0.1070.0000.0000.0000.000
107A112THR0-0.059-0.05623.1980.0090.0090.0000.0000.0000.000
108A113GLU-1-0.944-0.95425.800-0.025-0.0250.0000.0000.0000.000
109A114ASP-1-0.899-0.94021.604-0.065-0.0650.0000.0000.0000.000
110A115ASP-1-0.910-0.93924.521-0.054-0.0540.0000.0000.0000.000
111A116THR0-0.020-0.03923.978-0.006-0.0060.0000.0000.0000.000
112A117ALA0-0.0030.01626.4330.0040.0040.0000.0000.0000.000
113A118THR0-0.067-0.04227.048-0.009-0.0090.0000.0000.0000.000
114A119SER00.003-0.00527.0220.0020.0020.0000.0000.0000.000
115A120ALA0-0.018-0.00325.509-0.008-0.0080.0000.0000.0000.000
116A121SER00.0870.04325.027-0.007-0.0070.0000.0000.0000.000
117A122GLU-1-0.823-0.90023.399-0.055-0.0550.0000.0000.0000.000
118A123ARG10.8560.92922.4440.1590.1590.0000.0000.0000.000
119A124ALA00.031-0.00618.893-0.025-0.0250.0000.0000.0000.000
120A125ARG10.8010.86718.2940.0650.0650.0000.0000.0000.000
121A126ASP-1-0.827-0.90320.019-0.132-0.1320.0000.0000.0000.000
122A128GLN00.0300.01613.643-0.092-0.0920.0000.0000.0000.000
123A129LYS10.8520.91015.0070.1220.1220.0000.0000.0000.000
124A130LYS10.8510.91116.6720.3290.3290.0000.0000.0000.000
125A131LEU00.0130.0209.114-0.051-0.0510.0000.0000.0000.000
126A132THR0-0.063-0.02812.070-0.057-0.0570.0000.0000.0000.000
127A133GLU-1-0.942-0.98513.675-0.282-0.2820.0000.0000.0000.000
128A134TYR0-0.003-0.04512.9360.0000.0000.0000.0000.0000.000
129A135ARG10.8290.8726.2010.8800.8800.0000.0000.0000.000
130A136LYS10.8820.95010.7910.2010.2010.0000.0000.0000.000
131A137LEU00.0110.00513.6720.0140.0140.0000.0000.0000.000
132A138VAL0-0.0090.0088.9040.0190.0190.0000.0000.0000.000
133A139LEU00.0020.0029.2160.0250.0250.0000.0000.0000.000
134A140ALA0-0.0070.00612.1440.0500.0500.0000.0000.0000.000
135A141SER0-0.091-0.05613.5920.0250.0250.0000.0000.0000.000
136A142ALA0-0.028-0.00512.894-0.010-0.0100.0000.0000.0000.000
137A143VAL0-0.039-0.01913.8020.0640.0640.0000.0000.0000.000
138A144SER00.0390.01714.548-0.021-0.0210.0000.0000.0000.000
139A145PRO00.000-0.01014.0550.0060.0060.0000.0000.0000.000
140A146GLN0-0.040-0.00216.3860.0460.0460.0000.0000.0000.000
141A147LEU0-0.021-0.01716.093-0.001-0.0010.0000.0000.0000.000
142A148GLU-1-0.787-0.88420.004-0.034-0.0340.0000.0000.0000.000
143A149VAL0-0.037-0.00121.5380.0050.0050.0000.0000.0000.000
144A150GLU-1-0.896-0.96023.755-0.051-0.0510.0000.0000.0000.000
145A151ARG10.9040.94925.704-0.004-0.0040.0000.0000.0000.000
146A152ARG10.9170.96428.1050.0080.0080.0000.0000.0000.000
147A153SER00.0250.01729.8500.0060.0060.0000.0000.0000.000
148A154SER0-0.017-0.02729.611-0.004-0.0040.0000.0000.0000.000
149A155GLY00.0090.01531.6140.0050.0050.0000.0000.0000.000
150A156ARG10.8980.93833.920-0.027-0.0270.0000.0000.0000.000
151A157GLU-1-0.858-0.93135.9770.0310.0310.0000.0000.0000.000
152A158GLY00.0020.00936.5610.0020.0020.0000.0000.0000.000
153A159GLY0-0.0030.00832.3970.0000.0000.0000.0000.0000.000
154A160MET0-0.038-0.00929.912-0.009-0.0090.0000.0000.0000.000
155A161ARG10.8660.92523.8090.0040.0040.0000.0000.0000.000
156A162LEU00.0020.00624.035-0.010-0.0100.0000.0000.0000.000
157A163ARG10.8110.87520.5240.0340.0340.0000.0000.0000.000
158A164CYS0-0.091-0.02417.4420.0100.0100.0000.0000.0000.000
159A165PHE00.004-0.02117.9620.0000.0000.0000.0000.0000.000
160A166ALA00.0540.03514.3540.0090.0090.0000.0000.0000.000
161A167ARG10.8750.91615.7860.0800.0800.0000.0000.0000.000
162A168ASP-1-0.817-0.90917.554-0.201-0.2010.0000.0000.0000.000
163A169TYR0-0.049-0.0149.4220.0800.0800.0000.0000.0000.000
164A170TYR00.0380.02611.699-0.033-0.0330.0000.0000.0000.000
165A171PRO00.006-0.0087.7550.0990.0990.0000.0000.0000.000
166A172ALA00.0450.0047.4300.0730.0730.0000.0000.0000.000
167A173ASP-1-0.917-0.9582.459-4.306-2.0182.911-2.664-2.535-0.028
168A174LEU0-0.036-0.0125.1630.0140.021-0.001-0.003-0.0020.000
169A175GLU-1-0.831-0.8947.4550.7210.7210.0000.0000.0000.000
170A176ILE00.004-0.0238.661-0.082-0.0820.0000.0000.0000.000
171A177ARG10.8580.89811.919-0.473-0.4730.0000.0000.0000.000
172A178TRP00.0140.00214.569-0.029-0.0290.0000.0000.0000.000
173A179TRP0-0.042-0.02914.3550.0380.0380.0000.0000.0000.000
174A180LYS10.9020.95220.324-0.119-0.1190.0000.0000.0000.000
175A181ASP-1-0.799-0.86624.0610.1100.1100.0000.0000.0000.000
176A182ASP-1-0.845-0.92526.3780.1200.1200.0000.0000.0000.000
177A183GLY0-0.023-0.01028.836-0.006-0.0060.0000.0000.0000.000
178A184GLY0-0.014-0.01230.186-0.007-0.0070.0000.0000.0000.000
179A185GLY0-0.042-0.01227.8260.0020.0020.0000.0000.0000.000
180A186GLY00.0190.02225.4900.0120.0120.0000.0000.0000.000
181A187ALA0-0.043-0.04421.125-0.011-0.0110.0000.0000.0000.000
182A188LEU00.0220.01221.1680.0290.0290.0000.0000.0000.000
183A189PRO00.0090.00617.071-0.016-0.0160.0000.0000.0000.000
184A190GLN0-0.050-0.02218.712-0.028-0.0280.0000.0000.0000.000
185A191THR00.0090.00616.9450.0310.0310.0000.0000.0000.000
186A192SER0-0.0070.00015.641-0.025-0.0250.0000.0000.0000.000
187A193LYS10.9440.96517.418-0.073-0.0730.0000.0000.0000.000
188A194GLN0-0.045-0.03417.698-0.012-0.0120.0000.0000.0000.000
189A195HIS00.0460.0008.9900.0830.0830.0000.0000.0000.000
190A196HIS0-0.0390.00613.853-0.021-0.0210.0000.0000.0000.000
191A197ASP-1-0.845-0.9148.726-0.117-0.1170.0000.0000.0000.000
192A198PRO0-0.028-0.0128.4350.0470.0470.0000.0000.0000.000
193A199LEU0-0.009-0.00811.581-0.025-0.0250.0000.0000.0000.000
194A200PRO00.0150.00614.293-0.004-0.0040.0000.0000.0000.000
195A201SER0-0.004-0.03215.5800.0300.0300.0000.0000.0000.000
196A202GLY0-0.039-0.00618.5540.0260.0260.0000.0000.0000.000
197A203GLN0-0.012-0.02619.204-0.013-0.0130.0000.0000.0000.000
198A204GLY0-0.028-0.00716.9720.0020.0020.0000.0000.0000.000
199A205LEU0-0.072-0.00915.007-0.056-0.0560.0000.0000.0000.000
200A206TYR0-0.054-0.04311.2720.0250.0250.0000.0000.0000.000
201A207GLN00.0130.01214.2000.0440.0440.0000.0000.0000.000
202A208LYS10.9240.9779.3580.0250.0250.0000.0000.0000.000
203A209HIS0-0.011-0.01214.2030.0030.0030.0000.0000.0000.000
204A210ILE00.0060.03513.8910.0130.0130.0000.0000.0000.000
205A211ASP-1-0.818-0.87816.910-0.002-0.0020.0000.0000.0000.000
206A212VAL00.0040.01020.0240.0220.0220.0000.0000.0000.000
207A213TYR0-0.034-0.02722.443-0.019-0.0190.0000.0000.0000.000
208A214VAL0-0.0160.00026.0480.0090.0090.0000.0000.0000.000
209A215ASP-1-0.829-0.92028.5000.0570.0570.0000.0000.0000.000
210A216GLY00.0130.00432.2290.0000.0000.0000.0000.0000.000
211A217GLY0-0.021-0.01334.0240.0020.0020.0000.0000.0000.000
212A218LEU0-0.020-0.00831.0590.0020.0020.0000.0000.0000.000
213A219GLU-1-0.792-0.89828.7030.0350.0350.0000.0000.0000.000
214A220HIS0-0.003-0.01127.7770.0070.0070.0000.0000.0000.000
215A221VAL00.0000.02227.5860.0020.0020.0000.0000.0000.000
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