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: 5NNGZ

Calculation Name: 4Q25-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 4Q25

Chain ID: A

ChEMBL ID:

UniProt ID: Q51547

Base Structure: X-ray

Registration Date: 2023-09-27

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 211
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2450692.617084
FMO2-HF: Nuclear repulsion 2366762.474076
FMO2-HF: Total energy -83930.143008
FMO2-MP2: Total energy -84174.444742


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:12:SER)


Summations of interaction energy for fragment #1(A:12: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.
-5.3281.9412.444-4.753-4.9610.013
Interaction energy analysis for fragmet #1(A:12:SER)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.076 / q_NPA : 0.034
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].
3A14GLN00.005-0.0243.350-4.0701.3440.043-2.907-2.5500.017
4A15PHE0-0.001-0.0092.265-0.8690.4642.385-1.642-2.077-0.003
5A16ASN00.018-0.0263.7310.1850.7070.016-0.204-0.334-0.001
6A17ALA00.0090.0356.1480.2160.2160.0000.0000.0000.000
7A18GLU-1-0.850-0.9366.604-0.620-0.6200.0000.0000.0000.000
8A19LEU0-0.009-0.0087.8720.1420.1420.0000.0000.0000.000
9A20GLU-1-0.902-0.9529.6160.0290.0290.0000.0000.0000.000
10A21ASP-1-0.944-0.97411.818-0.349-0.3490.0000.0000.0000.000
11A22VAL00.0290.02212.1820.0480.0480.0000.0000.0000.000
12A23ARG10.8350.93013.7780.0470.0470.0000.0000.0000.000
13A24SER0-0.062-0.03115.8160.0240.0240.0000.0000.0000.000
14A25HIS0-0.030-0.02516.0610.0090.0090.0000.0000.0000.000
15A26LEU00.0450.03018.5110.0110.0110.0000.0000.0000.000
16A27LEU0-0.042-0.01419.5110.0070.0070.0000.0000.0000.000
17A28ALA00.0000.00021.7260.0060.0060.0000.0000.0000.000
18A29MET0-0.041-0.01623.0370.0040.0040.0000.0000.0000.000
19A30GLY00.018-0.00624.4320.0050.0050.0000.0000.0000.000
20A31GLY00.0290.01426.1380.0040.0040.0000.0000.0000.000
21A32LEU0-0.051-0.03227.7450.0020.0020.0000.0000.0000.000
22A33VAL00.0530.01729.0210.0030.0030.0000.0000.0000.000
23A34GLU-1-0.905-0.96030.042-0.006-0.0060.0000.0000.0000.000
24A35LYS10.8410.90432.2000.0320.0320.0000.0000.0000.000
25A36GLN0-0.004-0.01333.6380.0020.0020.0000.0000.0000.000
26A37VAL0-0.008-0.00134.4140.0020.0020.0000.0000.0000.000
27A38ASN0-0.033-0.01436.4900.0030.0030.0000.0000.0000.000
28A39ASP-1-0.836-0.91238.019-0.021-0.0210.0000.0000.0000.000
29A40ALA0-0.0010.01039.4470.0010.0010.0000.0000.0000.000
30A41VAL0-0.011-0.01240.6870.0010.0010.0000.0000.0000.000
31A42ASN00.001-0.00842.2360.0030.0030.0000.0000.0000.000
32A43ALA00.0260.02843.8680.0000.0000.0000.0000.0000.000
33A44LEU0-0.024-0.02245.4740.0010.0010.0000.0000.0000.000
34A45ILE0-0.120-0.06446.8480.0010.0010.0000.0000.0000.000
35A46ASP-1-0.926-0.95847.908-0.009-0.0090.0000.0000.0000.000
36A47ALA0-0.050-0.01950.093-0.001-0.0010.0000.0000.0000.000
37A48ASP-1-0.856-0.91547.426-0.017-0.0170.0000.0000.0000.000
38A49SER00.040-0.01947.2560.0000.0000.0000.0000.0000.000
39A50GLY0-0.038-0.00846.891-0.001-0.0010.0000.0000.0000.000
40A51LEU0-0.027-0.01341.521-0.002-0.0020.0000.0000.0000.000
41A52ALA00.013-0.00942.462-0.001-0.0010.0000.0000.0000.000
42A53GLN0-0.041-0.03942.4220.0020.0020.0000.0000.0000.000
43A54GLN0-0.029-0.01339.106-0.003-0.0030.0000.0000.0000.000
44A55VAL00.0230.01837.678-0.002-0.0020.0000.0000.0000.000
45A56ARG10.9160.95937.4120.0140.0140.0000.0000.0000.000
46A57GLU-1-0.908-0.94537.654-0.028-0.0280.0000.0000.0000.000
47A58ILE0-0.036-0.00532.654-0.003-0.0030.0000.0000.0000.000
48A59ASP-1-0.867-0.94832.787-0.019-0.0190.0000.0000.0000.000
49A60ASP-1-0.899-0.94232.405-0.029-0.0290.0000.0000.0000.000
50A61GLN0-0.058-0.03328.2250.0000.0000.0000.0000.0000.000
51A62ILE00.0100.00428.160-0.006-0.0060.0000.0000.0000.000
52A63ASN00.004-0.01527.423-0.001-0.0010.0000.0000.0000.000
53A64GLN0-0.060-0.02825.0930.0060.0060.0000.0000.0000.000
54A65MET0-0.066-0.03223.811-0.006-0.0060.0000.0000.0000.000
55A66GLU-1-0.918-0.95622.643-0.015-0.0150.0000.0000.0000.000
56A67ARG10.9730.98722.4630.0330.0330.0000.0000.0000.000
57A68ASN0-0.051-0.02920.6690.0000.0000.0000.0000.0000.000
58A69ILE00.0230.02117.764-0.015-0.0150.0000.0000.0000.000
59A70ASP-1-0.868-0.92917.4700.0070.0070.0000.0000.0000.000
60A71GLU-1-0.941-0.98517.810-0.027-0.0270.0000.0000.0000.000
61A72GLU-1-0.914-0.95413.490-0.200-0.2000.0000.0000.0000.000
62A73CYS0-0.023-0.02113.124-0.006-0.0060.0000.0000.0000.000
63A74VAL00.0020.01013.5260.0480.0480.0000.0000.0000.000
64A75ARG10.9050.94412.6100.2250.2250.0000.0000.0000.000
65A76ILE0-0.0150.0008.0180.0540.0540.0000.0000.0000.000
66A77LEU0-0.021-0.0168.7770.1310.1310.0000.0000.0000.000
67A78ALA0-0.0250.01110.8860.0900.0900.0000.0000.0000.000
68A79ARG10.8140.9157.0580.4100.4100.0000.0000.0000.000
69A80ARG10.9130.9605.303-1.009-1.0090.0000.0000.0000.000
70A81GLN00.0010.0018.425-0.024-0.0240.0000.0000.0000.000
71A82PRO00.0550.0437.3350.2330.2330.0000.0000.0000.000
72A83ALA00.0250.0057.648-0.049-0.0490.0000.0000.0000.000
73A84ALA00.035-0.0059.180-0.082-0.0820.0000.0000.0000.000
74A85SER00.005-0.01410.709-0.030-0.0300.0000.0000.0000.000
75A86ASP-1-0.851-0.9176.7820.4770.4770.0000.0000.0000.000
76A87LEU0-0.044-0.01210.325-0.064-0.0640.0000.0000.0000.000
77A88ARG10.8200.91912.841-0.296-0.2960.0000.0000.0000.000
78A89LEU00.0380.02211.295-0.030-0.0300.0000.0000.0000.000
79A90ILE00.0610.02810.845-0.032-0.0320.0000.0000.0000.000
80A91ILE0-0.048-0.02714.340-0.024-0.0240.0000.0000.0000.000
81A92SER0-0.014-0.01317.347-0.017-0.0170.0000.0000.0000.000
82A93ILE00.0030.00614.594-0.011-0.0110.0000.0000.0000.000
83A94SER00.0000.00318.130-0.009-0.0090.0000.0000.0000.000
84A95LYS10.9400.96219.778-0.098-0.0980.0000.0000.0000.000
85A96SER00.0080.01221.081-0.009-0.0090.0000.0000.0000.000
86A97VAL00.0620.02120.992-0.006-0.0060.0000.0000.0000.000
87A98ILE00.0130.02223.756-0.003-0.0030.0000.0000.0000.000
88A99ASP-1-0.852-0.92426.4420.0330.0330.0000.0000.0000.000
89A100LEU0-0.003-0.00924.159-0.003-0.0030.0000.0000.0000.000
90A101GLU-1-0.794-0.87227.704-0.006-0.0060.0000.0000.0000.000
91A102ARG10.8310.90829.377-0.011-0.0110.0000.0000.0000.000
92A103ILE0-0.015-0.00529.8370.0000.0000.0000.0000.0000.000
93A104GLY00.0410.02831.817-0.001-0.0010.0000.0000.0000.000
94A105ASP-1-0.816-0.90933.269-0.002-0.0020.0000.0000.0000.000
95A106GLU-1-0.933-0.98135.5140.0080.0080.0000.0000.0000.000
96A107ALA00.0060.00736.2010.0000.0000.0000.0000.0000.000
97A108SER00.0320.02037.533-0.001-0.0010.0000.0000.0000.000
98A109LYS10.8070.89438.989-0.002-0.0020.0000.0000.0000.000
99A110VAL0-0.0110.00441.1710.0000.0000.0000.0000.0000.000
100A111ALA00.0440.02841.7460.0000.0000.0000.0000.0000.000
101A112ARG10.8910.94143.1680.0040.0040.0000.0000.0000.000
102A113ARG10.8570.95045.4660.0000.0000.0000.0000.0000.000
103A114ALA00.0400.02346.2550.0000.0000.0000.0000.0000.000
104A115ILE00.0010.00946.0720.0000.0000.0000.0000.0000.000
105A116GLN0-0.0260.00349.5320.0000.0000.0000.0000.0000.000
106A117LEU00.003-0.01450.4040.0000.0000.0000.0000.0000.000
107A118CYS0-0.066-0.00551.3060.0000.0000.0000.0000.0000.000
108A119GLU-1-1.004-0.98953.178-0.008-0.0080.0000.0000.0000.000
109A120GLU-1-0.886-0.95755.639-0.001-0.0010.0000.0000.0000.000
110A121GLY0-0.037-0.00156.9980.0010.0010.0000.0000.0000.000
111A122GLU-1-0.915-0.96455.825-0.003-0.0030.0000.0000.0000.000
112A123SER0-0.034-0.05454.8920.0010.0010.0000.0000.0000.000
113A124PRO0-0.022-0.00556.7320.0000.0000.0000.0000.0000.000
114A125ARG10.9270.95256.316-0.005-0.0050.0000.0000.0000.000
115A126GLY00.0660.05252.7340.0000.0000.0000.0000.0000.000
116A127TYR00.0910.06250.7680.0010.0010.0000.0000.0000.000
117A128VAL0-0.026-0.00549.6850.0000.0000.0000.0000.0000.000
118A129GLU-1-0.857-0.94948.8650.0070.0070.0000.0000.0000.000
119A130VAL00.0090.00745.5060.0010.0010.0000.0000.0000.000
120A131ARG10.9200.96243.8070.0040.0040.0000.0000.0000.000
121A132HIS0-0.064-0.04444.264-0.001-0.0010.0000.0000.0000.000
122A133ILE00.0060.00142.1060.0010.0010.0000.0000.0000.000
123A134GLY00.0380.01540.8400.0010.0010.0000.0000.0000.000
124A135SER0-0.054-0.02739.4320.0000.0000.0000.0000.0000.000
125A136GLN0-0.037-0.04338.6190.0010.0010.0000.0000.0000.000
126A137VAL00.0200.00736.3520.0020.0020.0000.0000.0000.000
127A138GLN00.0330.02634.9600.0010.0010.0000.0000.0000.000
128A139LYS10.9220.97033.770-0.014-0.0140.0000.0000.0000.000
129A140MET0-0.039-0.01632.7140.0010.0010.0000.0000.0000.000
130A141VAL00.0180.01729.6260.0030.0030.0000.0000.0000.000
131A142GLN0-0.006-0.00128.9250.0000.0000.0000.0000.0000.000
132A143GLU-1-0.939-0.96728.1940.0250.0250.0000.0000.0000.000
133A144ALA00.0160.01326.9600.0050.0050.0000.0000.0000.000
134A145LEU0-0.0200.00424.3280.0050.0050.0000.0000.0000.000
135A146ASP-1-0.876-0.95423.4310.0210.0210.0000.0000.0000.000
136A147ALA0-0.037-0.02123.5710.0050.0050.0000.0000.0000.000
137A148PHE00.000-0.01917.2120.0130.0130.0000.0000.0000.000
138A149ALA0-0.031-0.02119.1540.0060.0060.0000.0000.0000.000
139A150ARG10.7810.88819.231-0.044-0.0440.0000.0000.0000.000
140A151PHE0-0.034-0.01114.2510.0180.0180.0000.0000.0000.000
141A152ASP-1-0.785-0.87219.5990.0760.0760.0000.0000.0000.000
142A153ALA0-0.017-0.04023.131-0.007-0.0070.0000.0000.0000.000
143A154ASP-1-0.939-0.96124.6780.0820.0820.0000.0000.0000.000
144A155LEU00.0060.01027.053-0.004-0.0040.0000.0000.0000.000
145A156ALA00.0250.04125.460-0.004-0.0040.0000.0000.0000.000
146A157LEU0-0.031-0.00727.615-0.002-0.0020.0000.0000.0000.000
147A158SER0-0.056-0.05530.048-0.004-0.0040.0000.0000.0000.000
148A159VAL00.0560.02429.830-0.003-0.0030.0000.0000.0000.000
149A160ALA00.013-0.00530.576-0.003-0.0030.0000.0000.0000.000
150A161GLN0-0.088-0.05332.512-0.003-0.0030.0000.0000.0000.000
151A162TYR0-0.053-0.03935.324-0.002-0.0020.0000.0000.0000.000
152A163ASP-1-0.743-0.88135.2650.0280.0280.0000.0000.0000.000
153A164LYS10.9190.97337.297-0.040-0.0400.0000.0000.0000.000
154A165THR0-0.116-0.06240.156-0.002-0.0020.0000.0000.0000.000
155A166VAL00.1020.05939.035-0.002-0.0020.0000.0000.0000.000
156A167ASP-1-0.800-0.90039.8250.0250.0250.0000.0000.0000.000
157A168ARG10.7750.88342.631-0.023-0.0230.0000.0000.0000.000
158A169GLU-1-0.787-0.87543.9810.0140.0140.0000.0000.0000.000
159A170TYR00.0500.03944.404-0.001-0.0010.0000.0000.0000.000
160A171LYS10.9200.95445.714-0.025-0.0250.0000.0000.0000.000
161A172THR0-0.050-0.03448.8040.0000.0000.0000.0000.0000.000
162A173ALA00.0560.03749.244-0.001-0.0010.0000.0000.0000.000
163A174LEU00.0140.01449.772-0.001-0.0010.0000.0000.0000.000
164A175ARG10.8690.94051.778-0.017-0.0170.0000.0000.0000.000
165A176GLU-1-0.888-0.93654.5210.0080.0080.0000.0000.0000.000
166A177LEU00.0130.00051.763-0.001-0.0010.0000.0000.0000.000
167A178VAL00.001-0.01054.537-0.001-0.0010.0000.0000.0000.000
168A179THR0-0.064-0.04357.092-0.001-0.0010.0000.0000.0000.000
169A180TYR00.0290.01258.862-0.001-0.0010.0000.0000.0000.000
170A181MET0-0.027-0.00755.855-0.001-0.0010.0000.0000.0000.000
171A182MET0-0.111-0.05760.5240.0000.0000.0000.0000.0000.000
172A183GLU-1-0.958-0.95963.3720.0050.0050.0000.0000.0000.000
173A184ASP-1-0.892-0.95163.3240.0020.0020.0000.0000.0000.000
174A185PRO00.0290.00163.0050.0000.0000.0000.0000.0000.000
175A186ARG10.9190.95462.940-0.002-0.0020.0000.0000.0000.000
176A187ALA00.0120.01060.051-0.001-0.0010.0000.0000.0000.000
177A188ILE0-0.0040.01257.9490.0000.0000.0000.0000.0000.000
178A189SER0-0.011-0.00456.5530.0000.0000.0000.0000.0000.000
179A190ARG10.8930.95654.9970.0000.0000.0000.0000.0000.000
180A191VAL00.014-0.00654.0980.0000.0000.0000.0000.0000.000
181A192LEU0-0.014-0.01752.7870.0010.0010.0000.0000.0000.000
182A193ASN0-0.013-0.01650.3420.0000.0000.0000.0000.0000.000
183A194ILE00.0500.03149.0060.0000.0000.0000.0000.0000.000
184A195ILE0-0.029-0.00948.4590.0010.0010.0000.0000.0000.000
185A196TRP0-0.053-0.04046.4960.0020.0020.0000.0000.0000.000
186A197ALA00.0320.02144.5980.0000.0000.0000.0000.0000.000
187A198LEU00.002-0.00143.6370.0010.0010.0000.0000.0000.000
188A199ARG10.8810.95541.214-0.017-0.0170.0000.0000.0000.000
189A200SER0-0.006-0.02140.3550.0010.0010.0000.0000.0000.000
190A201LEU0-0.026-0.01439.1150.0000.0000.0000.0000.0000.000
191A202GLU-1-0.858-0.94138.8690.0210.0210.0000.0000.0000.000
192A203ARG10.8130.92035.458-0.021-0.0210.0000.0000.0000.000
193A204ILE00.0000.00934.3640.0020.0020.0000.0000.0000.000
194A205GLY0-0.0050.01433.9220.0010.0010.0000.0000.0000.000
195A206ASP-1-0.771-0.90534.1680.0290.0290.0000.0000.0000.000
196A207HIS0-0.109-0.08230.7270.0030.0030.0000.0000.0000.000
197A208ALA00.0040.01229.6200.0020.0020.0000.0000.0000.000
198A209ARG10.8620.94829.266-0.035-0.0350.0000.0000.0000.000
199A210ASN0-0.023-0.00828.5070.0080.0080.0000.0000.0000.000
200A211ILE00.0290.00924.0360.0080.0080.0000.0000.0000.000
201A212ALA0-0.0060.00924.5750.0060.0060.0000.0000.0000.000
202A213GLU-1-0.929-0.98225.4440.0690.0690.0000.0000.0000.000
203A214LEU0-0.051-0.02221.9270.0140.0140.0000.0000.0000.000
204A215VAL00.0400.03020.9620.0160.0160.0000.0000.0000.000
205A216ILE0-0.0030.00321.3640.0150.0150.0000.0000.0000.000
206A217TYR0-0.058-0.03218.7480.0200.0200.0000.0000.0000.000
207A218LEU0-0.0090.00515.6400.0240.0240.0000.0000.0000.000
208A219VAL00.0010.00717.4890.0330.0330.0000.0000.0000.000
209A220ARG10.9220.95519.281-0.092-0.0920.0000.0000.0000.000
210A221GLY0-0.040-0.00218.9760.0100.0100.0000.0000.0000.000
211A222THR0-0.031-0.01919.933-0.003-0.0030.0000.0000.0000.000