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: 8NJ4Y

Calculation Name: 1QQG-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1QQG

Chain ID: A

ChEMBL ID:

UniProt ID: P35568

Base Structure: X-ray

Registration Date: 2023-09-26

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 207
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2422733.478123
FMO2-HF: Nuclear repulsion 2339265.795013
FMO2-HF: Total energy -83467.683111
FMO2-MP2: Total energy -83710.000965


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:ASP)


Summations of interaction energy for fragment #1(A:12:ASP)
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.
-249.807-243.18217.916-12.203-12.3360.106
Interaction energy analysis for fragmet #1(A:12:ASP)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : -1 / q_Mulliken : -0.800 / q_NPA : -0.896
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].
3A14ARG10.9200.9662.618-62.323-59.2141.013-1.777-2.3440.006
4A15LYS10.9180.9696.289-26.346-26.3460.0000.0000.0000.000
5A16VAL0-0.028-0.0058.8212.8032.8030.0000.0000.0000.000
6A17GLY00.0590.03410.947-2.117-2.1170.0000.0000.0000.000
7A18TYR0-0.022-0.02014.4080.2390.2390.0000.0000.0000.000
8A19LEU00.0860.07115.709-0.446-0.4460.0000.0000.0000.000
9A20ARG10.9090.93918.623-12.883-12.8830.0000.0000.0000.000
10A21LYS10.8790.94418.234-15.988-15.9880.0000.0000.0000.000
11A22PRO00.0720.03921.607-0.550-0.5500.0000.0000.0000.000
12A23LYS10.9530.98524.596-10.992-10.9920.0000.0000.0000.000
13A24SER0-0.013-0.02024.352-0.278-0.2780.0000.0000.0000.000
14A25MET00.0700.03725.2020.0600.0600.0000.0000.0000.000
15A26HIS0-0.0140.00422.5400.5410.5410.0000.0000.0000.000
16A27LYS10.9510.99220.129-15.075-15.0750.0000.0000.0000.000
17A28ARG10.8320.91816.512-16.343-16.3430.0000.0000.0000.000
18A29PHE00.0300.01210.403-0.562-0.5620.0000.0000.0000.000
19A30PHE00.0550.01611.9770.9500.9500.0000.0000.0000.000
20A31VAL0-0.002-0.0155.7950.0610.0610.0000.0000.0000.000
21A32LEU0-0.0030.0057.5700.1020.1020.0000.0000.0000.000
22A33ARG10.8030.8751.741-107.940-107.94116.484-8.953-7.5300.110
23A34ALA00.0330.0052.959-9.608-8.4350.113-0.455-0.8320.000
24A35ALA0-0.009-0.0092.8755.4007.1330.242-0.861-1.114-0.010
25A36SER0-0.010-0.0033.1441.3981.8020.065-0.125-0.3430.000
26A37GLU-1-0.889-0.9445.13528.11828.172-0.001-0.004-0.0480.000
27A38ALA0-0.035-0.0376.406-1.779-1.7790.0000.0000.0000.000
28A39GLY00.0010.0114.918-1.236-1.2360.0000.0000.0000.000
29A40GLY0-0.0110.0095.9241.3601.3600.0000.0000.0000.000
30A41PRO00.0650.0315.7643.7143.7140.0000.0000.0000.000
31A42ALA00.0380.0286.0005.5265.5260.0000.0000.0000.000
32A43ARG10.8100.8954.136-55.116-54.9630.000-0.028-0.1250.000
33A44LEU00.0230.0317.1653.9693.9690.0000.0000.0000.000
34A45GLU-1-0.759-0.8516.63942.94842.9480.0000.0000.0000.000
35A46TYR0-0.0160.0039.883-0.917-0.9170.0000.0000.0000.000
36A47TYR00.010-0.0207.395-0.937-0.9370.0000.0000.0000.000
37A48GLU-1-0.870-0.91313.79315.08215.0820.0000.0000.0000.000
38A49ASN00.023-0.01516.242-0.258-0.2580.0000.0000.0000.000
39A50GLU-1-0.795-0.88113.36421.89321.8930.0000.0000.0000.000
40A51LYN00.0310.02213.4141.9261.9260.0000.0000.0000.000
41A52LYS10.8730.92914.571-16.669-16.6690.0000.0000.0000.000
42A53TRP00.0410.0306.125-2.532-2.5320.0000.0000.0000.000
43A54ARG10.8420.9089.695-17.856-17.8560.0000.0000.0000.000
44A55HIS00.007-0.02311.4821.7191.7190.0000.0000.0000.000
45A56LYS10.9290.9807.583-34.062-34.0620.0000.0000.0000.000
46A57SER00.0530.03611.696-0.873-0.8730.0000.0000.0000.000
47A58SER0-0.110-0.07113.639-2.065-2.0650.0000.0000.0000.000
48A59ALA00.0650.05312.1682.0752.0750.0000.0000.0000.000
49A60PRO0-0.0190.0019.186-1.862-1.8620.0000.0000.0000.000
50A61LYS10.8410.89412.117-18.372-18.3720.0000.0000.0000.000
51A62ARG10.7790.84413.644-18.622-18.6220.0000.0000.0000.000
52A63SER00.019-0.0038.8811.7111.7110.0000.0000.0000.000
53A64ILE00.0060.00411.413-1.526-1.5260.0000.0000.0000.000
54A65PRO00.0600.03110.5761.8981.8980.0000.0000.0000.000
55A66LEU00.0240.0059.708-1.899-1.8990.0000.0000.0000.000
56A67GLU-1-0.879-0.92912.11421.61621.6160.0000.0000.0000.000
57A68SER0-0.065-0.03714.398-1.556-1.5560.0000.0000.0000.000
58A69CYS0-0.094-0.04815.263-0.966-0.9660.0000.0000.0000.000
59A70PHE00.0170.00317.8240.0460.0460.0000.0000.0000.000
60A71ASN0-0.036-0.03820.504-0.468-0.4680.0000.0000.0000.000
61A72ILE00.0300.01515.8200.4440.4440.0000.0000.0000.000
62A73ASN00.0290.02020.235-0.647-0.6470.0000.0000.0000.000
63A74LYS10.8970.97222.544-12.846-12.8460.0000.0000.0000.000
64A75ARG10.7760.85124.175-12.078-12.0780.0000.0000.0000.000
65A76ALA00.015-0.00826.6160.2440.2440.0000.0000.0000.000
66A77ASP-1-0.803-0.88228.99310.59210.5920.0000.0000.0000.000
67A78SER0-0.078-0.07231.488-0.043-0.0430.0000.0000.0000.000
68A79LYS10.7650.88730.450-10.309-10.3090.0000.0000.0000.000
69A80ASN0-0.056-0.04126.5170.4920.4920.0000.0000.0000.000
70A81LYS11.0321.00428.677-9.744-9.7440.0000.0000.0000.000
71A82HIS00.0070.01724.734-0.284-0.2840.0000.0000.0000.000
72A83LEU0-0.0070.01923.0160.7350.7350.0000.0000.0000.000
73A84VAL00.0220.02518.028-0.263-0.2630.0000.0000.0000.000
74A85ALA0-0.039-0.02420.0230.3780.3780.0000.0000.0000.000
75A86LEU00.0250.01814.4530.0500.0500.0000.0000.0000.000
76A87TYR0-0.009-0.02119.121-0.719-0.7190.0000.0000.0000.000
77A88THR00.0680.03617.580-0.067-0.0670.0000.0000.0000.000
78A89ARG10.8390.90020.477-13.743-13.7430.0000.0000.0000.000
79A90ASP-1-0.786-0.89221.95112.57912.5790.0000.0000.0000.000
80A91GLU-1-0.814-0.85618.80415.79615.7960.0000.0000.0000.000
81A92HIS00.0070.01522.1420.3490.3490.0000.0000.0000.000
82A93PHE0-0.020-0.00915.788-0.049-0.0490.0000.0000.0000.000
83A94ALA00.0260.01719.3490.3960.3960.0000.0000.0000.000
84A95ILE0-0.057-0.02915.8610.1050.1050.0000.0000.0000.000
85A96ALA0-0.009-0.01719.558-0.379-0.3790.0000.0000.0000.000
86A97ALA0-0.004-0.00220.6810.4390.4390.0000.0000.0000.000
87A98ASP-1-0.911-0.94721.92713.28713.2870.0000.0000.0000.000
88A99SER00.001-0.02224.040-0.552-0.5520.0000.0000.0000.000
89A100GLU-1-0.912-0.96924.26211.91611.9160.0000.0000.0000.000
90A101ALA00.0240.02023.3410.3660.3660.0000.0000.0000.000
91A102GLU-1-0.857-0.93118.96317.43617.4360.0000.0000.0000.000
92A103GLN0-0.020-0.03019.2670.7650.7650.0000.0000.0000.000
93A104ASP-1-0.807-0.90120.08115.01715.0170.0000.0000.0000.000
94A105SER00.0140.02116.6431.0811.0810.0000.0000.0000.000
95A106TRP0-0.009-0.02911.2531.8381.8380.0000.0000.0000.000
96A107TYR0-0.032-0.01015.4820.8460.8460.0000.0000.0000.000
97A108GLN00.0190.00116.7150.5300.5300.0000.0000.0000.000
98A109ALA0-0.035-0.00711.4740.6230.6230.0000.0000.0000.000
99A110LEU0-0.033-0.04111.9661.3021.3020.0000.0000.0000.000
100A111LEU00.0230.01413.4340.2750.2750.0000.0000.0000.000
101A112GLN0-0.050-0.01511.7810.9510.9510.0000.0000.0000.000
102A113LEU0-0.066-0.0336.8060.9780.9780.0000.0000.0000.000
103A114HIS0-0.055-0.00210.6580.0720.0720.0000.0000.0000.000
104A159ALA0-0.0020.00224.162-0.064-0.0640.0000.0000.0000.000
105A160PHE0-0.015-0.02825.391-0.569-0.5690.0000.0000.0000.000
106A161LYS10.9150.97426.069-9.547-9.5470.0000.0000.0000.000
107A162GLU-1-0.847-0.90127.23811.44411.4440.0000.0000.0000.000
108A163VAL0-0.011-0.00225.746-0.222-0.2220.0000.0000.0000.000
109A164TRP00.0700.04127.3670.2770.2770.0000.0000.0000.000
110A165GLN00.0350.01626.4560.1360.1360.0000.0000.0000.000
111A166VAL0-0.019-0.01329.385-0.121-0.1210.0000.0000.0000.000
112A167ILE0-0.001-0.00832.9600.0620.0620.0000.0000.0000.000
113A168LEU00.0130.00935.481-0.248-0.2480.0000.0000.0000.000
114A169LYS10.9160.96038.020-8.077-8.0770.0000.0000.0000.000
115A170PRO00.0210.00941.303-0.011-0.0110.0000.0000.0000.000
116A171LYS10.9100.96644.256-7.254-7.2540.0000.0000.0000.000
117A172GLY00.0440.01745.5350.1190.1190.0000.0000.0000.000
118A173LEU0-0.030-0.02344.694-0.055-0.0550.0000.0000.0000.000
119A174GLY00.0180.02642.7360.1090.1090.0000.0000.0000.000
120A175GLN00.0100.00043.6390.1170.1170.0000.0000.0000.000
121A176THR0-0.008-0.00346.1360.0030.0030.0000.0000.0000.000
122A177LYS10.8680.95443.680-6.844-6.8440.0000.0000.0000.000
123A178ASN0-0.017-0.00542.2840.1630.1630.0000.0000.0000.000
124A179LEU0-0.049-0.00938.4930.2140.2140.0000.0000.0000.000
125A180ILE00.003-0.01039.310-0.058-0.0580.0000.0000.0000.000
126A181GLY00.0130.01136.2150.1500.1500.0000.0000.0000.000
127A182ILE0-0.033-0.02429.711-0.020-0.0200.0000.0000.0000.000
128A183TYR00.0280.02031.8710.0920.0920.0000.0000.0000.000
129A184ARG10.8070.89723.991-12.128-12.1280.0000.0000.0000.000
130A185LEU0-0.0030.01630.274-0.169-0.1690.0000.0000.0000.000
131A186CYS0-0.032-0.01829.2330.4080.4080.0000.0000.0000.000
132A187LEU00.0240.01830.612-0.322-0.3220.0000.0000.0000.000
133A188THR00.0240.02430.3960.2230.2230.0000.0000.0000.000
134A189SER00.045-0.00232.234-0.085-0.0850.0000.0000.0000.000
135A190LYS11.0011.00134.148-9.030-9.0300.0000.0000.0000.000
136A191THR0-0.048-0.03034.665-0.223-0.2230.0000.0000.0000.000
137A192ILE00.0390.02334.8140.2430.2430.0000.0000.0000.000
138A193SER0-0.049-0.00832.456-0.157-0.1570.0000.0000.0000.000
139A194PHE00.0520.02333.2170.2320.2320.0000.0000.0000.000
140A195VAL00.0490.02628.603-0.181-0.1810.0000.0000.0000.000
141A196LYS10.9310.96930.845-9.623-9.6230.0000.0000.0000.000
142A197LEU0-0.008-0.01026.0280.2500.2500.0000.0000.0000.000
143A198ASN0-0.062-0.05625.864-0.758-0.7580.0000.0000.0000.000
144A199SER0-0.050-0.01327.374-0.105-0.1050.0000.0000.0000.000
145A200GLU-1-0.812-0.90325.21112.67612.6760.0000.0000.0000.000
146A201ALA0-0.0090.00728.0210.0350.0350.0000.0000.0000.000
147A202ALA0-0.028-0.02531.2680.0050.0050.0000.0000.0000.000
148A203ALA0-0.0330.00033.335-0.191-0.1910.0000.0000.0000.000
149A204VAL00.006-0.00736.548-0.214-0.2140.0000.0000.0000.000
150A205VAL00.002-0.00935.4300.2640.2640.0000.0000.0000.000
151A206LEU00.0050.00737.871-0.258-0.2580.0000.0000.0000.000
152A207GLN00.0410.01238.7740.2780.2780.0000.0000.0000.000
153A208LEU00.0440.01037.200-0.137-0.1370.0000.0000.0000.000
154A209MET00.0140.00741.076-0.139-0.1390.0000.0000.0000.000
155A210ASN0-0.046-0.01743.982-0.101-0.1010.0000.0000.0000.000
156A211ILE00.0120.01040.332-0.107-0.1070.0000.0000.0000.000
157A212ARG10.8290.91044.992-6.275-6.2750.0000.0000.0000.000
158A213ARG10.9140.94946.391-6.569-6.5690.0000.0000.0000.000
159A214CYS0-0.0420.00041.1410.0320.0320.0000.0000.0000.000
160A215GLY00.0390.01343.280-0.118-0.1180.0000.0000.0000.000
161A216HIS0-0.045-0.03240.9580.1510.1510.0000.0000.0000.000
162A217SER0-0.001-0.01442.888-0.217-0.2170.0000.0000.0000.000
163A218GLU-1-0.859-0.90642.9197.1807.1800.0000.0000.0000.000
164A219ASN0-0.066-0.02637.475-0.065-0.0650.0000.0000.0000.000
165A220PHE0-0.047-0.03538.6710.2170.2170.0000.0000.0000.000
166A221PHE00.0860.01937.574-0.030-0.0300.0000.0000.0000.000
167A222PHE0-0.0080.00440.3870.0230.0230.0000.0000.0000.000
168A223ILE00.0330.00738.5470.0530.0530.0000.0000.0000.000
169A224GLU-1-0.784-0.86043.0506.3596.3590.0000.0000.0000.000
170A225VAL00.0110.00043.6140.0300.0300.0000.0000.0000.000
171A226GLY00.029-0.00446.546-0.170-0.1700.0000.0000.0000.000
172A227ARG10.9570.95149.175-5.633-5.6330.0000.0000.0000.000
173A228SER0-0.023-0.00847.826-0.024-0.0240.0000.0000.0000.000
174A229ALA0-0.0130.01445.4830.1090.1090.0000.0000.0000.000
175A230VAL00.0590.03442.110-0.119-0.1190.0000.0000.0000.000
176A231THR0-0.038-0.01543.3100.0070.0070.0000.0000.0000.000
177A232GLY00.0100.00246.190-0.093-0.0930.0000.0000.0000.000
178A233PRO0-0.023-0.01748.2680.1100.1100.0000.0000.0000.000
179A234GLY00.0390.01448.928-0.043-0.0430.0000.0000.0000.000
180A235GLU-1-0.875-0.93045.8866.7546.7540.0000.0000.0000.000
181A236PHE00.0200.01440.820-0.019-0.0190.0000.0000.0000.000
182A237TRP00.038-0.01042.3710.1530.1530.0000.0000.0000.000
183A238MET0-0.049-0.00836.6350.1940.1940.0000.0000.0000.000
184A239GLN0-0.013-0.00337.506-0.221-0.2210.0000.0000.0000.000
185A240VAL00.0100.00433.6230.2700.2700.0000.0000.0000.000
186A241ASP-1-0.924-0.96330.22810.31710.3170.0000.0000.0000.000
187A242ASP-1-0.728-0.86233.5849.3849.3840.0000.0000.0000.000
188A243SER00.0530.00536.1220.1210.1210.0000.0000.0000.000
189A244VAL0-0.0100.01234.029-0.076-0.0760.0000.0000.0000.000
190A245VAL00.0210.00331.4750.0670.0670.0000.0000.0000.000
191A246ALA0-0.011-0.00234.1370.0280.0280.0000.0000.0000.000
192A247GLN0-0.045-0.02637.293-0.121-0.1210.0000.0000.0000.000
193A248ASN00.0280.01632.3810.1840.1840.0000.0000.0000.000
194A249MET0-0.0390.01133.6080.0920.0920.0000.0000.0000.000
195A250HIS00.0060.00835.645-0.035-0.0350.0000.0000.0000.000
196A251GLU-1-0.855-0.91737.5168.3998.3990.0000.0000.0000.000
197A252THR0-0.018-0.02832.4590.0000.0000.0000.0000.0000.000
198A253ILE0-0.023-0.02235.458-0.011-0.0110.0000.0000.0000.000
199A254LEU0-0.015-0.00437.502-0.141-0.1410.0000.0000.0000.000
200A255GLU-1-0.834-0.91737.7127.6347.6340.0000.0000.0000.000
201A256ALA0-0.031-0.01036.359-0.001-0.0010.0000.0000.0000.000
202A257MET0-0.074-0.04438.230-0.057-0.0570.0000.0000.0000.000
203A258ARG10.9010.93041.737-7.484-7.4840.0000.0000.0000.000
204A259ALA00.0350.02938.948-0.100-0.1000.0000.0000.0000.000
205A260MET0-0.078-0.03140.5270.0360.0360.0000.0000.0000.000
206A261SER0-0.102-0.03742.199-0.133-0.1330.0000.0000.0000.000
207A262ASP-1-0.973-0.98041.6397.2707.2700.0000.0000.0000.000