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: 1N2LZ

Calculation Name: 2PJQ-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2PJQ

Chain ID: A

ChEMBL ID:

UniProt ID: F9URF4

Base Structure: X-ray

Registration Date: 2023-09-20

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 206
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2343609.664899
FMO2-HF: Nuclear repulsion 2263043.66874
FMO2-HF: Total energy -80565.996159
FMO2-MP2: Total energy -80803.163335


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:1:MET)


Summations of interaction energy for fragment #1(A:1: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.
-29.261-29.26818.625-8.704-9.911-0.061
Interaction energy analysis for fragmet #1(A:1:MET)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.041 / q_NPA : -0.026
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].
3A3THR00.018-0.0163.8581.0762.989-0.015-0.926-0.9700.005
4A4GLU-1-0.799-0.9056.6020.3080.3080.0000.0000.0000.000
5A5THR00.000-0.0049.3820.1770.1770.0000.0000.0000.000
6A6GLN00.0560.0556.478-0.481-0.4810.0000.0000.0000.000
7A7LEU00.0170.0389.3740.2380.2380.0000.0000.0000.000
8A8THR0-0.017-0.01410.7820.1110.1110.0000.0000.0000.000
9A9ALA0-0.0010.01113.0510.1180.1180.0000.0000.0000.000
10A10ILE0-0.019-0.0209.6310.1080.1080.0000.0000.0000.000
11A11GLN0-0.077-0.04713.6890.1350.1350.0000.0000.0000.000
12A12THR00.0030.00416.1390.0680.0680.0000.0000.0000.000
13A13TYR00.0250.02016.7330.0640.0640.0000.0000.0000.000
14A14ALA00.0740.03617.4260.0480.0480.0000.0000.0000.000
15A15LEU00.0010.00019.2800.0480.0480.0000.0000.0000.000
16A16GLN0-0.090-0.05921.6650.0720.0720.0000.0000.0000.000
17A17LYS10.8280.90521.1330.3590.3590.0000.0000.0000.000
18A18LEU00.0250.01921.2770.0130.0130.0000.0000.0000.000
19A19ALA0-0.081-0.01924.8060.0280.0280.0000.0000.0000.000
20A20HIS0-0.023-0.02927.5230.0020.0020.0000.0000.0000.000
21A21ASP-1-0.786-0.87427.872-0.079-0.0790.0000.0000.0000.000
22A22HIS0-0.037-0.01829.9190.0100.0100.0000.0000.0000.000
23A23SER00.0480.01430.0870.0090.0090.0000.0000.0000.000
24A24GLY00.0400.02230.5130.0090.0090.0000.0000.0000.000
25A25HIS0-0.111-0.05725.4780.0340.0340.0000.0000.0000.000
26A26GLY00.1210.06425.873-0.021-0.0210.0000.0000.0000.000
27A27ARG10.8780.91924.1280.2050.2050.0000.0000.0000.000
28A28ASP-1-0.892-0.94923.989-0.034-0.0340.0000.0000.0000.000
29A29HIS10.7620.89022.5680.0090.0090.0000.0000.0000.000
30A30LEU00.0550.03619.1600.0310.0310.0000.0000.0000.000
31A31GLN0-0.006-0.00720.1550.0190.0190.0000.0000.0000.000
32A32ARG10.8040.88021.307-0.003-0.0030.0000.0000.0000.000
33A33VAL00.0660.03118.0830.0470.0470.0000.0000.0000.000
34A34ASN00.0080.00616.2420.0760.0760.0000.0000.0000.000
35A35ARG10.9270.96317.300-0.053-0.0530.0000.0000.0000.000
36A36LEU0-0.0040.00119.4520.0500.0500.0000.0000.0000.000
37A37ALA00.0720.03615.0230.0650.0650.0000.0000.0000.000
38A38ARG10.8590.92412.847-0.076-0.0760.0000.0000.0000.000
39A39ARG10.7740.88215.725-0.366-0.3660.0000.0000.0000.000
40A40LEU00.0310.00717.2490.0460.0460.0000.0000.0000.000
41A41ALA00.0100.00112.1730.0630.0630.0000.0000.0000.000
42A42LYS10.8830.93813.180-0.350-0.3500.0000.0000.0000.000
43A43ASP-1-0.807-0.88315.0490.5960.5960.0000.0000.0000.000
44A44GLU-1-0.889-0.95414.1160.8680.8680.0000.0000.0000.000
45A45GLY0-0.0410.00412.3940.0750.0750.0000.0000.0000.000
46A46ALA00.0080.0099.2180.4270.4270.0000.0000.0000.000
47A47ASN00.0400.0132.616-5.823-8.8486.888-1.431-2.4320.012
48A48LEU00.0330.0156.645-0.746-0.7460.0000.0000.0000.000
49A49ASN00.015-0.0235.159-0.950-0.9500.0000.0000.0000.000
50A50LEU00.0330.0213.204-1.456-0.9430.043-0.094-0.4620.000
51A51THR0-0.006-0.0096.470-0.646-0.6460.0000.0000.0000.000
52A52LEU0-0.038-0.03210.127-0.305-0.3050.0000.0000.0000.000
53A53ALA0-0.0150.0138.383-0.162-0.1620.0000.0000.0000.000
54A54ALA00.0290.00410.218-0.080-0.0800.0000.0000.0000.000
55A55ALA0-0.040-0.03411.970-0.040-0.0400.0000.0000.0000.000
56A56TRP0-0.064-0.03213.105-0.011-0.0110.0000.0000.0000.000
57A57LEU00.057-0.00212.100-0.001-0.0010.0000.0000.0000.000
58A58HIS10.8060.90315.9100.0490.0490.0000.0000.0000.000
59A59ASP-1-0.822-0.91617.636-0.034-0.0340.0000.0000.0000.000
60A60VAL0-0.062-0.02318.488-0.007-0.0070.0000.0000.0000.000
61A61ILE0-0.056-0.03218.606-0.017-0.0170.0000.0000.0000.000
62A62ASP-1-0.854-0.90221.629-0.055-0.0550.0000.0000.0000.000
63A72ALA00.0270.02121.8300.0080.0080.0000.0000.0000.000
64A73HIS0-0.031-0.03918.248-0.043-0.0430.0000.0000.0000.000
65A74GLN0-0.017-0.01218.835-0.054-0.0540.0000.0000.0000.000
66A75ASP-1-0.830-0.91019.457-0.442-0.4420.0000.0000.0000.000
67A76LEU00.0350.02214.218-0.066-0.0660.0000.0000.0000.000
68A77ILE00.0290.02714.533-0.142-0.1420.0000.0000.0000.000
69A78VAL00.0140.00614.617-0.135-0.1350.0000.0000.0000.000
70A79GLN0-0.032-0.00514.914-0.114-0.1140.0000.0000.0000.000
71A80LEU00.012-0.01710.224-0.090-0.0900.0000.0000.0000.000
72A81ASN00.0310.00610.849-0.348-0.3480.0000.0000.0000.000
73A82ALA0-0.0570.00112.346-0.132-0.1320.0000.0000.0000.000
74A83GLN0-0.055-0.05111.1600.0350.0350.0000.0000.0000.000
75A84ASN0-0.0050.0009.066-0.268-0.2680.0000.0000.0000.000
76A85VAL0-0.0270.0086.689-0.761-0.7610.0000.0000.0000.000
77A86THR00.0400.0002.919-0.2070.1750.047-0.121-0.3080.000
78A87ALA00.0780.0536.3540.0180.0180.0000.0000.0000.000
79A88ASP-1-0.867-0.9105.104-1.172-1.1720.0000.0000.0000.000
80A89ASP-1-0.752-0.8901.864-23.565-23.40711.663-6.128-5.692-0.078
81A90GLN0-0.048-0.0344.9941.0631.115-0.001-0.004-0.0470.000
82A91THR0-0.039-0.0428.4010.5230.5230.0000.0000.0000.000
83A92ALA0-0.036-0.0194.9610.4200.4200.0000.0000.0000.000
84A93ILE0-0.023-0.0196.8980.4940.4940.0000.0000.0000.000
85A94PHE0-0.016-0.0259.2630.2350.2350.0000.0000.0000.000
86A95ALA00.0020.0179.6080.1270.1270.0000.0000.0000.000
87A96ILE0-0.0100.0138.6120.1180.1180.0000.0000.0000.000
88A97ILE0-0.024-0.01012.3940.0130.0130.0000.0000.0000.000
89A98ASP-1-0.803-0.87714.586-0.213-0.2130.0000.0000.0000.000
90A99HIS0-0.097-0.04614.5450.0120.0120.0000.0000.0000.000
91A100MET00.0480.03516.1160.0520.0520.0000.0000.0000.000
92A101SER00.0060.01418.0800.0130.0130.0000.0000.0000.000
93A102PHE00.0800.02521.6230.0150.0150.0000.0000.0000.000
94A103SER00.0050.00824.6910.0000.0000.0000.0000.0000.000
95A104LYS10.8060.89819.4890.0780.0780.0000.0000.0000.000
96A105SER00.0330.03423.9090.0070.0070.0000.0000.0000.000
97A106PHE00.018-0.00325.0150.0060.0060.0000.0000.0000.000
98A107ASN0-0.118-0.05824.954-0.008-0.0080.0000.0000.0000.000
99A108GLY00.0450.03425.972-0.001-0.0010.0000.0000.0000.000
100A109PRO0-0.029-0.02222.611-0.002-0.0020.0000.0000.0000.000
101A110GLN00.0100.00218.2340.0020.0020.0000.0000.0000.000
102A111LYS10.9340.96015.670-0.419-0.4190.0000.0000.0000.000
103A112LEU0-0.020-0.00913.247-0.033-0.0330.0000.0000.0000.000
104A113SER0-0.0040.0058.259-0.044-0.0440.0000.0000.0000.000
105A114LEU00.0610.0449.451-0.128-0.1280.0000.0000.0000.000
106A115GLU-1-0.810-0.9216.5452.9742.9740.0000.0000.0000.000
107A116GLY00.023-0.01910.069-0.283-0.2830.0000.0000.0000.000
108A117GLN0-0.042-0.01611.988-0.152-0.1520.0000.0000.0000.000
109A118VAL00.0600.04513.217-0.120-0.1200.0000.0000.0000.000
110A119VAL00.020-0.00512.525-0.118-0.1180.0000.0000.0000.000
111A120GLN0-0.0180.00315.143-0.106-0.1060.0000.0000.0000.000
112A121ASP-1-0.727-0.82317.6590.3990.3990.0000.0000.0000.000
113A122ALA0-0.035-0.02417.816-0.050-0.0500.0000.0000.0000.000
114A123ASP-1-0.926-0.98119.1140.0350.0350.0000.0000.0000.000
115A124ARG10.8820.93820.913-0.230-0.2300.0000.0000.0000.000
116A125LEU00.0300.01621.767-0.026-0.0260.0000.0000.0000.000
117A126ASP-1-0.818-0.84723.9850.0530.0530.0000.0000.0000.000
118A127ALA0-0.031-0.00825.761-0.027-0.0270.0000.0000.0000.000
119A128ILE00.038-0.00527.636-0.007-0.0070.0000.0000.0000.000
120A129GLY00.0210.00830.0690.0020.0020.0000.0000.0000.000
121A130ALA00.011-0.00432.393-0.010-0.0100.0000.0000.0000.000
122A131ILE00.007-0.01629.179-0.010-0.0100.0000.0000.0000.000
123A132GLY00.0240.02130.871-0.011-0.0110.0000.0000.0000.000
124A133ILE00.0000.00531.687-0.009-0.0090.0000.0000.0000.000
125A134ALA0-0.009-0.00534.208-0.008-0.0080.0000.0000.0000.000
126A135ARG10.8220.89026.089-0.039-0.0390.0000.0000.0000.000
127A136ALA0-0.0010.01232.930-0.010-0.0100.0000.0000.0000.000
128A137LEU00.0240.01534.272-0.007-0.0070.0000.0000.0000.000
129A138TYR0-0.054-0.01734.431-0.005-0.0050.0000.0000.0000.000
130A139TYR0-0.033-0.00832.677-0.011-0.0110.0000.0000.0000.000
131A140SER00.003-0.03235.231-0.003-0.0030.0000.0000.0000.000
132A141GLY0-0.036-0.01738.236-0.003-0.0030.0000.0000.0000.000
133A142HIS0-0.064-0.02734.5060.0000.0000.0000.0000.0000.000
134A143VAL0-0.035-0.02236.555-0.007-0.0070.0000.0000.0000.000
135A144GLY0-0.0130.01238.921-0.002-0.0020.0000.0000.0000.000
136A145GLU-1-0.905-0.92337.010-0.001-0.0010.0000.0000.0000.000
137A146LYS10.8750.92041.0860.0010.0010.0000.0000.0000.000
138A147ILE00.0690.03341.9390.0030.0030.0000.0000.0000.000
139A148TYR00.003-0.00542.4170.0060.0060.0000.0000.0000.000
140A149ASP-1-0.777-0.88745.0310.0060.0060.0000.0000.0000.000
141A150PRO0-0.0120.00846.7060.0020.0020.0000.0000.0000.000
142A151ALA0-0.044-0.01549.1540.0020.0020.0000.0000.0000.000
143A152ILE0-0.037-0.02443.330-0.004-0.0040.0000.0000.0000.000
144A153ALA00.0260.03844.2060.0020.0020.0000.0000.0000.000
145A154PRO0-0.020-0.01239.386-0.003-0.0030.0000.0000.0000.000
146A155ARG10.7760.83936.557-0.015-0.0150.0000.0000.0000.000
147A156GLU-1-0.902-0.95237.4100.0740.0740.0000.0000.0000.000
148A157HIS0-0.074-0.03035.7290.0110.0110.0000.0000.0000.000
149A158MET0-0.0220.00833.493-0.003-0.0030.0000.0000.0000.000
150A159THR00.0620.02732.5260.0040.0040.0000.0000.0000.000
151A160ARG10.9890.98824.6040.0370.0370.0000.0000.0000.000
152A161GLU-1-0.977-0.97830.196-0.038-0.0380.0000.0000.0000.000
153A162GLN00.0360.02632.9060.0000.0000.0000.0000.0000.000
154A163TYR00.013-0.01328.740-0.002-0.0020.0000.0000.0000.000
155A164ARG10.9360.95827.7960.0620.0620.0000.0000.0000.000
156A165HIS0-0.038-0.02331.490-0.004-0.0040.0000.0000.0000.000
157A166GLN00.0270.03434.8380.0010.0010.0000.0000.0000.000
158A167PRO00.0390.02136.7940.0060.0060.0000.0000.0000.000
159A168GLY0-0.0010.00538.1650.0020.0020.0000.0000.0000.000
160A169THR0-0.043-0.02439.586-0.002-0.0020.0000.0000.0000.000
161A170ALA00.0870.02938.1410.0050.0050.0000.0000.0000.000
162A171ILE0-0.041-0.02938.0860.0070.0070.0000.0000.0000.000
163A172ASN0-0.051-0.03139.0500.0090.0090.0000.0000.0000.000
164A173HIS00.0680.03831.2950.0090.0090.0000.0000.0000.000
165A174PHE00.007-0.01234.0540.0090.0090.0000.0000.0000.000
166A175TYR00.0190.02634.8500.0090.0090.0000.0000.0000.000
167A176GLU-1-0.768-0.87234.3190.0420.0420.0000.0000.0000.000
168A177LYS10.9170.96426.168-0.057-0.0570.0000.0000.0000.000
169A178LEU0-0.004-0.00430.4070.0160.0160.0000.0000.0000.000
170A179PHE0-0.006-0.01831.1910.0130.0130.0000.0000.0000.000
171A180LYS10.8500.93230.085-0.077-0.0770.0000.0000.0000.000
172A181LEU0-0.046-0.01525.9510.0170.0170.0000.0000.0000.000
173A182ALA00.0520.01726.5160.0210.0210.0000.0000.0000.000
174A183ALA0-0.006-0.00127.1230.0210.0210.0000.0000.0000.000
175A184LEU0-0.042-0.02723.9980.0110.0110.0000.0000.0000.000
176A185MET0-0.118-0.02922.2890.0160.0160.0000.0000.0000.000
177A186ASN0-0.026-0.03818.361-0.001-0.0010.0000.0000.0000.000
178A187THR0-0.068-0.05218.0860.0380.0380.0000.0000.0000.000
179A188ASP-1-0.809-0.90719.9500.3680.3680.0000.0000.0000.000
180A189THR0-0.059-0.04021.025-0.056-0.0560.0000.0000.0000.000
181A190ALA00.000-0.00921.203-0.046-0.0460.0000.0000.0000.000
182A191LYS10.8700.93822.597-0.478-0.4780.0000.0000.0000.000
183A192ALA0-0.0080.00725.838-0.032-0.0320.0000.0000.0000.000
184A193LEU0-0.055-0.02924.941-0.030-0.0300.0000.0000.0000.000
185A194ALA00.002-0.01726.742-0.028-0.0280.0000.0000.0000.000
186A195ALA00.0400.04828.588-0.023-0.0230.0000.0000.0000.000
187A196HIS00.0390.01331.809-0.016-0.0160.0000.0000.0000.000
188A197ARG10.8780.93526.651-0.189-0.1890.0000.0000.0000.000
189A198THR00.024-0.01331.158-0.011-0.0110.0000.0000.0000.000
190A199ALA00.0160.02433.444-0.010-0.0100.0000.0000.0000.000
191A200VAL00.0260.00835.499-0.009-0.0090.0000.0000.0000.000
192A201MET0-0.090-0.00232.395-0.006-0.0060.0000.0000.0000.000
193A202HIS00.0290.01435.775-0.004-0.0040.0000.0000.0000.000
194A203GLU-1-0.917-0.94839.3000.0920.0920.0000.0000.0000.000
195A204PHE0-0.032-0.02739.252-0.007-0.0070.0000.0000.0000.000
196A205VAL0-0.022-0.02339.367-0.006-0.0060.0000.0000.0000.000
197A206ASP-1-0.930-0.96042.1380.0700.0700.0000.0000.0000.000
198A207GLN0-0.060-0.04944.965-0.002-0.0020.0000.0000.0000.000
199A208PHE00.0430.03944.395-0.005-0.0050.0000.0000.0000.000
200A209LYS10.9470.95944.153-0.058-0.0580.0000.0000.0000.000
201A210ALA0-0.0260.00547.889-0.003-0.0030.0000.0000.0000.000
202A211GLU-1-0.883-0.95948.6730.0360.0360.0000.0000.0000.000
203A212TRP0-0.083-0.04148.146-0.003-0.0030.0000.0000.0000.000
204A213THR0-0.010-0.01451.247-0.002-0.0020.0000.0000.0000.000
205A214ALA0-0.103-0.02953.964-0.001-0.0010.0000.0000.0000.000
206A215ASP-1-1.004-0.99454.3480.0170.0170.0000.0000.0000.000