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: G5L21

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 OptAll
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 -2348774.452673
FMO2-HF: Nuclear repulsion 2268207.073362
FMO2-HF: Total energy -80567.379311
FMO2-MP2: Total energy -80804.314023


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.
-27.482-28.40821.447-9.69-10.83-0.062
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 : -0.042 / 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].
3A3THR00.020-0.0033.8831.1092.994-0.008-0.903-0.9740.005
4A4GLU-1-0.719-0.8586.3520.4150.4150.0000.0000.0000.000
5A5THR00.0060.0119.4670.1220.1220.0000.0000.0000.000
6A6GLN00.0320.0396.302-0.558-0.5580.0000.0000.0000.000
7A7LEU0-0.0270.0069.1820.2130.2130.0000.0000.0000.000
8A8THR0-0.038-0.04410.6280.1340.1340.0000.0000.0000.000
9A9ALA00.0180.03212.9980.1140.1140.0000.0000.0000.000
10A10ILE00.007-0.0029.5420.1140.1140.0000.0000.0000.000
11A11GLN0-0.017-0.00513.6530.1390.1390.0000.0000.0000.000
12A12THR0-0.019-0.01416.0590.0830.0830.0000.0000.0000.000
13A13TYR00.0120.00316.5160.0610.0610.0000.0000.0000.000
14A14ALA00.0480.02117.0360.0490.0490.0000.0000.0000.000
15A15LEU0-0.016-0.01518.9370.0500.0500.0000.0000.0000.000
16A16GLN0-0.066-0.04721.4910.0690.0690.0000.0000.0000.000
17A17LYS10.8480.92420.7360.3450.3450.0000.0000.0000.000
18A18LEU00.0160.02221.2260.0180.0180.0000.0000.0000.000
19A19ALA0-0.044-0.01824.4980.0280.0280.0000.0000.0000.000
20A20HIS0-0.029-0.03327.2650.0040.0040.0000.0000.0000.000
21A21ASP-1-0.722-0.83427.501-0.056-0.0560.0000.0000.0000.000
22A22HIS0-0.029-0.01329.4950.0110.0110.0000.0000.0000.000
23A23SER00.0570.03729.8130.0110.0110.0000.0000.0000.000
24A24GLY00.0340.00730.2380.0120.0120.0000.0000.0000.000
25A25HIS0-0.101-0.06325.3780.0350.0350.0000.0000.0000.000
26A26GLY00.0360.01824.611-0.013-0.0130.0000.0000.0000.000
27A27ARG10.8700.92023.5810.1940.1940.0000.0000.0000.000
28A28ASP-1-0.887-0.93923.523-0.012-0.0120.0000.0000.0000.000
29A29HIS10.7510.87222.145-0.019-0.0190.0000.0000.0000.000
30A30LEU00.0380.02719.1000.0340.0340.0000.0000.0000.000
31A31GLN00.004-0.00419.7770.0200.0200.0000.0000.0000.000
32A32ARG10.8090.88121.071-0.028-0.0280.0000.0000.0000.000
33A33VAL00.0540.03117.8940.0490.0490.0000.0000.0000.000
34A34ASN00.009-0.00816.3640.0900.0900.0000.0000.0000.000
35A35ARG10.9210.96117.041-0.077-0.0770.0000.0000.0000.000
36A36LEU0-0.018-0.00519.3790.0470.0470.0000.0000.0000.000
37A37ALA00.0690.03614.7060.0670.0670.0000.0000.0000.000
38A38ARG10.8010.89112.720-0.061-0.0610.0000.0000.0000.000
39A39ARG10.7670.86215.781-0.469-0.4690.0000.0000.0000.000
40A40LEU00.0540.00816.9200.0520.0520.0000.0000.0000.000
41A41ALA00.0210.01211.7070.0630.0630.0000.0000.0000.000
42A42LYS10.8370.92412.924-0.402-0.4020.0000.0000.0000.000
43A43ASP-1-0.788-0.84115.2270.6010.6010.0000.0000.0000.000
44A44GLU-1-0.851-0.94014.1900.8640.8640.0000.0000.0000.000
45A45GLY0-0.0260.00212.5500.0830.0830.0000.0000.0000.000
46A46ALA0-0.0100.0119.3400.3780.3780.0000.0000.0000.000
47A47ASN00.0490.0172.561-5.382-8.7597.428-1.579-2.4720.012
48A48LEU00.0280.0206.593-0.805-0.8050.0000.0000.0000.000
49A49ASN00.025-0.0125.245-1.073-1.0730.0000.0000.0000.000
50A50LEU00.0070.0042.752-1.731-1.0460.251-0.160-0.7760.000
51A51THR0-0.019-0.0316.494-0.739-0.7390.0000.0000.0000.000
52A52LEU0-0.032-0.0279.900-0.351-0.3510.0000.0000.0000.000
53A53ALA0-0.0220.0018.308-0.178-0.1780.0000.0000.0000.000
54A54ALA00.0500.01310.171-0.103-0.1030.0000.0000.0000.000
55A55ALA0-0.033-0.02111.870-0.032-0.0320.0000.0000.0000.000
56A56TRP0-0.027-0.02713.259-0.030-0.0300.0000.0000.0000.000
57A57LEU00.016-0.00211.932-0.038-0.0380.0000.0000.0000.000
58A58HIS10.8170.90015.812-0.014-0.0140.0000.0000.0000.000
59A59ASP-1-0.795-0.90117.386-0.014-0.0140.0000.0000.0000.000
60A60VAL0-0.072-0.02218.537-0.011-0.0110.0000.0000.0000.000
61A61ILE0-0.047-0.02818.174-0.033-0.0330.0000.0000.0000.000
62A62ASP-1-0.878-0.91121.323-0.003-0.0030.0000.0000.0000.000
63A72ALA00.0200.00521.5770.0080.0080.0000.0000.0000.000
64A73HIS0-0.007-0.02117.640-0.057-0.0570.0000.0000.0000.000
65A74GLN0-0.0020.00018.075-0.067-0.0670.0000.0000.0000.000
66A75ASP-1-0.813-0.89819.039-0.427-0.4270.0000.0000.0000.000
67A76LEU0-0.0010.00013.914-0.066-0.0660.0000.0000.0000.000
68A77ILE00.0240.01214.210-0.158-0.1580.0000.0000.0000.000
69A78VAL00.0120.01414.302-0.137-0.1370.0000.0000.0000.000
70A79GLN0-0.018-0.00214.718-0.149-0.1490.0000.0000.0000.000
71A80LEU00.013-0.0109.762-0.090-0.0900.0000.0000.0000.000
72A81ASN0-0.029-0.02610.694-0.358-0.3580.0000.0000.0000.000
73A82ALA0-0.031-0.00412.274-0.068-0.0680.0000.0000.0000.000
74A83GLN0-0.039-0.02010.8060.0390.0390.0000.0000.0000.000
75A84ASN0-0.024-0.0109.213-0.258-0.2580.0000.0000.0000.000
76A85VAL0-0.0380.0006.155-0.762-0.7620.0000.0000.0000.000
77A86THR00.040-0.0022.7911.1062.1050.078-0.457-0.6200.000
78A87ALA00.0840.0285.5290.2730.2730.0000.0000.0000.000
79A88ASP-1-0.871-0.9164.926-1.152-1.1520.0000.0000.0000.000
80A89ASP-1-0.771-0.8691.845-23.129-24.31313.699-6.584-5.930-0.079
81A90GLN0-0.032-0.0164.8171.1731.239-0.001-0.007-0.0580.000
82A91THR0-0.023-0.0227.9710.5330.5330.0000.0000.0000.000
83A92ALA0-0.017-0.0084.8810.4100.4100.0000.0000.0000.000
84A93ILE00.001-0.0106.7920.4360.4360.0000.0000.0000.000
85A94PHE00.007-0.0089.0730.2400.2400.0000.0000.0000.000
86A95ALA0-0.0210.0029.3700.1250.1250.0000.0000.0000.000
87A96ILE0-0.0030.0118.2270.1210.1210.0000.0000.0000.000
88A97ILE00.002-0.00311.9200.0190.0190.0000.0000.0000.000
89A98ASP-1-0.841-0.90414.557-0.142-0.1420.0000.0000.0000.000
90A99HIS0-0.082-0.05014.2160.0050.0050.0000.0000.0000.000
91A100MET00.0100.03315.7280.0380.0380.0000.0000.0000.000
92A101SER00.0050.01517.5120.0030.0030.0000.0000.0000.000
93A102PHE00.0800.02220.9420.0070.0070.0000.0000.0000.000
94A103SER00.0150.01524.0020.0020.0020.0000.0000.0000.000
95A104LYS10.8050.89618.9760.0140.0140.0000.0000.0000.000
96A105SER00.0110.02023.7050.0040.0040.0000.0000.0000.000
97A106PHE00.0110.00324.7880.0030.0030.0000.0000.0000.000
98A107ASN0-0.073-0.04024.769-0.012-0.0120.0000.0000.0000.000
99A108GLY00.0240.02425.514-0.002-0.0020.0000.0000.0000.000
100A109PRO0-0.016-0.01322.309-0.003-0.0030.0000.0000.0000.000
101A110GLN00.0140.00017.7340.0130.0130.0000.0000.0000.000
102A111LYS10.9460.97415.259-0.420-0.4200.0000.0000.0000.000
103A112LEU0-0.017-0.00312.603-0.034-0.0340.0000.0000.0000.000
104A113SER00.0430.0187.657-0.079-0.0790.0000.0000.0000.000
105A114LEU00.0280.0449.680-0.145-0.1450.0000.0000.0000.000
106A115GLU-1-0.786-0.9206.5053.2783.2780.0000.0000.0000.000
107A116GLY00.008-0.0199.925-0.295-0.2950.0000.0000.0000.000
108A117GLN0-0.052-0.03211.578-0.185-0.1850.0000.0000.0000.000
109A118VAL00.0340.02212.854-0.123-0.1230.0000.0000.0000.000
110A119VAL0-0.008-0.01312.011-0.118-0.1180.0000.0000.0000.000
111A120GLN0-0.0070.00614.762-0.126-0.1260.0000.0000.0000.000
112A121ASP-1-0.718-0.81817.2800.4370.4370.0000.0000.0000.000
113A122ALA0-0.027-0.01617.472-0.053-0.0530.0000.0000.0000.000
114A123ASP-1-0.921-0.97318.9670.0690.0690.0000.0000.0000.000
115A124ARG10.8860.94120.797-0.278-0.2780.0000.0000.0000.000
116A125LEU00.0180.00521.384-0.023-0.0230.0000.0000.0000.000
117A126ASP-1-0.801-0.84823.5940.0730.0730.0000.0000.0000.000
118A127ALA0-0.0140.01225.358-0.029-0.0290.0000.0000.0000.000
119A128ILE00.0320.00527.178-0.008-0.0080.0000.0000.0000.000
120A129GLY00.0330.01129.6190.0030.0030.0000.0000.0000.000
121A130ALA00.0170.00332.341-0.009-0.0090.0000.0000.0000.000
122A131ILE0-0.014-0.00828.742-0.010-0.0100.0000.0000.0000.000
123A132GLY00.0340.02530.419-0.011-0.0110.0000.0000.0000.000
124A133ILE00.0100.00431.177-0.010-0.0100.0000.0000.0000.000
125A134ALA0-0.017-0.00533.937-0.009-0.0090.0000.0000.0000.000
126A135ARG10.8240.88625.460-0.063-0.0630.0000.0000.0000.000
127A136ALA0-0.0120.00732.416-0.010-0.0100.0000.0000.0000.000
128A137LEU00.001-0.00333.979-0.008-0.0080.0000.0000.0000.000
129A138TYR0-0.089-0.03633.688-0.005-0.0050.0000.0000.0000.000
130A139TYR00.0010.00732.226-0.011-0.0110.0000.0000.0000.000
131A140SER0-0.024-0.04634.628-0.004-0.0040.0000.0000.0000.000
132A141GLY0-0.014-0.00837.607-0.004-0.0040.0000.0000.0000.000
133A142HIS0-0.044-0.02334.136-0.001-0.0010.0000.0000.0000.000
134A143VAL0-0.037-0.01636.014-0.007-0.0070.0000.0000.0000.000
135A144GLY0-0.0050.00938.237-0.002-0.0020.0000.0000.0000.000
136A145GLU-1-0.889-0.90736.9970.0130.0130.0000.0000.0000.000
137A146LYS10.8680.91540.797-0.006-0.0060.0000.0000.0000.000
138A147ILE00.0600.02041.6810.0030.0030.0000.0000.0000.000
139A148TYR00.010-0.01041.9690.0060.0060.0000.0000.0000.000
140A149ASP-1-0.763-0.88044.3920.0120.0120.0000.0000.0000.000
141A150PRO0-0.0020.01846.3300.0020.0020.0000.0000.0000.000
142A151ALA0-0.035-0.01148.7150.0020.0020.0000.0000.0000.000
143A152ILE0-0.070-0.03842.668-0.003-0.0030.0000.0000.0000.000
144A153ALA00.0500.03443.5650.0030.0030.0000.0000.0000.000
145A154PRO0-0.027-0.01339.200-0.002-0.0020.0000.0000.0000.000
146A155ARG10.7820.85236.247-0.025-0.0250.0000.0000.0000.000
147A156GLU-1-0.914-0.95336.6610.0860.0860.0000.0000.0000.000
148A157HIS0-0.068-0.03635.3150.0110.0110.0000.0000.0000.000
149A158MET0-0.0170.01432.974-0.004-0.0040.0000.0000.0000.000
150A159THR00.0570.02132.0350.0040.0040.0000.0000.0000.000
151A160ARG10.9270.95323.8000.0110.0110.0000.0000.0000.000
152A161GLU-1-0.981-0.98529.614-0.029-0.0290.0000.0000.0000.000
153A162GLN00.0340.00832.4000.0000.0000.0000.0000.0000.000
154A163TYR00.033-0.01128.7960.0000.0000.0000.0000.0000.000
155A164ARG10.9260.96627.6840.0450.0450.0000.0000.0000.000
156A165HIS0-0.035-0.00731.376-0.006-0.0060.0000.0000.0000.000
157A166GLN00.0150.02734.7790.0010.0010.0000.0000.0000.000
158A167PRO00.0210.01536.5340.0060.0060.0000.0000.0000.000
159A168GLY0-0.004-0.00337.9820.0030.0030.0000.0000.0000.000
160A169THR0-0.051-0.04138.949-0.003-0.0030.0000.0000.0000.000
161A170ALA00.0550.03037.5200.0050.0050.0000.0000.0000.000
162A171ILE0-0.014-0.01437.4650.0080.0080.0000.0000.0000.000
163A172ASN0-0.049-0.01238.4550.0070.0070.0000.0000.0000.000
164A173HIS00.0520.02930.6650.0140.0140.0000.0000.0000.000
165A174PHE00.0070.00333.5740.0110.0110.0000.0000.0000.000
166A175TYR00.0580.04034.3810.0090.0090.0000.0000.0000.000
167A176GLU-1-0.772-0.87234.2270.0510.0510.0000.0000.0000.000
168A177LYS10.9200.96025.762-0.081-0.0810.0000.0000.0000.000
169A178LEU0-0.004-0.00530.0130.0170.0170.0000.0000.0000.000
170A179PHE00.009-0.01430.4920.0150.0150.0000.0000.0000.000
171A180LYS10.8570.93729.885-0.087-0.0870.0000.0000.0000.000
172A181LEU0-0.047-0.02125.6040.0170.0170.0000.0000.0000.000
173A182ALA00.0570.01925.9180.0250.0250.0000.0000.0000.000
174A183ALA0-0.035-0.01326.9390.0220.0220.0000.0000.0000.000
175A184LEU0-0.051-0.02823.7670.0070.0070.0000.0000.0000.000
176A185MET0-0.076-0.00621.7980.0080.0080.0000.0000.0000.000
177A186ASN0-0.063-0.05618.019-0.001-0.0010.0000.0000.0000.000
178A187THR0-0.029-0.03318.4140.0320.0320.0000.0000.0000.000
179A188ASP-1-0.824-0.90519.8670.3860.3860.0000.0000.0000.000
180A189THR0-0.061-0.06021.314-0.059-0.0590.0000.0000.0000.000
181A190ALA0-0.013-0.00620.974-0.042-0.0420.0000.0000.0000.000
182A191LYS10.8720.92422.054-0.501-0.5010.0000.0000.0000.000
183A192ALA00.0070.00625.835-0.033-0.0330.0000.0000.0000.000
184A193LEU0-0.057-0.02924.468-0.029-0.0290.0000.0000.0000.000
185A194ALA00.019-0.00726.276-0.027-0.0270.0000.0000.0000.000
186A195ALA00.0190.03728.160-0.024-0.0240.0000.0000.0000.000
187A196HIS00.0110.00031.470-0.016-0.0160.0000.0000.0000.000
188A197ARG10.8860.93527.089-0.203-0.2030.0000.0000.0000.000
189A198THR00.028-0.00630.953-0.012-0.0120.0000.0000.0000.000
190A199ALA00.0030.01533.195-0.011-0.0110.0000.0000.0000.000
191A200VAL00.0510.02335.374-0.009-0.0090.0000.0000.0000.000
192A201MET0-0.111-0.01931.852-0.006-0.0060.0000.0000.0000.000
193A202HIS00.0270.01435.796-0.004-0.0040.0000.0000.0000.000
194A203GLU-1-0.910-0.95739.2090.1010.1010.0000.0000.0000.000
195A204PHE0-0.004-0.00338.832-0.007-0.0070.0000.0000.0000.000
196A205VAL0-0.003-0.00438.711-0.007-0.0070.0000.0000.0000.000
197A206ASP-1-0.866-0.94341.6610.0750.0750.0000.0000.0000.000
198A207GLN0-0.070-0.04044.557-0.002-0.0020.0000.0000.0000.000
199A208PHE00.0230.01643.980-0.005-0.0050.0000.0000.0000.000
200A209LYS10.8290.90243.437-0.072-0.0720.0000.0000.0000.000
201A210ALA0-0.0150.01347.554-0.003-0.0030.0000.0000.0000.000
202A211GLU-1-0.886-0.94748.2560.0430.0430.0000.0000.0000.000
203A212TRP0-0.008-0.01347.517-0.003-0.0030.0000.0000.0000.000
204A213THR0-0.082-0.05951.006-0.002-0.0020.0000.0000.0000.000
205A214ALA0-0.075-0.02653.400-0.001-0.0010.0000.0000.0000.000
206A215ASP-1-1.002-0.98254.0330.0210.0210.0000.0000.0000.000