Manual

About

FMODB

FMODB: The database of quantum mechanical data based on the FMO method

Last updated: 2024-05-02

All entries: 37386

Number of unique PDB entries: 7781

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FMODB ID: 6GYVZ

Calculation Name: 2PL2-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2PL2

Chain ID: A

ChEMBL ID:

UniProt ID: Q72L02

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 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 194
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2097711.316977
FMO2-HF: Nuclear repulsion 2022776.352461
FMO2-HF: Total energy -74934.964516
FMO2-MP2: Total energy -75158.586807


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:28:ALA)


Summations of interaction energy for fragment #1(A:28:ALA)
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.
-10.953-6.0841.777-2.93-3.716-0.02
Interaction energy analysis for fragmet #1(A:28:ALA)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.003 / q_NPA : -0.002
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].
3A30GLN00.0280.0163.604-1.927-0.075-0.003-0.914-0.9360.002
4A31ASN00.0240.0094.545-1.150-0.924-0.001-0.014-0.2100.000
5A32PRO0-0.0080.0004.737-0.180-0.043-0.001-0.035-0.1010.000
6A33LEU00.0680.0427.2060.0740.0740.0000.0000.0000.000
7A34ARG10.8930.9428.928-1.135-1.1350.0000.0000.0000.000
8A35LEU0-0.008-0.00510.178-0.074-0.0740.0000.0000.0000.000
9A36GLY00.0490.02411.557-0.046-0.0460.0000.0000.0000.000
10A37VAL00.0170.00713.343-0.013-0.0130.0000.0000.0000.000
11A38GLN0-0.020-0.01613.8160.0510.0510.0000.0000.0000.000
12A39LEU00.013-0.00614.929-0.021-0.0210.0000.0000.0000.000
13A40TYR0-0.041-0.01717.472-0.012-0.0120.0000.0000.0000.000
14A41ALA0-0.016-0.00619.335-0.008-0.0080.0000.0000.0000.000
15A42LEU0-0.039-0.01219.364-0.006-0.0060.0000.0000.0000.000
16A43GLY00.0230.02422.403-0.011-0.0110.0000.0000.0000.000
17A44ARG10.7740.86620.2690.0070.0070.0000.0000.0000.000
18A45TYR00.0960.03319.734-0.010-0.0100.0000.0000.0000.000
19A46ASP-1-0.780-0.87819.503-0.079-0.0790.0000.0000.0000.000
20A47ALA0-0.0110.00217.139-0.027-0.0270.0000.0000.0000.000
21A48ALA0-0.006-0.00315.486-0.039-0.0390.0000.0000.0000.000
22A49LEU00.0170.02014.785-0.030-0.0300.0000.0000.0000.000
23A50THR00.0120.00214.019-0.055-0.0550.0000.0000.0000.000
24A51LEU0-0.077-0.02910.271-0.128-0.1280.0000.0000.0000.000
25A52PHE00.0370.0139.985-0.120-0.1200.0000.0000.0000.000
26A53GLU-1-0.893-0.95311.139-0.402-0.4020.0000.0000.0000.000
27A54ARG10.8770.9347.4360.5910.5910.0000.0000.0000.000
28A55ALA0-0.025-0.0116.670-0.406-0.4060.0000.0000.0000.000
29A56LEU00.0360.0086.891-0.199-0.1990.0000.0000.0000.000
30A57LYS10.8780.9507.0550.9750.9750.0000.0000.0000.000
31A58GLU-1-0.940-0.9712.596-7.386-4.8271.783-1.965-2.377-0.022
32A59ASN0-0.071-0.0454.9350.0590.154-0.001-0.002-0.0920.000
33A60PRO0-0.001-0.0047.4000.2080.2080.0000.0000.0000.000
34A61GLN0-0.027-0.01610.9680.1130.1130.0000.0000.0000.000
35A62ASP-1-0.798-0.88210.0760.0660.0660.0000.0000.0000.000
36A63PRO0-0.002-0.01412.133-0.008-0.0080.0000.0000.0000.000
37A64GLU-1-0.863-0.92212.9300.2460.2460.0000.0000.0000.000
38A65ALA00.005-0.01410.5350.0000.0000.0000.0000.0000.000
39A66LEU00.0040.00212.629-0.013-0.0130.0000.0000.0000.000
40A67TYR0-0.0420.00015.4900.0030.0030.0000.0000.0000.000
41A68TRP0-0.050-0.04114.660-0.010-0.0100.0000.0000.0000.000
42A69LEU0-0.0090.02414.9120.0030.0030.0000.0000.0000.000
43A70ALA00.0180.01416.9370.0110.0110.0000.0000.0000.000
44A71ARG10.8540.88720.304-0.015-0.0150.0000.0000.0000.000
45A72THR0-0.052-0.02618.4000.0220.0220.0000.0000.0000.000
46A73GLN00.030-0.00619.5190.0150.0150.0000.0000.0000.000
47A74LEU0-0.042-0.01622.4130.0050.0050.0000.0000.0000.000
48A75LYS10.8450.91823.782-0.003-0.0030.0000.0000.0000.000
49A76LEU0-0.0180.00521.2170.0030.0030.0000.0000.0000.000
50A77GLY00.0260.02125.479-0.005-0.0050.0000.0000.0000.000
51A78LEU0-0.0270.00022.419-0.003-0.0030.0000.0000.0000.000
52A79VAL00.017-0.01125.266-0.007-0.0070.0000.0000.0000.000
53A80ASN00.0230.00927.0270.0040.0040.0000.0000.0000.000
54A81PRO00.007-0.00522.206-0.001-0.0010.0000.0000.0000.000
55A82ALA00.0510.03922.657-0.007-0.0070.0000.0000.0000.000
56A83LEU0-0.0100.00023.7220.0050.0050.0000.0000.0000.000
57A84GLU-1-0.797-0.88623.349-0.093-0.0930.0000.0000.0000.000
58A85ASN00.0040.00018.718-0.018-0.0180.0000.0000.0000.000
59A86GLY00.008-0.00421.2690.0060.0060.0000.0000.0000.000
60A87LYS10.8050.88423.7430.0920.0920.0000.0000.0000.000
61A88THR00.0110.00019.4820.0020.0020.0000.0000.0000.000
62A89LEU0-0.0550.00017.6930.0040.0040.0000.0000.0000.000
63A90VAL0-0.018-0.00621.0090.0100.0100.0000.0000.0000.000
64A91ALA0-0.013-0.01023.9210.0060.0060.0000.0000.0000.000
65A92ARG10.8820.94616.8380.1590.1590.0000.0000.0000.000
66A93THR0-0.0080.00218.6830.0070.0070.0000.0000.0000.000
67A94PRO00.0680.04221.3240.0140.0140.0000.0000.0000.000
68A95ARG10.9430.97523.158-0.030-0.0300.0000.0000.0000.000
69A96TYR00.0380.01917.2110.0040.0040.0000.0000.0000.000
70A97LEU00.0330.00022.046-0.012-0.0120.0000.0000.0000.000
71A98GLY00.0370.02121.019-0.005-0.0050.0000.0000.0000.000
72A99GLY00.0360.00622.107-0.012-0.0120.0000.0000.0000.000
73A100TYR0-0.028-0.03623.123-0.010-0.0100.0000.0000.0000.000
74A101MET0-0.0270.00024.576-0.002-0.0020.0000.0000.0000.000
75A102VAL00.0120.01521.418-0.003-0.0030.0000.0000.0000.000
76A103LEU00.0010.00224.874-0.005-0.0050.0000.0000.0000.000
77A104SER00.0360.01327.354-0.001-0.0010.0000.0000.0000.000
78A105GLU-1-0.823-0.88426.0680.0050.0050.0000.0000.0000.000
79A106ALA00.0120.00327.175-0.002-0.0020.0000.0000.0000.000
80A107TYR00.009-0.00329.181-0.003-0.0030.0000.0000.0000.000
81A108VAL00.0110.00632.4270.0010.0010.0000.0000.0000.000
82A109ALA0-0.038-0.02030.9510.0010.0010.0000.0000.0000.000
83A110LEU0-0.032-0.02531.821-0.001-0.0010.0000.0000.0000.000
84A111TYR0-0.054-0.03434.6320.0010.0010.0000.0000.0000.000
85A112ARG10.9270.96135.0640.0120.0120.0000.0000.0000.000
86A113GLN0-0.056-0.01233.7170.0010.0010.0000.0000.0000.000
87A114ALA0-0.0080.00137.611-0.002-0.0020.0000.0000.0000.000
88A115GLU-1-0.926-0.93440.709-0.037-0.0370.0000.0000.0000.000
89A116ASP-1-0.837-0.91742.914-0.023-0.0230.0000.0000.0000.000
90A117ARG10.9640.97343.9620.0140.0140.0000.0000.0000.000
91A118GLU-1-0.943-0.97245.116-0.020-0.0200.0000.0000.0000.000
92A119ARG10.8380.89837.3350.0420.0420.0000.0000.0000.000
93A120GLY00.015-0.00940.227-0.001-0.0010.0000.0000.0000.000
94A121LYS10.8500.90440.0890.0110.0110.0000.0000.0000.000
95A122GLY00.0520.03440.8350.0010.0010.0000.0000.0000.000
96A123TYR00.0430.02335.692-0.001-0.0010.0000.0000.0000.000
97A124LEU0-0.0030.00236.2550.0010.0010.0000.0000.0000.000
98A125GLU-1-0.802-0.88938.213-0.008-0.0080.0000.0000.0000.000
99A126GLN0-0.045-0.02234.5530.0010.0010.0000.0000.0000.000
100A127ALA0-0.002-0.00433.5310.0010.0010.0000.0000.0000.000
101A128LEU00.0030.00534.4400.0040.0040.0000.0000.0000.000
102A129SER0-0.059-0.01635.5200.0030.0030.0000.0000.0000.000
103A130VAL00.0200.01329.6320.0030.0030.0000.0000.0000.000
104A131LEU00.0070.00030.8350.0050.0050.0000.0000.0000.000
105A132LYS10.8290.90632.878-0.009-0.0090.0000.0000.0000.000
106A133ASP-1-0.889-0.95032.094-0.004-0.0040.0000.0000.0000.000
107A134ALA00.0240.00128.8660.0040.0040.0000.0000.0000.000
108A135GLU-1-0.818-0.89130.2370.0310.0310.0000.0000.0000.000
109A136ARG10.8920.94332.579-0.008-0.0080.0000.0000.0000.000
110A137VAL0-0.048-0.00626.2410.0030.0030.0000.0000.0000.000
111A138ASN0-0.011-0.02026.7490.0060.0060.0000.0000.0000.000
112A139PRO00.0450.02529.9510.0000.0000.0000.0000.0000.000
113A140ARG10.9620.98731.484-0.083-0.0830.0000.0000.0000.000
114A141TYR00.0320.02223.9440.0100.0100.0000.0000.0000.000
115A142ALA00.0680.04129.682-0.008-0.0080.0000.0000.0000.000
116A143PRO00.0280.00326.932-0.007-0.0070.0000.0000.0000.000
117A144LEU00.0200.01028.502-0.008-0.0080.0000.0000.0000.000
118A145HIS0-0.0220.00431.503-0.009-0.0090.0000.0000.0000.000
119A146LEU00.0240.01730.950-0.004-0.0040.0000.0000.0000.000
120A147GLN0-0.001-0.00929.394-0.006-0.0060.0000.0000.0000.000
121A148ARG10.8090.89633.470-0.026-0.0260.0000.0000.0000.000
122A149GLY00.0200.00236.292-0.003-0.0030.0000.0000.0000.000
123A150LEU0-0.013-0.00134.193-0.003-0.0030.0000.0000.0000.000
124A151VAL00.015-0.01035.317-0.003-0.0030.0000.0000.0000.000
125A152TYR00.009-0.00838.168-0.001-0.0010.0000.0000.0000.000
126A153ALA0-0.0020.00140.899-0.001-0.0010.0000.0000.0000.000
127A154LEU0-0.054-0.01637.598-0.002-0.0020.0000.0000.0000.000
128A155LEU0-0.0040.00841.135-0.003-0.0030.0000.0000.0000.000
129A156GLY0-0.0120.01743.670-0.001-0.0010.0000.0000.0000.000
130A157GLU-1-0.857-0.92544.7690.0020.0020.0000.0000.0000.000
131A158ARG10.9330.94445.380-0.003-0.0030.0000.0000.0000.000
132A159ASP-1-0.770-0.88546.2250.0090.0090.0000.0000.0000.000
133A160LYS10.8160.88443.638-0.003-0.0030.0000.0000.0000.000
134A161ALA0-0.0070.01541.6660.0020.0020.0000.0000.0000.000
135A162GLU-1-0.727-0.82541.8050.0240.0240.0000.0000.0000.000
136A163ALA0-0.028-0.00943.2510.0030.0030.0000.0000.0000.000
137A164SER0-0.028-0.01838.5030.0030.0030.0000.0000.0000.000
138A165LEU00.0270.02037.4850.0040.0040.0000.0000.0000.000
139A166LYS10.9000.94739.132-0.022-0.0220.0000.0000.0000.000
140A167GLN0-0.020-0.01336.9880.0040.0040.0000.0000.0000.000
141A168ALA0-0.011-0.01434.8720.0040.0040.0000.0000.0000.000
142A169LEU0-0.044-0.01135.5420.0050.0050.0000.0000.0000.000
143A170ALA0-0.039-0.02137.9840.0030.0030.0000.0000.0000.000
144A171LEU0-0.121-0.04033.4180.0030.0030.0000.0000.0000.000
145A172GLU-1-0.908-0.96330.2750.1020.1020.0000.0000.0000.000
146A173ASP-1-0.775-0.88233.9880.0510.0510.0000.0000.0000.000
147A174THR00.0200.00331.4170.0020.0020.0000.0000.0000.000
148A175PRO00.0570.00833.501-0.005-0.0050.0000.0000.0000.000
149A176GLU-1-0.926-0.93429.8110.0500.0500.0000.0000.0000.000
150A177ILE00.0200.00532.975-0.007-0.0070.0000.0000.0000.000
151A178ARG10.7730.87036.163-0.050-0.0500.0000.0000.0000.000
152A179SER00.0480.00936.544-0.004-0.0040.0000.0000.0000.000
153A180ALA0-0.032-0.01036.264-0.004-0.0040.0000.0000.0000.000
154A181LEU0-0.032-0.02638.305-0.004-0.0040.0000.0000.0000.000
155A182ALA00.0210.02041.431-0.003-0.0030.0000.0000.0000.000
156A183GLU-1-0.796-0.88439.2700.0140.0140.0000.0000.0000.000
157A184LEU0-0.046-0.00641.996-0.003-0.0030.0000.0000.0000.000
158A185TYR0-0.059-0.05443.719-0.001-0.0010.0000.0000.0000.000
159A186LEU00.0270.01344.582-0.001-0.0010.0000.0000.0000.000
160A187SER0-0.103-0.06145.246-0.002-0.0020.0000.0000.0000.000
161A188MET0-0.102-0.04647.118-0.002-0.0020.0000.0000.0000.000
162A189GLY00.0250.01950.0880.0000.0000.0000.0000.0000.000
163A190ARG10.7590.85649.207-0.018-0.0180.0000.0000.0000.000
164A191LEU00.0470.00949.9470.0020.0020.0000.0000.0000.000
165A192ASP-1-0.874-0.93350.0500.0190.0190.0000.0000.0000.000
166A193GLU-1-0.860-0.92048.6890.0220.0220.0000.0000.0000.000
167A194ALA00.006-0.00445.9200.0030.0030.0000.0000.0000.000
168A195LEU0-0.0080.00145.5820.0020.0020.0000.0000.0000.000
169A196ALA00.0070.00746.9670.0020.0020.0000.0000.0000.000
170A197GLN0-0.0130.00842.6600.0060.0060.0000.0000.0000.000
171A198TYR00.018-0.02539.7160.0040.0040.0000.0000.0000.000
172A199ALA00.0010.01242.6140.0030.0030.0000.0000.0000.000
173A200LYS10.8420.93339.852-0.052-0.0520.0000.0000.0000.000
174A201ALA00.011-0.00338.6050.0040.0040.0000.0000.0000.000
175A202LEU0-0.028-0.01738.7540.0040.0040.0000.0000.0000.000
176A203GLU-1-0.927-0.96440.3480.0500.0500.0000.0000.0000.000
177A204GLN0-0.090-0.05036.5650.0000.0000.0000.0000.0000.000
178A205ALA0-0.0030.00235.0040.0070.0070.0000.0000.0000.000
179A206PRO00.0640.05136.605-0.003-0.0030.0000.0000.0000.000
180A207LYS10.8830.92235.686-0.072-0.0720.0000.0000.0000.000
181A208ASP-1-0.828-0.90134.1630.0480.0480.0000.0000.0000.000
182A209LEU00.011-0.01735.234-0.004-0.0040.0000.0000.0000.000
183A210ASP-1-0.825-0.86434.4300.0220.0220.0000.0000.0000.000
184A211LEU00.0290.01236.421-0.004-0.0040.0000.0000.0000.000
185A212ARG10.8660.92138.282-0.044-0.0440.0000.0000.0000.000
186A213VAL0-0.0180.00239.428-0.002-0.0020.0000.0000.0000.000
187A214ARG10.7990.86935.537-0.023-0.0230.0000.0000.0000.000
188A215TYR00.0090.00641.747-0.002-0.0020.0000.0000.0000.000
189A216ALA00.000-0.00544.308-0.001-0.0010.0000.0000.0000.000
190A217SER0-0.006-0.01644.417-0.002-0.0020.0000.0000.0000.000
191A218ALA0-0.023-0.00645.734-0.002-0.0020.0000.0000.0000.000
192A219LEU0-0.028-0.02247.458-0.001-0.0010.0000.0000.0000.000
193A220LEU0-0.041-0.00248.495-0.001-0.0010.0000.0000.0000.000
194A221LEU0-0.090-0.03350.894-0.003-0.0030.0000.0000.0000.000