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: 72J3K

Calculation Name: 5GPL-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 5GPL

Chain ID: A

ChEMBL ID:

UniProt ID: Q9HGN2

Base Structure: X-ray

Registration Date: 2023-06-21

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 206
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2401440.126277
FMO2-HF: Nuclear repulsion 2318104.503785
FMO2-HF: Total energy -83335.622492
FMO2-MP2: Total energy -83584.470983


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:2:GLU)


Summations of interaction energy for fragment #1(A:2:GLU)
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.
115.06121.0821.076-2.838-4.260.022
Interaction energy analysis for fragmet #1(A:2:GLU)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : -1 / q_Mulliken : -0.945 / q_NPA : -0.992
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].
3A4ALA00.0120.0123.638-4.171-2.082-0.016-0.895-1.1780.004
4A5GLN00.0730.0352.932-9.011-5.4151.092-1.872-2.8160.018
5A6ALA0-0.006-0.0024.131-6.754-6.4170.000-0.071-0.2660.000
6A7PHE00.012-0.0155.624-4.530-4.5300.0000.0000.0000.000
7A8GLU-1-0.941-0.9577.56333.66233.6620.0000.0000.0000.000
8A9ASN0-0.021-0.0126.179-3.725-3.7250.0000.0000.0000.000
9A10LEU0-0.013-0.0059.577-2.687-2.6870.0000.0000.0000.000
10A11ALA00.0330.03011.666-2.133-2.1330.0000.0000.0000.000
11A12ASN0-0.025-0.02411.554-2.849-2.8490.0000.0000.0000.000
12A13LEU0-0.017-0.00713.495-1.377-1.3770.0000.0000.0000.000
13A14GLU-1-0.902-0.95215.38016.05316.0530.0000.0000.0000.000
14A15GLN0-0.063-0.03117.704-1.055-1.0550.0000.0000.0000.000
15A16GLU-1-0.927-0.96918.01514.64014.6400.0000.0000.0000.000
16A17PHE00.0210.01116.678-0.810-0.8100.0000.0000.0000.000
17A18GLY00.0260.02221.354-0.745-0.7450.0000.0000.0000.000
18A19LYS10.8470.91721.389-15.121-15.1210.0000.0000.0000.000
19A20ALA00.0320.01924.079-0.545-0.5450.0000.0000.0000.000
20A21GLU-1-0.891-0.94225.47810.78410.7840.0000.0000.0000.000
21A22ILE0-0.034-0.02127.303-0.575-0.5750.0000.0000.0000.000
22A23GLU-1-0.977-0.98528.72810.41710.4170.0000.0000.0000.000
23A24ILE0-0.007-0.00828.915-0.469-0.4690.0000.0000.0000.000
24A25LEU00.0280.01531.054-0.453-0.4530.0000.0000.0000.000
25A26LYS10.9120.96132.661-9.988-9.9880.0000.0000.0000.000
26A27LYS10.9660.99234.448-8.787-8.7870.0000.0000.0000.000
27A28GLN0-0.015-0.01335.390-0.209-0.2090.0000.0000.0000.000
28A29ASN00.004-0.01137.195-0.372-0.3720.0000.0000.0000.000
29A30GLU-1-0.958-0.96839.0727.8877.8870.0000.0000.0000.000
30A31LEU0-0.070-0.04238.892-0.213-0.2130.0000.0000.0000.000
31A32PHE0-0.009-0.01839.060-0.179-0.1790.0000.0000.0000.000
32A33GLN00.0370.04243.094-0.083-0.0830.0000.0000.0000.000
33A34PRO00.0370.01945.042-0.171-0.1710.0000.0000.0000.000
34A35LEU0-0.008-0.00844.926-0.176-0.1760.0000.0000.0000.000
35A36PHE00.019-0.00542.458-0.146-0.1460.0000.0000.0000.000
36A37GLU-1-0.951-0.95948.0246.2486.2480.0000.0000.0000.000
37A38GLN0-0.008-0.01750.669-0.076-0.0760.0000.0000.0000.000
38A39ARG10.8260.91047.234-6.804-6.8040.0000.0000.0000.000
39A40ARG10.8750.95551.678-6.203-6.2030.0000.0000.0000.000
40A41ASP-1-0.876-0.94153.3095.7105.7100.0000.0000.0000.000
41A42ILE0-0.037-0.01954.852-0.124-0.1240.0000.0000.0000.000
42A43LEU0-0.002-0.00351.946-0.099-0.0990.0000.0000.0000.000
43A44LYS10.9120.98556.447-5.438-5.4380.0000.0000.0000.000
44A45THR0-0.127-0.07058.682-0.116-0.1160.0000.0000.0000.000
45A46ILE0-0.032-0.00357.292-0.094-0.0940.0000.0000.0000.000
46A47ASN0-0.046-0.04159.7250.0510.0510.0000.0000.0000.000
47A48ASN00.0380.02059.813-0.066-0.0660.0000.0000.0000.000
48A49PHE00.0460.02452.1920.0640.0640.0000.0000.0000.000
49A50TRP00.016-0.01849.2370.1220.1220.0000.0000.0000.000
50A51VAL00.0130.03053.7200.1170.1170.0000.0000.0000.000
51A52VAL00.0670.04154.9770.0430.0430.0000.0000.0000.000
52A53VAL0-0.051-0.02849.7080.0870.0870.0000.0000.0000.000
53A54LEU0-0.063-0.05149.6520.1200.1200.0000.0000.0000.000
54A55GLU-1-0.959-0.97550.9135.6645.6640.0000.0000.0000.000
55A56ALA0-0.0110.00551.390-0.007-0.0070.0000.0000.0000.000
56A57ALA0-0.074-0.02546.7150.1150.1150.0000.0000.0000.000
57A58GLY00.0450.01946.0810.1570.1570.0000.0000.0000.000
58A59ASP-1-0.922-0.98244.9426.6196.6190.0000.0000.0000.000
59A60GLU-1-0.938-0.96941.7047.5147.5140.0000.0000.0000.000
60A61ILE00.004-0.00244.450-0.018-0.0180.0000.0000.0000.000
61A62SER00.0140.00047.729-0.060-0.0600.0000.0000.0000.000
62A63GLN0-0.047-0.01344.137-0.018-0.0180.0000.0000.0000.000
63A64TYR0-0.044-0.01643.697-0.084-0.0840.0000.0000.0000.000
64A65ILE0-0.033-0.00750.459-0.112-0.1120.0000.0000.0000.000
65A66THR00.0070.01253.572-0.090-0.0900.0000.0000.0000.000
66A67PRO0-0.005-0.03056.841-0.015-0.0150.0000.0000.0000.000
67A68GLU-1-0.904-0.95859.3255.2405.2400.0000.0000.0000.000
68A69ASP-1-0.769-0.89754.9175.7895.7890.0000.0000.0000.000
69A70SER00.0450.01457.7900.0200.0200.0000.0000.0000.000
70A71VAL0-0.031-0.00558.895-0.046-0.0460.0000.0000.0000.000
71A72LEU0-0.064-0.02158.388-0.058-0.0580.0000.0000.0000.000
72A73LEU00.019-0.00654.2120.0040.0040.0000.0000.0000.000
73A74GLU-1-0.861-0.92558.1625.2605.2600.0000.0000.0000.000
74A75LYS10.8260.91661.027-4.960-4.9600.0000.0000.0000.000
75A76LEU0-0.039-0.00753.5750.0010.0010.0000.0000.0000.000
76A77GLU-1-0.933-0.97958.2705.3235.3230.0000.0000.0000.000
77A78ASN0-0.028-0.05654.1030.1030.1030.0000.0000.0000.000
78A79ILE00.0340.05148.7010.0020.0020.0000.0000.0000.000
79A80TYR0-0.054-0.03548.4710.0330.0330.0000.0000.0000.000
80A81VAL00.0270.01742.7010.0250.0250.0000.0000.0000.000
81A82GLU-1-0.930-0.96744.7966.7466.7460.0000.0000.0000.000
82A83ARG10.9340.97037.144-8.370-8.3700.0000.0000.0000.000
83A84PHE0-0.012-0.00741.4320.0380.0380.0000.0000.0000.000
84A85ASN0-0.102-0.06038.006-0.044-0.0440.0000.0000.0000.000
85A86GLU-1-0.858-0.93538.2418.1968.1960.0000.0000.0000.000
86A87LYS10.8320.91932.329-9.537-9.5370.0000.0000.0000.000
87A88GLU-1-0.849-0.92332.06510.50310.5030.0000.0000.0000.000
88A89PRO00.0660.04233.194-0.266-0.2660.0000.0000.0000.000
89A90ARG10.8990.92328.432-10.826-10.8260.0000.0000.0000.000
90A91ASP-1-0.818-0.88535.3028.6048.6040.0000.0000.0000.000
91A92VAL0-0.013-0.00838.291-0.078-0.0780.0000.0000.0000.000
92A93ARG10.8000.88641.395-6.925-6.9250.0000.0000.0000.000
93A94ILE00.0090.00943.250-0.043-0.0430.0000.0000.0000.000
94A95SER0-0.008-0.01046.971-0.088-0.0880.0000.0000.0000.000
95A96LEU00.0220.01350.1320.0010.0010.0000.0000.0000.000
96A97THR0-0.024-0.00253.269-0.075-0.0750.0000.0000.0000.000
97A98PHE00.0360.01555.765-0.006-0.0060.0000.0000.0000.000
98A99GLN0-0.0090.00059.743-0.099-0.0990.0000.0000.0000.000
99A100PRO00.0340.01263.3460.0200.0200.0000.0000.0000.000
100A101ASN00.0400.01362.169-0.037-0.0370.0000.0000.0000.000
101A102GLU-1-0.935-0.96665.9464.7334.7330.0000.0000.0000.000
102A103TYR00.0500.01161.899-0.035-0.0350.0000.0000.0000.000
103A104LEU00.0040.01458.8490.0120.0120.0000.0000.0000.000
104A105GLN0-0.0020.00062.848-0.148-0.1480.0000.0000.0000.000
105A106ASP-1-0.891-0.95563.4344.8754.8750.0000.0000.0000.000
106A107ASP-1-0.960-0.96563.6165.1795.1790.0000.0000.0000.000
107A108ASN0-0.034-0.03057.7420.1440.1440.0000.0000.0000.000
108A109LEU00.0360.02559.5130.0390.0390.0000.0000.0000.000
109A110THR0-0.049-0.01954.4500.0470.0470.0000.0000.0000.000
110A111LEU0-0.0080.01153.4640.0190.0190.0000.0000.0000.000
111A112VAL00.011-0.00449.2040.0880.0880.0000.0000.0000.000
112A113LYS10.8310.92644.904-7.000-7.0000.0000.0000.0000.000
113A114GLU-1-0.866-0.91744.0717.1687.1680.0000.0000.0000.000
114A115VAL0-0.0070.02039.0220.0120.0120.0000.0000.0000.000
115A116ARG10.8870.94737.893-7.743-7.7430.0000.0000.0000.000
116A117ILE00.0130.02131.7210.0620.0620.0000.0000.0000.000
117A118LYS10.8920.92231.448-9.548-9.5480.0000.0000.0000.000
118A119GLU-1-0.946-0.96324.21513.06013.0600.0000.0000.0000.000
119A120GLU-1-0.904-0.94828.22910.34810.3480.0000.0000.0000.000
120A121LYS10.8720.92023.278-11.829-11.8290.0000.0000.0000.000
121A122ALA00.0000.01025.431-0.434-0.4340.0000.0000.0000.000
122A123LYS10.8980.96023.961-11.648-11.6480.0000.0000.0000.000
123A124ASP-1-0.806-0.90421.19713.45613.4560.0000.0000.0000.000
124A125ASP-1-0.915-0.97724.70210.87210.8720.0000.0000.0000.000
125A126GLU-1-1.013-0.99018.27114.91414.9140.0000.0000.0000.000
126A127GLY0-0.041-0.01321.8160.1090.1090.0000.0000.0000.000
127A128LEU0-0.076-0.04016.3920.2670.2670.0000.0000.0000.000
128A129GLU-1-0.891-0.96620.45011.84311.8430.0000.0000.0000.000
129A130LYS10.9270.96720.170-12.694-12.6940.0000.0000.0000.000
130A131LYS10.9160.96020.081-15.585-15.5850.0000.0000.0000.000
131A132ILE00.0080.00523.4600.0360.0360.0000.0000.0000.000
132A133THR0-0.0150.00226.905-0.116-0.1160.0000.0000.0000.000
133A134LYS10.9580.98829.293-9.359-9.3590.0000.0000.0000.000
134A135TYR00.0420.01332.7630.0690.0690.0000.0000.0000.000
135A136THR0-0.020-0.00436.171-0.109-0.1090.0000.0000.0000.000
136A137SER0-0.024-0.04638.973-0.075-0.0750.0000.0000.0000.000
137A138GLN0-0.0100.00442.592-0.139-0.1390.0000.0000.0000.000
138A139PRO00.0130.01545.710-0.013-0.0130.0000.0000.0000.000
139A140VAL0-0.012-0.01748.565-0.056-0.0560.0000.0000.0000.000
140A141ASP-1-0.969-0.98651.2985.6185.6180.0000.0000.0000.000
141A142ILE00.0000.01254.025-0.039-0.0390.0000.0000.0000.000
142A143HIS0-0.072-0.03957.001-0.118-0.1180.0000.0000.0000.000
143A144TRP00.0310.01456.328-0.112-0.1120.0000.0000.0000.000
144A145LYS10.8280.90562.187-4.876-4.8760.0000.0000.0000.000
145A146PRO0-0.027-0.03365.3660.0390.0390.0000.0000.0000.000
146A147GLY0-0.051-0.02566.036-0.041-0.0410.0000.0000.0000.000
147A148LYS10.8960.95764.063-4.851-4.8510.0000.0000.0000.000
148A149SER0-0.040-0.01958.8700.0640.0640.0000.0000.0000.000
149A150LEU00.0440.03357.199-0.051-0.0510.0000.0000.0000.000
150A151PHE00.0040.03253.3460.0850.0850.0000.0000.0000.000
151A152ARG10.7790.90047.387-6.646-6.6460.0000.0000.0000.000
152A153LYS10.9070.94555.154-5.287-5.2870.0000.0000.0000.000
153A154ASN0-0.011-0.02153.792-0.001-0.0010.0000.0000.0000.000
154A155LYS11.0651.04847.839-6.584-6.5840.0000.0000.0000.000
155A156LYS10.8630.91648.864-6.318-6.3180.0000.0000.0000.000
156A157LEU00.000-0.00251.5390.0280.0280.0000.0000.0000.000
157A158PRO00.016-0.00350.4880.0480.0480.0000.0000.0000.000
158A159PRO0-0.0140.01947.653-0.140-0.1400.0000.0000.0000.000
159A160ASN00.005-0.00550.923-0.013-0.0130.0000.0000.0000.000
160A161PHE00.0600.01948.5640.1220.1220.0000.0000.0000.000
161A162PHE0-0.026-0.02750.4060.1210.1210.0000.0000.0000.000
162A163ASP-1-0.767-0.89049.9926.0906.0900.0000.0000.0000.000
163A164TYR00.001-0.00243.0730.0620.0620.0000.0000.0000.000
164A165PHE0-0.020-0.02947.0930.1330.1330.0000.0000.0000.000
165A166GLN0-0.066-0.03649.2970.0350.0350.0000.0000.0000.000
166A167TRP00.0690.07439.1860.0480.0480.0000.0000.0000.000
167A168THR0-0.005-0.00743.3300.0800.0800.0000.0000.0000.000
168A169GLY00.0060.00039.5110.1720.1720.0000.0000.0000.000
169A170GLU-1-0.994-1.01438.3178.2438.2430.0000.0000.0000.000
170A171GLU-1-0.979-0.98539.9446.9736.9730.0000.0000.0000.000
171A172GLU-1-1.015-1.00637.7268.2478.2470.0000.0000.0000.000
172A173ASP-1-0.958-0.99239.4797.4737.4730.0000.0000.0000.000
173A174ASP-1-0.913-0.93141.9456.7106.7100.0000.0000.0000.000
174A175ASP-1-0.796-0.91142.2736.9026.9020.0000.0000.0000.000
175A176PHE0-0.050-0.03543.2570.0810.0810.0000.0000.0000.000
176A177ASP-1-0.799-0.86238.3278.4318.4310.0000.0000.0000.000
177A178GLY00.033-0.00941.040-0.012-0.0120.0000.0000.0000.000
178A179ALA0-0.035-0.01036.2030.0070.0070.0000.0000.0000.000
179A180THR0-0.014-0.03237.4560.1990.1990.0000.0000.0000.000
180A181LEU00.0520.04738.470-0.036-0.0360.0000.0000.0000.000
181A182THR0-0.028-0.03139.528-0.135-0.1350.0000.0000.0000.000
182A183ILE0-0.038-0.01134.161-0.040-0.0400.0000.0000.0000.000
183A184PHE00.0490.03438.312-0.027-0.0270.0000.0000.0000.000
184A185LEU00.011-0.00140.622-0.113-0.1130.0000.0000.0000.000
185A186ALA0-0.028-0.02539.796-0.102-0.1020.0000.0000.0000.000
186A187GLU-1-1.008-1.01434.9809.1189.1180.0000.0000.0000.000
187A188ASP-1-0.859-0.90139.2387.6107.6100.0000.0000.0000.000
188A189LEU00.0180.01241.341-0.142-0.1420.0000.0000.0000.000
189A190PHE00.0270.00844.025-0.187-0.1870.0000.0000.0000.000
190A191PRO0-0.026-0.00940.941-0.189-0.1890.0000.0000.0000.000
191A192ASN0-0.078-0.04041.211-0.107-0.1070.0000.0000.0000.000
192A193ALA00.0620.05245.338-0.116-0.1160.0000.0000.0000.000
193A194VAL00.020-0.00648.747-0.096-0.0960.0000.0000.0000.000
194A195LYS10.8510.93743.570-7.288-7.2880.0000.0000.0000.000
195A196TYR00.0600.02043.541-0.104-0.1040.0000.0000.0000.000
196A197PHE00.0040.00949.837-0.108-0.1080.0000.0000.0000.000
197A198THR0-0.069-0.05652.636-0.129-0.1290.0000.0000.0000.000
198A199GLU-1-0.958-0.98249.1686.3246.3240.0000.0000.0000.000
199A200ALA00.0560.02752.792-0.071-0.0710.0000.0000.0000.000
200A201MET0-0.046-0.02754.747-0.145-0.1450.0000.0000.0000.000
201A202THR0-0.109-0.04755.142-0.101-0.1010.0000.0000.0000.000
202A203GLU-1-0.918-0.96254.8115.5245.5240.0000.0000.0000.000
203A204GLU-1-0.930-0.94357.0095.2505.2500.0000.0000.0000.000
204A205ALA0-0.104-0.05260.065-0.113-0.1130.0000.0000.0000.000
205A206SER0-0.152-0.06359.749-0.067-0.0670.0000.0000.0000.000
206A207ASP-1-0.958-0.98260.4715.1415.1410.0000.0000.0000.000