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: 6N3LZ

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 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. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2405147.566517
FMO2-HF: Nuclear repulsion 2321809.984486
FMO2-HF: Total energy -83337.582031
FMO2-MP2: Total energy -83586.523725


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.
113.174119.5512.129-3.199-5.3070.022
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 : -0.941 / q_NPA : -0.989
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].
3A4ALA0-0.0020.0203.826-4.443-2.470-0.011-0.873-1.0890.002
4A5GLN00.1000.0502.643-10.951-7.3762.131-2.078-3.6280.020
5A6ALA0-0.027-0.0103.441-5.289-4.6310.010-0.234-0.4340.000
6A7PHE00.021-0.0074.806-4.359-4.188-0.001-0.014-0.1560.000
7A8GLU-1-0.919-0.9586.86735.76635.7660.0000.0000.0000.000
8A9ASN0-0.032-0.0165.631-6.302-6.3020.0000.0000.0000.000
9A10LEU0-0.013-0.0088.923-2.824-2.8240.0000.0000.0000.000
10A11ALA00.0140.00910.965-2.058-2.0580.0000.0000.0000.000
11A12ASN0-0.067-0.04111.621-3.005-3.0050.0000.0000.0000.000
12A13LEU0-0.010-0.00113.235-1.345-1.3450.0000.0000.0000.000
13A14GLU-1-0.880-0.94214.95915.66615.6660.0000.0000.0000.000
14A15GLN0-0.0030.00617.174-1.249-1.2490.0000.0000.0000.000
15A16GLU-1-0.847-0.89817.41115.09115.0910.0000.0000.0000.000
16A17PHE00.008-0.00316.382-0.769-0.7690.0000.0000.0000.000
17A18GLY00.0280.02220.889-0.729-0.7290.0000.0000.0000.000
18A19LYS10.7420.84420.622-15.600-15.6000.0000.0000.0000.000
19A20ALA00.0160.00723.671-0.554-0.5540.0000.0000.0000.000
20A21GLU-1-0.866-0.93225.01110.67310.6730.0000.0000.0000.000
21A22ILE0-0.031-0.01426.897-0.558-0.5580.0000.0000.0000.000
22A23GLU-1-0.978-0.98628.51010.53210.5320.0000.0000.0000.000
23A24ILE0-0.004-0.00528.201-0.477-0.4770.0000.0000.0000.000
24A25LEU00.0180.00730.467-0.445-0.4450.0000.0000.0000.000
25A26LYS10.8310.91332.805-9.470-9.4700.0000.0000.0000.000
26A27LYS10.7880.87833.977-8.781-8.7810.0000.0000.0000.000
27A28GLN0-0.002-0.00234.255-0.369-0.3690.0000.0000.0000.000
28A29ASN00.0310.00936.601-0.343-0.3430.0000.0000.0000.000
29A30GLU-1-0.853-0.90238.5647.9577.9570.0000.0000.0000.000
30A31LEU0-0.037-0.02038.204-0.234-0.2340.0000.0000.0000.000
31A32PHE0-0.002-0.01538.448-0.173-0.1730.0000.0000.0000.000
32A33GLN00.0000.02042.355-0.037-0.0370.0000.0000.0000.000
33A34PRO00.0040.00244.361-0.182-0.1820.0000.0000.0000.000
34A35LEU00.0160.00344.048-0.175-0.1750.0000.0000.0000.000
35A36PHE00.0290.00141.752-0.143-0.1430.0000.0000.0000.000
36A37GLU-1-0.857-0.89747.4516.3136.3130.0000.0000.0000.000
37A38GLN0-0.022-0.02850.011-0.060-0.0600.0000.0000.0000.000
38A39ARG10.8130.90646.563-6.846-6.8460.0000.0000.0000.000
39A40ARG10.7750.86050.965-6.238-6.2380.0000.0000.0000.000
40A41ASP-1-0.829-0.88352.5945.7475.7470.0000.0000.0000.000
41A42ILE0-0.036-0.02054.179-0.123-0.1230.0000.0000.0000.000
42A43LEU00.0060.01151.535-0.104-0.1040.0000.0000.0000.000
43A44LYS10.9130.98755.871-5.439-5.4390.0000.0000.0000.000
44A45THR0-0.126-0.07658.181-0.117-0.1170.0000.0000.0000.000
45A46ILE0-0.035-0.00556.948-0.096-0.0960.0000.0000.0000.000
46A47ASN0-0.040-0.03159.1070.0540.0540.0000.0000.0000.000
47A48ASN00.023-0.01559.424-0.045-0.0450.0000.0000.0000.000
48A49PHE00.0240.01851.8180.0750.0750.0000.0000.0000.000
49A50TRP00.014-0.01248.6810.1280.1280.0000.0000.0000.000
50A51VAL00.0330.03453.1750.1170.1170.0000.0000.0000.000
51A52VAL00.0450.03054.6790.0620.0620.0000.0000.0000.000
52A53VAL0-0.060-0.03249.3840.0900.0900.0000.0000.0000.000
53A54LEU0-0.045-0.03349.1260.1230.1230.0000.0000.0000.000
54A55GLU-1-0.862-0.91950.4985.7015.7010.0000.0000.0000.000
55A56ALA0-0.0040.00451.5200.0160.0160.0000.0000.0000.000
56A57ALA0-0.068-0.02646.4840.0940.0940.0000.0000.0000.000
57A58GLY00.0350.02646.0920.1700.1700.0000.0000.0000.000
58A59ASP-1-0.875-0.94245.2166.5896.5890.0000.0000.0000.000
59A60GLU-1-0.856-0.93441.7517.4677.4670.0000.0000.0000.000
60A61ILE0-0.007-0.02044.458-0.008-0.0080.0000.0000.0000.000
61A62SER0-0.030-0.04147.862-0.109-0.1090.0000.0000.0000.000
62A63GLN0-0.102-0.03243.262-0.109-0.1090.0000.0000.0000.000
63A64TYR0-0.075-0.03543.377-0.042-0.0420.0000.0000.0000.000
64A65ILE0-0.047-0.01650.348-0.097-0.0970.0000.0000.0000.000
65A66THR0-0.016-0.01953.477-0.089-0.0890.0000.0000.0000.000
66A67PRO0-0.010-0.01756.633-0.016-0.0160.0000.0000.0000.000
67A68GLU-1-0.894-0.96659.1635.2405.2400.0000.0000.0000.000
68A69ASP-1-0.751-0.85854.7555.8225.8220.0000.0000.0000.000
69A70SER00.021-0.01357.3810.0050.0050.0000.0000.0000.000
70A71VAL0-0.071-0.03158.642-0.051-0.0510.0000.0000.0000.000
71A72LEU0-0.060-0.01957.763-0.063-0.0630.0000.0000.0000.000
72A73LEU00.009-0.00453.8530.0050.0050.0000.0000.0000.000
73A74GLU-1-0.854-0.90357.7395.1915.1910.0000.0000.0000.000
74A75LYS10.7990.89160.430-5.015-5.0150.0000.0000.0000.000
75A76LEU0-0.036-0.00753.1270.0010.0010.0000.0000.0000.000
76A77GLU-1-0.924-0.97057.7345.2415.2410.0000.0000.0000.000
77A78ASN0-0.051-0.07453.4610.0980.0980.0000.0000.0000.000
78A79ILE00.0440.04948.1390.0050.0050.0000.0000.0000.000
79A80TYR0-0.042-0.02648.3610.0160.0160.0000.0000.0000.000
80A81VAL00.0340.01242.1350.0250.0250.0000.0000.0000.000
81A82GLU-1-0.880-0.91543.8296.8366.8360.0000.0000.0000.000
82A83ARG10.8410.89835.285-8.572-8.5720.0000.0000.0000.000
83A84PHE0-0.031-0.02140.0950.0730.0730.0000.0000.0000.000
84A85ASN0-0.057-0.02637.076-0.045-0.0450.0000.0000.0000.000
85A86GLU-1-0.804-0.91037.1578.6058.6050.0000.0000.0000.000
86A87LYS10.8380.92630.597-9.814-9.8140.0000.0000.0000.000
87A88GLU-1-0.839-0.90430.93910.66210.6620.0000.0000.0000.000
88A89PRO00.0430.03732.358-0.254-0.2540.0000.0000.0000.000
89A90ARG10.8780.89327.362-10.786-10.7860.0000.0000.0000.000
90A91ASP-1-0.788-0.86234.6018.5208.5200.0000.0000.0000.000
91A92VAL0-0.013-0.01637.462-0.046-0.0460.0000.0000.0000.000
92A93ARG10.7700.86640.566-7.045-7.0450.0000.0000.0000.000
93A94ILE00.0270.03042.244-0.057-0.0570.0000.0000.0000.000
94A95SER0-0.008-0.02045.930-0.063-0.0630.0000.0000.0000.000
95A96LEU00.0430.03049.116-0.007-0.0070.0000.0000.0000.000
96A97THR0-0.032-0.02252.399-0.043-0.0430.0000.0000.0000.000
97A98PHE00.0310.01154.9280.0030.0030.0000.0000.0000.000
98A99GLN0-0.020-0.00359.051-0.117-0.1170.0000.0000.0000.000
99A100PRO00.008-0.00462.7830.0200.0200.0000.0000.0000.000
100A101ASN00.0220.00861.504-0.037-0.0370.0000.0000.0000.000
101A102GLU-1-0.829-0.91065.4534.7464.7460.0000.0000.0000.000
102A103TYR00.034-0.00161.210-0.019-0.0190.0000.0000.0000.000
103A104LEU00.0200.03557.8180.0210.0210.0000.0000.0000.000
104A105GLN0-0.012-0.01161.868-0.158-0.1580.0000.0000.0000.000
105A106ASP-1-0.829-0.92262.6784.9094.9090.0000.0000.0000.000
106A107ASP-1-0.908-0.93562.3885.1555.1550.0000.0000.0000.000
107A108ASN00.012-0.01157.9120.1370.1370.0000.0000.0000.000
108A109LEU0-0.0100.02058.4070.0680.0680.0000.0000.0000.000
109A110THR0-0.056-0.03553.7890.0340.0340.0000.0000.0000.000
110A111LEU00.0240.03852.7160.0240.0240.0000.0000.0000.000
111A112VAL0-0.005-0.00548.6330.1000.1000.0000.0000.0000.000
112A113LYS10.8240.90544.544-7.026-7.0260.0000.0000.0000.000
113A114GLU-1-0.810-0.87343.1337.3537.3530.0000.0000.0000.000
114A115VAL0-0.0230.01938.770-0.018-0.0180.0000.0000.0000.000
115A116ARG10.7900.88037.770-7.732-7.7320.0000.0000.0000.000
116A117ILE00.0100.01531.0960.0460.0460.0000.0000.0000.000
117A118LYS10.8010.87730.210-10.107-10.1070.0000.0000.0000.000
118A119GLU-1-0.858-0.90823.71513.42313.4230.0000.0000.0000.000
119A120GLU-1-0.818-0.88927.83110.16010.1600.0000.0000.0000.000
120A121LYS10.8480.90923.275-11.610-11.6100.0000.0000.0000.000
121A122ALA0-0.015-0.00325.408-0.427-0.4270.0000.0000.0000.000
122A123LYS10.8190.91023.083-12.376-12.3760.0000.0000.0000.000
123A124ASP-1-0.791-0.88921.49813.28213.2820.0000.0000.0000.000
124A125ASP-1-0.906-0.96024.76311.04711.0470.0000.0000.0000.000
125A126GLU-1-0.966-0.96418.28514.48914.4890.0000.0000.0000.000
126A127GLY0-0.032-0.01321.4020.2580.2580.0000.0000.0000.000
127A128LEU0-0.050-0.03016.6350.2380.2380.0000.0000.0000.000
128A129GLU-1-0.834-0.91620.26512.04412.0440.0000.0000.0000.000
129A130LYS10.8670.91919.900-12.628-12.6280.0000.0000.0000.000
130A131LYS10.8320.89619.848-15.160-15.1600.0000.0000.0000.000
131A132ILE00.0090.00123.4220.0140.0140.0000.0000.0000.000
132A133THR0-0.019-0.00326.786-0.108-0.1080.0000.0000.0000.000
133A134LYS10.8470.92628.857-8.991-8.9910.0000.0000.0000.000
134A135TYR00.0580.01831.5650.1120.1120.0000.0000.0000.000
135A136THR0-0.046-0.02435.482-0.104-0.1040.0000.0000.0000.000
136A137SER0-0.001-0.03838.643-0.081-0.0810.0000.0000.0000.000
137A138GLN0-0.0020.00442.240-0.095-0.0950.0000.0000.0000.000
138A139PRO00.0000.01445.435-0.002-0.0020.0000.0000.0000.000
139A140VAL0-0.019-0.01448.229-0.087-0.0870.0000.0000.0000.000
140A141ASP-1-0.915-0.95950.6695.6265.6260.0000.0000.0000.000
141A142ILE0-0.026-0.01053.2490.0210.0210.0000.0000.0000.000
142A143HIS0-0.067-0.02956.744-0.138-0.1380.0000.0000.0000.000
143A144TRP00.0290.00755.530-0.101-0.1010.0000.0000.0000.000
144A145LYS10.7550.86761.564-4.953-4.9530.0000.0000.0000.000
145A146PRO0-0.027-0.02364.8970.0340.0340.0000.0000.0000.000
146A147GLY0-0.058-0.03966.414-0.043-0.0430.0000.0000.0000.000
147A148LYS10.8120.91464.028-4.808-4.8080.0000.0000.0000.000
148A149SER0-0.029-0.02758.9120.0750.0750.0000.0000.0000.000
149A150LEU00.0400.02856.832-0.051-0.0510.0000.0000.0000.000
150A151PHE0-0.0070.02353.1570.0730.0730.0000.0000.0000.000
151A152ARG10.7490.83447.580-6.604-6.6040.0000.0000.0000.000
152A153LYS10.9020.94454.699-5.266-5.2660.0000.0000.0000.000
153A154ASN0-0.029-0.03553.6470.0270.0270.0000.0000.0000.000
154A155LYS10.8710.93045.469-6.940-6.9400.0000.0000.0000.000
155A156LYS10.8150.88846.785-6.530-6.5300.0000.0000.0000.000
156A157LEU0-0.0210.01151.543-0.044-0.0440.0000.0000.0000.000
157A158PRO00.0120.00050.5560.0710.0710.0000.0000.0000.000
158A159PRO0-0.0110.01147.599-0.133-0.1330.0000.0000.0000.000
159A160ASN0-0.0180.00050.9040.0110.0110.0000.0000.0000.000
160A161PHE00.0480.00748.6890.1280.1280.0000.0000.0000.000
161A162PHE0-0.008-0.01850.1970.1120.1120.0000.0000.0000.000
162A163ASP-1-0.761-0.87849.8406.1246.1240.0000.0000.0000.000
163A164TYR0-0.028-0.02142.3750.0480.0480.0000.0000.0000.000
164A165PHE00.012-0.01346.6430.1240.1240.0000.0000.0000.000
165A166GLN0-0.058-0.02848.6610.0580.0580.0000.0000.0000.000
166A167TRP00.0390.05038.8650.0750.0750.0000.0000.0000.000
167A168THR0-0.005-0.03443.1280.0950.0950.0000.0000.0000.000
168A169GLY00.0420.02239.1710.1620.1620.0000.0000.0000.000
169A170GLU-1-0.952-0.98138.0268.5228.5220.0000.0000.0000.000
170A171GLU-1-0.842-0.87639.8337.0097.0090.0000.0000.0000.000
171A172GLU-1-0.976-0.98838.1408.0828.0820.0000.0000.0000.000
172A173ASP-1-0.869-0.93139.7797.1587.1580.0000.0000.0000.000
173A174ASP-1-0.849-0.94242.2836.6206.6200.0000.0000.0000.000
174A175ASP-1-0.825-0.87342.5006.8346.8340.0000.0000.0000.000
175A176PHE00.0300.01943.6210.0350.0350.0000.0000.0000.000
176A177ASP-1-0.789-0.86637.8588.4668.4660.0000.0000.0000.000
177A178GLY00.0280.00340.903-0.032-0.0320.0000.0000.0000.000
178A179ALA0-0.0420.00035.8500.0200.0200.0000.0000.0000.000
179A180THR0-0.018-0.04137.0150.1610.1610.0000.0000.0000.000
180A181LEU00.0210.03538.077-0.016-0.0160.0000.0000.0000.000
181A182THR0-0.013-0.02538.867-0.136-0.1360.0000.0000.0000.000
182A183ILE0-0.045-0.01033.863-0.030-0.0300.0000.0000.0000.000
183A184PHE00.0300.02037.765-0.020-0.0200.0000.0000.0000.000
184A185LEU00.0220.00440.337-0.125-0.1250.0000.0000.0000.000
185A186ALA0-0.023-0.02439.353-0.119-0.1190.0000.0000.0000.000
186A187GLU-1-0.912-0.95134.6409.0809.0800.0000.0000.0000.000
187A188ASP-1-0.846-0.86638.6587.6947.6940.0000.0000.0000.000
188A189LEU00.0260.02240.821-0.137-0.1370.0000.0000.0000.000
189A190PHE00.0550.01943.498-0.183-0.1830.0000.0000.0000.000
190A191PRO0-0.033-0.01240.356-0.172-0.1720.0000.0000.0000.000
191A192ASN0-0.036-0.03540.965-0.137-0.1370.0000.0000.0000.000
192A193ALA00.0260.03144.928-0.127-0.1270.0000.0000.0000.000
193A194VAL00.017-0.00748.408-0.098-0.0980.0000.0000.0000.000
194A195LYS10.8210.92443.025-7.330-7.3300.0000.0000.0000.000
195A196TYR00.0600.01143.228-0.121-0.1210.0000.0000.0000.000
196A197PHE00.0190.01749.899-0.116-0.1160.0000.0000.0000.000
197A198THR0-0.054-0.04752.579-0.134-0.1340.0000.0000.0000.000
198A199GLU-1-0.952-0.96648.8206.4216.4210.0000.0000.0000.000
199A200ALA00.0600.03052.866-0.083-0.0830.0000.0000.0000.000
200A201MET0-0.034-0.02255.013-0.141-0.1410.0000.0000.0000.000
201A202THR0-0.095-0.05055.513-0.108-0.1080.0000.0000.0000.000
202A203GLU-1-0.927-0.95655.1665.6535.6530.0000.0000.0000.000
203A204GLU-1-0.917-0.96657.2665.3085.3080.0000.0000.0000.000
204A205ALA0-0.099-0.04160.221-0.115-0.1150.0000.0000.0000.000
205A206SER0-0.116-0.06159.391-0.063-0.0630.0000.0000.0000.000
206A207ASP-1-1.034-1.00860.9295.0885.0880.0000.0000.0000.000