FMODB

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

Last updated: 2024-07-23

All entries: 37450

Number of unique PDB entries: 7783

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FMODB ID: M375Z

Calculation Name: 5GHE-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 5GHE

Chain ID: A

ChEMBL ID:

UniProt ID: Q45757

Base Structure: X-ray

Registration Date: 2023-06-20

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 386
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -6219976.068305
FMO2-HF: Nuclear repulsion 6068975.853967
FMO2-HF: Total energy -151000.214338
FMO2-MP2: Total energy -151448.180445


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.
-16.36-9.79521.462-7.851-20.178-0.029
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 : -0.043 / q_NPA : -0.022
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].
3A3ILE0-0.037-0.0103.8541.5262.999-0.019-0.656-0.7980.001
4A4ASP-1-0.839-0.9106.9460.3030.3030.0000.0000.0000.000
5A5SER00.0390.0039.4950.0820.0820.0000.0000.0000.000
6A6LYS10.8100.88912.007-0.436-0.4360.0000.0000.0000.000
7A7THR0-0.0110.00416.065-0.008-0.0080.0000.0000.0000.000
8A8THR0-0.0140.00316.8370.0010.0010.0000.0000.0000.000
9A9LEU00.0230.02213.0610.0030.0030.0000.0000.0000.000
10A10PRO00.0360.00217.086-0.011-0.0110.0000.0000.0000.000
11A11ARG10.8500.89211.9540.4410.4410.0000.0000.0000.000
12A12HIS00.012-0.01111.9210.0040.0040.0000.0000.0000.000
13A13SER00.0190.01116.0160.0020.0020.0000.0000.0000.000
14A14LEU00.0080.03217.4750.0060.0060.0000.0000.0000.000
15A15ILE00.0230.00412.750-0.003-0.0030.0000.0000.0000.000
16A16HIS00.008-0.00616.0560.0010.0010.0000.0000.0000.000
17A17THR00.009-0.00618.4380.0100.0100.0000.0000.0000.000
18A18ILE0-0.0060.01116.1860.0020.0020.0000.0000.0000.000
19A19LYS10.8550.91813.1040.1660.1660.0000.0000.0000.000
20A20LEU0-0.054-0.01419.1730.0100.0100.0000.0000.0000.000
21A21ASN00.011-0.01022.1040.0150.0150.0000.0000.0000.000
22A22SER0-0.097-0.04719.890-0.001-0.0010.0000.0000.0000.000
23A23ASN0-0.034-0.02821.832-0.010-0.0100.0000.0000.0000.000
24A24LYS10.8290.92425.1930.1050.1050.0000.0000.0000.000
25A25LYS10.9260.97527.1410.0710.0710.0000.0000.0000.000
26A26TYR0-0.028-0.04629.149-0.001-0.0010.0000.0000.0000.000
27A27GLY00.0560.03525.977-0.006-0.0060.0000.0000.0000.000
28A28PRO0-0.059-0.03320.785-0.005-0.0050.0000.0000.0000.000
29A29GLY00.0660.03720.662-0.023-0.0230.0000.0000.0000.000
30A30ASP-1-0.755-0.85615.654-0.237-0.2370.0000.0000.0000.000
31A31MET0-0.053-0.00915.579-0.045-0.0450.0000.0000.0000.000
32A32THR0-0.067-0.05812.609-0.022-0.0220.0000.0000.0000.000
33A33ASN00.0090.0055.7090.3600.3600.0000.0000.0000.000
34A34GLY00.0470.0328.564-0.022-0.0220.0000.0000.0000.000
35A35ASN0-0.054-0.0349.344-0.089-0.0890.0000.0000.0000.000
36A36GLN00.0010.0106.767-0.202-0.2020.0000.0000.0000.000
37A37PHE00.0840.0289.9610.0590.0590.0000.0000.0000.000
38A38ILE0-0.063-0.02410.014-0.158-0.1580.0000.0000.0000.000
39A39ILE0-0.0080.0009.911-0.111-0.1110.0000.0000.0000.000
40A40SER0-0.005-0.0086.4100.0260.0260.0000.0000.0000.000
41A41LYS10.9060.9307.5560.1770.1770.0000.0000.0000.000
42A42GLN00.0490.0145.3410.0100.0100.0000.0000.0000.000
43A43GLU-1-0.863-0.9112.319-4.813-3.7451.083-0.530-1.620-0.004
44A44TRP00.0510.0123.728-0.542-0.1010.005-0.064-0.382-0.001
45A45ALA00.0060.0236.3980.3440.3440.0000.0000.0000.000
46A46THR0-0.015-0.0112.729-0.4440.4890.352-0.253-1.033-0.001
47A47ILE0-0.024-0.0162.2150.1180.4602.894-0.639-2.597-0.003
48A48GLY00.0300.0124.7390.2090.263-0.001-0.013-0.0400.000
49A49ALA0-0.0120.0017.7660.0410.0410.0000.0000.0000.000
50A50TYR0-0.049-0.0523.183-0.3850.3130.735-0.281-1.1520.002
51A51ILE00.0130.0108.325-0.157-0.1570.0000.0000.0000.000
52A52GLN0-0.0060.00310.448-0.082-0.0820.0000.0000.0000.000
53A53THR0-0.031-0.01811.295-0.064-0.0640.0000.0000.0000.000
54A54GLY00.0500.02912.607-0.045-0.0450.0000.0000.0000.000
55A55LEU0-0.058-0.04314.294-0.038-0.0380.0000.0000.0000.000
56A56GLY0-0.0150.00116.503-0.023-0.0230.0000.0000.0000.000
57A57LEU0-0.058-0.00615.1920.0080.0080.0000.0000.0000.000
58A58PRO0-0.036-0.00419.257-0.023-0.0230.0000.0000.0000.000
59A59VAL00.024-0.01022.2670.0030.0030.0000.0000.0000.000
60A60ASN0-0.002-0.00524.545-0.003-0.0030.0000.0000.0000.000
61A61GLU-1-0.757-0.87127.2620.0580.0580.0000.0000.0000.000
62A62GLN0-0.0030.00629.2740.0040.0040.0000.0000.0000.000
63A63GLN00.0310.01425.7230.0070.0070.0000.0000.0000.000
64A64LEU00.0270.01422.9140.0080.0080.0000.0000.0000.000
65A65ARG10.7940.87125.761-0.048-0.0480.0000.0000.0000.000
66A66THR0-0.030-0.02027.4870.0040.0040.0000.0000.0000.000
67A67HIS0-0.026-0.01418.788-0.010-0.0100.0000.0000.0000.000
68A68VAL0-0.012-0.00722.1440.0160.0160.0000.0000.0000.000
69A69ASN0-0.032-0.00124.4340.0050.0050.0000.0000.0000.000
70A70LEU00.0190.02627.8850.0020.0020.0000.0000.0000.000
71A71SER00.016-0.01429.854-0.006-0.0060.0000.0000.0000.000
72A72GLN0-0.037-0.03133.6780.0000.0000.0000.0000.0000.000
73A73ASP-1-0.878-0.92335.8580.0500.0500.0000.0000.0000.000
74A74ILE0-0.0510.00231.640-0.001-0.0010.0000.0000.0000.000
75A75SER00.0210.01234.1470.0000.0000.0000.0000.0000.000
76A76ILE00.0290.00729.0440.0070.0070.0000.0000.0000.000
77A77PRO0-0.0150.00630.138-0.006-0.0060.0000.0000.0000.000
78A78SER00.0590.02330.5140.0020.0020.0000.0000.0000.000
79A79ASP-1-0.844-0.89528.3000.0630.0630.0000.0000.0000.000
80A80PHE00.0500.01324.7160.0020.0020.0000.0000.0000.000
81A81SER0-0.074-0.04925.6840.0020.0020.0000.0000.0000.000
82A82GLN0-0.021-0.02423.712-0.006-0.0060.0000.0000.0000.000
83A83LEU00.0060.01220.350-0.001-0.0010.0000.0000.0000.000
84A84TYR0-0.0050.00421.4790.0020.0020.0000.0000.0000.000
85A85ASP-1-0.846-0.92622.7640.0070.0070.0000.0000.0000.000
86A86VAL0-0.050-0.01417.227-0.014-0.0140.0000.0000.0000.000
87A87TYR00.042-0.00117.1510.0060.0060.0000.0000.0000.000
88A88CYS00.0300.01618.628-0.005-0.0050.0000.0000.0000.000
89A89SER0-0.022-0.00318.107-0.009-0.0090.0000.0000.0000.000
90A90ASP-1-0.873-0.95012.7280.0800.0800.0000.0000.0000.000
91A91LYS10.8080.90815.037-0.009-0.0090.0000.0000.0000.000
92A92THR0-0.037-0.03317.359-0.023-0.0230.0000.0000.0000.000
93A93SER0-0.011-0.00412.908-0.042-0.0420.0000.0000.0000.000
94A94ALA00.0280.01112.936-0.049-0.0490.0000.0000.0000.000
95A95GLU-1-0.811-0.90213.930-0.076-0.0760.0000.0000.0000.000
96A96TRP0-0.061-0.02314.785-0.021-0.0210.0000.0000.0000.000
97A97TRP00.0430.0117.8520.0480.0480.0000.0000.0000.000
98A98ASN0-0.001-0.00413.735-0.061-0.0610.0000.0000.0000.000
99A99LYS10.8890.95614.8570.1470.1470.0000.0000.0000.000
100A100ASN0-0.060-0.04816.9060.0160.0160.0000.0000.0000.000
101A101LEU00.0060.02110.291-0.002-0.0020.0000.0000.0000.000
102A102TYR0-0.006-0.01910.778-0.052-0.0520.0000.0000.0000.000
103A103PRO00.017-0.00513.220-0.024-0.0240.0000.0000.0000.000
104A104LEU0-0.060-0.02615.4640.0230.0230.0000.0000.0000.000
105A105ILE00.0250.02510.5880.0110.0110.0000.0000.0000.000
106A106ILE00.0040.00613.8710.0070.0070.0000.0000.0000.000
107A107LYS10.9080.95616.1660.2730.2730.0000.0000.0000.000
108A108SER00.0540.03015.6180.0090.0090.0000.0000.0000.000
109A109ALA00.0100.01015.0120.0090.0090.0000.0000.0000.000
110A110ASN00.0310.01116.9280.0340.0340.0000.0000.0000.000
111A111ASP-1-0.893-0.92620.188-0.257-0.2570.0000.0000.0000.000
112A112ILE0-0.010-0.01016.6680.0260.0260.0000.0000.0000.000
113A113ALA0-0.007-0.00120.7340.0260.0260.0000.0000.0000.000
114A114SER0-0.072-0.04822.4050.0280.0280.0000.0000.0000.000
115A115TYR00.0100.00624.6150.0180.0180.0000.0000.0000.000
116A116GLY00.0420.02424.6670.0150.0150.0000.0000.0000.000
117A117PHE00.010-0.01323.5400.0130.0130.0000.0000.0000.000
118A118LYS10.7660.88728.0610.1470.1470.0000.0000.0000.000
119A119VAL0-0.043-0.01328.2310.0120.0120.0000.0000.0000.000
120A120ALA00.0960.04829.2830.0100.0100.0000.0000.0000.000
121A121GLY00.0060.00831.1460.0080.0080.0000.0000.0000.000
122A122ASP-1-0.898-0.94231.209-0.110-0.1100.0000.0000.0000.000
123A123PRO00.1060.06332.8370.0060.0060.0000.0000.0000.000
124A124SER0-0.069-0.05233.9290.0080.0080.0000.0000.0000.000
125A125ILE0-0.038-0.03633.3670.0060.0060.0000.0000.0000.000
126A126LYS10.8500.92337.2670.0710.0710.0000.0000.0000.000
127A127LYS10.8670.96332.1440.1120.1120.0000.0000.0000.000
128A128ASP-1-0.779-0.88635.757-0.079-0.0790.0000.0000.0000.000
129A129GLY00.0450.02834.022-0.001-0.0010.0000.0000.0000.000
130A130TYR0-0.080-0.06233.2510.0050.0050.0000.0000.0000.000
131A131PHE00.0230.00329.6050.0020.0020.0000.0000.0000.000
132A132LYS10.8750.92334.8820.0720.0720.0000.0000.0000.000
133A133LYS10.8420.90037.6240.0860.0860.0000.0000.0000.000
134A134LEU0-0.081-0.04135.4810.0010.0010.0000.0000.0000.000
135A135GLN00.006-0.01137.505-0.001-0.0010.0000.0000.0000.000
136A136ASP-1-0.799-0.87540.637-0.064-0.0640.0000.0000.0000.000
137A137GLU-1-0.946-0.97442.638-0.060-0.0600.0000.0000.0000.000
138A138LEU0-0.012-0.01240.0490.0020.0020.0000.0000.0000.000
139A139ASP-1-0.828-0.89744.169-0.053-0.0530.0000.0000.0000.000
140A140ASN0-0.097-0.06546.8550.0040.0040.0000.0000.0000.000
141A141ILE0-0.096-0.04845.7340.0010.0010.0000.0000.0000.000
142A142VAL00.0680.04247.5460.0010.0010.0000.0000.0000.000
143A143ASP-1-0.836-0.89050.138-0.038-0.0380.0000.0000.0000.000
144A144ASN0-0.100-0.06152.3910.0020.0020.0000.0000.0000.000
145A145ASN0-0.185-0.10555.6090.0030.0030.0000.0000.0000.000
146A146SER0-0.058-0.02452.2370.0000.0000.0000.0000.0000.000
147A147ASP-1-0.873-0.92755.493-0.039-0.0390.0000.0000.0000.000
148A148ASP-1-0.876-0.95855.503-0.039-0.0390.0000.0000.0000.000
149A149ASP-1-0.949-0.96654.799-0.042-0.0420.0000.0000.0000.000
150A150ALA0-0.064-0.03453.278-0.003-0.0030.0000.0000.0000.000
151A151ILE00.0690.04050.599-0.003-0.0030.0000.0000.0000.000
152A152ALA0-0.014-0.00749.941-0.003-0.0030.0000.0000.0000.000
153A153LYS10.7850.88147.4450.0560.0560.0000.0000.0000.000
154A154ALA00.0510.03746.923-0.003-0.0030.0000.0000.0000.000
155A155ILE00.0420.02345.398-0.004-0.0040.0000.0000.0000.000
156A156LYS10.8240.90444.7350.0570.0570.0000.0000.0000.000
157A157ASP-1-0.830-0.92244.148-0.067-0.0670.0000.0000.0000.000
158A158PHE00.0710.04338.856-0.006-0.0060.0000.0000.0000.000
159A159LYS10.9220.95739.8000.0600.0600.0000.0000.0000.000
160A160ALA0-0.044-0.01339.630-0.005-0.0050.0000.0000.0000.000
161A161ARG10.8800.94637.0430.0760.0760.0000.0000.0000.000
162A162CYS00.0340.02635.337-0.007-0.0070.0000.0000.0000.000
163A163GLY00.0190.00034.555-0.007-0.0070.0000.0000.0000.000
164A164ILE0-0.095-0.04133.301-0.006-0.0060.0000.0000.0000.000
165A165LEU00.0360.02730.512-0.008-0.0080.0000.0000.0000.000
166A166ILE00.0020.02129.918-0.013-0.0130.0000.0000.0000.000
167A167LYS10.9230.96430.2350.1120.1120.0000.0000.0000.000
168A168GLU-1-0.844-0.91028.155-0.150-0.1500.0000.0000.0000.000
169A169ALA00.0490.02925.732-0.016-0.0160.0000.0000.0000.000
170A170LYS10.8100.89225.3150.1550.1550.0000.0000.0000.000
171A171GLN0-0.035-0.03626.3660.0020.0020.0000.0000.0000.000
172A172TYR00.0270.01421.933-0.008-0.0080.0000.0000.0000.000
173A173GLU-1-0.810-0.87321.338-0.223-0.2230.0000.0000.0000.000
174A174GLU-1-0.812-0.88921.895-0.218-0.2180.0000.0000.0000.000
175A175ALA0-0.0090.00420.657-0.012-0.0120.0000.0000.0000.000
176A176ALA00.0140.00517.503-0.031-0.0310.0000.0000.0000.000
177A177LYS10.8300.89117.3290.1730.1730.0000.0000.0000.000
178A178ASN0-0.019-0.00219.0850.0030.0030.0000.0000.0000.000
179A179ILE00.0000.01913.327-0.003-0.0030.0000.0000.0000.000
180A180VAL00.0020.00614.398-0.046-0.0460.0000.0000.0000.000
181A181THR0-0.028-0.02715.4000.0000.0000.0000.0000.0000.000
182A182SER0-0.048-0.03415.4970.0290.0290.0000.0000.0000.000
183A183LEU0-0.010-0.0109.4570.0010.0010.0000.0000.0000.000
184A184ASP-1-0.832-0.90512.401-0.365-0.3650.0000.0000.0000.000
185A185GLN0-0.016-0.01114.4990.0400.0400.0000.0000.0000.000
186A186PHE0-0.0040.0038.1290.0330.0330.0000.0000.0000.000
187A187LEU0-0.0020.0128.1310.0460.0460.0000.0000.0000.000
188A188HIS10.7730.85512.0540.4180.4180.0000.0000.0000.000
189A189GLY00.0860.06615.6530.0360.0360.0000.0000.0000.000
190A190ASP-1-0.757-0.87418.061-0.154-0.1540.0000.0000.0000.000
191A191GLN0-0.049-0.03019.7050.0190.0190.0000.0000.0000.000
192A192LYS10.7650.88123.4330.1540.1540.0000.0000.0000.000
193A193LYS10.9070.93723.7320.1120.1120.0000.0000.0000.000
194A194LEU0-0.0390.00316.6650.0120.0120.0000.0000.0000.000
195A195GLU-1-0.734-0.82817.556-0.064-0.0640.0000.0000.0000.000
196A196GLY00.0420.01715.184-0.007-0.0070.0000.0000.0000.000
197A197VAL00.017-0.0078.7380.0370.0370.0000.0000.0000.000
198A198ILE0-0.0090.00812.2170.0410.0410.0000.0000.0000.000
199A199ASN0-0.084-0.05813.1490.0410.0410.0000.0000.0000.000
200A200ILE00.0160.01313.5230.0280.0280.0000.0000.0000.000
201A201GLN0-0.028-0.0328.8160.0110.0110.0000.0000.0000.000
202A202LYS10.8700.95012.6870.0590.0590.0000.0000.0000.000
203A203ARG10.8340.88615.9000.0420.0420.0000.0000.0000.000
204A204LEU00.0080.00112.8530.0170.0170.0000.0000.0000.000
205A205LYS10.8790.94410.293-0.089-0.0890.0000.0000.0000.000
206A206GLU-1-0.898-0.94416.0650.0150.0150.0000.0000.0000.000
207A207VAL00.0320.00919.5350.0070.0070.0000.0000.0000.000
208A208GLN0-0.039-0.02014.062-0.009-0.0090.0000.0000.0000.000
209A209THR0-0.038-0.02518.7380.0100.0100.0000.0000.0000.000
210A210ALA00.0010.00320.8500.0010.0010.0000.0000.0000.000
211A211LEU00.0230.00822.0100.0010.0010.0000.0000.0000.000
212A212ASN0-0.039-0.04318.7350.0120.0120.0000.0000.0000.000
213A213GLN0-0.036-0.01322.766-0.006-0.0060.0000.0000.0000.000
214A214ALA0-0.038-0.01125.640-0.003-0.0030.0000.0000.0000.000
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