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: QY87Y

Calculation Name: 5GNG-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 5GNG

Chain ID: A

ChEMBL ID:

UniProt ID: P44251

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 214
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2849035.006217
FMO2-HF: Nuclear repulsion 2761519.478776
FMO2-HF: Total energy -87515.527441
FMO2-MP2: Total energy -87772.827371


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.
-45.168-35.82536.25-16.515-29.078-0.129
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 : -0.100 / q_NPA : -0.023
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].
3A3THR00.034-0.0022.797-2.9870.0910.359-1.666-1.770-0.006
4A4LYS10.8060.8985.1410.0160.064-0.001-0.005-0.0420.000
5A5PHE00.0210.0138.8510.1910.1910.0000.0000.0000.000
6A6TYR0-0.087-0.05810.958-0.034-0.0340.0000.0000.0000.000
7A7ASP-1-0.838-0.89714.4710.0540.0540.0000.0000.0000.000
8A8TYR0-0.035-0.03216.923-0.004-0.0040.0000.0000.0000.000
9A9GLN0-0.091-0.06219.636-0.008-0.0080.0000.0000.0000.000
10A10GLY0-0.0160.00919.475-0.004-0.0040.0000.0000.0000.000
11A11GLU-1-0.754-0.85519.6640.0750.0750.0000.0000.0000.000
12A12HIS0-0.078-0.02918.7290.0020.0020.0000.0000.0000.000
13A13LEU00.0150.02511.369-0.003-0.0030.0000.0000.0000.000
14A14ILE0-0.042-0.01912.9470.0350.0350.0000.0000.0000.000
15A15LEU00.0320.0188.069-0.001-0.0010.0000.0000.0000.000
16A16TYR00.039-0.0068.887-0.044-0.0440.0000.0000.0000.000
17A17PHE00.0630.0292.945-1.114-0.4151.278-0.438-1.5390.001
18A18ALA00.0260.0186.911-0.790-0.7900.0000.0000.0000.000
19A19GLY00.0600.0348.0070.4670.4670.0000.0000.0000.000
20A20TRP0-0.014-0.0138.8120.0330.0330.0000.0000.0000.000
21A21GLY0-0.009-0.0099.184-0.100-0.1000.0000.0000.0000.000
22A22THR0-0.101-0.07010.421-0.087-0.0870.0000.0000.0000.000
23A23PRO00.0200.02010.3990.0410.0410.0000.0000.0000.000
24A24PRO00.0370.0028.5740.0650.0650.0000.0000.0000.000
25A25ASP-1-0.840-0.92810.8130.2500.2500.0000.0000.0000.000
26A26ALA0-0.0160.00714.083-0.029-0.0290.0000.0000.0000.000
27A27VAL00.0090.00312.866-0.006-0.0060.0000.0000.0000.000
28A28ASN0-0.0020.01115.753-0.013-0.0130.0000.0000.0000.000
29A29HIS0-0.055-0.02016.790-0.036-0.0360.0000.0000.0000.000
30A30LEU0-0.076-0.02016.648-0.023-0.0230.0000.0000.0000.000
31A31ILE00.0350.00719.0670.0020.0020.0000.0000.0000.000
32A32LEU0-0.0040.00416.6540.0300.0300.0000.0000.0000.000
33A33PRO0-0.065-0.02519.937-0.026-0.0260.0000.0000.0000.000
34A34GLU-1-0.805-0.90821.9200.1250.1250.0000.0000.0000.000
35A35ASN0-0.050-0.04023.0680.0110.0110.0000.0000.0000.000
36A36HIS0-0.112-0.07018.0850.0220.0220.0000.0000.0000.000
37A37ASP-1-0.680-0.80114.8100.1040.1040.0000.0000.0000.000
38A38LEU0-0.064-0.03812.0330.0740.0740.0000.0000.0000.000
39A39LEU00.0030.0106.978-0.097-0.0970.0000.0000.0000.000
40A40ILE0-0.033-0.0077.3500.4410.4410.0000.0000.0000.000
41A41CYS0-0.011-0.0053.005-2.486-1.8731.064-0.424-1.2540.004
42A42TYR00.012-0.0142.9510.3081.3100.079-0.268-0.814-0.001
43A43ASP-1-0.799-0.8972.557-5.197-3.3171.192-1.270-1.802-0.016
44A44TYR0-0.005-0.0312.595-4.952-4.4328.246-2.617-6.149-0.007
45A45GLN0-0.022-0.0343.517-0.573-0.3130.0120.065-0.3370.000
46A46ASP-1-0.824-0.8901.889-14.694-16.5658.609-3.386-3.352-0.036
47A47LEU0-0.030-0.0342.301-2.967-0.9602.758-2.106-2.658-0.018
48A48ASN0-0.058-0.0392.9251.6532.3320.6680.408-1.756-0.002
49A49LEU00.009-0.0152.040-11.896-11.6818.589-4.163-4.641-0.047
50A50ASP-1-0.941-0.9534.0400.2920.6550.001-0.055-0.3100.000
51A51PHE0-0.015-0.0226.4650.3140.3140.0000.0000.0000.000
52A52ASP-1-0.838-0.8858.696-0.197-0.1970.0000.0000.0000.000
53A53LEU0-0.008-0.0198.7040.1230.1230.0000.0000.0000.000
54A54SER0-0.097-0.07012.6280.0700.0700.0000.0000.0000.000
55A55ALA0-0.0020.00216.1510.0210.0210.0000.0000.0000.000
56A56TYR0-0.041-0.03014.0820.0190.0190.0000.0000.0000.000
57A57ARG10.7890.86218.149-0.076-0.0760.0000.0000.0000.000
58A58HIS0-0.042-0.03019.0630.0080.0080.0000.0000.0000.000
59A59ILE00.1060.06012.3830.0110.0110.0000.0000.0000.000
60A60ARG10.8040.89915.268-0.326-0.3260.0000.0000.0000.000
61A61LEU00.0280.0269.3120.0600.0600.0000.0000.0000.000
62A62VAL0-0.017-0.01011.672-0.158-0.1580.0000.0000.0000.000
63A63ALA00.0130.0139.4720.3320.3320.0000.0000.0000.000
64A64TRP0-0.035-0.02410.243-0.312-0.3120.0000.0000.0000.000
65A65SER0-0.0050.00110.7630.2270.2270.0000.0000.0000.000
66A66MET0-0.036-0.0359.7430.0190.0190.0000.0000.0000.000
67A67GLY00.0540.0426.7480.0320.0320.0000.0000.0000.000
68A68VAL0-0.051-0.0167.1780.2250.2250.0000.0000.0000.000
69A69TRP00.012-0.0026.546-0.014-0.0140.0000.0000.0000.000
70A70VAL00.0120.0122.574-1.054-0.7671.124-0.222-1.1900.001
71A71ALA00.0190.0104.827-0.447-0.399-0.001-0.005-0.0420.000
72A72GLU-1-0.858-0.9376.488-0.032-0.0320.0000.0000.0000.000
73A73ARG10.7270.8505.474-0.274-0.2740.0000.0000.0000.000
74A74VAL0-0.011-0.0082.156-0.316-0.8202.274-0.362-1.406-0.002
75A75LEU0-0.009-0.0065.385-0.103-0.084-0.001-0.001-0.0160.000
76A76GLN00.0550.0428.8260.0190.0190.0000.0000.0000.000
77A77GLY0-0.0090.00011.132-0.100-0.1000.0000.0000.0000.000
78A78ILE0-0.020-0.00210.454-0.020-0.0200.0000.0000.0000.000
79A79ARG10.8310.90713.404-0.086-0.0860.0000.0000.0000.000
80A80LEU00.0470.03011.7490.0090.0090.0000.0000.0000.000
81A81LYS10.8710.94115.839-0.252-0.2520.0000.0000.0000.000
82A82SER0-0.018-0.01917.286-0.050-0.0500.0000.0000.0000.000
83A83ALA00.0220.02914.0770.0480.0480.0000.0000.0000.000
84A84THR0-0.015-0.01514.937-0.076-0.0760.0000.0000.0000.000
85A85ALA00.0290.02113.9560.1410.1410.0000.0000.0000.000
86A86VAL0-0.008-0.01314.540-0.106-0.1060.0000.0000.0000.000
87A87ASN0-0.047-0.03515.1820.0640.0640.0000.0000.0000.000
88A88GLY00.0440.00914.0380.0490.0490.0000.0000.0000.000
89A89THR0-0.049-0.04314.006-0.029-0.0290.0000.0000.0000.000
90A90GLY00.0830.04112.5740.0830.0830.0000.0000.0000.000
91A91LEU0-0.023-0.01013.629-0.056-0.0560.0000.0000.0000.000
92A92PRO00.0130.00111.166-0.018-0.0180.0000.0000.0000.000
93A93CYS0-0.041-0.01414.454-0.017-0.0170.0000.0000.0000.000
94A94ASP-1-0.807-0.90816.6730.0860.0860.0000.0000.0000.000
95A95ASP-1-0.844-0.92919.7970.1270.1270.0000.0000.0000.000
96A96SER0-0.051-0.00722.654-0.003-0.0030.0000.0000.0000.000
97A97PHE0-0.022-0.01019.3350.0040.0040.0000.0000.0000.000
98A98GLY0-0.0010.02217.4840.0480.0480.0000.0000.0000.000
99A99ILE0-0.049-0.00515.679-0.023-0.0230.0000.0000.0000.000
100A100PRO00.001-0.00619.089-0.019-0.0190.0000.0000.0000.000
101A101TYR00.015-0.01119.3680.0100.0100.0000.0000.0000.000
102A102ALA0-0.009-0.00921.304-0.006-0.0060.0000.0000.0000.000
103A103ILE0-0.0060.00320.974-0.007-0.0070.0000.0000.0000.000
104A104PHE00.0490.02412.582-0.001-0.0010.0000.0000.0000.000
105A105LYS10.8240.89418.596-0.023-0.0230.0000.0000.0000.000
106A106GLY00.0130.01220.324-0.011-0.0110.0000.0000.0000.000
107A107THR0-0.044-0.04517.383-0.001-0.0010.0000.0000.0000.000
108A108LEU00.0140.00415.0240.0000.0000.0000.0000.0000.000
109A109GLU-1-0.838-0.90118.073-0.002-0.0020.0000.0000.0000.000
110A110ASN0-0.080-0.03521.359-0.012-0.0120.0000.0000.0000.000
111A111LEU0-0.0140.03814.8800.0130.0130.0000.0000.0000.000
112A112THR00.008-0.01419.474-0.019-0.0190.0000.0000.0000.000
113A113GLU-1-0.734-0.87218.3710.1220.1220.0000.0000.0000.000
114A114ASN0-0.003-0.00320.8440.0210.0210.0000.0000.0000.000
115A115THR0-0.031-0.04221.8540.0090.0090.0000.0000.0000.000
116A116ARG10.8320.90714.635-0.161-0.1610.0000.0000.0000.000
117A117LEU00.0410.02519.1320.0280.0280.0000.0000.0000.000
118A118LYS10.8220.90821.452-0.092-0.0920.0000.0000.0000.000
119A119PHE00.0420.02615.9650.0010.0010.0000.0000.0000.000
120A120GLU-1-0.731-0.86616.2010.2760.2760.0000.0000.0000.000
121A121ARG10.8320.91019.363-0.148-0.1480.0000.0000.0000.000
122A122ARG10.8280.89721.563-0.194-0.1940.0000.0000.0000.000
123A123ILE0-0.0010.00915.6890.0030.0030.0000.0000.0000.000
124A124CYS0-0.013-0.00219.9720.0150.0150.0000.0000.0000.000
125A125GLY00.0620.05622.523-0.013-0.0130.0000.0000.0000.000
126A126ASP-1-0.864-0.90025.6560.1560.1560.0000.0000.0000.000
127A127LYS10.8590.91826.883-0.112-0.1120.0000.0000.0000.000
128A128ALA00.0450.02128.0000.0000.0000.0000.0000.0000.000
129A129SER0-0.036-0.06924.5120.0050.0050.0000.0000.0000.000
130A130PHE0-0.039-0.01222.0530.0150.0150.0000.0000.0000.000
131A131GLU-1-0.813-0.92023.5670.1290.1290.0000.0000.0000.000
132A132ARG10.8580.93123.765-0.218-0.2180.0000.0000.0000.000
133A133TYR00.0110.00115.5840.0330.0330.0000.0000.0000.000
134A134GLN0-0.030-0.02619.910-0.006-0.0060.0000.0000.0000.000
135A135LEU0-0.044-0.00321.835-0.018-0.0180.0000.0000.0000.000
136A136PHE0-0.038-0.00116.7780.0010.0010.0000.0000.0000.000
137A137PRO00.004-0.01415.441-0.008-0.0080.0000.0000.0000.000
138A138ALA00.0160.02214.9130.0220.0220.0000.0000.0000.000
139A139ARG10.7810.8897.397-0.380-0.3800.0000.0000.0000.000
140A140PRO00.0320.00211.5680.0170.0170.0000.0000.0000.000
141A141PHE00.0240.02112.8500.0050.0050.0000.0000.0000.000
142A142ASP-1-0.846-0.93513.763-0.014-0.0140.0000.0000.0000.000
143A143GLU-1-0.866-0.9038.636-0.183-0.1830.0000.0000.0000.000
144A144ILE0-0.0180.0019.097-0.008-0.0080.0000.0000.0000.000
145A145HIS00.0180.01510.9080.0260.0260.0000.0000.0000.000
146A146GLN00.0020.0049.332-0.030-0.0300.0000.0000.0000.000
147A147GLU-1-0.732-0.8355.9060.9490.9490.0000.0000.0000.000
148A148LEU0-0.032-0.0078.3360.0220.0220.0000.0000.0000.000
149A149THR0-0.014-0.02111.511-0.006-0.0060.0000.0000.0000.000
150A150ALA00.0140.0158.123-0.003-0.0030.0000.0000.0000.000
151A151LEU0-0.010-0.0086.587-0.001-0.0010.0000.0000.0000.000
152A152PHE00.0130.0019.557-0.002-0.0020.0000.0000.0000.000
153A153ALA0-0.0180.01012.2730.0090.0090.0000.0000.0000.000
154A154MET00.0450.0155.694-0.032-0.0320.0000.0000.0000.000
155A155ILE00.0100.01310.0910.0350.0350.0000.0000.0000.000
156A156GLN0-0.074-0.04612.5190.0430.0430.0000.0000.0000.000
157A157GLN0-0.021-0.01413.415-0.027-0.0270.0000.0000.0000.000
158A158ASP-1-0.793-0.85011.029-0.225-0.2250.0000.0000.0000.000
159A159LYS10.8850.94112.8660.0280.0280.0000.0000.0000.000
160A160ARG10.8080.88411.0760.2640.2640.0000.0000.0000.000
161A161ILE00.0090.00914.2450.0350.0350.0000.0000.0000.000
162A162ASP-1-0.778-0.84415.0080.1620.1620.0000.0000.0000.000
163A163LEU0-0.037-0.00811.117-0.035-0.0350.0000.0000.0000.000
164A164ILE0-0.020-0.00710.339-0.027-0.0270.0000.0000.0000.000
165A165HIS0-0.0260.00114.0660.0050.0050.0000.0000.0000.000
166A166TRP0-0.008-0.02310.5600.0730.0730.0000.0000.0000.000
167A167ALA0-0.029-0.02016.873-0.045-0.0450.0000.0000.0000.000
168A168ASN0-0.041-0.01018.533-0.010-0.0100.0000.0000.0000.000
169A169ALA00.0770.04317.9850.0640.0640.0000.0000.0000.000
170A170TRP0-0.045-0.02818.798-0.070-0.0700.0000.0000.0000.000
171A171VAL00.0030.00019.5440.0390.0390.0000.0000.0000.000
172A172SER0-0.042-0.04621.782-0.028-0.0280.0000.0000.0000.000
173A173SER0-0.015-0.04823.6470.0010.0010.0000.0000.0000.000
174A174ARG10.8330.89126.209-0.207-0.2070.0000.0000.0000.000
175A175ASP-1-0.732-0.85220.0560.3720.3720.0000.0000.0000.000
176A176LYS10.7840.86522.724-0.227-0.2270.0000.0000.0000.000
177A177ILE0-0.058-0.01917.130-0.029-0.0290.0000.0000.0000.000
178A178PHE00.0580.02913.567-0.011-0.0110.0000.0000.0000.000
179A179THR00.0210.01819.6930.0060.0060.0000.0000.0000.000
180A180PRO00.0390.01322.9100.0050.0050.0000.0000.0000.000
181A181ALA00.0010.01124.3310.0040.0040.0000.0000.0000.000
182A182ASN0-0.015-0.00621.528-0.017-0.0170.0000.0000.0000.000
183A183GLN0-0.023-0.01819.0390.0370.0370.0000.0000.0000.000
184A184HIS0-0.040-0.04321.1660.0150.0150.0000.0000.0000.000
185A185GLN0-0.063-0.03024.160-0.017-0.0170.0000.0000.0000.000
186A186TYR0-0.028-0.02016.396-0.006-0.0060.0000.0000.0000.000
187A187TRP00.039-0.00714.890-0.023-0.0230.0000.0000.0000.000
188A188ALA0-0.0070.00121.519-0.007-0.0070.0000.0000.0000.000
189A189LEU0-0.055-0.02324.316-0.015-0.0150.0000.0000.0000.000
190A190ARG10.7480.84218.805-0.203-0.2030.0000.0000.0000.000
191A191CYS0-0.071-0.02520.2160.0100.0100.0000.0000.0000.000
192A192ALA00.0130.01922.321-0.016-0.0160.0000.0000.0000.000
193A193VAL00.0390.01122.3590.0310.0310.0000.0000.0000.000
194A194GLN0-0.012-0.00721.604-0.041-0.0410.0000.0000.0000.000
195A195GLU-1-0.847-0.90624.0230.2070.2070.0000.0000.0000.000
196A196ILE0-0.031-0.01823.275-0.011-0.0110.0000.0000.0000.000
197A197GLU-1-0.842-0.87826.3000.1820.1820.0000.0000.0000.000
198A198GLY00.0080.00524.9960.0030.0030.0000.0000.0000.000
199A199GLU-1-0.766-0.84023.5200.2020.2020.0000.0000.0000.000
200A200HIS00.0240.02216.1980.0780.0780.0000.0000.0000.000
201A201TYR0-0.027-0.00817.1380.0410.0410.0000.0000.0000.000
202A202VAL00.0320.00719.049-0.050-0.0500.0000.0000.0000.000
203A203PHE00.0820.02914.684-0.046-0.0460.0000.0000.0000.000
204A204SER0-0.017-0.00519.748-0.033-0.0330.0000.0000.0000.000
205A205ARG10.8320.91422.991-0.246-0.2460.0000.0000.0000.000
206A206PHE0-0.0220.00121.065-0.008-0.0080.0000.0000.0000.000
207A207THR00.033-0.01022.8020.0030.0030.0000.0000.0000.000
208A208HIS00.0300.03322.206-0.003-0.0030.0000.0000.0000.000
209A209TRP00.0580.01613.1130.0480.0480.0000.0000.0000.000
210A210SER00.0290.00619.2390.0270.0270.0000.0000.0000.000
211A211ALA0-0.021-0.00521.593-0.004-0.0040.0000.0000.0000.000
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