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: 6NZ2Z

Calculation Name: 1G8A-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1G8A

Chain ID: A

ChEMBL ID:

UniProt ID: O57811

Base Structure: X-ray

Registration Date: 2023-06-22

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 227
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2893391.149529
FMO2-HF: Nuclear repulsion 2804440.987832
FMO2-HF: Total energy -88950.161698
FMO2-MP2: Total energy -89215.308734


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.
-19.779-14.995.254-5.141-4.902-0.048
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 : -0.011 / q_NPA : -0.007
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].
3A3GLU-1-0.819-0.8653.725-2.2820.127-0.001-1.173-1.2360.006
4A4VAL0-0.002-0.0025.6660.1130.1130.0000.0000.0000.000
5A5LYS10.8400.9089.3601.6721.6720.0000.0000.0000.000
6A6LYS10.9480.96012.3030.3240.3240.0000.0000.0000.000
7A7HIS00.0230.02316.0810.0260.0260.0000.0000.0000.000
8A8LYS10.8220.91518.2910.3870.3870.0000.0000.0000.000
9A9PHE0-0.016-0.01121.6200.0490.0490.0000.0000.0000.000
10A10PRO00.0260.01221.514-0.036-0.0360.0000.0000.0000.000
11A11GLY00.0440.01021.1280.0190.0190.0000.0000.0000.000
12A12VAL0-0.036-0.01919.266-0.033-0.0330.0000.0000.0000.000
13A13TYR0-0.014-0.01514.2640.0530.0530.0000.0000.0000.000
14A14THR0-0.008-0.01813.0860.0830.0830.0000.0000.0000.000
15A15VAL0-0.024-0.0048.7730.0520.0520.0000.0000.0000.000
16A16ILE0-0.024-0.0186.5850.4100.4100.0000.0000.0000.000
17A17ASP-1-0.765-0.8754.472-4.744-4.595-0.001-0.033-0.1140.000
18A18ASP-1-0.854-0.9142.040-18.784-16.6285.257-3.930-3.483-0.054
19A19ASP-1-0.867-0.9084.984-0.378-0.303-0.001-0.005-0.0690.000
20A20GLY0-0.078-0.0637.9900.4580.4580.0000.0000.0000.000
21A21SER0-0.004-0.0257.6300.2360.2360.0000.0000.0000.000
22A22GLU-1-0.974-0.98010.092-0.603-0.6030.0000.0000.0000.000
23A23ARG10.7570.89111.8971.7081.7080.0000.0000.0000.000
24A24ILE00.0280.02013.942-0.086-0.0860.0000.0000.0000.000
25A25ALA0-0.018-0.01614.922-0.014-0.0140.0000.0000.0000.000
26A26THR0-0.033-0.02316.8780.0490.0490.0000.0000.0000.000
27A27LYS10.8090.91015.9890.4260.4260.0000.0000.0000.000
28A28ASN0-0.035-0.03318.3590.0660.0660.0000.0000.0000.000
29A29LEU0-0.023-0.00420.4300.0180.0180.0000.0000.0000.000
30A30VAL0-0.038-0.02023.4680.0320.0320.0000.0000.0000.000
31A31PRO0-0.020-0.01319.771-0.015-0.0150.0000.0000.0000.000
32A32GLY00.0280.00920.5030.0360.0360.0000.0000.0000.000
33A33GLN0-0.042-0.02221.771-0.010-0.0100.0000.0000.0000.000
34A34ARG10.8860.95220.7790.2670.2670.0000.0000.0000.000
35A35VAL00.0140.02122.5870.0220.0220.0000.0000.0000.000
36A36TYR0-0.014-0.02823.099-0.030-0.0300.0000.0000.0000.000
37A37GLY00.0230.01721.8770.0080.0080.0000.0000.0000.000
38A38GLU-1-0.890-0.94018.980-0.475-0.4750.0000.0000.0000.000
39A39ARG10.9320.96215.3050.7850.7850.0000.0000.0000.000
40A40VAL0-0.015-0.01015.153-0.048-0.0480.0000.0000.0000.000
41A41ILE00.0420.0328.9390.0530.0530.0000.0000.0000.000
42A42LYS10.8760.92510.7410.6040.6040.0000.0000.0000.000
43A43TRP00.021-0.0125.3090.1090.1090.0000.0000.0000.000
44A44GLU-1-0.916-0.9577.858-0.347-0.3470.0000.0000.0000.000
45A45GLY00.0020.01410.3260.1020.1020.0000.0000.0000.000
46A46GLU-1-0.816-0.87713.225-0.422-0.4220.0000.0000.0000.000
47A47GLU-1-0.805-0.90613.927-0.533-0.5330.0000.0000.0000.000
48A48TYR0-0.003-0.01712.6050.0550.0550.0000.0000.0000.000
49A49ARG10.8270.89514.5920.3820.3820.0000.0000.0000.000
50A50ILE00.0360.01212.8760.0420.0420.0000.0000.0000.000
51A51TRP0-0.086-0.07216.9150.1030.1030.0000.0000.0000.000
52A52ASN00.003-0.00919.980-0.018-0.0180.0000.0000.0000.000
53A53PRO00.0590.05520.3700.0540.0540.0000.0000.0000.000
54A54ASN00.012-0.00623.1480.0320.0320.0000.0000.0000.000
55A55ARG10.9030.95424.6740.4150.4150.0000.0000.0000.000
56A56SER00.0250.00425.0640.0050.0050.0000.0000.0000.000
57A57LYS10.8930.94326.4030.2330.2330.0000.0000.0000.000
58A58LEU00.0180.02127.491-0.003-0.0030.0000.0000.0000.000
59A59GLY00.0370.02423.611-0.011-0.0110.0000.0000.0000.000
60A60ALA00.003-0.01523.493-0.029-0.0290.0000.0000.0000.000
61A61ALA00.0200.01425.422-0.004-0.0040.0000.0000.0000.000
62A62ILE0-0.026-0.01921.5990.0030.0030.0000.0000.0000.000
63A63MET0-0.036-0.01417.894-0.013-0.0130.0000.0000.0000.000
64A64ASN0-0.057-0.03122.022-0.030-0.0300.0000.0000.0000.000
65A65GLY00.0130.01323.9810.0270.0270.0000.0000.0000.000
66A66LEU0-0.060-0.01424.9190.0250.0250.0000.0000.0000.000
67A67LYS10.9370.96226.7020.2020.2020.0000.0000.0000.000
68A68ASN0-0.052-0.04128.4000.0030.0030.0000.0000.0000.000
69A69PHE00.0660.02226.439-0.007-0.0070.0000.0000.0000.000
70A70PRO0-0.016-0.01329.024-0.001-0.0010.0000.0000.0000.000
71A71ILE0-0.0130.00128.3850.0120.0120.0000.0000.0000.000
72A72LYS10.9250.95727.1720.2140.2140.0000.0000.0000.000
73A73PRO00.0520.02024.9980.0130.0130.0000.0000.0000.000
74A74GLY00.0050.01527.8350.0130.0130.0000.0000.0000.000
75A75LYS10.7960.90231.1900.1760.1760.0000.0000.0000.000
76A76SER0-0.007-0.02433.250-0.001-0.0010.0000.0000.0000.000
77A77VAL0-0.012-0.02132.3780.0000.0000.0000.0000.0000.000
78A78LEU00.0120.02435.8080.0030.0030.0000.0000.0000.000
79A79TYR0-0.023-0.02631.630-0.017-0.0170.0000.0000.0000.000
80A80LEU00.0060.01636.8590.0050.0050.0000.0000.0000.000
81A81GLY00.0720.03537.728-0.007-0.0070.0000.0000.0000.000
82A82ILE0-0.034-0.01833.561-0.015-0.0150.0000.0000.0000.000
83A83ALA0-0.006-0.01333.292-0.015-0.0150.0000.0000.0000.000
84A84SER0-0.086-0.05133.324-0.010-0.0100.0000.0000.0000.000
85A85GLY0-0.008-0.00129.466-0.018-0.0180.0000.0000.0000.000
86A86THR0-0.038-0.04724.135-0.007-0.0070.0000.0000.0000.000
87A87THR00.0040.03026.385-0.025-0.0250.0000.0000.0000.000
88A88ALA00.0660.04927.574-0.010-0.0100.0000.0000.0000.000
89A89SER00.0270.00625.087-0.011-0.0110.0000.0000.0000.000
90A90HIS10.8350.91120.2030.5260.5260.0000.0000.0000.000
91A91VAL00.0420.01724.584-0.004-0.0040.0000.0000.0000.000
92A92SER0-0.024-0.01927.3300.0040.0040.0000.0000.0000.000
93A93ASP-1-0.700-0.81021.808-0.438-0.4380.0000.0000.0000.000
94A94ILE0-0.077-0.01623.1730.0020.0020.0000.0000.0000.000
95A95VAL0-0.026-0.00724.7410.0150.0150.0000.0000.0000.000
96A96GLY00.0520.02826.6890.0180.0180.0000.0000.0000.000
97A97TRP00.001-0.01726.4580.0150.0150.0000.0000.0000.000
98A98GLU-1-0.953-0.96529.114-0.155-0.1550.0000.0000.0000.000
99A99GLY00.0100.02231.2200.0100.0100.0000.0000.0000.000
100A100LYS10.8280.90932.7600.1600.1600.0000.0000.0000.000
101A101ILE00.0090.01230.106-0.004-0.0040.0000.0000.0000.000
102A102PHE00.0280.01534.7850.0020.0020.0000.0000.0000.000
103A103GLY00.031-0.00437.293-0.006-0.0060.0000.0000.0000.000
104A104ILE0-0.0150.00938.0000.0050.0050.0000.0000.0000.000
105A105GLU-1-0.823-0.92838.041-0.193-0.1930.0000.0000.0000.000
106A106PHE00.0640.03241.8060.0070.0070.0000.0000.0000.000
107A107SER00.0060.00043.1900.0080.0080.0000.0000.0000.000
108A108PRO00.0570.01343.153-0.006-0.0060.0000.0000.0000.000
109A109ARG10.8730.95742.4820.1260.1260.0000.0000.0000.000
110A110VAL00.0480.02438.276-0.004-0.0040.0000.0000.0000.000
111A111LEU00.0160.01038.579-0.008-0.0080.0000.0000.0000.000
112A112ARG10.7890.86438.9040.1350.1350.0000.0000.0000.000
113A113GLU-1-0.771-0.87637.084-0.153-0.1530.0000.0000.0000.000
114A114LEU0-0.0020.01133.153-0.012-0.0120.0000.0000.0000.000
115A115VAL00.0130.01533.908-0.010-0.0100.0000.0000.0000.000
116A116PRO00.0140.01131.965-0.005-0.0050.0000.0000.0000.000
117A117ILE0-0.074-0.02528.569-0.019-0.0190.0000.0000.0000.000
118A118VAL0-0.031-0.04129.457-0.017-0.0170.0000.0000.0000.000
119A119GLU-1-0.912-0.94031.895-0.174-0.1740.0000.0000.0000.000
120A120GLU-1-0.824-0.90227.726-0.233-0.2330.0000.0000.0000.000
121A121ARG10.7750.87723.2790.3460.3460.0000.0000.0000.000
122A122ARG10.9020.92830.3990.1630.1630.0000.0000.0000.000
123A123ASN0-0.024-0.00228.5550.0080.0080.0000.0000.0000.000
124A124ILE0-0.010-0.01330.1300.0020.0020.0000.0000.0000.000
125A125VAL0-0.024-0.01434.0490.0090.0090.0000.0000.0000.000
126A126PRO0-0.0070.00036.4450.0010.0010.0000.0000.0000.000
127A127ILE0-0.013-0.00838.9410.0090.0090.0000.0000.0000.000
128A128LEU0-0.019-0.01042.553-0.004-0.0040.0000.0000.0000.000
129A129GLY0-0.006-0.01645.1270.0050.0050.0000.0000.0000.000
130A130ASP-1-0.800-0.86545.800-0.120-0.1200.0000.0000.0000.000
131A131ALA00.0190.00544.0020.0020.0020.0000.0000.0000.000
132A132THR0-0.041-0.05145.9550.0010.0010.0000.0000.0000.000
133A133LYS10.8250.90549.2670.1050.1050.0000.0000.0000.000
134A134PRO00.0520.03547.0930.0010.0010.0000.0000.0000.000
135A135GLU-1-0.891-0.95348.688-0.099-0.0990.0000.0000.0000.000
136A136GLU-1-0.851-0.90850.630-0.097-0.0970.0000.0000.0000.000
137A137TYR0-0.017-0.02644.6270.0020.0020.0000.0000.0000.000
138A138ARG10.9140.94847.4180.0870.0870.0000.0000.0000.000
139A139ALA0-0.047-0.01448.9820.0010.0010.0000.0000.0000.000
140A140LEU0-0.042-0.02144.9770.0010.0010.0000.0000.0000.000
141A141VAL0-0.0150.00542.090-0.007-0.0070.0000.0000.0000.000
142A142PRO00.0010.01841.6550.0060.0060.0000.0000.0000.000
143A143LYS10.8740.91643.5250.1000.1000.0000.0000.0000.000
144A144VAL0-0.019-0.01238.681-0.001-0.0010.0000.0000.0000.000
145A145ASP-1-0.841-0.89335.919-0.145-0.1450.0000.0000.0000.000
146A146VAL0-0.007-0.01233.453-0.002-0.0020.0000.0000.0000.000
147A147ILE00.0300.03436.7150.0020.0020.0000.0000.0000.000
148A148PHE0-0.027-0.03232.106-0.008-0.0080.0000.0000.0000.000
149A149GLU-1-0.783-0.91135.968-0.156-0.1560.0000.0000.0000.000
150A150ASP-1-0.811-0.87233.604-0.257-0.2570.0000.0000.0000.000
151A151VAL00.0270.01936.7110.0000.0000.0000.0000.0000.000
152A152ALA0-0.0120.00539.6900.0040.0040.0000.0000.0000.000
153A153GLN00.004-0.01041.4330.0030.0030.0000.0000.0000.000
154A154PRO00.0520.02245.138-0.003-0.0030.0000.0000.0000.000
155A155THR00.0160.01347.3820.0000.0000.0000.0000.0000.000
156A156GLN0-0.004-0.01941.091-0.006-0.0060.0000.0000.0000.000
157A157ALA00.0220.01943.812-0.004-0.0040.0000.0000.0000.000
158A158LYS10.9230.93244.9520.1040.1040.0000.0000.0000.000
159A159ILE0-0.042-0.00243.8770.0030.0030.0000.0000.0000.000
160A160LEU00.0370.02839.7950.0010.0010.0000.0000.0000.000
161A161ILE0-0.0050.00143.6490.0010.0010.0000.0000.0000.000
162A162ASP-1-0.830-0.88746.735-0.105-0.1050.0000.0000.0000.000
163A163ASN0-0.033-0.03543.7530.0020.0020.0000.0000.0000.000
164A164ALA00.001-0.00543.7060.0000.0000.0000.0000.0000.000
165A165GLU-1-0.815-0.85045.053-0.097-0.0970.0000.0000.0000.000
166A166VAL0-0.014-0.00647.9100.0040.0040.0000.0000.0000.000
167A167TYR0-0.025-0.03443.4610.0030.0030.0000.0000.0000.000
168A168LEU0-0.0450.01439.772-0.001-0.0010.0000.0000.0000.000
169A169LYS10.8750.93338.8080.1420.1420.0000.0000.0000.000
170A170ARG11.0091.00142.9100.0890.0890.0000.0000.0000.000
171A171GLY0-0.026-0.01042.0010.0020.0020.0000.0000.0000.000
172A172GLY0-0.0070.00738.700-0.007-0.0070.0000.0000.0000.000
173A173TYR0-0.026-0.03136.0230.0040.0040.0000.0000.0000.000
174A174GLY00.0570.03138.1050.0020.0020.0000.0000.0000.000
175A175MET0-0.068-0.03130.437-0.008-0.0080.0000.0000.0000.000
176A176ILE00.0560.03236.0500.0010.0010.0000.0000.0000.000
177A177ALA0-0.014-0.00633.548-0.004-0.0040.0000.0000.0000.000
178A178VAL00.0230.03035.3610.0020.0020.0000.0000.0000.000
179A179LYS10.9350.97136.1870.2060.2060.0000.0000.0000.000
180A180SER00.0360.02038.9330.0120.0120.0000.0000.0000.000
181A181ARG10.9020.94341.0090.1580.1580.0000.0000.0000.000
182A182SER0-0.083-0.05341.8660.0020.0020.0000.0000.0000.000
183A183ILE0-0.029-0.00843.4060.0040.0040.0000.0000.0000.000
184A184ASP-1-0.779-0.87945.788-0.111-0.1110.0000.0000.0000.000
185A185VAL0-0.028-0.01345.598-0.006-0.0060.0000.0000.0000.000
186A186THR0-0.096-0.06747.1400.0000.0000.0000.0000.0000.000
187A187LYS10.8510.93047.5750.1150.1150.0000.0000.0000.000
188A188GLU-1-0.855-0.91543.916-0.135-0.1350.0000.0000.0000.000
189A189PRO00.023-0.00139.8120.0030.0030.0000.0000.0000.000
190A190GLU-1-0.760-0.86140.085-0.162-0.1620.0000.0000.0000.000
191A191GLN0-0.107-0.06041.8920.0070.0070.0000.0000.0000.000
192A192VAL00.0300.02143.5690.0020.0020.0000.0000.0000.000
193A193PHE0-0.038-0.01837.4880.0000.0000.0000.0000.0000.000
194A194ARG10.9520.95342.1850.1360.1360.0000.0000.0000.000
195A195GLU-1-0.903-0.93944.665-0.109-0.1090.0000.0000.0000.000
196A196VAL00.0490.02142.4160.0030.0030.0000.0000.0000.000
197A197GLU-1-0.869-0.93140.738-0.155-0.1550.0000.0000.0000.000
198A198ARG10.9160.96744.1360.1120.1120.0000.0000.0000.000
199A199GLU-1-0.836-0.91447.227-0.120-0.1200.0000.0000.0000.000
200A200LEU0-0.037-0.02241.5990.0010.0010.0000.0000.0000.000
201A201SER0-0.061-0.04945.6930.0030.0030.0000.0000.0000.000
202A202GLU-1-0.972-0.97046.901-0.093-0.0930.0000.0000.0000.000
203A203TYR0-0.103-0.08446.0910.0020.0020.0000.0000.0000.000
204A204PHE0-0.058-0.04042.928-0.002-0.0020.0000.0000.0000.000
205A205GLU-1-0.863-0.90941.255-0.127-0.1270.0000.0000.0000.000
206A206VAL00.013-0.01439.741-0.009-0.0090.0000.0000.0000.000
207A207ILE0-0.050-0.01235.159-0.001-0.0010.0000.0000.0000.000
208A208GLU-1-0.813-0.91131.055-0.258-0.2580.0000.0000.0000.000
209A209ARG10.8350.90535.4060.1710.1710.0000.0000.0000.000
210A210LEU0-0.043-0.00727.9950.0010.0010.0000.0000.0000.000
211A211ASN00.024-0.00132.192-0.008-0.0080.0000.0000.0000.000
212A212LEU00.0070.00129.356-0.019-0.0190.0000.0000.0000.000
213A213GLU-1-0.892-0.90029.013-0.270-0.2700.0000.0000.0000.000
214A214PRO00.0280.01125.329-0.007-0.0070.0000.0000.0000.000
215A215TYR0-0.008-0.02322.122-0.004-0.0040.0000.0000.0000.000
216A216GLU-1-0.852-0.94027.191-0.254-0.2540.0000.0000.0000.000
217A217LYS10.8660.92529.8690.2870.2870.0000.0000.0000.000
218A218ASP-1-0.839-0.90634.126-0.185-0.1850.0000.0000.0000.000
219A219HIS0-0.024-0.02433.7780.0120.0120.0000.0000.0000.000
220A220ALA0-0.005-0.00234.167-0.009-0.0090.0000.0000.0000.000
221A221LEU0-0.039-0.00930.5140.0050.0050.0000.0000.0000.000
222A222PHE00.0130.00433.9450.0000.0000.0000.0000.0000.000
223A223VAL0-0.058-0.03932.547-0.007-0.0070.0000.0000.0000.000
224A224VAL00.0120.01735.9930.0060.0060.0000.0000.0000.000
225A225ARG10.8840.93338.5600.1320.1320.0000.0000.0000.000
226A226LYS10.8550.94140.6990.1150.1150.0000.0000.0000.000
227A227THR0-0.039-0.03943.6450.0060.0060.0000.0000.0000.000