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: 85Q1Y

Calculation Name: 1GG3-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1GG3

Chain ID: A

ChEMBL ID:

UniProt ID: P11171

Base Structure: X-ray

Registration Date: 2023-06-26

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 279
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -3962426.418546
FMO2-HF: Nuclear repulsion 3849150.805021
FMO2-HF: Total energy -113275.613525
FMO2-MP2: Total energy -113606.860341


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.
-24.889-18.35615.508-7.32-14.723-0.057
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 : -0.075 / q_NPA : -0.052
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].
3A3CYS0-0.075-0.0343.792-1.992-0.172-0.018-0.710-1.091-0.001
4A4LYS10.9320.9735.5522.1172.1170.0000.0000.0000.000
5A5VAL0-0.021-0.0189.0410.0690.0690.0000.0000.0000.000
6A6SER0-0.037-0.01311.6360.1470.1470.0000.0000.0000.000
7A7LEU00.043-0.01115.085-0.018-0.0180.0000.0000.0000.000
8A8LEU0-0.058-0.04017.5730.0550.0550.0000.0000.0000.000
9A9ASP-1-0.819-0.91220.930-0.568-0.5680.0000.0000.0000.000
10A10ASP-1-0.924-0.95820.449-0.445-0.4450.0000.0000.0000.000
11A11THR00.0270.04917.8440.0120.0120.0000.0000.0000.000
12A12VAL0-0.068-0.04412.808-0.106-0.1060.0000.0000.0000.000
13A13TYR00.0430.02611.0700.0410.0410.0000.0000.0000.000
14A14GLU-1-0.839-0.9389.748-1.481-1.4810.0000.0000.0000.000
15A15CYS0-0.024-0.0017.6530.0400.0400.0000.0000.0000.000
16A16VAL00.0380.0172.462-2.000-1.0280.412-0.505-0.8790.001
17A17VAL0-0.0020.0182.6311.3292.8130.197-0.542-1.139-0.002
18A18GLU-1-0.879-0.9481.984-8.712-10.4827.509-3.143-2.597-0.034
19A19LYS10.9370.9442.796-4.632-3.3870.355-0.422-1.1790.001
20A20HIS0-0.063-0.0343.6810.7930.9140.0070.111-0.2400.000
21A21ALA00.0750.0575.5140.3750.3750.0000.0000.0000.000
22A22LYS10.8840.9437.3090.8920.8920.0000.0000.0000.000
23A23GLY00.0790.0209.326-0.311-0.3110.0000.0000.0000.000
24A24GLN00.0780.04110.853-0.140-0.1400.0000.0000.0000.000
25A25ASP-1-0.924-0.96212.025-0.979-0.9790.0000.0000.0000.000
26A26LEU0-0.046-0.0039.3670.0280.0280.0000.0000.0000.000
27A27LEU00.0360.0097.194-0.029-0.0290.0000.0000.0000.000
28A28LYS10.9100.9809.6351.1941.1940.0000.0000.0000.000
29A29ARG10.8860.95713.2530.8680.8680.0000.0000.0000.000
30A30VAL0-0.038-0.0159.4940.0640.0640.0000.0000.0000.000
31A31CYS0-0.034-0.04112.7500.0740.0740.0000.0000.0000.000
32A32GLU-1-0.833-0.90414.355-0.811-0.8110.0000.0000.0000.000
33A33HIS00.011-0.00915.2710.0830.0830.0000.0000.0000.000
34A34LEU0-0.058-0.01014.9660.0680.0680.0000.0000.0000.000
35A35ASN0-0.005-0.01217.1690.0930.0930.0000.0000.0000.000
36A36LEU0-0.063-0.02219.9390.0650.0650.0000.0000.0000.000
37A37LEU0-0.031-0.01720.8810.0460.0460.0000.0000.0000.000
38A38GLU-1-0.856-0.91022.137-0.505-0.5050.0000.0000.0000.000
39A39GLU-1-0.858-0.91824.348-0.370-0.3700.0000.0000.0000.000
40A40ASP-1-0.863-0.93619.540-0.745-0.7450.0000.0000.0000.000
41A41TYR0-0.084-0.06221.865-0.009-0.0090.0000.0000.0000.000
42A42PHE00.0270.01223.2690.0060.0060.0000.0000.0000.000
43A43GLY00.051-0.06422.962-0.036-0.0360.0000.0000.0000.000
44A44LEU00.0160.03220.394-0.026-0.0260.0000.0000.0000.000
45A45ALA00.013-0.02517.626-0.019-0.0190.0000.0000.0000.000
46A46ILE00.0110.03111.490-0.015-0.0150.0000.0000.0000.000
47A47TRP0-0.049-0.01014.2750.0630.0630.0000.0000.0000.000
48A48ASP-1-0.833-0.90511.202-1.095-1.0950.0000.0000.0000.000
49A49ASN0-0.034-0.02913.3000.0490.0490.0000.0000.0000.000
50A50ALA00.017-0.00915.8410.0250.0250.0000.0000.0000.000
51A51THR0-0.017-0.01018.1730.0330.0330.0000.0000.0000.000
52A52SER0-0.046-0.03720.8940.0180.0180.0000.0000.0000.000
53A53LYS10.9551.01218.3970.4720.4720.0000.0000.0000.000
54A54THR0-0.037-0.05015.7590.1270.1270.0000.0000.0000.000
55A55TRP0-0.0110.02715.647-0.057-0.0570.0000.0000.0000.000
56A56LEU00.0350.0319.6510.0740.0740.0000.0000.0000.000
57A57ASP-1-0.904-0.98913.775-0.539-0.5390.0000.0000.0000.000
58A58SER00.049-0.01113.633-0.132-0.1320.0000.0000.0000.000
59A59ALA00.0050.00614.459-0.045-0.0450.0000.0000.0000.000
60A60LYS10.8580.92613.0860.5310.5310.0000.0000.0000.000
61A61GLU-1-0.864-0.9367.942-0.308-0.3080.0000.0000.0000.000
62A62ILE00.0520.0325.8870.3910.3910.0000.0000.0000.000
63A63LYS10.9821.0044.863-3.023-3.0230.0000.0000.0000.000
64A64LYS10.8590.9076.2430.3950.3950.0000.0000.0000.000
65A65GLN0-0.046-0.0149.6580.2360.2360.0000.0000.0000.000
66A66VAL00.0740.0745.4030.0690.0690.0000.0000.0000.000
67A67ARG10.8860.9477.8280.0530.0530.0000.0000.0000.000
68A68GLY0-0.022-0.0068.499-0.068-0.0680.0000.0000.0000.000
69A69VAL00.012-0.0038.0880.0090.0090.0000.0000.0000.000
70A70PRO0-0.0150.0095.586-0.145-0.1450.0000.0000.0000.000
71A71TRP00.012-0.0022.470-6.439-3.7627.047-2.105-7.619-0.022
72A72ASN00.0130.0055.215-0.608-0.624-0.001-0.0040.0210.000
73A73PHE0-0.009-0.0316.5310.0440.0440.0000.0000.0000.000
74A74THR0-0.032-0.01011.4820.0470.0470.0000.0000.0000.000
75A75PHE00.0400.01615.008-0.049-0.0490.0000.0000.0000.000
76A76ASN0-0.058-0.04016.7280.0290.0290.0000.0000.0000.000
77A77VAL00.0740.08920.033-0.025-0.0250.0000.0000.0000.000
78A78LYS10.7150.85619.7960.6120.6120.0000.0000.0000.000
79A79PHE0-0.0590.00523.1030.0380.0380.0000.0000.0000.000
80A80TYR0-0.046-0.05626.098-0.011-0.0110.0000.0000.0000.000
81A81PRO00.0340.04829.0390.0180.0180.0000.0000.0000.000
82A82PRO0-0.0210.00131.5830.0060.0060.0000.0000.0000.000
83A83ASP-1-0.814-0.93435.185-0.212-0.2120.0000.0000.0000.000
84A84PRO00.0090.00032.928-0.005-0.0050.0000.0000.0000.000
85A85ALA00.0510.04434.307-0.011-0.0110.0000.0000.0000.000
86A86GLN0-0.087-0.03535.6440.0040.0040.0000.0000.0000.000
87A87LEU0-0.081-0.03129.601-0.005-0.0050.0000.0000.0000.000
88A88THR0-0.009-0.00631.1070.0220.0220.0000.0000.0000.000
89A89GLU-1-0.890-0.96227.495-0.398-0.3980.0000.0000.0000.000
90A90ASP-1-0.877-0.96931.410-0.283-0.2830.0000.0000.0000.000
91A91ILE00.0490.04625.878-0.001-0.0010.0000.0000.0000.000
92A92THR0-0.010-0.03226.579-0.031-0.0310.0000.0000.0000.000
93A93ARG10.8440.93127.7000.2780.2780.0000.0000.0000.000
94A94TYR00.0500.04425.686-0.009-0.0090.0000.0000.0000.000
95A95TYR00.0410.00322.561-0.009-0.0090.0000.0000.0000.000
96A96LEU0-0.051-0.02525.875-0.009-0.0090.0000.0000.0000.000
97A97CYS00.0170.01827.9260.0170.0170.0000.0000.0000.000
98A98LEU00.0410.02824.1070.0080.0080.0000.0000.0000.000
99A99GLN00.0200.02322.952-0.055-0.0550.0000.0000.0000.000
100A100LEU0-0.038-0.01125.8780.0170.0170.0000.0000.0000.000
101A101ARG10.9610.99428.6210.3450.3450.0000.0000.0000.000
102A102GLN00.0070.01123.2730.0470.0470.0000.0000.0000.000
103A103ASP-1-0.870-0.91926.604-0.379-0.3790.0000.0000.0000.000
104A104ILE0-0.024-0.02228.3780.0180.0180.0000.0000.0000.000
105A105VAL00.0200.02728.6280.0220.0220.0000.0000.0000.000
106A106ALA0-0.042-0.01726.8170.0110.0110.0000.0000.0000.000
107A107GLY0-0.025-0.01728.8840.0050.0050.0000.0000.0000.000
108A108ARG10.8220.91124.5430.3910.3910.0000.0000.0000.000
109A109LEU00.001-0.00630.2970.0020.0020.0000.0000.0000.000
110A110PRO0-0.033-0.00133.2270.0050.0050.0000.0000.0000.000
111A111CYS0-0.002-0.01336.3030.0020.0020.0000.0000.0000.000
112A112SER00.0120.01139.2590.0000.0000.0000.0000.0000.000
113A113PHE00.0880.05341.461-0.008-0.0080.0000.0000.0000.000
114A114ALA00.0040.00943.306-0.003-0.0030.0000.0000.0000.000
115A115THR00.006-0.02139.341-0.002-0.0020.0000.0000.0000.000
116A116LEU00.0050.00436.629-0.007-0.0070.0000.0000.0000.000
117A117ALA00.0730.02739.315-0.008-0.0080.0000.0000.0000.000
118A118LEU0-0.0380.00741.600-0.001-0.0010.0000.0000.0000.000
119A119LEU00.0050.03636.238-0.003-0.0030.0000.0000.0000.000
120A120GLY00.0370.01336.947-0.010-0.0100.0000.0000.0000.000
121A121SER0-0.026-0.05737.727-0.006-0.0060.0000.0000.0000.000
122A122TYR00.006-0.01838.0980.0010.0010.0000.0000.0000.000
123A123THR0-0.030-0.01133.100-0.015-0.0150.0000.0000.0000.000
124A124ILE00.010-0.00535.134-0.008-0.0080.0000.0000.0000.000
125A125GLN0-0.0160.00337.4060.0080.0080.0000.0000.0000.000
126A126SER0-0.021-0.02533.7220.0070.0070.0000.0000.0000.000
127A127GLU-1-0.971-0.98330.147-0.334-0.3340.0000.0000.0000.000
128A128LEU0-0.052-0.01433.9040.0010.0010.0000.0000.0000.000
129A129GLY00.0120.02137.1070.0040.0040.0000.0000.0000.000
130A130ASP-1-0.858-0.94139.624-0.154-0.1540.0000.0000.0000.000
131A131TYR0-0.021-0.02343.0770.0060.0060.0000.0000.0000.000
132A132ASP-1-0.773-0.88443.879-0.135-0.1350.0000.0000.0000.000
133A133PRO0-0.066-0.03845.190-0.002-0.0020.0000.0000.0000.000
134A134GLU-1-0.881-0.96342.167-0.148-0.1480.0000.0000.0000.000
135A135LEU0-0.0870.00340.405-0.003-0.0030.0000.0000.0000.000
136A136HIS0-0.147-0.09542.5970.0030.0030.0000.0000.0000.000
137A137GLY00.0500.03943.679-0.004-0.0040.0000.0000.0000.000
138A138VAL0-0.063-0.01044.677-0.005-0.0050.0000.0000.0000.000
139A139ASP-1-0.938-1.04042.878-0.126-0.1260.0000.0000.0000.000
140A140TYR00.0700.02139.9480.0000.0000.0000.0000.0000.000
141A141VAL0-0.013-0.02637.791-0.010-0.0100.0000.0000.0000.000
142A142SER0-0.042-0.01637.174-0.013-0.0130.0000.0000.0000.000
143A143ASP-1-0.889-0.92733.921-0.188-0.1880.0000.0000.0000.000
144A144PHE0-0.092-0.05131.941-0.023-0.0230.0000.0000.0000.000
145A145LYS10.8500.92826.0680.3520.3520.0000.0000.0000.000
146A146LEU00.032-0.00631.948-0.014-0.0140.0000.0000.0000.000
147A147ALA0-0.066-0.04934.6870.0020.0020.0000.0000.0000.000
148A148PRO0-0.037-0.00232.7760.0020.0020.0000.0000.0000.000
149A149ASN0-0.077-0.03233.799-0.001-0.0010.0000.0000.0000.000
150A150GLN00.1120.06634.749-0.008-0.0080.0000.0000.0000.000
151A151THR0-0.018-0.00637.9530.0050.0050.0000.0000.0000.000
152A152LYS11.0581.02141.6440.1220.1220.0000.0000.0000.000
153A153GLU-1-0.914-0.94743.809-0.115-0.1150.0000.0000.0000.000
154A154LEU0-0.061-0.05139.2360.0000.0000.0000.0000.0000.000
155A155GLU-1-0.880-0.94739.468-0.163-0.1630.0000.0000.0000.000
156A156GLU-1-0.881-0.94142.417-0.126-0.1260.0000.0000.0000.000
157A157LYS10.8880.95444.9000.1230.1230.0000.0000.0000.000
158A158VAL0-0.0080.02039.708-0.002-0.0020.0000.0000.0000.000
159A159MET00.0150.03842.3830.0020.0020.0000.0000.0000.000
160A160GLU-1-0.953-0.97344.464-0.116-0.1160.0000.0000.0000.000
161A161LEU0-0.058-0.03744.0980.0030.0030.0000.0000.0000.000
162A162HIS00.0400.05441.3630.0050.0050.0000.0000.0000.000
163A163LYS10.8670.95243.9250.1280.1280.0000.0000.0000.000
164A164SER0-0.136-0.06247.1650.0030.0030.0000.0000.0000.000
165A165TYR0-0.044-0.02842.2650.0030.0030.0000.0000.0000.000
166A166ARG10.9940.98745.5840.1330.1330.0000.0000.0000.000
167A167SER0-0.113-0.06645.1340.0020.0020.0000.0000.0000.000
168A168MET0-0.0270.02041.095-0.003-0.0030.0000.0000.0000.000
169A169THR0-0.002-0.02938.945-0.009-0.0090.0000.0000.0000.000
170A170PRO00.0850.02234.8820.0010.0010.0000.0000.0000.000
171A171ALA00.0610.04235.183-0.006-0.0060.0000.0000.0000.000
172A172GLN0-0.0200.00436.1770.0010.0010.0000.0000.0000.000
173A173ALA00.0290.01337.3730.0030.0030.0000.0000.0000.000
174A174ASP-1-0.807-0.92032.553-0.304-0.3040.0000.0000.0000.000
175A175LEU0-0.036-0.02835.569-0.006-0.0060.0000.0000.0000.000
176A176GLU-1-0.863-0.92137.604-0.178-0.1780.0000.0000.0000.000
177A177PHE0-0.0100.00233.1140.0030.0030.0000.0000.0000.000
178A178LEU0-0.045-0.04532.1260.0010.0010.0000.0000.0000.000
179A179GLU-1-0.825-0.90536.034-0.207-0.2070.0000.0000.0000.000
180A180ASN0-0.064-0.04939.2530.0160.0160.0000.0000.0000.000
181A181ALA0-0.009-0.01334.6640.0050.0050.0000.0000.0000.000
182A182LYS10.7760.90836.1950.2080.2080.0000.0000.0000.000
183A183LYS10.8690.92937.1310.1810.1810.0000.0000.0000.000
184A184LEU0-0.0350.01436.3500.0100.0100.0000.0000.0000.000
185A185SER0-0.0070.00237.851-0.007-0.0070.0000.0000.0000.000
186A186MET0-0.057-0.05834.1150.0010.0010.0000.0000.0000.000
187A187TYR00.006-0.03132.421-0.023-0.0230.0000.0000.0000.000
188A188GLY00.0410.00929.6450.0040.0040.0000.0000.0000.000
189A189VAL0-0.095-0.04730.6680.0070.0070.0000.0000.0000.000
190A190ASP-1-0.868-0.94524.892-0.386-0.3860.0000.0000.0000.000
191A191LEU00.0300.01328.0760.0220.0220.0000.0000.0000.000
192A192HIS0-0.082-0.02824.7530.0060.0060.0000.0000.0000.000
193A193LYS10.9800.98328.9080.1790.1790.0000.0000.0000.000
194A194ALA0-0.081-0.04730.341-0.003-0.0030.0000.0000.0000.000
195A195LYS10.9340.97532.9990.1030.1030.0000.0000.0000.000
196A196ASP-1-0.816-0.92036.456-0.103-0.1030.0000.0000.0000.000
197A197LEU0-0.079-0.03938.7910.0060.0060.0000.0000.0000.000
198A198GLU-1-0.855-0.92741.374-0.067-0.0670.0000.0000.0000.000
199A199GLY0-0.109-0.04340.4200.0030.0030.0000.0000.0000.000
200A200VAL0-0.0250.00040.588-0.003-0.0030.0000.0000.0000.000
201A201ASP-1-0.854-0.95036.978-0.112-0.1120.0000.0000.0000.000
202A202ILE0-0.0570.00135.196-0.003-0.0030.0000.0000.0000.000
203A203ILE0-0.035-0.03432.492-0.005-0.0050.0000.0000.0000.000
204A204LEU0-0.020-0.00431.7630.0020.0020.0000.0000.0000.000
205A205GLY00.0520.01631.462-0.008-0.0080.0000.0000.0000.000
206A206VAL0-0.034-0.02128.7070.0130.0130.0000.0000.0000.000
207A207CYS00.0580.05730.504-0.005-0.0050.0000.0000.0000.000
208A208SER00.1130.05331.8210.0140.0140.0000.0000.0000.000
209A209SER0-0.028-0.01733.3540.0150.0150.0000.0000.0000.000
210A210GLY00.032-0.03235.2490.0100.0100.0000.0000.0000.000
211A211LEU0-0.0110.00332.914-0.008-0.0080.0000.0000.0000.000
212A212LEU0-0.052-0.01534.8840.0170.0170.0000.0000.0000.000
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