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: N1KLQ

Calculation Name: 3GGY-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3GGY

Chain ID: A

ChEMBL ID:

UniProt ID: P53843

Base Structure: X-ray

Registration Date: 2023-06-19

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 186
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2027545.613811
FMO2-HF: Nuclear repulsion 1951761.600713
FMO2-HF: Total energy -75784.013098
FMO2-MP2: Total energy -76005.27904


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:6:ILE)


Summations of interaction energy for fragment #1(A:6:ILE)
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.
-5.061-1.80.106-1.329-2.0380.005
Interaction energy analysis for fragmet #1(A:6:ILE)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.060 / 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].
3A8PHE00.0370.0303.9301.2642.617-0.008-0.638-0.7070.002
4A9THR00.0940.0386.7770.5720.5720.0000.0000.0000.000
5A10ILE0-0.024-0.0133.632-0.892-0.3050.016-0.184-0.4180.001
6A11LYS10.8910.9463.038-2.691-1.3700.098-0.507-0.9130.002
7A12LEU00.0600.0436.008-0.623-0.6230.0000.0000.0000.000
8A13LYS10.9790.9907.898-1.713-1.7130.0000.0000.0000.000
9A14THR0-0.056-0.0447.019-0.383-0.3830.0000.0000.0000.000
10A15CYS00.0000.0099.605-0.322-0.3220.0000.0000.0000.000
11A16LEU00.0430.03011.460-0.172-0.1720.0000.0000.0000.000
12A17LYS10.9340.96812.596-0.782-0.7820.0000.0000.0000.000
13A18MET0-0.025-0.00113.096-0.098-0.0980.0000.0000.0000.000
14A19CYS0-0.002-0.00215.057-0.097-0.0970.0000.0000.0000.000
15A20ILE00.0170.01417.089-0.053-0.0530.0000.0000.0000.000
16A21GLN0-0.001-0.00918.361-0.047-0.0470.0000.0000.0000.000
17A22ARG10.7600.86118.353-0.366-0.3660.0000.0000.0000.000
18A23LEU00.0120.01521.093-0.031-0.0310.0000.0000.0000.000
19A24ARG10.8060.88422.094-0.324-0.3240.0000.0000.0000.000
20A25TYR0-0.043-0.01323.972-0.025-0.0250.0000.0000.0000.000
21A26ALA0-0.034-0.01525.122-0.022-0.0220.0000.0000.0000.000
22A27GLN00.003-0.01726.185-0.026-0.0260.0000.0000.0000.000
23A28GLU-1-0.909-0.94728.3050.1570.1570.0000.0000.0000.000
24A29LYS10.9310.96128.908-0.155-0.1550.0000.0000.0000.000
25A30GLN0-0.010-0.02729.020-0.017-0.0170.0000.0000.0000.000
26A31GLN00.0300.01632.546-0.014-0.0140.0000.0000.0000.000
27A32ALA0-0.030-0.00634.419-0.010-0.0100.0000.0000.0000.000
28A33ILE0-0.036-0.02433.465-0.009-0.0090.0000.0000.0000.000
29A34ALA00.0810.05236.812-0.008-0.0080.0000.0000.0000.000
30A35LYS10.9400.96138.730-0.088-0.0880.0000.0000.0000.000
31A36GLN0-0.038-0.02139.450-0.009-0.0090.0000.0000.0000.000
32A37SER00.0410.00940.384-0.007-0.0070.0000.0000.0000.000
33A38ARG10.8530.92142.143-0.086-0.0860.0000.0000.0000.000
34A39ARG10.9220.97044.656-0.068-0.0680.0000.0000.0000.000
35A40GLN0-0.027-0.01442.990-0.003-0.0030.0000.0000.0000.000
36A41VAL00.0430.03246.310-0.003-0.0030.0000.0000.0000.000
37A42ALA00.0660.03848.729-0.003-0.0030.0000.0000.0000.000
38A43GLN0-0.046-0.02050.195-0.002-0.0020.0000.0000.0000.000
39A44LEU0-0.043-0.02048.830-0.003-0.0030.0000.0000.0000.000
40A45LEU00.0720.05252.663-0.002-0.0020.0000.0000.0000.000
41A46LEU00.0200.01153.977-0.003-0.0030.0000.0000.0000.000
42A47THR0-0.119-0.06254.957-0.002-0.0020.0000.0000.0000.000
43A48ASN00.0250.01057.477-0.002-0.0020.0000.0000.0000.000
44A49LYS10.8590.94253.912-0.042-0.0420.0000.0000.0000.000
45A50GLU-1-0.723-0.87853.8420.0420.0420.0000.0000.0000.000
46A51GLN00.0290.02853.0300.0020.0020.0000.0000.0000.000
47A52LYS10.9480.97050.124-0.044-0.0440.0000.0000.0000.000
48A53ALA0-0.020-0.00849.1180.0030.0030.0000.0000.0000.000
49A54HIS00.009-0.00248.9940.0040.0040.0000.0000.0000.000
50A55TYR00.0540.01646.8910.0020.0020.0000.0000.0000.000
51A56ARG10.8080.90142.410-0.066-0.0660.0000.0000.0000.000
52A57VAL00.0140.00844.1570.0050.0050.0000.0000.0000.000
53A58GLU-1-0.887-0.95044.3230.0620.0620.0000.0000.0000.000
54A59THR0-0.097-0.05339.8450.0030.0030.0000.0000.0000.000
55A60LEU0-0.018-0.01039.8610.0050.0050.0000.0000.0000.000
56A61ILE0-0.0010.01040.1280.0050.0050.0000.0000.0000.000
57A62HIS0-0.038-0.01934.2090.0080.0080.0000.0000.0000.000
58A63ASP-1-0.881-0.94635.7480.1050.1050.0000.0000.0000.000
59A64ASP-1-0.796-0.88335.2730.1030.1030.0000.0000.0000.000
60A65ILE0-0.0070.00835.1390.0070.0070.0000.0000.0000.000
61A66HIS10.8150.89428.893-0.140-0.1400.0000.0000.0000.000
62A67ILE0-0.019-0.01230.9610.0130.0130.0000.0000.0000.000
63A68GLU-1-0.777-0.87730.9140.1280.1280.0000.0000.0000.000
64A69LEU0-0.031-0.00928.0870.0110.0110.0000.0000.0000.000
65A70LEU0-0.021-0.01425.9650.0200.0200.0000.0000.0000.000
66A71GLU-1-0.869-0.93726.1310.1760.1760.0000.0000.0000.000
67A72ILE0-0.027-0.02027.3640.0110.0110.0000.0000.0000.000
68A73LEU00.014-0.00323.5800.0170.0170.0000.0000.0000.000
69A74GLU-1-0.775-0.85622.5470.2970.2970.0000.0000.0000.000
70A75LEU00.0160.00722.4500.0290.0290.0000.0000.0000.000
71A76TYR0-0.055-0.05322.4330.0120.0120.0000.0000.0000.000
72A77CYS0-0.034-0.01418.3700.0410.0410.0000.0000.0000.000
73A78GLU-1-0.861-0.92918.2580.3830.3830.0000.0000.0000.000
74A79LEU0-0.038-0.00320.0070.0180.0180.0000.0000.0000.000
75A80LEU00.017-0.00516.8990.0140.0140.0000.0000.0000.000
76A81LEU0-0.064-0.03313.8890.0720.0720.0000.0000.0000.000
77A82ALA0-0.022-0.01515.7150.0430.0430.0000.0000.0000.000
78A83ARG10.8720.93917.953-0.275-0.2750.0000.0000.0000.000
79A84VAL0-0.0070.00111.1220.0180.0180.0000.0000.0000.000
80A85GLN0-0.055-0.02413.3230.0340.0340.0000.0000.0000.000
81A86VAL00.0540.02014.569-0.034-0.0340.0000.0000.0000.000
82A87ILE00.0260.00714.230-0.024-0.0240.0000.0000.0000.000
83A88ASN0-0.124-0.07111.1270.0310.0310.0000.0000.0000.000
84A89ASP-1-0.841-0.90213.7330.1530.1530.0000.0000.0000.000
85A90ILE0-0.052-0.00716.522-0.033-0.0330.0000.0000.0000.000
86A91SER0-0.021-0.02516.0720.0080.0080.0000.0000.0000.000
87A92THR00.0320.00217.604-0.016-0.0160.0000.0000.0000.000
88A93GLU-1-0.768-0.88220.9060.1300.1300.0000.0000.0000.000
89A94GLU-1-0.820-0.88423.3850.0700.0700.0000.0000.0000.000
90A95GLN00.002-0.00320.262-0.003-0.0030.0000.0000.0000.000
91A96LEU0-0.040-0.01220.2300.0120.0120.0000.0000.0000.000
92A97VAL00.009-0.00123.2430.0070.0070.0000.0000.0000.000
93A98LYS10.8110.87526.996-0.067-0.0670.0000.0000.0000.000
94A99GLU-1-0.853-0.90622.9020.1210.1210.0000.0000.0000.000
95A100HIS10.7520.84622.138-0.178-0.1780.0000.0000.0000.000
96A101MET00.0330.03724.9490.0180.0180.0000.0000.0000.000
97A102ASP-1-0.960-0.96927.9320.1410.1410.0000.0000.0000.000
98A103ASP-1-0.767-0.87823.1560.2280.2280.0000.0000.0000.000
99A104GLY00.0720.03724.9030.0200.0200.0000.0000.0000.000
100A105ILE0-0.059-0.03519.4260.0180.0180.0000.0000.0000.000
101A106ASN0-0.007-0.01322.1700.0170.0170.0000.0000.0000.000
102A107GLU-1-0.706-0.81424.1780.1630.1630.0000.0000.0000.000
103A108ALA00.0140.01221.9430.0020.0020.0000.0000.0000.000
104A109ILE0-0.017-0.02316.4610.0180.0180.0000.0000.0000.000
105A110ARG10.7950.88320.505-0.140-0.1400.0000.0000.0000.000
106A111SER0-0.010-0.01823.242-0.014-0.0140.0000.0000.0000.000
107A112LEU0-0.039-0.02519.141-0.001-0.0010.0000.0000.0000.000
108A113ILE0-0.033-0.01817.5880.0040.0040.0000.0000.0000.000
109A114TYR00.0360.01321.007-0.013-0.0130.0000.0000.0000.000
110A115ALA00.0310.00323.636-0.011-0.0110.0000.0000.0000.000
111A116ILE0-0.067-0.01818.805-0.001-0.0010.0000.0000.0000.000
112A117LEU0-0.046-0.01122.596-0.005-0.0050.0000.0000.0000.000
113A118PHE0-0.003-0.00825.905-0.013-0.0130.0000.0000.0000.000
114A119VAL0-0.014-0.00423.998-0.004-0.0040.0000.0000.0000.000
115A120ASP-1-0.792-0.87823.5420.1810.1810.0000.0000.0000.000
116A121GLU-1-0.787-0.86823.5340.1860.1860.0000.0000.0000.000
117A122VAL0-0.046-0.01819.0930.0180.0180.0000.0000.0000.000
118A123LYS10.8840.92419.041-0.164-0.1640.0000.0000.0000.000
119A124GLU-1-0.791-0.87814.9030.3720.3720.0000.0000.0000.000
120A125LEU00.0230.00415.0620.0740.0740.0000.0000.0000.000
121A126SER0-0.029-0.02616.3520.0060.0060.0000.0000.0000.000
122A127GLN00.028-0.00410.001-0.063-0.0630.0000.0000.0000.000
123A128LEU0-0.004-0.00212.2830.0740.0740.0000.0000.0000.000
124A129LYS10.9180.95814.366-0.235-0.2350.0000.0000.0000.000
125A130ASP-1-0.843-0.91012.3430.2130.2130.0000.0000.0000.000
126A131LEU0-0.084-0.0527.6660.0270.0270.0000.0000.0000.000
127A132MET00.0110.00011.356-0.058-0.0580.0000.0000.0000.000
128A133ALA0-0.0050.00714.820-0.045-0.0450.0000.0000.0000.000
129A134TRP0-0.074-0.0338.082-0.032-0.0320.0000.0000.0000.000
130A135LYS10.7570.88811.218-0.294-0.2940.0000.0000.0000.000
131A136ILE0-0.0350.00013.570-0.020-0.0200.0000.0000.0000.000
132A137ASN00.0250.01117.329-0.018-0.0180.0000.0000.0000.000
133A138VAL00.0310.00818.4340.0260.0260.0000.0000.0000.000
134A139GLU-1-0.906-0.95720.1910.0480.0480.0000.0000.0000.000
135A140PHE00.0420.02118.8580.0130.0130.0000.0000.0000.000
136A141VAL0-0.031-0.01817.9080.0090.0090.0000.0000.0000.000
137A142ASN0-0.003-0.00721.3280.0090.0090.0000.0000.0000.000
138A143GLY00.0520.03824.373-0.001-0.0010.0000.0000.0000.000
139A144VAL0-0.058-0.02822.9490.0020.0020.0000.0000.0000.000
140A145ILE0-0.051-0.04221.3020.0030.0030.0000.0000.0000.000
141A146ALA0-0.059-0.01925.787-0.004-0.0040.0000.0000.0000.000
142A147ASP-1-0.907-0.95728.9750.0670.0670.0000.0000.0000.000
143A148HIS0-0.042-0.01528.575-0.001-0.0010.0000.0000.0000.000
144A149ILE00.0420.02028.0450.0030.0030.0000.0000.0000.000
145A150ASP-1-0.834-0.92127.6790.1310.1310.0000.0000.0000.000
146A151VAL0-0.050-0.01126.6070.0150.0150.0000.0000.0000.000
147A152PRO0-0.023-0.01128.396-0.012-0.0120.0000.0000.0000.000
148A153GLU-1-0.807-0.91231.4070.0960.0960.0000.0000.0000.000
149A154LYS10.7610.86730.351-0.154-0.1540.0000.0000.0000.000
150A155ILE00.0100.00827.6340.0040.0040.0000.0000.0000.000
151A156ILE00.0810.04831.0500.0010.0010.0000.0000.0000.000
152A157LYS10.8270.89932.664-0.089-0.0890.0000.0000.0000.000
153A158LYS10.7830.87832.300-0.124-0.1240.0000.0000.0000.000
154A159CYS0-0.0360.00129.1920.0070.0070.0000.0000.0000.000
155A160SER0-0.046-0.02131.595-0.006-0.0060.0000.0000.0000.000
156A161PRO00.0250.03035.038-0.005-0.0050.0000.0000.0000.000
157A162SER0-0.049-0.03537.939-0.002-0.0020.0000.0000.0000.000
158A163VAL00.0230.01641.5080.0020.0020.0000.0000.0000.000
159A164PRO00.0180.01142.9410.0000.0000.0000.0000.0000.000
160A165LYS10.8290.90845.349-0.059-0.0590.0000.0000.0000.000
161A166GLU-1-0.749-0.88148.7050.0520.0520.0000.0000.0000.000
162A167GLU-1-0.822-0.90151.4980.0530.0530.0000.0000.0000.000
163A168LEU0-0.026-0.00543.9460.0000.0000.0000.0000.0000.000
164A169VAL00.0440.02347.7290.0020.0020.0000.0000.0000.000
165A170ASP-1-0.779-0.88549.4120.0490.0490.0000.0000.0000.000
166A171LEU00.0020.00548.136-0.001-0.0010.0000.0000.0000.000
167A172TYR0-0.015-0.04941.5850.0000.0000.0000.0000.0000.000
168A173LEU0-0.017-0.00848.3740.0010.0010.0000.0000.0000.000
169A174LYS10.8290.90051.280-0.049-0.0490.0000.0000.0000.000
170A175GLU-1-0.889-0.93146.1550.0730.0730.0000.0000.0000.000
171A176ILE0-0.041-0.01346.2210.0000.0000.0000.0000.0000.000
172A177ALA0-0.011-0.01649.438-0.001-0.0010.0000.0000.0000.000
173A178LYS10.9600.98051.951-0.059-0.0590.0000.0000.0000.000
174A179THR0-0.094-0.05546.5620.0010.0010.0000.0000.0000.000
175A180TYR0-0.061-0.04044.8290.0030.0030.0000.0000.0000.000
176A181ASP-1-0.904-0.93451.7590.0490.0490.0000.0000.0000.000
177A182VAL0-0.035-0.00953.464-0.002-0.0020.0000.0000.0000.000
178A183PRO0-0.011-0.01256.2990.0000.0000.0000.0000.0000.000
179A184TYR0-0.017-0.03159.9290.0000.0000.0000.0000.0000.000
180A185SER00.0230.00760.8290.0010.0010.0000.0000.0000.000
181A186LYS10.7910.87958.156-0.038-0.0380.0000.0000.0000.000
182A187LEU00.0110.02354.8710.0010.0010.0000.0000.0000.000
183A188GLU-1-0.808-0.89757.6440.0410.0410.0000.0000.0000.000
184A189ASN0-0.072-0.03359.977-0.001-0.0010.0000.0000.0000.000
185A190SER0-0.099-0.05954.8200.0000.0000.0000.0000.0000.000
186A191LEU0-0.069-0.00355.5460.0010.0010.0000.0000.0000.000