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

tag_button

FMODB ID: LZ299

Calculation Name: 3GRP-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3GRP

Chain ID: A

ChEMBL ID:

UniProt ID: A0A0H3

Base Structure: X-ray

Registration Date: 2023-09-20

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 OptHSide
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 236
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2796812.709731
FMO2-HF: Nuclear repulsion 2705203.091906
FMO2-HF: Total energy -91609.617826
FMO2-MP2: Total energy -91869.9997


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:0:SER)


Summations of interaction energy for fragment #1(A:0:SER)
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.
-0.9630.571.182-1.077-1.639-0.001
Interaction energy analysis for fragmet #1(A:0:SER)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.033 / q_NPA : -0.030
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].
3A2PHE0-0.037-0.0373.8290.5851.570-0.012-0.371-0.6030.002
4A3LYS10.8470.9332.496-0.940-0.3931.195-0.703-1.039-0.003
5A4LEU00.000-0.0035.081-0.081-0.080-0.001-0.0030.0030.000
6A5THR0-0.004-0.0135.7390.2600.2600.0000.0000.0000.000
7A6GLY0-0.0130.0078.357-0.112-0.1120.0000.0000.0000.000
8A7ARG10.8450.91710.4291.0021.0020.0000.0000.0000.000
9A8LYS10.8650.93513.0670.4330.4330.0000.0000.0000.000
10A9ALA0-0.020-0.01415.7100.0100.0100.0000.0000.0000.000
11A10LEU00.0160.01917.7210.0180.0180.0000.0000.0000.000
12A11VAL00.006-0.00418.7550.0080.0080.0000.0000.0000.000
13A12THR00.0550.03021.7890.0090.0090.0000.0000.0000.000
14A13GLY00.003-0.00124.7780.0120.0120.0000.0000.0000.000
15A14ALA00.008-0.00622.8370.0150.0150.0000.0000.0000.000
16A15THR00.0050.00924.2610.0050.0050.0000.0000.0000.000
17A16GLY00.010-0.00326.7550.0060.0060.0000.0000.0000.000
18A17GLY0-0.022-0.01525.474-0.002-0.0020.0000.0000.0000.000
19A18ILE00.0320.01721.8180.0100.0100.0000.0000.0000.000
20A19GLY00.0610.02921.3160.0080.0080.0000.0000.0000.000
21A20GLU-1-0.820-0.89321.1240.0770.0770.0000.0000.0000.000
22A21ALA0-0.003-0.00719.3540.0070.0070.0000.0000.0000.000
23A22ILE0-0.024-0.02516.9740.0300.0300.0000.0000.0000.000
24A23ALA00.0050.01716.017-0.010-0.0100.0000.0000.0000.000
25A24ARG10.7900.86616.155-0.130-0.1300.0000.0000.0000.000
26A25CYS0-0.053-0.01412.8810.0500.0500.0000.0000.0000.000
27A26PHE00.024-0.02011.5380.0110.0110.0000.0000.0000.000
28A27HIS0-0.0240.01011.486-0.035-0.0350.0000.0000.0000.000
29A28ALA00.0300.02210.823-0.050-0.0500.0000.0000.0000.000
30A29GLN0-0.068-0.0375.7450.2590.2590.0000.0000.0000.000
31A30GLY00.0300.0067.361-0.366-0.3660.0000.0000.0000.000
32A31ALA0-0.0200.0099.381-0.120-0.1200.0000.0000.0000.000
33A32ILE00.0030.00912.2160.0690.0690.0000.0000.0000.000
34A33VAL0-0.006-0.00915.2750.0050.0050.0000.0000.0000.000
35A34GLY00.0420.01817.8490.0100.0100.0000.0000.0000.000
36A35LEU0-0.024-0.02320.0050.0140.0140.0000.0000.0000.000
37A36HIS00.0570.01523.3570.0010.0010.0000.0000.0000.000
38A37GLY0-0.005-0.01026.5880.0130.0130.0000.0000.0000.000
39A38THR0-0.021-0.01529.265-0.004-0.0040.0000.0000.0000.000
40A39ARG10.8130.87531.788-0.010-0.0100.0000.0000.0000.000
41A40GLU-1-0.739-0.86430.957-0.042-0.0420.0000.0000.0000.000
42A41ASP-1-0.791-0.86930.8190.0030.0030.0000.0000.0000.000
43A42LYS10.8650.92028.636-0.032-0.0320.0000.0000.0000.000
44A43LEU00.012-0.00126.0990.0070.0070.0000.0000.0000.000
45A44LYS10.8810.93625.9150.0410.0410.0000.0000.0000.000
46A45GLU-1-0.864-0.90826.7300.0290.0290.0000.0000.0000.000
47A46ILE0-0.0180.00021.7990.0030.0030.0000.0000.0000.000
48A47ALA00.011-0.00322.1480.0010.0010.0000.0000.0000.000
49A48ALA0-0.058-0.02522.249-0.009-0.0090.0000.0000.0000.000
50A49ASP-1-0.860-0.91822.0730.0890.0890.0000.0000.0000.000
51A50LEU0-0.056-0.01616.7890.0130.0130.0000.0000.0000.000
52A51GLY00.0210.01518.253-0.007-0.0070.0000.0000.0000.000
53A52LYS10.8290.88615.0440.3080.3080.0000.0000.0000.000
54A53ASP-1-0.865-0.90815.421-0.337-0.3370.0000.0000.0000.000
55A54VAL00.0210.00817.649-0.001-0.0010.0000.0000.0000.000
56A55PHE00.0100.01520.2410.0020.0020.0000.0000.0000.000
57A56VAL0-0.020-0.00523.3710.0120.0120.0000.0000.0000.000
58A57PHE00.0140.00923.955-0.003-0.0030.0000.0000.0000.000
59A58SER00.031-0.00128.6330.0120.0120.0000.0000.0000.000
60A59ALA0-0.005-0.00831.729-0.006-0.0060.0000.0000.0000.000
61A60ASN00.0300.03233.3200.0080.0080.0000.0000.0000.000
62A61LEU00.023-0.00629.627-0.003-0.0030.0000.0000.0000.000
63A62SER00.0270.00834.2310.0020.0020.0000.0000.0000.000
64A63ASP-1-0.867-0.93337.401-0.039-0.0390.0000.0000.0000.000
65A64ARG10.9680.98737.1620.0370.0370.0000.0000.0000.000
66A65LYS10.9410.95936.8340.0360.0360.0000.0000.0000.000
67A66SER00.0380.02136.152-0.005-0.0050.0000.0000.0000.000
68A67ILE0-0.033-0.00331.574-0.005-0.0050.0000.0000.0000.000
69A68LYS10.8040.87132.1900.0710.0710.0000.0000.0000.000
70A69GLN00.0130.02133.068-0.004-0.0040.0000.0000.0000.000
71A70LEU0-0.017-0.00228.005-0.006-0.0060.0000.0000.0000.000
72A71ALA00.0030.00028.301-0.009-0.0090.0000.0000.0000.000
73A72GLU-1-0.858-0.90228.356-0.116-0.1160.0000.0000.0000.000
74A73VAL0-0.017-0.01529.552-0.011-0.0110.0000.0000.0000.000
75A74ALA00.0330.02025.173-0.009-0.0090.0000.0000.0000.000
76A75GLU-1-0.813-0.88624.308-0.229-0.2290.0000.0000.0000.000
77A76ARG10.8250.88425.1050.1040.1040.0000.0000.0000.000
78A77GLU-1-0.931-0.97426.211-0.133-0.1330.0000.0000.0000.000
79A78MET0-0.054-0.01719.387-0.003-0.0030.0000.0000.0000.000
80A79GLU-1-0.920-0.94721.019-0.317-0.3170.0000.0000.0000.000
81A80GLY0-0.075-0.01721.349-0.038-0.0380.0000.0000.0000.000
82A81ILE00.001-0.00819.922-0.017-0.0170.0000.0000.0000.000
83A82ASP-1-0.833-0.90415.909-0.455-0.4550.0000.0000.0000.000
84A83ILE0-0.031-0.01913.3940.0190.0190.0000.0000.0000.000
85A84LEU00.0060.02118.1160.0110.0110.0000.0000.0000.000
86A85VAL0-0.006-0.00818.2820.0130.0130.0000.0000.0000.000
87A86ASN0-0.056-0.03421.4140.0020.0020.0000.0000.0000.000
88A87ASN0-0.035-0.03823.4710.0250.0250.0000.0000.0000.000
89A88ALA0-0.047-0.01225.4920.0090.0090.0000.0000.0000.000
90A89GLY00.0570.02828.713-0.001-0.0010.0000.0000.0000.000
91A90ILE0-0.056-0.02131.7780.0010.0010.0000.0000.0000.000
92A91THR00.016-0.02132.8270.0010.0010.0000.0000.0000.000
93A92ARG10.8710.95635.178-0.014-0.0140.0000.0000.0000.000
94A93ASP-1-0.767-0.87738.8210.0190.0190.0000.0000.0000.000
95A94GLY0-0.028-0.00242.0500.0020.0020.0000.0000.0000.000
96A95LEU0-0.0250.00645.966-0.002-0.0020.0000.0000.0000.000
97A96PHE00.030-0.00748.1800.0010.0010.0000.0000.0000.000
98A97VAL00.0230.04052.8960.0010.0010.0000.0000.0000.000
99A98ARG10.7350.81644.216-0.018-0.0180.0000.0000.0000.000
100A99MET00.0410.02450.1570.0010.0010.0000.0000.0000.000
101A100GLN00.0290.00148.5300.0000.0000.0000.0000.0000.000
102A101ASP-1-0.874-0.93547.5570.0060.0060.0000.0000.0000.000
103A102GLN00.0150.00047.119-0.001-0.0010.0000.0000.0000.000
104A103ASP-1-0.795-0.86344.2340.0130.0130.0000.0000.0000.000
105A104TRP0-0.065-0.04242.8330.0030.0030.0000.0000.0000.000
106A105ASP-1-0.880-0.94742.282-0.005-0.0050.0000.0000.0000.000
107A106ASP-1-0.930-0.96540.984-0.002-0.0020.0000.0000.0000.000
108A107VAL0-0.074-0.03637.509-0.001-0.0010.0000.0000.0000.000
109A108LEU0-0.009-0.00137.226-0.001-0.0010.0000.0000.0000.000
110A109ALA0-0.0020.00637.150-0.004-0.0040.0000.0000.0000.000
111A110VAL0-0.037-0.02534.188-0.005-0.0050.0000.0000.0000.000
112A111ASN00.011-0.00432.811-0.003-0.0030.0000.0000.0000.000
113A112LEU0-0.0320.00532.5130.0010.0010.0000.0000.0000.000
114A113THR0-0.017-0.01433.336-0.006-0.0060.0000.0000.0000.000
115A114ALA00.0360.03932.650-0.008-0.0080.0000.0000.0000.000
116A115ALA00.0370.02528.768-0.008-0.0080.0000.0000.0000.000
117A116SER0-0.026-0.00329.534-0.012-0.0120.0000.0000.0000.000
118A117THR0-0.058-0.05131.796-0.008-0.0080.0000.0000.0000.000
119A118LEU00.0380.02126.926-0.007-0.0070.0000.0000.0000.000
120A119THR0-0.004-0.03126.240-0.013-0.0130.0000.0000.0000.000
121A120ARG10.8310.89527.8960.0620.0620.0000.0000.0000.000
122A121GLU-1-0.837-0.89930.059-0.093-0.0930.0000.0000.0000.000
123A122LEU00.0250.01424.565-0.008-0.0080.0000.0000.0000.000
124A123ILE00.0080.00824.874-0.019-0.0190.0000.0000.0000.000
125A124HIS00.0150.02325.891-0.019-0.0190.0000.0000.0000.000
126A125SER0-0.020-0.05824.384-0.011-0.0110.0000.0000.0000.000
127A126MET0-0.0020.02420.614-0.016-0.0160.0000.0000.0000.000
128A127MET00.0090.00122.403-0.016-0.0160.0000.0000.0000.000
129A128ARG10.8480.93424.9360.2160.2160.0000.0000.0000.000
130A129ARG10.8210.89619.1020.3270.3270.0000.0000.0000.000
131A130ARG10.8210.92120.2650.2220.2220.0000.0000.0000.000
132A131TYR0-0.011-0.02212.219-0.004-0.0040.0000.0000.0000.000
133A132GLY00.0340.01918.0660.0120.0120.0000.0000.0000.000
134A133ARG10.7850.91713.2200.3770.3770.0000.0000.0000.000
135A134ILE00.0150.00818.5810.0050.0050.0000.0000.0000.000
136A135ILE0-0.011-0.01016.5870.0170.0170.0000.0000.0000.000
137A136ASN00.001-0.00821.237-0.007-0.0070.0000.0000.0000.000
138A137ILE00.0150.00820.7320.0160.0160.0000.0000.0000.000
139A138THR0-0.013-0.00724.799-0.005-0.0050.0000.0000.0000.000
140A139SER00.0810.02627.9950.0060.0060.0000.0000.0000.000
141A140ILE0-0.041-0.01028.035-0.001-0.0010.0000.0000.0000.000
142A148GLY00.0630.02143.4680.0000.0000.0000.0000.0000.000
143A149GLN00.005-0.01439.410-0.001-0.0010.0000.0000.0000.000
144A150THR00.0510.02639.7090.0010.0010.0000.0000.0000.000
145A151ASN00.0720.04141.085-0.001-0.0010.0000.0000.0000.000
146A152TYR00.002-0.01935.556-0.003-0.0030.0000.0000.0000.000
147A153CYS0-0.080-0.04336.0940.0010.0010.0000.0000.0000.000
148A154ALA00.0410.02836.794-0.001-0.0010.0000.0000.0000.000
149A155ALA00.0280.01935.623-0.004-0.0040.0000.0000.0000.000
150A156LYS10.8990.95730.118-0.070-0.0700.0000.0000.0000.000
151A157ALA00.002-0.00632.511-0.002-0.0020.0000.0000.0000.000
152A158GLY00.0360.01834.257-0.004-0.0040.0000.0000.0000.000
153A159LEU00.0050.01128.545-0.007-0.0070.0000.0000.0000.000
154A160ILE00.0030.00128.927-0.007-0.0070.0000.0000.0000.000
155A161GLY0-0.0110.00130.485-0.004-0.0040.0000.0000.0000.000
156A162PHE00.000-0.01229.141-0.007-0.0070.0000.0000.0000.000
157A163SER0-0.016-0.02926.717-0.010-0.0100.0000.0000.0000.000
158A164LYS10.8760.92928.075-0.028-0.0280.0000.0000.0000.000
159A165ALA00.0180.01129.545-0.005-0.0050.0000.0000.0000.000
160A166LEU00.0180.01427.168-0.007-0.0070.0000.0000.0000.000
161A167ALA0-0.020-0.01525.634-0.012-0.0120.0000.0000.0000.000
162A168GLN0-0.039-0.02426.624-0.011-0.0110.0000.0000.0000.000
163A169GLU-1-0.897-0.91529.318-0.086-0.0860.0000.0000.0000.000
164A170ILE00.000-0.01624.839-0.009-0.0090.0000.0000.0000.000
165A171ALA00.0560.04523.894-0.021-0.0210.0000.0000.0000.000
166A172SER0-0.008-0.00223.491-0.023-0.0230.0000.0000.0000.000
167A173ARG10.8440.91523.8820.1690.1690.0000.0000.0000.000
168A174ASN0-0.033-0.02718.759-0.001-0.0010.0000.0000.0000.000
169A175ILE00.0090.02319.023-0.035-0.0350.0000.0000.0000.000
170A176THR0-0.037-0.01018.0590.0210.0210.0000.0000.0000.000
171A177VAL00.0290.00920.743-0.005-0.0050.0000.0000.0000.000
172A178ASN0-0.027-0.01519.6190.0300.0300.0000.0000.0000.000
173A179CYS0-0.050-0.00622.719-0.008-0.0080.0000.0000.0000.000
174A180ILE00.0440.02918.7830.0150.0150.0000.0000.0000.000
175A181ALA0-0.031-0.01023.388-0.014-0.0140.0000.0000.0000.000
176A182PRO0-0.015-0.00424.5290.0150.0150.0000.0000.0000.000
177A183GLY00.0190.00826.360-0.013-0.0130.0000.0000.0000.000
178A184PHE00.009-0.00828.959-0.005-0.0050.0000.0000.0000.000
179A185ILE0-0.0240.00224.6470.0150.0150.0000.0000.0000.000
180A186LYS10.8670.91927.525-0.157-0.1570.0000.0000.0000.000
181A187SER0-0.025-0.01828.064-0.003-0.0030.0000.0000.0000.000
182A188ALA00.0800.03230.559-0.001-0.0010.0000.0000.0000.000
183A189MET0-0.051-0.03133.707-0.003-0.0030.0000.0000.0000.000
184A190THR00.0450.01432.175-0.002-0.0020.0000.0000.0000.000
185A191ASP-1-0.817-0.89832.5180.1250.1250.0000.0000.0000.000
186A192LYS10.9320.97435.297-0.062-0.0620.0000.0000.0000.000
187A193LEU0-0.0620.00336.269-0.005-0.0050.0000.0000.0000.000
188A194ASN00.0660.02839.8270.0030.0030.0000.0000.0000.000
189A195GLU-1-0.768-0.89441.5040.0980.0980.0000.0000.0000.000
190A196LYS10.9550.97842.482-0.058-0.0580.0000.0000.0000.000
191A197GLN0-0.032-0.01141.1100.0020.0020.0000.0000.0000.000
192A198LYS10.8990.94736.927-0.103-0.1030.0000.0000.0000.000
193A199GLU-1-0.908-0.96338.4630.1130.1130.0000.0000.0000.000
194A200ALA0-0.017-0.01440.3280.0020.0020.0000.0000.0000.000
195A201ILE0-0.013-0.02035.0030.0010.0010.0000.0000.0000.000
196A202MET00.0090.01232.9460.0090.0090.0000.0000.0000.000
197A203ALA00.0110.02136.2230.0070.0070.0000.0000.0000.000
198A204MET0-0.043-0.01236.440-0.003-0.0030.0000.0000.0000.000
199A205ILE0-0.021-0.00830.7120.0020.0020.0000.0000.0000.000
200A206PRO0-0.023-0.00531.7760.0040.0040.0000.0000.0000.000
201A207MET0-0.025-0.00924.9800.0080.0080.0000.0000.0000.000
202A208LYS10.8350.91630.402-0.124-0.1240.0000.0000.0000.000
203A209ARG10.8350.88622.973-0.272-0.2720.0000.0000.0000.000
204A210MET0-0.040-0.01129.300-0.006-0.0060.0000.0000.0000.000
205A211GLY00.0310.01425.1990.0170.0170.0000.0000.0000.000
206A212ILE00.007-0.01021.131-0.028-0.0280.0000.0000.0000.000
207A213GLY00.0290.00322.1860.0090.0090.0000.0000.0000.000
208A214GLU-1-0.871-0.95017.3520.3800.3800.0000.0000.0000.000
209A215GLU-1-0.741-0.82817.2890.3270.3270.0000.0000.0000.000
210A216ILE0-0.042-0.02018.3690.0040.0040.0000.0000.0000.000
211A217ALA00.0380.02716.206-0.017-0.0170.0000.0000.0000.000
212A218PHE00.006-0.00313.009-0.011-0.0110.0000.0000.0000.000
213A219ALA00.0070.01013.6210.0060.0060.0000.0000.0000.000
214A220THR0-0.029-0.03015.702-0.050-0.0500.0000.0000.0000.000
215A221VAL00.0460.0219.553-0.073-0.0730.0000.0000.0000.000
216A222TYR0-0.020-0.00311.514-0.107-0.1070.0000.0000.0000.000
217A223LEU0-0.028-0.01312.521-0.094-0.0940.0000.0000.0000.000
218A224ALA0-0.005-0.00912.929-0.051-0.0510.0000.0000.0000.000
219A225SER0-0.007-0.0038.957-0.101-0.1010.0000.0000.0000.000
220A226ASP-1-0.754-0.8618.723-0.934-0.9340.0000.0000.0000.000
221A227GLU-1-0.791-0.9026.445-0.956-0.9560.0000.0000.0000.000
222A228ALA0-0.057-0.00810.9820.1260.1260.0000.0000.0000.000
223A229ALA00.0090.00113.9890.0210.0210.0000.0000.0000.000
224A230TYR0-0.041-0.02015.7550.0170.0170.0000.0000.0000.000
225A231LEU0-0.0280.01117.6560.0340.0340.0000.0000.0000.000
226A232THR00.0740.01619.661-0.020-0.0200.0000.0000.0000.000
227A233GLY00.0370.03222.4040.0120.0120.0000.0000.0000.000
228A234GLN0-0.0150.00222.6140.0100.0100.0000.0000.0000.000
229A235THR0-0.010-0.02024.200-0.010-0.0100.0000.0000.0000.000
230A236LEU00.0130.01118.6010.0100.0100.0000.0000.0000.000
231A237HIS00.010-0.00523.157-0.003-0.0030.0000.0000.0000.000
232A238ILE00.0080.01120.0170.0140.0140.0000.0000.0000.000
233A239ASN00.034-0.00824.2240.0070.0070.0000.0000.0000.000
234A240GLY00.0640.02926.259-0.008-0.0080.0000.0000.0000.000
235A241GLY0-0.0020.00027.764-0.001-0.0010.0000.0000.0000.000
236A242MET0-0.0310.00629.866-0.010-0.0100.0000.0000.0000.000