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: 3958L

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 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 236
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2794025.059426
FMO2-HF: Nuclear repulsion 2702416.669676
FMO2-HF: Total energy -91608.38975
FMO2-MP2: Total energy -91868.768186


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.
-1.159-0.4242.925-1.508-2.152-0.003
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 : -0.019 / q_NPA : -0.029
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].
3A2PHE0-0.036-0.0343.8291.7222.718-0.012-0.349-0.6350.001
4A3LYS10.8800.9612.3370.221-0.0452.938-1.154-1.518-0.004
5A4LEU00.004-0.0025.081-0.181-0.176-0.001-0.0050.0010.000
6A5THR00.001-0.0105.3480.2880.2880.0000.0000.0000.000
7A6GLY0-0.0170.0078.203-0.092-0.0920.0000.0000.0000.000
8A7ARG10.8650.94210.2311.3221.3220.0000.0000.0000.000
9A8LYS10.8450.91513.0100.4570.4570.0000.0000.0000.000
10A9ALA0-0.006-0.00815.753-0.012-0.0120.0000.0000.0000.000
11A10LEU00.0170.01617.7160.0350.0350.0000.0000.0000.000
12A11VAL00.001-0.00518.775-0.007-0.0070.0000.0000.0000.000
13A12THR00.0370.02421.7930.0190.0190.0000.0000.0000.000
14A13GLY00.005-0.01224.7870.0040.0040.0000.0000.0000.000
15A14ALA00.010-0.00422.8210.0100.0100.0000.0000.0000.000
16A15THR0-0.025-0.00524.2710.0090.0090.0000.0000.0000.000
17A16GLY00.0320.01026.7840.0110.0110.0000.0000.0000.000
18A17GLY0-0.016-0.01425.490-0.007-0.0070.0000.0000.0000.000
19A18ILE00.0310.01521.8580.0070.0070.0000.0000.0000.000
20A19GLY00.0590.02221.334-0.004-0.0040.0000.0000.0000.000
21A20GLU-1-0.828-0.89121.1360.0010.0010.0000.0000.0000.000
22A21ALA0-0.001-0.00419.3290.0040.0040.0000.0000.0000.000
23A22ILE0-0.024-0.02916.9500.0140.0140.0000.0000.0000.000
24A23ALA00.0090.01716.029-0.025-0.0250.0000.0000.0000.000
25A24ARG10.8030.86616.162-0.058-0.0580.0000.0000.0000.000
26A25CYS0-0.053-0.01012.9730.0360.0360.0000.0000.0000.000
27A26PHE00.016-0.02111.552-0.024-0.0240.0000.0000.0000.000
28A27HIS0-0.0140.01311.488-0.057-0.0570.0000.0000.0000.000
29A28ALA00.0260.02110.759-0.027-0.0270.0000.0000.0000.000
30A29GLN0-0.091-0.0545.9430.3550.3550.0000.0000.0000.000
31A30GLY00.0240.0017.356-0.414-0.4140.0000.0000.0000.000
32A31ALA0-0.0190.0099.371-0.086-0.0860.0000.0000.0000.000
33A32ILE00.0160.01612.2070.0920.0920.0000.0000.0000.000
34A33VAL0-0.016-0.01215.384-0.016-0.0160.0000.0000.0000.000
35A34GLY00.0440.01817.8440.0270.0270.0000.0000.0000.000
36A35LEU0-0.020-0.02220.281-0.002-0.0020.0000.0000.0000.000
37A36HIS00.0670.02623.3570.0050.0050.0000.0000.0000.000
38A37GLY0-0.008-0.01726.5890.0060.0060.0000.0000.0000.000
39A38THR0-0.026-0.01729.270-0.001-0.0010.0000.0000.0000.000
40A39ARG10.7770.86131.8040.0270.0270.0000.0000.0000.000
41A40GLU-1-0.781-0.89930.961-0.064-0.0640.0000.0000.0000.000
42A41ASP-1-0.788-0.86930.820-0.026-0.0260.0000.0000.0000.000
43A42LYS10.9770.97529.1050.0170.0170.0000.0000.0000.000
44A43LEU0-0.015-0.00726.0830.0040.0040.0000.0000.0000.000
45A44LYS10.9420.97425.9170.0500.0500.0000.0000.0000.000
46A45GLU-1-0.924-0.95026.731-0.001-0.0010.0000.0000.0000.000
47A46ILE0-0.022-0.00121.8050.0050.0050.0000.0000.0000.000
48A47ALA00.007-0.00822.1490.0010.0010.0000.0000.0000.000
49A48ALA0-0.059-0.02522.247-0.003-0.0030.0000.0000.0000.000
50A49ASP-1-0.857-0.91421.8530.0550.0550.0000.0000.0000.000
51A50LEU0-0.070-0.02316.9580.0110.0110.0000.0000.0000.000
52A51GLY00.0180.01618.2510.0020.0020.0000.0000.0000.000
53A52LYS10.8900.93014.8550.1920.1920.0000.0000.0000.000
54A53ASP-1-0.906-0.94415.483-0.280-0.2800.0000.0000.0000.000
55A54VAL00.0150.00117.639-0.019-0.0190.0000.0000.0000.000
56A55PHE00.0100.01320.2270.0100.0100.0000.0000.0000.000
57A56VAL0-0.017-0.00523.3620.0010.0010.0000.0000.0000.000
58A57PHE00.0280.01924.0520.0000.0000.0000.0000.0000.000
59A58SER00.0350.01128.6290.0060.0060.0000.0000.0000.000
60A59ALA0-0.020-0.01831.728-0.004-0.0040.0000.0000.0000.000
61A60ASN00.0380.04033.3220.0010.0010.0000.0000.0000.000
62A61LEU00.037-0.01029.551-0.001-0.0010.0000.0000.0000.000
63A62SER0-0.0010.00034.235-0.001-0.0010.0000.0000.0000.000
64A63ASP-1-0.891-0.94237.410-0.067-0.0670.0000.0000.0000.000
65A64ARG10.9770.98437.1620.0770.0770.0000.0000.0000.000
66A65LYS10.9510.96036.8310.0600.0600.0000.0000.0000.000
67A66SER00.0560.03935.736-0.004-0.0040.0000.0000.0000.000
68A67ILE0-0.029-0.00531.566-0.005-0.0050.0000.0000.0000.000
69A68LYS10.9080.94732.1860.1000.1000.0000.0000.0000.000
70A69GLN00.0140.02233.026-0.005-0.0050.0000.0000.0000.000
71A70LEU0-0.024-0.00327.800-0.004-0.0040.0000.0000.0000.000
72A71ALA00.0040.00028.257-0.009-0.0090.0000.0000.0000.000
73A72GLU-1-0.884-0.93328.307-0.130-0.1300.0000.0000.0000.000
74A73VAL0-0.033-0.02929.481-0.007-0.0070.0000.0000.0000.000
75A74ALA00.0330.01625.092-0.004-0.0040.0000.0000.0000.000
76A75GLU-1-0.864-0.89124.536-0.236-0.2360.0000.0000.0000.000
77A76ARG10.8810.93825.0330.1170.1170.0000.0000.0000.000
78A77GLU-1-0.956-0.98425.965-0.134-0.1340.0000.0000.0000.000
79A78MET0-0.060-0.01919.305-0.001-0.0010.0000.0000.0000.000
80A79GLU-1-0.903-0.93620.912-0.265-0.2650.0000.0000.0000.000
81A80GLY0-0.064-0.02021.304-0.034-0.0340.0000.0000.0000.000
82A81ILE0-0.0020.00719.893-0.019-0.0190.0000.0000.0000.000
83A82ASP-1-0.869-0.94015.804-0.551-0.5510.0000.0000.0000.000
84A83ILE0-0.037-0.02613.476-0.002-0.0020.0000.0000.0000.000
85A84LEU00.0010.01718.1220.0310.0310.0000.0000.0000.000
86A85VAL00.001-0.00518.358-0.002-0.0020.0000.0000.0000.000
87A86ASN0-0.064-0.04021.4200.0240.0240.0000.0000.0000.000
88A87ASN0-0.005-0.00723.5000.0100.0100.0000.0000.0000.000
89A88ALA0-0.070-0.02925.5040.0130.0130.0000.0000.0000.000
90A89GLY00.0710.03228.724-0.004-0.0040.0000.0000.0000.000
91A90ILE0-0.058-0.02231.7910.0050.0050.0000.0000.0000.000
92A91THR00.031-0.00932.787-0.002-0.0020.0000.0000.0000.000
93A92ARG10.8820.96035.1970.0330.0330.0000.0000.0000.000
94A93ASP-1-0.796-0.89138.829-0.025-0.0250.0000.0000.0000.000
95A94GLY0-0.030-0.00542.1360.0020.0020.0000.0000.0000.000
96A95LEU0-0.040-0.01046.064-0.002-0.0020.0000.0000.0000.000
97A96PHE00.0550.00748.1210.0010.0010.0000.0000.0000.000
98A97VAL00.0200.04052.9000.0010.0010.0000.0000.0000.000
99A98ARG10.7320.82144.6240.0220.0220.0000.0000.0000.000
100A99MET00.0160.01450.1650.0010.0010.0000.0000.0000.000
101A100GLN00.023-0.00648.545-0.002-0.0020.0000.0000.0000.000
102A101ASP-1-0.862-0.92747.572-0.032-0.0320.0000.0000.0000.000
103A102GLN00.0090.00047.131-0.002-0.0020.0000.0000.0000.000
104A103ASP-1-0.764-0.84744.232-0.029-0.0290.0000.0000.0000.000
105A104TRP0-0.072-0.03542.847-0.002-0.0020.0000.0000.0000.000
106A105ASP-1-0.881-0.95042.295-0.048-0.0480.0000.0000.0000.000
107A106ASP-1-0.920-0.96340.994-0.046-0.0460.0000.0000.0000.000
108A107VAL0-0.070-0.03537.444-0.004-0.0040.0000.0000.0000.000
109A108LEU00.0020.00237.238-0.006-0.0060.0000.0000.0000.000
110A109ALA0-0.023-0.00637.159-0.008-0.0080.0000.0000.0000.000
111A110VAL0-0.037-0.02134.087-0.007-0.0070.0000.0000.0000.000
112A111ASN00.015-0.00132.823-0.007-0.0070.0000.0000.0000.000
113A112LEU0-0.0440.00532.525-0.005-0.0050.0000.0000.0000.000
114A113THR0-0.020-0.02433.343-0.009-0.0090.0000.0000.0000.000
115A114ALA00.0220.02932.624-0.008-0.0080.0000.0000.0000.000
116A115ALA00.0390.02928.699-0.008-0.0080.0000.0000.0000.000
117A116SER0-0.0330.00029.537-0.014-0.0140.0000.0000.0000.000
118A117THR0-0.063-0.05431.799-0.005-0.0050.0000.0000.0000.000
119A118LEU00.0400.02026.967-0.003-0.0030.0000.0000.0000.000
120A119THR0-0.005-0.03026.349-0.016-0.0160.0000.0000.0000.000
121A120ARG10.9140.95227.9580.1190.1190.0000.0000.0000.000
122A121GLU-1-0.921-0.95730.120-0.134-0.1340.0000.0000.0000.000
123A122LEU00.0220.01624.451-0.005-0.0050.0000.0000.0000.000
124A123ILE00.0000.00024.922-0.022-0.0220.0000.0000.0000.000
125A124HIS00.0450.03625.995-0.021-0.0210.0000.0000.0000.000
126A125SER0-0.058-0.09624.565-0.006-0.0060.0000.0000.0000.000
127A126MET0-0.0240.01520.576-0.017-0.0170.0000.0000.0000.000
128A127MET00.0140.00022.532-0.020-0.0200.0000.0000.0000.000
129A128ARG10.8710.94525.0030.2380.2380.0000.0000.0000.000
130A129ARG10.9230.95619.5640.3650.3650.0000.0000.0000.000
131A130ARG10.8360.93720.3760.2970.2970.0000.0000.0000.000
132A131TYR00.0500.02012.964-0.013-0.0130.0000.0000.0000.000
133A132GLY00.0320.02318.1680.0350.0350.0000.0000.0000.000
134A133ARG10.7970.92513.2280.7160.7160.0000.0000.0000.000
135A134ILE00.0260.01718.6850.0240.0240.0000.0000.0000.000
136A135ILE0-0.012-0.01316.6700.0040.0040.0000.0000.0000.000
137A136ASN0-0.006-0.01121.2470.0100.0100.0000.0000.0000.000
138A137ILE00.0090.00620.8700.0060.0060.0000.0000.0000.000
139A138THR00.011-0.00324.8150.0050.0050.0000.0000.0000.000
140A139SER00.0180.00228.0150.0050.0050.0000.0000.0000.000
141A140ILE0-0.056-0.01827.9430.0000.0000.0000.0000.0000.000
142A148GLY00.0610.02243.4820.0000.0000.0000.0000.0000.000
143A149GLN00.016-0.01339.505-0.004-0.0040.0000.0000.0000.000
144A150THR00.0440.02339.730-0.002-0.0020.0000.0000.0000.000
145A151ASN00.0830.04441.104-0.003-0.0030.0000.0000.0000.000
146A152TYR0-0.020-0.03535.669-0.006-0.0060.0000.0000.0000.000
147A153CYS0-0.073-0.03936.112-0.004-0.0040.0000.0000.0000.000
148A154ALA00.0430.03136.813-0.004-0.0040.0000.0000.0000.000
149A155ALA00.0290.02035.557-0.005-0.0050.0000.0000.0000.000
150A156LYS10.9560.98730.3230.0360.0360.0000.0000.0000.000
151A157ALA0-0.009-0.01332.527-0.008-0.0080.0000.0000.0000.000
152A158GLY00.0370.01834.272-0.006-0.0060.0000.0000.0000.000
153A159LEU00.0170.01228.509-0.008-0.0080.0000.0000.0000.000
154A160ILE0-0.005-0.00828.963-0.012-0.0120.0000.0000.0000.000
155A161GLY0-0.014-0.00230.497-0.009-0.0090.0000.0000.0000.000
156A162PHE00.004-0.01129.165-0.005-0.0050.0000.0000.0000.000
157A163SER0-0.012-0.02526.700-0.013-0.0130.0000.0000.0000.000
158A164LYS10.9070.95927.9380.0980.0980.0000.0000.0000.000
159A165ALA00.0160.01129.343-0.006-0.0060.0000.0000.0000.000
160A166LEU00.0400.02127.345-0.005-0.0050.0000.0000.0000.000
161A167ALA0-0.034-0.02125.142-0.012-0.0120.0000.0000.0000.000
162A168GLN0-0.041-0.02526.227-0.011-0.0110.0000.0000.0000.000
163A169GLU-1-0.988-0.97628.865-0.160-0.1600.0000.0000.0000.000
164A170ILE00.004-0.01024.743-0.004-0.0040.0000.0000.0000.000
165A171ALA00.0460.04123.458-0.027-0.0270.0000.0000.0000.000
166A172SER0-0.011-0.00522.979-0.030-0.0300.0000.0000.0000.000
167A173ARG10.8550.91923.6040.2340.2340.0000.0000.0000.000
168A174ASN0-0.020-0.00818.210-0.009-0.0090.0000.0000.0000.000
169A175ILE00.0100.02018.844-0.052-0.0520.0000.0000.0000.000
170A176THR0-0.032-0.00617.8410.0350.0350.0000.0000.0000.000
171A177VAL00.0300.00920.5330.0010.0010.0000.0000.0000.000
172A178ASN0-0.018-0.01119.5560.0440.0440.0000.0000.0000.000
173A179CYS0-0.060-0.01022.7310.0060.0060.0000.0000.0000.000
174A180ILE00.0370.02718.8670.0020.0020.0000.0000.0000.000
175A181ALA0-0.015-0.00123.4080.0010.0010.0000.0000.0000.000
176A182PRO0-0.013-0.00324.7750.0110.0110.0000.0000.0000.000
177A183GLY00.0210.00726.385-0.003-0.0030.0000.0000.0000.000
178A184PHE00.017-0.00828.986-0.003-0.0030.0000.0000.0000.000
179A185ILE0-0.0190.00424.7270.0100.0100.0000.0000.0000.000
180A186LYS10.9560.97427.373-0.084-0.0840.0000.0000.0000.000
181A187SER0-0.013-0.00728.090-0.004-0.0040.0000.0000.0000.000
182A188ALA00.1160.05230.5840.0020.0020.0000.0000.0000.000
183A189MET0-0.053-0.03433.731-0.001-0.0010.0000.0000.0000.000
184A190THR00.0410.00532.2760.0000.0000.0000.0000.0000.000
185A191ASP-1-0.925-0.95432.8350.0500.0500.0000.0000.0000.000
186A192LYS10.8930.95335.324-0.009-0.0090.0000.0000.0000.000
187A193LEU0-0.062-0.00836.541-0.002-0.0020.0000.0000.0000.000
188A194ASN00.0330.01339.8550.0040.0040.0000.0000.0000.000
189A195GLU-1-0.845-0.94241.7890.0410.0410.0000.0000.0000.000
190A196LYS10.9851.00342.515-0.015-0.0150.0000.0000.0000.000
191A197GLN0-0.037-0.01841.1610.0010.0010.0000.0000.0000.000
192A198LYS11.0050.99935.495-0.054-0.0540.0000.0000.0000.000
193A199GLU-1-0.908-0.95838.4960.0430.0430.0000.0000.0000.000
194A200ALA0-0.010-0.00740.3610.0000.0000.0000.0000.0000.000
195A201ILE0-0.022-0.03435.025-0.001-0.0010.0000.0000.0000.000
196A202MET0-0.0090.00333.4060.0030.0030.0000.0000.0000.000
197A203ALA00.0300.02636.2580.0030.0030.0000.0000.0000.000
198A204MET0-0.051-0.00436.374-0.004-0.0040.0000.0000.0000.000
199A205ILE0-0.036-0.01430.828-0.003-0.0030.0000.0000.0000.000
200A206PRO0-0.023-0.00631.7490.0060.0060.0000.0000.0000.000
201A207MET0-0.018-0.00725.4080.0080.0080.0000.0000.0000.000
202A208LYS10.8420.92630.402-0.040-0.0400.0000.0000.0000.000
203A209ARG10.8350.90122.879-0.124-0.1240.0000.0000.0000.000
204A210MET0-0.036-0.00829.332-0.007-0.0070.0000.0000.0000.000
205A211GLY00.0300.01925.2140.0130.0130.0000.0000.0000.000
206A212ILE0-0.015-0.02221.004-0.015-0.0150.0000.0000.0000.000
207A213GLY00.0380.00822.215-0.002-0.0020.0000.0000.0000.000
208A214GLU-1-0.854-0.94317.4350.2050.2050.0000.0000.0000.000
209A215GLU-1-0.773-0.86217.3170.1400.1400.0000.0000.0000.000
210A216ILE0-0.042-0.01618.398-0.016-0.0160.0000.0000.0000.000
211A217ALA00.0360.02316.156-0.036-0.0360.0000.0000.0000.000
212A218PHE00.019-0.00213.091-0.049-0.0490.0000.0000.0000.000
213A219ALA00.0050.00813.647-0.050-0.0500.0000.0000.0000.000
214A220THR0-0.020-0.01715.723-0.063-0.0630.0000.0000.0000.000
215A221VAL00.0350.0129.666-0.084-0.0840.0000.0000.0000.000
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