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: 2LJ9R

Calculation Name: 5H2T-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 5H2T

Chain ID: A

ChEMBL ID:

UniProt ID: D1ABU6

Base Structure: X-ray

Registration Date: 2023-09-26

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 544
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -12575379.40202
FMO2-HF: Nuclear repulsion 12352663.802548
FMO2-HF: Total energy -222715.599473
FMO2-MP2: Total energy -223362.331698


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:17:PRO)


Summations of interaction energy for fragment #1(A:17:PRO)
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.
-5.577-3.118-0.029-1.106-1.3240.006
Interaction energy analysis for fragmet #1(A:17:PRO)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.005 / q_NPA : 0.000
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].
3A19ASP-1-0.908-0.9633.785-3.573-1.114-0.029-1.106-1.3240.006
4A20PRO00.002-0.0106.0860.3250.3250.0000.0000.0000.000
5A21TYR00.0130.0009.5100.1660.1660.0000.0000.0000.000
6A22TRP00.0210.0168.8520.1630.1630.0000.0000.0000.000
7A23TYR0-0.023-0.05110.4920.0820.0820.0000.0000.0000.000
8A24LYS10.8940.95613.4680.4680.4680.0000.0000.0000.000
9A25HIS10.8380.9269.0281.0901.0900.0000.0000.0000.000
10A26ALA0-0.032-0.00214.093-0.014-0.0140.0000.0000.0000.000
11A27VAL0-0.001-0.00815.4050.0640.0640.0000.0000.0000.000
12A28PHE00.006-0.01117.319-0.035-0.0350.0000.0000.0000.000
13A29TYR0-0.057-0.07020.2690.0360.0360.0000.0000.0000.000
14A30GLU-1-0.781-0.87422.656-0.231-0.2310.0000.0000.0000.000
15A31VAL0-0.002-0.01024.0510.0200.0200.0000.0000.0000.000
16A32LEU00.0170.02026.757-0.004-0.0040.0000.0000.0000.000
17A33VAL00.0240.01126.2690.0050.0050.0000.0000.0000.000
18A34ARG10.9750.99228.8270.1370.1370.0000.0000.0000.000
19A35GLY00.0310.01431.7210.0100.0100.0000.0000.0000.000
20A36PHE0-0.027-0.01325.5330.0010.0010.0000.0000.0000.000
21A37SER0-0.022-0.03329.4380.0050.0050.0000.0000.0000.000
22A38ASP-1-0.683-0.80831.171-0.116-0.1160.0000.0000.0000.000
23A39SER0-0.112-0.05631.0130.0040.0040.0000.0000.0000.000
24A40ASN0-0.093-0.02933.0860.0080.0080.0000.0000.0000.000
25A41ASP-1-0.892-0.94935.715-0.088-0.0880.0000.0000.0000.000
26A42ASP-1-0.902-0.96037.222-0.099-0.0990.0000.0000.0000.000
27A43GLY0-0.082-0.04138.6840.0030.0030.0000.0000.0000.000
28A44THR0-0.006-0.01834.842-0.002-0.0020.0000.0000.0000.000
29A45GLY0-0.0280.00632.5070.0000.0000.0000.0000.0000.000
30A46ASP-1-0.676-0.85130.182-0.147-0.1470.0000.0000.0000.000
31A47LEU00.009-0.01524.213-0.012-0.0120.0000.0000.0000.000
32A48ARG10.7930.87124.7790.1550.1550.0000.0000.0000.000
33A49GLY00.033-0.00926.881-0.003-0.0030.0000.0000.0000.000
34A50LEU0-0.052-0.03522.866-0.005-0.0050.0000.0000.0000.000
35A51ILE0-0.007-0.00421.697-0.017-0.0170.0000.0000.0000.000
36A52ASN0-0.047-0.02523.036-0.009-0.0090.0000.0000.0000.000
37A53ARG10.8790.96225.2010.1610.1610.0000.0000.0000.000
38A54LEU00.0280.01318.490-0.012-0.0120.0000.0000.0000.000
39A55ASP-1-0.934-0.97220.307-0.221-0.2210.0000.0000.0000.000
40A56TYR0-0.039-0.03221.730-0.002-0.0020.0000.0000.0000.000
41A57LEU00.0410.01320.258-0.003-0.0030.0000.0000.0000.000
42A58GLN00.0110.00815.1070.0040.0040.0000.0000.0000.000
43A59TRP0-0.075-0.02818.658-0.003-0.0030.0000.0000.0000.000
44A60LEU0-0.028-0.00421.4570.0120.0120.0000.0000.0000.000
45A61GLY00.0160.01318.0020.0090.0090.0000.0000.0000.000
46A62ILE0-0.0510.00817.569-0.031-0.0310.0000.0000.0000.000
47A63ASP-1-0.842-0.92713.810-0.626-0.6260.0000.0000.0000.000
48A64CYS0-0.047-0.01914.258-0.102-0.1020.0000.0000.0000.000
49A65ILE00.0150.01916.7280.0570.0570.0000.0000.0000.000
50A66TRP0-0.067-0.05919.400-0.037-0.0370.0000.0000.0000.000
51A67LEU0-0.034-0.02121.9270.0240.0240.0000.0000.0000.000
52A68LEU00.0150.00824.2560.0030.0030.0000.0000.0000.000
53A69PRO0-0.031-0.01727.556-0.005-0.0050.0000.0000.0000.000
54A70ILE00.0320.02024.9070.0090.0090.0000.0000.0000.000
55A71TYR0-0.037-0.06425.8570.0060.0060.0000.0000.0000.000
56A72GLN00.0370.03030.5690.0050.0050.0000.0000.0000.000
57A73SER00.013-0.02233.9160.0000.0000.0000.0000.0000.000
58A74PRO0-0.037-0.01536.4440.0020.0020.0000.0000.0000.000
59A75LEU0-0.041-0.00735.5620.0020.0020.0000.0000.0000.000
60A76ARG10.8970.95239.0580.0850.0850.0000.0000.0000.000
61A77ASP-1-0.806-0.90838.799-0.111-0.1110.0000.0000.0000.000
62A78GLY0-0.0140.00036.625-0.007-0.0070.0000.0000.0000.000
63A79GLY00.0130.00334.218-0.008-0.0080.0000.0000.0000.000
64A80TYR0-0.055-0.02330.817-0.006-0.0060.0000.0000.0000.000
65A81ASP-1-0.786-0.90134.406-0.112-0.1120.0000.0000.0000.000
66A82ILE00.0150.02430.4600.0030.0030.0000.0000.0000.000
67A83SER0-0.041-0.03934.6030.0080.0080.0000.0000.0000.000
68A84ASP-1-0.821-0.95132.751-0.116-0.1160.0000.0000.0000.000
69A85TYR00.0100.00228.910-0.003-0.0030.0000.0000.0000.000
70A86THR0-0.037-0.00127.326-0.012-0.0120.0000.0000.0000.000
71A87LYS10.9470.98328.7310.1080.1080.0000.0000.0000.000
72A88ILE00.0060.00225.473-0.005-0.0050.0000.0000.0000.000
73A89LEU0-0.037-0.01129.8970.0110.0110.0000.0000.0000.000
74A90PRO0-0.007-0.00732.420-0.003-0.0030.0000.0000.0000.000
75A91GLU-1-0.914-0.95234.024-0.114-0.1140.0000.0000.0000.000
76A92PHE0-0.026-0.02229.644-0.002-0.0020.0000.0000.0000.000
77A93GLY00.0430.03129.508-0.012-0.0120.0000.0000.0000.000
78A94ASP-1-0.887-0.95328.441-0.134-0.1340.0000.0000.0000.000
79A95LEU0-0.021-0.03425.103-0.013-0.0130.0000.0000.0000.000
80A96GLY0-0.034-0.00323.902-0.017-0.0170.0000.0000.0000.000
81A97ASP-1-0.789-0.90523.615-0.173-0.1730.0000.0000.0000.000
82A98PHE0-0.011-0.01519.758-0.022-0.0220.0000.0000.0000.000
83A99VAL0-0.0020.00118.665-0.030-0.0300.0000.0000.0000.000
84A100GLU-1-0.762-0.83418.464-0.219-0.2190.0000.0000.0000.000
85A101LEU0-0.012-0.01319.058-0.022-0.0220.0000.0000.0000.000
86A102VAL0-0.024-0.00614.576-0.049-0.0490.0000.0000.0000.000
87A103ASP-1-0.909-0.95214.371-0.453-0.4530.0000.0000.0000.000
88A104GLU-1-0.945-0.98614.427-0.312-0.3120.0000.0000.0000.000
89A105ALA0-0.029-0.01515.647-0.010-0.0100.0000.0000.0000.000
90A106HIS10.8360.89710.5640.7060.7060.0000.0000.0000.000
91A107ARG10.8990.95910.8400.2080.2080.0000.0000.0000.000
92A108ARG10.8260.92012.5120.3250.3250.0000.0000.0000.000
93A109GLY0-0.057-0.01610.0700.0170.0170.0000.0000.0000.000
94A110ILE0-0.057-0.01711.043-0.037-0.0370.0000.0000.0000.000
95A111ARG10.9360.9717.2641.6921.6920.0000.0000.0000.000
96A112VAL00.022-0.00213.6580.0780.0780.0000.0000.0000.000
97A113ILE0-0.0010.00416.652-0.033-0.0330.0000.0000.0000.000
98A114ALA00.0290.00819.0540.0240.0240.0000.0000.0000.000
99A115ASP-1-0.708-0.82322.728-0.239-0.2390.0000.0000.0000.000
100A116LEU0-0.0090.02625.1790.0040.0040.0000.0000.0000.000
101A117VAL00.0060.02527.277-0.002-0.0020.0000.0000.0000.000
102A118MET0-0.0030.00827.1960.0040.0040.0000.0000.0000.000
103A119ASN0-0.0030.01030.7420.0090.0090.0000.0000.0000.000
104A120HIS00.0500.03734.3630.0090.0090.0000.0000.0000.000
105A121THR00.0280.02834.741-0.006-0.0060.0000.0000.0000.000
106A122SER0-0.005-0.00536.8360.0060.0060.0000.0000.0000.000
107A123ASP-1-0.844-0.93939.358-0.080-0.0800.0000.0000.0000.000
108A124GLN0-0.057-0.03640.8960.0040.0040.0000.0000.0000.000
109A125HIS0-0.0070.01134.006-0.001-0.0010.0000.0000.0000.000
110A126PRO0-0.004-0.00437.6630.0050.0050.0000.0000.0000.000
111A127TRP00.010-0.01132.4560.0040.0040.0000.0000.0000.000
112A128PHE00.0300.03139.8500.0040.0040.0000.0000.0000.000
113A129GLN0-0.017-0.02942.4110.0080.0080.0000.0000.0000.000
114A130ALA0-0.0090.00342.8960.0040.0040.0000.0000.0000.000
115A131SER0-0.0250.00443.0090.0030.0030.0000.0000.0000.000
116A132ARG10.8170.89245.0490.0640.0640.0000.0000.0000.000
117A133THR0-0.046-0.03347.8750.0030.0030.0000.0000.0000.000
118A134ASP-1-0.933-0.97247.499-0.044-0.0440.0000.0000.0000.000
119A135PRO0-0.037-0.01247.399-0.002-0.0020.0000.0000.0000.000
120A136ASP-1-0.887-0.93847.758-0.043-0.0430.0000.0000.0000.000
121A137GLY0-0.051-0.01645.8090.0010.0010.0000.0000.0000.000
122A138PRO0-0.037-0.04040.743-0.001-0.0010.0000.0000.0000.000
123A139TYR00.0190.00436.572-0.001-0.0010.0000.0000.0000.000
124A140GLY00.0320.04341.609-0.003-0.0030.0000.0000.0000.000
125A141ASP-1-0.883-0.93642.516-0.058-0.0580.0000.0000.0000.000
126A142PHE0-0.026-0.02735.596-0.003-0.0030.0000.0000.0000.000
127A143TYR00.014-0.00438.562-0.004-0.0040.0000.0000.0000.000
128A144MET0-0.019-0.00340.0080.0050.0050.0000.0000.0000.000
129A145TRP00.0200.01543.9390.0010.0010.0000.0000.0000.000
130A146SER0-0.078-0.05447.5520.0020.0020.0000.0000.0000.000
131A147ASP-1-0.863-0.93150.858-0.044-0.0440.0000.0000.0000.000
132A148THR0-0.142-0.09453.3730.0010.0010.0000.0000.0000.000
133A149ASP-1-0.878-0.95653.015-0.055-0.0550.0000.0000.0000.000
134A150ASP-1-0.864-0.90753.652-0.047-0.0470.0000.0000.0000.000
135A151LYS10.8640.95648.7860.0540.0540.0000.0000.0000.000
136A152TYR0-0.019-0.01544.863-0.002-0.0020.0000.0000.0000.000
137A153PRO00.0320.02148.342-0.002-0.0020.0000.0000.0000.000
138A154ASP-1-0.921-0.94948.251-0.058-0.0580.0000.0000.0000.000
139A155ALA0-0.066-0.02944.631-0.003-0.0030.0000.0000.0000.000
140A156ARG10.8910.94041.2970.0940.0940.0000.0000.0000.000
141A157ILE00.0150.00845.725-0.003-0.0030.0000.0000.0000.000
142A158ILE0-0.042-0.01440.0330.0010.0010.0000.0000.0000.000
143A159PHE00.0180.01139.9330.0000.0000.0000.0000.0000.000
144A160VAL00.0260.00645.6630.0030.0030.0000.0000.0000.000
145A161ASP-1-0.938-0.95648.891-0.068-0.0680.0000.0000.0000.000
146A162THR0-0.138-0.07247.8670.0010.0010.0000.0000.0000.000
147A163GLU-1-0.839-0.92646.566-0.073-0.0730.0000.0000.0000.000
148A164VAL0-0.020-0.00749.9440.0010.0010.0000.0000.0000.000
149A165SER00.0370.02451.2750.0000.0000.0000.0000.0000.000
150A166ASN00.0110.00846.377-0.004-0.0040.0000.0000.0000.000
151A167TRP0-0.056-0.04547.019-0.003-0.0030.0000.0000.0000.000
152A168THR00.0020.01348.9520.0000.0000.0000.0000.0000.000
153A169TYR0-0.0170.00950.4670.0000.0000.0000.0000.0000.000
154A170ASP-1-0.775-0.87649.523-0.060-0.0600.0000.0000.0000.000
155A171PRO0-0.036-0.03152.0520.0020.0020.0000.0000.0000.000
156A172VAL0-0.078-0.03251.5580.0020.0020.0000.0000.0000.000
157A173ARG10.8280.91446.7570.0580.0580.0000.0000.0000.000
158A174GLY0-0.038-0.01152.4070.0020.0020.0000.0000.0000.000
159A175GLN0-0.023-0.00351.020-0.001-0.0010.0000.0000.0000.000
160A176TYR00.0140.01451.083-0.001-0.0010.0000.0000.0000.000
161A177TYR0-0.058-0.07545.0670.0010.0010.0000.0000.0000.000
162A178TRP00.0440.00042.0120.0020.0020.0000.0000.0000.000
163A179HIS10.8430.90142.4850.0750.0750.0000.0000.0000.000
164A180ARG10.8740.97240.2210.0930.0930.0000.0000.0000.000
165A181PHE00.0130.00936.612-0.002-0.0020.0000.0000.0000.000
166A182PHE00.0190.02141.6220.0060.0060.0000.0000.0000.000
167A183SER0-0.0020.00243.504-0.002-0.0020.0000.0000.0000.000
168A184HIS00.0080.05241.4770.0060.0060.0000.0000.0000.000
169A185GLN0-0.082-0.07937.7870.0000.0000.0000.0000.0000.000
170A186PRO0-0.042-0.00141.0790.0000.0000.0000.0000.0000.000
171A187ASP-1-0.750-0.90739.037-0.104-0.1040.0000.0000.0000.000
172A188LEU0-0.034-0.02134.2140.0060.0060.0000.0000.0000.000
173A189ASN0-0.008-0.01637.984-0.002-0.0020.0000.0000.0000.000
174A190TYR00.043-0.01031.158-0.002-0.0020.0000.0000.0000.000
175A191ASP-1-0.827-0.90136.082-0.077-0.0770.0000.0000.0000.000
176A192ASN0-0.053-0.03038.3540.0040.0040.0000.0000.0000.000
177A193PRO0-0.007-0.02134.989-0.006-0.0060.0000.0000.0000.000
178A194ALA00.0180.00033.786-0.005-0.0050.0000.0000.0000.000
179A195VAL00.0260.03833.890-0.005-0.0050.0000.0000.0000.000
180A196GLN0-0.068-0.04931.297-0.011-0.0110.0000.0000.0000.000
181A197GLU-1-0.930-0.96727.929-0.131-0.1310.0000.0000.0000.000
182A198ALA00.0300.01629.224-0.007-0.0070.0000.0000.0000.000
183A199MET00.0100.00828.982-0.012-0.0120.0000.0000.0000.000
184A200LEU0-0.010-0.00623.627-0.018-0.0180.0000.0000.0000.000
185A201GLU-1-0.962-0.96724.535-0.133-0.1330.0000.0000.0000.000
186A202VAL0-0.027-0.01225.495-0.012-0.0120.0000.0000.0000.000
187A203LEU0-0.024-0.02522.448-0.016-0.0160.0000.0000.0000.000
188A204ARG10.9050.94720.6340.1310.1310.0000.0000.0000.000
189A205PHE00.0340.04020.805-0.014-0.0140.0000.0000.0000.000
190A206TRP0-0.025-0.02121.090-0.014-0.0140.0000.0000.0000.000
191A207LEU0-0.057-0.02416.254-0.038-0.0380.0000.0000.0000.000
192A208ASP-1-0.878-0.93216.411-0.289-0.2890.0000.0000.0000.000
193A209LEU0-0.088-0.03517.499-0.004-0.0040.0000.0000.0000.000
194A210GLY0-0.019-0.00214.572-0.016-0.0160.0000.0000.0000.000
195A211ILE0-0.0340.00314.437-0.078-0.0780.0000.0000.0000.000
196A212ASP-1-0.804-0.89311.632-0.943-0.9430.0000.0000.0000.000
197A213GLY00.020-0.01314.444-0.043-0.0430.0000.0000.0000.000
198A214PHE00.0030.00217.5410.0230.0230.0000.0000.0000.000
199A215ARG10.8430.94021.2260.2080.2080.0000.0000.0000.000
200A216LEU0-0.026-0.01823.8760.0160.0160.0000.0000.0000.000
201A217ASP-1-0.788-0.93626.328-0.198-0.1980.0000.0000.0000.000
202A218ALA00.020-0.01129.7650.0070.0070.0000.0000.0000.000
203A219VAL00.006-0.00728.2390.0080.0080.0000.0000.0000.000
204A220PRO0-0.038-0.02131.6060.0060.0060.0000.0000.0000.000
205A221TYR0-0.013-0.01334.3100.0050.0050.0000.0000.0000.000
206A222LEU0-0.0480.01630.6560.0030.0030.0000.0000.0000.000
207A223TYR0-0.028-0.00733.2630.0030.0030.0000.0000.0000.000
208A224ALA00.0500.02537.807-0.001-0.0010.0000.0000.0000.000
209A225ARG10.7940.88239.7540.0770.0770.0000.0000.0000.000
210A226GLU-1-0.848-0.92943.848-0.056-0.0560.0000.0000.0000.000
211A227GLY0-0.024-0.01747.2150.0010.0010.0000.0000.0000.000
212A228THR0-0.054-0.02643.100-0.002-0.0020.0000.0000.0000.000
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