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: 94232

Calculation Name: 5H76-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 5H76

Chain ID: A

ChEMBL ID:

UniProt ID: P38507

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 197
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -1980241.881104
FMO2-HF: Nuclear repulsion 1906028.316703
FMO2-HF: Total energy -74213.564401
FMO2-MP2: Total energy -74433.272771


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:13:ASP)


Summations of interaction energy for fragment #1(A:13:ASP)
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.
73.16782.2941.54-4.688-5.980.039
Interaction energy analysis for fragmet #1(A:13:ASP)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : -1 / q_Mulliken : -0.937 / q_NPA : -0.984
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].
3A15GLY00.0790.0502.820-13.356-9.7370.220-1.740-2.0990.012
4A16ARG10.8840.9292.329-73.965-69.0161.316-2.754-3.5120.027
5A17LYS10.9210.9544.040-53.138-52.5790.004-0.194-0.3690.000
6A18LEU00.0320.0275.924-5.287-5.2870.0000.0000.0000.000
7A19LEU00.0140.0086.776-3.469-3.4690.0000.0000.0000.000
8A20GLU-1-0.886-0.9376.91335.48435.4840.0000.0000.0000.000
9A21ALA00.0120.0069.806-2.786-2.7860.0000.0000.0000.000
10A22ALA0-0.0030.00111.807-2.131-2.1310.0000.0000.0000.000
11A23ARG10.9320.96411.167-26.359-26.3590.0000.0000.0000.000
12A24ALA0-0.039-0.02114.073-1.380-1.3800.0000.0000.0000.000
13A25GLY00.0150.01415.776-1.027-1.0270.0000.0000.0000.000
14A26GLN0-0.050-0.02412.375-1.234-1.2340.0000.0000.0000.000
15A27ASP-1-0.794-0.91715.38617.04317.0430.0000.0000.0000.000
16A28ASP-1-0.949-0.98516.80215.93215.9320.0000.0000.0000.000
17A29GLU-1-0.953-0.98612.18323.27923.2790.0000.0000.0000.000
18A30VAL00.0330.02011.9142.1052.1050.0000.0000.0000.000
19A31ARG10.9340.96713.168-14.914-14.9140.0000.0000.0000.000
20A32ILE0-0.040-0.02210.7900.0130.0130.0000.0000.0000.000
21A33LEU0-0.0020.0026.8321.3811.3810.0000.0000.0000.000
22A34MET0-0.022-0.0049.7641.6601.6600.0000.0000.0000.000
23A35ALA0-0.044-0.00812.444-0.508-0.5080.0000.0000.0000.000
24A36ASN0-0.108-0.0558.056-0.515-0.5150.0000.0000.0000.000
25A37GLY0-0.009-0.0068.8681.4131.4130.0000.0000.0000.000
26A38ALA0-0.059-0.0257.4722.0972.0970.0000.0000.0000.000
27A39ASP-1-0.891-0.9457.47225.78625.7860.0000.0000.0000.000
28A40VAL00.0300.0049.2511.8011.8010.0000.0000.0000.000
29A41ASN0-0.022-0.00311.687-1.175-1.1750.0000.0000.0000.000
30A42ALA0-0.0090.0066.7650.5890.5890.0000.0000.0000.000
31A43ALA00.0530.0158.773-1.033-1.0330.0000.0000.0000.000
32A44ASP-1-0.841-0.8708.62430.31830.3180.0000.0000.0000.000
33A45ASN0-0.051-0.0469.558-0.616-0.6160.0000.0000.0000.000
34A46THR0-0.087-0.06911.968-2.066-2.0660.0000.0000.0000.000
35A47GLY00.0460.02413.263-1.778-1.7780.0000.0000.0000.000
36A48THR0-0.0090.00212.981-1.518-1.5180.0000.0000.0000.000
37A49THR00.010-0.02811.7252.6772.6770.0000.0000.0000.000
38A50PRO0-0.010-0.02710.019-1.098-1.0980.0000.0000.0000.000
39A51LEU00.0420.02112.707-1.058-1.0580.0000.0000.0000.000
40A52HIS00.0360.05215.5000.0470.0470.0000.0000.0000.000
41A53LEU0-0.027-0.01111.937-0.898-0.8980.0000.0000.0000.000
42A54ALA00.0240.01816.135-0.828-0.8280.0000.0000.0000.000
43A55ALA00.0090.00017.955-0.936-0.9360.0000.0000.0000.000
44A56TYR0-0.068-0.03218.520-0.449-0.4490.0000.0000.0000.000
45A57SER0-0.050-0.03918.310-0.570-0.5700.0000.0000.0000.000
46A58GLY0-0.0130.01020.925-0.515-0.5150.0000.0000.0000.000
47A59HIS0-0.0100.00718.256-0.876-0.8760.0000.0000.0000.000
48A60LEU00.0590.02421.0590.6450.6450.0000.0000.0000.000
49A61GLU-1-0.862-0.93222.11213.68213.6820.0000.0000.0000.000
50A62ILE0-0.048-0.02016.0370.5910.5910.0000.0000.0000.000
51A63VAL00.0060.00718.2650.8000.8000.0000.0000.0000.000
52A64GLU-1-0.911-0.95420.23912.51012.5100.0000.0000.0000.000
53A65VAL0-0.104-0.05717.068-0.067-0.0670.0000.0000.0000.000
54A66LEU0-0.023-0.01513.6330.4150.4150.0000.0000.0000.000
55A67LEU00.0470.02517.1730.1980.1980.0000.0000.0000.000
56A68LYS10.8780.95820.231-14.177-14.1770.0000.0000.0000.000
57A69HIS0-0.114-0.07515.659-1.258-1.2580.0000.0000.0000.000
58A70GLY0-0.0010.00617.1310.6730.6730.0000.0000.0000.000
59A71ALA0-0.040-0.02316.0850.5510.5510.0000.0000.0000.000
60A72ASP-1-0.900-0.96216.66515.19415.1940.0000.0000.0000.000
61A73VAL0-0.019-0.01318.6360.4660.4660.0000.0000.0000.000
62A74ASP-1-0.862-0.91721.40212.44812.4480.0000.0000.0000.000
63A75ALA0-0.0120.01117.0010.0360.0360.0000.0000.0000.000
64A76SER0-0.032-0.03219.116-0.386-0.3860.0000.0000.0000.000
65A77ASP-1-0.840-0.91517.45517.04917.0490.0000.0000.0000.000
66A78VAL0-0.063-0.04717.831-0.909-0.9090.0000.0000.0000.000
67A79PHE0-0.066-0.03919.615-0.743-0.7430.0000.0000.0000.000
68A80GLY00.0080.00721.803-0.823-0.8230.0000.0000.0000.000
69A81TYR0-0.065-0.03021.438-0.504-0.5040.0000.0000.0000.000
70A82THR00.0760.02720.9390.7960.7960.0000.0000.0000.000
71A83PRO00.012-0.01618.864-0.264-0.2640.0000.0000.0000.000
72A84LEU00.0410.02921.419-0.289-0.2890.0000.0000.0000.000
73A85HIS00.0120.02724.2860.0300.0300.0000.0000.0000.000
74A86LEU0-0.030-0.00519.477-0.334-0.3340.0000.0000.0000.000
75A87ALA00.0340.01323.783-0.232-0.2320.0000.0000.0000.000
76A88ALA0-0.014-0.00525.511-0.420-0.4200.0000.0000.0000.000
77A89TYR0-0.022-0.02126.258-0.548-0.5480.0000.0000.0000.000
78A90TRP0-0.050-0.03823.588-0.301-0.3010.0000.0000.0000.000
79A91GLY00.0130.02027.424-0.034-0.0340.0000.0000.0000.000
80A92HIS0-0.015-0.00224.222-0.548-0.5480.0000.0000.0000.000
81A93LEU00.0300.00228.3500.1410.1410.0000.0000.0000.000
82A94GLU-1-0.875-0.94329.08210.60310.6030.0000.0000.0000.000
83A95ILE0-0.0040.00622.8640.1780.1780.0000.0000.0000.000
84A96VAL0-0.012-0.00226.2890.2150.2150.0000.0000.0000.000
85A97GLU-1-0.933-0.97328.4339.6559.6550.0000.0000.0000.000
86A98VAL0-0.038-0.01824.798-0.081-0.0810.0000.0000.0000.000
87A99LEU00.001-0.00921.9440.1610.1610.0000.0000.0000.000
88A100LEU00.0140.01125.814-0.038-0.0380.0000.0000.0000.000
89A101LYS10.8830.95528.997-10.312-10.3120.0000.0000.0000.000
90A102ASN0-0.105-0.06624.774-0.044-0.0440.0000.0000.0000.000
91A103GLY0-0.020-0.01125.9450.3540.3540.0000.0000.0000.000
92A104ALA0-0.0010.01025.6020.0650.0650.0000.0000.0000.000
93A105ASP-1-0.883-0.95326.74910.18910.1890.0000.0000.0000.000
94A106VAL0-0.046-0.02328.7450.1920.1920.0000.0000.0000.000
95A107ASN0-0.038-0.02531.205-0.254-0.2540.0000.0000.0000.000
96A108ALA00.0490.04226.696-0.071-0.0710.0000.0000.0000.000
97A109MET0-0.065-0.05428.778-0.280-0.2800.0000.0000.0000.000
98A110ASP-1-0.799-0.88426.12911.81111.8110.0000.0000.0000.000
99A111SER0-0.036-0.02725.937-0.235-0.2350.0000.0000.0000.000
100A112ASP-1-1.010-0.99727.74010.47410.4740.0000.0000.0000.000
101A113GLY0-0.017-0.02330.648-0.446-0.4460.0000.0000.0000.000
102A114MET0-0.067-0.02830.536-0.298-0.2980.0000.0000.0000.000
103A115THR00.0330.01030.1710.3450.3450.0000.0000.0000.000
104A116PRO00.031-0.00628.229-0.088-0.0880.0000.0000.0000.000
105A117LEU00.0310.01930.562-0.090-0.0900.0000.0000.0000.000
106A118HIS00.0180.02833.1610.0510.0510.0000.0000.0000.000
107A119LEU0-0.014-0.00727.803-0.138-0.1380.0000.0000.0000.000
108A120ALA00.0200.01031.869-0.021-0.0210.0000.0000.0000.000
109A121ALA00.002-0.01033.459-0.191-0.1910.0000.0000.0000.000
110A122LYS10.8900.95331.529-10.101-10.1010.0000.0000.0000.000
111A123TRP0-0.071-0.04130.104-0.280-0.2800.0000.0000.0000.000
112A124GLY0-0.032-0.01035.118-0.096-0.0960.0000.0000.0000.000
113A125TYR0-0.030-0.00330.926-0.189-0.1890.0000.0000.0000.000
114A126LEU00.0430.02736.1630.0630.0630.0000.0000.0000.000
115A127GLU-1-0.846-0.93436.2768.5828.5820.0000.0000.0000.000
116A128ILE0-0.0100.00030.7020.0510.0510.0000.0000.0000.000
117A129VAL00.0200.01134.5030.0760.0760.0000.0000.0000.000
118A130GLU-1-0.933-0.97036.9647.8207.8200.0000.0000.0000.000
119A131VAL0-0.046-0.02933.100-0.113-0.1130.0000.0000.0000.000
120A132LEU00.0180.01931.1780.0370.0370.0000.0000.0000.000
121A133LEU00.005-0.00435.049-0.072-0.0720.0000.0000.0000.000
122A134LYS10.8590.94237.586-8.520-8.5200.0000.0000.0000.000
123A135HIS0-0.097-0.05633.313-0.004-0.0040.0000.0000.0000.000
124A136GLY0-0.0100.00435.7790.1390.1390.0000.0000.0000.000
125A137ALA0-0.0020.00435.3990.0620.0620.0000.0000.0000.000
126A138VAL0-0.033-0.01636.459-0.319-0.3190.0000.0000.0000.000
127A139ASN0-0.053-0.02437.7560.2940.2940.0000.0000.0000.000
128A140ALA00.0100.00436.486-0.129-0.1290.0000.0000.0000.000
129A141GLN0-0.075-0.04538.624-0.007-0.0070.0000.0000.0000.000
130A142ASP-1-0.757-0.85534.9308.9398.9390.0000.0000.0000.000
131A143LYS10.9310.96432.405-10.042-10.0420.0000.0000.0000.000
132A144PHE0-0.116-0.06335.029-0.174-0.1740.0000.0000.0000.000
133A145GLY0-0.018-0.00639.042-0.246-0.2460.0000.0000.0000.000
134A146LYS10.8780.93739.263-8.012-8.0120.0000.0000.0000.000
135A147THR00.0090.00139.1020.2320.2320.0000.0000.0000.000
136A148ALA00.0640.02538.0680.0200.0200.0000.0000.0000.000
137A149PHE00.0450.02239.597-0.046-0.0460.0000.0000.0000.000
138A150ASP-1-0.822-0.91942.1827.3457.3450.0000.0000.0000.000
139A151ILE0-0.0080.00136.449-0.027-0.0270.0000.0000.0000.000
140A152SER0-0.054-0.04840.6330.0160.0160.0000.0000.0000.000
141A153ILE0-0.067-0.02142.663-0.141-0.1410.0000.0000.0000.000
142A154ASP-1-0.946-0.96841.9947.5127.5120.0000.0000.0000.000
143A155ASN0-0.062-0.03138.634-0.074-0.0740.0000.0000.0000.000
144A156GLY00.0070.00943.024-0.127-0.1270.0000.0000.0000.000
145A157ASN0-0.048-0.02640.770-0.179-0.1790.0000.0000.0000.000
146A158GLU-1-0.845-0.93844.6016.4076.4070.0000.0000.0000.000
147A159ASP-1-0.873-0.93544.5757.0537.0530.0000.0000.0000.000
148A160LEU0-0.033-0.00139.4390.0190.0190.0000.0000.0000.000
149A161ALA00.0490.01943.3940.0190.0190.0000.0000.0000.000
150A162GLN0-0.043-0.02845.9700.0020.0020.0000.0000.0000.000
151A163ILE0-0.001-0.00242.583-0.089-0.0890.0000.0000.0000.000
152A164LEU00.005-0.00140.328-0.031-0.0310.0000.0000.0000.000
153A165ALA00.0210.02044.376-0.050-0.0500.0000.0000.0000.000
154A166PHE0-0.031-0.02146.669-0.169-0.1690.0000.0000.0000.000
155A167TYR00.001-0.00842.862-0.096-0.0960.0000.0000.0000.000
156A168GLU-1-0.856-0.94245.3287.0637.0630.0000.0000.0000.000
157A169ILE0-0.012-0.01847.388-0.119-0.1190.0000.0000.0000.000
158A170LEU0-0.094-0.03947.292-0.133-0.1330.0000.0000.0000.000
159A171HIS0-0.068-0.02944.9830.0030.0030.0000.0000.0000.000
160A172LEU0-0.051-0.00748.7940.0010.0010.0000.0000.0000.000
161A173PRO0-0.051-0.02851.096-0.077-0.0770.0000.0000.0000.000
162A174ASN0-0.032-0.01753.447-0.092-0.0920.0000.0000.0000.000
163A175LEU0-0.0060.01754.985-0.134-0.1340.0000.0000.0000.000
164A176ASN0-0.006-0.00457.4090.0670.0670.0000.0000.0000.000
165A177GLU-1-0.931-0.98558.1655.6065.6060.0000.0000.0000.000
166A178GLU-1-0.972-0.98159.2475.1585.1580.0000.0000.0000.000
167A179GLN00.0680.00559.7120.0830.0830.0000.0000.0000.000
168A180ARG10.9681.00052.880-5.926-5.9260.0000.0000.0000.000
169A181ASN0-0.008-0.02356.1440.1750.1750.0000.0000.0000.000
170A182ALA00.0110.02357.8840.0170.0170.0000.0000.0000.000
171A183PHE00.0250.01255.3900.0150.0150.0000.0000.0000.000
172A184ILE00.0150.01052.5740.0690.0690.0000.0000.0000.000
173A185GLN0-0.040-0.01854.8970.0670.0670.0000.0000.0000.000
174A186SER0-0.022-0.02957.699-0.055-0.0550.0000.0000.0000.000
175A187LEU0-0.0250.00150.6250.0340.0340.0000.0000.0000.000
176A188LYS10.8480.92852.259-6.101-6.1010.0000.0000.0000.000
177A189ASP-1-1.008-0.98255.2395.4015.4010.0000.0000.0000.000
178A190ASP-1-0.790-0.86456.7355.7785.7780.0000.0000.0000.000
179A191PRO00.003-0.00251.2990.0230.0230.0000.0000.0000.000
180A192SER0-0.018-0.03352.1310.0850.0850.0000.0000.0000.000
181A193GLN0-0.0090.00953.4970.0180.0180.0000.0000.0000.000
182A194SER0-0.002-0.00649.361-0.032-0.0320.0000.0000.0000.000
183A195ALA00.0250.01550.4440.0280.0280.0000.0000.0000.000
184A196ASN0-0.092-0.05951.7030.0120.0120.0000.0000.0000.000
185A197LEU00.0150.01654.536-0.043-0.0430.0000.0000.0000.000
186A198LEU00.0190.03848.531-0.083-0.0830.0000.0000.0000.000
187A199ALA0-0.0020.00452.831-0.021-0.0210.0000.0000.0000.000
188A200GLU-1-0.971-0.99554.4965.3715.3710.0000.0000.0000.000
189A201ALA00.004-0.00854.098-0.063-0.0630.0000.0000.0000.000
190A202LYS10.9410.96548.432-6.750-6.7500.0000.0000.0000.000
191A203LYS10.9560.97554.548-5.414-5.4140.0000.0000.0000.000
192A204LEU0-0.016-0.00557.908-0.072-0.0720.0000.0000.0000.000
193A205ASN00.023-0.00653.057-0.110-0.1100.0000.0000.0000.000
194A206ASP-1-0.909-0.95754.8576.0156.0150.0000.0000.0000.000
195A207ALA0-0.106-0.04657.630-0.081-0.0810.0000.0000.0000.000
196A208GLN0-0.076-0.02060.184-0.171-0.1710.0000.0000.0000.000
197A209ALA0-0.0120.01057.343-0.036-0.0360.0000.0000.0000.000