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: MV25Z

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 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 197
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -1981275.005747
FMO2-HF: Nuclear repulsion 1907060.267428
FMO2-HF: Total energy -74214.738319
FMO2-MP2: Total energy -74434.455993


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.
36.68939.97819.985-10.898-12.3780.124
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 : -0.874 / q_NPA : -0.948
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].
3A15GLY00.0640.0422.995-9.843-6.6720.182-1.542-1.8120.006
4A16ARG10.8180.8781.872-114.078-114.81119.779-9.037-10.0090.115
5A17LYS10.9260.9623.852-57.622-56.7710.024-0.319-0.5570.003
6A18LEU00.0270.0205.903-6.576-6.5760.0000.0000.0000.000
7A19LEU00.0140.0126.226-3.953-3.9530.0000.0000.0000.000
8A20GLU-1-0.879-0.9276.60043.80343.8030.0000.0000.0000.000
9A21ALA00.0140.0059.630-3.366-3.3660.0000.0000.0000.000
10A22ALA00.0010.00211.214-2.486-2.4860.0000.0000.0000.000
11A23ARG10.9310.96810.297-29.066-29.0660.0000.0000.0000.000
12A24ALA0-0.035-0.01813.856-1.618-1.6180.0000.0000.0000.000
13A25GLY00.0260.02615.623-1.184-1.1840.0000.0000.0000.000
14A26GLN0-0.089-0.06913.205-0.698-0.6980.0000.0000.0000.000
15A27ASP-1-0.738-0.86915.38017.31417.3140.0000.0000.0000.000
16A28ASP-1-0.851-0.92616.71116.25116.2510.0000.0000.0000.000
17A29GLU-1-0.919-0.94911.94624.18324.1830.0000.0000.0000.000
18A30VAL00.0360.02211.7462.1352.1350.0000.0000.0000.000
19A31ARG10.7590.85513.093-15.570-15.5700.0000.0000.0000.000
20A32ILE0-0.040-0.02310.542-0.087-0.0870.0000.0000.0000.000
21A33LEU0-0.011-0.0106.6801.1961.1960.0000.0000.0000.000
22A34MET0-0.0070.0129.6551.2051.2050.0000.0000.0000.000
23A35ALA0-0.054-0.01512.335-0.671-0.6710.0000.0000.0000.000
24A36ASN0-0.118-0.0607.989-0.096-0.0960.0000.0000.0000.000
25A37GLY0-0.006-0.0038.8281.0911.0910.0000.0000.0000.000
26A38ALA0-0.062-0.0247.4531.6731.6730.0000.0000.0000.000
27A39ASP-1-0.883-0.9417.75924.92124.9210.0000.0000.0000.000
28A40VAL00.0280.0059.2792.1622.1620.0000.0000.0000.000
29A41ASN0-0.034-0.00811.843-0.563-0.5630.0000.0000.0000.000
30A42ALA0-0.0100.0086.6310.4640.4640.0000.0000.0000.000
31A43ALA00.0460.0118.776-0.501-0.5010.0000.0000.0000.000
32A44ASP-1-0.835-0.8808.78530.84730.8470.0000.0000.0000.000
33A45ASN0-0.043-0.0439.636-0.655-0.6550.0000.0000.0000.000
34A46THR0-0.092-0.06112.459-2.327-2.3270.0000.0000.0000.000
35A47GLY00.0430.02113.325-1.754-1.7540.0000.0000.0000.000
36A48THR0-0.035-0.00712.691-1.411-1.4110.0000.0000.0000.000
37A49THR00.036-0.01011.3192.8832.8830.0000.0000.0000.000
38A50PRO0-0.010-0.0269.613-0.711-0.7110.0000.0000.0000.000
39A51LEU00.0420.02012.234-1.066-1.0660.0000.0000.0000.000
40A52HIS00.0390.04815.1000.1590.1590.0000.0000.0000.000
41A53LEU0-0.026-0.00911.357-0.814-0.8140.0000.0000.0000.000
42A54ALA00.0220.02515.471-0.836-0.8360.0000.0000.0000.000
43A55ALA00.0080.00117.327-0.974-0.9740.0000.0000.0000.000
44A56TYR0-0.074-0.03117.555-0.382-0.3820.0000.0000.0000.000
45A57SER0-0.063-0.05817.555-0.505-0.5050.0000.0000.0000.000
46A58GLY0-0.0010.01220.237-0.538-0.5380.0000.0000.0000.000
47A59HIS0-0.029-0.00617.573-0.957-0.9570.0000.0000.0000.000
48A60LEU00.0530.02020.4820.6150.6150.0000.0000.0000.000
49A61GLU-1-0.856-0.92721.48314.14414.1440.0000.0000.0000.000
50A62ILE0-0.015-0.00815.4870.5430.5430.0000.0000.0000.000
51A63VAL0-0.0040.00217.8650.7540.7540.0000.0000.0000.000
52A64GLU-1-0.909-0.95319.81412.63212.6320.0000.0000.0000.000
53A65VAL0-0.083-0.04716.824-0.075-0.0750.0000.0000.0000.000
54A66LEU0-0.017-0.01913.1120.3500.3500.0000.0000.0000.000
55A67LEU00.0380.02016.9500.0870.0870.0000.0000.0000.000
56A68LYS10.8890.96120.076-14.369-14.3690.0000.0000.0000.000
57A69HIS0-0.119-0.07616.004-1.154-1.1540.0000.0000.0000.000
58A70GLY0-0.0040.00517.2590.5950.5950.0000.0000.0000.000
59A71ALA0-0.033-0.02016.0490.4900.4900.0000.0000.0000.000
60A72ASP-1-0.915-0.97016.62915.00715.0070.0000.0000.0000.000
61A73VAL0-0.017-0.01318.6150.5350.5350.0000.0000.0000.000
62A74ASP-1-0.858-0.91621.25412.45912.4590.0000.0000.0000.000
63A75ALA0-0.0190.00816.8520.0230.0230.0000.0000.0000.000
64A76SER0-0.027-0.03218.984-0.328-0.3280.0000.0000.0000.000
65A77ASP-1-0.843-0.91517.22217.16017.1600.0000.0000.0000.000
66A78VAL0-0.052-0.04017.882-0.952-0.9520.0000.0000.0000.000
67A79PHE0-0.069-0.03819.703-0.815-0.8150.0000.0000.0000.000
68A80GLY00.0120.00421.652-0.854-0.8540.0000.0000.0000.000
69A81TYR0-0.068-0.03421.135-0.497-0.4970.0000.0000.0000.000
70A82THR00.0810.02320.5890.8350.8350.0000.0000.0000.000
71A83PRO00.008-0.02018.510-0.167-0.1670.0000.0000.0000.000
72A84LEU00.0360.02620.997-0.252-0.2520.0000.0000.0000.000
73A85HIS00.0180.03623.9000.0490.0490.0000.0000.0000.000
74A86LEU0-0.034-0.00918.997-0.305-0.3050.0000.0000.0000.000
75A87ALA00.0280.00923.210-0.210-0.2100.0000.0000.0000.000
76A88ALA0-0.010-0.00124.935-0.421-0.4210.0000.0000.0000.000
77A89TYR0-0.021-0.02425.749-0.534-0.5340.0000.0000.0000.000
78A90TRP0-0.053-0.04923.286-0.316-0.3160.0000.0000.0000.000
79A91GLY00.0190.02926.799-0.015-0.0150.0000.0000.0000.000
80A92HIS0-0.0030.00623.722-0.510-0.5100.0000.0000.0000.000
81A93LEU00.018-0.00127.7140.1250.1250.0000.0000.0000.000
82A94GLU-1-0.879-0.94428.40210.86710.8670.0000.0000.0000.000
83A95ILE00.0010.00922.2470.1640.1640.0000.0000.0000.000
84A96VAL0-0.013-0.00325.8460.1900.1900.0000.0000.0000.000
85A97GLU-1-0.927-0.97027.9689.6989.6980.0000.0000.0000.000
86A98VAL0-0.035-0.01824.391-0.099-0.0990.0000.0000.0000.000
87A99LEU00.005-0.00721.4950.1440.1440.0000.0000.0000.000
88A100LEU00.0040.00425.492-0.061-0.0610.0000.0000.0000.000
89A101LYS10.8890.96028.804-10.397-10.3970.0000.0000.0000.000
90A102ASN0-0.098-0.06624.592-0.215-0.2150.0000.0000.0000.000
91A103GLY0-0.027-0.01325.8420.3390.3390.0000.0000.0000.000
92A104ALA00.0000.01225.3880.0510.0510.0000.0000.0000.000
93A105ASP-1-0.854-0.94226.55510.14110.1410.0000.0000.0000.000
94A106VAL0-0.050-0.02628.4970.2110.2110.0000.0000.0000.000
95A107ASN0-0.063-0.03830.936-0.282-0.2820.0000.0000.0000.000
96A108ALA00.0480.04426.446-0.068-0.0680.0000.0000.0000.000
97A109MET0-0.075-0.05428.551-0.243-0.2430.0000.0000.0000.000
98A110ASP-1-0.801-0.88725.90811.92311.9230.0000.0000.0000.000
99A111SER0-0.023-0.02525.988-0.270-0.2700.0000.0000.0000.000
100A112ASP-1-0.902-0.93827.71210.30710.3070.0000.0000.0000.000
101A113GLY00.001-0.00730.494-0.436-0.4360.0000.0000.0000.000
102A114MET0-0.056-0.01530.320-0.261-0.2610.0000.0000.0000.000
103A115THR00.0480.01729.7910.3750.3750.0000.0000.0000.000
104A116PRO00.038-0.00327.847-0.062-0.0620.0000.0000.0000.000
105A117LEU00.0260.01730.116-0.082-0.0820.0000.0000.0000.000
106A118HIS00.0170.02932.6960.0450.0450.0000.0000.0000.000
107A119LEU0-0.022-0.01027.319-0.117-0.1170.0000.0000.0000.000
108A120ALA00.0080.00531.377-0.008-0.0080.0000.0000.0000.000
109A121ALA0-0.002-0.00832.881-0.191-0.1910.0000.0000.0000.000
110A122LYS10.8740.94731.020-10.335-10.3350.0000.0000.0000.000
111A123TRP0-0.061-0.03229.487-0.286-0.2860.0000.0000.0000.000
112A124GLY0-0.024-0.00434.654-0.090-0.0900.0000.0000.0000.000
113A125TYR0-0.033-0.00430.154-0.189-0.1890.0000.0000.0000.000
114A126LEU00.0440.02735.5240.0370.0370.0000.0000.0000.000
115A127GLU-1-0.871-0.94935.5668.7838.7830.0000.0000.0000.000
116A128ILE00.0060.00730.0620.0310.0310.0000.0000.0000.000
117A129VAL00.0150.00733.9610.0470.0470.0000.0000.0000.000
118A130GLU-1-0.882-0.92636.4547.9237.9230.0000.0000.0000.000
119A131VAL0-0.023-0.01532.532-0.118-0.1180.0000.0000.0000.000
120A132LEU00.0160.01330.7030.0290.0290.0000.0000.0000.000
121A133LEU0-0.009-0.01234.646-0.080-0.0800.0000.0000.0000.000
122A134LYS10.8010.90337.284-8.571-8.5710.0000.0000.0000.000
123A135HIS0-0.096-0.05133.627-0.043-0.0430.0000.0000.0000.000
124A136GLY0-0.0110.00335.5360.1330.1330.0000.0000.0000.000
125A137ALA0-0.007-0.00135.0690.0600.0600.0000.0000.0000.000
126A138VAL0-0.038-0.01736.171-0.327-0.3270.0000.0000.0000.000
127A139ASN0-0.059-0.03237.4240.3080.3080.0000.0000.0000.000
128A140ALA00.0140.00736.181-0.130-0.1300.0000.0000.0000.000
129A141GLN0-0.089-0.05838.296-0.044-0.0440.0000.0000.0000.000
130A142ASP-1-0.765-0.87234.7349.0269.0260.0000.0000.0000.000
131A143LYS10.7930.88431.912-10.400-10.4000.0000.0000.0000.000
132A144PHE0-0.113-0.06134.474-0.194-0.1940.0000.0000.0000.000
133A145GLY0-0.0090.00539.033-0.251-0.2510.0000.0000.0000.000
134A146LYS10.7970.88339.203-8.124-8.1240.0000.0000.0000.000
135A147THR00.011-0.02238.7850.2320.2320.0000.0000.0000.000
136A148ALA00.0590.01737.5850.0200.0200.0000.0000.0000.000
137A149PHE00.0430.02839.108-0.047-0.0470.0000.0000.0000.000
138A150ASP-1-0.809-0.88641.9377.4047.4040.0000.0000.0000.000
139A151ILE00.0080.01536.060-0.038-0.0380.0000.0000.0000.000
140A152SER0-0.037-0.04040.2960.0270.0270.0000.0000.0000.000
141A153ILE0-0.056-0.01642.213-0.135-0.1350.0000.0000.0000.000
142A154ASP-1-0.882-0.91141.5677.7137.7130.0000.0000.0000.000
143A155ASN0-0.101-0.05338.6710.0320.0320.0000.0000.0000.000
144A156GLY00.0190.01242.645-0.133-0.1330.0000.0000.0000.000
145A157ASN0-0.039-0.01840.297-0.179-0.1790.0000.0000.0000.000
146A158GLU-1-0.830-0.93544.1096.4746.4740.0000.0000.0000.000
147A159ASP-1-0.903-0.94743.9227.1537.1530.0000.0000.0000.000
148A160LEU0-0.020-0.00639.0920.0100.0100.0000.0000.0000.000
149A161ALA00.0500.02242.8030.0220.0220.0000.0000.0000.000
150A162GLN0-0.038-0.02145.404-0.002-0.0020.0000.0000.0000.000
151A163ILE00.0080.00042.001-0.090-0.0900.0000.0000.0000.000
152A164LEU00.012-0.00339.684-0.042-0.0420.0000.0000.0000.000
153A165ALA00.0130.01743.892-0.058-0.0580.0000.0000.0000.000
154A166PHE0-0.034-0.01946.303-0.168-0.1680.0000.0000.0000.000
155A167TYR00.0230.00342.710-0.078-0.0780.0000.0000.0000.000
156A168GLU-1-0.781-0.87444.9947.0777.0770.0000.0000.0000.000
157A169ILE0-0.023-0.02347.000-0.124-0.1240.0000.0000.0000.000
158A170LEU0-0.080-0.03146.797-0.134-0.1340.0000.0000.0000.000
159A171HIS0-0.081-0.04744.809-0.006-0.0060.0000.0000.0000.000
160A172LEU0-0.0430.00148.4930.0070.0070.0000.0000.0000.000
161A173PRO0-0.042-0.02650.827-0.080-0.0800.0000.0000.0000.000
162A174ASN0-0.043-0.02753.209-0.082-0.0820.0000.0000.0000.000
163A175LEU0-0.0050.02254.724-0.138-0.1380.0000.0000.0000.000
164A176ASN0-0.002-0.00257.1250.0530.0530.0000.0000.0000.000
165A177GLU-1-0.821-0.90957.0245.8115.8110.0000.0000.0000.000
166A178GLU-1-0.979-0.98858.9265.1965.1960.0000.0000.0000.000
167A179GLN00.0740.02159.4320.0890.0890.0000.0000.0000.000
168A180ARG10.8890.94552.495-5.938-5.9380.0000.0000.0000.000
169A181ASN0-0.025-0.03355.7350.1690.1690.0000.0000.0000.000
170A182ALA00.0040.02157.4770.0160.0160.0000.0000.0000.000
171A183PHE00.0250.01354.9360.0050.0050.0000.0000.0000.000
172A184ILE00.0130.01052.0960.0750.0750.0000.0000.0000.000
173A185GLN0-0.022-0.01054.4340.0910.0910.0000.0000.0000.000
174A186SER0-0.041-0.04357.157-0.056-0.0560.0000.0000.0000.000
175A187LEU0-0.023-0.00450.3720.0360.0360.0000.0000.0000.000
176A188LYS10.8630.93651.469-6.188-6.1880.0000.0000.0000.000
177A189ASP-1-1.002-0.97754.6835.4335.4330.0000.0000.0000.000
178A190ASP-1-0.811-0.90055.8325.8555.8550.0000.0000.0000.000
179A191PRO00.0080.00450.7110.0180.0180.0000.0000.0000.000
180A192SER00.0140.00651.5330.0910.0910.0000.0000.0000.000
181A193GLN0-0.060-0.02053.0010.0050.0050.0000.0000.0000.000
182A194SER00.000-0.01149.624-0.005-0.0050.0000.0000.0000.000
183A195ALA00.0100.00550.0330.0290.0290.0000.0000.0000.000
184A196ASN0-0.063-0.03651.2130.0070.0070.0000.0000.0000.000
185A197LEU0-0.0020.00454.085-0.065-0.0650.0000.0000.0000.000
186A198LEU00.0300.03847.868-0.081-0.0810.0000.0000.0000.000
187A199ALA00.0060.01052.373-0.024-0.0240.0000.0000.0000.000
188A200GLU-1-0.857-0.90954.0485.3425.3420.0000.0000.0000.000
189A201ALA00.011-0.00853.708-0.066-0.0660.0000.0000.0000.000
190A202LYS10.8770.91447.722-6.847-6.8470.0000.0000.0000.000
191A203LYS10.8030.88954.176-5.473-5.4730.0000.0000.0000.000
192A204LEU0-0.013-0.00957.538-0.073-0.0730.0000.0000.0000.000
193A205ASN0-0.018-0.03253.493-0.067-0.0670.0000.0000.0000.000
194A206ASP-1-0.872-0.93454.3536.0526.0520.0000.0000.0000.000
195A207ALA0-0.088-0.03457.340-0.080-0.0800.0000.0000.0000.000
196A208GLN0-0.090-0.04259.844-0.189-0.1890.0000.0000.0000.000
197A209ALA0-0.0180.00857.195-0.035-0.0350.0000.0000.0000.000