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: 72Z9K

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 OptAll
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 -1985746.366969
FMO2-HF: Nuclear repulsion 1911531.257081
FMO2-HF: Total energy -74215.109888
FMO2-MP2: Total energy -74434.724497


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.
38.40836.05729.788-13.402-14.0350.148
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 : -0.847 / q_NPA : -0.931
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].
3A15GLY00.0400.0342.203-16.085-13.1302.878-2.761-3.0710.025
4A16ARG10.8330.8751.764-114.000-120.40426.887-10.130-10.3540.118
5A17LYS10.8560.9413.398-51.989-50.8910.023-0.511-0.6100.005
6A18LEU00.0290.0205.428-7.838-7.8380.0000.0000.0000.000
7A19LEU00.0210.0106.443-4.260-4.2600.0000.0000.0000.000
8A20GLU-1-0.891-0.9346.52543.72343.7230.0000.0000.0000.000
9A21ALA00.0040.0039.383-3.577-3.5770.0000.0000.0000.000
10A22ALA00.004-0.00510.935-2.528-2.5280.0000.0000.0000.000
11A23ARG10.9480.9919.801-29.927-29.9270.0000.0000.0000.000
12A24ALA0-0.019-0.00913.593-1.722-1.7220.0000.0000.0000.000
13A25GLY00.0590.04115.300-1.356-1.3560.0000.0000.0000.000
14A26GLN0-0.105-0.07013.219-0.775-0.7750.0000.0000.0000.000
15A27ASP-1-0.738-0.86814.67317.92517.9250.0000.0000.0000.000
16A28ASP-1-0.831-0.90716.30116.37316.3730.0000.0000.0000.000
17A29GLU-1-0.886-0.93311.76826.08426.0840.0000.0000.0000.000
18A30VAL00.0180.02011.8422.1292.1290.0000.0000.0000.000
19A31ARG10.7590.84012.900-15.838-15.8380.0000.0000.0000.000
20A32ILE0-0.042-0.02410.618-0.230-0.2300.0000.0000.0000.000
21A33LEU0-0.006-0.0076.8270.8400.8400.0000.0000.0000.000
22A34MET0-0.0040.0169.9760.8870.8870.0000.0000.0000.000
23A35ALA0-0.050-0.01712.689-0.539-0.5390.0000.0000.0000.000
24A36ASN0-0.123-0.0677.8490.2860.2860.0000.0000.0000.000
25A37GLY0-0.0030.0028.5491.1681.1680.0000.0000.0000.000
26A38ALA0-0.055-0.0267.2371.6781.6780.0000.0000.0000.000
27A39ASP-1-0.867-0.9367.98124.68124.6810.0000.0000.0000.000
28A40VAL00.010-0.0048.9822.7862.7860.0000.0000.0000.000
29A41ASN0-0.027-0.01311.504-1.085-1.0850.0000.0000.0000.000
30A42ALA0-0.010-0.0016.238-0.018-0.0180.0000.0000.0000.000
31A43ALA00.0180.0158.0722.4342.4340.0000.0000.0000.000
32A44ASP-1-0.839-0.8828.51631.94131.9410.0000.0000.0000.000
33A45ASN0-0.057-0.0559.502-0.671-0.6710.0000.0000.0000.000
34A46THR0-0.070-0.04212.136-2.400-2.4000.0000.0000.0000.000
35A47GLY00.0290.01213.411-1.742-1.7420.0000.0000.0000.000
36A48THR0-0.037-0.02112.616-1.191-1.1910.0000.0000.0000.000
37A49THR00.041-0.01211.4222.9742.9740.0000.0000.0000.000
38A50PRO0-0.007-0.0279.188-0.801-0.8010.0000.0000.0000.000
39A51LEU00.0400.02211.869-1.062-1.0620.0000.0000.0000.000
40A52HIS00.0360.04815.0940.1530.1530.0000.0000.0000.000
41A53LEU0-0.031-0.01011.218-0.819-0.8190.0000.0000.0000.000
42A54ALA00.0240.02815.275-0.915-0.9150.0000.0000.0000.000
43A55ALA0-0.004-0.00817.047-0.940-0.9400.0000.0000.0000.000
44A56TYR0-0.063-0.02417.379-0.476-0.4760.0000.0000.0000.000
45A57SER0-0.051-0.04817.320-0.549-0.5490.0000.0000.0000.000
46A58GLY00.0120.01220.011-0.582-0.5820.0000.0000.0000.000
47A59HIS0-0.040-0.01816.946-1.064-1.0640.0000.0000.0000.000
48A60LEU00.0570.02220.0260.6860.6860.0000.0000.0000.000
49A61GLU-1-0.849-0.92820.93914.33314.3330.0000.0000.0000.000
50A62ILE0-0.029-0.01215.0630.5490.5490.0000.0000.0000.000
51A63VAL0-0.0010.00317.5040.7670.7670.0000.0000.0000.000
52A64GLU-1-0.915-0.95319.46612.72712.7270.0000.0000.0000.000
53A65VAL0-0.089-0.04916.206-0.006-0.0060.0000.0000.0000.000
54A66LEU0-0.019-0.02012.8090.4630.4630.0000.0000.0000.000
55A67LEU00.0310.01816.5920.0870.0870.0000.0000.0000.000
56A68LYS10.8500.93319.845-15.072-15.0720.0000.0000.0000.000
57A69HIS0-0.066-0.05015.948-1.240-1.2400.0000.0000.0000.000
58A70GLY0-0.0110.00616.9040.5570.5570.0000.0000.0000.000
59A71ALA0-0.030-0.01615.8260.6520.6520.0000.0000.0000.000
60A72ASP-1-0.903-0.95816.64714.93714.9370.0000.0000.0000.000
61A73VAL0-0.030-0.02018.3890.6350.6350.0000.0000.0000.000
62A74ASP-1-0.830-0.91321.06012.66312.6630.0000.0000.0000.000
63A75ALA0-0.0240.00416.867-0.079-0.0790.0000.0000.0000.000
64A76SER0-0.023-0.01618.993-0.161-0.1610.0000.0000.0000.000
65A77ASP-1-0.839-0.92217.35417.21117.2110.0000.0000.0000.000
66A78VAL0-0.051-0.03918.061-0.875-0.8750.0000.0000.0000.000
67A79PHE0-0.091-0.04019.633-0.795-0.7950.0000.0000.0000.000
68A80GLY00.0180.00321.855-0.813-0.8130.0000.0000.0000.000
69A81TYR0-0.071-0.04421.268-0.395-0.3950.0000.0000.0000.000
70A82THR00.0680.02420.4970.8660.8660.0000.0000.0000.000
71A83PRO00.004-0.02118.178-0.155-0.1550.0000.0000.0000.000
72A84LEU00.0330.02620.669-0.270-0.2700.0000.0000.0000.000
73A85HIS00.0140.03323.9040.0650.0650.0000.0000.0000.000
74A86LEU0-0.020-0.00718.953-0.296-0.2960.0000.0000.0000.000
75A87ALA00.0200.00823.088-0.278-0.2780.0000.0000.0000.000
76A88ALA0-0.008-0.00624.693-0.408-0.4080.0000.0000.0000.000
77A89TYR0-0.017-0.01125.492-0.591-0.5910.0000.0000.0000.000
78A90TRP0-0.056-0.04523.033-0.346-0.3460.0000.0000.0000.000
79A91GLY00.0510.04326.437-0.019-0.0190.0000.0000.0000.000
80A92HIS0-0.0120.00223.400-0.635-0.6350.0000.0000.0000.000
81A93LEU00.022-0.00227.1660.1900.1900.0000.0000.0000.000
82A94GLU-1-0.890-0.94928.03110.95310.9530.0000.0000.0000.000
83A95ILE0-0.0130.00421.8700.1730.1730.0000.0000.0000.000
84A96VAL0-0.019-0.00425.5060.1820.1820.0000.0000.0000.000
85A97GLU-1-0.927-0.96927.6689.6879.6870.0000.0000.0000.000
86A98VAL0-0.028-0.01524.183-0.105-0.1050.0000.0000.0000.000
87A99LEU00.001-0.00821.2910.1200.1200.0000.0000.0000.000
88A100LEU00.0090.01225.299-0.046-0.0460.0000.0000.0000.000
89A101LYS10.8970.96128.834-10.595-10.5950.0000.0000.0000.000
90A102ASN0-0.083-0.06124.307-0.290-0.2900.0000.0000.0000.000
91A103GLY0-0.053-0.02225.9880.2740.2740.0000.0000.0000.000
92A104ALA0-0.0020.00725.250-0.038-0.0380.0000.0000.0000.000
93A105ASP-1-0.837-0.93126.58310.03410.0340.0000.0000.0000.000
94A106VAL0-0.031-0.02028.5860.2370.2370.0000.0000.0000.000
95A107ASN0-0.078-0.04330.930-0.386-0.3860.0000.0000.0000.000
96A108ALA00.0420.04026.474-0.077-0.0770.0000.0000.0000.000
97A109MET0-0.097-0.06428.192-0.266-0.2660.0000.0000.0000.000
98A110ASP-1-0.756-0.85026.15811.85611.8560.0000.0000.0000.000
99A111SER0-0.046-0.04726.393-0.262-0.2620.0000.0000.0000.000
100A112ASP-1-0.883-0.93428.09410.35210.3520.0000.0000.0000.000
101A113GLY00.0140.00930.688-0.442-0.4420.0000.0000.0000.000
102A114MET0-0.069-0.02530.378-0.243-0.2430.0000.0000.0000.000
103A115THR00.0700.01629.8510.3850.3850.0000.0000.0000.000
104A116PRO00.032-0.00627.733-0.049-0.0490.0000.0000.0000.000
105A117LEU00.0240.01830.006-0.075-0.0750.0000.0000.0000.000
106A118HIS00.0010.02432.8460.0280.0280.0000.0000.0000.000
107A119LEU0-0.031-0.01227.321-0.118-0.1180.0000.0000.0000.000
108A120ALA00.0190.01331.364-0.016-0.0160.0000.0000.0000.000
109A121ALA0-0.011-0.00832.846-0.178-0.1780.0000.0000.0000.000
110A122LYS10.8720.94730.948-10.406-10.4060.0000.0000.0000.000
111A123TRP0-0.064-0.03529.218-0.233-0.2330.0000.0000.0000.000
112A124GLY0-0.013-0.00234.343-0.054-0.0540.0000.0000.0000.000
113A125TYR0-0.035-0.00729.640-0.226-0.2260.0000.0000.0000.000
114A126LEU00.0390.02135.1720.0760.0760.0000.0000.0000.000
115A127GLU-1-0.878-0.94935.1848.8258.8250.0000.0000.0000.000
116A128ILE00.0060.00829.7910.0430.0430.0000.0000.0000.000
117A129VAL00.0040.00033.6610.0390.0390.0000.0000.0000.000
118A130GLU-1-0.895-0.94036.2198.0128.0120.0000.0000.0000.000
119A131VAL0-0.020-0.01432.085-0.108-0.1080.0000.0000.0000.000
120A132LEU00.0130.01230.4200.0370.0370.0000.0000.0000.000
121A133LEU0-0.010-0.01034.370-0.088-0.0880.0000.0000.0000.000
122A134LYS10.8110.91136.906-8.700-8.7000.0000.0000.0000.000
123A135HIS0-0.080-0.04433.363-0.019-0.0190.0000.0000.0000.000
124A136GLY0-0.023-0.00435.5830.1040.1040.0000.0000.0000.000
125A137ALA0-0.021-0.01435.0240.0330.0330.0000.0000.0000.000
126A138VAL0-0.031-0.01236.205-0.311-0.3110.0000.0000.0000.000
127A139ASN0-0.034-0.01837.2150.3420.3420.0000.0000.0000.000
128A140ALA00.0160.00936.436-0.153-0.1530.0000.0000.0000.000
129A141GLN0-0.101-0.07238.505-0.044-0.0440.0000.0000.0000.000
130A142ASP-1-0.754-0.87234.9458.9758.9750.0000.0000.0000.000
131A143LYS10.7760.87731.493-10.500-10.5000.0000.0000.0000.000
132A144PHE0-0.100-0.05134.074-0.166-0.1660.0000.0000.0000.000
133A145GLY0-0.026-0.00139.053-0.260-0.2600.0000.0000.0000.000
134A146LYS10.7990.90139.411-8.168-8.1680.0000.0000.0000.000
135A147THR00.020-0.01538.7770.2410.2410.0000.0000.0000.000
136A148ALA00.0590.02337.3300.0310.0310.0000.0000.0000.000
137A149PHE00.0370.02538.829-0.052-0.0520.0000.0000.0000.000
138A150ASP-1-0.812-0.88841.9567.4207.4200.0000.0000.0000.000
139A151ILE00.0030.00935.941-0.053-0.0530.0000.0000.0000.000
140A152SER0-0.043-0.03940.1070.0800.0800.0000.0000.0000.000
141A153ILE0-0.043-0.01341.996-0.172-0.1720.0000.0000.0000.000
142A154ASP-1-0.903-0.93241.0297.7907.7900.0000.0000.0000.000
143A155ASN0-0.078-0.04038.8510.0670.0670.0000.0000.0000.000
144A156GLY0-0.0030.00542.726-0.132-0.1320.0000.0000.0000.000
145A157ASN0-0.024-0.02140.171-0.132-0.1320.0000.0000.0000.000
146A158GLU-1-0.818-0.93144.1016.5176.5170.0000.0000.0000.000
147A159ASP-1-0.905-0.94243.9957.1047.1040.0000.0000.0000.000
148A160LEU0-0.0020.00539.0580.0140.0140.0000.0000.0000.000
149A161ALA00.0350.01742.6650.0230.0230.0000.0000.0000.000
150A162GLN0-0.060-0.03745.2130.0140.0140.0000.0000.0000.000
151A163ILE00.0170.00841.775-0.086-0.0860.0000.0000.0000.000
152A164LEU00.0210.00239.524-0.022-0.0220.0000.0000.0000.000
153A165ALA00.0050.01143.703-0.059-0.0590.0000.0000.0000.000
154A166PHE0-0.034-0.02246.037-0.156-0.1560.0000.0000.0000.000
155A167TYR00.0320.00542.478-0.078-0.0780.0000.0000.0000.000
156A168GLU-1-0.792-0.86944.8437.1367.1360.0000.0000.0000.000
157A169ILE0-0.014-0.02046.716-0.118-0.1180.0000.0000.0000.000
158A170LEU0-0.075-0.03546.421-0.146-0.1460.0000.0000.0000.000
159A171HIS0-0.073-0.04844.621-0.012-0.0120.0000.0000.0000.000
160A172LEU0-0.0340.00148.5920.0020.0020.0000.0000.0000.000
161A173PRO0-0.031-0.01850.540-0.106-0.1060.0000.0000.0000.000
162A174ASN0-0.055-0.03253.011-0.063-0.0630.0000.0000.0000.000
163A175LEU0-0.0190.01454.431-0.143-0.1430.0000.0000.0000.000
164A176ASN00.005-0.00556.8580.0550.0550.0000.0000.0000.000
165A177GLU-1-0.789-0.88656.4135.8805.8800.0000.0000.0000.000
166A178GLU-1-0.941-0.96958.8225.2445.2440.0000.0000.0000.000
167A179GLN00.0360.01259.3010.1110.1110.0000.0000.0000.000
168A180ARG10.8570.92152.561-5.939-5.9390.0000.0000.0000.000
169A181ASN0-0.047-0.04155.4580.1530.1530.0000.0000.0000.000
170A182ALA00.0060.01757.1140.0260.0260.0000.0000.0000.000
171A183PHE00.0240.01954.7760.0050.0050.0000.0000.0000.000
172A184ILE00.0080.01051.8090.0750.0750.0000.0000.0000.000
173A185GLN0-0.003-0.00954.0530.1150.1150.0000.0000.0000.000
174A186SER0-0.019-0.03056.800-0.032-0.0320.0000.0000.0000.000
175A187LEU0-0.022-0.00750.2220.0160.0160.0000.0000.0000.000
176A188LYS10.8580.93251.166-6.205-6.2050.0000.0000.0000.000
177A189ASP-1-1.000-0.97554.4245.4275.4270.0000.0000.0000.000
178A190ASP-1-0.796-0.87955.6465.8545.8540.0000.0000.0000.000
179A191PRO0-0.0050.00350.3470.0290.0290.0000.0000.0000.000
180A192SER00.0030.00251.2810.0900.0900.0000.0000.0000.000
181A193GLN0-0.077-0.03952.8290.0130.0130.0000.0000.0000.000
182A194SER0-0.005-0.01249.3430.0090.0090.0000.0000.0000.000
183A195ALA00.0240.01649.8200.0100.0100.0000.0000.0000.000
184A196ASN0-0.038-0.03051.0770.0020.0020.0000.0000.0000.000
185A197LEU0-0.014-0.01253.658-0.088-0.0880.0000.0000.0000.000
186A198LEU00.0030.01947.461-0.073-0.0730.0000.0000.0000.000
187A199ALA0-0.023-0.00851.995-0.011-0.0110.0000.0000.0000.000
188A200GLU-1-0.850-0.90253.8435.3715.3710.0000.0000.0000.000
189A201ALA00.0300.00953.542-0.071-0.0710.0000.0000.0000.000
190A202LYS10.8720.91547.456-6.875-6.8750.0000.0000.0000.000
191A203LYS10.8150.89053.806-5.479-5.4790.0000.0000.0000.000
192A204LEU0-0.026-0.01757.165-0.089-0.0890.0000.0000.0000.000
193A205ASN00.010-0.01653.460-0.067-0.0670.0000.0000.0000.000
194A206ASP-1-0.877-0.92954.0676.0646.0640.0000.0000.0000.000
195A207ALA0-0.086-0.04056.950-0.076-0.0760.0000.0000.0000.000
196A208GLN0-0.083-0.03459.425-0.198-0.1980.0000.0000.0000.000
197A209ALA0-0.040-0.00457.056-0.029-0.0290.0000.0000.0000.000