Manual

About

FMODB

FMODB: The database of quantum mechanical data based on the FMO method

Last updated: 2024-04-05

All entries: 36946

Number of unique PDB entries: 7781

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FMODB ID: ZVY1N

Calculation Name: 1SUL-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1SUL

Chain ID: A

ChEMBL ID:

UniProt ID: P38424

Base Structure: X-ray

Registration Date: 2023-09-21

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 186
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2107545.135747
FMO2-HF: Nuclear repulsion 2034388.205884
FMO2-HF: Total energy -73156.929864
FMO2-MP2: Total energy -73373.289053


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:1:MET)


Summations of interaction energy for fragment #1(A:1:MET)
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.
-19.823-15.75627.395-10.112-21.349-0.067
Interaction energy analysis for fragmet #1(A:1:MET)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.061 / q_NPA : -0.011
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].
3A3VAL00.0120.0222.149-0.2941.6881.629-1.078-2.5330.002
4A4THR0-0.055-0.0264.3960.2150.4060.000-0.028-0.1620.000
5A5LYS10.7550.8556.0540.5830.5830.0000.0000.0000.000
6A6SER0-0.022-0.0276.188-0.695-0.6950.0000.0000.0000.000
7A7GLU-1-0.842-0.8868.587-0.477-0.4770.0000.0000.0000.000
8A8ILE0-0.016-0.01311.670-0.123-0.1230.0000.0000.0000.000
9A9VAL0-0.034-0.00712.8780.0600.0600.0000.0000.0000.000
10A10ILE00.009-0.00215.6280.0740.0740.0000.0000.0000.000
11A11SER0-0.035-0.01717.920-0.071-0.0710.0000.0000.0000.000
12A12ALA0-0.025-0.01020.4830.0460.0460.0000.0000.0000.000
13A13VAL00.005-0.02622.278-0.021-0.0210.0000.0000.0000.000
14A14LYS10.8090.89724.5740.2240.2240.0000.0000.0000.000
15A15PRO00.0890.02623.056-0.012-0.0120.0000.0000.0000.000
16A16GLU-1-0.832-0.89323.308-0.211-0.2110.0000.0000.0000.000
17A17GLN0-0.005-0.00422.933-0.004-0.0040.0000.0000.0000.000
18A18TYR00.0200.01418.679-0.049-0.0490.0000.0000.0000.000
19A19PRO0-0.0060.00315.0230.0390.0390.0000.0000.0000.000
20A20GLU-1-0.880-0.92817.380-0.148-0.1480.0000.0000.0000.000
21A21GLY0-0.029-0.02615.530-0.046-0.0460.0000.0000.0000.000
22A22GLY00.0050.00615.4080.0460.0460.0000.0000.0000.000
23A23LEU0-0.044-0.0109.4560.0270.0270.0000.0000.0000.000
24A24PRO00.0110.0158.439-0.077-0.0770.0000.0000.0000.000
25A25GLU-1-0.717-0.8459.437-0.858-0.8580.0000.0000.0000.000
26A26ILE0-0.038-0.0067.5110.0040.0040.0000.0000.0000.000
27A27ALA00.0650.04210.401-0.140-0.1400.0000.0000.0000.000
28A28LEU0-0.074-0.0359.997-0.068-0.0680.0000.0000.0000.000
29A29ALA00.0700.03213.9970.0950.0950.0000.0000.0000.000
30A30GLY00.0510.00417.459-0.056-0.0560.0000.0000.0000.000
31A31ARG10.7980.89819.9550.4320.4320.0000.0000.0000.000
32A32SER0-0.025-0.02321.9750.0310.0310.0000.0000.0000.000
33A33ASN00.1150.05619.949-0.082-0.0820.0000.0000.0000.000
34A34VAL00.0310.02918.939-0.063-0.0630.0000.0000.0000.000
35A35GLY0-0.029-0.02118.753-0.044-0.0440.0000.0000.0000.000
36A36LYS10.8200.91615.3050.6470.6470.0000.0000.0000.000
37A37SER00.0890.03014.287-0.147-0.1470.0000.0000.0000.000
38A38SER0-0.057-0.01214.101-0.115-0.1150.0000.0000.0000.000
39A39PHE00.0450.0229.686-0.099-0.0990.0000.0000.0000.000
40A40ILE00.0670.0389.325-0.272-0.2720.0000.0000.0000.000
41A41ASN0-0.005-0.0149.041-0.338-0.3380.0000.0000.0000.000
42A42SER0-0.024-0.02410.256-0.105-0.1050.0000.0000.0000.000
43A43LEU00.0300.0275.932-0.046-0.0460.0000.0000.0000.000
44A44ILE00.0090.0135.265-1.162-1.1620.0000.0000.0000.000
45A45ASN0-0.0280.0126.5820.1830.1830.0000.0000.0000.000
46A46ARG10.9310.9679.3711.2991.2990.0000.0000.0000.000
47A47LYS10.8930.92812.1810.6540.6540.0000.0000.0000.000
48A48ASN0-0.011-0.00815.1480.0180.0180.0000.0000.0000.000
49A49LEU0-0.0090.02211.2120.0510.0510.0000.0000.0000.000
50A50ALA00.0170.00812.6160.1020.1020.0000.0000.0000.000
51A60GLN0-0.109-0.07925.140-0.029-0.0290.0000.0000.0000.000
52A61THR00.009-0.01521.5010.0330.0330.0000.0000.0000.000
53A62LEU00.0050.00718.330-0.037-0.0370.0000.0000.0000.000
54A63ASN0-0.0180.01516.7740.0850.0850.0000.0000.0000.000
55A64PHE00.0190.01613.850-0.113-0.1130.0000.0000.0000.000
56A65TYR00.013-0.00310.3860.0880.0880.0000.0000.0000.000
57A66ILE00.0540.0638.604-0.261-0.2610.0000.0000.0000.000
58A67ILE0-0.031-0.0422.937-0.664-0.2800.108-0.089-0.4050.000
59A68ASN0-0.044-0.0552.352-1.921-0.9281.378-0.663-1.707-0.007
60A69ASP-1-0.822-0.8844.8070.2320.281-0.001-0.007-0.0420.000
61A70GLU-1-0.774-0.8862.504-1.3382.3511.869-2.645-2.913-0.035
62A71LEU0-0.027-0.0113.170-0.605-0.2080.068-0.085-0.380-0.001
63A72HIS00.0460.0277.093-0.324-0.3240.0000.0000.0000.000
64A73PHE0-0.030-0.0235.837-0.229-0.2290.0000.0000.0000.000
65A74VAL00.0100.0079.5060.1580.1580.0000.0000.0000.000
66A75ASP-1-0.843-0.91413.304-0.797-0.7970.0000.0000.0000.000
67A76VAL00.0700.04015.3180.0880.0880.0000.0000.0000.000
68A77PRO0-0.020-0.01218.540-0.027-0.0270.0000.0000.0000.000
69A78GLY0-0.018-0.01521.6670.0040.0040.0000.0000.0000.000
70A79TYR00.003-0.01320.8390.0180.0180.0000.0000.0000.000
71A80GLY0-0.011-0.00424.9960.0250.0250.0000.0000.0000.000
72A81PHE00.0560.00727.3070.0170.0170.0000.0000.0000.000
73A82ALA0-0.032-0.00630.5550.0180.0180.0000.0000.0000.000
74A83LYS10.9120.95232.5900.2460.2460.0000.0000.0000.000
75A84VAL00.0500.04829.9700.0020.0020.0000.0000.0000.000
76A85SER00.0350.01633.1500.0070.0070.0000.0000.0000.000
77A86LYS10.9070.93234.2730.1600.1600.0000.0000.0000.000
78A87SER00.0510.02134.9840.0000.0000.0000.0000.0000.000
79A88GLU-1-0.833-0.91330.780-0.279-0.2790.0000.0000.0000.000
80A89ARG10.8500.93130.2220.2160.2160.0000.0000.0000.000
81A90GLU-1-0.783-0.86830.232-0.192-0.1920.0000.0000.0000.000
82A91ALA0-0.050-0.01230.162-0.002-0.0020.0000.0000.0000.000
83A92TRP0-0.011-0.01522.8730.0050.0050.0000.0000.0000.000
84A93GLY00.0290.01725.883-0.016-0.0160.0000.0000.0000.000
85A94ARG10.9010.92827.0110.2010.2010.0000.0000.0000.000
86A95MET0-0.0150.03422.8340.0010.0010.0000.0000.0000.000
87A96ILE00.006-0.00219.524-0.016-0.0160.0000.0000.0000.000
88A97GLU-1-0.836-0.90522.638-0.260-0.2600.0000.0000.0000.000
89A98THR0-0.035-0.00524.8290.0170.0170.0000.0000.0000.000
90A99TYR0-0.074-0.04214.830-0.009-0.0090.0000.0000.0000.000
91A100ILE0-0.031-0.02418.927-0.004-0.0040.0000.0000.0000.000
92A101THR0-0.042-0.03821.2180.0190.0190.0000.0000.0000.000
93A102THR0-0.078-0.05622.6080.0220.0220.0000.0000.0000.000
94A103ARG10.7470.85515.3120.4460.4460.0000.0000.0000.000
95A104GLU-1-0.855-0.92418.075-0.167-0.1670.0000.0000.0000.000
96A105GLU-1-0.818-0.90913.834-0.292-0.2920.0000.0000.0000.000
97A106LEU0-0.047-0.01913.382-0.081-0.0810.0000.0000.0000.000
98A107LYS10.8170.90011.4410.2920.2920.0000.0000.0000.000
99A108ALA0-0.017-0.01111.6990.0370.0370.0000.0000.0000.000
100A109VAL00.0000.01012.952-0.086-0.0860.0000.0000.0000.000
101A110VAL0-0.025-0.00610.254-0.005-0.0050.0000.0000.0000.000
102A111GLN00.003-0.01513.6140.0490.0490.0000.0000.0000.000
103A112ILE0-0.045-0.01813.8010.0010.0010.0000.0000.0000.000
104A113VAL00.0350.01217.1750.0780.0780.0000.0000.0000.000
105A114ASP-1-0.803-0.85919.347-0.535-0.5350.0000.0000.0000.000
106A115LEU00.0250.01419.3520.0410.0410.0000.0000.0000.000
107A116ARG10.8070.86122.2170.4460.4460.0000.0000.0000.000
108A117HIS0-0.0220.00225.4240.0270.0270.0000.0000.0000.000
109A118ALA00.0580.02926.173-0.020-0.0200.0000.0000.0000.000
110A119PRO0-0.053-0.02123.939-0.003-0.0030.0000.0000.0000.000
111A120SER0-0.034-0.03426.3240.0290.0290.0000.0000.0000.000
112A121ASN00.0720.01928.066-0.002-0.0020.0000.0000.0000.000
113A122ASP-1-0.842-0.92027.618-0.304-0.3040.0000.0000.0000.000
114A123ASP-1-0.742-0.82123.797-0.458-0.4580.0000.0000.0000.000
115A124VAL00.0350.02024.490-0.022-0.0220.0000.0000.0000.000
116A125GLN00.0320.02626.5700.0120.0120.0000.0000.0000.000
117A126MET0-0.043-0.01320.3410.0110.0110.0000.0000.0000.000
118A127TYR0-0.033-0.04119.999-0.003-0.0030.0000.0000.0000.000
119A128GLU-1-0.906-0.96523.375-0.242-0.2420.0000.0000.0000.000
120A129PHE0-0.036-0.01322.3600.0100.0100.0000.0000.0000.000
121A130LEU0-0.022-0.01418.668-0.001-0.0010.0000.0000.0000.000
122A131LYS10.8160.88820.1450.3660.3660.0000.0000.0000.000
123A132TYR0-0.039-0.00424.0540.0280.0280.0000.0000.0000.000
124A133TYR0-0.084-0.06623.1730.0220.0220.0000.0000.0000.000
125A134GLY0-0.0020.00623.1740.0020.0020.0000.0000.0000.000
126A135ILE0-0.031-0.00717.324-0.004-0.0040.0000.0000.0000.000
127A136PRO00.0330.01815.345-0.009-0.0090.0000.0000.0000.000
128A137VAL0-0.021-0.01715.860-0.082-0.0820.0000.0000.0000.000
129A138ILE0-0.021-0.0099.706-0.010-0.0100.0000.0000.0000.000
130A139VAL00.0330.01413.785-0.072-0.0720.0000.0000.0000.000
131A140ILE0-0.012-0.01011.203-0.020-0.0200.0000.0000.0000.000
132A141ALA00.0190.00815.1350.0620.0620.0000.0000.0000.000
133A142THR0-0.019-0.02915.4860.0180.0180.0000.0000.0000.000
134A143LYS10.8480.91117.7370.6810.6810.0000.0000.0000.000
135A144ALA00.0800.03717.4500.0650.0650.0000.0000.0000.000
136A145ASP-1-0.826-0.87518.613-0.520-0.5200.0000.0000.0000.000
137A146LYS10.8170.88820.3330.4560.4560.0000.0000.0000.000
138A147ILE00.0040.02222.4570.0320.0320.0000.0000.0000.000
139A148PRO00.0320.01423.510-0.008-0.0080.0000.0000.0000.000
140A149LYS11.0531.01919.5770.2870.2870.0000.0000.0000.000
141A150GLY00.0380.02723.680-0.001-0.0010.0000.0000.0000.000
142A151LYS10.8680.91725.8060.2020.2020.0000.0000.0000.000
143A152TRP00.0220.01817.769-0.016-0.0160.0000.0000.0000.000
144A153ASP-1-0.775-0.86423.174-0.261-0.2610.0000.0000.0000.000
145A154LYS10.9670.99024.2540.1920.1920.0000.0000.0000.000
146A155HIS0-0.015-0.01923.8830.0110.0110.0000.0000.0000.000
147A156ALA00.0280.00921.256-0.017-0.0170.0000.0000.0000.000
148A157LYS10.8390.91122.7110.2230.2230.0000.0000.0000.000
149A158VAL00.0170.01925.9440.0030.0030.0000.0000.0000.000
150A159VAL00.0110.01120.8230.0010.0010.0000.0000.0000.000
151A160ARG10.8590.90519.3340.3600.3600.0000.0000.0000.000
152A161GLN0-0.015-0.01424.0530.0100.0100.0000.0000.0000.000
153A162THR0-0.065-0.04626.9500.0150.0150.0000.0000.0000.000
154A163LEU0-0.027-0.01821.7400.0010.0010.0000.0000.0000.000
155A164ASN0-0.0180.00325.5610.0090.0090.0000.0000.0000.000
156A165ILE0-0.059-0.02419.8830.0020.0020.0000.0000.0000.000
157A166ASP-1-0.787-0.90121.492-0.235-0.2350.0000.0000.0000.000
158A167PRO0-0.033-0.02821.494-0.029-0.0290.0000.0000.0000.000
159A168GLU-1-0.826-0.87918.504-0.199-0.1990.0000.0000.0000.000
160A169ASP-1-0.729-0.79817.009-0.456-0.4560.0000.0000.0000.000
161A170GLU-1-0.811-0.89312.234-0.669-0.6690.0000.0000.0000.000
162A171LEU0-0.046-0.02015.587-0.032-0.0320.0000.0000.0000.000
163A172ILE0-0.039-0.00610.5410.0320.0320.0000.0000.0000.000
164A173LEU0-0.009-0.00914.378-0.024-0.0240.0000.0000.0000.000
165A174PHE00.0420.0199.5650.0350.0350.0000.0000.0000.000
166A175SER0-0.049-0.04513.4980.1460.1460.0000.0000.0000.000
167A176SER00.0410.00713.581-0.099-0.0990.0000.0000.0000.000
168A177GLU-1-0.865-0.92514.599-0.675-0.6750.0000.0000.0000.000
169A178THR0-0.019-0.02815.5870.0170.0170.0000.0000.0000.000
170A179LYS10.8560.93210.1020.9170.9170.0000.0000.0000.000
171A180LYS10.8630.93210.1850.5690.5690.0000.0000.0000.000
172A181GLY00.019-0.00710.7150.0490.0490.0000.0000.0000.000
173A182LYS10.8030.8935.0313.3873.3870.0000.0000.0000.000
174A183ASP-1-0.857-0.9294.304-3.611-3.566-0.001-0.017-0.0260.000
175A184GLU-1-0.828-0.9125.367-1.199-1.111-0.001-0.001-0.0850.000
176A185ALA00.0100.0027.8560.1610.1610.0000.0000.0000.000
177A186TRP00.017-0.0182.456-6.637-4.1568.451-2.501-8.431-0.029
178A187GLY00.0230.0154.0980.3800.649-0.001-0.031-0.2370.000
179A188ALA0-0.026-0.0245.8830.4490.4490.0000.0000.0000.000
180A189ILE00.0110.0014.8390.1830.1830.0000.0000.0000.000
181A190LYS10.8080.8812.285-8.637-15.13813.896-2.967-4.4280.003
182A191LYS10.7800.8846.4410.8970.8970.0000.0000.0000.000
183A192MET0-0.0190.0009.7610.1520.1520.0000.0000.0000.000
184A193ILE0-0.006-0.0065.6050.0460.0460.0000.0000.0000.000
185A194ASN0-0.085-0.0449.5300.1790.1790.0000.0000.0000.000
186A195ARG10.8290.91611.7290.2480.2480.0000.0000.0000.000