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: QV71Y

Calculation Name: 1X42-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1X42

Chain ID: A

ChEMBL ID:

UniProt ID: O58216

Base Structure: X-ray

Registration Date: 2023-09-20

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 229
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -3016231.304141
FMO2-HF: Nuclear repulsion 2923031.57739
FMO2-HF: Total energy -93199.72675
FMO2-MP2: Total energy -93471.420799


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.
-15.797-7.4955.604-4.532-9.372-0.034
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 : -0.012 / q_NPA : 0.001
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].
3A3ARG10.8000.8782.398-3.878-0.0743.091-2.344-4.551-0.006
4A4ALA00.0020.0043.4771.3741.5690.0120.089-0.2960.000
5A5VAL00.001-0.0017.047-0.396-0.3960.0000.0000.0000.000
6A6PHE0-0.040-0.0069.8080.3120.3120.0000.0000.0000.000
7A7PHE00.0350.01213.384-0.044-0.0440.0000.0000.0000.000
8A8ASP-1-0.758-0.87416.833-0.475-0.4750.0000.0000.0000.000
9A9PHE0-0.001-0.02320.471-0.006-0.0060.0000.0000.0000.000
10A10VAL00.0500.01223.0220.0120.0120.0000.0000.0000.000
11A11GLY00.0160.02725.223-0.023-0.0230.0000.0000.0000.000
12A12THR0-0.045-0.03419.400-0.022-0.0220.0000.0000.0000.000
13A13LEU0-0.035-0.02118.828-0.017-0.0170.0000.0000.0000.000
14A14LEU0-0.0090.00122.9870.0280.0280.0000.0000.0000.000
15A15SER0-0.018-0.00726.6990.0000.0000.0000.0000.0000.000
16A16VAL00.0680.02328.6460.0150.0150.0000.0000.0000.000
17A17GLU-1-0.791-0.86530.978-0.272-0.2720.0000.0000.0000.000
18A18GLY00.0200.00332.1860.0170.0170.0000.0000.0000.000
19A19GLU-1-0.763-0.86130.976-0.245-0.2450.0000.0000.0000.000
20A20ALA00.0250.02533.6350.0150.0150.0000.0000.0000.000
21A21LYS10.7520.86935.2150.2210.2210.0000.0000.0000.000
22A22THR0-0.020-0.02734.9280.0140.0140.0000.0000.0000.000
23A23HIS0-0.014-0.02734.1130.0220.0220.0000.0000.0000.000
24A24LEU0-0.025-0.01238.8680.0110.0110.0000.0000.0000.000
25A25LYS10.7840.86740.9580.1460.1460.0000.0000.0000.000
26A26ILE0-0.0070.02137.8680.0070.0070.0000.0000.0000.000
27A27MET0-0.015-0.00741.0030.0090.0090.0000.0000.0000.000
28A28GLU-1-0.825-0.91044.977-0.125-0.1250.0000.0000.0000.000
29A29GLU-1-0.804-0.86844.994-0.122-0.1220.0000.0000.0000.000
30A30VAL0-0.043-0.02444.9740.0040.0040.0000.0000.0000.000
31A31LEU0-0.065-0.01847.7800.0040.0040.0000.0000.0000.000
32A32GLY00.0230.01150.5500.0050.0050.0000.0000.0000.000
33A33ASP-1-0.952-0.98152.509-0.089-0.0890.0000.0000.0000.000
34A34TYR0-0.067-0.04053.9550.0040.0040.0000.0000.0000.000
35A35PRO0-0.0130.00454.854-0.003-0.0030.0000.0000.0000.000
36A36LEU0-0.036-0.02550.8730.0000.0000.0000.0000.0000.000
37A37ASN00.0170.00249.743-0.003-0.0030.0000.0000.0000.000
38A38PRO00.0880.04246.887-0.004-0.0040.0000.0000.0000.000
39A39LYS10.9410.96345.3050.1310.1310.0000.0000.0000.000
40A40THR00.0070.01145.696-0.004-0.0040.0000.0000.0000.000
41A41LEU00.0210.01045.547-0.003-0.0030.0000.0000.0000.000
42A42LEU00.0040.01039.841-0.003-0.0030.0000.0000.0000.000
43A43ASP-1-0.831-0.90442.226-0.163-0.1630.0000.0000.0000.000
44A44GLU-1-0.808-0.86943.096-0.139-0.1390.0000.0000.0000.000
45A45TYR0-0.002-0.04738.1850.0020.0020.0000.0000.0000.000
46A46GLU-1-0.831-0.88936.833-0.224-0.2240.0000.0000.0000.000
47A47LYS10.7820.88138.3610.1450.1450.0000.0000.0000.000
48A48LEU0-0.010-0.01239.871-0.004-0.0040.0000.0000.0000.000
49A49THR0-0.008-0.01736.596-0.007-0.0070.0000.0000.0000.000
50A50ARG10.8200.90034.0060.2310.2310.0000.0000.0000.000
51A51GLU-1-0.836-0.91635.409-0.209-0.2090.0000.0000.0000.000
52A52ALA0-0.0090.00537.398-0.001-0.0010.0000.0000.0000.000
53A53PHE00.008-0.02332.388-0.005-0.0050.0000.0000.0000.000
54A54SER0-0.054-0.00732.565-0.021-0.0210.0000.0000.0000.000
55A55ASN0-0.062-0.04633.317-0.001-0.0010.0000.0000.0000.000
56A56TYR00.0310.02233.0610.0100.0100.0000.0000.0000.000
57A57ALA0-0.0070.00329.012-0.016-0.0160.0000.0000.0000.000
58A58GLY0-0.052-0.02027.0470.0130.0130.0000.0000.0000.000
59A59LYS10.8370.91528.0750.2290.2290.0000.0000.0000.000
60A60PRO0-0.010-0.02430.161-0.015-0.0150.0000.0000.0000.000
61A61TYR0-0.042-0.04429.8900.0060.0060.0000.0000.0000.000
62A62ARG10.7470.84231.8840.1840.1840.0000.0000.0000.000
63A63PRO0-0.0030.00533.847-0.014-0.0140.0000.0000.0000.000
64A64ILE00.027-0.00330.0350.0060.0060.0000.0000.0000.000
65A65ARG10.8520.91934.4410.1570.1570.0000.0000.0000.000
66A66ASP-1-0.859-0.93037.274-0.157-0.1570.0000.0000.0000.000
67A67ILE0-0.020-0.00534.9730.0080.0080.0000.0000.0000.000
68A68GLU-1-0.777-0.86135.406-0.212-0.2120.0000.0000.0000.000
69A69GLU-1-0.759-0.84239.285-0.130-0.1300.0000.0000.0000.000
70A70GLU-1-0.865-0.88842.063-0.147-0.1470.0000.0000.0000.000
71A71VAL0-0.035-0.01840.5820.0070.0070.0000.0000.0000.000
72A72MET00.0000.00443.2430.0090.0090.0000.0000.0000.000
73A73ARG10.7700.85444.9590.1290.1290.0000.0000.0000.000
74A74LYS11.0111.01046.6290.1390.1390.0000.0000.0000.000
75A75LEU0-0.039-0.01844.7740.0040.0040.0000.0000.0000.000
76A76ALA0-0.013-0.01348.7200.0040.0040.0000.0000.0000.000
77A77GLU-1-0.982-0.98650.901-0.100-0.1000.0000.0000.0000.000
78A78LYS10.7900.89350.0320.1250.1250.0000.0000.0000.000
79A79TYR0-0.069-0.07049.6910.0040.0040.0000.0000.0000.000
80A80GLY00.0200.03554.2100.0030.0030.0000.0000.0000.000
81A81PHE00.0130.03048.4680.0030.0030.0000.0000.0000.000
82A82LYS10.8920.91452.6950.0940.0940.0000.0000.0000.000
83A83TYR00.002-0.01844.845-0.001-0.0010.0000.0000.0000.000
84A84PRO00.0090.03046.7610.0050.0050.0000.0000.0000.000
85A85GLU-1-0.801-0.90647.145-0.114-0.1140.0000.0000.0000.000
86A86ASN0-0.052-0.02445.162-0.001-0.0010.0000.0000.0000.000
87A87PHE00.0230.01041.055-0.004-0.0040.0000.0000.0000.000
88A88TRP00.0580.01734.461-0.002-0.0020.0000.0000.0000.000
89A89GLU-1-0.872-0.92439.047-0.129-0.1290.0000.0000.0000.000
90A90ILE0-0.036-0.01740.352-0.004-0.0040.0000.0000.0000.000
91A91HIS00.0130.00934.668-0.002-0.0020.0000.0000.0000.000
92A92LEU00.0480.03433.613-0.010-0.0100.0000.0000.0000.000
93A93ARG10.8090.87335.9850.1270.1270.0000.0000.0000.000
94A94MET0-0.040-0.02637.867-0.001-0.0010.0000.0000.0000.000
95A95HIS10.8010.87332.3170.2240.2240.0000.0000.0000.000
96A96GLN0-0.056-0.03433.118-0.002-0.0020.0000.0000.0000.000
97A97ARG10.8790.95434.2570.1510.1510.0000.0000.0000.000
98A98TYR0-0.057-0.04335.9460.0090.0090.0000.0000.0000.000
99A99GLY00.0640.05432.195-0.001-0.0010.0000.0000.0000.000
100A100GLU-1-0.825-0.89130.210-0.226-0.2260.0000.0000.0000.000
101A101LEU00.0260.00523.854-0.015-0.0150.0000.0000.0000.000
102A102TYR0-0.038-0.04424.1670.0180.0180.0000.0000.0000.000
103A103PRO0-0.010-0.00824.605-0.013-0.0130.0000.0000.0000.000
104A104GLU-1-0.756-0.85520.497-0.458-0.4580.0000.0000.0000.000
105A105VAL0-0.0120.00720.144-0.042-0.0420.0000.0000.0000.000
106A106VAL00.0350.00919.241-0.041-0.0410.0000.0000.0000.000
107A107GLU-1-0.875-0.93419.084-0.429-0.4290.0000.0000.0000.000
108A108VAL00.0250.00314.893-0.030-0.0300.0000.0000.0000.000
109A109LEU00.0430.03314.670-0.091-0.0910.0000.0000.0000.000
110A110LYS10.9030.94514.6130.3140.3140.0000.0000.0000.000
111A111SER0-0.085-0.04413.825-0.004-0.0040.0000.0000.0000.000
112A112LEU00.0090.0059.421-0.094-0.0940.0000.0000.0000.000
113A113LYS10.8130.8869.7200.3910.3910.0000.0000.0000.000
114A114GLY0-0.0270.00110.0570.1230.1230.0000.0000.0000.000
115A115LYS10.7640.8776.3661.5931.5930.0000.0000.0000.000
116A116TYR0-0.033-0.0412.872-1.233-0.5340.180-0.118-0.761-0.001
117A117HIS0-0.009-0.0056.3330.4530.4530.0000.0000.0000.000
118A118VAL00.0110.0088.830-0.285-0.2850.0000.0000.0000.000
119A119GLY00.0150.00011.7190.1730.1730.0000.0000.0000.000
120A120MET0-0.056-0.01814.129-0.005-0.0050.0000.0000.0000.000
121A121ILE0-0.020-0.01215.2220.0270.0270.0000.0000.0000.000
122A122THR0-0.0080.00719.214-0.011-0.0110.0000.0000.0000.000
123A123ASP-1-0.713-0.85422.878-0.381-0.3810.0000.0000.0000.000
124A124SER0-0.054-0.04526.0610.0030.0030.0000.0000.0000.000
125A125ASP-1-0.693-0.79727.992-0.234-0.2340.0000.0000.0000.000
126A126THR0-0.017-0.04825.782-0.016-0.0160.0000.0000.0000.000
127A127GLU-1-0.946-0.96628.299-0.175-0.1750.0000.0000.0000.000
128A128TYR0-0.009-0.03030.748-0.004-0.0040.0000.0000.0000.000
129A129LEU00.0130.00223.612-0.002-0.0020.0000.0000.0000.000
130A130MET0-0.022-0.00923.589-0.009-0.0090.0000.0000.0000.000
131A131ALA00.0240.01927.7040.0030.0030.0000.0000.0000.000
132A132HIS0-0.001-0.00128.8820.0040.0040.0000.0000.0000.000
133A133LEU00.029-0.00522.734-0.004-0.0040.0000.0000.0000.000
134A134ASP-1-0.823-0.90226.144-0.243-0.2430.0000.0000.0000.000
135A135ALA0-0.075-0.02328.1960.0090.0090.0000.0000.0000.000
136A136LEU0-0.033-0.01726.5650.0040.0040.0000.0000.0000.000
137A137GLY0-0.0260.00126.736-0.011-0.0110.0000.0000.0000.000
138A138ILE0-0.021-0.02621.630-0.011-0.0110.0000.0000.0000.000
139A139LYS10.8130.91221.1510.2060.2060.0000.0000.0000.000
140A140ASP-1-0.850-0.93720.666-0.283-0.2830.0000.0000.0000.000
141A141LEU0-0.080-0.04018.014-0.001-0.0010.0000.0000.0000.000
142A142PHE00.003-0.00515.567-0.080-0.0800.0000.0000.0000.000
143A143ASP-1-0.808-0.88312.332-0.548-0.5480.0000.0000.0000.000
144A144SER0-0.032-0.01414.7640.0150.0150.0000.0000.0000.000
145A145ILE00.0180.02016.441-0.076-0.0760.0000.0000.0000.000
146A146THR0-0.015-0.00217.9540.0510.0510.0000.0000.0000.000
147A147THR00.009-0.00120.632-0.028-0.0280.0000.0000.0000.000
148A148SER00.0470.01724.070-0.004-0.0040.0000.0000.0000.000
149A149GLU-1-0.865-0.88726.412-0.225-0.2250.0000.0000.0000.000
150A150GLU-1-0.799-0.89223.096-0.351-0.3510.0000.0000.0000.000
151A151ALA0-0.0110.00323.3970.0090.0090.0000.0000.0000.000
152A152GLY00.0200.02324.9910.0130.0130.0000.0000.0000.000
153A153PHE0-0.048-0.03126.2260.0220.0220.0000.0000.0000.000
154A154PHE00.0110.01626.362-0.026-0.0260.0000.0000.0000.000
155A155LYS10.7980.88621.7640.5440.5440.0000.0000.0000.000
156A156PRO0-0.005-0.00922.9350.0360.0360.0000.0000.0000.000
157A157HIS00.0070.00622.348-0.048-0.0480.0000.0000.0000.000
158A158PRO00.0530.01719.890-0.028-0.0280.0000.0000.0000.000
159A159ARG10.8960.93719.8140.2540.2540.0000.0000.0000.000
160A160ILE0-0.0080.00020.904-0.006-0.0060.0000.0000.0000.000
161A161PHE00.0390.01416.309-0.029-0.0290.0000.0000.0000.000
162A162GLU-1-0.897-0.94316.215-0.487-0.4870.0000.0000.0000.000
163A163LEU0-0.041-0.00916.933-0.011-0.0110.0000.0000.0000.000
164A164ALA00.0240.01315.8200.0160.0160.0000.0000.0000.000
165A165LEU0-0.0080.00010.898-0.038-0.0380.0000.0000.0000.000
166A166LYS10.8500.90612.8020.4980.4980.0000.0000.0000.000
167A167LYS10.7320.84215.3610.4910.4910.0000.0000.0000.000
168A168ALA00.0000.01710.7540.0560.0560.0000.0000.0000.000
169A169GLY0-0.0220.01110.440-0.016-0.0160.0000.0000.0000.000
170A170VAL0-0.051-0.0246.6900.0970.0970.0000.0000.0000.000
171A171LYS10.8450.9275.3541.9741.9740.0000.0000.0000.000
172A172GLY00.0750.0198.114-0.506-0.5060.0000.0000.0000.000
173A173GLU-1-0.856-0.9455.771-1.754-1.7540.0000.0000.0000.000
174A174GLU-1-0.825-0.8843.605-3.365-2.8550.002-0.105-0.4070.000
175A175ALA0-0.004-0.0075.331-0.326-0.281-0.001-0.012-0.0310.000
176A176VAL00.0330.0208.2930.2140.2140.0000.0000.0000.000
177A177TYR0-0.050-0.03910.5130.1720.1720.0000.0000.0000.000
178A178VAL0-0.005-0.00114.2210.0530.0530.0000.0000.0000.000
179A179GLY00.0350.00816.5960.0460.0460.0000.0000.0000.000
180A180ASP-1-0.870-0.91620.139-0.411-0.4110.0000.0000.0000.000
181A181ASN00.0810.03023.4500.0300.0300.0000.0000.0000.000
182A182PRO00.0390.00622.333-0.032-0.0320.0000.0000.0000.000
183A183VAL0-0.0010.00822.431-0.025-0.0250.0000.0000.0000.000
184A184LYS10.8460.89723.2770.3470.3470.0000.0000.0000.000
185A185ASP-1-0.726-0.85419.928-0.591-0.5910.0000.0000.0000.000
186A186CYS0-0.069-0.00717.726-0.111-0.1110.0000.0000.0000.000
187A187GLY00.0470.02717.989-0.037-0.0370.0000.0000.0000.000
188A188GLY0-0.015-0.01219.9070.0100.0100.0000.0000.0000.000
189A189SER0-0.025-0.03414.897-0.033-0.0330.0000.0000.0000.000
190A190LYS10.8330.89512.6281.0051.0050.0000.0000.0000.000
191A191ASN0-0.072-0.03315.0260.0200.0200.0000.0000.0000.000
192A192LEU0-0.064-0.02713.7200.0660.0660.0000.0000.0000.000
193A193GLY00.0000.00110.973-0.096-0.0960.0000.0000.0000.000
194A194MET0-0.064-0.0049.857-0.129-0.1290.0000.0000.0000.000
195A195THR00.0020.0188.4370.2840.2840.0000.0000.0000.000
196A196SER0-0.040-0.04610.9140.0340.0340.0000.0000.0000.000
197A197ILE00.000-0.01411.6730.0370.0370.0000.0000.0000.000
198A198LEU00.007-0.00415.8310.0330.0330.0000.0000.0000.000
199A199LEU0-0.0140.00819.6600.0130.0130.0000.0000.0000.000
200A200ASP-1-0.757-0.89121.597-0.332-0.3320.0000.0000.0000.000
201A201ARG10.8160.89923.1910.4580.4580.0000.0000.0000.000
202A202LYS10.8560.92726.5470.3060.3060.0000.0000.0000.000
203A203GLY0-0.070-0.01627.3430.0190.0190.0000.0000.0000.000
204A204GLU-1-0.932-0.97928.372-0.278-0.2780.0000.0000.0000.000
205A205LYS10.7700.85825.0760.4440.4440.0000.0000.0000.000
206A206ARG10.9070.95026.6050.2750.2750.0000.0000.0000.000
207A207GLU-1-0.960-0.97027.242-0.250-0.2500.0000.0000.0000.000
208A208PHE0-0.018-0.00925.8390.0000.0000.0000.0000.0000.000
209A209TRP0-0.003-0.02622.567-0.031-0.0310.0000.0000.0000.000
210A210ASP-1-0.797-0.87921.117-0.403-0.4030.0000.0000.0000.000
211A211LYS10.7510.86221.4450.3730.3730.0000.0000.0000.000
212A213ASP-1-0.768-0.82812.927-1.065-1.0650.0000.0000.0000.000
213A214PHE00.0230.00710.5780.0110.0110.0000.0000.0000.000
214A215ILE0-0.026-0.01315.8070.0140.0140.0000.0000.0000.000
215A216VAL0-0.0220.00016.837-0.017-0.0170.0000.0000.0000.000
216A217SER0-0.075-0.05119.8670.0460.0460.0000.0000.0000.000
217A218ASP-1-0.772-0.88621.027-0.435-0.4350.0000.0000.0000.000
218A219LEU00.0540.01817.671-0.061-0.0610.0000.0000.0000.000
219A220ARG10.7300.83016.4060.3210.3210.0000.0000.0000.000
220A221GLU-1-0.797-0.87716.403-0.546-0.5460.0000.0000.0000.000
221A222VAL00.0390.02412.222-0.076-0.0760.0000.0000.0000.000
222A223ILE0-0.004-0.00910.693-0.187-0.1870.0000.0000.0000.000
223A224LYS10.8430.92910.1180.4990.4990.0000.0000.0000.000
224A225ILE00.0740.04510.357-0.043-0.0430.0000.0000.0000.000
225A226VAL0-0.015-0.0106.110-0.154-0.1540.0000.0000.0000.000
226A227ASP-1-0.823-0.8826.382-2.393-2.3930.0000.0000.0000.000
227A228GLU-1-0.990-0.9897.518-0.625-0.6250.0000.0000.0000.000
228A229LEU0-0.046-0.0275.1470.2940.2940.0000.0000.0000.000
229A230ASN0-0.097-0.0272.504-4.763-1.7142.320-2.042-3.326-0.027