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: 98L72

Calculation Name: 1XB4-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1XB4

Chain ID: A

ChEMBL ID:

UniProt ID: P47142

Base Structure: X-ray

Registration Date: 2023-09-22

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 184
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2100649.785914
FMO2-HF: Nuclear repulsion 2023899.711954
FMO2-HF: Total energy -76750.073961
FMO2-MP2: Total energy -76971.588621


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.
-1.1362.6430.291-1.96-2.1080
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 : 0.051 / q_NPA : 0.027
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].
3A3ALA0-0.0140.0073.886-1.4781.478-0.024-1.673-1.2580.002
4A4LEU00.0280.0086.0720.1690.1690.0000.0000.0000.000
5A5PRO00.0190.0159.343-0.047-0.0470.0000.0000.0000.000
6A6PRO00.0650.02310.8820.1240.1240.0000.0000.0000.000
7A7VAL0-0.002-0.00513.6760.0670.0670.0000.0000.0000.000
8A8TYR00.004-0.00613.4710.0400.0400.0000.0000.0000.000
9A9SER00.0630.02915.4710.0410.0410.0000.0000.0000.000
10A10PHE00.0230.01717.7240.0320.0320.0000.0000.0000.000
11A11PRO00.0680.02420.5070.0000.0000.0000.0000.0000.000
12A12PRO0-0.035-0.02723.5110.0050.0050.0000.0000.0000.000
13A13LEU0-0.0080.01517.4060.0070.0070.0000.0000.0000.000
14A14TYR00.006-0.01917.8230.0100.0100.0000.0000.0000.000
15A15THR0-0.0270.00023.6160.0120.0120.0000.0000.0000.000
16A16ARG10.8440.92126.8770.0720.0720.0000.0000.0000.000
17A17GLN00.0130.00426.6710.0110.0110.0000.0000.0000.000
18A18PRO00.0100.00929.0700.0010.0010.0000.0000.0000.000
19A19ASN00.033-0.00631.1020.0080.0080.0000.0000.0000.000
20A20SER00.0040.01130.183-0.008-0.0080.0000.0000.0000.000
21A21LEU00.0330.01729.093-0.007-0.0070.0000.0000.0000.000
22A22THR00.0440.01126.630-0.007-0.0070.0000.0000.0000.000
23A23ARG10.8330.92125.5800.0770.0770.0000.0000.0000.000
24A24ARG10.9020.95523.1780.1290.1290.0000.0000.0000.000
25A25GLN00.0390.03122.323-0.026-0.0260.0000.0000.0000.000
26A26GLN00.0060.00020.824-0.015-0.0150.0000.0000.0000.000
27A27ILE00.005-0.00420.430-0.014-0.0140.0000.0000.0000.000
28A28SER0-0.027-0.03119.250-0.008-0.0080.0000.0000.0000.000
29A29THR0-0.019-0.01716.304-0.033-0.0330.0000.0000.0000.000
30A30TRP00.009-0.00715.438-0.051-0.0510.0000.0000.0000.000
31A31ILE0-0.036-0.01715.685-0.011-0.0110.0000.0000.0000.000
32A32ASP-1-0.918-0.94211.407-0.668-0.6680.0000.0000.0000.000
33A33ILE00.0180.01011.324-0.066-0.0660.0000.0000.0000.000
34A34ILE0-0.001-0.00511.259-0.021-0.0210.0000.0000.0000.000
35A35SER0-0.014-0.01411.5210.0590.0590.0000.0000.0000.000
36A36GLN00.0440.0155.8660.1840.1840.0000.0000.0000.000
37A37TYR00.0490.0346.559-0.020-0.0200.0000.0000.0000.000
38A38CYS0-0.067-0.0298.3180.1670.1670.0000.0000.0000.000
39A39LYS10.9510.9775.4940.8490.8490.0000.0000.0000.000
40A40THR0-0.089-0.0702.557-0.769-0.0690.316-0.284-0.732-0.002
41A41LYS10.9030.9594.9720.3290.452-0.001-0.003-0.1180.000
42A42LYS10.8280.9257.572-0.767-0.7670.0000.0000.0000.000
43A43ILE00.0080.02010.169-0.073-0.0730.0000.0000.0000.000
44A44TRP00.0560.02212.854-0.043-0.0430.0000.0000.0000.000
45A45TYR00.0220.00115.666-0.023-0.0230.0000.0000.0000.000
46A46MET0-0.0070.00916.5050.0010.0010.0000.0000.0000.000
47A47SER00.001-0.02519.0940.0020.0020.0000.0000.0000.000
48A48VAL00.016-0.00622.168-0.010-0.0100.0000.0000.0000.000
49A49ASP-1-0.691-0.79423.565-0.039-0.0390.0000.0000.0000.000
50A50GLY00.0010.00120.084-0.010-0.0100.0000.0000.0000.000
51A51THR0-0.062-0.05118.790-0.002-0.0020.0000.0000.0000.000
52A52VAL0-0.0110.00314.235-0.001-0.0010.0000.0000.0000.000
53A53ILE0-0.070-0.04017.4810.0060.0060.0000.0000.0000.000
54A54ASN0-0.012-0.01415.7950.0050.0050.0000.0000.0000.000
55A55ASP-1-0.850-0.90916.4290.1210.1210.0000.0000.0000.000
56A73LYS10.9100.94516.725-0.005-0.0050.0000.0000.0000.000
57A74ASN0-0.033-0.03018.340-0.009-0.0090.0000.0000.0000.000
58A75LEU00.0410.03913.048-0.005-0.0050.0000.0000.0000.000
59A76PHE00.0180.00416.590-0.034-0.0340.0000.0000.0000.000
60A77ASN0-0.040-0.03019.546-0.005-0.0050.0000.0000.0000.000
61A78ASN0-0.0140.00517.2380.0210.0210.0000.0000.0000.000
62A79GLU-1-0.808-0.91819.450-0.031-0.0310.0000.0000.0000.000
63A80ASP-1-0.941-0.96316.871-0.056-0.0560.0000.0000.0000.000
64A81ILE0-0.103-0.04819.308-0.002-0.0020.0000.0000.0000.000
65A82GLN0-0.0160.00121.9690.0000.0000.0000.0000.0000.000
66A83ARG10.8460.92722.6060.0920.0920.0000.0000.0000.000
67A84SER00.0630.02722.505-0.002-0.0020.0000.0000.0000.000
68A85VAL0-0.085-0.01921.5130.0000.0000.0000.0000.0000.000
69A86SER00.0110.00724.5620.0070.0070.0000.0000.0000.000
70A87GLN00.027-0.01325.978-0.004-0.0040.0000.0000.0000.000
71A88VAL00.0270.00827.901-0.003-0.0030.0000.0000.0000.000
72A89PHE0-0.033-0.01823.926-0.003-0.0030.0000.0000.0000.000
73A90ILE00.0310.02022.850-0.009-0.0090.0000.0000.0000.000
74A91ASP-1-0.794-0.89524.073-0.063-0.0630.0000.0000.0000.000
75A92GLU-1-0.808-0.86426.553-0.086-0.0860.0000.0000.0000.000
76A93ILE0-0.015-0.00119.574-0.007-0.0070.0000.0000.0000.000
77A94TRP00.0230.00018.697-0.010-0.0100.0000.0000.0000.000
78A95SER0-0.035-0.02123.2230.0010.0010.0000.0000.0000.000
79A96GLN0-0.0010.00322.8220.0110.0110.0000.0000.0000.000
80A97MET0-0.012-0.00415.5750.0010.0010.0000.0000.0000.000
81A98THR0-0.001-0.01621.0220.0060.0060.0000.0000.0000.000
82A99LYS10.8430.92123.6060.0910.0910.0000.0000.0000.000
83A100GLU-1-0.872-0.91820.252-0.165-0.1650.0000.0000.0000.000
84A101GLY00.0070.00420.877-0.008-0.0080.0000.0000.0000.000
85A102LYS10.8790.93716.3310.1960.1960.0000.0000.0000.000
86A103CYS0-0.055-0.01216.990-0.002-0.0020.0000.0000.0000.000
87A104LEU00.0040.00919.4450.0010.0010.0000.0000.0000.000
88A105PRO00.009-0.00522.3800.0060.0060.0000.0000.0000.000
89A106ILE0-0.028-0.00622.5740.0040.0040.0000.0000.0000.000
90A107ASP-1-0.722-0.85026.478-0.007-0.0070.0000.0000.0000.000
91A108GLN0-0.041-0.03127.7830.0010.0010.0000.0000.0000.000
92A109SER0-0.092-0.04728.6610.0040.0040.0000.0000.0000.000
93A110GLY00.009-0.01527.7330.0030.0030.0000.0000.0000.000
94A111ARG10.9470.97426.5020.0280.0280.0000.0000.0000.000
95A112ARG10.9000.96328.2360.0140.0140.0000.0000.0000.000
96A113SER00.0300.00828.342-0.001-0.0010.0000.0000.0000.000
97A114SER0-0.024-0.00230.1120.0010.0010.0000.0000.0000.000
98A115ASN00.0260.01833.4750.0020.0020.0000.0000.0000.000
99A116THR00.013-0.00633.103-0.001-0.0010.0000.0000.0000.000
100A117THR00.006-0.00532.6370.0010.0010.0000.0000.0000.000
101A118THR0-0.0070.00927.4860.0020.0020.0000.0000.0000.000
102A119THR0-0.013-0.00726.982-0.001-0.0010.0000.0000.0000.000
103A120ARG10.8670.93922.451-0.013-0.0130.0000.0000.0000.000
104A121TYR00.0130.00920.170-0.002-0.0020.0000.0000.0000.000
105A122PHE00.0460.02616.2860.0020.0020.0000.0000.0000.000
106A123ILE00.012-0.01513.637-0.016-0.0160.0000.0000.0000.000
107A124LEU0-0.0300.00014.9320.0210.0210.0000.0000.0000.000
108A125TRP0-0.012-0.00810.255-0.006-0.0060.0000.0000.0000.000
109A126LYS10.8560.92611.546-0.095-0.0950.0000.0000.0000.000
110A127SER00.0270.01714.3280.0080.0080.0000.0000.0000.000
111A128LEU00.0460.01618.1430.0140.0140.0000.0000.0000.000
112A129ASP-1-0.850-0.92320.686-0.021-0.0210.0000.0000.0000.000
113A130SER0-0.068-0.02016.4600.0050.0050.0000.0000.0000.000
114A131TRP00.0600.00712.4530.0170.0170.0000.0000.0000.000
115A132ALA00.0090.01318.4040.0080.0080.0000.0000.0000.000
116A133SER0-0.044-0.04320.0570.0020.0020.0000.0000.0000.000
117A134LEU0-0.029-0.00814.3820.0050.0050.0000.0000.0000.000
118A135ILE00.0140.00718.6670.0070.0070.0000.0000.0000.000
119A136LEU0-0.022-0.01620.876-0.001-0.0010.0000.0000.0000.000
120A137GLN00.0090.00218.3790.0090.0090.0000.0000.0000.000
121A138TRP0-0.0010.00518.740-0.003-0.0030.0000.0000.0000.000
122A139PHE00.019-0.01020.914-0.002-0.0020.0000.0000.0000.000
123A140GLU-1-0.939-0.96024.5470.0080.0080.0000.0000.0000.000
124A141ASP-1-0.870-0.93620.9050.0280.0280.0000.0000.0000.000
125A142SER0-0.043-0.01721.8290.0020.0020.0000.0000.0000.000
126A143GLY0-0.026-0.00423.8940.0000.0000.0000.0000.0000.000
127A144LYS10.8720.92824.811-0.045-0.0450.0000.0000.0000.000
128A145LEU0-0.018-0.00428.259-0.001-0.0010.0000.0000.0000.000
129A146ASN0-0.043-0.02129.588-0.004-0.0040.0000.0000.0000.000
130A147GLN0-0.016-0.00830.5260.0000.0000.0000.0000.0000.000
131A148VAL0-0.029-0.02131.679-0.001-0.0010.0000.0000.0000.000
132A149ILE00.0050.01725.0290.0000.0000.0000.0000.0000.000
133A150THR00.0260.00428.198-0.001-0.0010.0000.0000.0000.000
134A151LEU0-0.020-0.02725.6130.0030.0030.0000.0000.0000.000
135A152TYR0-0.029-0.01223.3830.0050.0050.0000.0000.0000.000
136A153GLU-1-0.818-0.91323.2210.0480.0480.0000.0000.0000.000
137A154LEU0-0.052-0.02022.5110.0030.0030.0000.0000.0000.000
138A155SER0-0.065-0.05919.4040.0080.0080.0000.0000.0000.000
139A156GLU-1-0.862-0.93119.0180.0820.0820.0000.0000.0000.000
140A157GLY00.0610.01819.4950.0080.0080.0000.0000.0000.000
141A158ASP-1-0.844-0.89220.7050.0480.0480.0000.0000.0000.000
142A159GLU-1-0.920-0.94918.7920.0900.0900.0000.0000.0000.000
143A160THR0-0.133-0.08418.891-0.002-0.0020.0000.0000.0000.000
144A161VAL0-0.048-0.00218.084-0.001-0.0010.0000.0000.0000.000
145A162ASN00.026-0.00411.2200.0290.0290.0000.0000.0000.000
146A163TRP00.0010.00412.4620.0260.0260.0000.0000.0000.000
147A164GLU-1-0.869-0.9408.7270.4370.4370.0000.0000.0000.000
148A165PHE00.003-0.00512.3820.0190.0190.0000.0000.0000.000
149A166HIS00.0760.05213.918-0.016-0.0160.0000.0000.0000.000
150A167ARG10.7960.88014.927-0.093-0.0930.0000.0000.0000.000
151A168MET0-0.0480.00716.665-0.013-0.0130.0000.0000.0000.000
152A169PRO00.0210.00517.962-0.011-0.0110.0000.0000.0000.000
153A170GLU-1-0.729-0.86021.3890.0310.0310.0000.0000.0000.000
154A171SER0-0.015-0.00824.477-0.003-0.0030.0000.0000.0000.000
155A172LEU0-0.040-0.02619.310-0.009-0.0090.0000.0000.0000.000
156A173LEU00.0840.03220.158-0.007-0.0070.0000.0000.0000.000
157A174TYR00.0170.00822.334-0.005-0.0050.0000.0000.0000.000
158A175TYR0-0.017-0.01323.513-0.007-0.0070.0000.0000.0000.000
159A176CYS0-0.094-0.03920.066-0.006-0.0060.0000.0000.0000.000
160A177LEU00.0650.03222.4410.0000.0000.0000.0000.0000.000
161A178LYS10.8490.91725.6170.0070.0070.0000.0000.0000.000
162A179PRO0-0.001-0.00924.202-0.001-0.0010.0000.0000.0000.000
163A180LEU0-0.0110.00524.804-0.002-0.0020.0000.0000.0000.000
164A181CYS0-0.0490.00328.1280.0010.0010.0000.0000.0000.000
165A182ASP-1-0.780-0.87329.976-0.012-0.0120.0000.0000.0000.000
166A183ARG10.8670.91726.5260.0100.0100.0000.0000.0000.000
167A184ASN0-0.034-0.01831.838-0.001-0.0010.0000.0000.0000.000
168A185ARG10.8320.93129.238-0.006-0.0060.0000.0000.0000.000
169A186ALA00.0320.01829.6320.0030.0030.0000.0000.0000.000
170A187THR0-0.065-0.04231.787-0.002-0.0020.0000.0000.0000.000
171A188MET00.0130.01030.2420.0030.0030.0000.0000.0000.000
172A189LEU0-0.023-0.01332.891-0.002-0.0020.0000.0000.0000.000
173A190LYS10.8340.90733.834-0.005-0.0050.0000.0000.0000.000
174A191ASP-1-0.797-0.89635.7320.0160.0160.0000.0000.0000.000
175A192GLU-1-0.932-0.97338.1540.0120.0120.0000.0000.0000.000
176A193ASN0-0.083-0.03637.954-0.002-0.0020.0000.0000.0000.000
177A194ASP-1-0.893-0.93938.1660.0050.0050.0000.0000.0000.000
178A195LYS10.8180.90129.710-0.027-0.0270.0000.0000.0000.000
179A196VAL0-0.006-0.01630.3350.0010.0010.0000.0000.0000.000
180A197ILE00.0190.01730.9890.0030.0030.0000.0000.0000.000
181A198ALA00.0030.00530.2930.0040.0040.0000.0000.0000.000
182A199ILE0-0.035-0.01227.495-0.004-0.0040.0000.0000.0000.000
183A200LYS10.9671.00030.931-0.008-0.0080.0000.0000.0000.000
184A201VAL00.0280.02227.784-0.003-0.0030.0000.0000.0000.000