FMODB

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

Last updated: 2024-04-25

All entries: 37426

Number of unique PDB entries: 7782

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FMODB ID: ZVRYN

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 OptH
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 -3005685.460329
FMO2-HF: Nuclear repulsion 2912488.001341
FMO2-HF: Total energy -93197.458989
FMO2-MP2: Total energy -93469.246346


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.
-14.801-7.6367.013-4.701-9.478-0.042
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 : -0.050 / q_NPA : -0.034
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].
3A3ARG10.8020.8692.406-3.905-0.6053.089-2.137-4.251-0.010
4A4ALA0-0.0100.0023.7401.2271.5160.006-0.030-0.2650.000
5A5VAL00.0160.0137.271-0.193-0.1930.0000.0000.0000.000
6A6PHE0-0.047-0.0209.9500.2290.2290.0000.0000.0000.000
7A7PHE00.022-0.00213.147-0.006-0.0060.0000.0000.0000.000
8A8ASP-1-0.763-0.87616.767-0.349-0.3490.0000.0000.0000.000
9A9PHE0-0.002-0.03820.389-0.018-0.0180.0000.0000.0000.000
10A10VAL00.0270.00622.959-0.002-0.0020.0000.0000.0000.000
11A11GLY00.0170.02525.671-0.004-0.0040.0000.0000.0000.000
12A12THR0-0.034-0.01419.413-0.020-0.0200.0000.0000.0000.000
13A13LEU0-0.038-0.03418.628-0.016-0.0160.0000.0000.0000.000
14A14LEU0-0.015-0.01022.6780.0210.0210.0000.0000.0000.000
15A15SER00.0250.01926.3580.0020.0020.0000.0000.0000.000
16A16VAL00.0550.02428.6670.0140.0140.0000.0000.0000.000
17A17GLU-1-0.897-0.96430.940-0.218-0.2180.0000.0000.0000.000
18A18GLY00.0390.01432.1670.0140.0140.0000.0000.0000.000
19A19GLU-1-0.789-0.86531.888-0.192-0.1920.0000.0000.0000.000
20A20ALA00.0730.05933.8020.0120.0120.0000.0000.0000.000
21A21LYS10.9350.97536.6780.1600.1600.0000.0000.0000.000
22A22THR0-0.046-0.03035.0880.0100.0100.0000.0000.0000.000
23A23HIS0-0.012-0.04034.6950.0130.0130.0000.0000.0000.000
24A24LEU0-0.014-0.00938.9850.0080.0080.0000.0000.0000.000
25A25LYS10.8860.94340.8040.1250.1250.0000.0000.0000.000
26A26ILE0-0.0020.01538.1100.0060.0060.0000.0000.0000.000
27A27MET0-0.0130.00241.3040.0070.0070.0000.0000.0000.000
28A28GLU-1-0.933-0.97745.030-0.101-0.1010.0000.0000.0000.000
29A29GLU-1-0.888-0.93945.206-0.097-0.0970.0000.0000.0000.000
30A30VAL0-0.070-0.04145.1530.0040.0040.0000.0000.0000.000
31A31LEU0-0.073-0.02747.9030.0040.0040.0000.0000.0000.000
32A32GLY00.0100.01550.5650.0040.0040.0000.0000.0000.000
33A33ASP-1-0.925-0.97152.535-0.070-0.0700.0000.0000.0000.000
34A34TYR0-0.106-0.07853.9630.0030.0030.0000.0000.0000.000
35A35PRO00.0010.00754.768-0.002-0.0020.0000.0000.0000.000
36A36LEU0-0.035-0.01750.8640.0010.0010.0000.0000.0000.000
37A37ASN00.005-0.00850.268-0.004-0.0040.0000.0000.0000.000
38A38PRO00.1090.05347.011-0.002-0.0020.0000.0000.0000.000
39A39LYS10.9480.97045.1170.1030.1030.0000.0000.0000.000
40A40THR0-0.019-0.00145.815-0.002-0.0020.0000.0000.0000.000
41A41LEU0-0.0020.00046.690-0.003-0.0030.0000.0000.0000.000
42A42LEU00.006-0.00539.806-0.001-0.0010.0000.0000.0000.000
43A43ASP-1-0.919-0.95142.160-0.114-0.1140.0000.0000.0000.000
44A44GLU-1-0.813-0.90942.839-0.094-0.0940.0000.0000.0000.000
45A45TYR0-0.035-0.06238.4100.0030.0030.0000.0000.0000.000
46A46GLU-1-0.920-0.95137.966-0.150-0.1500.0000.0000.0000.000
47A47LYS10.9220.96438.7160.0960.0960.0000.0000.0000.000
48A48LEU0-0.055-0.03940.0960.0010.0010.0000.0000.0000.000
49A49THR00.000-0.00737.123-0.003-0.0030.0000.0000.0000.000
50A50ARG10.9510.97533.5470.1700.1700.0000.0000.0000.000
51A51GLU-1-0.937-0.96435.785-0.120-0.1200.0000.0000.0000.000
52A52ALA0-0.032-0.01637.7500.0010.0010.0000.0000.0000.000
53A53PHE00.002-0.02032.768-0.001-0.0010.0000.0000.0000.000
54A54SER0-0.028-0.00433.274-0.009-0.0090.0000.0000.0000.000
55A55ASN00.0000.00633.9170.0000.0000.0000.0000.0000.000
56A56TYR0-0.038-0.02033.4440.0080.0080.0000.0000.0000.000
57A57ALA00.0380.03429.478-0.009-0.0090.0000.0000.0000.000
58A58GLY0-0.058-0.02527.6630.0130.0130.0000.0000.0000.000
59A59LYS10.8690.93828.6990.1260.1260.0000.0000.0000.000
60A60PRO0-0.016-0.02130.549-0.011-0.0110.0000.0000.0000.000
61A61TYR0-0.038-0.04130.0830.0030.0030.0000.0000.0000.000
62A62ARG10.8080.90031.9810.1240.1240.0000.0000.0000.000
63A63PRO00.0100.01034.164-0.009-0.0090.0000.0000.0000.000
64A64ILE00.0170.00530.1290.0060.0060.0000.0000.0000.000
65A65ARG10.8920.93234.5860.1230.1230.0000.0000.0000.000
66A66ASP-1-0.916-0.96037.186-0.109-0.1090.0000.0000.0000.000
67A67ILE0-0.054-0.02535.3040.0060.0060.0000.0000.0000.000
68A68GLU-1-0.789-0.88435.230-0.157-0.1570.0000.0000.0000.000
69A69GLU-1-0.871-0.92639.468-0.103-0.1030.0000.0000.0000.000
70A70GLU-1-0.884-0.92642.325-0.094-0.0940.0000.0000.0000.000
71A71VAL0-0.030-0.01040.8550.0060.0060.0000.0000.0000.000
72A72MET00.007-0.00243.5090.0070.0070.0000.0000.0000.000
73A73ARG10.8590.94045.2030.0920.0920.0000.0000.0000.000
74A74LYS10.9891.00246.5460.0920.0920.0000.0000.0000.000
75A75LEU0-0.042-0.02544.8710.0040.0040.0000.0000.0000.000
76A76ALA0-0.0080.00148.9730.0030.0030.0000.0000.0000.000
77A77GLU-1-0.967-0.97651.192-0.066-0.0660.0000.0000.0000.000
78A78LYS10.8130.91750.1370.0830.0830.0000.0000.0000.000
79A79TYR0-0.044-0.05549.5050.0030.0030.0000.0000.0000.000
80A80GLY00.0210.05354.3040.0020.0020.0000.0000.0000.000
81A81PHE00.0090.03448.8720.0020.0020.0000.0000.0000.000
82A82LYS10.9060.91552.5480.0730.0730.0000.0000.0000.000
83A83TYR00.0650.02445.117-0.003-0.0030.0000.0000.0000.000
84A84PRO0-0.0290.01646.7080.0040.0040.0000.0000.0000.000
85A85GLU-1-0.801-0.94547.379-0.084-0.0840.0000.0000.0000.000
86A86ASN00.0160.03345.4270.0000.0000.0000.0000.0000.000
87A87PHE00.028-0.00140.930-0.004-0.0040.0000.0000.0000.000
88A88TRP00.0500.02634.879-0.002-0.0020.0000.0000.0000.000
89A89GLU-1-0.924-0.96339.240-0.109-0.1090.0000.0000.0000.000
90A90ILE0-0.071-0.03340.409-0.005-0.0050.0000.0000.0000.000
91A91HIS00.0390.04434.621-0.005-0.0050.0000.0000.0000.000
92A92LEU00.0450.04833.383-0.009-0.0090.0000.0000.0000.000
93A93ARG10.8770.94536.0230.1040.1040.0000.0000.0000.000
94A94MET0-0.059-0.03537.710-0.004-0.0040.0000.0000.0000.000
95A95HIS10.7640.83132.3560.1780.1780.0000.0000.0000.000
96A96GLN0-0.033-0.01332.927-0.002-0.0020.0000.0000.0000.000
97A97ARG10.9230.97333.7910.1290.1290.0000.0000.0000.000
98A98TYR0-0.084-0.06235.8280.0050.0050.0000.0000.0000.000
99A99GLY00.0360.05131.629-0.002-0.0020.0000.0000.0000.000
100A100GLU-1-0.951-0.97730.090-0.200-0.2000.0000.0000.0000.000
101A101LEU00.0200.00123.647-0.009-0.0090.0000.0000.0000.000
102A102TYR0-0.0160.00423.9450.0180.0180.0000.0000.0000.000
103A103PRO0-0.026-0.02624.658-0.015-0.0150.0000.0000.0000.000
104A104GLU-1-0.754-0.85020.415-0.406-0.4060.0000.0000.0000.000
105A105VAL00.0200.02020.028-0.049-0.0490.0000.0000.0000.000
106A106VAL00.0390.01818.928-0.052-0.0520.0000.0000.0000.000
107A107GLU-1-0.937-0.96418.218-0.474-0.4740.0000.0000.0000.000
108A108VAL00.0280.01214.643-0.054-0.0540.0000.0000.0000.000
109A109LEU00.0310.01714.345-0.115-0.1150.0000.0000.0000.000
110A110LYS10.9300.94914.0690.3470.3470.0000.0000.0000.000
111A111SER0-0.092-0.03713.328-0.059-0.0590.0000.0000.0000.000
112A112LEU00.0430.0129.071-0.103-0.1030.0000.0000.0000.000
113A113LYS10.9320.9769.2780.4130.4130.0000.0000.0000.000
114A114GLY0-0.063-0.01610.0220.0540.0540.0000.0000.0000.000
115A115LYS10.8500.9315.7431.4971.4970.0000.0000.0000.000
116A116TYR0-0.029-0.0183.142-1.190-0.6250.058-0.083-0.5400.000
117A117HIS00.000-0.0016.3400.4730.4730.0000.0000.0000.000
118A118VAL0-0.008-0.0128.869-0.225-0.2250.0000.0000.0000.000
119A119GLY00.0170.00211.6790.1670.1670.0000.0000.0000.000
120A120MET0-0.0440.00014.277-0.016-0.0160.0000.0000.0000.000
121A121ILE0-0.028-0.02215.4820.0250.0250.0000.0000.0000.000
122A122THR0-0.017-0.00919.327-0.004-0.0040.0000.0000.0000.000
123A123ASP-1-0.740-0.86222.953-0.256-0.2560.0000.0000.0000.000
124A124SER0-0.061-0.06526.466-0.006-0.0060.0000.0000.0000.000
125A125ASP-1-0.679-0.79728.153-0.171-0.1710.0000.0000.0000.000
126A126THR00.019-0.01426.273-0.016-0.0160.0000.0000.0000.000
127A127GLU-1-0.942-0.96228.376-0.153-0.1530.0000.0000.0000.000
128A128TYR0-0.001-0.03430.878-0.006-0.0060.0000.0000.0000.000
129A129LEU00.0140.00623.726-0.003-0.0030.0000.0000.0000.000
130A130MET0-0.038-0.00923.568-0.011-0.0110.0000.0000.0000.000
131A131ALA00.0330.02227.663-0.003-0.0030.0000.0000.0000.000
132A132HIS00.003-0.01628.6390.0010.0010.0000.0000.0000.000
133A133LEU00.013-0.00922.574-0.006-0.0060.0000.0000.0000.000
134A134ASP-1-0.910-0.96726.201-0.226-0.2260.0000.0000.0000.000
135A135ALA0-0.051-0.00828.0140.0040.0040.0000.0000.0000.000
136A136LEU0-0.061-0.02726.3470.0040.0040.0000.0000.0000.000
137A137GLY0-0.0170.00826.475-0.009-0.0090.0000.0000.0000.000
138A138ILE0-0.023-0.02721.354-0.017-0.0170.0000.0000.0000.000
139A139LYS10.9350.99121.0910.1960.1960.0000.0000.0000.000
140A140ASP-1-0.903-0.95920.939-0.294-0.2940.0000.0000.0000.000
141A141LEU0-0.118-0.06817.618-0.015-0.0150.0000.0000.0000.000
142A142PHE0-0.021-0.01015.725-0.083-0.0830.0000.0000.0000.000
143A143ASP-1-0.830-0.90811.795-0.703-0.7030.0000.0000.0000.000
144A144SER0-0.030-0.00914.7610.0260.0260.0000.0000.0000.000
145A145ILE00.0050.00516.519-0.046-0.0460.0000.0000.0000.000
146A146THR0-0.041-0.02718.3140.0390.0390.0000.0000.0000.000
147A147THR00.0140.00820.734-0.017-0.0170.0000.0000.0000.000
148A148SER00.0620.02724.1070.0020.0020.0000.0000.0000.000
149A149GLU-1-0.912-0.93526.389-0.162-0.1620.0000.0000.0000.000
150A150GLU-1-0.871-0.92523.096-0.278-0.2780.0000.0000.0000.000
151A151ALA0-0.024-0.01223.3410.0130.0130.0000.0000.0000.000
152A152GLY0-0.005-0.00525.2020.0180.0180.0000.0000.0000.000
153A153PHE0-0.062-0.03926.3040.0210.0210.0000.0000.0000.000
154A154PHE00.0180.01826.522-0.022-0.0220.0000.0000.0000.000
155A155LYS10.8200.92421.8090.3920.3920.0000.0000.0000.000
156A156PRO0-0.030-0.02823.5350.0180.0180.0000.0000.0000.000
157A157HIS00.0000.00123.170-0.013-0.0130.0000.0000.0000.000
158A158PRO00.0480.01520.678-0.028-0.0280.0000.0000.0000.000
159A159ARG10.9700.98620.1140.1400.1400.0000.0000.0000.000
160A160ILE0-0.0150.00421.229-0.014-0.0140.0000.0000.0000.000
161A161PHE00.0260.01416.669-0.032-0.0320.0000.0000.0000.000
162A162GLU-1-0.943-0.97816.632-0.263-0.2630.0000.0000.0000.000
163A163LEU0-0.025-0.01217.153-0.017-0.0170.0000.0000.0000.000
164A164ALA0-0.0160.00116.043-0.002-0.0020.0000.0000.0000.000
165A165LEU00.0190.01211.260-0.047-0.0470.0000.0000.0000.000
166A166LYS10.9110.94613.0320.2240.2240.0000.0000.0000.000
167A167LYS10.8010.89315.3790.3840.3840.0000.0000.0000.000
168A168ALA0-0.0010.00810.8560.0320.0320.0000.0000.0000.000
169A169GLY0-0.0220.01611.023-0.015-0.0150.0000.0000.0000.000
170A170VAL0-0.062-0.0367.306-0.005-0.0050.0000.0000.0000.000
171A171LYS10.8960.9585.2450.4650.4650.0000.0000.0000.000
172A172GLY00.0710.0278.459-0.346-0.3460.0000.0000.0000.000
173A173GLU-1-0.859-0.9516.595-0.407-0.4070.0000.0000.0000.000
174A174GLU-1-0.892-0.9213.685-2.226-1.7990.000-0.070-0.3580.000
175A175ALA00.006-0.0065.474-1.107-1.1070.0000.0000.0000.000
176A176VAL00.0630.0408.1850.3280.3280.0000.0000.0000.000
177A177TYR0-0.060-0.04810.5610.0680.0680.0000.0000.0000.000
178A178VAL0-0.0030.00014.0850.0540.0540.0000.0000.0000.000
179A179GLY00.0360.00916.6870.0280.0280.0000.0000.0000.000
180A180ASP-1-0.863-0.91920.314-0.311-0.3110.0000.0000.0000.000
181A181ASN00.0390.01823.3260.0440.0440.0000.0000.0000.000
182A182PRO00.047-0.00322.264-0.015-0.0150.0000.0000.0000.000
183A183VAL0-0.0040.00222.344-0.003-0.0030.0000.0000.0000.000
184A184LYS10.9540.96623.5670.2340.2340.0000.0000.0000.000
185A185ASP-1-0.731-0.87020.039-0.397-0.3970.0000.0000.0000.000
186A186CYS0-0.114-0.03218.037-0.057-0.0570.0000.0000.0000.000
187A187GLY00.0250.01518.4160.0030.0030.0000.0000.0000.000
188A188GLY0-0.011-0.01720.2780.0170.0170.0000.0000.0000.000
189A189SER0-0.030-0.01715.396-0.009-0.0090.0000.0000.0000.000
190A190LYS10.9801.00013.5950.2210.2210.0000.0000.0000.000
191A191ASN0-0.049-0.02516.0760.0660.0660.0000.0000.0000.000
192A192LEU0-0.065-0.02514.3400.0420.0420.0000.0000.0000.000
193A193GLY0-0.013-0.00712.199-0.025-0.0250.0000.0000.0000.000
194A194MET0-0.081-0.01810.7660.0410.0410.0000.0000.0000.000
195A195THR0-0.0040.0078.8700.1990.1990.0000.0000.0000.000
196A196SER0-0.040-0.02311.087-0.128-0.1280.0000.0000.0000.000
197A197ILE00.0240.00111.7250.0240.0240.0000.0000.0000.000
198A198LEU0-0.011-0.02415.6630.0100.0100.0000.0000.0000.000
199A199LEU0-0.0250.00819.445-0.001-0.0010.0000.0000.0000.000
200A200ASP-1-0.765-0.90121.468-0.212-0.2120.0000.0000.0000.000
201A201ARG10.8510.90423.2150.3640.3640.0000.0000.0000.000
202A202LYS10.9190.96426.4780.2270.2270.0000.0000.0000.000
203A203GLY0-0.0370.00227.3630.0150.0150.0000.0000.0000.000
204A204GLU-1-0.972-1.00128.330-0.183-0.1830.0000.0000.0000.000
205A205LYS10.8130.88825.3060.3010.3010.0000.0000.0000.000
206A206ARG10.9240.95626.7270.1780.1780.0000.0000.0000.000
207A207GLU-1-0.989-0.97627.398-0.126-0.1260.0000.0000.0000.000
208A208PHE0-0.009-0.02025.8510.0050.0050.0000.0000.0000.000
209A209TRP00.007-0.01222.804-0.012-0.0120.0000.0000.0000.000
210A210ASP-1-0.908-0.93721.457-0.167-0.1670.0000.0000.0000.000
211A211LYS10.8680.94121.4630.1810.1810.0000.0000.0000.000
212A213ASP-1-0.819-0.88313.191-0.378-0.3780.0000.0000.0000.000
213A214PHE00.0160.00510.963-0.004-0.0040.0000.0000.0000.000
214A215ILE0-0.029-0.01116.020-0.005-0.0050.0000.0000.0000.000
215A216VAL0-0.0100.01116.786-0.008-0.0080.0000.0000.0000.000
216A217SER0-0.077-0.03419.8730.0330.0330.0000.0000.0000.000
217A218ASP-1-0.764-0.88820.863-0.400-0.4000.0000.0000.0000.000
218A219LEU00.0550.00717.834-0.051-0.0510.0000.0000.0000.000
219A220ARG10.7980.89116.3480.3020.3020.0000.0000.0000.000
220A221GLU-1-0.874-0.96515.796-0.479-0.4790.0000.0000.0000.000
221A222VAL00.0300.01611.794-0.053-0.0530.0000.0000.0000.000
222A223ILE0-0.040-0.01810.318-0.184-0.1840.0000.0000.0000.000
223A224LYS10.9150.9649.9070.4640.4640.0000.0000.0000.000
224A225ILE00.0650.04310.100-0.027-0.0270.0000.0000.0000.000
225A226VAL0-0.012-0.0085.629-0.065-0.0650.0000.0000.0000.000
226A227ASP-1-0.964-0.9876.235-2.283-2.2830.0000.0000.0000.000
227A228GLU-1-1.019-1.0037.498-0.366-0.3660.0000.0000.0000.000
228A229LEU0-0.064-0.0285.3470.2710.2710.0000.0000.0000.000
229A230ASN0-0.0420.0122.528-4.500-1.9163.860-2.381-4.064-0.032