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: JLRY9

Calculation Name: 4V16-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 4V16

Chain ID: A

ChEMBL ID:

UniProt ID: Q6CN23

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 305
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -4756961.006382
FMO2-HF: Nuclear repulsion 4634009.044019
FMO2-HF: Total energy -122951.962363
FMO2-MP2: Total energy -123311.168204


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:14:SER)


Summations of interaction energy for fragment #1(A:14:SER)
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.
-1.260.103-0.014-0.591-0.7590.002
Interaction energy analysis for fragmet #1(A:14:SER)
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 : -0.003
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].
3A16PRO00.0270.0233.8610.7682.131-0.014-0.591-0.7590.002
4A17ILE0-0.038-0.0276.4440.2680.2680.0000.0000.0000.000
5A18VAL0-0.049-0.01410.049-0.181-0.1810.0000.0000.0000.000
6A19ASP-1-0.774-0.87412.9850.3090.3090.0000.0000.0000.000
7A20TYR0-0.080-0.08614.5110.1630.1630.0000.0000.0000.000
8A21GLU-1-0.747-0.84016.5150.2970.2970.0000.0000.0000.000
9A22PHE0-0.012-0.01419.8270.0470.0470.0000.0000.0000.000
10A23ASN0-0.019-0.01921.993-0.011-0.0110.0000.0000.0000.000
11A24GLN00.014-0.00424.6720.0130.0130.0000.0000.0000.000
12A25ASP-1-0.813-0.86727.7230.2810.2810.0000.0000.0000.000
13A26GLN0-0.031-0.02324.394-0.026-0.0260.0000.0000.0000.000
14A27SER0-0.025-0.01424.3550.0280.0280.0000.0000.0000.000
15A28CYS0-0.053-0.03321.2780.0260.0260.0000.0000.0000.000
16A29LEU00.0040.00215.063-0.018-0.0180.0000.0000.0000.000
17A30ILE0-0.013-0.00117.1660.0450.0450.0000.0000.0000.000
18A31VAL0-0.006-0.01211.7290.0160.0160.0000.0000.0000.000
19A32SER00.021-0.00113.7100.0190.0190.0000.0000.0000.000
20A33THR00.004-0.0078.4920.1310.1310.0000.0000.0000.000
21A34PRO00.010-0.0088.261-0.101-0.1010.0000.0000.0000.000
22A35LYS10.7850.8748.389-0.341-0.3410.0000.0000.0000.000
23A36SER0-0.011-0.00410.5930.0290.0290.0000.0000.0000.000
24A37PHE00.0230.01512.5460.0090.0090.0000.0000.0000.000
25A38ASP-1-0.810-0.86411.1861.2521.2520.0000.0000.0000.000
26A39ILE00.0480.01714.167-0.012-0.0120.0000.0000.0000.000
27A40TYR00.0050.00010.8850.1420.1420.0000.0000.0000.000
28A41ASN00.0490.03717.264-0.078-0.0780.0000.0000.0000.000
29A42VAL0-0.018-0.00618.8640.0670.0670.0000.0000.0000.000
30A43HIS00.0260.01320.4780.0460.0460.0000.0000.0000.000
31A44PRO0-0.0090.00121.997-0.029-0.0290.0000.0000.0000.000
32A45LEU00.000-0.00814.641-0.009-0.0090.0000.0000.0000.000
33A46LYS10.9340.95216.477-0.506-0.5060.0000.0000.0000.000
34A47ARG10.8690.9488.777-1.609-1.6090.0000.0000.0000.000
35A48ILE0-0.077-0.03315.733-0.071-0.0710.0000.0000.0000.000
36A49MET0-0.038-0.00217.405-0.039-0.0390.0000.0000.0000.000
37A50SER0-0.033-0.05012.4420.0880.0880.0000.0000.0000.000
38A51GLN00.023-0.00114.730-0.092-0.0920.0000.0000.0000.000
39A52GLU-1-0.789-0.86812.1770.3610.3610.0000.0000.0000.000
40A53MET0-0.022-0.00414.087-0.075-0.0750.0000.0000.0000.000
41A54PRO00.0280.03214.4110.0360.0360.0000.0000.0000.000
42A55ASP-1-0.835-0.91915.335-0.022-0.0220.0000.0000.0000.000
43A56ALA00.0310.02615.556-0.009-0.0090.0000.0000.0000.000
44A57GLY00.0300.00915.6750.0150.0150.0000.0000.0000.000
45A58THR00.0190.01417.4660.0550.0550.0000.0000.0000.000
46A59ILE0-0.028-0.01517.018-0.028-0.0280.0000.0000.0000.000
47A60ARG10.7870.87720.316-0.286-0.2860.0000.0000.0000.000
48A61MET00.0380.02022.2270.0150.0150.0000.0000.0000.000
49A62LEU00.0230.03724.207-0.016-0.0160.0000.0000.0000.000
50A63HIS00.0430.01627.7740.0020.0020.0000.0000.0000.000
51A64ARG10.8840.92423.833-0.328-0.3280.0000.0000.0000.000
52A65THR0-0.036-0.02327.273-0.008-0.0080.0000.0000.0000.000
53A66ASN0-0.028-0.01426.0150.0210.0210.0000.0000.0000.000
54A67TYR0-0.025-0.00126.509-0.009-0.0090.0000.0000.0000.000
55A68ILE0-0.0040.00320.4500.0180.0180.0000.0000.0000.000
56A69ALA00.0070.01123.765-0.029-0.0290.0000.0000.0000.000
57A70PHE00.002-0.01020.1040.0340.0340.0000.0000.0000.000
58A71VAL00.0660.04021.695-0.027-0.0270.0000.0000.0000.000
59A72SER0-0.070-0.02920.3690.0040.0040.0000.0000.0000.000
60A73THR00.0530.00717.690-0.024-0.0240.0000.0000.0000.000
61A74LYS10.8240.90418.1630.0640.0640.0000.0000.0000.000
62A75LYS10.8340.90521.540-0.088-0.0880.0000.0000.0000.000
63A76GLU-1-0.857-0.92124.3580.0690.0690.0000.0000.0000.000
64A77LEU0-0.0090.00425.289-0.005-0.0050.0000.0000.0000.000
65A78LEU00.0440.03025.0610.0160.0160.0000.0000.0000.000
66A79HIS0-0.011-0.02823.895-0.030-0.0300.0000.0000.0000.000
67A80ILE00.0190.01425.6840.0220.0220.0000.0000.0000.000
68A81TRP0-0.013-0.02021.434-0.021-0.0210.0000.0000.0000.000
69A82ASP-1-0.736-0.87025.6250.1910.1910.0000.0000.0000.000
70A83ASP-1-0.788-0.91121.4160.3570.3570.0000.0000.0000.000
71A84VAL0-0.041-0.02923.9750.0150.0150.0000.0000.0000.000
72A85LYS10.8500.91426.726-0.153-0.1530.0000.0000.0000.000
73A86LYS10.7590.89220.339-0.348-0.3480.0000.0000.0000.000
74A87GLN00.0240.01424.568-0.013-0.0130.0000.0000.0000.000
75A88ASP-1-0.785-0.86525.2570.1490.1490.0000.0000.0000.000
76A89ILE0-0.057-0.02627.394-0.011-0.0110.0000.0000.0000.000
77A90THR0-0.007-0.01629.922-0.010-0.0100.0000.0000.0000.000
78A91ARG10.8300.90027.247-0.071-0.0710.0000.0000.0000.000
79A92VAL00.0130.01829.657-0.010-0.0100.0000.0000.0000.000
80A93LYS10.8100.89728.927-0.033-0.0330.0000.0000.0000.000
81A94LEU0-0.0130.01027.0390.0050.0050.0000.0000.0000.000
82A95ASP-1-0.859-0.93530.8920.0430.0430.0000.0000.0000.000
83A96ALA0-0.053-0.03130.074-0.010-0.0100.0000.0000.0000.000
84A97ALA00.0340.02824.9770.0100.0100.0000.0000.0000.000
85A98VAL0-0.027-0.01824.4940.0000.0000.0000.0000.0000.000
86A99LYS10.8190.91424.492-0.078-0.0780.0000.0000.0000.000
87A100ASP-1-0.821-0.90624.9660.2400.2400.0000.0000.0000.000
88A101LEU0-0.055-0.02624.065-0.018-0.0180.0000.0000.0000.000
89A102PHE00.0360.01326.4980.0210.0210.0000.0000.0000.000
90A103LEU0-0.004-0.00526.293-0.013-0.0130.0000.0000.0000.000
91A104SER0-0.025-0.02530.0870.0040.0040.0000.0000.0000.000
92A105ARG10.8750.91833.005-0.146-0.1460.0000.0000.0000.000
93A106GLU-1-0.795-0.88235.0780.1310.1310.0000.0000.0000.000
94A107PHE00.0190.00635.886-0.006-0.0060.0000.0000.0000.000
95A108ILE0-0.021-0.00130.2650.0150.0150.0000.0000.0000.000
96A109VAL00.0000.00731.511-0.012-0.0120.0000.0000.0000.000
97A110VAL00.028-0.00128.4140.0170.0170.0000.0000.0000.000
98A111SER00.0130.01629.044-0.016-0.0160.0000.0000.0000.000
99A112GLN00.031-0.00128.7040.0080.0080.0000.0000.0000.000
100A113GLY00.0560.01629.466-0.008-0.0080.0000.0000.0000.000
101A114ASP-1-0.936-0.95631.0670.0550.0550.0000.0000.0000.000
102A115VAL00.0020.00333.688-0.003-0.0030.0000.0000.0000.000
103A116ILE0-0.021-0.00233.3380.0090.0090.0000.0000.0000.000
104A117SER00.015-0.00533.649-0.006-0.0060.0000.0000.0000.000
105A118ILE0-0.025-0.02134.1990.0110.0110.0000.0000.0000.000
106A119PHE00.015-0.00633.028-0.008-0.0080.0000.0000.0000.000
107A120LYS10.8990.94636.125-0.081-0.0810.0000.0000.0000.000
108A121PHE0-0.020-0.00530.2900.0040.0040.0000.0000.0000.000
109A122GLY00.0430.00534.880-0.004-0.0040.0000.0000.0000.000
110A123ASN00.0000.01036.535-0.005-0.0050.0000.0000.0000.000
111A124PRO0-0.028-0.01338.6320.0000.0000.0000.0000.0000.000
112A125TRP00.0220.00732.3460.0000.0000.0000.0000.0000.000
113A126ASN00.0030.00236.4190.0030.0030.0000.0000.0000.000
114A127LYS10.8730.92037.662-0.054-0.0540.0000.0000.0000.000
115A128ILE0-0.046-0.02038.933-0.004-0.0040.0000.0000.0000.000
116A129THR0-0.0140.00040.345-0.002-0.0020.0000.0000.0000.000
117A130GLU-1-0.845-0.90041.5070.0520.0520.0000.0000.0000.000
118A131ASP-1-0.798-0.88137.6600.0720.0720.0000.0000.0000.000
119A132ILE0-0.018-0.00538.417-0.004-0.0040.0000.0000.0000.000
120A133LYS10.8790.94737.758-0.040-0.0400.0000.0000.0000.000
121A134PHE0-0.007-0.00831.5750.0030.0030.0000.0000.0000.000
122A135GLY00.0230.01736.530-0.003-0.0030.0000.0000.0000.000
123A136GLY0-0.075-0.03832.6290.0010.0010.0000.0000.0000.000
124A137VAL0-0.016-0.01130.7720.0090.0090.0000.0000.0000.000
125A138CYS0-0.025-0.01930.868-0.009-0.0090.0000.0000.0000.000
126A139GLU-1-0.831-0.88729.9780.2030.2030.0000.0000.0000.000
127A140PHE0-0.003-0.00231.732-0.013-0.0130.0000.0000.0000.000
128A141ALA00.0140.00631.9360.0150.0150.0000.0000.0000.000
129A142ASN0-0.056-0.03933.848-0.008-0.0080.0000.0000.0000.000
130A143GLY00.0470.02936.507-0.007-0.0070.0000.0000.0000.000
131A144LEU0-0.065-0.02337.530-0.010-0.0100.0000.0000.0000.000
132A145LEU00.0000.01035.5430.0100.0100.0000.0000.0000.000
133A146VAL00.007-0.00136.294-0.007-0.0070.0000.0000.0000.000
134A147TYR00.0140.00735.6700.0060.0060.0000.0000.0000.000
135A148SER00.0200.01635.908-0.004-0.0040.0000.0000.0000.000
136A149ASN00.022-0.00138.044-0.004-0.0040.0000.0000.0000.000
137A150GLU-1-0.876-0.96039.2330.0500.0500.0000.0000.0000.000
138A151PHE00.0050.01740.093-0.003-0.0030.0000.0000.0000.000
139A152ASN0-0.028-0.00842.138-0.002-0.0020.0000.0000.0000.000
140A153LEU00.0280.00636.6910.0040.0040.0000.0000.0000.000
141A154GLY0-0.020-0.00638.3990.0060.0060.0000.0000.0000.000
142A155GLN0-0.054-0.03740.7780.0010.0010.0000.0000.0000.000
143A156ILE00.0000.00038.0480.0020.0020.0000.0000.0000.000
144A157HIS00.0140.02340.507-0.007-0.0070.0000.0000.0000.000
145A158VAL00.009-0.00240.4490.0070.0070.0000.0000.0000.000
146A159THR0-0.003-0.00140.907-0.006-0.0060.0000.0000.0000.000
147A160ARG10.9540.97141.147-0.100-0.1000.0000.0000.0000.000
148A161LEU0-0.0180.00637.734-0.004-0.0040.0000.0000.0000.000
149A162GLN0-0.100-0.07142.0450.0020.0020.0000.0000.0000.000
150A163THR0-0.038-0.04544.8030.0020.0020.0000.0000.0000.000
151A164ASP-1-0.833-0.89247.4280.0710.0710.0000.0000.0000.000
152A165ALA00.0090.01748.333-0.003-0.0030.0000.0000.0000.000
153A166GLU-1-0.814-0.90048.4370.0590.0590.0000.0000.0000.000
154A167GLN0-0.050-0.03447.1080.0020.0020.0000.0000.0000.000
155A168VAL0-0.014-0.00142.2500.0030.0030.0000.0000.0000.000
156A169VAL0-0.030-0.02141.3240.0060.0060.0000.0000.0000.000
157A170GLY00.0420.03043.8520.0010.0010.0000.0000.0000.000
158A171LYS10.8400.89646.394-0.063-0.0630.0000.0000.0000.000
159A172GLY00.0480.02246.4570.0010.0010.0000.0000.0000.000
160A173VAL0-0.0060.02045.608-0.004-0.0040.0000.0000.0000.000
161A174LEU0-0.006-0.00145.1580.0020.0020.0000.0000.0000.000
162A175VAL00.0430.03043.466-0.003-0.0030.0000.0000.0000.000
163A176LYS10.8340.92443.331-0.059-0.0590.0000.0000.0000.000
164A177ALA00.0310.03040.537-0.001-0.0010.0000.0000.0000.000
165A178HIS00.0600.02538.7940.0050.0050.0000.0000.0000.000
166A179ALA0-0.0100.00141.836-0.003-0.0030.0000.0000.0000.000
167A180ASN00.013-0.02438.440-0.006-0.0060.0000.0000.0000.000
168A181PRO00.0070.00335.9490.0040.0040.0000.0000.0000.000
169A182VAL00.004-0.00334.3620.0030.0030.0000.0000.0000.000
170A183LYS10.8380.93127.680-0.128-0.1280.0000.0000.0000.000
171A184MET0-0.025-0.01027.5230.0070.0070.0000.0000.0000.000
172A185VAL00.0290.00631.336-0.010-0.0100.0000.0000.0000.000
173A186ARG10.8170.88225.647-0.218-0.2180.0000.0000.0000.000
174A187LEU00.0260.02532.712-0.010-0.0100.0000.0000.0000.000
175A188ASN0-0.016-0.01333.4860.0150.0150.0000.0000.0000.000
176A189ARG10.8750.92128.795-0.235-0.2350.0000.0000.0000.000
177A190LYS10.8760.95534.835-0.132-0.1320.0000.0000.0000.000
178A191GLY00.0370.02238.257-0.003-0.0030.0000.0000.0000.000
179A192ASP-1-0.807-0.87739.0870.1150.1150.0000.0000.0000.000
180A193MET0-0.032-0.01139.733-0.005-0.0050.0000.0000.0000.000
181A194VAL00.0050.00436.6030.0090.0090.0000.0000.0000.000
182A195ALA00.0010.01534.466-0.007-0.0070.0000.0000.0000.000
183A196THR0-0.018-0.01635.2330.0030.0030.0000.0000.0000.000
184A197CYS00.0130.01332.6370.0000.0000.0000.0000.0000.000
185A198SER00.0540.03234.968-0.001-0.0010.0000.0000.0000.000
186A199GLN00.010-0.01231.2620.0110.0110.0000.0000.0000.000
187A200ASP-1-0.829-0.89332.7000.0720.0720.0000.0000.0000.000
188A201GLY00.0350.02232.7780.0010.0010.0000.0000.0000.000
189A202THR0-0.029-0.01433.8030.0060.0060.0000.0000.0000.000
190A203LEU0-0.018-0.01036.9240.0010.0010.0000.0000.0000.000
191A204ILE0-0.028-0.01233.6370.0030.0030.0000.0000.0000.000
192A205ARG10.7780.87437.396-0.081-0.0810.0000.0000.0000.000
193A206VAL00.0150.00238.2840.0080.0080.0000.0000.0000.000
194A207PHE0-0.010-0.00540.360-0.007-0.0070.0000.0000.0000.000
195A208GLN00.001-0.00741.8790.0050.0050.0000.0000.0000.000
196A209THR0-0.081-0.06140.384-0.005-0.0050.0000.0000.0000.000
197A210ASP-1-0.874-0.92543.5220.0890.0890.0000.0000.0000.000
198A211ASN0-0.009-0.02447.109-0.001-0.0010.0000.0000.0000.000
199A212GLY00.0150.01745.364-0.003-0.0030.0000.0000.0000.000
200A213VAL0-0.029-0.00946.449-0.001-0.0010.0000.0000.0000.000
201A214LEU0-0.014-0.01643.7180.0050.0050.0000.0000.0000.000
202A215VAL00.0140.01743.604-0.003-0.0030.0000.0000.0000.000
203A216ARG10.8490.90941.959-0.097-0.0970.0000.0000.0000.000
204A217GLU-1-0.791-0.87941.7650.0810.0810.0000.0000.0000.000
205A218PHE00.0170.02538.141-0.002-0.0020.0000.0000.0000.000
206A219ARG10.8460.91839.160-0.081-0.0810.0000.0000.0000.000
207A220ARG10.8580.93131.558-0.119-0.1190.0000.0000.0000.000
208A221GLY00.0180.00035.2250.0040.0040.0000.0000.0000.000
209A222LEU0-0.026-0.00336.960-0.004-0.0040.0000.0000.0000.000
210A223ASP-1-0.799-0.89434.0860.0930.0930.0000.0000.0000.000
211A224ARG10.8900.93534.764-0.055-0.0550.0000.0000.0000.000
212A225THR0-0.061-0.02529.930-0.001-0.0010.0000.0000.0000.000
213A226SER0-0.055-0.05726.8880.0040.0040.0000.0000.0000.000
214A227ILE0-0.014-0.02227.1620.0100.0100.0000.0000.0000.000
215A228ILE0-0.058-0.01821.581-0.006-0.0060.0000.0000.0000.000
216A229ASP-1-0.679-0.82223.6530.3050.3050.0000.0000.0000.000
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