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

tag_button

FMODB ID: M9MGZ

Calculation Name: 2D3V-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2D3V

Chain ID: A

ChEMBL ID:

UniProt ID: A6NI73

Base Structure: X-ray

Registration Date: 2023-09-26

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 OptHSide
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 180
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -1864007.233107
FMO2-HF: Nuclear repulsion 1791441.955456
FMO2-HF: Total energy -72565.277651
FMO2-MP2: Total energy -72777.252157


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:3:LEU)


Summations of interaction energy for fragment #1(A:3:LEU)
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.
-4.604-0.2771.859-2.54-3.646-0.003
Interaction energy analysis for fragmet #1(A:3:LEU)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.036 / q_NPA : 0.020
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].
3A5LYS10.8730.9233.828-0.1882.344-0.019-1.319-1.1940.007
4A6ALA00.0050.0076.2260.2390.2390.0000.0000.0000.000
5A7THR0-0.048-0.0199.797-0.072-0.0720.0000.0000.0000.000
6A8LEU00.0170.00012.8180.0800.0800.0000.0000.0000.000
7A9TRP0-0.068-0.04715.763-0.009-0.0090.0000.0000.0000.000
8A10ALA00.0220.00319.3270.0140.0140.0000.0000.0000.000
9A11GLU-1-0.828-0.86222.946-0.259-0.2590.0000.0000.0000.000
10A12PRO00.036-0.00225.9880.0060.0060.0000.0000.0000.000
11A13GLY00.0460.00725.953-0.003-0.0030.0000.0000.0000.000
12A14SER0-0.010-0.00323.4830.0050.0050.0000.0000.0000.000
13A15VAL00.0120.01325.5370.0020.0020.0000.0000.0000.000
14A16ILE0-0.020-0.00428.7210.0070.0070.0000.0000.0000.000
15A17SER00.0490.03131.3610.0020.0020.0000.0000.0000.000
16A18ARG10.8980.94634.6020.1040.1040.0000.0000.0000.000
17A19GLY0-0.053-0.02635.2730.0060.0060.0000.0000.0000.000
18A20ASN0-0.013-0.00134.3650.0070.0070.0000.0000.0000.000
19A21SER0-0.031-0.02931.943-0.002-0.0020.0000.0000.0000.000
20A22VAL0-0.013-0.00126.085-0.004-0.0040.0000.0000.0000.000
21A23THR0-0.053-0.02724.3050.0080.0080.0000.0000.0000.000
22A24ILE00.0360.02619.698-0.014-0.0140.0000.0000.0000.000
23A25ARG10.8220.89919.9480.2790.2790.0000.0000.0000.000
24A26CYS00.0050.01313.1570.0190.0190.0000.0000.0000.000
25A27GLN0-0.023-0.01013.9320.1170.1170.0000.0000.0000.000
26A28GLY00.0480.01711.178-0.138-0.1380.0000.0000.0000.000
27A29THR0-0.049-0.0589.114-0.038-0.0380.0000.0000.0000.000
28A30LEU00.016-0.00712.2660.0220.0220.0000.0000.0000.000
29A31GLU-1-0.856-0.90311.582-0.152-0.1520.0000.0000.0000.000
30A32ALA0-0.052-0.00312.6880.0270.0270.0000.0000.0000.000
31A33GLN0-0.046-0.04513.7620.0460.0460.0000.0000.0000.000
32A34GLU-1-0.820-0.90214.977-0.172-0.1720.0000.0000.0000.000
33A35TYR0-0.049-0.05013.676-0.080-0.0800.0000.0000.0000.000
34A36ARG10.9110.94814.5140.2900.2900.0000.0000.0000.000
35A37LEU0-0.023-0.00314.960-0.071-0.0710.0000.0000.0000.000
36A38VAL00.0230.00415.0970.0380.0380.0000.0000.0000.000
37A39LYS10.8660.93917.6440.1670.1670.0000.0000.0000.000
38A40GLU-1-0.774-0.85317.919-0.321-0.3210.0000.0000.0000.000
39A41GLY0-0.003-0.00420.4250.0150.0150.0000.0000.0000.000
40A42SER0-0.050-0.02621.8270.0230.0230.0000.0000.0000.000
41A43PRO0-0.011-0.00720.770-0.017-0.0170.0000.0000.0000.000
42A44GLU-1-0.941-0.95419.934-0.129-0.1290.0000.0000.0000.000
43A45PRO0-0.065-0.05218.190-0.017-0.0170.0000.0000.0000.000
44A46TRP00.0050.00820.0000.0150.0150.0000.0000.0000.000
45A47ASP-1-0.829-0.91620.407-0.183-0.1830.0000.0000.0000.000
46A48THR0-0.089-0.05918.634-0.033-0.0330.0000.0000.0000.000
47A49GLN00.0070.00719.1160.0090.0090.0000.0000.0000.000
48A50ASN00.000-0.00718.828-0.021-0.0210.0000.0000.0000.000
49A51PRO0-0.0250.01218.5290.0190.0190.0000.0000.0000.000
50A52LEU00.013-0.01921.2470.0100.0100.0000.0000.0000.000
51A53GLU-1-0.925-0.97822.165-0.129-0.1290.0000.0000.0000.000
52A54PRO00.0110.03720.4110.0020.0020.0000.0000.0000.000
53A55LYS10.9000.95516.8900.1280.1280.0000.0000.0000.000
54A56ASN00.0160.01815.069-0.007-0.0070.0000.0000.0000.000
55A57LYS10.8860.93815.8780.2970.2970.0000.0000.0000.000
56A58ALA00.0480.04917.6720.0330.0330.0000.0000.0000.000
57A59ARG10.9140.94919.2780.1560.1560.0000.0000.0000.000
58A60PHE00.0060.00317.7720.0130.0130.0000.0000.0000.000
59A61SER00.0040.00023.192-0.005-0.0050.0000.0000.0000.000
60A62ILE00.0220.01025.4390.0070.0070.0000.0000.0000.000
61A63PRO00.005-0.00428.8590.0020.0020.0000.0000.0000.000
62A64SER00.0010.01032.5050.0050.0050.0000.0000.0000.000
63A65MET0-0.0120.01228.155-0.004-0.0040.0000.0000.0000.000
64A66THR00.015-0.01231.5560.0110.0110.0000.0000.0000.000
65A67GLU-1-0.805-0.92931.306-0.121-0.1210.0000.0000.0000.000
66A68HIS0-0.009-0.00530.269-0.014-0.0140.0000.0000.0000.000
67A69HIS00.1040.07327.203-0.006-0.0060.0000.0000.0000.000
68A70ALA00.0050.04526.062-0.020-0.0200.0000.0000.0000.000
69A71GLY00.003-0.01424.4590.0080.0080.0000.0000.0000.000
70A72ARG10.7860.85917.7090.3170.3170.0000.0000.0000.000
71A73TYR0-0.037-0.03618.3670.0110.0110.0000.0000.0000.000
72A74ARG10.8650.92412.1470.4760.4760.0000.0000.0000.000
73A76TYR00.0280.0209.034-0.116-0.1160.0000.0000.0000.000
74A77TYR00.0480.0177.645-0.026-0.0260.0000.0000.0000.000
75A78TYR00.0390.0299.661-0.076-0.0760.0000.0000.0000.000
76A79SER0-0.001-0.0069.1380.0360.0360.0000.0000.0000.000
77A80PRO00.0510.01711.1070.0230.0230.0000.0000.0000.000
78A81ALA0-0.0320.0006.3840.0650.0650.0000.0000.0000.000
79A82GLY00.0050.0136.8310.1080.1080.0000.0000.0000.000
80A83TRP0-0.066-0.0498.200-0.059-0.0590.0000.0000.0000.000
81A84SER0-0.046-0.0165.3840.0000.0000.0000.0000.0000.000
82A85GLU-1-0.875-0.9482.391-4.361-2.6021.879-1.219-2.419-0.010
83A86PRO0-0.025-0.0125.0190.1790.215-0.001-0.002-0.0330.000
84A87SER0-0.025-0.0128.301-0.171-0.1710.0000.0000.0000.000
85A88ASP-1-0.847-0.91710.594-1.001-1.0010.0000.0000.0000.000
86A89PRO0-0.053-0.02012.3430.0460.0460.0000.0000.0000.000
87A90LEU00.0130.01715.5400.0130.0130.0000.0000.0000.000
88A91GLU-1-0.861-0.91718.513-0.242-0.2420.0000.0000.0000.000
89A92LEU0-0.039-0.01721.7340.0060.0060.0000.0000.0000.000
90A93VAL00.0180.00024.5150.0090.0090.0000.0000.0000.000
91A94VAL0-0.0110.01427.9860.0020.0020.0000.0000.0000.000
92A95THR0-0.019-0.00731.3890.0040.0040.0000.0000.0000.000
93A96GLY00.0830.01834.5800.0020.0020.0000.0000.0000.000
94A97PHE0-0.054-0.02234.6480.0060.0060.0000.0000.0000.000
95A98TYR0-0.046-0.02735.2820.0070.0070.0000.0000.0000.000
96A99ASN00.0390.00940.722-0.003-0.0030.0000.0000.0000.000
97A100LYS10.8640.94341.6320.0770.0770.0000.0000.0000.000
98A101PRO0-0.054-0.01139.7820.0050.0050.0000.0000.0000.000
99A102THR0-0.018-0.01443.0810.0010.0010.0000.0000.0000.000
100A103LEU00.029-0.01140.207-0.001-0.0010.0000.0000.0000.000
101A104SER00.0020.00443.9470.0020.0020.0000.0000.0000.000
102A105ALA00.0260.02445.221-0.001-0.0010.0000.0000.0000.000
103A117VAL00.0390.01942.7340.0010.0010.0000.0000.0000.000
104A118THR0-0.042-0.03942.261-0.005-0.0050.0000.0000.0000.000
105A119LEU00.0060.01339.9180.0030.0030.0000.0000.0000.000
106A120GLN00.015-0.00341.843-0.001-0.0010.0000.0000.0000.000
107A121CYS0-0.0510.00036.741-0.004-0.0040.0000.0000.0000.000
108A122GLY00.0320.00241.7340.0010.0010.0000.0000.0000.000
109A123SER0-0.016-0.01843.4940.0010.0010.0000.0000.0000.000
110A124ARG10.9630.98445.2020.0580.0580.0000.0000.0000.000
111A125LEU0-0.0340.00142.9940.0010.0010.0000.0000.0000.000
112A126ARG10.8670.92137.9410.0830.0830.0000.0000.0000.000
113A127PHE00.0010.01937.981-0.004-0.0040.0000.0000.0000.000
114A128ASP-1-0.757-0.83434.944-0.094-0.0940.0000.0000.0000.000
115A129ARG10.9080.95827.1870.1530.1530.0000.0000.0000.000
116A130PHE0-0.020-0.00734.7690.0040.0040.0000.0000.0000.000
117A131ILE0-0.014-0.00830.596-0.003-0.0030.0000.0000.0000.000
118A132LEU00.0120.02033.5360.0050.0050.0000.0000.0000.000
119A133THR0-0.021-0.03531.446-0.011-0.0110.0000.0000.0000.000
120A134GLU-1-0.806-0.90432.792-0.111-0.1110.0000.0000.0000.000
121A135GLU-1-0.830-0.90633.194-0.125-0.1250.0000.0000.0000.000
122A136GLY0-0.011-0.02533.967-0.001-0.0010.0000.0000.0000.000
123A137ASP-1-0.897-0.91635.048-0.113-0.1130.0000.0000.0000.000
124A138HIS0-0.056-0.03032.623-0.011-0.0110.0000.0000.0000.000
125A139LYS10.9290.95725.8650.2170.2170.0000.0000.0000.000
126A140LEU0-0.006-0.00427.413-0.015-0.0150.0000.0000.0000.000
127A141SER0-0.040-0.02227.7610.0060.0060.0000.0000.0000.000
128A142TRP00.0430.03929.234-0.007-0.0070.0000.0000.0000.000
129A143THR0-0.015-0.01129.1000.0040.0040.0000.0000.0000.000
130A144LEU0-0.0040.00631.0800.0010.0010.0000.0000.0000.000
131A145ASP-1-0.766-0.85532.358-0.123-0.1230.0000.0000.0000.000
132A146SER0-0.076-0.05034.8890.0030.0030.0000.0000.0000.000
133A147GLN00.000-0.00738.402-0.001-0.0010.0000.0000.0000.000
134A148LEU00.0170.00541.5010.0000.0000.0000.0000.0000.000
135A149THR00.0210.01444.7200.0020.0020.0000.0000.0000.000
136A150PRO00.0430.01247.8680.0000.0000.0000.0000.0000.000
137A151SER0-0.024-0.00850.8920.0010.0010.0000.0000.0000.000
138A152GLY0-0.030-0.01548.9650.0000.0000.0000.0000.0000.000
139A153GLN0-0.022-0.00147.3080.0010.0010.0000.0000.0000.000
140A154PHE00.0480.02141.8370.0000.0000.0000.0000.0000.000
141A155GLN0-0.004-0.02642.2700.0010.0010.0000.0000.0000.000
142A156ALA00.0460.02537.932-0.001-0.0010.0000.0000.0000.000
143A157LEU0-0.023-0.01339.8600.0020.0020.0000.0000.0000.000
144A158PHE00.0360.00234.253-0.002-0.0020.0000.0000.0000.000
145A159PRO0-0.0010.00337.3200.0030.0030.0000.0000.0000.000
146A160VAL00.0040.02037.388-0.005-0.0050.0000.0000.0000.000
147A161GLY00.017-0.00537.160-0.006-0.0060.0000.0000.0000.000
148A162PRO0-0.0390.00737.3220.0060.0060.0000.0000.0000.000
149A163VAL00.0480.02040.132-0.003-0.0030.0000.0000.0000.000
150A164THR00.017-0.00141.3450.0050.0050.0000.0000.0000.000
151A165PRO0-0.013-0.01043.485-0.002-0.0020.0000.0000.0000.000
152A166SER0-0.026-0.02041.4690.0000.0000.0000.0000.0000.000
153A167HIS00.0030.00037.497-0.001-0.0010.0000.0000.0000.000
154A168ARG10.9100.96740.0210.0760.0760.0000.0000.0000.000
155A169TRP0-0.019-0.00434.785-0.006-0.0060.0000.0000.0000.000
156A170MET00.004-0.00838.3790.0050.0050.0000.0000.0000.000
157A171LEU00.0330.01936.519-0.006-0.0060.0000.0000.0000.000
158A172ARG10.8440.91937.3980.1100.1100.0000.0000.0000.000
159A174TYR00.0560.03134.0240.0050.0050.0000.0000.0000.000
160A175GLY00.0460.01836.3600.0000.0000.0000.0000.0000.000
161A176SER0-0.003-0.00432.713-0.005-0.0050.0000.0000.0000.000
162A177ARG10.8620.90334.2080.1000.1000.0000.0000.0000.000
163A178ARG10.7800.84731.0350.1120.1120.0000.0000.0000.000
164A179HIS0-0.0040.00230.752-0.007-0.0070.0000.0000.0000.000
165A180ILE0-0.009-0.00129.859-0.005-0.0050.0000.0000.0000.000
166A181LEU00.0230.01226.5580.0020.0020.0000.0000.0000.000
167A182GLN0-0.046-0.02624.9000.0090.0090.0000.0000.0000.000
168A183VAL00.0160.01928.365-0.001-0.0010.0000.0000.0000.000
169A184TRP0-0.015-0.02628.6580.0060.0060.0000.0000.0000.000
170A185SER0-0.034-0.03134.1390.0020.0020.0000.0000.0000.000
171A186GLU-1-0.871-0.94537.001-0.106-0.1060.0000.0000.0000.000
172A187PRO0-0.0140.01737.5240.0010.0010.0000.0000.0000.000
173A188SER0-0.005-0.01239.1420.0040.0040.0000.0000.0000.000
174A189ASP-1-0.861-0.93141.657-0.081-0.0810.0000.0000.0000.000
175A190LEU0-0.030-0.00240.499-0.002-0.0020.0000.0000.0000.000
176A191LEU0-0.024-0.01242.1560.0050.0050.0000.0000.0000.000
177A192GLU-1-0.908-0.94942.359-0.087-0.0870.0000.0000.0000.000
178A193ILE0-0.048-0.00542.8620.0050.0050.0000.0000.0000.000
179A194PRO0-0.020-0.02843.526-0.003-0.0030.0000.0000.0000.000
180A195VAL00.0200.00846.8950.0030.0030.0000.0000.0000.000