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

tag_button

FMODB ID: 9MY32

Calculation Name: 2BA0-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2BA0

Chain ID: A

ChEMBL ID:

UniProt ID: O29757

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 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 218
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2379783.142507
FMO2-HF: Nuclear repulsion 2296048.341979
FMO2-HF: Total energy -83734.800528
FMO2-MP2: Total energy -83982.094283


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:2:ARG)


Summations of interaction energy for fragment #1(A:2:ARG)
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.
18.60623.28321.178-10.954-14.897-0.104
Interaction energy analysis for fragmet #1(A:2:ARG)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 1 / q_Mulliken : 0.912 / q_NPA : 0.947
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].
3A4ILE00.0320.0113.895-4.602-2.731-0.009-0.890-0.9710.004
4A5VAL0-0.051-0.0216.1182.2612.2610.0000.0000.0000.000
5A6LEU00.0380.0118.5120.0570.0570.0000.0000.0000.000
6A7PRO0-0.048-0.02212.098-0.319-0.3190.0000.0000.0000.000
7A8GLY00.0630.02914.6480.9910.9910.0000.0000.0000.000
8A9ASP-1-0.841-0.93110.678-22.973-22.9730.0000.0000.0000.000
9A10LEU0-0.031-0.01712.897-0.589-0.5890.0000.0000.0000.000
10A11LEU0-0.073-0.0328.419-1.259-1.2590.0000.0000.0000.000
11A12SER00.0230.00210.691-0.359-0.3590.0000.0000.0000.000
12A13THR00.0200.00213.2721.0741.0740.0000.0000.0000.000
13A14ASN00.0250.02014.5590.2820.2820.0000.0000.0000.000
14A15PRO00.0590.01316.191-0.816-0.8160.0000.0000.0000.000
15A16ARG10.9220.96017.22213.41313.4130.0000.0000.0000.000
16A17ALA00.0310.03812.9500.0700.0700.0000.0000.0000.000
17A18ALA0-0.0020.01112.552-2.036-2.0360.0000.0000.0000.000
18A19GLY00.0450.02111.8050.6120.6120.0000.0000.0000.000
19A20TYR0-0.031-0.02510.4470.1360.1360.0000.0000.0000.000
20A21GLY00.0390.01710.168-2.256-2.2560.0000.0000.0000.000
21A22THR0-0.041-0.02210.4880.4140.4140.0000.0000.0000.000
22A23TYR0-0.077-0.05413.0350.5750.5750.0000.0000.0000.000
23A24VAL00.0210.00916.104-0.709-0.7090.0000.0000.0000.000
24A25GLU-1-0.836-0.90618.664-12.787-12.7870.0000.0000.0000.000
25A26GLY00.0200.00821.070-0.310-0.3100.0000.0000.0000.000
26A27GLY0-0.017-0.00621.9940.0930.0930.0000.0000.0000.000
27A28LYS10.9250.97017.63013.50213.5020.0000.0000.0000.000
28A29VAL00.0050.00412.7330.2970.2970.0000.0000.0000.000
29A30TYR00.0550.02713.889-0.671-0.6710.0000.0000.0000.000
30A31ALA00.0330.01510.477-0.442-0.4420.0000.0000.0000.000
31A32LYS10.8740.92812.36220.30620.3060.0000.0000.0000.000
32A33ILE0-0.047-0.01710.8231.1511.1510.0000.0000.0000.000
33A34ILE00.0260.02210.764-0.837-0.8370.0000.0000.0000.000
34A35GLY00.001-0.0137.9150.5230.5230.0000.0000.0000.000
35A36LEU0-0.018-0.0032.192-2.745-1.1132.194-0.947-2.878-0.004
36A37PHE00.0030.0083.868-2.015-1.3270.007-0.148-0.5460.000
37A38ASP-1-0.856-0.9221.723-119.026-119.48017.795-8.659-8.682-0.104
38A39GLN00.0300.0083.3229.98910.0110.0290.121-0.172-0.001
39A40THR0-0.024-0.0146.028-1.210-1.2100.0000.0000.0000.000
40A41GLU-1-0.909-0.9558.316-18.333-18.3330.0000.0000.0000.000
41A42THR0-0.035-0.01410.6271.5411.5410.0000.0000.0000.000
42A43HIS0-0.073-0.0305.1906.1356.1350.0000.0000.0000.000
43A44VAL00.0150.0058.466-2.388-2.3880.0000.0000.0000.000
44A45ARG10.8720.9266.62133.79733.7970.0000.0000.0000.000
45A46VAL00.0180.0106.216-2.973-2.9730.0000.0000.0000.000
46A47ILE0-0.0090.0002.9591.8652.7831.162-0.431-1.6480.001
47A48PRO00.0190.0126.8070.0340.0340.0000.0000.0000.000
48A49LEU00.0220.0067.748-1.526-1.5260.0000.0000.0000.000
49A50LYS10.9300.96110.85818.59218.5920.0000.0000.0000.000
50A51GLY00.0180.01314.635-0.382-0.3820.0000.0000.0000.000
51A52ARG10.9570.98317.44513.37313.3730.0000.0000.0000.000
52A53TYR00.009-0.03116.843-0.244-0.2440.0000.0000.0000.000
53A54THR0-0.015-0.00916.1360.4750.4750.0000.0000.0000.000
54A55PRO0-0.0020.02016.849-1.022-1.0220.0000.0000.0000.000
55A56SER0-0.061-0.05015.277-0.270-0.2700.0000.0000.0000.000
56A57VAL00.027-0.00317.2660.5840.5840.0000.0000.0000.000
57A58GLY00.0160.01417.627-0.687-0.6870.0000.0000.0000.000
58A59ASP-1-0.792-0.83716.089-18.801-18.8010.0000.0000.0000.000
59A60VAL0-0.001-0.00618.2850.9550.9550.0000.0000.0000.000
60A61VAL0-0.013-0.00419.516-0.691-0.6910.0000.0000.0000.000
61A62ILE0-0.024-0.00922.1890.4980.4980.0000.0000.0000.000
62A63GLY00.0450.02024.939-0.321-0.3210.0000.0000.0000.000
63A64ILE0-0.021-0.00327.7810.2110.2110.0000.0000.0000.000
64A65ILE0-0.015-0.00431.455-0.148-0.1480.0000.0000.0000.000
65A66ARG10.9010.93832.8009.6619.6610.0000.0000.0000.000
66A67GLU-1-0.920-0.96735.564-8.006-8.0060.0000.0000.0000.000
67A68VAL0-0.017-0.00637.533-0.213-0.2130.0000.0000.0000.000
68A69ALA00.0250.02140.0630.1830.1830.0000.0000.0000.000
69A70ALA00.005-0.00941.477-0.051-0.0510.0000.0000.0000.000
70A71ASN00.0290.00838.3840.1260.1260.0000.0000.0000.000
71A72GLY0-0.010-0.01136.836-0.228-0.2280.0000.0000.0000.000
72A73TRP0-0.0080.00234.8110.1320.1320.0000.0000.0000.000
73A74ALA00.0260.02433.689-0.322-0.3220.0000.0000.0000.000
74A75VAL0-0.037-0.02528.8680.0970.0970.0000.0000.0000.000
75A76ASP-1-0.834-0.91329.082-10.981-10.9810.0000.0000.0000.000
76A77ILE00.016-0.00323.299-0.181-0.1810.0000.0000.0000.000
77A78TYR0-0.052-0.01822.116-0.460-0.4600.0000.0000.0000.000
78A79SER0-0.055-0.01822.434-0.718-0.7180.0000.0000.0000.000
79A80PRO0-0.024-0.01522.9820.4500.4500.0000.0000.0000.000
80A81TYR0-0.018-0.00421.2610.0200.0200.0000.0000.0000.000
81A82GLN00.0310.01725.8510.2020.2020.0000.0000.0000.000
82A83ALA00.0110.00027.162-0.273-0.2730.0000.0000.0000.000
83A84PHE0-0.0030.01329.0930.3490.3490.0000.0000.0000.000
84A85LEU00.0090.02030.334-0.377-0.3770.0000.0000.0000.000
85A86PRO00.0180.00731.8350.3160.3160.0000.0000.0000.000
86A87VAL00.0610.00834.860-0.121-0.1210.0000.0000.0000.000
87A88SER0-0.060-0.03334.3780.0600.0600.0000.0000.0000.000
88A89GLU-1-0.835-0.88631.190-9.904-9.9040.0000.0000.0000.000
89A90ASN00.0520.02332.461-0.375-0.3750.0000.0000.0000.000
90A91PRO00.0120.00433.9070.2620.2620.0000.0000.0000.000
91A92GLU-1-0.792-0.85336.732-8.162-8.1620.0000.0000.0000.000
92A93MET0-0.046-0.00738.5720.2000.2000.0000.0000.0000.000
93A94LYS10.9570.98140.7016.8046.8040.0000.0000.0000.000
94A95PRO00.031-0.00743.0620.1050.1050.0000.0000.0000.000
95A96ASN0-0.028-0.00245.3190.0090.0090.0000.0000.0000.000
96A97LYS10.8390.92943.6157.3037.3030.0000.0000.0000.000
97A98LYS10.9170.94045.2576.3186.3180.0000.0000.0000.000
98A99PRO00.0610.00840.762-0.041-0.0410.0000.0000.0000.000
99A100ASN00.022-0.00141.376-0.059-0.0590.0000.0000.0000.000
100A101GLU-1-0.839-0.88043.225-6.589-6.5890.0000.0000.0000.000
101A102VAL0-0.109-0.05338.7040.0510.0510.0000.0000.0000.000
102A103LEU0-0.034-0.01434.905-0.221-0.2210.0000.0000.0000.000
103A104ASP-1-0.775-0.88338.834-7.340-7.3400.0000.0000.0000.000
104A105ILE0-0.045-0.03438.340-0.270-0.2700.0000.0000.0000.000
105A106GLY0-0.0110.00236.7990.1620.1620.0000.0000.0000.000
106A107ASP-1-0.856-0.91935.496-8.506-8.5060.0000.0000.0000.000
107A108ALA0-0.013-0.00130.996-0.266-0.2660.0000.0000.0000.000
108A109ILE0-0.005-0.00129.0160.1580.1580.0000.0000.0000.000
109A110ILE0-0.028-0.01325.148-0.438-0.4380.0000.0000.0000.000
110A111ALA00.036-0.00425.3490.3720.3720.0000.0000.0000.000
111A112LYS10.8520.90520.65413.44913.4490.0000.0000.0000.000
112A113VAL0-0.031-0.00420.7880.6550.6550.0000.0000.0000.000
113A114LEU0-0.0080.00622.291-0.406-0.4060.0000.0000.0000.000
114A115ASN00.022-0.00923.918-0.535-0.5350.0000.0000.0000.000
115A116ILE00.0070.00720.3530.0990.0990.0000.0000.0000.000
116A117ASP-1-0.787-0.86824.419-10.904-10.9040.0000.0000.0000.000
117A118PRO00.0520.01026.337-0.253-0.2530.0000.0000.0000.000
118A119LYS10.9110.96527.4329.2669.2660.0000.0000.0000.000
119A120MET0-0.033-0.01423.633-0.071-0.0710.0000.0000.0000.000
120A121LYS10.8400.91926.74110.23710.2370.0000.0000.0000.000
121A122VAL0-0.004-0.01223.931-0.269-0.2690.0000.0000.0000.000
122A123THR0-0.025-0.00726.3470.5580.5580.0000.0000.0000.000
123A124LEU00.003-0.00725.232-0.536-0.5360.0000.0000.0000.000
124A125THR00.005-0.04126.3160.4510.4510.0000.0000.0000.000
125A126MET00.014-0.01327.542-0.453-0.4530.0000.0000.0000.000
126A127LYS10.8300.92829.6549.6079.6070.0000.0000.0000.000
127A128ASP-1-0.786-0.91024.115-13.219-13.2190.0000.0000.0000.000
128A129ARG10.9690.98825.27611.73811.7380.0000.0000.0000.000
129A130ILE0-0.043-0.01922.4660.1800.1800.0000.0000.0000.000
130A131CYS0-0.0490.03025.469-0.055-0.0550.0000.0000.0000.000
131A132ARG10.8700.94327.32111.12111.1210.0000.0000.0000.000
132A133PRO00.0610.03930.299-0.288-0.2880.0000.0000.0000.000
133A134ILE0-0.066-0.04028.3250.0090.0090.0000.0000.0000.000
134A135ARG10.8030.85632.6018.5008.5000.0000.0000.0000.000
135A136PHE0-0.0010.00433.3610.2190.2190.0000.0000.0000.000
136A137GLY00.0110.01832.071-0.309-0.3090.0000.0000.0000.000
137A138ARG10.8380.89330.8899.4609.4600.0000.0000.0000.000
138A139ILE00.008-0.00627.285-0.290-0.2900.0000.0000.0000.000
139A140VAL0-0.0140.00524.6750.2390.2390.0000.0000.0000.000
140A141ALA0-0.010-0.00924.091-0.325-0.3250.0000.0000.0000.000
141A142ILE00.0380.03018.0970.0550.0550.0000.0000.0000.000
142A143ASN00.001-0.01118.241-0.794-0.7940.0000.0000.0000.000
143A144PRO00.0580.01716.849-0.677-0.6770.0000.0000.0000.000
144A145ALA0-0.050-0.01913.879-1.282-1.2820.0000.0000.0000.000
145A146ARG10.8390.91613.57416.76216.7620.0000.0000.0000.000
146A147VAL00.0710.05113.7010.1240.1240.0000.0000.0000.000
147A148PRO0-0.005-0.0149.4660.2200.2200.0000.0000.0000.000
148A149ARG10.7480.88111.41417.44917.4490.0000.0000.0000.000
149A150VAL00.0640.02813.2930.5590.5590.0000.0000.0000.000
150A151ILE0-0.0150.01212.3420.7240.7240.0000.0000.0000.000
151A152GLY00.0740.03512.0500.8110.8110.0000.0000.0000.000
152A153LYS10.9900.9878.38525.88625.8860.0000.0000.0000.000
153A154LYS10.9740.9839.44226.14426.1440.0000.0000.0000.000
154A155GLY00.0410.02411.2721.6921.6920.0000.0000.0000.000
155A156SER0-0.047-0.04113.1441.2831.2830.0000.0000.0000.000
156A157MET00.0260.03815.1241.3121.3120.0000.0000.0000.000
157A158ILE00.0260.01416.1960.9840.9840.0000.0000.0000.000
158A159LYS10.8460.92315.37518.31118.3110.0000.0000.0000.000
159A160LEU00.0220.04419.5420.6680.6680.0000.0000.0000.000
160A161LEU00.0270.00120.6000.6140.6140.0000.0000.0000.000
161A162LYS10.8450.93920.66314.21614.2160.0000.0000.0000.000
162A163SER0-0.036-0.03323.4110.5430.5430.0000.0000.0000.000
163A164GLU-1-0.818-0.90225.404-10.609-10.6090.0000.0000.0000.000
164A165LEU0-0.018-0.00926.5730.4160.4160.0000.0000.0000.000
165A166ASP-1-0.866-0.90928.756-9.393-9.3930.0000.0000.0000.000
166A167VAL0-0.0360.00426.1660.2400.2400.0000.0000.0000.000
167A168GLN0-0.010-0.00726.482-0.401-0.4010.0000.0000.0000.000
168A169ILE00.0430.00621.808-0.014-0.0140.0000.0000.0000.000
169A170VAL0-0.048-0.02921.556-0.413-0.4130.0000.0000.0000.000
170A171VAL00.0340.01616.9670.3450.3450.0000.0000.0000.000
171A172GLY00.0190.02618.567-0.592-0.5920.0000.0000.0000.000
172A173GLN0-0.043-0.04213.856-1.569-1.5690.0000.0000.0000.000
173A174ASN0-0.026-0.03916.929-0.990-0.9900.0000.0000.0000.000
174A175GLY00.009-0.00219.1430.1460.1460.0000.0000.0000.000
175A176LEU0-0.0360.00719.9600.4870.4870.0000.0000.0000.000
176A177ILE0-0.005-0.01119.984-0.488-0.4880.0000.0000.0000.000
177A178TRP0-0.008-0.00223.3080.3340.3340.0000.0000.0000.000
178A179VAL00.011-0.00625.235-0.441-0.4410.0000.0000.0000.000
179A180ASN0-0.003-0.01727.5640.5560.5560.0000.0000.0000.000
180A181GLY00.0640.02830.233-0.263-0.2630.0000.0000.0000.000
181A182ASP-1-0.794-0.88432.878-8.181-8.1810.0000.0000.0000.000
182A183ARG11.0010.98834.0037.4867.4860.0000.0000.0000.000
183A184ARG10.9110.95434.6457.8907.8900.0000.0000.0000.000
184A185LYS10.9110.95731.2509.0059.0050.0000.0000.0000.000
185A186VAL0-0.023-0.01429.916-0.344-0.3440.0000.0000.0000.000
186A187SER0-0.007-0.00429.700-0.245-0.2450.0000.0000.0000.000
187A188ILE00.0380.02128.608-0.235-0.2350.0000.0000.0000.000
188A189ALA00.0080.00025.854-0.411-0.4110.0000.0000.0000.000
189A190GLU-1-0.848-0.91425.432-10.374-10.3740.0000.0000.0000.000
190A191GLU-1-0.809-0.87326.357-10.030-10.0300.0000.0000.0000.000
191A192ALA00.0150.00823.826-0.318-0.3180.0000.0000.0000.000
192A193ILE0-0.033-0.02021.465-0.696-0.6960.0000.0000.0000.000
193A194TYR00.0410.01221.762-0.627-0.6270.0000.0000.0000.000
194A195LEU00.0120.01923.276-0.310-0.3100.0000.0000.0000.000
195A196ILE0-0.016-0.00617.297-0.604-0.6040.0000.0000.0000.000
196A197GLU-1-0.856-0.93318.273-15.321-15.3210.0000.0000.0000.000
197A198GLN0-0.014-0.02119.488-0.447-0.4470.0000.0000.0000.000
198A199GLU-1-0.826-0.86818.585-14.146-14.1460.0000.0000.0000.000
199A200ALA00.0010.00418.573-0.908-0.9080.0000.0000.0000.000
200A201HIS0-0.009-0.00617.184-1.449-1.4490.0000.0000.0000.000
201A202THR0-0.063-0.05613.0300.0300.0300.0000.0000.0000.000
202A203GLU-1-0.803-0.88214.044-16.582-16.5820.0000.0000.0000.000
203A204GLY00.0620.02416.513-0.353-0.3530.0000.0000.0000.000
204A205LEU0-0.031-0.01116.5360.5560.5560.0000.0000.0000.000
205A206THR00.003-0.01916.0690.2300.2300.0000.0000.0000.000
206A207ASP-1-0.834-0.91818.618-14.067-14.0670.0000.0000.0000.000
207A208ARG10.7870.86920.05014.62614.6260.0000.0000.0000.000
208A209VAL0-0.012-0.00120.1230.5160.5160.0000.0000.0000.000
209A210ALA00.0440.02322.8640.4720.4720.0000.0000.0000.000
210A211GLU-1-0.882-0.92024.848-9.906-9.9060.0000.0000.0000.000
211A212PHE0-0.023-0.01025.8700.4430.4430.0000.0000.0000.000
212A213ILE00.024-0.00224.4670.4320.4320.0000.0000.0000.000
213A214LYS10.8210.89828.30710.73410.7340.0000.0000.0000.000
214A215ARG10.9590.97530.6009.3759.3750.0000.0000.0000.000
215A216ARG10.7490.83230.9339.4339.4330.0000.0000.0000.000
216A217LYS10.7890.85829.72810.37810.3780.0000.0000.0000.000
217A218ALA0-0.0500.00034.1960.2000.2000.0000.0000.0000.000
218A219ASP-1-0.958-0.95336.420-7.773-7.7730.0000.0000.0000.000