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: 894MY

Calculation Name: 3R2P-A-Xray372

Preferred Name: Apolipoprotein A-I

Target Type: SINGLE PROTEIN

Ligand Name:

ligand 3-letter code:

PDB ID: 3R2P

Chain ID: A

ChEMBL ID: CHEMBL5984

UniProt ID: P02647

Base Structure: X-ray

Registration Date: 2023-09-23

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 -1411925.809937
FMO2-HF: Nuclear repulsion 1338643.569763
FMO2-HF: Total energy -73282.240175
FMO2-MP2: Total energy -73498.561506


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:PRO)


Summations of interaction energy for fragment #1(A:3:PRO)
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.
-0.561.269-0.004-0.759-1.0660.003
Interaction energy analysis for fragmet #1(A:3:PRO)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.023 / q_NPA : -0.010
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].
3A5GLN00.0070.0023.315-0.4201.409-0.004-0.759-1.0660.003
4A6SER00.0110.0056.2340.4770.4770.0000.0000.0000.000
5A7PRO00.0680.0349.199-0.072-0.0720.0000.0000.0000.000
6A8TRP00.009-0.00812.4600.0110.0110.0000.0000.0000.000
7A9ASP-1-0.844-0.9219.557-0.737-0.7370.0000.0000.0000.000
8A10ARG10.8320.88212.9320.5260.5260.0000.0000.0000.000
9A11VAL00.0060.00716.0420.0340.0340.0000.0000.0000.000
10A12LYS10.8320.90911.6250.5380.5380.0000.0000.0000.000
11A13ASP-1-0.859-0.92016.689-0.326-0.3260.0000.0000.0000.000
12A14LEU00.0130.00218.2180.0260.0260.0000.0000.0000.000
13A15ALA0-0.021-0.01620.5730.0220.0220.0000.0000.0000.000
14A16THR00.0100.00119.7960.0050.0050.0000.0000.0000.000
15A17VAL0-0.022-0.01221.2710.0150.0150.0000.0000.0000.000
16A18TYR0-0.009-0.00523.7850.0060.0060.0000.0000.0000.000
17A19VAL0-0.031-0.00925.5020.0160.0160.0000.0000.0000.000
18A20ASP-1-0.858-0.91122.848-0.154-0.1540.0000.0000.0000.000
19A21VAL00.0650.04426.0890.0060.0060.0000.0000.0000.000
20A22LEU0-0.0090.00827.6150.0070.0070.0000.0000.0000.000
21A23LYS10.8670.92328.9530.0970.0970.0000.0000.0000.000
22A24ASP-1-0.856-0.93325.172-0.161-0.1610.0000.0000.0000.000
23A25SER0-0.026-0.00828.8320.0050.0050.0000.0000.0000.000
24A26GLY00.011-0.00931.8900.0060.0060.0000.0000.0000.000
25A27ARG10.8140.88927.8320.1250.1250.0000.0000.0000.000
26A28ASP-1-0.855-0.92230.437-0.136-0.1360.0000.0000.0000.000
27A29TYR0-0.030-0.02332.9310.0030.0030.0000.0000.0000.000
28A30VAL0-0.047-0.01434.9190.0060.0060.0000.0000.0000.000
29A31SER00.0330.00332.6990.0030.0030.0000.0000.0000.000
30A32GLN0-0.0300.01235.1200.0040.0040.0000.0000.0000.000
31A33PHE00.000-0.00237.9310.0040.0040.0000.0000.0000.000
32A34GLU-1-0.794-0.91234.917-0.082-0.0820.0000.0000.0000.000
33A35GLY0-0.016-0.00637.6960.0010.0010.0000.0000.0000.000
34A36SER0-0.020-0.01338.4770.0020.0020.0000.0000.0000.000
35A37ALA0-0.014-0.02142.0270.0010.0010.0000.0000.0000.000
36A38LEU0-0.015-0.02044.6310.0020.0020.0000.0000.0000.000
37A39GLY00.0670.04042.4340.0020.0020.0000.0000.0000.000
38A40LYS10.8890.94438.2490.0840.0840.0000.0000.0000.000
39A41GLN0-0.0040.02642.2710.0040.0040.0000.0000.0000.000
40A42LEU0-0.019-0.00944.9050.0020.0020.0000.0000.0000.000
41A43ASN0-0.078-0.03039.551-0.001-0.0010.0000.0000.0000.000
42A44LEU0-0.028-0.00140.4190.0010.0010.0000.0000.0000.000
43A45LYS10.8590.90433.4330.0630.0630.0000.0000.0000.000
44A46LEU0-0.050-0.03136.3310.0040.0040.0000.0000.0000.000
45A47LEU00.0110.01131.6580.0000.0000.0000.0000.0000.000
46A48ASP-1-0.857-0.90431.631-0.072-0.0720.0000.0000.0000.000
47A49ASN0-0.069-0.04431.1800.0050.0050.0000.0000.0000.000
48A50TRP00.0150.03629.5060.0070.0070.0000.0000.0000.000
49A51ASP-1-0.794-0.87426.166-0.118-0.1180.0000.0000.0000.000
50A52SER0-0.021-0.00826.9040.0090.0090.0000.0000.0000.000
51A53VAL00.019-0.00425.604-0.008-0.0080.0000.0000.0000.000
52A54THR00.0090.01423.797-0.005-0.0050.0000.0000.0000.000
53A55SER00.0500.03319.6610.0030.0030.0000.0000.0000.000
54A56THR00.054-0.01822.9100.0170.0170.0000.0000.0000.000
55A57PHE00.0080.00114.6230.0030.0030.0000.0000.0000.000
56A58SER0-0.038-0.03319.8390.0080.0080.0000.0000.0000.000
57A59LYS10.9460.97120.7010.0940.0940.0000.0000.0000.000
58A60LEU00.0080.01621.6850.0090.0090.0000.0000.0000.000
59A61ARG10.9070.96213.4930.0680.0680.0000.0000.0000.000
60A62GLU-1-0.985-0.99320.519-0.012-0.0120.0000.0000.0000.000
61A63GLN0-0.054-0.02223.0430.0100.0100.0000.0000.0000.000
62A64LEU0-0.035-0.02121.7590.0060.0060.0000.0000.0000.000
63A65GLY00.0370.04222.4150.0110.0110.0000.0000.0000.000
64A66PRO0-0.079-0.04919.115-0.013-0.0130.0000.0000.0000.000
65A67VAL00.0180.01218.145-0.002-0.0020.0000.0000.0000.000
66A68THR0-0.034-0.05318.3040.0120.0120.0000.0000.0000.000
67A69GLN0-0.040-0.04515.441-0.010-0.0100.0000.0000.0000.000
68A70GLU-1-0.811-0.87518.324-0.022-0.0220.0000.0000.0000.000
69A71PHE0-0.0060.01319.457-0.016-0.0160.0000.0000.0000.000
70A72TRP00.034-0.00415.592-0.045-0.0450.0000.0000.0000.000
71A73ASP-1-0.823-0.89918.872-0.150-0.1500.0000.0000.0000.000
72A74ASN0-0.070-0.05720.918-0.004-0.0040.0000.0000.0000.000
73A75LEU0-0.018-0.00118.743-0.004-0.0040.0000.0000.0000.000
74A76GLU-1-0.802-0.85117.803-0.387-0.3870.0000.0000.0000.000
75A77LYS10.8190.91721.4410.1020.1020.0000.0000.0000.000
76A78GLU-1-0.856-0.93125.080-0.105-0.1050.0000.0000.0000.000
77A79THR0-0.035-0.02521.635-0.005-0.0050.0000.0000.0000.000
78A80GLU-1-0.917-0.96824.344-0.165-0.1650.0000.0000.0000.000
79A81GLY00.0140.01026.9950.0070.0070.0000.0000.0000.000
80A82LEU00.0110.00824.5520.0070.0070.0000.0000.0000.000
81A83ARG10.8690.92220.8400.2660.2660.0000.0000.0000.000
82A84GLN0-0.039-0.02427.2570.0120.0120.0000.0000.0000.000
83A85GLU-1-0.852-0.92130.903-0.087-0.0870.0000.0000.0000.000
84A86MET00.0290.01726.8820.0090.0090.0000.0000.0000.000
85A87SER0-0.025-0.02029.932-0.001-0.0010.0000.0000.0000.000
86A88LYS10.7400.86431.0500.0960.0960.0000.0000.0000.000
87A89ASP-1-0.843-0.90832.431-0.086-0.0860.0000.0000.0000.000
88A90LEU0-0.023-0.00829.0060.0040.0040.0000.0000.0000.000
89A91GLU-1-0.836-0.90532.668-0.115-0.1150.0000.0000.0000.000
90A92GLU-1-0.815-0.87935.672-0.067-0.0670.0000.0000.0000.000
91A93VAL0-0.004-0.01334.3800.0060.0060.0000.0000.0000.000
92A94LYS10.8500.89132.3990.1250.1250.0000.0000.0000.000
93A95ALA0-0.0260.00036.3960.0030.0030.0000.0000.0000.000
94A96LYS10.7480.85038.6650.0730.0730.0000.0000.0000.000
95A97VAL0-0.025-0.01536.3290.0040.0040.0000.0000.0000.000
96A98GLN0-0.034-0.01238.584-0.003-0.0030.0000.0000.0000.000
97A99PRO00.0230.01040.4830.0010.0010.0000.0000.0000.000
98A100TYR0-0.0130.00240.5580.0020.0020.0000.0000.0000.000
99A101LEU0-0.0120.01236.2030.0010.0010.0000.0000.0000.000
100A102ASP-1-0.832-0.91640.388-0.074-0.0740.0000.0000.0000.000
101A103ASP-1-0.967-1.00443.501-0.050-0.0500.0000.0000.0000.000
102A104PHE0-0.014-0.01339.3290.0020.0020.0000.0000.0000.000
103A105GLN0-0.057-0.03740.5240.0020.0020.0000.0000.0000.000
104A106LYS10.9030.94343.2840.0520.0520.0000.0000.0000.000
105A107LYS10.8170.91546.4450.0470.0470.0000.0000.0000.000
106A108TRP00.0370.02341.2150.0030.0030.0000.0000.0000.000
107A109GLN0-0.019-0.01045.2590.0010.0010.0000.0000.0000.000
108A110GLU-1-0.858-0.91747.546-0.045-0.0450.0000.0000.0000.000
109A111GLU-1-0.829-0.91148.330-0.043-0.0430.0000.0000.0000.000
110A112MET0-0.036-0.01846.1250.0020.0020.0000.0000.0000.000
111A113GLU-1-0.740-0.81449.375-0.044-0.0440.0000.0000.0000.000
112A114LEU0-0.008-0.01152.4520.0020.0020.0000.0000.0000.000
113A115TYR0-0.055-0.03550.3440.0030.0030.0000.0000.0000.000
114A116ARG10.8220.86952.2170.0460.0460.0000.0000.0000.000
115A117GLN0-0.074-0.05653.8640.0030.0030.0000.0000.0000.000
116A118LYS10.9180.96556.5170.0330.0330.0000.0000.0000.000
117A119VAL0-0.0130.00153.6730.0010.0010.0000.0000.0000.000
118A120GLU-1-0.872-0.93354.307-0.043-0.0430.0000.0000.0000.000
119A121PRO0-0.0070.00256.7700.0000.0000.0000.0000.0000.000
120A122LEU00.0430.02759.7730.0010.0010.0000.0000.0000.000
121A123ARG10.8430.90651.9880.0440.0440.0000.0000.0000.000
122A124ALA0-0.005-0.00958.5580.0000.0000.0000.0000.0000.000
123A125GLU-1-0.925-0.96260.134-0.028-0.0280.0000.0000.0000.000
124A126LEU0-0.010-0.00560.3710.0010.0010.0000.0000.0000.000
125A127GLN0-0.0040.00056.3960.0000.0000.0000.0000.0000.000
126A128GLU-1-0.801-0.88460.845-0.031-0.0310.0000.0000.0000.000
127A129GLY00.0580.03063.9570.0010.0010.0000.0000.0000.000
128A130ALA0-0.018-0.01462.2580.0010.0010.0000.0000.0000.000
129A131ARG10.8310.91662.5550.0320.0320.0000.0000.0000.000
130A132GLN0-0.102-0.06564.3020.0010.0010.0000.0000.0000.000
131A133LYS10.8800.92367.4560.0260.0260.0000.0000.0000.000
132A134LEU00.0000.01562.3460.0010.0010.0000.0000.0000.000
133A135HIS0-0.003-0.02366.5790.0000.0000.0000.0000.0000.000
134A136GLU-1-0.830-0.88568.215-0.023-0.0230.0000.0000.0000.000
135A137LEU0-0.018-0.01867.3730.0010.0010.0000.0000.0000.000
136A138GLN0-0.029-0.01063.6650.0000.0000.0000.0000.0000.000
137A139GLU-1-0.882-0.95568.608-0.025-0.0250.0000.0000.0000.000
138A140LYS10.8210.90472.1210.0240.0240.0000.0000.0000.000
139A141LEU0-0.009-0.00768.5000.0010.0010.0000.0000.0000.000
140A142SER0-0.0310.00470.5270.0000.0000.0000.0000.0000.000
141A143PRO00.0270.00971.5150.0000.0000.0000.0000.0000.000
142A144LEU00.0110.00772.4830.0000.0000.0000.0000.0000.000
143A145GLY00.0150.00170.1820.0000.0000.0000.0000.0000.000
144A146GLU-1-0.784-0.87769.997-0.026-0.0260.0000.0000.0000.000
145A147GLU-1-0.825-0.87472.722-0.019-0.0190.0000.0000.0000.000
146A148MET0-0.020-0.01171.4900.0010.0010.0000.0000.0000.000
147A149ARG10.8070.87766.9530.0270.0270.0000.0000.0000.000
148A150ASP-1-0.857-0.91871.520-0.022-0.0220.0000.0000.0000.000
149A151ARG10.7780.87174.9210.0190.0190.0000.0000.0000.000
150A152ALA0-0.008-0.00170.5820.0000.0000.0000.0000.0000.000
151A153ARG10.8910.92369.3000.0230.0230.0000.0000.0000.000
152A154ALA00.0270.02473.1760.0000.0000.0000.0000.0000.000
153A155HIS0-0.044-0.04074.3670.0010.0010.0000.0000.0000.000
154A156VAL00.0080.01070.1410.0000.0000.0000.0000.0000.000
155A157ASP-1-0.780-0.86873.310-0.020-0.0200.0000.0000.0000.000
156A158ALA00.0040.02475.7260.0010.0010.0000.0000.0000.000
157A159LEU00.0110.01272.1820.0010.0010.0000.0000.0000.000
158A160ARG10.8300.89472.8530.0190.0190.0000.0000.0000.000
159A161THR0-0.039-0.04874.9710.0000.0000.0000.0000.0000.000
160A162HIS0-0.002-0.00378.5970.0010.0010.0000.0000.0000.000
161A163LEU00.006-0.00273.2220.0010.0010.0000.0000.0000.000
162A164ALA00.0000.01577.1930.0000.0000.0000.0000.0000.000
163A165PRO00.0570.02178.1440.0000.0000.0000.0000.0000.000
164A166TYR00.0130.00578.3350.0000.0000.0000.0000.0000.000
165A167SER0-0.023-0.00875.0320.0000.0000.0000.0000.0000.000
166A168ASP-1-0.819-0.89576.753-0.015-0.0150.0000.0000.0000.000
167A169GLU-1-0.849-0.89579.487-0.011-0.0110.0000.0000.0000.000
168A170LEU0-0.007-0.01174.9760.0000.0000.0000.0000.0000.000
169A171ARG10.8270.90176.3120.0150.0150.0000.0000.0000.000
170A172GLN00.0110.00077.4720.0000.0000.0000.0000.0000.000
171A173ARG10.8200.88879.9420.0110.0110.0000.0000.0000.000
172A174LEU0-0.023-0.00273.4530.0000.0000.0000.0000.0000.000
173A175ALA00.0230.00877.9580.0000.0000.0000.0000.0000.000
174A176ALA00.0200.01179.4640.0000.0000.0000.0000.0000.000
175A177ARG10.9310.96178.7630.0100.0100.0000.0000.0000.000
176A178LEU00.001-0.00174.7730.0000.0000.0000.0000.0000.000
177A179GLU-1-0.809-0.88678.852-0.011-0.0110.0000.0000.0000.000
178A180ALA0-0.045-0.01182.0690.0000.0000.0000.0000.0000.000
179A181LEU0-0.061-0.02476.9180.0000.0000.0000.0000.0000.000
180A182LYS10.7760.88580.6860.0120.0120.0000.0000.0000.000