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: NNJQQ

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 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 180
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -1414829.199669
FMO2-HF: Nuclear repulsion 1341546.533174
FMO2-HF: Total energy -73282.666496
FMO2-MP2: Total energy -73498.936381


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.
-0.7570.9720.071-0.686-1.1150.002
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 : 0.009 / q_NPA : -0.018
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].
3A5GLN0-0.005-0.0102.973-0.8460.8830.071-0.686-1.1150.002
4A6SER00.0140.0116.4700.4220.4220.0000.0000.0000.000
5A7PRO00.0270.0199.871-0.036-0.0360.0000.0000.0000.000
6A8TRP00.036-0.00113.014-0.004-0.0040.0000.0000.0000.000
7A9ASP-1-0.848-0.92810.258-0.558-0.5580.0000.0000.0000.000
8A10ARG10.8110.87313.0590.2950.2950.0000.0000.0000.000
9A11VAL00.0250.01016.6300.0200.0200.0000.0000.0000.000
10A12LYS10.8240.91612.2830.4410.4410.0000.0000.0000.000
11A13ASP-1-0.790-0.88017.124-0.237-0.2370.0000.0000.0000.000
12A14LEU0-0.006-0.00518.7860.0200.0200.0000.0000.0000.000
13A15ALA0-0.002-0.00521.1550.0150.0150.0000.0000.0000.000
14A16THR0-0.002-0.00720.6230.0030.0030.0000.0000.0000.000
15A17VAL0-0.033-0.01921.5400.0110.0110.0000.0000.0000.000
16A18TYR0-0.007-0.00524.1430.0050.0050.0000.0000.0000.000
17A19VAL0-0.025-0.00326.0160.0120.0120.0000.0000.0000.000
18A20ASP-1-0.849-0.90823.045-0.138-0.1380.0000.0000.0000.000
19A21VAL00.0570.02926.1680.0070.0070.0000.0000.0000.000
20A22LEU0-0.0060.01327.6670.0060.0060.0000.0000.0000.000
21A23LYS10.8240.91529.1110.0910.0910.0000.0000.0000.000
22A24ASP-1-0.873-0.95225.723-0.138-0.1380.0000.0000.0000.000
23A25SER0-0.021-0.01029.2260.0050.0050.0000.0000.0000.000
24A26GLY00.0340.00632.3240.0050.0050.0000.0000.0000.000
25A27ARG10.7940.87528.1270.1180.1180.0000.0000.0000.000
26A28ASP-1-0.855-0.91730.445-0.118-0.1180.0000.0000.0000.000
27A29TYR0-0.017-0.01532.9990.0030.0030.0000.0000.0000.000
28A30VAL0-0.051-0.01835.3690.0050.0050.0000.0000.0000.000
29A31SER00.021-0.00732.6570.0010.0010.0000.0000.0000.000
30A32GLN0-0.049-0.00335.0490.0030.0030.0000.0000.0000.000
31A33PHE00.0040.00437.8190.0040.0040.0000.0000.0000.000
32A34GLU-1-0.782-0.90735.294-0.079-0.0790.0000.0000.0000.000
33A35GLY00.007-0.00137.3520.0010.0010.0000.0000.0000.000
34A36SER0-0.006-0.00538.1650.0010.0010.0000.0000.0000.000
35A37ALA0-0.024-0.02641.7650.0000.0000.0000.0000.0000.000
36A38LEU0-0.013-0.01444.3150.0010.0010.0000.0000.0000.000
37A39GLY00.0640.03742.3390.0020.0020.0000.0000.0000.000
38A40LYS10.8850.93337.8170.0790.0790.0000.0000.0000.000
39A41GLN0-0.0020.02742.2610.0030.0030.0000.0000.0000.000
40A42LEU0-0.0140.00144.9990.0020.0020.0000.0000.0000.000
41A43ASN0-0.083-0.04139.253-0.001-0.0010.0000.0000.0000.000
42A44LEU0-0.0160.01040.5540.0000.0000.0000.0000.0000.000
43A45LYS10.8050.87933.7780.0710.0710.0000.0000.0000.000
44A46LEU0-0.042-0.02236.5240.0040.0040.0000.0000.0000.000
45A47LEU00.0160.01531.8940.0000.0000.0000.0000.0000.000
46A48ASP-1-0.846-0.89431.798-0.080-0.0800.0000.0000.0000.000
47A49ASN0-0.053-0.03930.9670.0050.0050.0000.0000.0000.000
48A50TRP00.0190.03330.0310.0070.0070.0000.0000.0000.000
49A51ASP-1-0.770-0.84926.518-0.112-0.1120.0000.0000.0000.000
50A52SER0-0.040-0.02627.0660.0060.0060.0000.0000.0000.000
51A53VAL00.0370.01125.201-0.007-0.0070.0000.0000.0000.000
52A54THR00.0150.02123.838-0.008-0.0080.0000.0000.0000.000
53A55SER00.0740.04319.8720.0070.0070.0000.0000.0000.000
54A56THR00.026-0.02223.1020.0120.0120.0000.0000.0000.000
55A57PHE00.0270.01214.9710.0020.0020.0000.0000.0000.000
56A58SER0-0.044-0.02420.0890.0050.0050.0000.0000.0000.000
57A59LYS10.9160.95220.9520.0930.0930.0000.0000.0000.000
58A60LEU00.0170.01822.4880.0100.0100.0000.0000.0000.000
59A61ARG10.9190.96414.1700.0790.0790.0000.0000.0000.000
60A62GLU-1-0.991-0.99620.964-0.027-0.0270.0000.0000.0000.000
61A63GLN0-0.057-0.02723.4650.0090.0090.0000.0000.0000.000
62A64LEU0-0.026-0.01321.9810.0050.0050.0000.0000.0000.000
63A65GLY00.0250.03522.5010.0110.0110.0000.0000.0000.000
64A66PRO0-0.076-0.05119.399-0.007-0.0070.0000.0000.0000.000
65A67VAL00.0140.01018.545-0.001-0.0010.0000.0000.0000.000
66A68THR0-0.036-0.05118.5100.0100.0100.0000.0000.0000.000
67A69GLN0-0.045-0.04715.708-0.005-0.0050.0000.0000.0000.000
68A70GLU-1-0.817-0.87718.4970.0340.0340.0000.0000.0000.000
69A71PHE0-0.0040.01119.782-0.015-0.0150.0000.0000.0000.000
70A72TRP00.022-0.00515.941-0.042-0.0420.0000.0000.0000.000
71A73ASP-1-0.822-0.90019.032-0.007-0.0070.0000.0000.0000.000
72A74ASN0-0.056-0.04920.973-0.011-0.0110.0000.0000.0000.000
73A75LEU00.0000.01219.125-0.008-0.0080.0000.0000.0000.000
74A76GLU-1-0.798-0.84817.474-0.218-0.2180.0000.0000.0000.000
75A77LYS10.8100.90021.3640.0370.0370.0000.0000.0000.000
76A78GLU-1-0.835-0.91124.968-0.049-0.0490.0000.0000.0000.000
77A79THR0-0.056-0.03121.698-0.008-0.0080.0000.0000.0000.000
78A80GLU-1-0.927-0.96924.497-0.100-0.1000.0000.0000.0000.000
79A81GLY00.0220.02427.0790.0020.0020.0000.0000.0000.000
80A82LEU00.0140.00124.6350.0010.0010.0000.0000.0000.000
81A83ARG10.8220.88820.4870.1870.1870.0000.0000.0000.000
82A84GLN0-0.043-0.02627.1210.0040.0040.0000.0000.0000.000
83A85GLU-1-0.848-0.92030.869-0.057-0.0570.0000.0000.0000.000
84A86MET00.0380.01226.9540.0050.0050.0000.0000.0000.000
85A87SER0-0.0120.00230.035-0.003-0.0030.0000.0000.0000.000
86A88LYS10.7300.85031.2040.0640.0640.0000.0000.0000.000
87A89ASP-1-0.841-0.90932.615-0.060-0.0600.0000.0000.0000.000
88A90LEU0-0.027-0.00729.0100.0020.0020.0000.0000.0000.000
89A91GLU-1-0.833-0.90432.645-0.089-0.0890.0000.0000.0000.000
90A92GLU-1-0.822-0.87735.651-0.050-0.0500.0000.0000.0000.000
91A93VAL00.005-0.01334.4700.0040.0040.0000.0000.0000.000
92A94LYS10.8510.89332.5320.0960.0960.0000.0000.0000.000
93A95ALA0-0.028-0.00436.6670.0020.0020.0000.0000.0000.000
94A96LYS10.7490.85739.1380.0550.0550.0000.0000.0000.000
95A97VAL0-0.011-0.00536.3680.0020.0020.0000.0000.0000.000
96A98GLN0-0.049-0.03538.332-0.002-0.0020.0000.0000.0000.000
97A99PRO00.0360.01240.3580.0000.0000.0000.0000.0000.000
98A100TYR0-0.043-0.01440.9830.0020.0020.0000.0000.0000.000
99A101LEU0-0.0250.00236.3050.0000.0000.0000.0000.0000.000
100A102ASP-1-0.814-0.90740.494-0.061-0.0610.0000.0000.0000.000
101A103ASP-1-0.881-0.94543.508-0.044-0.0440.0000.0000.0000.000
102A104PHE0-0.004-0.00539.5670.0010.0010.0000.0000.0000.000
103A105GLN0-0.050-0.03440.2680.0020.0020.0000.0000.0000.000
104A106LYS10.8270.91143.4900.0450.0450.0000.0000.0000.000
105A107LYS10.7840.88746.7780.0420.0420.0000.0000.0000.000
106A108TRP00.0320.00941.4030.0020.0020.0000.0000.0000.000
107A109GLN0-0.028-0.01945.4400.0020.0020.0000.0000.0000.000
108A110GLU-1-0.847-0.91647.757-0.040-0.0400.0000.0000.0000.000
109A111GLU-1-0.802-0.88948.797-0.040-0.0400.0000.0000.0000.000
110A112MET0-0.041-0.01446.1690.0010.0010.0000.0000.0000.000
111A113GLU-1-0.737-0.81249.539-0.041-0.0410.0000.0000.0000.000
112A114LEU0-0.005-0.01052.4800.0020.0020.0000.0000.0000.000
113A115TYR0-0.054-0.04350.3660.0020.0020.0000.0000.0000.000
114A116ARG10.8220.87052.1430.0420.0420.0000.0000.0000.000
115A117GLN0-0.064-0.05453.8750.0020.0020.0000.0000.0000.000
116A118LYS10.8880.95156.3740.0320.0320.0000.0000.0000.000
117A119VAL0-0.0110.00454.2090.0010.0010.0000.0000.0000.000
118A120GLU-1-0.868-0.92454.152-0.041-0.0410.0000.0000.0000.000
119A121PRO0-0.011-0.00757.0280.0000.0000.0000.0000.0000.000
120A122LEU00.0650.03660.0830.0000.0000.0000.0000.0000.000
121A123ARG10.8190.89752.0970.0430.0430.0000.0000.0000.000
122A124ALA00.010-0.00458.4910.0000.0000.0000.0000.0000.000
123A125GLU-1-0.941-0.96660.298-0.028-0.0280.0000.0000.0000.000
124A126LEU0-0.012-0.01160.4120.0010.0010.0000.0000.0000.000
125A127GLN0-0.018-0.00356.3870.0000.0000.0000.0000.0000.000
126A128GLU-1-0.788-0.87660.881-0.029-0.0290.0000.0000.0000.000
127A129GLY00.0470.02964.0710.0010.0010.0000.0000.0000.000
128A130ALA0-0.012-0.00962.0660.0010.0010.0000.0000.0000.000
129A131ARG10.8160.90062.2570.0310.0310.0000.0000.0000.000
130A132GLN0-0.063-0.04963.9340.0010.0010.0000.0000.0000.000
131A133LYS10.8660.91767.3960.0250.0250.0000.0000.0000.000
132A134LEU00.0070.02362.1730.0000.0000.0000.0000.0000.000
133A135HIS00.0210.00266.3860.0000.0000.0000.0000.0000.000
134A136GLU-1-0.835-0.89668.084-0.023-0.0230.0000.0000.0000.000
135A137LEU0-0.018-0.00967.7600.0010.0010.0000.0000.0000.000
136A138GLN00.002-0.01264.1540.0000.0000.0000.0000.0000.000
137A139GLU-1-0.884-0.95868.694-0.024-0.0240.0000.0000.0000.000
138A140LYS10.7850.88871.9880.0230.0230.0000.0000.0000.000
139A141LEU0-0.010-0.00868.6390.0010.0010.0000.0000.0000.000
140A142SER0-0.0270.00770.5770.0000.0000.0000.0000.0000.000
141A143PRO00.0260.01271.5450.0000.0000.0000.0000.0000.000
142A144LEU00.0080.00273.0220.0000.0000.0000.0000.0000.000
143A145GLY00.0060.00470.3680.0000.0000.0000.0000.0000.000
144A146GLU-1-0.780-0.86270.187-0.026-0.0260.0000.0000.0000.000
145A147GLU-1-0.801-0.84972.960-0.020-0.0200.0000.0000.0000.000
146A148MET00.0020.00072.0320.0010.0010.0000.0000.0000.000
147A149ARG10.7950.86867.3410.0270.0270.0000.0000.0000.000
148A150ASP-1-0.864-0.92871.936-0.022-0.0220.0000.0000.0000.000
149A151ARG10.7350.82675.3580.0200.0200.0000.0000.0000.000
150A152ALA00.000-0.00270.8540.0000.0000.0000.0000.0000.000
151A153ARG10.8720.91669.5510.0230.0230.0000.0000.0000.000
152A154ALA00.0330.02373.6980.0000.0000.0000.0000.0000.000
153A155HIS0-0.041-0.03174.6240.0010.0010.0000.0000.0000.000
154A156VAL00.0110.00970.2720.0000.0000.0000.0000.0000.000
155A157ASP-1-0.773-0.86773.385-0.021-0.0210.0000.0000.0000.000
156A158ALA0-0.0030.02075.7710.0000.0000.0000.0000.0000.000
157A159LEU00.0070.00472.4170.0000.0000.0000.0000.0000.000
158A160ARG10.8330.89272.8310.0200.0200.0000.0000.0000.000
159A161THR0-0.042-0.03674.9910.0000.0000.0000.0000.0000.000
160A162HIS00.003-0.00478.6940.0010.0010.0000.0000.0000.000
161A163LEU00.0160.00673.0760.0000.0000.0000.0000.0000.000
162A164ALA00.0110.03477.1170.0000.0000.0000.0000.0000.000
163A165PRO00.0450.02378.1020.0000.0000.0000.0000.0000.000
164A166TYR00.0370.01078.7150.0000.0000.0000.0000.0000.000
165A167SER0-0.024-0.01575.2350.0000.0000.0000.0000.0000.000
166A168ASP-1-0.815-0.89276.990-0.016-0.0160.0000.0000.0000.000
167A169GLU-1-0.863-0.90579.582-0.013-0.0130.0000.0000.0000.000
168A170LEU0-0.008-0.00975.2630.0000.0000.0000.0000.0000.000
169A171ARG10.8290.89476.6000.0160.0160.0000.0000.0000.000
170A172GLN00.0110.00977.6680.0000.0000.0000.0000.0000.000
171A173ARG10.8160.88279.9790.0130.0130.0000.0000.0000.000
172A174LEU0-0.0050.01173.6400.0000.0000.0000.0000.0000.000
173A175ALA00.0280.00878.0550.0000.0000.0000.0000.0000.000
174A176ALA00.0210.00479.6620.0000.0000.0000.0000.0000.000
175A177ARG10.8790.93578.6640.0130.0130.0000.0000.0000.000
176A178LEU00.0110.00674.8720.0000.0000.0000.0000.0000.000
177A179GLU-1-0.817-0.89178.872-0.013-0.0130.0000.0000.0000.000
178A180ALA0-0.039-0.01682.2890.0000.0000.0000.0000.0000.000
179A181LEU0-0.042-0.00876.8080.0000.0000.0000.0000.0000.000
180A182LYS10.7670.87980.5280.0130.0130.0000.0000.0000.000