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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: G5ZG1

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 OptH
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 -1410168.735969
FMO2-HF: Nuclear repulsion 1336888.257404
FMO2-HF: Total energy -73280.478564
FMO2-MP2: Total energy -73496.738935


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.
-1.6080.487-0.018-0.966-1.1120.005
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 : 0.013 / q_NPA : 0.005
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].
3A5GLN00.0520.0273.834-1.3700.725-0.018-0.966-1.1120.005
4A6SER0-0.003-0.0026.2920.4500.4500.0000.0000.0000.000
5A7PRO00.0720.0229.233-0.038-0.0380.0000.0000.0000.000
6A8TRP0-0.001-0.00712.5070.0300.0300.0000.0000.0000.000
7A9ASP-1-0.907-0.9519.623-0.865-0.8650.0000.0000.0000.000
8A10ARG10.9770.98612.3860.7640.7640.0000.0000.0000.000
9A11VAL00.0150.01516.1000.0420.0420.0000.0000.0000.000
10A12LYS10.8930.94611.9540.5250.5250.0000.0000.0000.000
11A13ASP-1-0.916-0.96416.738-0.356-0.3560.0000.0000.0000.000
12A14LEU00.0300.00818.2710.0330.0330.0000.0000.0000.000
13A15ALA0-0.024-0.01620.6230.0260.0260.0000.0000.0000.000
14A16THR00.0050.00219.8030.0160.0160.0000.0000.0000.000
15A17VAL0-0.021-0.01221.3820.0200.0200.0000.0000.0000.000
16A18TYR0-0.016-0.00723.8380.0060.0060.0000.0000.0000.000
17A19VAL0-0.029-0.00725.5110.0160.0160.0000.0000.0000.000
18A20ASP-1-0.848-0.89122.964-0.156-0.1560.0000.0000.0000.000
19A21VAL00.0600.04526.1220.0090.0090.0000.0000.0000.000
20A22LEU0-0.0190.00127.6570.0090.0090.0000.0000.0000.000
21A23LYS10.9500.97328.9640.0940.0940.0000.0000.0000.000
22A24ASP-1-0.852-0.92525.346-0.155-0.1550.0000.0000.0000.000
23A25SER0-0.033-0.01928.8620.0070.0070.0000.0000.0000.000
24A26GLY00.015-0.00631.9270.0070.0070.0000.0000.0000.000
25A27ARG10.8870.94528.0110.1100.1100.0000.0000.0000.000
26A28ASP-1-0.868-0.93530.374-0.125-0.1250.0000.0000.0000.000
27A29TYR0-0.021-0.02132.9610.0040.0040.0000.0000.0000.000
28A30VAL0-0.027-0.00434.9110.0060.0060.0000.0000.0000.000
29A31SER00.0260.00232.7160.0040.0040.0000.0000.0000.000
30A32GLN0-0.0210.02535.1410.0040.0040.0000.0000.0000.000
31A33PHE0-0.014-0.01537.9580.0040.0040.0000.0000.0000.000
32A34GLU-1-0.813-0.91534.898-0.063-0.0630.0000.0000.0000.000
33A35GLY0-0.033-0.00937.7180.0030.0030.0000.0000.0000.000
34A36SER0-0.021-0.00938.4960.0020.0020.0000.0000.0000.000
35A37ALA0-0.011-0.02342.0490.0020.0020.0000.0000.0000.000
36A38LEU0-0.027-0.02344.6510.0020.0020.0000.0000.0000.000
37A39GLY00.0620.03842.4480.0030.0030.0000.0000.0000.000
38A40LYS10.9460.97038.6010.0660.0660.0000.0000.0000.000
39A41GLN0-0.0100.00942.2810.0050.0050.0000.0000.0000.000
40A42LEU0-0.014-0.00944.8830.0020.0020.0000.0000.0000.000
41A43ASN0-0.073-0.02839.824-0.001-0.0010.0000.0000.0000.000
42A44LEU0-0.039-0.00940.3400.0020.0020.0000.0000.0000.000
43A45LYS10.9770.98533.6740.0400.0400.0000.0000.0000.000
44A46LEU0-0.058-0.04336.3250.0040.0040.0000.0000.0000.000
45A47LEU0-0.011-0.00331.619-0.001-0.0010.0000.0000.0000.000
46A48ASP-1-0.920-0.95131.631-0.049-0.0490.0000.0000.0000.000
47A49ASN0-0.092-0.05731.2140.0030.0030.0000.0000.0000.000
48A50TRP0-0.0350.00929.4730.0040.0040.0000.0000.0000.000
49A51ASP-1-0.869-0.93426.191-0.108-0.1080.0000.0000.0000.000
50A52SER0-0.059-0.03026.8700.0100.0100.0000.0000.0000.000
51A53VAL00.0320.00125.620-0.007-0.0070.0000.0000.0000.000
52A54THR0-0.016-0.00123.722-0.002-0.0020.0000.0000.0000.000
53A55SER00.0310.01419.656-0.001-0.0010.0000.0000.0000.000
54A56THR00.045-0.03322.9150.0150.0150.0000.0000.0000.000
55A57PHE00.001-0.00214.9190.0000.0000.0000.0000.0000.000
56A58SER0-0.024-0.01919.7200.0040.0040.0000.0000.0000.000
57A59LYS10.9981.00020.7040.0900.0900.0000.0000.0000.000
58A60LEU00.0020.01321.6460.0080.0080.0000.0000.0000.000
59A61ARG10.9170.96613.2270.1470.1470.0000.0000.0000.000
60A62GLU-1-0.981-0.99420.530-0.027-0.0270.0000.0000.0000.000
61A63GLN0-0.055-0.01923.0430.0100.0100.0000.0000.0000.000
62A64LEU0-0.042-0.02521.8580.0040.0040.0000.0000.0000.000
63A65GLY00.0350.04122.3840.0090.0090.0000.0000.0000.000
64A66PRO0-0.078-0.04519.076-0.019-0.0190.0000.0000.0000.000
65A67VAL00.0310.01817.9830.0020.0020.0000.0000.0000.000
66A68THR0-0.004-0.00818.306-0.001-0.0010.0000.0000.0000.000
67A69GLN0-0.010-0.01815.258-0.015-0.0150.0000.0000.0000.000
68A70GLU-1-0.870-0.93618.345-0.113-0.1130.0000.0000.0000.000
69A71PHE0-0.0180.00119.253-0.008-0.0080.0000.0000.0000.000
70A72TRP00.018-0.00715.796-0.038-0.0380.0000.0000.0000.000
71A73ASP-1-0.853-0.92518.874-0.302-0.3020.0000.0000.0000.000
72A74ASN0-0.028-0.02820.9180.0020.0020.0000.0000.0000.000
73A75LEU0-0.038-0.01018.7290.0030.0030.0000.0000.0000.000
74A76GLU-1-0.931-0.93018.636-0.455-0.4550.0000.0000.0000.000
75A77LYS10.8760.94921.5100.1700.1700.0000.0000.0000.000
76A78GLU-1-0.925-0.97625.102-0.153-0.1530.0000.0000.0000.000
77A79THR0-0.051-0.05521.687-0.002-0.0020.0000.0000.0000.000
78A80GLU-1-0.944-0.97624.414-0.203-0.2030.0000.0000.0000.000
79A81GLY00.0440.01827.0700.0110.0110.0000.0000.0000.000
80A82LEU00.0240.01024.7250.0100.0100.0000.0000.0000.000
81A83ARG10.9190.95621.6830.3010.3010.0000.0000.0000.000
82A84GLN0-0.044-0.01827.3230.0050.0050.0000.0000.0000.000
83A85GLU-1-0.906-0.96030.982-0.112-0.1120.0000.0000.0000.000
84A86MET00.0160.00727.0030.0100.0100.0000.0000.0000.000
85A87SER0-0.054-0.03129.8780.0070.0070.0000.0000.0000.000
86A88LYS10.9070.96531.1120.1170.1170.0000.0000.0000.000
87A89ASP-1-0.876-0.92732.431-0.107-0.1070.0000.0000.0000.000
88A90LEU0-0.049-0.02629.1560.0060.0060.0000.0000.0000.000
89A91GLU-1-0.922-0.97332.720-0.121-0.1210.0000.0000.0000.000
90A92GLU-1-0.959-0.96835.727-0.081-0.0810.0000.0000.0000.000
91A93VAL0-0.038-0.03334.5460.0080.0080.0000.0000.0000.000
92A94LYS10.9420.96631.7650.1390.1390.0000.0000.0000.000
93A95ALA0-0.0110.00636.4430.0050.0050.0000.0000.0000.000
94A96LYS10.8930.93938.8520.0830.0830.0000.0000.0000.000
95A97VAL0-0.003-0.00536.3950.0050.0050.0000.0000.0000.000
96A98GLN0-0.0260.00338.717-0.003-0.0030.0000.0000.0000.000
97A99PRO00.0050.00140.5250.0020.0020.0000.0000.0000.000
98A100TYR0-0.0040.00540.5620.0030.0030.0000.0000.0000.000
99A101LEU0-0.0220.00536.1340.0020.0020.0000.0000.0000.000
100A102ASP-1-0.846-0.92640.422-0.073-0.0730.0000.0000.0000.000
101A103ASP-1-1.009-1.01643.539-0.048-0.0480.0000.0000.0000.000
102A104PHE0-0.009-0.00739.5890.0020.0020.0000.0000.0000.000
103A105GLN0-0.057-0.05040.8390.0030.0030.0000.0000.0000.000
104A106LYS10.9850.98543.3150.0510.0510.0000.0000.0000.000
105A107LYS10.9580.99846.4210.0430.0430.0000.0000.0000.000
106A108TRP00.0360.02341.3580.0040.0040.0000.0000.0000.000
107A109GLN0-0.022-0.01445.2970.0000.0000.0000.0000.0000.000
108A110GLU-1-0.954-0.97747.572-0.042-0.0420.0000.0000.0000.000
109A111GLU-1-0.905-0.96348.328-0.037-0.0370.0000.0000.0000.000
110A112MET0-0.042-0.01246.0570.0020.0020.0000.0000.0000.000
111A113GLU-1-0.758-0.84249.394-0.038-0.0380.0000.0000.0000.000
112A114LEU0-0.016-0.01652.4750.0020.0020.0000.0000.0000.000
113A115TYR0-0.041-0.01850.8650.0030.0030.0000.0000.0000.000
114A116ARG10.8380.90052.2500.0390.0390.0000.0000.0000.000
115A117GLN0-0.069-0.05953.8810.0020.0020.0000.0000.0000.000
116A118LYS10.9220.96556.6640.0270.0270.0000.0000.0000.000
117A119VAL0-0.0140.00453.6750.0010.0010.0000.0000.0000.000
118A120GLU-1-0.931-0.98255.049-0.033-0.0330.0000.0000.0000.000
119A121PRO0-0.0100.00256.7860.0010.0010.0000.0000.0000.000
120A122LEU00.0420.02459.7130.0010.0010.0000.0000.0000.000
121A123ARG10.8950.95451.8790.0340.0340.0000.0000.0000.000
122A124ALA0-0.001-0.00158.5680.0000.0000.0000.0000.0000.000
123A125GLU-1-0.919-0.96160.149-0.021-0.0210.0000.0000.0000.000
124A126LEU0-0.023-0.01260.1660.0010.0010.0000.0000.0000.000
125A127GLN0-0.006-0.00156.3200.0000.0000.0000.0000.0000.000
126A128GLU-1-0.925-0.96460.856-0.022-0.0220.0000.0000.0000.000
127A129GLY00.0730.03463.9710.0000.0000.0000.0000.0000.000
128A130ALA0-0.032-0.02062.2710.0010.0010.0000.0000.0000.000
129A131ARG10.9270.97462.7340.0250.0250.0000.0000.0000.000
130A132GLN0-0.085-0.05264.3140.0010.0010.0000.0000.0000.000
131A133LYS10.9500.97667.4790.0180.0180.0000.0000.0000.000
132A134LEU0-0.0070.01162.3390.0010.0010.0000.0000.0000.000
133A135HIS0-0.013-0.02966.6380.0000.0000.0000.0000.0000.000
134A136GLU-1-0.925-0.94068.239-0.016-0.0160.0000.0000.0000.000
135A137LEU0-0.020-0.03067.5290.0010.0010.0000.0000.0000.000
136A138GLN0-0.023-0.00963.3830.0010.0010.0000.0000.0000.000
137A139GLU-1-0.905-0.96068.651-0.018-0.0180.0000.0000.0000.000
138A140LYS10.9020.95072.1490.0150.0150.0000.0000.0000.000
139A141LEU0-0.019-0.01368.3540.0010.0010.0000.0000.0000.000
140A142SER0-0.0310.00070.5580.0000.0000.0000.0000.0000.000
141A143PRO00.0180.00671.5500.0000.0000.0000.0000.0000.000
142A144LEU00.0190.01772.8250.0000.0000.0000.0000.0000.000
143A145GLY00.012-0.00370.2350.0000.0000.0000.0000.0000.000
144A146GLU-1-0.897-0.97570.707-0.017-0.0170.0000.0000.0000.000
145A147GLU-1-0.866-0.90772.755-0.011-0.0110.0000.0000.0000.000
146A148MET0-0.077-0.04671.4680.0010.0010.0000.0000.0000.000
147A149ARG10.9070.95766.7850.0170.0170.0000.0000.0000.000
148A150ASP-1-0.841-0.90671.578-0.014-0.0140.0000.0000.0000.000
149A151ARG10.8790.94374.9670.0110.0110.0000.0000.0000.000
150A152ALA0-0.014-0.00570.6840.0000.0000.0000.0000.0000.000
151A153ARG10.9480.95868.9540.0140.0140.0000.0000.0000.000
152A154ALA00.0350.03673.2340.0000.0000.0000.0000.0000.000
153A155HIS0-0.054-0.04474.4100.0010.0010.0000.0000.0000.000
154A156VAL00.0020.00770.1850.0010.0010.0000.0000.0000.000
155A157ASP-1-0.915-0.96373.401-0.011-0.0110.0000.0000.0000.000
156A158ALA0-0.010-0.00275.7920.0000.0000.0000.0000.0000.000
157A159LEU00.0060.01172.2200.0000.0000.0000.0000.0000.000
158A160ARG10.9330.96172.7380.0110.0110.0000.0000.0000.000
159A161THR0-0.034-0.01975.0580.0000.0000.0000.0000.0000.000
160A162HIS0-0.008-0.01178.7080.0000.0000.0000.0000.0000.000
161A163LEU0-0.002-0.01173.2530.0000.0000.0000.0000.0000.000
162A164ALA00.0000.01677.2820.0000.0000.0000.0000.0000.000
163A165PRO00.0630.02578.2330.0000.0000.0000.0000.0000.000
164A166TYR00.0160.00978.5080.0010.0010.0000.0000.0000.000
165A167SER0-0.031-0.01275.0460.0000.0000.0000.0000.0000.000
166A168ASP-1-0.927-0.95576.864-0.006-0.0060.0000.0000.0000.000
167A169GLU-1-0.871-0.93779.579-0.003-0.0030.0000.0000.0000.000
168A170LEU0-0.004-0.01274.9580.0000.0000.0000.0000.0000.000
169A171ARG10.9650.98376.2750.0060.0060.0000.0000.0000.000
170A172GLN0-0.037-0.02477.5730.0000.0000.0000.0000.0000.000
171A173ARG10.8660.93780.0690.0020.0020.0000.0000.0000.000
172A174LEU0-0.0230.00073.5660.0000.0000.0000.0000.0000.000
173A175ALA00.0190.00478.0820.0000.0000.0000.0000.0000.000
174A176ALA00.0270.01279.5570.0000.0000.0000.0000.0000.000
175A177ARG10.9260.96079.0650.0010.0010.0000.0000.0000.000
176A178LEU0-0.004-0.00574.8740.0000.0000.0000.0000.0000.000
177A179GLU-1-0.876-0.94478.959-0.003-0.0030.0000.0000.0000.000
178A180ALA0-0.047-0.01182.1590.0000.0000.0000.0000.0000.000
179A181LEU0-0.065-0.02677.1310.0000.0000.0000.0000.0000.000
180A182LYS10.8600.95280.6720.0040.0040.0000.0000.0000.000