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

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FMODB ID: QN15Y

Calculation Name: 3ERB-A-Xray372

Preferred Name: Complement C2

Target Type: SINGLE PROTEIN

Ligand Name:

ligand 3-letter code:

PDB ID: 3ERB

Chain ID: A

ChEMBL ID: CHEMBL4295701

UniProt ID: P06681

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 182
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -1724340.313998
FMO2-HF: Nuclear repulsion 1651221.573567
FMO2-HF: Total energy -73118.740431
FMO2-MP2: Total energy -73323.998374


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:SER)


Summations of interaction energy for fragment #1(A:3:SER)
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.
-11.496-5.0812.649-4.173-4.891-0.021
Interaction energy analysis for fragmet #1(A:3:SER)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.017 / q_NPA : -0.022
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].
3A5PRO00.0080.0153.649-1.2560.226-0.012-0.725-0.7460.002
4A6GLN00.0620.0125.6940.5120.5120.0000.0000.0000.000
5A7ASN0-0.0330.0048.1050.1290.1290.0000.0000.0000.000
6A8VAL0-0.004-0.0089.5560.0830.0830.0000.0000.0000.000
7A9ASN00.0480.03912.2290.0650.0650.0000.0000.0000.000
8A10ILE0-0.0110.00515.121-0.022-0.0220.0000.0000.0000.000
9A11SER0-0.048-0.03118.2210.0120.0120.0000.0000.0000.000
10A12GLY00.0490.01621.6860.0120.0120.0000.0000.0000.000
11A13GLY00.0290.00821.2290.0240.0240.0000.0000.0000.000
12A14THR0-0.048-0.01217.915-0.017-0.0170.0000.0000.0000.000
13A15PHE00.023-0.01110.339-0.027-0.0270.0000.0000.0000.000
14A16THR00.0130.02713.9250.0280.0280.0000.0000.0000.000
15A17LEU0-0.025-0.0207.363-0.075-0.0750.0000.0000.0000.000
16A18SER00.010-0.00110.9970.0530.0530.0000.0000.0000.000
17A19HIS00.0500.0409.1070.0470.0470.0000.0000.0000.000
18A20GLY00.0390.0216.9040.3240.3240.0000.0000.0000.000
19A21TRP00.0520.0212.466-1.310-0.2690.479-0.621-0.8990.001
20A22ALA00.0330.0302.376-8.700-5.9201.703-2.286-2.197-0.026
21A23PRO00.051-0.0102.612-1.803-1.1930.244-0.268-0.5860.000
22A24GLY0-0.029-0.0065.483-0.052-0.0520.0000.0000.0000.000
23A25SER0-0.072-0.0317.040-0.095-0.0950.0000.0000.0000.000
24A26LEU00.0410.0088.832-0.201-0.2010.0000.0000.0000.000
25A27LEU0-0.042-0.0149.8740.0050.0050.0000.0000.0000.000
26A28THR00.0390.00411.9550.0300.0300.0000.0000.0000.000
27A29TYR0-0.049-0.04914.017-0.029-0.0290.0000.0000.0000.000
28A30SER00.0170.00617.6260.0410.0410.0000.0000.0000.000
29A31CYS0-0.0430.01220.877-0.023-0.0230.0000.0000.0000.000
30A32PRO00.0500.02723.7960.0140.0140.0000.0000.0000.000
31A33GLN00.0610.01727.039-0.004-0.0040.0000.0000.0000.000
32A34GLY00.0160.01729.943-0.002-0.0020.0000.0000.0000.000
33A35LEU0-0.028-0.01027.092-0.005-0.0050.0000.0000.0000.000
34A36TYR00.003-0.00525.1740.0000.0000.0000.0000.0000.000
35A37PRO00.0210.01420.203-0.012-0.0120.0000.0000.0000.000
36A38SER0-0.0030.03422.0430.0180.0180.0000.0000.0000.000
37A39PRO0-0.047-0.04917.078-0.020-0.0200.0000.0000.0000.000
38A40ALA00.1230.05219.171-0.018-0.0180.0000.0000.0000.000
39A41SER00.0110.01315.6230.0040.0040.0000.0000.0000.000
40A42ARG10.8520.91311.5340.5830.5830.0000.0000.0000.000
41A43LEU00.0410.02710.570-0.013-0.0130.0000.0000.0000.000
42A45LYS10.9230.9597.2120.5790.5790.0000.0000.0000.000
43A46SER00.0460.0055.8360.7310.7310.0000.0000.0000.000
44A47SER0-0.036-0.0365.9960.7210.7210.0000.0000.0000.000
45A48GLY00.0540.0383.0480.2410.7800.229-0.325-0.4420.001
46A49GLN0-0.0180.0003.820-3.259-3.2960.0060.052-0.0210.001
47A50TRP00.008-0.0206.6670.4700.4700.0000.0000.0000.000
48A51GLN0-0.0140.0049.3120.0800.0800.0000.0000.0000.000
49A52THR00.0020.00612.523-0.009-0.0090.0000.0000.0000.000
50A53PRO00.0420.03515.3380.0180.0180.0000.0000.0000.000
51A61LYS10.8930.94117.2520.3650.3650.0000.0000.0000.000
52A62ALA00.0070.01516.9530.0430.0430.0000.0000.0000.000
53A63VAL0-0.003-0.02118.7060.0010.0010.0000.0000.0000.000
54A65LYS10.8890.94524.3730.1820.1820.0000.0000.0000.000
55A66PRO00.0450.01227.6460.0060.0060.0000.0000.0000.000
56A67VAL0-0.0030.01429.948-0.002-0.0020.0000.0000.0000.000
57A68ARG10.8810.93332.0560.0850.0850.0000.0000.0000.000
58A69CYS0-0.0860.01035.4490.0000.0000.0000.0000.0000.000
59A70PRO00.0140.00137.489-0.003-0.0030.0000.0000.0000.000
60A71ALA00.0370.02939.7890.0020.0020.0000.0000.0000.000
61A72PRO00.0000.00443.1800.0010.0010.0000.0000.0000.000
62A73VAL0-0.045-0.01444.084-0.002-0.0020.0000.0000.0000.000
63A74SER0-0.038-0.02746.7430.0000.0000.0000.0000.0000.000
64A75PHE0-0.027-0.01549.9520.0000.0000.0000.0000.0000.000
65A76GLU-1-0.839-0.89152.400-0.019-0.0190.0000.0000.0000.000
66A77ASN0-0.040-0.03155.8160.0010.0010.0000.0000.0000.000
67A78GLY00.1050.04557.1260.0010.0010.0000.0000.0000.000
68A79ILE0-0.076-0.01355.111-0.002-0.0020.0000.0000.0000.000
69A80TYR00.008-0.00948.0130.0000.0000.0000.0000.0000.000
70A81THR0-0.0470.00651.311-0.002-0.0020.0000.0000.0000.000
71A82PRO00.0890.03646.9240.0010.0010.0000.0000.0000.000
72A83ARG11.0041.01746.5560.0440.0440.0000.0000.0000.000
73A84LEU0-0.030-0.01843.284-0.002-0.0020.0000.0000.0000.000
74A85GLY0-0.006-0.00942.6020.0020.0020.0000.0000.0000.000
75A86SER0-0.055-0.01738.317-0.004-0.0040.0000.0000.0000.000
76A87TYR00.035-0.01939.536-0.001-0.0010.0000.0000.0000.000
77A88PRO00.0120.01437.718-0.003-0.0030.0000.0000.0000.000
78A89VAL00.0390.00134.0760.0040.0040.0000.0000.0000.000
79A90GLY0-0.020-0.00537.459-0.002-0.0020.0000.0000.0000.000
80A91GLY0-0.036-0.00440.4480.0020.0020.0000.0000.0000.000
81A92ASN00.017-0.00742.9170.0020.0020.0000.0000.0000.000
82A93VAL0-0.062-0.02546.079-0.002-0.0020.0000.0000.0000.000
83A94SER0-0.020-0.01247.9070.0020.0020.0000.0000.0000.000
84A95PHE0-0.052-0.04147.842-0.002-0.0020.0000.0000.0000.000
85A96GLU-1-0.895-0.94653.616-0.019-0.0190.0000.0000.0000.000
86A97CYS0-0.0340.01654.4700.0000.0000.0000.0000.0000.000
87A98GLU-1-0.833-0.90159.611-0.018-0.0180.0000.0000.0000.000
88A99ASP-1-0.879-0.95362.587-0.014-0.0140.0000.0000.0000.000
89A100GLY0-0.048-0.02865.9610.0000.0000.0000.0000.0000.000
90A101PHE0-0.072-0.03961.1530.0010.0010.0000.0000.0000.000
91A102ILE00.0020.00261.2610.0000.0000.0000.0000.0000.000
92A103LEU0-0.006-0.01154.4680.0000.0000.0000.0000.0000.000
93A104ARG10.8380.92153.6550.0110.0110.0000.0000.0000.000
94A105GLY00.0450.01452.428-0.001-0.0010.0000.0000.0000.000
95A106SER0-0.033-0.02649.4920.0000.0000.0000.0000.0000.000
96A107PRO00.0670.03851.379-0.002-0.0020.0000.0000.0000.000
97A108VAL0-0.011-0.00449.227-0.002-0.0020.0000.0000.0000.000
98A109ARG10.8340.93044.6350.0230.0230.0000.0000.0000.000
99A110GLN00.0350.01442.134-0.004-0.0040.0000.0000.0000.000
100A112ARG10.9770.98537.4090.0210.0210.0000.0000.0000.000
101A113PRO00.0540.00233.258-0.004-0.0040.0000.0000.0000.000
102A114ASN00.0180.00332.068-0.008-0.0080.0000.0000.0000.000
103A115GLY00.0300.00533.130-0.001-0.0010.0000.0000.0000.000
104A116MET0-0.0350.00234.9960.0030.0030.0000.0000.0000.000
105A117TRP00.015-0.00638.005-0.001-0.0010.0000.0000.0000.000
106A118ASP-1-0.872-0.92541.597-0.021-0.0210.0000.0000.0000.000
107A119GLY00.0690.04343.354-0.001-0.0010.0000.0000.0000.000
108A120GLU-1-0.955-0.98045.695-0.009-0.0090.0000.0000.0000.000
109A121THR0-0.046-0.08146.941-0.002-0.0020.0000.0000.0000.000
110A122ALA0-0.0020.02848.6980.0020.0020.0000.0000.0000.000
111A123VAL0-0.044-0.02851.791-0.001-0.0010.0000.0000.0000.000
112A125ASP-1-0.811-0.92657.929-0.009-0.0090.0000.0000.0000.000
113A126ASN00.0410.02060.1440.0010.0010.0000.0000.0000.000
114A127GLY0-0.020-0.00162.7500.0000.0000.0000.0000.0000.000
115A128ALA0-0.032-0.01564.2970.0010.0010.0000.0000.0000.000
116A129GLY0-0.049-0.01162.3580.0000.0000.0000.0000.0000.000
117A130HIS0-0.027-0.02462.1670.0000.0000.0000.0000.0000.000
118A131CYS0-0.118-0.00554.5710.0020.0020.0000.0000.0000.000
119A132PRO00.0390.02357.189-0.001-0.0010.0000.0000.0000.000
120A133ASN00.0650.04055.6750.0000.0000.0000.0000.0000.000
121A134PRO0-0.045-0.00752.1050.0000.0000.0000.0000.0000.000
122A135GLY00.0510.02351.6550.0000.0000.0000.0000.0000.000
123A136ILE0-0.047-0.03047.5100.0010.0010.0000.0000.0000.000
124A137SER0-0.015-0.00644.401-0.002-0.0020.0000.0000.0000.000
125A138LEU00.003-0.01543.301-0.002-0.0020.0000.0000.0000.000
126A139GLY00.0420.02441.377-0.001-0.0010.0000.0000.0000.000
127A140ALA00.0080.00442.256-0.002-0.0020.0000.0000.0000.000
128A141VAL0-0.033-0.02144.121-0.001-0.0010.0000.0000.0000.000
129A142ARG10.8280.89546.6010.0170.0170.0000.0000.0000.000
130A143THR0-0.053-0.02349.439-0.001-0.0010.0000.0000.0000.000
131A144GLY00.0540.02051.8650.0010.0010.0000.0000.0000.000
132A145PHE0-0.008-0.02455.235-0.001-0.0010.0000.0000.0000.000
133A146ARG10.9471.00058.1980.0080.0080.0000.0000.0000.000
134A147PHE00.0430.00456.3000.0000.0000.0000.0000.0000.000
135A148GLY00.0420.02160.0950.0000.0000.0000.0000.0000.000
136A149HIS00.035-0.00560.9180.0000.0000.0000.0000.0000.000
137A150GLY00.0060.00759.5830.0000.0000.0000.0000.0000.000
138A151ASP-1-0.873-0.92358.714-0.006-0.0060.0000.0000.0000.000
139A152LYS10.8020.87753.0610.0010.0010.0000.0000.0000.000
140A153VAL0-0.050-0.00751.359-0.001-0.0010.0000.0000.0000.000
141A154ARG10.8990.93148.2500.0100.0100.0000.0000.0000.000
142A155TYR0-0.022-0.03745.269-0.001-0.0010.0000.0000.0000.000
143A156ARG10.9410.97841.4980.0340.0340.0000.0000.0000.000
144A157CYS0-0.0320.02238.5390.0010.0010.0000.0000.0000.000
145A158SER0-0.058-0.03839.907-0.002-0.0020.0000.0000.0000.000
146A159SER0-0.009-0.02037.026-0.003-0.0030.0000.0000.0000.000
147A160ASN00.010-0.00131.3860.0060.0060.0000.0000.0000.000
148A161LEU0-0.0250.00033.413-0.001-0.0010.0000.0000.0000.000
149A162VAL00.0040.00431.5560.0030.0030.0000.0000.0000.000
150A163LEU00.0290.00235.0220.0010.0010.0000.0000.0000.000
151A164THR0-0.055-0.02536.5350.0030.0030.0000.0000.0000.000
152A165GLY00.0760.04938.666-0.002-0.0020.0000.0000.0000.000
153A166SER0-0.037-0.01942.0570.0000.0000.0000.0000.0000.000
154A167SER00.0410.01942.906-0.001-0.0010.0000.0000.0000.000
155A168GLU-1-0.839-0.91344.848-0.006-0.0060.0000.0000.0000.000
156A169ARG10.8360.92248.3360.0060.0060.0000.0000.0000.000
157A170GLU-1-0.842-0.92351.0170.0000.0000.0000.0000.0000.000
158A172GLN00.009-0.00654.8070.0010.0010.0000.0000.0000.000
159A173GLY00.0800.02758.798-0.001-0.0010.0000.0000.0000.000
160A174ASN0-0.025-0.02357.766-0.001-0.0010.0000.0000.0000.000
161A175GLY00.0750.04360.8110.0000.0000.0000.0000.0000.000
162A176VAL0-0.028-0.01554.612-0.001-0.0010.0000.0000.0000.000
163A177TRP0-0.020-0.00952.7700.0010.0010.0000.0000.0000.000
164A178SER00.0400.02352.0830.0000.0000.0000.0000.0000.000
165A179GLY00.0020.00948.199-0.002-0.0020.0000.0000.0000.000
166A180THR0-0.001-0.01344.5330.0000.0000.0000.0000.0000.000
167A181GLU-1-0.813-0.89446.153-0.014-0.0140.0000.0000.0000.000
168A182PRO0-0.0120.00943.0680.0000.0000.0000.0000.0000.000
169A183ILE00.0120.01939.254-0.002-0.0020.0000.0000.0000.000
170A185ARG10.9420.94833.9410.0180.0180.0000.0000.0000.000
171A186GLN00.008-0.01231.825-0.004-0.0040.0000.0000.0000.000
172A187PRO00.0230.02229.1640.0030.0030.0000.0000.0000.000
173A188TYR00.0390.01026.7480.0030.0030.0000.0000.0000.000
174A189SER0-0.046-0.03426.8760.0010.0010.0000.0000.0000.000
175A190TYR0-0.016-0.01927.7250.0060.0060.0000.0000.0000.000
176A191ASP-1-0.909-0.95122.707-0.096-0.0960.0000.0000.0000.000
177A192PHE0-0.138-0.06523.616-0.005-0.0050.0000.0000.0000.000
178A193PRO00.0070.00923.0000.0060.0060.0000.0000.0000.000
179A194GLU-1-0.911-0.94825.793-0.004-0.0040.0000.0000.0000.000
180A195ASP-1-0.960-0.97927.5080.0210.0210.0000.0000.0000.000
181A196VAL0-0.055-0.02725.6100.0010.0010.0000.0000.0000.000
182A197ALA0-0.018-0.00727.208-0.003-0.0030.0000.0000.0000.000