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: K23Q3

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 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 182
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -1726057.280275
FMO2-HF: Nuclear repulsion 1652938.249322
FMO2-HF: Total energy -73119.030953
FMO2-MP2: Total energy -73324.194568


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.
-17.114-13.65511.482-7.49-7.449-0.037
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 : -0.028 / q_NPA : -0.040
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].
3A5PRO00.0220.0203.844-1.1540.149-0.011-0.636-0.6550.003
4A6GLN00.0680.0185.7900.4610.4610.0000.0000.0000.000
5A7ASN0-0.0290.0048.3470.1060.1060.0000.0000.0000.000
6A8VAL0-0.012-0.0109.7170.1070.1070.0000.0000.0000.000
7A9ASN00.0330.03112.4020.0490.0490.0000.0000.0000.000
8A10ILE0-0.0160.01115.243-0.006-0.0060.0000.0000.0000.000
9A11SER0-0.036-0.02818.2260.0080.0080.0000.0000.0000.000
10A12GLY00.0400.01721.6860.0130.0130.0000.0000.0000.000
11A13GLY00.029-0.00321.3570.0210.0210.0000.0000.0000.000
12A14THR0-0.044-0.01018.037-0.013-0.0130.0000.0000.0000.000
13A15PHE00.011-0.01810.297-0.026-0.0260.0000.0000.0000.000
14A16THR00.0050.02713.5500.0390.0390.0000.0000.0000.000
15A17LEU00.002-0.0137.231-0.092-0.0920.0000.0000.0000.000
16A18SER00.0030.00010.5890.0650.0650.0000.0000.0000.000
17A19HIS00.0600.0418.4560.0470.0470.0000.0000.0000.000
18A20GLY00.0230.0196.6430.3500.3500.0000.0000.0000.000
19A21TRP00.0700.0252.423-1.730-0.0090.746-1.179-1.2870.003
20A22ALA00.0360.0401.904-13.095-14.0919.703-4.687-4.021-0.047
21A23PRO00.025-0.0292.316-1.932-1.2140.840-0.593-0.9650.000
22A24GLY0-0.0170.0045.154-0.126-0.100-0.001-0.003-0.0220.000
23A25SER0-0.062-0.0256.777-0.040-0.0400.0000.0000.0000.000
24A26LEU00.0380.0068.532-0.181-0.1810.0000.0000.0000.000
25A27LEU0-0.028-0.0079.5790.0140.0140.0000.0000.0000.000
26A28THR00.0230.00311.4970.0470.0470.0000.0000.0000.000
27A29TYR0-0.037-0.05014.106-0.026-0.0260.0000.0000.0000.000
28A30SER00.000-0.00717.1820.0450.0450.0000.0000.0000.000
29A31CYS0-0.0220.01720.570-0.026-0.0260.0000.0000.0000.000
30A32PRO00.0550.03023.6000.0130.0130.0000.0000.0000.000
31A33GLN00.0550.02426.954-0.004-0.0040.0000.0000.0000.000
32A34GLY00.0350.02629.6880.0000.0000.0000.0000.0000.000
33A35LEU0-0.052-0.02726.934-0.005-0.0050.0000.0000.0000.000
34A36TYR00.0220.00825.204-0.001-0.0010.0000.0000.0000.000
35A37PRO00.0310.01020.123-0.012-0.0120.0000.0000.0000.000
36A38SER0-0.0080.01821.6700.0180.0180.0000.0000.0000.000
37A39PRO0-0.038-0.03517.141-0.015-0.0150.0000.0000.0000.000
38A40ALA00.1150.04918.784-0.024-0.0240.0000.0000.0000.000
39A41SER00.0130.01315.374-0.003-0.0030.0000.0000.0000.000
40A42ARG10.8210.88611.3100.5640.5640.0000.0000.0000.000
41A43LEU00.0530.04310.239-0.054-0.0540.0000.0000.0000.000
42A45LYS10.9030.9446.9520.5360.5360.0000.0000.0000.000
43A46SER00.0490.0065.8900.8100.8100.0000.0000.0000.000
44A47SER0-0.033-0.0196.0420.6930.6930.0000.0000.0000.000
45A48GLY00.0510.0393.254-0.6540.0310.202-0.423-0.4640.003
46A49GLN0-0.003-0.0083.919-3.049-3.0470.0030.031-0.0350.001
47A50TRP00.000-0.0236.4300.4330.4330.0000.0000.0000.000
48A51GLN00.0080.0069.1470.1330.1330.0000.0000.0000.000
49A52THR0-0.0100.00412.331-0.003-0.0030.0000.0000.0000.000
50A53PRO00.0250.03115.2450.0210.0210.0000.0000.0000.000
51A61LYS10.8860.93716.6620.3340.3340.0000.0000.0000.000
52A62ALA00.0550.04016.9250.0470.0470.0000.0000.0000.000
53A63VAL0-0.019-0.01118.707-0.004-0.0040.0000.0000.0000.000
54A65LYS10.8860.94424.3050.1640.1640.0000.0000.0000.000
55A66PRO00.0380.00527.6690.0060.0060.0000.0000.0000.000
56A67VAL00.0010.02529.776-0.001-0.0010.0000.0000.0000.000
57A68ARG10.8730.92332.0040.0800.0800.0000.0000.0000.000
58A69CYS0-0.0600.02135.4750.0000.0000.0000.0000.0000.000
59A70PRO00.0340.01137.127-0.002-0.0020.0000.0000.0000.000
60A71ALA00.0360.02739.6650.0020.0020.0000.0000.0000.000
61A72PRO00.0310.01843.1940.0010.0010.0000.0000.0000.000
62A73VAL0-0.050-0.01243.561-0.001-0.0010.0000.0000.0000.000
63A74SER0-0.020-0.01346.3020.0000.0000.0000.0000.0000.000
64A75PHE0-0.033-0.02249.6080.0000.0000.0000.0000.0000.000
65A76GLU-1-0.786-0.85352.253-0.016-0.0160.0000.0000.0000.000
66A77ASN0-0.049-0.03955.6600.0000.0000.0000.0000.0000.000
67A78GLY00.1120.04957.3160.0010.0010.0000.0000.0000.000
68A79ILE0-0.079-0.01555.045-0.001-0.0010.0000.0000.0000.000
69A80TYR0-0.019-0.02747.6890.0000.0000.0000.0000.0000.000
70A81THR0-0.0250.00451.181-0.002-0.0020.0000.0000.0000.000
71A82PRO00.0830.03946.8890.0010.0010.0000.0000.0000.000
72A83ARG10.9541.00246.2020.0390.0390.0000.0000.0000.000
73A84LEU0-0.014-0.00842.947-0.002-0.0020.0000.0000.0000.000
74A85GLY00.004-0.00442.3260.0020.0020.0000.0000.0000.000
75A86SER0-0.052-0.01838.094-0.003-0.0030.0000.0000.0000.000
76A87TYR00.030-0.01339.697-0.002-0.0020.0000.0000.0000.000
77A88PRO00.0130.00737.326-0.002-0.0020.0000.0000.0000.000
78A89VAL00.0480.01833.9180.0040.0040.0000.0000.0000.000
79A90GLY0-0.0010.01137.309-0.001-0.0010.0000.0000.0000.000
80A91GLY0-0.037-0.01940.4390.0020.0020.0000.0000.0000.000
81A92ASN0-0.030-0.01942.4420.0030.0030.0000.0000.0000.000
82A93VAL0-0.063-0.02845.614-0.002-0.0020.0000.0000.0000.000
83A94SER00.0050.00747.7240.0020.0020.0000.0000.0000.000
84A95PHE0-0.041-0.03347.650-0.002-0.0020.0000.0000.0000.000
85A96GLU-1-0.901-0.94853.447-0.018-0.0180.0000.0000.0000.000
86A97CYS0-0.0410.01154.2290.0000.0000.0000.0000.0000.000
87A98GLU-1-0.824-0.89559.565-0.016-0.0160.0000.0000.0000.000
88A99ASP-1-0.908-0.96662.733-0.013-0.0130.0000.0000.0000.000
89A100GLY0-0.019-0.00966.0760.0000.0000.0000.0000.0000.000
90A101PHE0-0.086-0.05060.8590.0010.0010.0000.0000.0000.000
91A102ILE00.0180.00960.7770.0000.0000.0000.0000.0000.000
92A103LEU00.0090.00154.2250.0000.0000.0000.0000.0000.000
93A104ARG10.8240.90453.3820.0100.0100.0000.0000.0000.000
94A105GLY00.0430.01852.548-0.001-0.0010.0000.0000.0000.000
95A106SER0-0.004-0.01249.3710.0000.0000.0000.0000.0000.000
96A107PRO00.0400.02651.049-0.001-0.0010.0000.0000.0000.000
97A108VAL0-0.015-0.01549.005-0.001-0.0010.0000.0000.0000.000
98A109ARG10.8090.91944.4340.0210.0210.0000.0000.0000.000
99A110GLN00.005-0.01841.885-0.004-0.0040.0000.0000.0000.000
100A112ARG10.9340.95537.0660.0200.0200.0000.0000.0000.000
101A113PRO00.036-0.01232.978-0.003-0.0030.0000.0000.0000.000
102A114ASN00.0170.00731.627-0.007-0.0070.0000.0000.0000.000
103A115GLY00.0180.00232.647-0.001-0.0010.0000.0000.0000.000
104A116MET0-0.0010.01134.3360.0030.0030.0000.0000.0000.000
105A117TRP00.018-0.00237.6220.0000.0000.0000.0000.0000.000
106A118ASP-1-0.831-0.88141.198-0.021-0.0210.0000.0000.0000.000
107A119GLY00.0790.03742.937-0.001-0.0010.0000.0000.0000.000
108A120GLU-1-0.946-0.97045.317-0.009-0.0090.0000.0000.0000.000
109A121THR0-0.047-0.08946.403-0.002-0.0020.0000.0000.0000.000
110A122ALA0-0.0160.01848.4630.0010.0010.0000.0000.0000.000
111A123VAL0-0.041-0.02851.538-0.001-0.0010.0000.0000.0000.000
112A125ASP-1-0.802-0.91957.650-0.008-0.0080.0000.0000.0000.000
113A126ASN00.0400.03059.9170.0010.0010.0000.0000.0000.000
114A127GLY0-0.0100.00062.4130.0000.0000.0000.0000.0000.000
115A128ALA0-0.042-0.01363.8830.0010.0010.0000.0000.0000.000
116A129GLY0-0.044-0.01762.4010.0000.0000.0000.0000.0000.000
117A130HIS0-0.050-0.03662.0310.0000.0000.0000.0000.0000.000
118A131CYS0-0.0940.00154.4440.0020.0020.0000.0000.0000.000
119A132PRO00.0460.02557.185-0.001-0.0010.0000.0000.0000.000
120A133ASN00.0430.03955.6820.0000.0000.0000.0000.0000.000
121A134PRO0-0.0210.00252.1070.0000.0000.0000.0000.0000.000
122A135GLY00.0580.03251.4280.0000.0000.0000.0000.0000.000
123A136ILE0-0.049-0.03347.1460.0010.0010.0000.0000.0000.000
124A137SER00.0050.00543.954-0.001-0.0010.0000.0000.0000.000
125A138LEU00.001-0.01143.159-0.002-0.0020.0000.0000.0000.000
126A139GLY00.0340.00940.853-0.001-0.0010.0000.0000.0000.000
127A140ALA0-0.017-0.00341.553-0.002-0.0020.0000.0000.0000.000
128A141VAL0-0.018-0.01443.734-0.001-0.0010.0000.0000.0000.000
129A142ARG10.7670.85346.4650.0150.0150.0000.0000.0000.000
130A143THR0-0.064-0.03849.211-0.001-0.0010.0000.0000.0000.000
131A144GLY00.0590.01751.3850.0010.0010.0000.0000.0000.000
132A145PHE0-0.017-0.01354.765-0.001-0.0010.0000.0000.0000.000
133A146ARG10.9420.99957.8950.0070.0070.0000.0000.0000.000
134A147PHE00.0600.01056.2460.0000.0000.0000.0000.0000.000
135A148GLY00.0440.02059.9970.0000.0000.0000.0000.0000.000
136A149HIS00.033-0.00360.9650.0000.0000.0000.0000.0000.000
137A150GLY00.0050.01159.6110.0000.0000.0000.0000.0000.000
138A151ASP-1-0.862-0.92158.535-0.005-0.0050.0000.0000.0000.000
139A152LYS10.7860.86952.7750.0010.0010.0000.0000.0000.000
140A153VAL0-0.045-0.01251.268-0.001-0.0010.0000.0000.0000.000
141A154ARG10.8930.93347.9620.0080.0080.0000.0000.0000.000
142A155TYR0-0.005-0.03045.071-0.001-0.0010.0000.0000.0000.000
143A156ARG10.9110.96240.9090.0300.0300.0000.0000.0000.000
144A157CYS0-0.0160.02838.2880.0010.0010.0000.0000.0000.000
145A158SER0-0.032-0.02640.427-0.001-0.0010.0000.0000.0000.000
146A159SER0-0.031-0.03635.760-0.002-0.0020.0000.0000.0000.000
147A160ASN00.0190.01131.1600.0050.0050.0000.0000.0000.000
148A161LEU0-0.0250.00233.096-0.002-0.0020.0000.0000.0000.000
149A162VAL0-0.0060.00131.1860.0030.0030.0000.0000.0000.000
150A163LEU00.0430.00834.6690.0000.0000.0000.0000.0000.000
151A164THR0-0.079-0.05236.0710.0020.0020.0000.0000.0000.000
152A165GLY00.0690.04838.312-0.001-0.0010.0000.0000.0000.000
153A166SER0-0.046-0.01541.8420.0010.0010.0000.0000.0000.000
154A167SER00.0380.01542.573-0.001-0.0010.0000.0000.0000.000
155A168GLU-1-0.839-0.90844.573-0.004-0.0040.0000.0000.0000.000
156A169ARG10.8340.91948.1180.0050.0050.0000.0000.0000.000
157A170GLU-1-0.847-0.92250.7950.0000.0000.0000.0000.0000.000
158A172GLN00.004-0.01054.5560.0010.0010.0000.0000.0000.000
159A173GLY00.0800.02858.5320.0000.0000.0000.0000.0000.000
160A174ASN0-0.030-0.01857.108-0.001-0.0010.0000.0000.0000.000
161A175GLY00.0790.04660.5850.0000.0000.0000.0000.0000.000
162A176VAL0-0.047-0.02954.211-0.001-0.0010.0000.0000.0000.000
163A177TRP0-0.013-0.00952.5300.0010.0010.0000.0000.0000.000
164A178SER00.0430.02651.9480.0000.0000.0000.0000.0000.000
165A179GLY00.0120.01547.948-0.001-0.0010.0000.0000.0000.000
166A180THR00.002-0.01444.2720.0000.0000.0000.0000.0000.000
167A181GLU-1-0.788-0.88845.411-0.014-0.0140.0000.0000.0000.000
168A182PRO0-0.034-0.00142.4770.0000.0000.0000.0000.0000.000
169A183ILE00.0410.04139.006-0.003-0.0030.0000.0000.0000.000
170A185ARG10.9240.93733.8340.0190.0190.0000.0000.0000.000
171A186GLN00.0340.00131.600-0.003-0.0030.0000.0000.0000.000
172A187PRO00.0030.01928.7490.0020.0020.0000.0000.0000.000
173A188TYR00.0220.00226.4910.0030.0030.0000.0000.0000.000
174A189SER0-0.060-0.04926.757-0.001-0.0010.0000.0000.0000.000
175A190TYR00.012-0.00227.4610.0060.0060.0000.0000.0000.000
176A191ASP-1-0.923-0.95922.364-0.095-0.0950.0000.0000.0000.000
177A192PHE0-0.107-0.04623.151-0.009-0.0090.0000.0000.0000.000
178A193PRO0-0.0070.00222.4380.0070.0070.0000.0000.0000.000
179A194GLU-1-0.889-0.94125.321-0.009-0.0090.0000.0000.0000.000
180A195ASP-1-0.952-0.98127.1110.0150.0150.0000.0000.0000.000
181A196VAL0-0.077-0.03025.1540.0000.0000.0000.0000.0000.000
182A197ALA0-0.029-0.00927.393-0.005-0.0050.0000.0000.0000.000