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: RY548

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 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 182
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -1724207.103738
FMO2-HF: Nuclear repulsion 1651088.959696
FMO2-HF: Total energy -73118.144042
FMO2-MP2: Total energy -73323.485091


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.
-2.6612.0511.067-2.417-3.363-0.002
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 : 0.004 / q_NPA : -0.019
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].
3A5PRO00.0100.0173.8440.0431.130-0.014-0.481-0.5920.002
4A6GLN00.0630.0165.5640.9290.9290.0000.0000.0000.000
5A7ASN0-0.0360.0018.4460.0840.0840.0000.0000.0000.000
6A8VAL00.000-0.00210.3500.0740.0740.0000.0000.0000.000
7A9ASN00.0470.04612.9370.1200.1200.0000.0000.0000.000
8A10ILE0-0.0230.00015.967-0.014-0.0140.0000.0000.0000.000
9A11SER0-0.053-0.03719.219-0.011-0.0110.0000.0000.0000.000
10A12GLY00.0510.01622.5140.0170.0170.0000.0000.0000.000
11A13GLY00.0260.00622.4480.0150.0150.0000.0000.0000.000
12A14THR0-0.053-0.01219.069-0.014-0.0140.0000.0000.0000.000
13A15PHE00.026-0.01611.615-0.007-0.0070.0000.0000.0000.000
14A16THR00.0190.03215.007-0.007-0.0070.0000.0000.0000.000
15A17LEU0-0.021-0.0218.400-0.002-0.0020.0000.0000.0000.000
16A18SER0-0.002-0.00711.864-0.018-0.0180.0000.0000.0000.000
17A19HIS00.0570.0479.210-0.045-0.0450.0000.0000.0000.000
18A20GLY00.0370.0187.4960.6050.6050.0000.0000.0000.000
19A21TRP00.0470.0143.293-1.387-0.6720.071-0.290-0.4950.002
20A22ALA00.0300.0302.8601.0942.8880.528-1.107-1.215-0.008
21A23PRO00.045-0.0112.610-2.462-1.8620.238-0.268-0.5700.000
22A24GLY0-0.026-0.0065.521-0.380-0.3800.0000.0000.0000.000
23A25SER0-0.075-0.0307.194-0.572-0.5720.0000.0000.0000.000
24A26LEU00.0410.0068.828-0.081-0.0810.0000.0000.0000.000
25A27LEU0-0.035-0.01110.900-0.040-0.0400.0000.0000.0000.000
26A28THR00.0370.00412.575-0.046-0.0460.0000.0000.0000.000
27A29TYR0-0.060-0.06214.905-0.031-0.0310.0000.0000.0000.000
28A30SER00.0290.01418.5600.0140.0140.0000.0000.0000.000
29A31CYS0-0.0570.00021.985-0.001-0.0010.0000.0000.0000.000
30A32PRO00.0480.02824.9730.0110.0110.0000.0000.0000.000
31A33GLN00.0630.01928.261-0.002-0.0020.0000.0000.0000.000
32A34GLY00.0090.01231.113-0.008-0.0080.0000.0000.0000.000
33A35LEU0-0.021-0.00728.107-0.008-0.0080.0000.0000.0000.000
34A36TYR0-0.002-0.00525.5390.0100.0100.0000.0000.0000.000
35A37PRO00.0260.01320.937-0.021-0.0210.0000.0000.0000.000
36A38SER00.0020.02422.4320.0190.0190.0000.0000.0000.000
37A39PRO0-0.066-0.05717.420-0.038-0.0380.0000.0000.0000.000
38A40ALA00.1230.05319.665-0.012-0.0120.0000.0000.0000.000
39A41SER0-0.0020.00615.6990.0270.0270.0000.0000.0000.000
40A42ARG10.8710.92211.714-0.081-0.0810.0000.0000.0000.000
41A43LEU00.0420.02810.5760.0480.0480.0000.0000.0000.000
42A45LYS10.9490.9797.240-0.258-0.2580.0000.0000.0000.000
43A46SER00.0380.0015.9031.0501.0500.0000.0000.0000.000
44A47SER0-0.033-0.0255.9960.8100.8100.0000.0000.0000.000
45A48GLY00.0620.0412.912-0.0950.4550.239-0.329-0.4610.001
46A49GLN0-0.013-0.0043.677-3.085-3.1190.0050.058-0.0300.001
47A50TRP0-0.005-0.0307.0040.6250.6250.0000.0000.0000.000
48A51GLN0-0.031-0.0139.340-0.119-0.1190.0000.0000.0000.000
49A52THR0-0.009-0.00112.5600.0640.0640.0000.0000.0000.000
50A53PRO00.0450.03915.366-0.033-0.0330.0000.0000.0000.000
51A61LYS10.9120.95517.5160.1990.1990.0000.0000.0000.000
52A62ALA00.0030.01117.6570.0220.0220.0000.0000.0000.000
53A63VAL0-0.007-0.01819.441-0.027-0.0270.0000.0000.0000.000
54A65LYS10.9030.96125.342-0.016-0.0160.0000.0000.0000.000
55A66PRO00.0490.01628.4430.0090.0090.0000.0000.0000.000
56A67VAL0-0.0090.01330.7530.0030.0030.0000.0000.0000.000
57A68ARG10.8960.94432.755-0.026-0.0260.0000.0000.0000.000
58A69CYS0-0.0880.00835.9300.0130.0130.0000.0000.0000.000
59A70PRO00.0110.00237.938-0.006-0.0060.0000.0000.0000.000
60A71ALA00.0420.02740.095-0.001-0.0010.0000.0000.0000.000
61A72PRO0-0.0050.00243.4910.0030.0030.0000.0000.0000.000
62A73VAL0-0.044-0.01344.132-0.002-0.0020.0000.0000.0000.000
63A74SER0-0.044-0.02746.786-0.002-0.0020.0000.0000.0000.000
64A75PHE0-0.027-0.01850.0650.0020.0020.0000.0000.0000.000
65A76GLU-1-0.931-0.96352.5660.0310.0310.0000.0000.0000.000
66A77ASN0-0.034-0.01255.9190.0020.0020.0000.0000.0000.000
67A78GLY00.1100.04757.4440.0000.0000.0000.0000.0000.000
68A79ILE0-0.078-0.00955.4920.0000.0000.0000.0000.0000.000
69A80TYR00.005-0.01548.3810.0010.0010.0000.0000.0000.000
70A81THR0-0.0430.00851.885-0.002-0.0020.0000.0000.0000.000
71A82PRO00.0830.03347.6390.0010.0010.0000.0000.0000.000
72A83ARG11.0151.01746.983-0.010-0.0100.0000.0000.0000.000
73A84LEU0-0.040-0.02343.843-0.003-0.0030.0000.0000.0000.000
74A85GLY0-0.006-0.01042.9120.0020.0020.0000.0000.0000.000
75A86SER0-0.067-0.03038.7580.0030.0030.0000.0000.0000.000
76A87TYR00.032-0.01540.081-0.004-0.0040.0000.0000.0000.000
77A88PRO00.0100.01538.5080.0040.0040.0000.0000.0000.000
78A89VAL00.042-0.00234.9120.0030.0030.0000.0000.0000.000
79A90GLY0-0.025-0.00538.361-0.005-0.0050.0000.0000.0000.000
80A91GLY0-0.0310.00141.453-0.002-0.0020.0000.0000.0000.000
81A92ASN00.026-0.00343.8180.0060.0060.0000.0000.0000.000
82A93VAL0-0.067-0.02746.691-0.003-0.0030.0000.0000.0000.000
83A94SER0-0.023-0.01548.5830.0020.0020.0000.0000.0000.000
84A95PHE0-0.045-0.03948.280-0.001-0.0010.0000.0000.0000.000
85A96GLU-1-0.895-0.94754.1420.0160.0160.0000.0000.0000.000
86A97CYS0-0.0400.01754.7090.0000.0000.0000.0000.0000.000
87A98GLU-1-0.861-0.93059.9960.0190.0190.0000.0000.0000.000
88A99ASP-1-0.878-0.95662.9240.0170.0170.0000.0000.0000.000
89A100GLY0-0.056-0.03066.2160.0000.0000.0000.0000.0000.000
90A101PHE0-0.068-0.03261.3990.0020.0020.0000.0000.0000.000
91A102ILE00.0040.00161.608-0.001-0.0010.0000.0000.0000.000
92A103LEU0-0.009-0.01654.9280.0010.0010.0000.0000.0000.000
93A104ARG10.8600.93153.838-0.040-0.0400.0000.0000.0000.000
94A105GLY00.0440.01552.8210.0000.0000.0000.0000.0000.000
95A106SER0-0.032-0.02050.066-0.001-0.0010.0000.0000.0000.000
96A107PRO00.0740.04151.9220.0000.0000.0000.0000.0000.000
97A108VAL0-0.009-0.00249.988-0.002-0.0020.0000.0000.0000.000
98A109ARG10.8570.94445.008-0.043-0.0430.0000.0000.0000.000
99A110GLN00.0370.01442.925-0.005-0.0050.0000.0000.0000.000
100A112ARG11.0271.00737.314-0.070-0.0700.0000.0000.0000.000
101A113PRO00.0530.00434.2970.0010.0010.0000.0000.0000.000
102A114ASN00.002-0.01132.771-0.005-0.0050.0000.0000.0000.000
103A115GLY00.0220.00033.7490.0060.0060.0000.0000.0000.000
104A116MET0-0.068-0.02835.6020.0000.0000.0000.0000.0000.000
105A117TRP00.001-0.01438.518-0.003-0.0030.0000.0000.0000.000
106A118ASP-1-0.882-0.92642.1640.0450.0450.0000.0000.0000.000
107A119GLY00.0520.02244.016-0.002-0.0020.0000.0000.0000.000
108A120GLU-1-0.940-0.97946.1960.0500.0500.0000.0000.0000.000
109A121THR0-0.081-0.10147.369-0.003-0.0030.0000.0000.0000.000
110A122ALA00.0000.02749.0120.0000.0000.0000.0000.0000.000
111A123VAL0-0.041-0.02952.1020.0010.0010.0000.0000.0000.000
112A125ASP-1-0.835-0.93158.1690.0350.0350.0000.0000.0000.000
113A126ASN00.0410.02060.3070.0000.0000.0000.0000.0000.000
114A127GLY0-0.020-0.00362.861-0.001-0.0010.0000.0000.0000.000
115A128ALA0-0.030-0.01664.3990.0000.0000.0000.0000.0000.000
116A129GLY0-0.059-0.01562.3730.0000.0000.0000.0000.0000.000
117A130HIS0-0.029-0.02062.199-0.001-0.0010.0000.0000.0000.000
118A131CYS0-0.132-0.00554.5920.0020.0020.0000.0000.0000.000
119A132PRO00.0480.02957.146-0.001-0.0010.0000.0000.0000.000
120A133ASN00.1020.05955.6660.0040.0040.0000.0000.0000.000
121A134PRO0-0.039-0.00252.1340.0000.0000.0000.0000.0000.000
122A135GLY00.0450.01751.6770.0020.0020.0000.0000.0000.000
123A136ILE0-0.023-0.02047.6040.0030.0030.0000.0000.0000.000
124A137SER0-0.009-0.00744.387-0.002-0.0020.0000.0000.0000.000
125A138LEU00.001-0.01643.551-0.001-0.0010.0000.0000.0000.000
126A139GLY00.0390.02441.4520.0040.0040.0000.0000.0000.000
127A140ALA00.0180.00942.2700.0020.0020.0000.0000.0000.000
128A141VAL0-0.034-0.02344.136-0.004-0.0040.0000.0000.0000.000
129A142ARG10.8920.95646.620-0.037-0.0370.0000.0000.0000.000
130A143THR0-0.054-0.02049.460-0.003-0.0030.0000.0000.0000.000
131A144GLY00.0420.01151.8890.0020.0020.0000.0000.0000.000
132A145PHE0-0.004-0.01655.2590.0000.0000.0000.0000.0000.000
133A146ARG10.9450.99258.219-0.034-0.0340.0000.0000.0000.000
134A147PHE00.0440.00356.3530.0020.0020.0000.0000.0000.000
135A148GLY00.0410.02460.112-0.001-0.0010.0000.0000.0000.000
136A149HIS00.028-0.00760.9390.0020.0020.0000.0000.0000.000
137A150GLY00.0080.01459.609-0.001-0.0010.0000.0000.0000.000
138A151ASP-1-0.901-0.93658.9160.0400.0400.0000.0000.0000.000
139A152LYS10.9340.95653.542-0.053-0.0530.0000.0000.0000.000
140A153VAL0-0.052-0.00651.295-0.002-0.0020.0000.0000.0000.000
141A154ARG10.9550.96548.287-0.051-0.0510.0000.0000.0000.000
142A155TYR0-0.013-0.03245.234-0.003-0.0030.0000.0000.0000.000
143A156ARG10.9460.98341.840-0.048-0.0480.0000.0000.0000.000
144A157CYS0-0.0390.01538.5500.0020.0020.0000.0000.0000.000
145A158SER0-0.064-0.04439.9290.0000.0000.0000.0000.0000.000
146A159SER00.000-0.01236.8880.0030.0030.0000.0000.0000.000
147A160ASN00.011-0.00131.4100.0010.0010.0000.0000.0000.000
148A161LEU0-0.031-0.00433.4310.0070.0070.0000.0000.0000.000
149A162VAL00.0150.00731.5800.0010.0010.0000.0000.0000.000
150A163LEU00.019-0.00335.038-0.003-0.0030.0000.0000.0000.000
151A164THR0-0.051-0.02336.4910.0100.0100.0000.0000.0000.000
152A165GLY00.0720.04438.680-0.006-0.0060.0000.0000.0000.000
153A166SER0-0.031-0.01342.0760.0020.0020.0000.0000.0000.000
154A167SER00.0330.01442.909-0.003-0.0030.0000.0000.0000.000
155A168GLU-1-0.943-0.97744.8710.0580.0580.0000.0000.0000.000
156A169ARG10.8390.92048.470-0.058-0.0580.0000.0000.0000.000
157A170GLU-1-0.893-0.96351.0380.0520.0520.0000.0000.0000.000
158A172GLN00.0280.00654.9030.0010.0010.0000.0000.0000.000
159A173GLY00.0780.02658.817-0.002-0.0020.0000.0000.0000.000
160A174ASN0-0.023-0.02757.760-0.002-0.0020.0000.0000.0000.000
161A175GLY00.0720.04360.823-0.001-0.0010.0000.0000.0000.000
162A176VAL0-0.031-0.01854.5950.0000.0000.0000.0000.0000.000
163A177TRP0-0.026-0.02052.8300.0020.0020.0000.0000.0000.000
164A178SER00.0460.02752.0060.0020.0020.0000.0000.0000.000
165A179GLY0-0.0040.00448.2140.0000.0000.0000.0000.0000.000
166A180THR0-0.012-0.01844.4450.0000.0000.0000.0000.0000.000
167A181GLU-1-0.790-0.87645.7220.0570.0570.0000.0000.0000.000
168A182PRO0-0.0150.00943.0790.0040.0040.0000.0000.0000.000
169A183ILE0-0.0020.01839.308-0.005-0.0050.0000.0000.0000.000
170A185ARG10.9770.98733.975-0.103-0.1030.0000.0000.0000.000
171A186GLN00.020-0.00132.1200.0040.0040.0000.0000.0000.000
172A187PRO00.0240.02129.1680.0080.0080.0000.0000.0000.000
173A188TYR00.0500.01126.9540.0080.0080.0000.0000.0000.000
174A189SER0-0.046-0.03327.1910.0080.0080.0000.0000.0000.000
175A190TYR0-0.019-0.02227.6720.0000.0000.0000.0000.0000.000
176A191ASP-1-0.909-0.94723.0160.1970.1970.0000.0000.0000.000
177A192PHE0-0.144-0.06624.0330.0040.0040.0000.0000.0000.000
178A193PRO0-0.0100.01024.4220.0050.0050.0000.0000.0000.000
179A194GLU-1-0.895-0.94926.3380.1300.1300.0000.0000.0000.000
180A195ASP-1-0.961-0.98428.2470.1530.1530.0000.0000.0000.000
181A196VAL0-0.048-0.02126.5940.0040.0040.0000.0000.0000.000
182A197ALA0-0.024-0.01028.288-0.016-0.0160.0000.0000.0000.000