FMODB

FMODB: The database of quantum mechanical data based on the FMO method

Last updated: 2025-10-17

All entries: 77277

Number of unique PDB entries: 32023

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FMODB ID: MRG3Z

Calculation Name: 2BV8-B-Xray547

Preferred Name:

Target Type:

Ligand Name: phycocyanobilin | phycoerythrobilin | n-methyl asparagine

Ligand 3-letter code: CYC | PEB | MEN

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 2BV8

Chain ID: B

ChEMBL ID:

UniProt ID: Q6B8L6

Base Structure: X-ray

Registration Date: 2025-10-03

Reference: Sci Data 11, 1164 (2024).

DOI: https://doi.org/10.1038/s41597-024-03999-2

Apendix: None


IFIE MAP

IFIE Diagram


Modeling method
Optimization MOE:Amber10:EHT
Restraint OptAll
Protonation MOE:Protonate 3D
Complement MOE:Homology Modeling
Water No
Procedure Manual calculation
Remarks
ac.sh, 23 2024 Oct; Missing atoms/residues were imported from a 100% homology model, which was constructed by MOE.
FMO calculation
FMO method FMO2-MP2/6-31G(d)
Fragmentation Auto
Number of fragment 172
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922
Total energy (hartree)
FMO2-HF: Electronic energy -1523968.709854
FMO2-HF: Nuclear repulsion 1458831.81306
FMO2-HF: Total energy -65136.896794
FMO2-MP2: Total energy -65322.551796


3D Structure Molmil
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:1:MET)


Summations of interaction energy for fragment #1(A:1:MET)
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.
-145.75-139.3925.683-3.585-8.454-0.021
Interaction energy analysis for fragmet #1(A:1:MET)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 1 / q_Mulliken : 0.813 / q_NPA : 0.903
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].
3A3ASP-1-0.758-0.8573.697-36.302-33.913-0.010-1.000-1.379-0.005
92A92TYR00.008-0.0014.738-2.613-2.520-0.001-0.002-0.0890.000
99A99ALA0-0.039-0.0085.609-0.232-0.170-0.001-0.006-0.0540.000
103A103SER0-0.020-0.0113.232-8.364-6.9060.063-0.786-0.735-0.005
104A104VAL0-0.021-0.0242.534-3.147-2.5274.076-1.200-3.496-0.007
105A105LEU00.0010.0073.5502.7632.8750.0320.011-0.1550.000
107A107ASP-1-0.927-0.9773.772-53.038-52.5320.001-0.191-0.316-0.001
108A108ARG10.8550.9212.97046.92248.0401.523-0.411-2.230-0.003
4A4ALA00.0320.0055.624-0.653-0.6530.0000.0000.0000.000
5A5PHE00.017-0.0018.9641.8781.8780.0000.0000.0000.000
6A6ALA0-0.011-0.0156.0780.8990.8990.0000.0000.0000.000
7A7LYS10.8260.9137.94232.62132.6210.0000.0000.0000.000
8A8VAL00.0150.0038.9262.0112.0110.0000.0000.0000.000
9A9VAL0-0.006-0.00111.1201.7081.7080.0000.0000.0000.000
10A10ALA00.0100.0108.3871.5301.5300.0000.0000.0000.000
11A11GLN0-0.050-0.03810.4861.9891.9890.0000.0000.0000.000
12A12ALA0-0.0220.00013.1101.5891.5890.0000.0000.0000.000
13A13ASP-1-0.900-0.94712.773-20.996-20.9960.0000.0000.0000.000
14A14ALA0-0.019-0.01113.1151.2481.2480.0000.0000.0000.000
15A15ARG10.7550.86015.02018.45718.4570.0000.0000.0000.000
16A16GLY0-0.0150.00617.8251.0151.0150.0000.0000.0000.000
17A17GLU-1-0.912-0.93218.628-14.280-14.2800.0000.0000.0000.000
18A18PHE0-0.014-0.01418.407-0.850-0.8500.0000.0000.0000.000
19A19LEU0-0.005-0.00315.2020.0320.0320.0000.0000.0000.000
20A20SER00.008-0.00919.5060.8580.8580.0000.0000.0000.000
21A21ASN00.038-0.01021.491-0.710-0.7100.0000.0000.0000.000
22A22THR00.0350.02422.6990.0180.0180.0000.0000.0000.000
23A23GLN00.0400.03817.1690.5060.5060.0000.0000.0000.000
24A24LEU0-0.014-0.00418.017-0.694-0.6940.0000.0000.0000.000
25A25ASP-1-0.903-0.94819.497-13.186-13.1860.0000.0000.0000.000
26A26ALA0-0.009-0.00718.188-0.132-0.1320.0000.0000.0000.000
27A27LEU00.005-0.00213.064-0.416-0.4160.0000.0000.0000.000
28A28ALA00.0050.00216.355-0.211-0.2110.0000.0000.0000.000
29A29ASN0-0.036-0.02419.2170.6540.6540.0000.0000.0000.000
30A30MET0-0.0040.00511.839-0.193-0.1930.0000.0000.0000.000
31A31ILE0-0.058-0.01914.951-0.252-0.2520.0000.0000.0000.000
32A32ALA0-0.043-0.01517.4610.4020.4020.0000.0000.0000.000
33A33GLU-1-0.860-0.91916.233-16.381-16.3810.0000.0000.0000.000
34A34GLY00.0340.01616.159-0.124-0.1240.0000.0000.0000.000
35A35ASN0-0.021-0.02516.761-0.655-0.6550.0000.0000.0000.000
36A36LYS10.9320.96319.15712.43012.4300.0000.0000.0000.000
37A37ARG10.7540.83812.22920.04720.0470.0000.0000.0000.000
38A38LEU0-0.018-0.01313.885-0.507-0.5070.0000.0000.0000.000
39A39ASP-1-0.905-0.95715.923-12.836-12.8360.0000.0000.0000.000
40A40ILE0-0.015-0.00416.3070.2940.2940.0000.0000.0000.000
41A41VAL00.0210.00611.8580.0610.0610.0000.0000.0000.000
42A42ASN0-0.029-0.01314.971-0.003-0.0030.0000.0000.0000.000
43A43ARG10.8850.95117.61512.05012.0500.0000.0000.0000.000
44A44ILE00.0350.01214.7480.2690.2690.0000.0000.0000.000
45A45ASN0-0.052-0.04213.185-0.195-0.1950.0000.0000.0000.000
46A46SER0-0.073-0.03916.4570.4800.4800.0000.0000.0000.000
47A47ASN0-0.027-0.01219.9360.7510.7510.0000.0000.0000.000
48A48ALA00.0210.02916.8440.2720.2720.0000.0000.0000.000
49A49SER00.013-0.00218.6940.1020.1020.0000.0000.0000.000
50A50ALA00.0030.01221.2620.3550.3550.0000.0000.0000.000
51A51ILE00.0370.02519.1540.3280.3280.0000.0000.0000.000
52A52VAL00.0290.02618.4420.2250.2250.0000.0000.0000.000
53A53SER0-0.031-0.03721.3500.3990.3990.0000.0000.0000.000
54A54ASN0-0.032-0.01624.8860.6330.6330.0000.0000.0000.000
55A55SER00.0410.01823.1070.3560.3560.0000.0000.0000.000
56A56ALA00.0050.00524.2140.2000.2000.0000.0000.0000.000
57A57ARG10.8650.92025.9529.6849.6840.0000.0000.0000.000
58A58ALA00.0180.01328.4960.3160.3160.0000.0000.0000.000
59A59LEU00.0370.02325.2860.2520.2520.0000.0000.0000.000
60A60PHE0-0.025-0.04826.3600.1780.1780.0000.0000.0000.000
61A61ALA0-0.028-0.00331.2150.3010.3010.0000.0000.0000.000
62A62GLU-1-0.865-0.92730.865-9.430-9.4300.0000.0000.0000.000
63A63GLN00.0250.02629.1910.0400.0400.0000.0000.0000.000
64A64PRO00.0440.02732.502-0.162-0.1620.0000.0000.0000.000
65A65GLN00.018-0.00634.718-0.155-0.1550.0000.0000.0000.000
66A66LEU0-0.027-0.00528.134-0.036-0.0360.0000.0000.0000.000
67A67ILE0-0.023-0.01830.640-0.141-0.1410.0000.0000.0000.000
68A68GLN00.0030.02133.0350.1790.1790.0000.0000.0000.000
69A69PRO0-0.001-0.02735.572-0.203-0.2030.0000.0000.0000.000
70A70GLY0-0.014-0.00335.8170.1150.1150.0000.0000.0000.000
71A71GLY00.0450.04733.380-0.160-0.1600.0000.0000.0000.000
72A72ASN00.0260.02126.574-0.334-0.3340.0000.0000.0000.000
73A73ALA00.0650.03027.418-0.247-0.2470.0000.0000.0000.000
74A74TYR00.0140.02528.5530.0980.0980.0000.0000.0000.000
75A75THR0-0.065-0.04330.621-0.201-0.2010.0000.0000.0000.000
76A76ASN00.0730.01829.346-0.264-0.2640.0000.0000.0000.000
77A77ARG10.9700.99125.26710.48810.4880.0000.0000.0000.000
78A78ARG10.8430.91825.0849.2879.2870.0000.0000.0000.000
79A79MET00.0280.03725.051-0.434-0.4340.0000.0000.0000.000
80A80ALA00.003-0.00623.367-0.315-0.3150.0000.0000.0000.000
81A81ALA0-0.032-0.01220.881-0.471-0.4710.0000.0000.0000.000
82A82CYS00.0470.03020.207-0.500-0.5000.0000.0000.0000.000
83A83LEU00.009-0.00120.668-0.380-0.3800.0000.0000.0000.000
84A84ARG10.8520.90816.37214.34914.3490.0000.0000.0000.000
85A85ASP-1-0.767-0.84916.132-15.931-15.9310.0000.0000.0000.000
86A86MET0-0.049-0.01515.933-0.548-0.5480.0000.0000.0000.000
87A87GLU-1-0.882-0.95214.533-15.964-15.9640.0000.0000.0000.000
88A88ILE0-0.083-0.04011.107-1.036-1.0360.0000.0000.0000.000
89A89VAL00.0520.01711.196-1.581-1.5810.0000.0000.0000.000
90A90LEU00.0160.02112.408-0.968-0.9680.0000.0000.0000.000
91A91ARG10.8980.9518.47620.25920.2590.0000.0000.0000.000
93A93VAL00.0190.0158.653-2.041-2.0410.0000.0000.0000.000
94A94SER0-0.034-0.02110.103-0.401-0.4010.0000.0000.0000.000
95A95TYR0-0.037-0.0265.266-0.459-0.4590.0000.0000.0000.000
96A96ALA00.0060.0066.662-2.113-2.1130.0000.0000.0000.000
97A97GLU-1-0.853-0.9338.013-18.965-18.9650.0000.0000.0000.000
98A98ILE0-0.027-0.0177.4220.5400.5400.0000.0000.0000.000
100A100GLY00.0460.0277.467-0.441-0.4410.0000.0000.0000.000
101A101ASP-1-0.806-0.8905.701-41.670-41.6700.0000.0000.0000.000
102A102SER00.005-0.0196.542-0.991-0.9910.0000.0000.0000.000
106A106ASP-1-0.753-0.8537.001-26.447-26.4470.0000.0000.0000.000
109A109CYS0-0.067-0.0156.9683.0813.0810.0000.0000.0000.000
110A110LEU00.0020.01910.0042.0212.0210.0000.0000.0000.000
111A111ASN0-0.009-0.00410.6753.1153.1150.0000.0000.0000.000
112A112GLY00.0220.02312.559-0.093-0.0930.0000.0000.0000.000
113A113LEU0-0.0160.01314.3431.1771.1770.0000.0000.0000.000
114A114ARG10.8830.94216.62516.21016.2100.0000.0000.0000.000
115A115GLU-1-0.863-0.94318.602-15.437-15.4370.0000.0000.0000.000
116A116THR0-0.047-0.03117.6340.6870.6870.0000.0000.0000.000
117A117TYR0-0.058-0.06618.3890.5870.5870.0000.0000.0000.000
118A118GLN0-0.011-0.01222.1760.4360.4360.0000.0000.0000.000
119A119ALA0-0.028-0.00823.1750.5620.5620.0000.0000.0000.000
120A120LEU0-0.072-0.03421.0650.4380.4380.0000.0000.0000.000
121A121GLY0-0.0250.00125.2680.4140.4140.0000.0000.0000.000
122A122THR0-0.079-0.05323.1460.3410.3410.0000.0000.0000.000
123A123PRO0-0.019-0.01525.379-0.233-0.2330.0000.0000.0000.000
124A124GLY00.1110.04923.139-0.085-0.0850.0000.0000.0000.000
125A125SER00.0100.00523.588-0.280-0.2800.0000.0000.0000.000
126A126SER0-0.015-0.03026.0770.0370.0370.0000.0000.0000.000
127A127VAL0-0.007-0.00119.8150.0370.0370.0000.0000.0000.000
128A128ALA00.0330.02221.538-0.348-0.3480.0000.0000.0000.000
129A129VAL0-0.010-0.00122.608-0.061-0.0610.0000.0000.0000.000
130A130ALA0-0.008-0.01822.0310.0840.0840.0000.0000.0000.000
131A131ILE0-0.028-0.01417.518-0.137-0.1370.0000.0000.0000.000
132A132GLU-1-0.801-0.90420.439-13.453-13.4530.0000.0000.0000.000
133A133LYS10.8380.92222.81110.38710.3870.0000.0000.0000.000
134A134MET0-0.0340.00217.5900.0650.0650.0000.0000.0000.000
135A135LYS10.7900.91219.87913.26813.2680.0000.0000.0000.000
136A136GLU-1-0.928-0.97221.034-10.661-10.6610.0000.0000.0000.000
137A137ALA0-0.034-0.01722.7190.1960.1960.0000.0000.0000.000
138A138SER00.012-0.02018.849-0.004-0.0040.0000.0000.0000.000
139A139VAL0-0.004-0.00520.721-0.129-0.1290.0000.0000.0000.000
140A140SER0-0.032-0.01322.4690.4320.4320.0000.0000.0000.000
141A141ASP-1-0.886-0.94522.275-11.679-11.6790.0000.0000.0000.000
142A142ALA0-0.070-0.03720.3890.1220.1220.0000.0000.0000.000
143A143ASN0-0.033-0.00722.285-0.155-0.1550.0000.0000.0000.000
144A144ASP-1-0.875-0.91725.790-9.453-9.4530.0000.0000.0000.000
145A145SER0-0.019-0.01326.467-0.183-0.1830.0000.0000.0000.000
146A146SER0-0.015-0.00628.4250.1190.1190.0000.0000.0000.000
147A147GLY0-0.009-0.00327.513-0.313-0.3130.0000.0000.0000.000
148A148THR0-0.0250.00123.798-0.382-0.3820.0000.0000.0000.000
149A149PRO0-0.024-0.02326.0320.3790.3790.0000.0000.0000.000
150A150SER0-0.0150.00127.971-0.292-0.2920.0000.0000.0000.000
151A151GLY00.019-0.00628.6180.1270.1270.0000.0000.0000.000
152A152ASP-1-0.825-0.88326.845-11.413-11.4130.0000.0000.0000.000
153A153CYS00.0180.01022.364-0.375-0.3750.0000.0000.0000.000
154A154SER0-0.015-0.02522.378-0.667-0.6670.0000.0000.0000.000
155A155SER00.010-0.00219.737-0.156-0.1560.0000.0000.0000.000
156A156LEU00.0040.01316.442-0.434-0.4340.0000.0000.0000.000
157A157SER0-0.001-0.01218.124-0.695-0.6950.0000.0000.0000.000
158A158ALA0-0.018-0.00320.155-0.056-0.0560.0000.0000.0000.000
159A159GLU-1-0.768-0.81612.863-21.016-21.0160.0000.0000.0000.000
160A160LEU00.0570.02515.141-0.695-0.6950.0000.0000.0000.000
161A161GLY0-0.019-0.01816.129-0.251-0.2510.0000.0000.0000.000
162A162THR00.013-0.00114.9150.0190.0190.0000.0000.0000.000
163A163TYR0-0.084-0.07010.259-1.574-1.5740.0000.0000.0000.000
164A164PHE00.023-0.00113.539-0.541-0.5410.0000.0000.0000.000
165A165ASP-1-0.809-0.88516.324-14.116-14.1160.0000.0000.0000.000
166A166ARG10.7800.87310.59824.17624.1760.0000.0000.0000.000
167A167ALA00.0220.00213.929-0.029-0.0290.0000.0000.0000.000
168A168ALA0-0.013-0.01515.3480.4380.4380.0000.0000.0000.000
169A169SER0-0.044-0.03417.8170.8280.8280.0000.0000.0000.000
170A170ALA0-0.046-0.02015.2450.1810.1810.0000.0000.0000.000
171A171VAL0-0.040-0.01617.203-0.032-0.0320.0000.0000.0000.000
172A172SER-1-0.890-0.92119.490-12.765-12.7650.0000.0000.0000.000