FMODB

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

Last updated: 2025-09-03

All entries: 45600

Number of unique PDB entries: 8613

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FMODB ID: G8VV1

Calculation Name: 1B8D-A-Xray547

Preferred Name:

Target Type:

Ligand Name: phycourobilin | phycoerythrobilin | n-methyl asparagine

Ligand 3-letter code: PUB | PEB | MEN

Ligand of Interest (LOI):

PDB ID: 1B8D

Chain ID: A

ChEMBL ID:

UniProt ID: O36005

Base Structure: X-ray

Registration Date: 2025-09-02

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
FMO calculation
FMO method FMO2-MP2/6-31G(d)
Fragmentation Auto
Number of fragment 164
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922
Total energy (hartree)
FMO2-HF: Electronic energy -1461686.979925
FMO2-HF: Nuclear repulsion 1398840.787321
FMO2-HF: Total energy -62846.192605
FMO2-MP2: Total energy -63026.913473


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: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.
-150.897-145.35124.044-11.171-18.42-0.132
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 : 0.842 / q_NPA : 0.922
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].
3A3SER00.0420.0083.8786.6308.134-0.010-0.528-0.9670.000
6A6THR00.014-0.0063.1885.1176.0300.022-0.401-0.5350.000
99A99VAL0-0.055-0.0222.563-0.977-0.1570.306-0.212-0.914-0.001
103A103GLY0-0.0210.0092.761-0.829-0.4690.769-0.297-0.832-0.001
104A104PRO00.022-0.0092.891-0.554-0.8555.900-1.107-4.492-0.004
105A105VAL00.0340.0203.7632.7711.1580.0971.801-0.2850.000
107A107GLU-1-0.876-0.9511.918-123.729-120.44913.489-9.529-7.240-0.114
108A108TRP0-0.059-0.0362.599-1.048-0.4653.471-0.898-3.155-0.012
4A4VAL00.0630.0465.6440.4160.4160.0000.0000.0000.000
5A5ILE00.0250.0117.3730.7230.7230.0000.0000.0000.000
7A7THR0-0.0250.0026.425-0.206-0.2060.0000.0000.0000.000
8A8THR0-0.009-0.0228.5461.8251.8250.0000.0000.0000.000
9A9ILE00.0070.0019.0771.4131.4130.0000.0000.0000.000
10A10SER0-0.013-0.0166.8970.2640.2640.0000.0000.0000.000
11A11ALA0-0.028-0.0129.5121.7361.7360.0000.0000.0000.000
12A12ALA0-0.030-0.01412.8301.5931.5930.0000.0000.0000.000
13A13ASP-1-0.914-0.95611.672-22.012-22.0120.0000.0000.0000.000
14A14ALA0-0.0010.00212.6821.2591.2590.0000.0000.0000.000
15A15ALA0-0.055-0.02314.4091.2501.2500.0000.0000.0000.000
16A16GLY0-0.0070.00116.9201.0791.0790.0000.0000.0000.000
17A17ARG10.8320.91417.43916.46016.4600.0000.0000.0000.000
18A18PHE00.0290.01317.143-0.890-0.8900.0000.0000.0000.000
19A19PRO0-0.030-0.02015.4050.0960.0960.0000.0000.0000.000
20A20SER0-0.020-0.01817.6981.1951.1950.0000.0000.0000.000
21A21SER00.0430.00619.429-0.671-0.6710.0000.0000.0000.000
22A22SER00.0970.04618.4220.0870.0870.0000.0000.0000.000
23A23ASP-1-0.798-0.84415.225-19.817-19.8170.0000.0000.0000.000
24A24LEU0-0.002-0.01515.541-0.852-0.8520.0000.0000.0000.000
25A25GLU-1-0.960-0.96717.913-13.920-13.9200.0000.0000.0000.000
26A26SER00.003-0.01714.281-0.157-0.1570.0000.0000.0000.000
27A27ILE0-0.039-0.03012.293-0.862-0.8620.0000.0000.0000.000
28A28GLN00.0150.01614.7210.1580.1580.0000.0000.0000.000
29A29GLY00.0520.02316.3790.4250.4250.0000.0000.0000.000
30A30ASN0-0.013-0.0099.873-0.340-0.3400.0000.0000.0000.000
31A31ILE0-0.036-0.01213.7240.1360.1360.0000.0000.0000.000
32A32GLN0-0.044-0.02316.6160.7350.7350.0000.0000.0000.000
33A33ARG10.7950.87714.44916.42616.4260.0000.0000.0000.000
34A34ALA00.002-0.00113.5180.0250.0250.0000.0000.0000.000
35A35ALA00.0310.01114.496-0.122-0.1220.0000.0000.0000.000
36A36ALA00.0210.01517.4230.2010.2010.0000.0000.0000.000
37A37ARG10.8850.9349.73523.66023.6600.0000.0000.0000.000
38A38LEU00.0180.00412.001-0.367-0.3670.0000.0000.0000.000
39A39GLU-1-0.779-0.85214.794-12.320-12.3200.0000.0000.0000.000
40A40ALA00.0470.01515.4560.3450.3450.0000.0000.0000.000
41A41ALA0-0.0180.00112.6640.1590.1590.0000.0000.0000.000
42A42GLN0-0.022-0.00914.5580.1930.1930.0000.0000.0000.000
43A43LYS10.8040.87117.50312.63912.6390.0000.0000.0000.000
44A44LEU0-0.0240.00014.2520.4070.4070.0000.0000.0000.000
45A45SER0-0.042-0.02815.2350.1980.1980.0000.0000.0000.000
46A46GLY00.002-0.00916.7950.3610.3610.0000.0000.0000.000
47A47ASN00.000-0.00120.1030.8350.8350.0000.0000.0000.000
48A48HIS10.8090.89517.49114.38614.3860.0000.0000.0000.000
49A49GLU-1-0.824-0.91019.533-12.754-12.7540.0000.0000.0000.000
50A50ALA00.0080.00422.1860.2480.2480.0000.0000.0000.000
51A51VAL00.0040.00119.9050.1970.1970.0000.0000.0000.000
52A52VAL0-0.0140.00018.5520.0990.0990.0000.0000.0000.000
53A53LYS10.8130.90021.35010.15210.1520.0000.0000.0000.000
54A54GLU-1-0.813-0.90624.994-10.058-10.0580.0000.0000.0000.000
55A55ALA00.0160.02122.1710.2270.2270.0000.0000.0000.000
56A56GLY00.032-0.00424.0520.0290.0290.0000.0000.0000.000
57A57ASP-1-0.826-0.86924.817-9.650-9.6500.0000.0000.0000.000
58A58ALA0-0.0020.00226.8990.3230.3230.0000.0000.0000.000
59A59CYS0-0.0180.00425.1160.1390.1390.0000.0000.0000.000
60A60PHE0-0.022-0.03226.0800.2990.2990.0000.0000.0000.000
61A61ALA0-0.0200.00429.8300.3380.3380.0000.0000.0000.000
62A62LYS10.9010.96529.07210.13510.1350.0000.0000.0000.000
63A63TYR0-0.026-0.03027.7050.0880.0880.0000.0000.0000.000
64A64SER00.0490.03231.183-0.143-0.1430.0000.0000.0000.000
65A65TYR00.0370.00929.7800.0360.0360.0000.0000.0000.000
66A66LEU00.0070.00627.1580.0080.0080.0000.0000.0000.000
67A67LYS10.9080.95930.9419.1009.1000.0000.0000.0000.000
68A68ASN0-0.0070.00633.1490.3020.3020.0000.0000.0000.000
69A69ALA00.000-0.01334.034-0.230-0.2300.0000.0000.0000.000
70A70GLY00.0070.01033.2850.1260.1260.0000.0000.0000.000
71A71GLU-1-0.900-0.93530.770-9.748-9.7480.0000.0000.0000.000
72A72ALA00.005-0.01625.562-0.041-0.0410.0000.0000.0000.000
73A73GLY0-0.015-0.01526.552-0.339-0.3390.0000.0000.0000.000
74A74ASP-1-0.845-0.89428.849-9.215-9.2150.0000.0000.0000.000
75A75SER00.0290.00930.5810.1950.1950.0000.0000.0000.000
76A76PRO00.0130.00529.653-0.303-0.3030.0000.0000.0000.000
77A77GLU-1-0.877-0.94527.100-9.790-9.7900.0000.0000.0000.000
78A78LYS10.7420.86925.3929.5339.5330.0000.0000.0000.000
79A79ILE00.0020.00125.042-0.400-0.4000.0000.0000.0000.000
80A80ASN0-0.004-0.01324.448-0.333-0.3330.0000.0000.0000.000
81A81LYS10.9160.96121.09511.60811.6080.0000.0000.0000.000
82A82CYS00.0330.03820.216-0.724-0.7240.0000.0000.0000.000
83A83TYR0-0.027-0.04720.533-0.427-0.4270.0000.0000.0000.000
84A84ARG10.8300.89717.01914.27314.2730.0000.0000.0000.000
85A85ASP-1-0.778-0.87115.953-15.941-15.9410.0000.0000.0000.000
86A86ILE00.0270.02215.563-0.961-0.9610.0000.0000.0000.000
87A87ASP-1-0.859-0.91415.823-16.073-16.0730.0000.0000.0000.000
88A88HIS00.0220.01911.941-1.571-1.5710.0000.0000.0000.000
89A89TYR00.0350.02711.426-1.091-1.0910.0000.0000.0000.000
90A90MET0-0.0020.01312.513-1.030-1.0300.0000.0000.0000.000
91A91ARG10.8840.9258.71120.89220.8920.0000.0000.0000.000
92A92LEU0-0.014-0.0046.175-1.381-1.3810.0000.0000.0000.000
93A93ILE00.0370.0378.205-2.147-2.1470.0000.0000.0000.000
94A94ASN0-0.047-0.03110.493-1.438-1.4380.0000.0000.0000.000
95A95TYR00.0310.0145.697-0.502-0.5020.0000.0000.0000.000
96A96SER00.000-0.0195.980-2.701-2.7010.0000.0000.0000.000
97A97LEU0-0.036-0.0027.051-0.596-0.5960.0000.0000.0000.000
98A98VAL00.0100.0078.0660.7990.7990.0000.0000.0000.000
100A100GLY0-0.035-0.0135.862-0.230-0.2300.0000.0000.0000.000
101A101GLY0-0.031-0.0356.077-0.124-0.1240.0000.0000.0000.000
102A102THR0-0.008-0.0225.721-0.582-0.5820.0000.0000.0000.000
106A106ASP-1-0.760-0.8455.389-34.802-34.8020.0000.0000.0000.000
109A109GLY00.0240.0186.5372.7132.7130.0000.0000.0000.000
110A110ILE0-0.0040.0219.6252.0492.0490.0000.0000.0000.000
111A111ALA00.0180.0229.5302.1302.1300.0000.0000.0000.000
112A112GLY00.0080.01011.5550.5860.5860.0000.0000.0000.000
113A113SER0-0.016-0.01313.8691.9271.9270.0000.0000.0000.000
114A114ARG10.9670.96515.48918.29818.2980.0000.0000.0000.000
115A115GLU-1-0.874-0.92117.461-16.059-16.0590.0000.0000.0000.000
116A116VAL00.0180.00316.0630.9210.9210.0000.0000.0000.000
117A117TYR00.004-0.03215.0420.7890.7890.0000.0000.0000.000
118A118ARG10.8330.92220.77214.60714.6070.0000.0000.0000.000
119A119ALA0-0.020-0.01222.3650.5650.5650.0000.0000.0000.000
120A120LEU0-0.050-0.02420.5010.4420.4420.0000.0000.0000.000
121A121ASN0-0.051-0.01124.2500.1010.1010.0000.0000.0000.000
122A122LEU00.0020.00420.5690.1870.1870.0000.0000.0000.000
123A123PRO00.0270.01422.932-0.495-0.4950.0000.0000.0000.000
124A124GLY00.0680.02021.786-0.096-0.0960.0000.0000.0000.000
125A125SER00.0200.00722.537-0.305-0.3050.0000.0000.0000.000
126A126ALA00.0190.00323.9420.1790.1790.0000.0000.0000.000
127A127TYR0-0.014-0.01318.4420.1170.1170.0000.0000.0000.000
128A128ILE00.0420.02920.942-0.067-0.0670.0000.0000.0000.000
129A129ALA0-0.037-0.00422.1390.1490.1490.0000.0000.0000.000
130A130ALA00.0240.02321.4090.1870.1870.0000.0000.0000.000
131A131PHE00.001-0.00116.925-0.054-0.0540.0000.0000.0000.000
132A132THR00.005-0.01120.517-0.035-0.0350.0000.0000.0000.000
133A133PHE0-0.019-0.00723.5550.2670.2670.0000.0000.0000.000
134A134THR0-0.032-0.05119.7250.1460.1460.0000.0000.0000.000
135A135ARG10.7710.85021.19012.52312.5230.0000.0000.0000.000
136A136ASP-1-0.837-0.89922.499-11.268-11.2680.0000.0000.0000.000
137A137ARG10.7810.89225.07110.60510.6050.0000.0000.0000.000
138A138LEU0-0.053-0.00521.9540.2380.2380.0000.0000.0000.000
139A139CYS0-0.013-0.01225.1040.3390.3390.0000.0000.0000.000
140A140VAL0-0.0180.01324.837-0.197-0.1970.0000.0000.0000.000
141A141PRO0-0.025-0.03327.3780.3070.3070.0000.0000.0000.000
142A142ARG10.8470.91027.7349.7389.7380.0000.0000.0000.000
143A143ASP-1-0.765-0.85024.339-10.835-10.8350.0000.0000.0000.000
144A144MET0-0.031-0.01419.280-0.501-0.5010.0000.0000.0000.000
145A145SER00.024-0.01022.0170.3360.3360.0000.0000.0000.000
146A146SER00.0370.00222.898-0.432-0.4320.0000.0000.0000.000
147A147GLN00.0440.02620.106-0.820-0.8200.0000.0000.0000.000
148A148ALA00.0250.02318.183-0.700-0.7000.0000.0000.0000.000
149A149GLY00.0580.01618.400-0.567-0.5670.0000.0000.0000.000
150A150VAL00.0010.01618.657-0.237-0.2370.0000.0000.0000.000
151A151GLU-1-0.831-0.88913.529-19.250-19.2500.0000.0000.0000.000
152A152PHE00.010-0.01015.224-0.934-0.9340.0000.0000.0000.000
153A153THR0-0.020-0.02016.820-0.110-0.1100.0000.0000.0000.000
154A154SER0-0.003-0.01415.472-0.044-0.0440.0000.0000.0000.000
155A155ALA0-0.037-0.01412.623-0.791-0.7910.0000.0000.0000.000
156A156LEU0-0.014-0.00513.940-0.532-0.5320.0000.0000.0000.000
157A157ASP-1-0.788-0.89216.766-14.005-14.0050.0000.0000.0000.000
158A158TYR0-0.113-0.0659.5530.7290.7290.0000.0000.0000.000
159A159VAL00.0080.00012.378-0.308-0.3080.0000.0000.0000.000
160A160ILE0-0.0070.01014.8430.3060.3060.0000.0000.0000.000
161A161ASN0-0.021-0.03917.2780.7330.7330.0000.0000.0000.000
162A162SER0-0.093-0.04214.129-0.402-0.4020.0000.0000.0000.000
163A163LEU0-0.090-0.05416.048-0.016-0.0160.0000.0000.0000.000
164A164CYS-1-0.988-0.97219.179-13.402-13.4020.0000.0000.0000.000