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

tag_button

FMODB ID: 5YQ1Z

Calculation Name: 4XK8-D-Xray547

Preferred Name:

Target Type:

Ligand Name: chlorophyll a | chlorophyll b | digalactosyl diacyl glycerol (dgdg) | (3s,5r,6s,3's,5'r,6's)-5,6,5',6'-diepoxy-5,6,5',6'-tetrahydro-beta,beta-carotene-3,3'-diol | (3r,3'r,6s)-4,5-didehydro-5,6-dihydro-beta,beta-carotene-3,3'-diol | beta-carotene | 1,2-distearoyl-monogalactosyl-diglyceride | 1,2-dipalmitoyl-phosphatidyl-glycerole | dodecyl-beta-d-maltoside | phylloquinone | iron/sulfur cluster | heptyl 1-thio-beta-d-glucopyranoside

Ligand 3-letter code: CLA | CHL | DGD | XAT | LUT | BCR | LMG | LHG | LMT | PQN | SF4 | HTG

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 4XK8

Chain ID: D

ChEMBL ID:

UniProt ID: Q01667

Base Structure: X-ray

Registration Date: 2025-10-04

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 141
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922
Total energy (hartree)
FMO2-HF: Electronic energy -1145864.390184
FMO2-HF: Nuclear repulsion 1090989.828717
FMO2-HF: Total energy -54874.561468
FMO2-MP2: Total energy -55036.451982


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:70:THR)


Summations of interaction energy for fragment #1(A:70:THR)
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.
54.04458.290.236-2.158-2.323-0.018
Interaction energy analysis for fragmet #1(A:70:THR)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 1 / q_Mulliken : 0.836 / q_NPA : 0.907
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].
3A72PRO0-0.010-0.0063.202-4.552-2.5410.058-0.929-1.140-0.004
101A170ASP-1-0.716-0.8253.787-38.863-38.5810.001-0.051-0.2320.000
102A171GLY00.0170.0162.746-12.867-11.0000.178-1.175-0.869-0.014
103A172VAL0-0.058-0.0324.6785.7025.788-0.001-0.003-0.0820.000
4A73GLU-1-0.866-0.9255.674-27.955-27.9550.0000.0000.0000.000
5A74LEU0-0.018-0.0108.0940.6510.6510.0000.0000.0000.000
6A75ASP-1-0.901-0.96211.341-17.249-17.2490.0000.0000.0000.000
7A76PRO00.0110.01814.6390.9090.9090.0000.0000.0000.000
8A77ASN0-0.005-0.01517.609-0.037-0.0370.0000.0000.0000.000
9A78THR0-0.045-0.02718.0490.4650.4650.0000.0000.0000.000
10A79PRO00.0340.01821.1890.3210.3210.0000.0000.0000.000
11A80SER00.0250.01223.637-0.293-0.2930.0000.0000.0000.000
12A81PRO0-0.036-0.01724.1260.3700.3700.0000.0000.0000.000
13A82ILE00.0180.02427.1410.1630.1630.0000.0000.0000.000
14A83PHE0-0.009-0.02430.774-0.022-0.0220.0000.0000.0000.000
15A84GLY00.0240.01932.6430.0480.0480.0000.0000.0000.000
16A85GLY0-0.0060.01434.0210.1260.1260.0000.0000.0000.000
17A86SER0-0.015-0.01833.5420.1340.1340.0000.0000.0000.000
18A87THR00.0230.00135.391-0.149-0.1490.0000.0000.0000.000
19A88GLY00.0060.02033.3460.0130.0130.0000.0000.0000.000
20A89GLY0-0.026-0.01330.489-0.341-0.3410.0000.0000.0000.000
21A90LEU0-0.029-0.01826.132-0.078-0.0780.0000.0000.0000.000
22A91LEU00.0590.02730.2170.3240.3240.0000.0000.0000.000
23A92ARG10.9830.98131.3508.5748.5740.0000.0000.0000.000
24A93LYS10.8680.94425.08711.95311.9530.0000.0000.0000.000
25A94ALA00.000-0.00627.189-0.265-0.2650.0000.0000.0000.000
26A95GLN0-0.034-0.02227.852-0.065-0.0650.0000.0000.0000.000
27A96VAL0-0.034-0.01130.3020.0670.0670.0000.0000.0000.000
28A97GLU-1-0.916-0.95427.135-10.903-10.9030.0000.0000.0000.000
29A98GLU-1-0.721-0.83922.602-14.211-14.2110.0000.0000.0000.000
30A99PHE0-0.069-0.02622.6570.5580.5580.0000.0000.0000.000
31A100TYR0-0.056-0.05818.371-0.973-0.9730.0000.0000.0000.000
32A101VAL00.0270.01717.1180.9110.9110.0000.0000.0000.000
33A102ILE0-0.037-0.02716.795-1.086-1.0860.0000.0000.0000.000
34A103THR00.0590.02914.1120.7170.7170.0000.0000.0000.000
35A104TRP0-0.032-0.05315.996-0.789-0.7890.0000.0000.0000.000
36A105ASP-1-0.878-0.93216.806-14.958-14.9580.0000.0000.0000.000
37A106SER0-0.028-0.03418.493-0.055-0.0550.0000.0000.0000.000
38A107PRO0-0.004-0.01521.5190.2700.2700.0000.0000.0000.000
39A108LYS10.9761.00123.81510.58810.5880.0000.0000.0000.000
40A109GLU-1-0.874-0.91326.462-10.169-10.1690.0000.0000.0000.000
41A110GLN0-0.071-0.05924.9890.5620.5620.0000.0000.0000.000
42A111ILE00.0390.03128.935-0.242-0.2420.0000.0000.0000.000
43A112PHE0-0.035-0.01025.881-0.278-0.2780.0000.0000.0000.000
44A113GLU-1-0.893-0.93928.626-9.539-9.5390.0000.0000.0000.000
45A114MET00.0020.00327.727-0.708-0.7080.0000.0000.0000.000
46A115PRO0-0.049-0.03724.6540.2420.2420.0000.0000.0000.000
47A116THR0-0.040-0.01127.7990.0290.0290.0000.0000.0000.000
48A117GLY00.0560.03930.5140.3080.3080.0000.0000.0000.000
49A118GLY00.0420.01233.2770.0190.0190.0000.0000.0000.000
50A119ALA0-0.022-0.01532.096-0.267-0.2670.0000.0000.0000.000
51A120ALA00.0100.00729.2440.1980.1980.0000.0000.0000.000
52A121ILE00.0220.00830.118-0.050-0.0500.0000.0000.0000.000
53A122MET0-0.108-0.01124.375-0.320-0.3200.0000.0000.0000.000
54A123ARG10.9790.96425.43511.07211.0720.0000.0000.0000.000
55A124GLU-1-0.918-0.94724.886-11.163-11.1630.0000.0000.0000.000
56A125GLY00.0480.03421.2060.0470.0470.0000.0000.0000.000
57A126PRO00.0120.00618.058-0.110-0.1100.0000.0000.0000.000
58A127ASN0-0.044-0.02019.7581.1191.1190.0000.0000.0000.000
59A128LEU00.0450.02518.497-0.792-0.7920.0000.0000.0000.000
60A129LEU0-0.011-0.02020.7610.8540.8540.0000.0000.0000.000
61A130LYS10.9780.99521.36310.74210.7420.0000.0000.0000.000
62A131LEU0-0.027-0.02421.8940.5820.5820.0000.0000.0000.000
63A132ALA00.0990.04123.943-0.311-0.3110.0000.0000.0000.000
64A133ARG10.8320.89223.77611.40411.4040.0000.0000.0000.000
65A134LYS11.0231.01815.42017.83017.8300.0000.0000.0000.000
66A135GLU-1-0.841-0.89719.940-12.029-12.0290.0000.0000.0000.000
67A136GLN00.0550.02422.334-0.215-0.2150.0000.0000.0000.000
68A137CYS00.0140.02618.1560.0400.0400.0000.0000.0000.000
69A138LEU00.0120.00516.243-0.321-0.3210.0000.0000.0000.000
70A139ALA00.0180.02418.941-0.033-0.0330.0000.0000.0000.000
71A140LEU00.0020.00821.3650.2440.2440.0000.0000.0000.000
72A141GLY00.0630.01117.7520.0900.0900.0000.0000.0000.000
73A142THR0-0.067-0.04118.637-0.317-0.3170.0000.0000.0000.000
74A143ARG10.9190.94820.07711.35211.3520.0000.0000.0000.000
75A144LEU00.0020.00619.6340.3230.3230.0000.0000.0000.000
76A145ARG10.8570.91814.65117.63317.6330.0000.0000.0000.000
77A146SER0-0.051-0.02019.1330.1860.1860.0000.0000.0000.000
78A147LYS10.9290.96122.21110.74710.7470.0000.0000.0000.000
79A148TYR0-0.051-0.05722.7670.4990.4990.0000.0000.0000.000
80A149LYS10.8330.93520.60212.36912.3690.0000.0000.0000.000
81A150ILE00.0490.04518.037-0.366-0.3660.0000.0000.0000.000
82A151LYS10.8800.9377.94628.78428.7840.0000.0000.0000.000
83A152TYR00.0310.02613.8600.2050.2050.0000.0000.0000.000
84A153GLN0-0.019-0.01310.0160.1430.1430.0000.0000.0000.000
85A154PHE0-0.026-0.02312.4321.7041.7040.0000.0000.0000.000
86A155TYR00.0450.02411.553-2.403-2.4030.0000.0000.0000.000
87A156ARG10.8150.89915.02817.32717.3270.0000.0000.0000.000
88A157VAL00.0210.00917.559-0.915-0.9150.0000.0000.0000.000
89A158PHE00.0410.01118.5270.6810.6810.0000.0000.0000.000
90A159PRO0-0.023-0.01522.986-0.094-0.0940.0000.0000.0000.000
91A160ASN0-0.036-0.00922.4460.0540.0540.0000.0000.0000.000
92A161GLY00.0280.02022.9970.1700.1700.0000.0000.0000.000
93A162GLU-1-0.948-0.95918.136-17.334-17.3340.0000.0000.0000.000
94A163VAL00.0120.00214.8200.3330.3330.0000.0000.0000.000
95A164GLN00.0380.02613.853-0.506-0.5060.0000.0000.0000.000
96A165TYR00.004-0.0186.7550.9350.9350.0000.0000.0000.000
97A166LEU0-0.113-0.05611.014-0.806-0.8060.0000.0000.0000.000
98A167HIS0-0.034-0.01310.249-1.569-1.5690.0000.0000.0000.000
99A168PRO00.0630.0257.8470.9620.9620.0000.0000.0000.000
100A169LYS10.9400.9856.85726.07826.0780.0000.0000.0000.000
104A173TYR0-0.038-0.0317.2050.7490.7490.0000.0000.0000.000
105A174PRO00.0230.00410.729-0.562-0.5620.0000.0000.0000.000
106A175GLU-1-0.802-0.88712.433-18.233-18.2330.0000.0000.0000.000
107A176LYS10.9330.98710.91222.94622.9460.0000.0000.0000.000
108A177VAL00.0410.01512.097-1.437-1.4370.0000.0000.0000.000
109A178ASN0-0.025-0.0365.5341.4311.4310.0000.0000.0000.000
110A179ALA00.0300.0238.8441.3141.3140.0000.0000.0000.000
111A180GLY00.003-0.0017.848-3.650-3.6500.0000.0000.0000.000
112A181ARG10.7500.8507.76528.83628.8360.0000.0000.0000.000
113A182GLN00.0230.01710.3882.1652.1650.0000.0000.0000.000
114A183GLY0-0.014-0.00313.278-0.010-0.0100.0000.0000.0000.000
115A184VAL00.004-0.01215.6800.2300.2300.0000.0000.0000.000
116A185GLY00.0090.00618.4340.0960.0960.0000.0000.0000.000
117A186GLN0-0.031-0.00220.9590.7680.7680.0000.0000.0000.000
118A187ASN00.0300.00722.774-0.272-0.2720.0000.0000.0000.000
119A188PHE00.0000.00221.5850.1730.1730.0000.0000.0000.000
120A189ARG10.7990.87227.49010.49910.4990.0000.0000.0000.000
121A190SER00.0070.00530.607-0.080-0.0800.0000.0000.0000.000
122A191ILE00.0670.01731.0470.2140.2140.0000.0000.0000.000
123A192GLY00.0010.00033.0590.1160.1160.0000.0000.0000.000
124A193LYS10.9080.95935.1418.9468.9460.0000.0000.0000.000
125A194ASN00.0120.01932.781-0.318-0.3180.0000.0000.0000.000
126A195VAL00.0480.03735.7150.2090.2090.0000.0000.0000.000
127A196SER00.0590.02038.202-0.080-0.0800.0000.0000.0000.000
128A197PRO00.028-0.00639.952-0.018-0.0180.0000.0000.0000.000
129A198ILE0-0.024-0.01541.001-0.015-0.0150.0000.0000.0000.000
130A199GLU-1-0.898-0.94939.936-7.418-7.4180.0000.0000.0000.000
131A200VAL0-0.0150.00736.165-0.107-0.1070.0000.0000.0000.000
132A201LYS10.9110.97839.3236.9576.9570.0000.0000.0000.000
133A202PHE0-0.022-0.02842.1060.1070.1070.0000.0000.0000.000
134A203THR0-0.0080.00437.273-0.137-0.1370.0000.0000.0000.000
135A204GLY0-0.002-0.00835.0740.0510.0510.0000.0000.0000.000
136A205LYS10.9030.95629.65110.02010.0200.0000.0000.0000.000
137A206GLN00.0360.02332.1820.4710.4710.0000.0000.0000.000
138A207PRO0-0.007-0.01133.018-0.233-0.2330.0000.0000.0000.000
139A208TYR0-0.023-0.01629.0750.1040.1040.0000.0000.0000.000
140A209ASP-1-0.871-0.92628.374-11.012-11.0120.0000.0000.0000.000
141A210LEU-1-0.913-0.92928.343-10.939-10.9390.0000.0000.0000.000