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: K8Z43

Calculation Name: 4XK8-L-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: L

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 153
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922
Total energy (hartree)
FMO2-HF: Electronic energy -1156095.292267
FMO2-HF: Nuclear repulsion 1101008.823606
FMO2-HF: Total energy -55086.468661
FMO2-MP2: Total energy -55251.655215


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:4:TYR)


Summations of interaction energy for fragment #1(A:4:TYR)
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.
-30.523-25.356.203-4.526-6.848-0.044
Interaction energy analysis for fragmet #1(A:4:TYR)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 1 / q_Mulliken : 0.828 / q_NPA : 0.904
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].
3A6VAL00.0260.0103.111-0.9142.1651.826-1.479-3.425-0.002
4A7ILE00.0050.0065.3883.0983.253-0.001-0.007-0.1460.000
5A8GLN0-0.010-0.0012.011-25.020-23.0814.378-3.040-3.277-0.042
6A9PRO00.0540.0326.3071.9771.9770.0000.0000.0000.000
7A10ILE00.0050.0158.548-0.961-0.9610.0000.0000.0000.000
8A11ASN0-0.045-0.0479.7990.4650.4650.0000.0000.0000.000
9A12GLY0-0.024-0.0038.7710.4980.4980.0000.0000.0000.000
10A13ASP-1-0.867-0.9399.673-15.878-15.8780.0000.0000.0000.000
11A14PRO0-0.069-0.04912.442-0.358-0.3580.0000.0000.0000.000
12A15PHE0-0.030-0.01813.6120.3090.3090.0000.0000.0000.000
13A16ILE0-0.0110.01315.5750.9230.9230.0000.0000.0000.000
14A17GLY00.0140.01515.842-0.772-0.7720.0000.0000.0000.000
15A18SER0-0.056-0.04314.8900.2660.2660.0000.0000.0000.000
16A19LEU00.002-0.00210.864-0.779-0.7790.0000.0000.0000.000
17A20GLU-1-0.893-0.9337.159-22.481-22.4810.0000.0000.0000.000
18A21THR00.035-0.0057.792-2.201-2.2010.0000.0000.0000.000
19A22PRO00.024-0.0066.9311.2531.2530.0000.0000.0000.000
20A23VAL00.0100.0219.2671.1301.1300.0000.0000.0000.000
21A24THR00.0100.00210.9550.7000.7000.0000.0000.0000.000
22A25SER00.0060.0088.9201.4731.4730.0000.0000.0000.000
23A26SER00.0150.0068.503-1.463-1.4630.0000.0000.0000.000
24A27PRO00.010-0.0158.9491.1751.1750.0000.0000.0000.000
25A28LEU00.0270.02612.1690.9050.9050.0000.0000.0000.000
26A29ILE00.0130.01812.9390.9710.9710.0000.0000.0000.000
27A30ALA00.0440.01913.3860.7570.7570.0000.0000.0000.000
28A31TRP00.0020.01715.4130.7330.7330.0000.0000.0000.000
29A32TYR00.0360.01717.9100.6330.6330.0000.0000.0000.000
30A33LEU00.0080.00517.7530.6140.6140.0000.0000.0000.000
31A34SER0-0.057-0.05018.8670.6160.6160.0000.0000.0000.000
32A35ASN0-0.046-0.05121.1170.9050.9050.0000.0000.0000.000
33A36LEU00.0300.02723.3380.4120.4120.0000.0000.0000.000
34A37PRO0-0.0170.00025.529-0.071-0.0710.0000.0000.0000.000
35A38ALA00.002-0.00926.5960.1170.1170.0000.0000.0000.000
36A39TYR00.0250.01322.0030.0360.0360.0000.0000.0000.000
37A40ARG10.8940.99024.6749.9699.9690.0000.0000.0000.000
38A41THR0-0.019-0.04224.5330.2350.2350.0000.0000.0000.000
39A42ALA0-0.0020.01227.3130.1270.1270.0000.0000.0000.000
40A43VAL0-0.0080.00929.7430.2450.2450.0000.0000.0000.000
41A44SER00.0270.00432.247-0.046-0.0460.0000.0000.0000.000
42A45PRO00.0330.00833.676-0.036-0.0360.0000.0000.0000.000
43A46LEU00.0480.03834.970-0.041-0.0410.0000.0000.0000.000
44A47LEU00.005-0.00335.2020.0230.0230.0000.0000.0000.000
45A48ARG10.7610.85629.0718.9598.9590.0000.0000.0000.000
46A49GLY00.0520.03033.280-0.097-0.0970.0000.0000.0000.000
47A50ILE0-0.0130.00136.1470.0270.0270.0000.0000.0000.000
48A51GLU-1-0.906-0.96030.350-9.069-9.0690.0000.0000.0000.000
49A52VAL0-0.014-0.01431.041-0.083-0.0830.0000.0000.0000.000
50A53GLY00.0630.03333.603-0.003-0.0030.0000.0000.0000.000
51A54LEU0-0.030-0.00836.7150.0630.0630.0000.0000.0000.000
52A55ALA0-0.013-0.00632.8450.0650.0650.0000.0000.0000.000
53A56HIS0-0.048-0.04331.402-0.132-0.1320.0000.0000.0000.000
54A57GLY00.0280.00236.0940.0960.0960.0000.0000.0000.000
55A58TYR0-0.037-0.00636.6250.0570.0570.0000.0000.0000.000
56A59LEU0-0.052-0.01933.2170.0680.0680.0000.0000.0000.000
57A60LEU0-0.009-0.01337.2300.0520.0520.0000.0000.0000.000
58A61VAL00.0150.01139.7910.1200.1200.0000.0000.0000.000
59A62GLY00.0160.01840.2230.1190.1190.0000.0000.0000.000
60A63PRO0-0.004-0.00638.9570.1230.1230.0000.0000.0000.000
61A64PHE00.0000.00741.5090.1420.1420.0000.0000.0000.000
62A65VAL0-0.0060.00744.7380.1520.1520.0000.0000.0000.000
63A66LYS10.9230.96543.3576.6596.6590.0000.0000.0000.000
64A67ALA0-0.002-0.00643.4640.0430.0430.0000.0000.0000.000
65A68GLY00.0170.02045.5450.0700.0700.0000.0000.0000.000
66A69PRO0-0.015-0.01848.0970.0400.0400.0000.0000.0000.000
67A70LEU00.0300.00851.7800.0640.0640.0000.0000.0000.000
68A71ARG10.9050.99048.0086.2626.2620.0000.0000.0000.000
69A72ASN0-0.031-0.01850.561-0.115-0.1150.0000.0000.0000.000
70A73THR0-0.017-0.02553.4110.1290.1290.0000.0000.0000.000
71A74GLU-1-0.894-0.94954.374-5.183-5.1830.0000.0000.0000.000
72A75ILE00.0240.01555.299-0.036-0.0360.0000.0000.0000.000
73A76ALA0-0.0280.00250.420-0.062-0.0620.0000.0000.0000.000
74A77GLY00.0580.01549.184-0.107-0.1070.0000.0000.0000.000
75A78GLN00.0300.02549.653-0.063-0.0630.0000.0000.0000.000
76A79ALA00.013-0.00251.200-0.058-0.0580.0000.0000.0000.000
77A80GLY00.012-0.00447.618-0.058-0.0580.0000.0000.0000.000
78A81SER00.033-0.00946.494-0.174-0.1740.0000.0000.0000.000
79A82LEU0-0.031-0.01247.406-0.048-0.0480.0000.0000.0000.000
80A83ALA0-0.0170.00147.284-0.024-0.0240.0000.0000.0000.000
81A84ALA00.0050.00743.132-0.093-0.0930.0000.0000.0000.000
82A85GLY00.0230.00843.946-0.107-0.1070.0000.0000.0000.000
83A86GLY00.0260.01046.078-0.006-0.0060.0000.0000.0000.000
84A87LEU0-0.002-0.01140.521-0.030-0.0300.0000.0000.0000.000
85A88VAL00.0120.02140.862-0.115-0.1150.0000.0000.0000.000
86A89VAL00.0020.01842.627-0.052-0.0520.0000.0000.0000.000
87A90ILE00.0140.00542.985-0.024-0.0240.0000.0000.0000.000
88A91LEU00.0210.01337.685-0.061-0.0610.0000.0000.0000.000
89A92SER00.005-0.01840.208-0.118-0.1180.0000.0000.0000.000
90A93LEU0-0.0160.01541.982-0.003-0.0030.0000.0000.0000.000
91A94CYS0-0.036-0.03339.8150.0040.0040.0000.0000.0000.000
92A95LEU00.0030.00435.458-0.079-0.0790.0000.0000.0000.000
93A96THR00.001-0.00539.048-0.036-0.0360.0000.0000.0000.000
94A97ILE0-0.005-0.00841.9540.0210.0210.0000.0000.0000.000
95A98TYR00.0130.03532.714-0.036-0.0360.0000.0000.0000.000
96A99GLY00.0100.00638.293-0.074-0.0740.0000.0000.0000.000
97A100ILE0-0.032-0.02639.2880.0080.0080.0000.0000.0000.000
98A101SER0-0.065-0.04240.4810.0270.0270.0000.0000.0000.000
99A102SER0-0.048-0.01735.699-0.102-0.1020.0000.0000.0000.000
100A103PHE0-0.043-0.02233.734-0.129-0.1290.0000.0000.0000.000
101A104ASN0-0.0030.00238.9340.0900.0900.0000.0000.0000.000
102A105GLU-1-0.871-0.96140.972-6.749-6.7490.0000.0000.0000.000
103A106GLY0-0.0160.00242.568-0.002-0.0020.0000.0000.0000.000
104A107ALA0-0.051-0.01637.936-0.051-0.0510.0000.0000.0000.000
105A108PRO0-0.007-0.00434.999-0.040-0.0400.0000.0000.0000.000
106A109SER0-0.017-0.03631.202-0.143-0.1430.0000.0000.0000.000
107A110THR00.0230.01031.018-0.124-0.1240.0000.0000.0000.000
108A111ALA0-0.0080.00927.208-0.298-0.2980.0000.0000.0000.000
109A112PRO00.016-0.00422.6110.0350.0350.0000.0000.0000.000
110A113SER0-0.008-0.00324.742-0.001-0.0010.0000.0000.0000.000
111A114LEU00.0300.01921.0590.1240.1240.0000.0000.0000.000
112A115THR0-0.039-0.02718.547-0.114-0.1140.0000.0000.0000.000
113A116LEU00.0850.03813.3060.2000.2000.0000.0000.0000.000
114A117THR0-0.0010.00514.752-0.185-0.1850.0000.0000.0000.000
115A118GLY00.0660.04516.0300.0750.0750.0000.0000.0000.000
116A119ARG10.8950.95718.74911.90111.9010.0000.0000.0000.000
117A120LYS10.9460.97121.5059.4489.4480.0000.0000.0000.000
118A121LYS10.8360.92522.38710.91310.9130.0000.0000.0000.000
119A122GLU-1-0.877-0.94326.056-8.545-8.5450.0000.0000.0000.000
120A123PRO0-0.034-0.02127.592-0.295-0.2950.0000.0000.0000.000
121A124ASP-1-0.746-0.84427.450-9.032-9.0320.0000.0000.0000.000
122A125GLN00.0600.03529.4010.1720.1720.0000.0000.0000.000
123A126LEU0-0.0320.00530.1030.2320.2320.0000.0000.0000.000
124A127GLN0-0.032-0.01328.7850.2690.2690.0000.0000.0000.000
125A128THR00.016-0.01332.6320.1120.1120.0000.0000.0000.000
126A129ALA00.0600.04136.295-0.027-0.0270.0000.0000.0000.000
127A130ASP-1-0.787-0.86339.804-6.861-6.8610.0000.0000.0000.000
128A131GLY0-0.006-0.00636.5400.0020.0020.0000.0000.0000.000
129A132TRP0-0.003-0.01932.142-0.169-0.1690.0000.0000.0000.000
130A133ALA00.0270.02337.2600.0260.0260.0000.0000.0000.000
131A134LYS10.8320.88838.8396.9926.9920.0000.0000.0000.000
132A135PHE0-0.0190.00432.852-0.011-0.0110.0000.0000.0000.000
133A136THR0-0.034-0.02637.2970.0380.0380.0000.0000.0000.000
134A137GLY00.0230.01139.8430.0680.0680.0000.0000.0000.000
135A138GLY0-0.004-0.01739.2490.0870.0870.0000.0000.0000.000
136A139PHE0-0.012-0.00535.836-0.012-0.0120.0000.0000.0000.000
137A140PHE00.0070.00438.9030.0380.0380.0000.0000.0000.000
138A141PHE0-0.022-0.00942.6090.0550.0550.0000.0000.0000.000
139A142GLY00.0200.00339.6720.0560.0560.0000.0000.0000.000
140A143GLY00.0280.01040.351-0.016-0.0160.0000.0000.0000.000
141A144ILE0-0.014-0.01641.1080.0380.0380.0000.0000.0000.000
142A145SER00.0030.01142.7350.0890.0890.0000.0000.0000.000
143A146GLY00.0290.01140.5840.0280.0280.0000.0000.0000.000
144A147VAL0-0.014-0.01241.489-0.013-0.0130.0000.0000.0000.000
145A148ILE0-0.024-0.01243.9220.0750.0750.0000.0000.0000.000
146A149TRP0-0.006-0.00140.6520.1160.1160.0000.0000.0000.000
147A150ALA00.011-0.00441.3530.0070.0070.0000.0000.0000.000
148A151TYR0-0.036-0.01843.1680.0470.0470.0000.0000.0000.000
149A152PHE0-0.003-0.00746.3310.0580.0580.0000.0000.0000.000
150A153LEU0-0.011-0.01241.8560.0340.0340.0000.0000.0000.000
151A154LEU0-0.098-0.04142.961-0.076-0.0760.0000.0000.0000.000
152A155TYR0-0.108-0.05146.6570.0360.0360.0000.0000.0000.000
153A156VAL-1-0.932-0.93349.938-5.757-5.7570.0000.0000.0000.000