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: Y1M82

Calculation Name: 4XK8-1-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: 1

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 195
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922
Total energy (hartree)
FMO2-HF: Electronic energy -1780915.155034
FMO2-HF: Nuclear repulsion 1706858.428252
FMO2-HF: Total energy -74056.726782
FMO2-MP2: Total energy -74274.760261


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:35:ALA)


Summations of interaction energy for fragment #1(A:35:ALA)
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.
-60.246-57.315-0.016-1.394-1.519-0.005
Interaction energy analysis for fragmet #1(A:35:ALA)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 1 / q_Mulliken : 0.854 / q_NPA : 0.914
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].
3A37TRP00.0730.0343.8660.0192.180-0.020-1.111-1.029-0.005
9A43ARG10.7410.8363.65955.89256.2930.000-0.175-0.2250.000
21A55PHE0-0.038-0.0283.637-9.679-9.3100.004-0.108-0.2650.000
4A38MET00.0300.0356.6303.4503.4500.0000.0000.0000.000
5A39PRO0-0.033-0.0276.090-1.740-1.7400.0000.0000.0000.000
6A40GLY0-0.0010.0027.1483.5643.5640.0000.0000.0000.000
7A41GLU-1-0.891-0.9358.700-20.745-20.7450.0000.0000.0000.000
8A42PRO0-0.075-0.0378.591-4.456-4.4560.0000.0000.0000.000
10A44PRO00.0410.0129.0311.3421.3420.0000.0000.0000.000
11A45ALA00.0090.00311.096-1.490-1.4900.0000.0000.0000.000
12A46TYR0-0.044-0.03913.3920.2350.2350.0000.0000.0000.000
13A47LEU0-0.048-0.0119.0990.2270.2270.0000.0000.0000.000
14A48ASP-1-0.780-0.8548.453-33.116-33.1160.0000.0000.0000.000
15A49GLY0-0.052-0.0275.319-5.910-5.9100.0000.0000.0000.000
16A50SER0-0.122-0.0806.096-0.467-0.4670.0000.0000.0000.000
17A51ALA00.0040.0078.8682.8112.8110.0000.0000.0000.000
18A52PRO00.0360.0118.392-4.057-4.0570.0000.0000.0000.000
19A53GLY00.007-0.0057.4121.6961.6960.0000.0000.0000.000
20A54ASP-1-0.779-0.8566.870-39.093-39.0930.0000.0000.0000.000
22A56GLY00.0470.0105.685-0.901-0.9010.0000.0000.0000.000
23A57PHE0-0.041-0.0237.9752.1432.1430.0000.0000.0000.000
24A58ASP-1-0.733-0.85010.779-18.352-18.3520.0000.0000.0000.000
25A59PRO0-0.032-0.01214.0830.6060.6060.0000.0000.0000.000
26A60LEU0-0.017-0.00516.0730.8850.8850.0000.0000.0000.000
27A61GLY00.0470.04017.6980.8520.8520.0000.0000.0000.000
28A62LEU0-0.009-0.00418.4880.7000.7000.0000.0000.0000.000
29A63GLY0-0.076-0.06116.7750.7710.7710.0000.0000.0000.000
30A64GLU-1-0.934-0.95717.780-15.612-15.6120.0000.0000.0000.000
31A65VAL0-0.024-0.00319.1660.4770.4770.0000.0000.0000.000
32A66PRO00.0400.00119.056-0.177-0.1770.0000.0000.0000.000
33A67ALA00.004-0.00320.049-0.272-0.2720.0000.0000.0000.000
34A68ASN0-0.0020.00121.6070.4730.4730.0000.0000.0000.000
35A69LEU00.0580.03914.252-0.159-0.1590.0000.0000.0000.000
36A70GLU-1-0.827-0.89817.642-18.062-18.0620.0000.0000.0000.000
37A71ARG10.9910.98919.35612.04212.0420.0000.0000.0000.000
38A72TYR0-0.023-0.00317.8660.6270.6270.0000.0000.0000.000
39A73LYS10.9000.96013.64820.06820.0680.0000.0000.0000.000
40A74GLU-1-0.817-0.90617.459-12.396-12.3960.0000.0000.0000.000
41A75SER0-0.021-0.04021.0040.1220.1220.0000.0000.0000.000
42A76GLU-1-0.771-0.84114.351-21.524-21.5240.0000.0000.0000.000
43A77LEU00.0130.00715.8830.0880.0880.0000.0000.0000.000
44A78ILE0-0.032-0.00918.8630.4600.4600.0000.0000.0000.000
45A79HIS0-0.029-0.02320.5880.7670.7670.0000.0000.0000.000
46A80CYS0-0.059-0.01016.820-0.131-0.1310.0000.0000.0000.000
47A81ARG10.7660.84319.37015.05515.0550.0000.0000.0000.000
48A82TRP00.0460.01822.1460.4220.4220.0000.0000.0000.000
49A83ALA00.0110.01220.8830.4140.4140.0000.0000.0000.000
50A84MET0-0.045-0.03318.4810.0450.0450.0000.0000.0000.000
51A85LEU0-0.0310.00122.4220.3500.3500.0000.0000.0000.000
52A86ALA00.0130.00225.8910.3780.3780.0000.0000.0000.000
53A87VAL00.0030.00222.3740.3020.3020.0000.0000.0000.000
54A88PRO0-0.019-0.00824.7430.3170.3170.0000.0000.0000.000
55A89GLY00.000-0.00227.5970.3930.3930.0000.0000.0000.000
56A90ILE0-0.024-0.00527.9670.3790.3790.0000.0000.0000.000
57A91LEU00.0390.01226.4480.2570.2570.0000.0000.0000.000
58A92VAL0-0.022-0.00230.1840.2600.2600.0000.0000.0000.000
59A93PRO0-0.027-0.01732.6010.2910.2910.0000.0000.0000.000
60A94GLU-1-0.820-0.90632.553-9.141-9.1410.0000.0000.0000.000
61A95ALA0-0.017-0.01333.3100.2040.2040.0000.0000.0000.000
62A96LEU0-0.061-0.03334.3840.1900.1900.0000.0000.0000.000
63A97GLY0-0.029-0.01537.6500.2200.2200.0000.0000.0000.000
64A98TYR0-0.045-0.01239.1060.1960.1960.0000.0000.0000.000
65A99GLY00.0270.03038.9230.1690.1690.0000.0000.0000.000
66A100ASN00.0440.00236.465-0.159-0.1590.0000.0000.0000.000
67A101TRP00.017-0.00231.0130.1290.1290.0000.0000.0000.000
68A102VAL00.0320.02834.9320.0010.0010.0000.0000.0000.000
69A103LYS10.8930.92437.1577.2187.2180.0000.0000.0000.000
70A104ALA0-0.041-0.01637.6800.1990.1990.0000.0000.0000.000
71A105GLN0-0.006-0.01136.8440.0550.0550.0000.0000.0000.000
72A106GLU-1-0.875-0.91840.484-6.925-6.9250.0000.0000.0000.000
73A107TRP0-0.035-0.00441.8700.2650.2650.0000.0000.0000.000
74A108ALA0-0.0030.00243.6180.1660.1660.0000.0000.0000.000
75A109ALA0-0.017-0.02345.4540.0240.0240.0000.0000.0000.000
76A110LEU0-0.0130.02047.3240.1630.1630.0000.0000.0000.000
77A111PRO0-0.017-0.03050.477-0.034-0.0340.0000.0000.0000.000
78A112GLY0-0.0180.00352.5990.0770.0770.0000.0000.0000.000
79A113GLY00.0070.00648.9370.0220.0220.0000.0000.0000.000
80A114GLN0-0.016-0.03049.330-0.030-0.0300.0000.0000.0000.000
81A115ALA00.0220.03543.944-0.056-0.0560.0000.0000.0000.000
82A116THR0-0.011-0.02244.4900.0930.0930.0000.0000.0000.000
83A117TYR0-0.001-0.00737.173-0.158-0.1580.0000.0000.0000.000
84A118LEU0-0.017-0.01838.9020.1260.1260.0000.0000.0000.000
85A119GLY00.0470.04142.2680.0980.0980.0000.0000.0000.000
86A120ASN0-0.014-0.00945.2810.2030.2030.0000.0000.0000.000
87A121PRO00.0170.00646.541-0.134-0.1340.0000.0000.0000.000
88A122VAL00.0220.02044.7090.0520.0520.0000.0000.0000.000
89A123PRO0-0.012-0.00247.9280.0330.0330.0000.0000.0000.000
90A124TRP00.011-0.00544.1010.1510.1510.0000.0000.0000.000
91A125GLY0-0.0120.00445.952-0.114-0.1140.0000.0000.0000.000
92A126THR00.0550.02546.941-0.014-0.0140.0000.0000.0000.000
93A127LEU00.0430.01544.058-0.056-0.0560.0000.0000.0000.000
94A128PRO00.007-0.00845.437-0.126-0.1260.0000.0000.0000.000
95A129THR0-0.017-0.00446.813-0.030-0.0300.0000.0000.0000.000
96A130ILE0-0.002-0.00941.641-0.078-0.0780.0000.0000.0000.000
97A131LEU00.0510.03840.912-0.142-0.1420.0000.0000.0000.000
98A132ALA0-0.003-0.00142.320-0.130-0.1300.0000.0000.0000.000
99A133ILE0-0.020-0.01641.672-0.064-0.0640.0000.0000.0000.000
100A134GLU-1-0.941-0.96437.165-8.547-8.5470.0000.0000.0000.000
101A135PHE0-0.006-0.00638.549-0.187-0.1870.0000.0000.0000.000
102A136LEU0-0.012-0.01439.582-0.115-0.1150.0000.0000.0000.000
103A137ALA0-0.0080.00238.313-0.082-0.0820.0000.0000.0000.000
104A138ILE00.008-0.00332.145-0.210-0.2100.0000.0000.0000.000
105A139ALA00.0280.01635.129-0.237-0.2370.0000.0000.0000.000
106A140PHE0-0.021-0.00436.960-0.110-0.1100.0000.0000.0000.000
107A141VAL0-0.003-0.00832.949-0.088-0.0880.0000.0000.0000.000
108A142GLU-1-0.826-0.89229.866-11.049-11.0490.0000.0000.0000.000
109A143HIS0-0.012-0.00832.541-0.252-0.2520.0000.0000.0000.000
110A144GLN0-0.039-0.03434.321-0.023-0.0230.0000.0000.0000.000
111A145ARG10.8010.89926.66711.33311.3330.0000.0000.0000.000
112A146SER0-0.060-0.03929.661-0.430-0.4300.0000.0000.0000.000
113A147MET0-0.051-0.01331.7330.1910.1910.0000.0000.0000.000
114A148GLU-1-0.868-0.90728.018-10.658-10.6580.0000.0000.0000.000
115A149LYS10.9030.93629.51110.16810.1680.0000.0000.0000.000
116A150ASP-1-0.862-0.93324.964-12.915-12.9150.0000.0000.0000.000
117A151PRO0-0.010-0.00521.965-0.079-0.0790.0000.0000.0000.000
118A152GLU-1-0.796-0.89618.248-17.915-17.9150.0000.0000.0000.000
119A153LYS10.9110.93521.78511.36511.3650.0000.0000.0000.000
120A154LYS10.8320.91824.47211.79711.7970.0000.0000.0000.000
121A155LYS10.8020.90917.05917.23117.2310.0000.0000.0000.000
122A156TYR0-0.010-0.00415.631-0.609-0.6090.0000.0000.0000.000
123A157PRO00.0570.05122.1480.1490.1490.0000.0000.0000.000
124A158GLY00.0250.00725.5710.1910.1910.0000.0000.0000.000
125A159GLY00.003-0.00926.5200.3560.3560.0000.0000.0000.000
126A160ALA00.0130.00230.141-0.004-0.0040.0000.0000.0000.000
127A161PHE0-0.002-0.00327.1400.1050.1050.0000.0000.0000.000
128A162ASP-1-0.798-0.87625.610-12.804-12.8040.0000.0000.0000.000
129A163PRO00.0030.00927.6070.1080.1080.0000.0000.0000.000
130A164LEU0-0.010-0.00226.7100.2540.2540.0000.0000.0000.000
131A165GLY0-0.059-0.03227.4940.0430.0430.0000.0000.0000.000
132A166TYR0-0.004-0.01822.209-0.137-0.1370.0000.0000.0000.000
133A167SER0-0.082-0.07721.829-0.615-0.6150.0000.0000.0000.000
134A168LYS10.9260.97122.84610.50810.5080.0000.0000.0000.000
135A169ASP-1-0.834-0.89920.177-15.190-15.1900.0000.0000.0000.000
136A170PRO00.0520.00619.296-0.623-0.6230.0000.0000.0000.000
137A171LYS10.9460.98212.44222.20022.2000.0000.0000.0000.000
138A172LYS10.9550.96615.69114.27114.2710.0000.0000.0000.000
139A173LEU00.0240.02817.215-0.440-0.4400.0000.0000.0000.000
140A174GLU-1-0.887-0.95011.305-25.099-25.0990.0000.0000.0000.000
141A175GLU-1-0.918-0.96112.502-20.924-20.9240.0000.0000.0000.000
142A176LEU0-0.039-0.02613.259-0.555-0.5550.0000.0000.0000.000
143A177LYS10.8760.95513.95218.91418.9140.0000.0000.0000.000
144A178VAL0-0.0020.0008.192-0.694-0.6940.0000.0000.0000.000
145A179LYS10.8330.91010.85919.01419.0140.0000.0000.0000.000
146A180GLU-1-0.785-0.85913.142-15.796-15.7960.0000.0000.0000.000
147A181ILE00.0150.00610.5870.3920.3920.0000.0000.0000.000
148A182LYS10.9140.9597.20930.43430.4340.0000.0000.0000.000
149A183ASN0-0.036-0.02811.7810.9880.9880.0000.0000.0000.000
150A184GLY00.0520.01315.4040.8150.8150.0000.0000.0000.000
151A185ARG10.8040.8489.25126.78726.7870.0000.0000.0000.000
152A186LEU0-0.028-0.00214.4710.4780.4780.0000.0000.0000.000
153A187ALA00.0120.00615.9700.7850.7850.0000.0000.0000.000
154A188LEU00.005-0.00917.5260.7570.7570.0000.0000.0000.000
155A189LEU0-0.0130.00215.5480.5450.5450.0000.0000.0000.000
156A190ALA0-0.0030.00119.0050.5980.5980.0000.0000.0000.000
157A191PHE00.0250.01221.6250.5910.5910.0000.0000.0000.000
158A192VAL00.005-0.00121.5280.5370.5370.0000.0000.0000.000
159A193GLY00.0150.00822.8380.4300.4300.0000.0000.0000.000
160A194PHE00.014-0.00924.2570.3880.3880.0000.0000.0000.000
161A195CYS0-0.031-0.01227.0550.5230.5230.0000.0000.0000.000
162A196VAL0-0.016-0.00825.6250.3680.3680.0000.0000.0000.000
163A197GLN00.001-0.00626.0540.4760.4760.0000.0000.0000.000
164A198GLN00.0110.02729.9000.5180.5180.0000.0000.0000.000
165A199SER0-0.049-0.02931.4900.3920.3920.0000.0000.0000.000
166A200ALA0-0.0090.00231.5060.2300.2300.0000.0000.0000.000
167A201TYR0-0.015-0.00331.7740.3270.3270.0000.0000.0000.000
168A202PRO00.0240.01935.5860.0080.0080.0000.0000.0000.000
169A203GLY0-0.045-0.03037.5770.1810.1810.0000.0000.0000.000
170A204THR0-0.026-0.00335.264-0.040-0.0400.0000.0000.0000.000
171A205GLY0-0.043-0.03233.774-0.184-0.1840.0000.0000.0000.000
172A206PRO0-0.024-0.00828.354-0.031-0.0310.0000.0000.0000.000
173A207LEU0-0.030-0.01929.718-0.222-0.2220.0000.0000.0000.000
174A208GLU-1-0.824-0.91331.365-8.183-8.1830.0000.0000.0000.000
175A209ASN0-0.009-0.01230.8330.1650.1650.0000.0000.0000.000
176A210LEU0-0.043-0.01027.033-0.073-0.0730.0000.0000.0000.000
177A211ALA0-0.004-0.01830.1080.0060.0060.0000.0000.0000.000
178A212THR0-0.005-0.01433.4700.2180.2180.0000.0000.0000.000
179A213HIS0-0.085-0.04227.697-0.190-0.1900.0000.0000.0000.000
180A214LEU0-0.059-0.04829.022-0.007-0.0070.0000.0000.0000.000
181A215ALA0-0.057-0.00332.2480.1320.1320.0000.0000.0000.000
182A216ASP-1-0.859-0.93234.705-7.918-7.9180.0000.0000.0000.000
183A217PRO0-0.039-0.00729.474-0.114-0.1140.0000.0000.0000.000
184A218TRP0-0.063-0.04528.349-0.381-0.3810.0000.0000.0000.000
185A219HIS0-0.0080.00432.281-0.088-0.0880.0000.0000.0000.000
186A220ASN00.0430.03233.6730.0730.0730.0000.0000.0000.000
187A221ASN0-0.014-0.02128.398-0.419-0.4190.0000.0000.0000.000
188A222ILE00.0090.00226.1270.0450.0450.0000.0000.0000.000
189A223GLY00.0120.00629.5150.0150.0150.0000.0000.0000.000
190A224ASP-1-0.861-0.93931.457-8.586-8.5860.0000.0000.0000.000
191A225ILE0-0.063-0.02631.1300.1380.1380.0000.0000.0000.000
192A226LEU0-0.090-0.04226.569-0.092-0.0920.0000.0000.0000.000
193A227ILE0-0.075-0.04731.1410.0060.0060.0000.0000.0000.000
194A228GLY00.0070.01833.7510.1890.1890.0000.0000.0000.000
195A229PHE-1-0.996-0.97936.628-7.568-7.5680.0000.0000.0000.000