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: 67Q2Z

Calculation Name: 7S3D-l-Other547

Preferred Name:

Target Type:

Ligand Name: chlorophyll f | chlorophyll a | chlorophyll a isomer | beta-carotene | 1,2-distearoyl-monogalactosyl-diglyceride | 1,2-dipalmitoyl-phosphatidyl-glycerole | dodecyl-beta-d-maltoside | phylloquinone | iron/sulfur cluster | fe2/s2 (inorganic) cluster | calcium ion

Ligand 3-letter code: F6C | CLA | CL0 | BCR | LMG | LHG | LMT | PQN | SF4 | FES | CA

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 7S3D

Chain ID: l

ChEMBL ID:

UniProt ID:

Base Structure: ElectronMicroscopy

Registration Date: 2025-10-05

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 170
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922
Total energy (hartree)
FMO2-HF: Electronic energy -1376270.125573
FMO2-HF: Nuclear repulsion 1313022.103747
FMO2-HF: Total energy -63248.021826
FMO2-MP2: Total energy -63435.130054


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:SER)


Summations of interaction energy for fragment #1(A:4:SER)
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.
8.58612.034-0.017-1.592-1.839-0.004
Interaction energy analysis for fragmet #1(A:4:SER)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 1 / q_Mulliken : 0.805 / q_NPA : 0.867
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].
3A6ALA0-0.043-0.0173.41710.03513.164-0.015-1.523-1.591-0.004
4A7TYR0-0.025-0.0255.387-1.065-0.976-0.001-0.009-0.0790.000
5A8ILE0-0.031-0.0024.2850.3200.550-0.001-0.060-0.1690.000
6A9SER0-0.028-0.0097.0474.1964.1960.0000.0000.0000.000
7A10ASP-1-0.907-0.9379.202-21.353-21.3530.0000.0000.0000.000
8A11ASP-1-0.878-0.94812.011-23.918-23.9180.0000.0000.0000.000
9A12PRO0-0.025-0.02914.1171.0101.0100.0000.0000.0000.000
10A13ILE0-0.093-0.03515.4551.5911.5910.0000.0000.0000.000
11A14GLN00.0600.04914.829-1.205-1.2050.0000.0000.0000.000
12A15PRO00.0590.02113.5431.0081.0080.0000.0000.0000.000
13A16TYR00.0140.01316.3201.0851.0850.0000.0000.0000.000
14A17GLN0-0.051-0.04319.9130.5110.5110.0000.0000.0000.000
15A18GLY00.0530.03717.6950.3280.3280.0000.0000.0000.000
16A19ASN0-0.021-0.01116.611-1.645-1.6450.0000.0000.0000.000
17A20PRO00.0210.00612.2980.6070.6070.0000.0000.0000.000
18A21GLN0-0.0020.00314.3450.0130.0130.0000.0000.0000.000
19A22LEU0-0.052-0.01716.3761.2431.2430.0000.0000.0000.000
20A23GLY00.0220.01718.507-0.622-0.6220.0000.0000.0000.000
21A24ASN0-0.059-0.04119.7740.5870.5870.0000.0000.0000.000
22A25LEU00.0470.02715.422-0.658-0.6580.0000.0000.0000.000
23A26ALA0-0.032-0.00818.9501.1151.1150.0000.0000.0000.000
24A27THR00.0510.02119.784-0.417-0.4170.0000.0000.0000.000
25A28PRO00.050-0.00121.4060.6290.6290.0000.0000.0000.000
26A29ILE00.0250.02424.5210.5530.5530.0000.0000.0000.000
27A30ASN0-0.0030.00423.1750.2890.2890.0000.0000.0000.000
28A31SER00.0170.00323.5510.1700.1700.0000.0000.0000.000
29A32SER0-0.004-0.00125.6500.1020.1020.0000.0000.0000.000
30A33ASN00.020-0.01327.2040.0750.0750.0000.0000.0000.000
31A34LEU00.0470.03530.2060.2800.2800.0000.0000.0000.000
32A35ALA00.0390.02929.4100.3180.3180.0000.0000.0000.000
33A36LYS10.8750.93526.68012.07612.0760.0000.0000.0000.000
34A37ALA0-0.0140.00131.9390.2680.2680.0000.0000.0000.000
35A38PHE00.0560.03534.8900.3020.3020.0000.0000.0000.000
36A39ILE00.0310.01032.7060.2370.2370.0000.0000.0000.000
37A40ASN0-0.019-0.03031.7760.0950.0950.0000.0000.0000.000
38A41ASN0-0.030-0.02535.7200.3110.3110.0000.0000.0000.000
39A42LEU00.0550.04737.4830.3060.3060.0000.0000.0000.000
40A43PRO00.0290.02740.392-0.120-0.1200.0000.0000.0000.000
41A44ALA0-0.024-0.01139.1510.0540.0540.0000.0000.0000.000
42A45TYR0-0.105-0.06134.954-0.107-0.1070.0000.0000.0000.000
43A46ARG10.7430.85238.2707.3537.3530.0000.0000.0000.000
44A47PRO00.0390.00538.1440.1500.1500.0000.0000.0000.000
45A48GLY00.0090.00840.7540.1490.1490.0000.0000.0000.000
46A49LEU00.0010.00944.0770.1610.1610.0000.0000.0000.000
47A50THR00.0480.02045.173-0.133-0.1330.0000.0000.0000.000
48A51PRO00.019-0.00445.2450.0180.0180.0000.0000.0000.000
49A52PHE00.0440.03947.060-0.046-0.0460.0000.0000.0000.000
50A53LEU00.0180.01749.1660.0260.0260.0000.0000.0000.000
51A54ARG10.7800.88541.3497.5907.5900.0000.0000.0000.000
52A55GLY00.0250.00746.503-0.056-0.0560.0000.0000.0000.000
53A56LEU0-0.0020.00248.3210.0210.0210.0000.0000.0000.000
54A57GLU-1-0.760-0.84745.861-7.071-7.0710.0000.0000.0000.000
55A58ILE0-0.024-0.01643.404-0.045-0.0450.0000.0000.0000.000
56A59GLY00.0250.00747.018-0.008-0.0080.0000.0000.0000.000
57A60MET0-0.021-0.00950.4060.0470.0470.0000.0000.0000.000
58A61ALA0-0.022-0.00147.2490.0530.0530.0000.0000.0000.000
59A62HIS0-0.064-0.05144.300-0.120-0.1200.0000.0000.0000.000
60A63GLY00.0260.01649.1830.0410.0410.0000.0000.0000.000
61A64TYR0-0.032-0.00952.2640.0600.0600.0000.0000.0000.000
62A65PHE0-0.006-0.00646.0890.0420.0420.0000.0000.0000.000
63A66LEU0-0.043-0.03148.9170.0220.0220.0000.0000.0000.000
64A67VAL0-0.0200.01252.1540.0500.0500.0000.0000.0000.000
65A68GLY00.0120.01453.9340.0730.0730.0000.0000.0000.000
66A69PRO0-0.024-0.02651.0970.0610.0610.0000.0000.0000.000
67A70GLU-1-0.870-0.95053.720-5.720-5.7200.0000.0000.0000.000
68A71VAL0-0.0350.00157.1330.0900.0900.0000.0000.0000.000
69A72VAL0-0.0110.00454.9490.0710.0710.0000.0000.0000.000
70A73PHE0-0.049-0.04452.1220.0360.0360.0000.0000.0000.000
71A74GLY00.0800.05956.6340.0170.0170.0000.0000.0000.000
72A75PRO0-0.101-0.06358.8460.0560.0560.0000.0000.0000.000
73A76LEU00.0280.02362.1740.0830.0830.0000.0000.0000.000
74A77LYS10.8670.94258.7385.5205.5200.0000.0000.0000.000
75A78GLU-1-0.926-0.96162.868-4.937-4.9370.0000.0000.0000.000
76A79GLY00.006-0.00366.1470.0870.0870.0000.0000.0000.000
77A80SER0-0.018-0.00265.095-0.062-0.0620.0000.0000.0000.000
78A81HIS0-0.003-0.01465.177-0.019-0.0190.0000.0000.0000.000
79A82GLY00.0420.02066.447-0.029-0.0290.0000.0000.0000.000
80A83ALA00.0220.02061.957-0.070-0.0700.0000.0000.0000.000
81A84ASN0-0.003-0.01461.670-0.182-0.1820.0000.0000.0000.000
82A85LEU00.0010.00261.866-0.084-0.0840.0000.0000.0000.000
83A86SER0-0.023-0.02261.347-0.068-0.0680.0000.0000.0000.000
84A87GLY00.0690.04057.945-0.093-0.0930.0000.0000.0000.000
85A88LEU0-0.022-0.01157.888-0.099-0.0990.0000.0000.0000.000
86A89ILE0-0.007-0.01459.175-0.067-0.0670.0000.0000.0000.000
87A90THR00.0130.00254.751-0.059-0.0590.0000.0000.0000.000
88A91ALA00.0160.01054.412-0.112-0.1120.0000.0000.0000.000
89A92ILE0-0.0090.00854.881-0.097-0.0970.0000.0000.0000.000
90A93TYR00.0240.01354.916-0.026-0.0260.0000.0000.0000.000
91A94ILE00.0120.01450.241-0.087-0.0870.0000.0000.0000.000
92A95THR0-0.016-0.00251.758-0.152-0.1520.0000.0000.0000.000
93A96VAL00.0170.00652.744-0.076-0.0760.0000.0000.0000.000
94A97SER0-0.023-0.01851.847-0.032-0.0320.0000.0000.0000.000
95A98ALA0-0.0110.00248.292-0.104-0.1040.0000.0000.0000.000
96A99CYS0-0.042-0.01349.059-0.119-0.1190.0000.0000.0000.000
97A100LEU00.0280.03651.306-0.021-0.0210.0000.0000.0000.000
98A101GLY00.0360.01348.323-0.039-0.0390.0000.0000.0000.000
99A102ILE0-0.023-0.01845.747-0.119-0.1190.0000.0000.0000.000
100A103SER0-0.015-0.02447.514-0.046-0.0460.0000.0000.0000.000
101A104ILE00.012-0.00548.6090.0030.0030.0000.0000.0000.000
102A105PHE0-0.0110.01340.118-0.086-0.0860.0000.0000.0000.000
103A106ALA0-0.017-0.00845.354-0.114-0.1140.0000.0000.0000.000
104A107LEU0-0.029-0.02046.807-0.028-0.0280.0000.0000.0000.000
105A108ALA00.0060.01646.0420.0150.0150.0000.0000.0000.000
106A109THR0-0.039-0.01841.150-0.155-0.1550.0000.0000.0000.000
107A110PHE0-0.072-0.04341.957-0.111-0.1110.0000.0000.0000.000
108A111GLN0-0.053-0.02045.2350.3000.3000.0000.0000.0000.000
109A112GLY00.0120.01145.629-0.057-0.0570.0000.0000.0000.000
110A113ASP-1-0.806-0.88939.356-8.173-8.1730.0000.0000.0000.000
111A114PRO00.0020.01439.629-0.043-0.0430.0000.0000.0000.000
112A115ARG10.9930.98637.9177.5727.5720.0000.0000.0000.000
113A116GLY00.0240.01734.0720.0160.0160.0000.0000.0000.000
114A117THR00.0200.00532.0620.0110.0110.0000.0000.0000.000
115A118TYR00.0230.00834.307-0.144-0.1440.0000.0000.0000.000
116A119ASN0-0.0200.01935.2010.0160.0160.0000.0000.0000.000
117A120SER0-0.039-0.06336.191-0.235-0.2350.0000.0000.0000.000
118A121HIS00.0080.00832.622-0.318-0.3180.0000.0000.0000.000
119A122SER0-0.124-0.05431.605-0.561-0.5610.0000.0000.0000.000
120A123ARG10.9730.97025.08911.77011.7700.0000.0000.0000.000
121A124ASP-1-0.811-0.89429.248-10.518-10.5180.0000.0000.0000.000
122A125ARG10.9150.94927.86211.19911.1990.0000.0000.0000.000
123A126LEU00.0250.02429.1450.1880.1880.0000.0000.0000.000
124A127ARG10.8550.92331.4179.9829.9820.0000.0000.0000.000
125A128PRO00.0470.02335.4920.0600.0600.0000.0000.0000.000
126A129LEU00.0120.02037.3450.1390.1390.0000.0000.0000.000
127A130ARG10.8610.92235.5308.7868.7860.0000.0000.0000.000
128A131LYS10.9250.97040.5937.5227.5220.0000.0000.0000.000
129A132LYS10.9390.95844.3306.4956.4950.0000.0000.0000.000
130A133GLU-1-0.803-0.89447.128-6.542-6.5420.0000.0000.0000.000
131A134ASP-1-0.826-0.93843.499-7.238-7.2380.0000.0000.0000.000
132A135TRP0-0.019-0.02040.5160.0770.0770.0000.0000.0000.000
133A136TYR00.002-0.00646.7700.0530.0530.0000.0000.0000.000
134A137GLN0-0.012-0.00349.4210.1140.1140.0000.0000.0000.000
135A138LEU0-0.0030.00244.3020.0560.0560.0000.0000.0000.000
136A139SER0-0.028-0.01648.3010.0510.0510.0000.0000.0000.000
137A140GLY00.0450.01850.5280.0720.0720.0000.0000.0000.000
138A141GLY00.0280.00751.2010.0950.0950.0000.0000.0000.000
139A142ILE0-0.015-0.00946.3290.0510.0510.0000.0000.0000.000
140A143LEU00.0230.00150.9320.0600.0600.0000.0000.0000.000
141A144MET0-0.021-0.01754.3730.1130.1130.0000.0000.0000.000
142A145GLY00.0140.00453.1060.0680.0680.0000.0000.0000.000
143A146SER0-0.046-0.02651.858-0.008-0.0080.0000.0000.0000.000
144A147LEU00.000-0.00453.7960.0510.0510.0000.0000.0000.000
145A148GLY00.0220.01657.3170.0870.0870.0000.0000.0000.000
146A149GLY00.004-0.00954.7760.0530.0530.0000.0000.0000.000
147A150ALA00.0200.01255.8530.0300.0300.0000.0000.0000.000
148A151ILE0-0.001-0.01157.3140.0680.0680.0000.0000.0000.000
149A152PHE0-0.0090.00156.8580.0730.0730.0000.0000.0000.000
150A153ALA00.0310.01056.4070.0480.0480.0000.0000.0000.000
151A154TYR00.001-0.00158.5320.0440.0440.0000.0000.0000.000
152A155ALA00.0050.00861.6090.0740.0740.0000.0000.0000.000
153A156LEU0-0.020-0.01058.7360.0680.0680.0000.0000.0000.000
154A157LEU0-0.035-0.00558.6470.0210.0210.0000.0000.0000.000
155A158GLU-1-0.803-0.88562.724-4.804-4.8040.0000.0000.0000.000
156A159ASN0-0.080-0.04365.8320.1450.1450.0000.0000.0000.000
157A160PHE00.0290.02261.2000.0020.0020.0000.0000.0000.000
158A161GLU-1-0.914-0.95865.342-4.599-4.5990.0000.0000.0000.000
159A162LEU0-0.0060.00368.5760.0310.0310.0000.0000.0000.000
160A163LEU00.000-0.00462.903-0.004-0.0040.0000.0000.0000.000
161A164ASP-1-0.845-0.91164.844-5.003-5.0030.0000.0000.0000.000
162A165SER0-0.017-0.02265.7660.0330.0330.0000.0000.0000.000
163A166ILE0-0.002-0.01465.9600.0310.0310.0000.0000.0000.000
164A167LEU0-0.048-0.02560.997-0.013-0.0130.0000.0000.0000.000
165A168ARG10.8030.90063.2424.9974.9970.0000.0000.0000.000
166A169GLY0-0.021-0.00167.0870.0440.0440.0000.0000.0000.000
167A170ALA0-0.005-0.01069.5120.0680.0680.0000.0000.0000.000
168A171VAL0-0.024-0.01070.8360.0600.0600.0000.0000.0000.000
169A172ASN0-0.129-0.05970.7590.0360.0360.0000.0000.0000.000
170A173VAL-1-0.937-0.95074.951-4.091-4.0910.0000.0000.0000.000