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: 1V56Z

Calculation Name: 7F9O-d-Other547

Preferred Name:

Target Type:

Ligand Name: chlorophyll a | chlorophyll b | chlorophyll a isomer | 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 | 1,2-di-o-acyl-3-o-[6-deoxy-6-sulfo-alpha-d-glucopyranosyl]-sn-glycerol | beta-carotene | 1,2-distearoyl-monogalactosyl-diglyceride | 1,2-dipalmitoyl-phosphatidyl-glycerole | phylloquinone | iron/sulfur cluster

Ligand 3-letter code: CLA | CHL | CL0 | DGD | XAT | LUT | SQD | BCR | LMG | LHG | PQN | SF4

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 7F9O

Chain ID: d

ChEMBL ID:

UniProt ID:

Base Structure: ElectronMicroscopy

Registration Date: 2025-10-06

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 172
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922
Total energy (hartree)
FMO2-HF: Electronic energy -1746533.019973
FMO2-HF: Nuclear repulsion 1680133.039732
FMO2-HF: Total energy -66399.980241
FMO2-MP2: Total energy -66591.794607


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:71:GLN)


Summations of interaction energy for fragment #1(A:71:GLN)
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.
-60.087-50.2973.243-5.088-7.945-0.05
Interaction energy analysis for fragmet #1(A:71:GLN)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 1 / q_Mulliken : 0.811 / q_NPA : 0.902
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].
3A73LYS10.9851.0033.62725.34227.085-0.009-0.750-0.9840.000
30A100TYR00.0430.0182.609-8.461-5.7030.859-1.523-2.093-0.017
95A165LEU0-0.071-0.0263.042-6.381-5.7500.022-0.220-0.434-0.002
96A166VAL00.0700.0374.5553.8143.913-0.001-0.003-0.0950.000
97A167HIS0-0.018-0.0254.899-10.328-10.244-0.001-0.001-0.0820.000
98A168THR0-0.026-0.0103.095-2.083-1.5620.046-0.133-0.434-0.001
136A206GLN0-0.032-0.0112.463-29.296-25.3422.327-2.458-3.823-0.030
4A74VAL0-0.027-0.0085.771-1.440-1.4400.0000.0000.0000.000
5A75THR0-0.030-0.0067.7682.7222.7220.0000.0000.0000.000
6A76ASN0-0.007-0.00811.1171.0211.0210.0000.0000.0000.000
7A77LYS10.9620.97510.46119.47519.4750.0000.0000.0000.000
8A78VAL00.0130.00912.8711.5611.5610.0000.0000.0000.000
9A79TYR0-0.036-0.00914.068-0.949-0.9490.0000.0000.0000.000
10A80PHE00.004-0.00615.5180.4840.4840.0000.0000.0000.000
11A81ASP-1-0.780-0.87318.721-13.300-13.3000.0000.0000.0000.000
12A82ILE00.001-0.00219.234-0.227-0.2270.0000.0000.0000.000
13A83ASN0-0.017-0.00322.4740.1030.1030.0000.0000.0000.000
14A84ILE00.0280.01625.321-0.057-0.0570.0000.0000.0000.000
15A85GLY0-0.031-0.01528.0170.3030.3030.0000.0000.0000.000
16A86ASN00.001-0.01731.789-0.173-0.1730.0000.0000.0000.000
17A87PRO0-0.0210.02834.2520.0970.0970.0000.0000.0000.000
18A88VAL00.034-0.00533.646-0.050-0.0500.0000.0000.0000.000
19A89GLY00.0340.02329.6560.0110.0110.0000.0000.0000.000
20A90LYS10.9470.97129.3449.7879.7870.0000.0000.0000.000
21A91ASN00.0400.00324.656-0.538-0.5380.0000.0000.0000.000
22A92VAL0-0.055-0.02823.2280.4240.4240.0000.0000.0000.000
23A93GLY00.0120.00621.097-0.092-0.0920.0000.0000.0000.000
24A94ARG10.8260.91717.81914.68214.6820.0000.0000.0000.000
25A95ILE0-0.024-0.00513.611-0.395-0.3950.0000.0000.0000.000
26A96VAL00.0370.02012.1480.7280.7280.0000.0000.0000.000
27A97ILE0-0.004-0.0039.698-1.794-1.7940.0000.0000.0000.000
28A98GLY00.0290.0267.7262.0752.0750.0000.0000.0000.000
29A99LEU00.016-0.0037.825-2.725-2.7250.0000.0000.0000.000
31A101GLY00.002-0.0107.6640.8800.8800.0000.0000.0000.000
32A102ASP-1-0.900-0.9549.360-24.148-24.1480.0000.0000.0000.000
33A103ASP-1-0.907-0.9457.799-36.410-36.4100.0000.0000.0000.000
34A104VAL0-0.059-0.0298.8031.1091.1090.0000.0000.0000.000
35A105PRO00.0450.02811.5410.5500.5500.0000.0000.0000.000
36A106GLN0-0.037-0.02414.2901.0061.0060.0000.0000.0000.000
37A107THR0-0.018-0.01813.2170.6370.6370.0000.0000.0000.000
38A108VAL00.0040.00510.1300.3230.3230.0000.0000.0000.000
39A109GLU-1-0.827-0.89213.279-14.869-14.8690.0000.0000.0000.000
40A110ASN00.0850.02516.6641.3821.3820.0000.0000.0000.000
41A111PHE00.005-0.00114.0320.4510.4510.0000.0000.0000.000
42A112ARG10.9190.95615.23716.43116.4310.0000.0000.0000.000
43A113ALA00.0210.02516.9510.7560.7560.0000.0000.0000.000
44A114LEU0-0.042-0.01719.8400.7360.7360.0000.0000.0000.000
45A115CYS0-0.074-0.04217.5790.3300.3300.0000.0000.0000.000
46A116THR0-0.024-0.01919.8910.1230.1230.0000.0000.0000.000
47A117GLY00.001-0.01522.4140.5990.5990.0000.0000.0000.000
48A118GLU-1-0.915-0.94924.431-12.740-12.7400.0000.0000.0000.000
49A119LYS10.9190.95626.9129.6939.6930.0000.0000.0000.000
50A120GLY00.0180.01028.3370.3340.3340.0000.0000.0000.000
51A121PHE0-0.066-0.03626.9010.2720.2720.0000.0000.0000.000
52A122GLY00.0990.04923.830-0.463-0.4630.0000.0000.0000.000
53A123TYR0-0.070-0.06117.8770.1850.1850.0000.0000.0000.000
54A124LYS10.8350.89823.34911.11911.1190.0000.0000.0000.000
55A125GLY0-0.018-0.00325.8500.3850.3850.0000.0000.0000.000
56A126SER0-0.043-0.01223.9870.1020.1020.0000.0000.0000.000
57A127SER0-0.050-0.04325.3530.1760.1760.0000.0000.0000.000
58A128PHE00.008-0.00817.747-0.417-0.4170.0000.0000.0000.000
59A129HIS0-0.024-0.00823.3170.4680.4680.0000.0000.0000.000
60A130ARG10.8770.93123.05613.53513.5350.0000.0000.0000.000
61A131VAL0-0.017-0.00521.683-0.847-0.8470.0000.0000.0000.000
62A132ILE00.0280.03021.0380.5790.5790.0000.0000.0000.000
63A133LYS11.0190.98820.62611.82211.8220.0000.0000.0000.000
64A134ASP-1-0.959-0.98318.497-16.102-16.1020.0000.0000.0000.000
65A135PHE00.0020.00717.472-0.675-0.6750.0000.0000.0000.000
66A136MET0-0.047-0.02716.030-1.301-1.3010.0000.0000.0000.000
67A137ILE0-0.0220.02116.6011.4121.4120.0000.0000.0000.000
68A138GLN00.0350.00917.499-0.473-0.4730.0000.0000.0000.000
69A139GLY00.0390.01819.7920.8790.8790.0000.0000.0000.000
70A140GLY00.0680.04120.733-0.563-0.5630.0000.0000.0000.000
71A141ASP-1-0.716-0.84322.069-11.219-11.2190.0000.0000.0000.000
72A142PHE00.012-0.00624.1640.3830.3830.0000.0000.0000.000
73A143ASP-1-0.895-0.92727.509-9.803-9.8030.0000.0000.0000.000
74A144LYS10.8430.89829.94010.00110.0010.0000.0000.0000.000
75A145GLY0-0.0030.02628.4740.2460.2460.0000.0000.0000.000
76A146ASN0-0.083-0.06629.4030.1490.1490.0000.0000.0000.000
77A147GLY00.0290.02425.979-0.023-0.0230.0000.0000.0000.000
78A148THR0-0.054-0.03326.669-0.110-0.1100.0000.0000.0000.000
79A149GLY0-0.0130.00228.5130.3430.3430.0000.0000.0000.000
80A150GLY0-0.0160.00326.031-0.497-0.4970.0000.0000.0000.000
81A151LYS10.8490.93225.70110.80110.8010.0000.0000.0000.000
82A152SER00.016-0.01122.025-0.870-0.8700.0000.0000.0000.000
83A153ILE00.0360.03921.3340.5740.5740.0000.0000.0000.000
84A154TYR0-0.042-0.02520.3920.8840.8840.0000.0000.0000.000
85A155GLY0-0.018-0.00725.1300.0720.0720.0000.0000.0000.000
86A156ARG10.8540.90626.89011.33211.3320.0000.0000.0000.000
87A157THR00.0070.00523.667-0.088-0.0880.0000.0000.0000.000
88A158PHE0-0.0240.00017.5480.6050.6050.0000.0000.0000.000
89A159LYS10.9450.97519.97213.61613.6160.0000.0000.0000.000
90A160ASP-1-0.765-0.87415.888-18.219-18.2190.0000.0000.0000.000
91A161GLU-1-0.882-0.93214.067-17.947-17.9470.0000.0000.0000.000
92A162ASN00.001-0.02111.8020.5170.5170.0000.0000.0000.000
93A163PHE0-0.025-0.01210.229-1.077-1.0770.0000.0000.0000.000
94A164GLN00.0300.0267.9091.3301.3300.0000.0000.0000.000
99A169GLY0-0.059-0.0515.9915.1185.1180.0000.0000.0000.000
100A170PRO0-0.047-0.0178.018-0.574-0.5740.0000.0000.0000.000
101A171GLY00.0130.0217.141-1.918-1.9180.0000.0000.0000.000
102A172VAL0-0.015-0.0175.330-5.813-5.8130.0000.0000.0000.000
103A173LEU0-0.013-0.0028.0184.3774.3770.0000.0000.0000.000
104A174SER00.0380.0039.639-2.829-2.8290.0000.0000.0000.000
105A175MET0-0.0060.00812.1121.2151.2150.0000.0000.0000.000
106A176ALA0-0.047-0.03315.267-0.021-0.0210.0000.0000.0000.000
107A177ASN0-0.036-0.00717.9201.0431.0430.0000.0000.0000.000
108A178ALA0-0.011-0.00219.8480.1810.1810.0000.0000.0000.000
109A179GLY00.0160.01421.9340.6650.6650.0000.0000.0000.000
110A180PRO00.025-0.01319.859-0.242-0.2420.0000.0000.0000.000
111A181ASN0-0.050-0.03019.9170.1890.1890.0000.0000.0000.000
112A182THR0-0.0190.01521.4710.6600.6600.0000.0000.0000.000
113A183ASN0-0.028-0.03317.402-0.648-0.6480.0000.0000.0000.000
114A184GLY00.0580.00519.8960.9120.9120.0000.0000.0000.000
115A185SER0-0.033-0.02120.060-0.708-0.7080.0000.0000.0000.000
116A186GLN0-0.0240.00420.325-0.456-0.4560.0000.0000.0000.000
117A187PHE00.0380.03115.019-0.744-0.7440.0000.0000.0000.000
118A188PHE0-0.013-0.02214.2651.1221.1220.0000.0000.0000.000
119A189ILE00.0140.01311.583-1.765-1.7650.0000.0000.0000.000
120A190CYS0-0.0220.00410.9952.2032.2030.0000.0000.0000.000
121A191THR00.013-0.01911.602-1.910-1.9100.0000.0000.0000.000
122A192VAL00.0100.00712.832-0.294-0.2940.0000.0000.0000.000
123A193LYS10.9310.9679.90326.25326.2530.0000.0000.0000.000
124A194THR00.0300.01511.0971.4531.4530.0000.0000.0000.000
125A195PRO0-0.004-0.00311.701-0.971-0.9710.0000.0000.0000.000
126A196TRP00.0310.00612.703-0.231-0.2310.0000.0000.0000.000
127A197LEU0-0.063-0.03013.0151.3461.3460.0000.0000.0000.000
128A198ASP-1-0.767-0.8699.141-31.798-31.7980.0000.0000.0000.000
129A199GLY0-0.036-0.02112.0871.9701.9700.0000.0000.0000.000
130A200ARG10.9040.95314.09518.17818.1780.0000.0000.0000.000
131A201HIS0-0.016-0.01613.2050.2960.2960.0000.0000.0000.000
132A202VAL00.0600.03910.711-1.632-1.6320.0000.0000.0000.000
133A203VAL0-0.0110.0115.2280.8750.8750.0000.0000.0000.000
134A204PHE00.006-0.0067.617-1.792-1.7920.0000.0000.0000.000
135A205GLY00.0670.0206.7751.1621.1620.0000.0000.0000.000
137A207VAL0-0.0130.0036.2242.8162.8160.0000.0000.0000.000
138A208LEU0-0.049-0.0236.166-2.597-2.5970.0000.0000.0000.000
139A209GLU-1-0.899-0.9478.811-17.978-17.9780.0000.0000.0000.000
140A210GLY00.0630.02112.153-0.028-0.0280.0000.0000.0000.000
141A211MET0-0.014-0.0146.6311.0541.0540.0000.0000.0000.000
142A212ASP-1-0.866-0.93512.618-17.115-17.1150.0000.0000.0000.000
143A213ILE0-0.017-0.00816.0180.8480.8480.0000.0000.0000.000
144A214VAL00.0150.01013.1970.5650.5650.0000.0000.0000.000
145A215ARG10.9240.95410.95721.73621.7360.0000.0000.0000.000
146A216MET00.0010.02117.0650.7200.7200.0000.0000.0000.000
147A217ILE0-0.014-0.01018.8240.6800.6800.0000.0000.0000.000
148A218GLU0-0.027-0.01917.7110.0600.0600.0000.0000.0000.000
149A219SER0-0.064-0.04220.1090.3530.3530.0000.0000.0000.000
150A220SER0-0.065-0.02822.7600.7090.7090.0000.0000.0000.000
151A221GLU-1-0.877-0.92725.474-9.515-9.5150.0000.0000.0000.000
152A222THR00.0000.00226.1110.0040.0040.0000.0000.0000.000
153A223ASP-1-0.886-0.95529.237-9.727-9.7270.0000.0000.0000.000
154A224ARG10.9340.95331.3208.6278.6270.0000.0000.0000.000
155A225GLY00.0040.01731.1790.0120.0120.0000.0000.0000.000
156A226ASP-1-0.850-0.91525.817-12.561-12.5610.0000.0000.0000.000
157A227ARG10.8990.95226.43910.17310.1730.0000.0000.0000.000
158A228PRO00.0080.01825.8330.3060.3060.0000.0000.0000.000
159A229LYS10.8590.91728.0299.5169.5160.0000.0000.0000.000
160A230LYS10.8970.94529.31810.16110.1610.0000.0000.0000.000
161A231LYS10.9840.99528.5799.3479.3470.0000.0000.0000.000
162A232VAL00.0520.01822.8920.1310.1310.0000.0000.0000.000
163A233VAL0-0.020-0.02425.456-0.102-0.1020.0000.0000.0000.000
164A234ILE00.0350.03719.972-0.188-0.1880.0000.0000.0000.000
165A235SER0-0.054-0.02623.9830.3600.3600.0000.0000.0000.000
166A236GLU-1-0.812-0.89624.111-11.399-11.3990.0000.0000.0000.000
167A237CYS0-0.079-0.03520.280-0.490-0.4900.0000.0000.0000.000
168A238GLY00.0900.04919.6110.7210.7210.0000.0000.0000.000
169A239GLU-1-0.846-0.90616.578-18.102-18.1020.0000.0000.0000.000
170A240LEU0-0.045-0.03016.8811.0101.0100.0000.0000.0000.000
171A241PRO0-0.032-0.01516.160-1.074-1.0740.0000.0000.0000.000
172A242VAL-1-0.926-0.95612.749-16.598-16.5980.0000.0000.0000.000