FMODB

FMODB: The database of quantum mechanical data based on the FMO method

Last updated: 2025-12-18

All entries: 87239

Number of unique PDB entries: 32030

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FMODB ID: MZ95Z

Calculation Name: 7WG5-A-Other547

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 | 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 | dodecyl-alpha-d-maltoside | phylloquinone | iron/sulfur cluster | fe2/s2 (inorganic) cluster

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

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 7WG5

Chain ID: A

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 221
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922
Total energy (hartree)
FMO2-HF: Electronic energy -2208157.917074
FMO2-HF: Nuclear repulsion 2125074.278463
FMO2-HF: Total energy -83083.638611
FMO2-MP2: Total energy -83328.856979


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:53:ARG)


Summations of interaction energy for fragment #1(A:53:ARG)
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.
-287.453-284.25542.734-15.664-30.272-0.189
Interaction energy analysis for fragmet #1(A:53:ARG)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 2 / q_Mulliken : 1.675 / q_NPA : 1.823
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].
3A55LEU00.0230.0062.497-19.718-15.7981.970-1.916-3.974-0.010
4A56TRP0-0.034-0.0094.3999.7929.946-0.001-0.017-0.1360.000
6A58ALA00.0010.0184.1760.0800.201-0.001-0.024-0.0960.000
11A63LEU0-0.044-0.0462.342-10.244-10.9484.044-0.809-2.532-0.003
12A64SER0-0.050-0.0244.062-0.971-0.894-0.001-0.007-0.0690.000
14A66LEU0-0.082-0.0022.442-5.192-3.3811.267-1.336-1.743-0.006
15A67ASP-1-0.808-0.9091.828-140.711-142.14216.948-8.515-7.003-0.116
16A68GLY0-0.076-0.0562.3861.8963.2402.933-1.654-2.624-0.008
17A69SER0-0.0120.0032.82217.61815.3330.3662.322-0.402-0.002
21A73ASP-1-0.795-0.8922.970-133.245-128.1762.152-3.077-4.144-0.030
22A74TYR00.019-0.0082.163-22.127-21.3824.520-1.836-3.430-0.024
23A75GLY0-0.015-0.0021.924-8.153-9.1947.632-3.059-3.5330.008
24A76PHE00.0070.0142.36815.74911.1670.9054.264-0.5860.002
5A57PHE0-0.001-0.0126.452-1.167-1.1670.0000.0000.0000.000
7A59SER00.0410.0295.8534.0494.0490.0000.0000.0000.000
8A60SER00.000-0.0176.864-6.154-6.1540.0000.0000.0000.000
9A61GLN0-0.0210.0048.918-0.310-0.3100.0000.0000.0000.000
10A62SER0-0.005-0.0045.194-5.108-5.1080.0000.0000.0000.000
13A65TYR00.0600.0245.6562.8762.8760.0000.0000.0000.000
18A70LEU00.0660.0296.4846.5736.5730.0000.0000.0000.000
19A71PRO0-0.039-0.0046.435-5.991-5.9910.0000.0000.0000.000
20A72GLY00.0540.0176.5301.0841.0840.0000.0000.0000.000
25A77ASP-1-0.696-0.8316.141-44.197-44.1970.0000.0000.0000.000
26A78PRO0-0.036-0.0267.8540.0070.0070.0000.0000.0000.000
27A79LEU0-0.031-0.01510.3662.5702.5700.0000.0000.0000.000
28A80GLY00.0360.02910.7911.7981.7980.0000.0000.0000.000
29A81LEU0-0.046-0.03111.6922.0512.0510.0000.0000.0000.000
30A82SER0-0.086-0.0668.9100.8390.8390.0000.0000.0000.000
31A83ASP-1-0.793-0.89010.175-44.521-44.5210.0000.0000.0000.000
32A84PRO0-0.026-0.02110.1361.9121.9120.0000.0000.0000.000
33A85GLU-1-0.954-0.95713.144-28.292-28.2920.0000.0000.0000.000
34A86GLY00.0030.00115.8931.1831.1830.0000.0000.0000.000
35A87THR0-0.101-0.04515.073-0.228-0.2280.0000.0000.0000.000
36A88GLY00.0990.04817.941-0.459-0.4590.0000.0000.0000.000
37A89GLY0-0.052-0.02820.6470.2940.2940.0000.0000.0000.000
38A90PHE0-0.014-0.02020.646-0.050-0.0500.0000.0000.0000.000
39A91ILE0-0.030-0.01016.176-1.224-1.2240.0000.0000.0000.000
40A92GLU-1-0.756-0.88915.697-30.029-30.0290.0000.0000.0000.000
41A93PRO00.0270.01210.864-0.286-0.2860.0000.0000.0000.000
42A94ARG10.8280.93612.60028.42428.4240.0000.0000.0000.000
43A95TRP00.0220.00214.970-0.002-0.0020.0000.0000.0000.000
44A96LEU00.0030.01313.2630.4660.4660.0000.0000.0000.000
45A97ALA00.0100.01011.484-0.294-0.2940.0000.0000.0000.000
46A98TYR0-0.039-0.01613.1021.0831.0830.0000.0000.0000.000
47A99GLY00.0590.02916.8071.2841.2840.0000.0000.0000.000
48A100GLU-1-0.806-0.86311.192-48.074-48.0740.0000.0000.0000.000
49A101ILE0-0.045-0.01913.3200.9040.9040.0000.0000.0000.000
50A102ILE0-0.032-0.01216.3351.3751.3750.0000.0000.0000.000
51A103ASN0-0.023-0.02518.6512.0812.0810.0000.0000.0000.000
52A104GLY00.0260.01317.3100.7690.7690.0000.0000.0000.000
53A105ARG10.7700.85218.13531.65031.6500.0000.0000.0000.000
54A106PHE00.0330.00921.0150.9660.9660.0000.0000.0000.000
55A107ALA00.0100.01720.4921.0071.0070.0000.0000.0000.000
56A108MET0-0.035-0.02218.4690.4150.4150.0000.0000.0000.000
57A109LEU0-0.022-0.00422.6470.8780.8780.0000.0000.0000.000
58A110GLY00.0370.02425.6470.8980.8980.0000.0000.0000.000
59A111ALA0-0.011-0.01523.8790.7370.7370.0000.0000.0000.000
60A112ALA00.0160.02125.9400.5080.5080.0000.0000.0000.000
61A113GLY00.0260.00028.1180.7330.7330.0000.0000.0000.000
62A114ALA0-0.034-0.02829.2670.6930.6930.0000.0000.0000.000
63A115ILE00.0000.00229.1000.3800.3800.0000.0000.0000.000
64A116ALA0-0.0010.01231.9370.4300.4300.0000.0000.0000.000
65A117PRO00.0290.01233.5490.3460.3460.0000.0000.0000.000
66A118GLU-1-0.844-0.94234.376-16.979-16.9790.0000.0000.0000.000
67A119ILE0-0.021-0.02531.0810.3300.3300.0000.0000.0000.000
68A120LEU0-0.014-0.00935.1400.1810.1810.0000.0000.0000.000
69A121GLY00.0310.03137.7130.3770.3770.0000.0000.0000.000
70A122LYS10.8740.93137.25016.59116.5910.0000.0000.0000.000
71A123ALA0-0.032-0.00439.1100.2420.2420.0000.0000.0000.000
72A124GLY0-0.0010.00041.1160.2180.2180.0000.0000.0000.000
73A125LEU0-0.057-0.02339.4070.2130.2130.0000.0000.0000.000
74A126ILE0-0.047-0.01539.3090.0950.0950.0000.0000.0000.000
75A127PRO00.0240.01642.6050.0500.0500.0000.0000.0000.000
76A128ALA00.0440.01544.028-0.287-0.2870.0000.0000.0000.000
77A129GLU-1-0.890-0.95244.522-13.368-13.3680.0000.0000.0000.000
78A130THR0-0.063-0.03842.184-0.102-0.1020.0000.0000.0000.000
79A131ALA0-0.012-0.00540.178-0.391-0.3910.0000.0000.0000.000
80A132LEU0-0.0320.00039.847-0.161-0.1610.0000.0000.0000.000
81A133PRO00.0070.01435.688-0.445-0.4450.0000.0000.0000.000
82A134TRP00.024-0.00231.6130.2570.2570.0000.0000.0000.000
83A135PHE0-0.024-0.01334.4550.1440.1440.0000.0000.0000.000
84A136GLN00.0090.00236.0090.4280.4280.0000.0000.0000.000
85A137THR00.000-0.00336.7500.3870.3870.0000.0000.0000.000
86A138GLY00.0380.01239.4380.3420.3420.0000.0000.0000.000
87A139VAL0-0.0130.01533.9200.1350.1350.0000.0000.0000.000
88A140ILE00.0140.00234.460-0.184-0.1840.0000.0000.0000.000
89A141PRO00.0410.02338.6510.2190.2190.0000.0000.0000.000
90A142PRO0-0.077-0.04540.8690.2250.2250.0000.0000.0000.000
91A143ALA0-0.0210.00539.4420.1020.1020.0000.0000.0000.000
92A144GLY00.0140.01341.5220.0820.0820.0000.0000.0000.000
93A145THR0-0.043-0.04542.024-0.228-0.2280.0000.0000.0000.000
94A146TYR00.0080.02743.1360.3270.3270.0000.0000.0000.000
95A147THR0-0.028-0.01944.827-0.023-0.0230.0000.0000.0000.000
96A148TYR00.0190.01539.9730.0790.0790.0000.0000.0000.000
97A149TRP0-0.017-0.01043.4370.3500.3500.0000.0000.0000.000
98A150ALA0-0.015-0.00446.0330.2600.2600.0000.0000.0000.000
99A151ASP-1-0.824-0.92546.495-13.407-13.4070.0000.0000.0000.000
100A152ASN0-0.019-0.02641.265-0.445-0.4450.0000.0000.0000.000
101A153TYR00.0190.01442.061-0.454-0.4540.0000.0000.0000.000
102A154THR0-0.027-0.01343.038-0.235-0.2350.0000.0000.0000.000
103A155LEU00.0120.01040.760-0.204-0.2040.0000.0000.0000.000
104A156PHE00.0470.02935.554-0.284-0.2840.0000.0000.0000.000
105A157VAL0-0.009-0.00638.832-0.296-0.2960.0000.0000.0000.000
106A158LEU0-0.014-0.01340.386-0.152-0.1520.0000.0000.0000.000
107A159GLU-1-0.928-0.96033.977-18.271-18.2710.0000.0000.0000.000
108A160MET0-0.022-0.01433.448-0.413-0.4130.0000.0000.0000.000
109A161ALA0-0.018-0.00236.704-0.183-0.1830.0000.0000.0000.000
110A162LEU0-0.041-0.02536.476-0.186-0.1860.0000.0000.0000.000
111A163MET00.014-0.00129.145-0.412-0.4120.0000.0000.0000.000
112A164GLY00.0420.03932.545-0.518-0.5180.0000.0000.0000.000
113A165PHE0-0.049-0.04034.127-0.206-0.2060.0000.0000.0000.000
114A166ALA0-0.031-0.00930.612-0.230-0.2300.0000.0000.0000.000
115A167GLU-1-0.769-0.86027.123-23.326-23.3260.0000.0000.0000.000
116A168HIS00.0150.01029.254-0.822-0.8220.0000.0000.0000.000
117A169ARG10.8920.94631.21417.84117.8410.0000.0000.0000.000
118A170ARG10.8330.88023.15824.13324.1330.0000.0000.0000.000
119A171LEU00.0020.00625.868-0.887-0.8870.0000.0000.0000.000
120A172GLN0-0.029-0.03527.248-0.604-0.6040.0000.0000.0000.000
121A173ASP-1-0.883-0.94024.606-24.015-24.0150.0000.0000.0000.000
122A174TRP0-0.004-0.01618.364-1.023-1.0230.0000.0000.0000.000
123A175TYR0-0.011-0.00523.298-1.121-1.1210.0000.0000.0000.000
124A176ASN0-0.039-0.02825.576-0.331-0.3310.0000.0000.0000.000
125A177PRO00.0780.03623.1100.8220.8220.0000.0000.0000.000
126A178GLY0-0.0190.01526.1960.2420.2420.0000.0000.0000.000
127A179SER0-0.065-0.03429.2321.1941.1940.0000.0000.0000.000
128A180MET0-0.046-0.02029.8220.1440.1440.0000.0000.0000.000
129A181GLY00.0660.02932.024-0.153-0.1530.0000.0000.0000.000
130A182LYS10.9110.96033.68018.50518.5050.0000.0000.0000.000
131A183GLN00.0040.02036.2030.3910.3910.0000.0000.0000.000
132A184TYR00.0300.00437.508-0.286-0.2860.0000.0000.0000.000
133A185PHE00.000-0.02236.7310.0090.0090.0000.0000.0000.000
134A186LEU00.0380.01838.974-0.252-0.2520.0000.0000.0000.000
135A187GLY00.0080.01540.5460.0680.0680.0000.0000.0000.000
136A188LEU00.0130.00436.258-0.269-0.2690.0000.0000.0000.000
137A189GLU-1-0.831-0.91034.633-17.015-17.0150.0000.0000.0000.000
138A190LYS10.8540.91333.65915.86115.8610.0000.0000.0000.000
139A191GLY0-0.034-0.01231.465-0.411-0.4110.0000.0000.0000.000
140A192LEU0-0.041-0.04229.772-0.620-0.6200.0000.0000.0000.000
141A193ALA0-0.0030.01029.143-0.425-0.4250.0000.0000.0000.000
142A194GLY00.0690.04625.092-0.218-0.2180.0000.0000.0000.000
143A195SER0-0.113-0.08023.154-1.593-1.5930.0000.0000.0000.000
144A196GLY00.0450.02821.3790.5130.5130.0000.0000.0000.000
145A197ASN0-0.054-0.02416.985-2.157-2.1570.0000.0000.0000.000
146A198PRO00.0650.05818.7770.2400.2400.0000.0000.0000.000
147A199ALA00.008-0.00116.6380.5820.5820.0000.0000.0000.000
148A200TYR0-0.052-0.03913.577-0.087-0.0870.0000.0000.0000.000
149A201PRO00.0870.05419.3610.1070.1070.0000.0000.0000.000
150A202GLY00.0020.01322.6540.4760.4760.0000.0000.0000.000
151A203GLY00.0550.03723.4880.4980.4980.0000.0000.0000.000
152A204PRO00.024-0.00727.325-0.254-0.2540.0000.0000.0000.000
153A205PHE00.0000.00529.9660.3550.3550.0000.0000.0000.000
154A206PHE0-0.030-0.01125.101-0.019-0.0190.0000.0000.0000.000
155A207ASN0-0.042-0.02523.706-1.352-1.3520.0000.0000.0000.000
156A208PRO00.0100.01925.8140.1620.1620.0000.0000.0000.000
157A209LEU00.0070.01128.1370.4760.4760.0000.0000.0000.000
158A210GLY00.0210.01725.178-0.748-0.7480.0000.0000.0000.000
159A211PHE00.0330.01220.528-0.255-0.2550.0000.0000.0000.000
160A212GLY0-0.016-0.00919.114-0.572-0.5720.0000.0000.0000.000
161A213LYS10.8390.90920.01226.21926.2190.0000.0000.0000.000
162A214ASP-1-0.785-0.89016.898-33.305-33.3050.0000.0000.0000.000
163A215GLU-1-0.776-0.85613.193-39.677-39.6770.0000.0000.0000.000
164A216LYS10.9680.99112.58335.35635.3560.0000.0000.0000.000
165A217SER0-0.107-0.08013.541-0.765-0.7650.0000.0000.0000.000
166A218LEU00.0570.02115.566-0.161-0.1610.0000.0000.0000.000
167A219LYS10.8230.9015.91169.53469.5340.0000.0000.0000.000
168A220GLU-1-0.881-0.92511.035-47.648-47.6480.0000.0000.0000.000
169A221LEU0-0.013-0.01512.257-0.099-0.0990.0000.0000.0000.000
170A222LYS10.8960.94412.13641.51941.5190.0000.0000.0000.000
171A223LEU0-0.0160.0056.961-1.690-1.6900.0000.0000.0000.000
172A224LYS10.8620.90510.86938.02038.0200.0000.0000.0000.000
173A225GLU-1-0.794-0.86613.970-32.198-32.1980.0000.0000.0000.000
174A226VAL00.0270.0139.6831.2911.2910.0000.0000.0000.000
175A227LYS10.8630.9379.61451.74651.7460.0000.0000.0000.000
176A228ASN0-0.021-0.02012.8742.3142.3140.0000.0000.0000.000
177A229GLY00.0420.02715.9831.4811.4810.0000.0000.0000.000
178A230ARG10.7590.8267.91155.40255.4020.0000.0000.0000.000
179A231LEU0-0.017-0.00215.0141.1181.1180.0000.0000.0000.000
180A232ALA00.0190.00917.2221.4351.4350.0000.0000.0000.000
181A233MET0-0.008-0.00515.5601.4091.4090.0000.0000.0000.000
182A234LEU0-0.024-0.00615.2911.0031.0030.0000.0000.0000.000
183A235ALA0-0.0070.00519.4771.1511.1510.0000.0000.0000.000
184A236ILE00.0060.01022.5621.1131.1130.0000.0000.0000.000
185A237LEU00.0040.00720.7970.9120.9120.0000.0000.0000.000
186A238GLY00.0150.00223.4960.8180.8180.0000.0000.0000.000
187A239TYR0-0.028-0.04025.2300.7670.7670.0000.0000.0000.000
188A240PHE0-0.019-0.01126.3050.7630.7630.0000.0000.0000.000
189A241ILE00.0120.00825.9580.7460.7460.0000.0000.0000.000
190A242GLN00.0160.00527.6810.8010.8010.0000.0000.0000.000
191A243GLY00.0180.03230.8970.6260.6260.0000.0000.0000.000
192A244LEU0-0.058-0.02730.9520.5450.5450.0000.0000.0000.000
193A245VAL0-0.025-0.01531.7030.4560.4560.0000.0000.0000.000
194A246THR00.0410.00334.0380.5310.5310.0000.0000.0000.000
195A247GLY0-0.0130.01236.1560.4840.4840.0000.0000.0000.000
196A248VAL0-0.024-0.01936.4780.3870.3870.0000.0000.0000.000
197A249GLY00.0190.00935.042-0.453-0.4530.0000.0000.0000.000
198A250PRO00.0160.01829.9800.0240.0240.0000.0000.0000.000
199A251TYR00.004-0.00831.775-0.080-0.0800.0000.0000.0000.000
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201A253ASN0-0.015-0.01631.9200.0800.0800.0000.0000.0000.000
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