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: Y7NL2

Calculation Name: 7F9O-s-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: s

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 211
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922
Total energy (hartree)
FMO2-HF: Electronic energy -2130115.331124
FMO2-HF: Nuclear repulsion 2046008.911034
FMO2-HF: Total energy -84106.42009
FMO2-MP2: Total energy -84349.763312


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:56:THR)


Summations of interaction energy for fragment #1(A:56:THR)
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.
-127.287-126.6149.185-5.637-4.223-0.036
Interaction energy analysis for fragmet #1(A:56:THR)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 1 / q_Mulliken : 0.823 / q_NPA : 0.883
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].
3A58CYS00.0070.0133.835-2.024-0.142-0.014-0.887-0.982-0.003
26A81SER0-0.079-0.0504.759-2.591-2.558-0.001-0.008-0.0240.000
138A193ASP-1-0.844-0.8984.792-49.352-49.147-0.001-0.010-0.1940.000
161A216MET00.0520.0462.607-5.850-7.4079.202-4.717-2.928-0.033
164A219ARG10.8580.9174.23844.11344.223-0.001-0.015-0.0950.000
4A59GLU-1-0.876-0.9315.940-37.194-37.1940.0000.0000.0000.000
5A60PRO00.0360.0269.3861.6841.6840.0000.0000.0000.000
6A61LEU0-0.012-0.02411.7260.9170.9170.0000.0000.0000.000
7A62GLY00.0520.02315.5510.1230.1230.0000.0000.0000.000
8A63PRO0-0.074-0.03117.4470.2820.2820.0000.0000.0000.000
9A64ASP-1-0.874-0.94312.776-21.494-21.4940.0000.0000.0000.000
10A65ARG10.7690.88712.43320.93820.9380.0000.0000.0000.000
11A66PRO0-0.016-0.00515.3131.2611.2610.0000.0000.0000.000
12A67VAL0-0.031-0.01418.250-0.302-0.3020.0000.0000.0000.000
13A68TRP0-0.022-0.01719.5250.9170.9170.0000.0000.0000.000
14A69PHE0-0.0240.00521.3700.6760.6760.0000.0000.0000.000
15A70PRO00.033-0.00524.076-0.144-0.1440.0000.0000.0000.000
16A71GLY0-0.006-0.00625.0790.3890.3890.0000.0000.0000.000
17A72THR0-0.0300.00323.5690.4390.4390.0000.0000.0000.000
18A73ALA0-0.004-0.00421.500-0.506-0.5060.0000.0000.0000.000
19A74PRO00.0090.00717.2280.3530.3530.0000.0000.0000.000
20A75PRO00.0160.01418.1490.0630.0630.0000.0000.0000.000
21A76PRO00.004-0.01917.052-0.841-0.8410.0000.0000.0000.000
22A77TRP0-0.0270.00315.102-0.449-0.4490.0000.0000.0000.000
23A78LEU0-0.058-0.01613.470-0.914-0.9140.0000.0000.0000.000
24A79ASP-1-0.814-0.9038.073-30.402-30.4020.0000.0000.0000.000
25A80GLY00.0290.0139.8740.3520.3520.0000.0000.0000.000
27A82LEU0-0.009-0.0035.741-4.519-4.5190.0000.0000.0000.000
28A83PRO00.003-0.0136.0341.9281.9280.0000.0000.0000.000
29A84GLY00.0230.0078.8061.9821.9820.0000.0000.0000.000
30A85ASP-1-0.776-0.85811.436-18.968-18.9680.0000.0000.0000.000
31A86PHE0-0.040-0.02313.241-0.559-0.5590.0000.0000.0000.000
32A87GLY00.0370.00715.4240.9360.9360.0000.0000.0000.000
33A88PHE0-0.063-0.03916.9400.9710.9710.0000.0000.0000.000
34A89ASP-1-0.729-0.87718.646-14.814-14.8140.0000.0000.0000.000
35A90PRO0-0.052-0.03020.5190.2070.2070.0000.0000.0000.000
36A91LEU0-0.031-0.00623.7400.4930.4930.0000.0000.0000.000
37A92GLY0-0.0100.00721.3500.2720.2720.0000.0000.0000.000
38A93PHE0-0.018-0.02221.4110.1440.1440.0000.0000.0000.000
39A94GLY0-0.005-0.00117.204-0.056-0.0560.0000.0000.0000.000
40A95SER0-0.034-0.01316.806-0.640-0.6400.0000.0000.0000.000
41A96GLU-1-0.832-0.90217.410-15.691-15.6910.0000.0000.0000.000
42A97PRO00.0320.00412.675-0.383-0.3830.0000.0000.0000.000
43A98GLU-1-0.976-0.98613.541-16.049-16.0490.0000.0000.0000.000
44A99SER0-0.031-0.03915.815-0.330-0.3300.0000.0000.0000.000
45A100LEU00.0230.02211.820-0.204-0.2040.0000.0000.0000.000
46A101ARG10.8930.94211.15718.35718.3570.0000.0000.0000.000
47A102TRP0-0.033-0.00312.469-0.259-0.2590.0000.0000.0000.000
48A103PHE00.008-0.01715.9830.3620.3620.0000.0000.0000.000
49A104ALA00.0360.03410.9680.2230.2230.0000.0000.0000.000
50A105GLN0-0.041-0.04210.9440.9040.9040.0000.0000.0000.000
51A106ALA00.0080.01014.2110.6180.6180.0000.0000.0000.000
52A107GLU-1-0.823-0.88714.362-18.302-18.3020.0000.0000.0000.000
53A108LEU0-0.029-0.00911.2550.4840.4840.0000.0000.0000.000
54A109MET0-0.040-0.01314.9940.2010.2010.0000.0000.0000.000
55A110HIS0-0.024-0.03018.0871.1651.1650.0000.0000.0000.000
56A111GLY00.0050.00918.1820.5430.5430.0000.0000.0000.000
57A112ARG10.7760.85912.39420.78820.7880.0000.0000.0000.000
58A113TRP00.0280.00319.4970.6020.6020.0000.0000.0000.000
59A114ALA00.0100.01122.4830.5320.5320.0000.0000.0000.000
60A115MET0-0.004-0.00120.8090.5690.5690.0000.0000.0000.000
61A116LEU0-0.023-0.01622.6490.4190.4190.0000.0000.0000.000
62A117ALA0-0.0090.01025.5320.4710.4710.0000.0000.0000.000
63A118VAL00.005-0.00625.7810.3730.3730.0000.0000.0000.000
64A119ALA0-0.027-0.00826.8960.3200.3200.0000.0000.0000.000
65A120GLY0-0.008-0.01328.8100.3270.3270.0000.0000.0000.000
66A121ILE0-0.029-0.00431.1740.2830.2830.0000.0000.0000.000
67A122LEU0-0.003-0.00230.5440.2330.2330.0000.0000.0000.000
68A123ILE0-0.048-0.02530.7230.2170.2170.0000.0000.0000.000
69A124PRO0-0.029-0.01633.7730.2010.2010.0000.0000.0000.000
70A125GLU-1-0.766-0.88536.843-7.881-7.8810.0000.0000.0000.000
71A126ILE00.021-0.00335.3190.1760.1760.0000.0000.0000.000
72A127LEU0-0.102-0.04937.8580.1560.1560.0000.0000.0000.000
73A128GLN0-0.077-0.02839.7920.0930.0930.0000.0000.0000.000
74A129LYS00.0120.02141.8510.2140.2140.0000.0000.0000.000
75A130TRP0-0.057-0.03840.7180.2270.2270.0000.0000.0000.000
76A131GLY0-0.0250.00042.1290.0120.0120.0000.0000.0000.000
77A132PHE0-0.065-0.03343.0150.1650.1650.0000.0000.0000.000
78A133MET0-0.024-0.02042.3140.0950.0950.0000.0000.0000.000
79A134GLU-1-0.824-0.92243.215-6.748-6.7480.0000.0000.0000.000
80A135GLU-1-0.899-0.95039.093-7.994-7.9940.0000.0000.0000.000
81A136PHE0-0.008-0.01041.863-0.086-0.0860.0000.0000.0000.000
82A137SER00.012-0.00241.477-0.091-0.0910.0000.0000.0000.000
83A138TRP00.0990.03734.845-0.056-0.0560.0000.0000.0000.000
84A139TYR0-0.050-0.02137.626-0.134-0.1340.0000.0000.0000.000
85A140THR00.0070.01039.1840.0070.0070.0000.0000.0000.000
86A141ALA0-0.0080.00238.8130.1490.1490.0000.0000.0000.000
87A142GLY0-0.062-0.02939.136-0.077-0.0770.0000.0000.0000.000
88A143GLU-1-0.901-0.96739.860-7.292-7.2920.0000.0000.0000.000
89A144ARG10.8350.92839.5267.8237.8230.0000.0000.0000.000
90A145GLU-1-0.926-0.96043.957-6.677-6.6770.0000.0000.0000.000
91A146TYR0-0.034-0.01440.471-0.074-0.0740.0000.0000.0000.000
92A147PHE0-0.049-0.03441.4310.1350.1350.0000.0000.0000.000
93A148ALA0-0.022-0.00443.7670.1360.1360.0000.0000.0000.000
94A149ASP-1-0.770-0.85144.821-7.035-7.0350.0000.0000.0000.000
95A150PRO00.0860.02341.473-0.146-0.1460.0000.0000.0000.000
96A151TRP0-0.045-0.02040.428-0.144-0.1440.0000.0000.0000.000
97A152THR0-0.011-0.04240.831-0.213-0.2130.0000.0000.0000.000
98A153LEU00.0210.02837.679-0.199-0.1990.0000.0000.0000.000
99A154PHE00.0210.01935.486-0.269-0.2690.0000.0000.0000.000
100A155VAL0-0.006-0.01435.937-0.255-0.2550.0000.0000.0000.000
101A156THR0-0.052-0.02936.348-0.232-0.2320.0000.0000.0000.000
102A157GLN00.010-0.00232.782-0.097-0.0970.0000.0000.0000.000
103A158MET0-0.008-0.00431.693-0.469-0.4690.0000.0000.0000.000
104A159ALA0-0.0190.00131.712-0.259-0.2590.0000.0000.0000.000
105A160LEU0-0.022-0.01430.903-0.260-0.2600.0000.0000.0000.000
106A161MET00.0140.01024.130-0.375-0.3750.0000.0000.0000.000
107A162GLY00.0400.01726.840-0.441-0.4410.0000.0000.0000.000
108A163TRP0-0.043-0.01727.628-0.279-0.2790.0000.0000.0000.000
109A164VAL0-0.017-0.01523.091-0.333-0.3330.0000.0000.0000.000
110A165GLU-1-0.748-0.84021.736-14.439-14.4390.0000.0000.0000.000
111A166GLY00.0190.01522.775-0.402-0.4020.0000.0000.0000.000
112A167ARG10.8860.94122.78612.20212.2020.0000.0000.0000.000
113A168ARG10.8510.88916.50115.14315.1430.0000.0000.0000.000
114A169TRP0-0.002-0.00318.448-0.749-0.7490.0000.0000.0000.000
115A170MET0-0.002-0.01419.720-0.226-0.2260.0000.0000.0000.000
116A171ASP-1-0.868-0.92515.473-18.903-18.9030.0000.0000.0000.000
117A172TYR00.0070.00013.646-1.328-1.3280.0000.0000.0000.000
118A173LEU0-0.057-0.02115.575-0.530-0.5300.0000.0000.0000.000
119A174ASN0-0.064-0.03417.356-0.587-0.5870.0000.0000.0000.000
120A175PRO00.0300.01512.6920.1720.1720.0000.0000.0000.000
121A176GLY0-0.046-0.02314.798-0.097-0.0970.0000.0000.0000.000
122A177SER0-0.046-0.01615.8710.8300.8300.0000.0000.0000.000
123A178VAL0-0.072-0.04418.6951.0181.0180.0000.0000.0000.000
124A179ASP-1-0.922-0.94216.998-16.605-16.6050.0000.0000.0000.000
125A180ILE0-0.037-0.03218.5830.9670.9670.0000.0000.0000.000
126A181GLU-1-0.811-0.90717.497-17.223-17.2230.0000.0000.0000.000
127A182PRO0-0.048-0.00119.8670.3230.3230.0000.0000.0000.000
128A183ARG10.9160.94220.94513.29213.2920.0000.0000.0000.000
129A184PHE00.0240.02123.2370.5180.5180.0000.0000.0000.000
130A185PRO00.0470.00224.417-0.516-0.5160.0000.0000.0000.000
131A186ASN0-0.010-0.00423.4230.2900.2900.0000.0000.0000.000
132A187ARG10.9480.99218.26614.92314.9230.0000.0000.0000.000
133A188LYS10.9310.95816.81717.24817.2480.0000.0000.0000.000
134A189ASN00.0400.02616.6910.0570.0570.0000.0000.0000.000
135A190PRO00.0030.00211.983-0.737-0.7370.0000.0000.0000.000
136A191THR0-0.005-0.0018.1090.9480.9480.0000.0000.0000.000
137A192PRO00.0700.01510.232-1.312-1.3120.0000.0000.0000.000
139A194VAL00.0840.0397.6510.3310.3310.0000.0000.0000.000
140A195GLY00.0350.0429.666-0.862-0.8620.0000.0000.0000.000
141A196TYR0-0.045-0.0407.4120.0830.0830.0000.0000.0000.000
142A197PRO00.0200.01310.416-1.281-1.2810.0000.0000.0000.000
143A198GLY00.0000.01512.418-0.220-0.2200.0000.0000.0000.000
144A199GLY00.0250.00313.1021.2491.2490.0000.0000.0000.000
145A200LEU0-0.074-0.05516.082-0.028-0.0280.0000.0000.0000.000
146A201TRP00.0210.01218.8980.9640.9640.0000.0000.0000.000
147A202PHE0-0.010-0.01316.4740.6100.6100.0000.0000.0000.000
148A203ASP-1-0.821-0.89512.514-23.763-23.7630.0000.0000.0000.000
149A204TRP0-0.022-0.00416.078-0.431-0.4310.0000.0000.0000.000
150A205GLY0-0.018-0.00418.3620.5970.5970.0000.0000.0000.000
151A206ASN0-0.106-0.05712.892-0.208-0.2080.0000.0000.0000.000
152A207TRP00.0400.02810.056-0.413-0.4130.0000.0000.0000.000
153A208GLY00.003-0.00910.363-1.468-1.4680.0000.0000.0000.000
154A209ARG10.8290.8998.29225.78325.7830.0000.0000.0000.000
155A210GLY00.0390.0167.8171.6281.6280.0000.0000.0000.000
156A211SER0-0.020-0.0168.6090.3020.3020.0000.0000.0000.000
157A212PRO0-0.0040.00812.0010.9920.9920.0000.0000.0000.000
158A213GLU-1-0.869-0.95610.783-23.229-23.2290.0000.0000.0000.000
159A214PRO0-0.0110.0027.278-2.978-2.9780.0000.0000.0000.000
160A215VAL00.0260.0094.812-0.101-0.1010.0000.0000.0000.000
162A217VAL00.0470.0485.8824.1084.1080.0000.0000.0000.000
163A218LEU0-0.029-0.0119.2132.7472.7470.0000.0000.0000.000
165A220THR00.019-0.0069.1772.3962.3960.0000.0000.0000.000
166A221LYS10.9010.95011.32521.16521.1650.0000.0000.0000.000
167A222GLU-1-0.806-0.87412.513-20.587-20.5870.0000.0000.0000.000
168A223ILE00.0110.02212.0851.5881.5880.0000.0000.0000.000
169A224LYS10.9200.96514.61518.96918.9690.0000.0000.0000.000
170A225ASN0-0.039-0.03517.1211.6711.6710.0000.0000.0000.000
171A226GLY00.0460.03417.8140.7760.7760.0000.0000.0000.000
172A227ARG10.8050.86514.78519.04919.0490.0000.0000.0000.000
173A228LEU0-0.014-0.00220.3510.6630.6630.0000.0000.0000.000
174A229ALA00.0210.01322.3420.6190.6190.0000.0000.0000.000
175A230MET00.003-0.00619.1460.6030.6030.0000.0000.0000.000
176A231LEU0-0.023-0.01223.9310.5240.5240.0000.0000.0000.000
177A232ALA0-0.0030.00626.5310.4750.4750.0000.0000.0000.000
178A233PHE00.0050.01027.3530.3830.3830.0000.0000.0000.000
179A234VAL0-0.001-0.00528.5610.3920.3920.0000.0000.0000.000
180A235GLY00.0070.00730.3320.3600.3600.0000.0000.0000.000
181A236PHE0-0.007-0.02031.1280.3060.3060.0000.0000.0000.000
182A237TRP00.0150.00633.0830.2280.2280.0000.0000.0000.000
183A238PHE0-0.015-0.01634.3920.2700.2700.0000.0000.0000.000
184A239GLN0-0.0070.00035.2000.3730.3730.0000.0000.0000.000
185A240VAL00.0020.01537.9090.1960.1960.0000.0000.0000.000
186A241VAL0-0.055-0.01338.3170.1860.1860.0000.0000.0000.000
187A242TYR0-0.075-0.02840.7790.1950.1950.0000.0000.0000.000
188A243THR0-0.056-0.04741.4660.2380.2380.0000.0000.0000.000
189A244GLY0-0.0030.00543.009-0.112-0.1120.0000.0000.0000.000
190A245GLN0-0.0180.00143.0460.0760.0760.0000.0000.0000.000
191A246GLY00.0220.02339.820-0.154-0.1540.0000.0000.0000.000
192A247PRO0-0.057-0.03535.5190.0260.0260.0000.0000.0000.000
193A248LEU00.0030.00637.554-0.055-0.0550.0000.0000.0000.000
194A249ASP-1-0.830-0.90939.160-7.251-7.2510.0000.0000.0000.000
195A250ASN00.002-0.01639.0690.2870.2870.0000.0000.0000.000
196A251LEU0-0.040-0.00535.3940.0130.0130.0000.0000.0000.000
197A252PHE00.012-0.02039.2350.0360.0360.0000.0000.0000.000
198A253ALA00.0140.01342.4260.1580.1580.0000.0000.0000.000
199A254HIS0-0.046-0.01639.6050.0270.0270.0000.0000.0000.000
200A255LEU0-0.057-0.04338.7270.0280.0280.0000.0000.0000.000
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