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: 3G2ZL

Calculation Name: 2E74-B-Xray549

Preferred Name:

Target Type:

Ligand Name: chlorophyll a | protoporphyrin ix containing fe | (7r,17e)-4-hydroxy-n,n,n,7-tetramethyl-7-[(8e)-octadec-8-enoyloxy]-10-oxo-3,5,9-trioxa-4-phosphaheptacos-17-en-1-aminium 4-oxide | 1,2-di-o-acyl-3-o-[6-deoxy-6-sulfo-alpha-d-glucopyranosyl]-sn-glycerol | beta-carotene | undecyl-maltoside | fe2/s2 (inorganic) cluster | cadmium ion

Ligand 3-letter code: CLA | HEM | OPC | SQD | BCR | UMQ | FES | CD

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 2E74

Chain ID: B

ChEMBL ID:

UniProt ID: P83791

Base Structure: X-ray

Registration Date: 2025-10-11

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 OptH
Protonation MOE:Protonate 3D
Complement ac.sh, 23 2024 Oct
Water No
Procedure Manual calculation
Remarks
FMO calculation
FMO method FMO2-MP2/6-31G(d)
Fragmentation Auto
Number of fragment 160
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922
Total energy (hartree)
FMO2-HF: Electronic energy -1175457.657101
FMO2-HF: Nuclear repulsion 1114232.318709
FMO2-HF: Total energy -61225.338391
FMO2-MP2: Total energy -61404.562709


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(B:1:MET)


Summations of interaction energy for fragment #1(B:1:MET)
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.
29.14332.5371.201-1.773-2.823-0.019
Interaction energy analysis for fragmet #1(B:1:MET)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 1 / q_Mulliken : 0.850 / q_NPA : 0.918
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].
3B3THR00.0330.0002.475-0.7382.4931.202-1.746-2.687-0.019
4B4LEU0-0.0060.0074.5552.5872.750-0.001-0.027-0.1360.000
5B5LYS10.9260.9796.68220.12420.1240.0000.0000.0000.000
6B6LYS10.9850.9768.49825.85325.8530.0000.0000.0000.000
7B7PRO00.0170.00011.6880.8020.8020.0000.0000.0000.000
8B8ASP-1-0.830-0.90915.532-15.582-15.5820.0000.0000.0000.000
9B9LEU0-0.047-0.04117.3950.8700.8700.0000.0000.0000.000
10B10SER00.0280.01919.6360.7170.7170.0000.0000.0000.000
11B11ASP-1-0.846-0.91421.143-11.846-11.8460.0000.0000.0000.000
12B12PRO00.000-0.01522.977-0.078-0.0780.0000.0000.0000.000
13B13LYS10.9440.97424.88010.93210.9320.0000.0000.0000.000
14B14LEU00.0180.02118.3840.0780.0780.0000.0000.0000.000
15B15ARG10.9500.97622.97912.18212.1820.0000.0000.0000.000
16B16ALA00.0240.01024.8660.1540.1540.0000.0000.0000.000
17B17LYS10.8960.96424.13812.13812.1380.0000.0000.0000.000
18B18LEU0-0.002-0.00220.3900.1050.1050.0000.0000.0000.000
19B19ALA0-0.0170.00024.5430.0970.0970.0000.0000.0000.000
20B20LYS10.8950.94728.10710.53410.5340.0000.0000.0000.000
21B21GLY0-0.0160.00025.7140.1140.1140.0000.0000.0000.000
22B22MET0-0.034-0.02025.226-0.247-0.2470.0000.0000.0000.000
23B23GLY00.025-0.00722.1410.1580.1580.0000.0000.0000.000
24B24HIS00.012-0.00218.922-1.075-1.0750.0000.0000.0000.000
25B25ASN00.0650.04417.818-0.694-0.6940.0000.0000.0000.000
26B26TYR00.0130.01117.7000.0670.0670.0000.0000.0000.000
27B27TYR0-0.106-0.06713.555-0.360-0.3600.0000.0000.0000.000
28B28GLY00.0610.04011.2370.7070.7070.0000.0000.0000.000
29B29GLU-1-0.843-0.9128.090-33.980-33.9800.0000.0000.0000.000
30B30PRO0-0.060-0.0348.4222.4032.4030.0000.0000.0000.000
31B31ALA00.0540.00911.474-0.007-0.0070.0000.0000.0000.000
32B32TRP00.0350.02214.2420.5230.5230.0000.0000.0000.000
33B33PRO0-0.027-0.00311.4770.1800.1800.0000.0000.0000.000
34B34ASN0-0.022-0.0457.1772.0902.0900.0000.0000.0000.000
35B35ASP-1-0.812-0.91911.264-21.856-21.8560.0000.0000.0000.000
36B36LEU0-0.049-0.02814.1831.0721.0720.0000.0000.0000.000
37B37LEU0-0.049-0.00915.9350.9460.9460.0000.0000.0000.000
38B38TYR0-0.019-0.00512.1390.8720.8720.0000.0000.0000.000
39B39VAL00.0360.02113.6250.7200.7200.0000.0000.0000.000
40B40PHE0-0.016-0.00616.4381.1061.1060.0000.0000.0000.000
41B41PRO0-0.003-0.00218.7510.6940.6940.0000.0000.0000.000
42B42VAL00.0290.02617.9760.6040.6040.0000.0000.0000.000
43B43VAL00.0100.00819.4770.5620.5620.0000.0000.0000.000
44B44ILE0-0.0100.01122.1080.6880.6880.0000.0000.0000.000
45B45MET0-0.018-0.01624.0380.4190.4190.0000.0000.0000.000
46B46GLY00.0300.02024.3170.4250.4250.0000.0000.0000.000
47B47THR0-0.019-0.02125.3510.4350.4350.0000.0000.0000.000
48B48PHE0-0.008-0.00827.6340.4200.4200.0000.0000.0000.000
49B49ALA00.0140.00528.1940.3780.3780.0000.0000.0000.000
50B50CYS0-0.038-0.02027.7750.2380.2380.0000.0000.0000.000
51B51ILE00.0290.01730.7640.3230.3230.0000.0000.0000.000
52B52VAL0-0.0180.00533.3780.3530.3530.0000.0000.0000.000
53B53ALA0-0.003-0.00633.0580.2640.2640.0000.0000.0000.000
54B54LEU00.004-0.00633.7540.2220.2220.0000.0000.0000.000
55B55SER0-0.024-0.02336.6400.2810.2810.0000.0000.0000.000
56B56VAL0-0.074-0.03238.4450.2380.2380.0000.0000.0000.000
57B57LEU0-0.076-0.04136.1380.1600.1600.0000.0000.0000.000
58B58ASP-1-0.953-0.96740.145-7.423-7.4230.0000.0000.0000.000
59B59PRO0-0.0350.00241.954-0.050-0.0500.0000.0000.0000.000
60B60ALA0-0.005-0.01043.8530.1120.1120.0000.0000.0000.000
61B61MET00.0060.00145.6800.0920.0920.0000.0000.0000.000
62B62VAL0-0.047-0.01649.358-0.028-0.0280.0000.0000.0000.000
63B63GLY00.0080.00452.4930.0210.0210.0000.0000.0000.000
64B64GLU-1-0.931-0.96954.464-5.393-5.3930.0000.0000.0000.000
65B65PRO0-0.051-0.03657.837-0.051-0.0510.0000.0000.0000.000
66B66ALA0-0.0050.00358.7770.0300.0300.0000.0000.0000.000
67B67ASP-1-0.807-0.90260.527-4.844-4.8440.0000.0000.0000.000
68B68PRO0-0.077-0.04863.562-0.033-0.0330.0000.0000.0000.000
69B69PHE0-0.064-0.03565.3790.0410.0410.0000.0000.0000.000
70B70ALA0-0.0210.00264.8150.0320.0320.0000.0000.0000.000
71B71THR0-0.029-0.01461.136-0.094-0.0940.0000.0000.0000.000
72B72PRO00.0150.00758.0540.0450.0450.0000.0000.0000.000
73B73LEU0-0.020-0.01159.1220.0020.0020.0000.0000.0000.000
74B74GLU-1-0.921-0.96252.512-6.097-6.0970.0000.0000.0000.000
75B75ILE0-0.043-0.01154.025-0.092-0.0920.0000.0000.0000.000
76B76LEU00.007-0.00448.801-0.010-0.0100.0000.0000.0000.000
77B77PRO0-0.050-0.02148.072-0.031-0.0310.0000.0000.0000.000
78B78GLU-1-0.788-0.87443.271-7.506-7.5060.0000.0000.0000.000
79B79TRP00.0620.00936.9020.0410.0410.0000.0000.0000.000
80B80TYR0-0.116-0.06839.917-0.011-0.0110.0000.0000.0000.000
81B81LEU0-0.024-0.01441.6600.0280.0280.0000.0000.0000.000
82B82TYR00.0070.03044.2890.1080.1080.0000.0000.0000.000
83B83PRO00.0310.00042.3730.1580.1580.0000.0000.0000.000
84B84VAL0-0.015-0.00445.2770.1370.1370.0000.0000.0000.000
85B85PHE00.0390.00847.7200.1680.1680.0000.0000.0000.000
86B86GLN00.0370.02448.6810.1380.1380.0000.0000.0000.000
87B87ILE0-0.028-0.02347.0360.1440.1440.0000.0000.0000.000
88B88LEU0-0.036-0.03251.1400.1400.1400.0000.0000.0000.000
89B89ARG10.7850.90652.3526.2476.2470.0000.0000.0000.000
90B90SER00.0050.00953.6610.0740.0740.0000.0000.0000.000
91B91VAL0-0.036-0.00953.7270.0130.0130.0000.0000.0000.000
92B92PRO00.0100.00356.7450.0380.0380.0000.0000.0000.000
93B93ASN0-0.018-0.00159.7490.0950.0950.0000.0000.0000.000
94B94LYS11.0601.00658.4595.0945.0940.0000.0000.0000.000
95B95LEU00.0230.02257.329-0.096-0.0960.0000.0000.0000.000
96B96LEU00.0210.00854.532-0.089-0.0890.0000.0000.0000.000
97B97GLY00.0620.03853.733-0.126-0.1260.0000.0000.0000.000
98B98VAL00.0230.00252.459-0.137-0.1370.0000.0000.0000.000
99B99LEU0-0.007-0.00452.019-0.124-0.1240.0000.0000.0000.000
100B100LEU0-0.0010.02349.936-0.151-0.1510.0000.0000.0000.000
101B101MET0-0.0090.00048.060-0.133-0.1330.0000.0000.0000.000
102B102ALA00.0220.01147.101-0.167-0.1670.0000.0000.0000.000
103B103SER0-0.038-0.06146.845-0.110-0.1100.0000.0000.0000.000
104B104VAL0-0.0050.02041.898-0.158-0.1580.0000.0000.0000.000
105B105PRO0-0.0040.00041.634-0.203-0.2030.0000.0000.0000.000
106B106LEU0-0.001-0.00542.073-0.131-0.1310.0000.0000.0000.000
107B107GLY00.0390.02142.943-0.041-0.0410.0000.0000.0000.000
108B108LEU0-0.018-0.02537.315-0.163-0.1630.0000.0000.0000.000
109B109ILE0-0.024-0.00538.173-0.223-0.2230.0000.0000.0000.000
110B110LEU00.003-0.00139.908-0.066-0.0660.0000.0000.0000.000
111B111VAL00.0100.01635.173-0.062-0.0620.0000.0000.0000.000
112B112PRO0-0.008-0.00234.636-0.125-0.1250.0000.0000.0000.000
113B113PHE0-0.043-0.03236.025-0.070-0.0700.0000.0000.0000.000
114B114ILE0-0.0170.00439.0900.0850.0850.0000.0000.0000.000
115B115GLU-1-0.822-0.91333.422-9.589-9.5890.0000.0000.0000.000
116B116ASN0-0.044-0.01934.546-0.426-0.4260.0000.0000.0000.000
117B117VAL0-0.0140.01235.9260.0380.0380.0000.0000.0000.000
118B118ASN0-0.027-0.01431.940-0.347-0.3470.0000.0000.0000.000
119B119LYS10.9910.99226.91611.28611.2860.0000.0000.0000.000
120B120PHE0-0.039-0.02227.466-0.634-0.6340.0000.0000.0000.000
121B121GLN00.0460.02423.503-0.127-0.1270.0000.0000.0000.000
122B122ASN0-0.004-0.01221.7090.5800.5800.0000.0000.0000.000
123B123PRO00.1290.05524.8450.2550.2550.0000.0000.0000.000
124B124PHE00.0250.02724.0280.3930.3930.0000.0000.0000.000
125B125ARG10.8960.94721.93313.25313.2530.0000.0000.0000.000
126B126ARG10.8070.89428.02710.75610.7560.0000.0000.0000.000
127B127PRO00.0460.02231.8560.1060.1060.0000.0000.0000.000
128B128VAL00.0350.03433.4560.0920.0920.0000.0000.0000.000
129B129ALA00.0430.03133.3110.1160.1160.0000.0000.0000.000
130B130THR0-0.022-0.02830.5480.0170.0170.0000.0000.0000.000
131B131THR00.008-0.00233.0400.0300.0300.0000.0000.0000.000
132B132ILE00.0060.00336.3740.1450.1450.0000.0000.0000.000
133B133PHE0-0.0020.00630.5170.0830.0830.0000.0000.0000.000
134B134LEU00.0040.00431.5470.0510.0510.0000.0000.0000.000
135B135PHE00.0120.01635.5610.1200.1200.0000.0000.0000.000
136B136GLY00.0510.02239.0240.1490.1490.0000.0000.0000.000
137B137THR0-0.046-0.02234.3020.0560.0560.0000.0000.0000.000
138B138LEU00.0060.00237.5100.0660.0660.0000.0000.0000.000
139B139VAL00.0140.00439.4620.1560.1560.0000.0000.0000.000
140B140THR0-0.030-0.02939.5520.1820.1820.0000.0000.0000.000
141B141ILE0-0.008-0.01136.2530.0920.0920.0000.0000.0000.000
142B142TRP0-0.0270.00340.8770.0990.0990.0000.0000.0000.000
143B143LEU00.008-0.00144.1930.1630.1630.0000.0000.0000.000
144B144GLY0-0.015-0.01243.3750.1260.1260.0000.0000.0000.000
145B145ILE00.0280.00841.8030.0670.0670.0000.0000.0000.000
146B146GLY00.0720.03745.5400.1340.1340.0000.0000.0000.000
147B147ALA0-0.047-0.02547.8340.1740.1740.0000.0000.0000.000
148B148THR0-0.057-0.03846.9040.1140.1140.0000.0000.0000.000
149B149PHE00.0020.02148.4690.1190.1190.0000.0000.0000.000
150B150PRO00.0290.00252.8330.0300.0300.0000.0000.0000.000
151B151LEU00.007-0.00155.821-0.056-0.0560.0000.0000.0000.000
152B152ASP-1-0.879-0.95157.140-5.487-5.4870.0000.0000.0000.000
153B153LYS10.9040.94455.1295.6255.6250.0000.0000.0000.000
154B154THR0-0.0540.00152.211-0.120-0.1200.0000.0000.0000.000
155B155LEU00.021-0.00151.414-0.124-0.1240.0000.0000.0000.000
156B156THR00.0190.00650.778-0.144-0.1440.0000.0000.0000.000
157B157LEU0-0.0100.00646.283-0.087-0.0870.0000.0000.0000.000
158B158GLY0-0.058-0.01950.9450.0030.0030.0000.0000.0000.000
159B159LEU0-0.072-0.03748.116-0.023-0.0230.0000.0000.0000.000
160B160PHE-1-0.920-0.95549.684-5.786-5.7860.0000.0000.0000.000