FMODB

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

Last updated: 2025-10-06

All entries: 70436

Number of unique PDB entries: 28101

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FMODB ID: YR6V2

Calculation Name: 1GCV-A-Xray547

Preferred Name:

Target Type:

Ligand Name: protoporphyrin ix containing fe

Ligand 3-letter code: HEM

Ligand of Interest (LOI):

PDB ID: 1GCV

Chain ID: A

ChEMBL ID:

UniProt ID: Q9YGW2

Base Structure: X-ray

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
FMO calculation
FMO method FMO2-MP2/6-31G(d)
Fragmentation Auto
Number of fragment 140
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922
Total energy (hartree)
FMO2-HF: Electronic energy -1225097.244137
FMO2-HF: Nuclear repulsion 1171092.691826
FMO2-HF: Total energy -54004.552311
FMO2-MP2: Total energy -54160.787527


3D Structure
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:1:ALA)


Summations of interaction energy for fragment #1(A:1:ALA)
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.
-17.787-16.072-0.023-0.732-0.961-0.001
Interaction energy analysis for fragmet #1(A:1:ALA)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 1 / q_Mulliken : 0.849 / q_NPA : 0.917
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].
3A3THR00.0290.0043.8434.2535.755-0.021-0.680-0.801-0.001
74A74ASP-1-0.855-0.9135.185-47.230-47.235-0.001-0.0010.0070.000
126A126LYS10.8400.9034.00551.21651.434-0.001-0.051-0.1670.000
4A4ALA00.0440.0106.6770.3240.3240.0000.0000.0000.000
5A5CYS00.0250.0119.9171.6351.6350.0000.0000.0000.000
6A6GLU-1-0.720-0.8166.241-45.616-45.6160.0000.0000.0000.000
7A7LYS10.8400.9036.16139.70939.7090.0000.0000.0000.000
8A8GLN00.0240.0089.4311.0101.0100.0000.0000.0000.000
9A9THR0-0.039-0.01912.4872.3482.3480.0000.0000.0000.000
10A10ILE00.0110.0087.8451.5391.5390.0000.0000.0000.000
11A11GLY00.0330.01812.0161.5351.5350.0000.0000.0000.000
12A12LYS10.8740.93814.19019.12019.1200.0000.0000.0000.000
13A13ILE00.0180.00815.0501.3771.3770.0000.0000.0000.000
14A14ALA00.0200.01614.7170.9960.9960.0000.0000.0000.000
15A15GLN00.0250.00116.7241.6321.6320.0000.0000.0000.000
16A16VAL0-0.034-0.00519.6601.0481.0480.0000.0000.0000.000
17A17LEU00.012-0.00417.0010.8230.8230.0000.0000.0000.000
18A18ALA00.011-0.00220.5770.6190.6190.0000.0000.0000.000
19A19LYS10.8490.93222.21413.96213.9620.0000.0000.0000.000
20A20SER0-0.019-0.00424.9580.5870.5870.0000.0000.0000.000
21A21PRO00.0020.00522.764-0.003-0.0030.0000.0000.0000.000
22A22GLU-1-0.784-0.86724.253-12.111-12.1110.0000.0000.0000.000
23A23ALA00.0090.00827.1350.0560.0560.0000.0000.0000.000
24A24TYR00.0210.01422.5640.0350.0350.0000.0000.0000.000
25A25GLY00.0590.02323.023-0.223-0.2230.0000.0000.0000.000
26A26ALA0-0.008-0.00123.9280.0480.0480.0000.0000.0000.000
27A27GLU-1-0.773-0.84525.946-11.528-11.5280.0000.0000.0000.000
28A28CYS0-0.053-0.00921.786-0.164-0.1640.0000.0000.0000.000
29A29LEU00.003-0.00323.7960.0260.0260.0000.0000.0000.000
30A30ALA00.0120.01325.8420.2500.2500.0000.0000.0000.000
31A31ARG10.8660.91724.93512.14212.1420.0000.0000.0000.000
32A32LEU00.0360.03022.9040.1070.1070.0000.0000.0000.000
33A33PHE0-0.045-0.04125.7490.2820.2820.0000.0000.0000.000
34A34VAL0-0.032-0.00829.3540.4160.4160.0000.0000.0000.000
35A35THR0-0.026-0.03526.1720.0660.0660.0000.0000.0000.000
36A36HIS10.9240.96323.72512.62212.6220.0000.0000.0000.000
37A37PRO00.0410.03627.977-0.108-0.1080.0000.0000.0000.000
38A38GLY00.0280.01630.6640.1640.1640.0000.0000.0000.000
39A39SER00.0260.00926.3490.0920.0920.0000.0000.0000.000
40A40LYS10.9230.95328.0539.2789.2780.0000.0000.0000.000
41A41SER0-0.042-0.02130.3230.1410.1410.0000.0000.0000.000
42A42TYR00.0280.03226.4570.1190.1190.0000.0000.0000.000
43A43PHE0-0.027-0.01325.640-0.095-0.0950.0000.0000.0000.000
44A44GLU-1-0.857-0.91131.823-8.339-8.3390.0000.0000.0000.000
45A45TYR0-0.087-0.04929.1150.0950.0950.0000.0000.0000.000
46A46LYS10.9620.96535.8777.8267.8260.0000.0000.0000.000
47A47ASP-1-0.793-0.86836.641-8.695-8.6950.0000.0000.0000.000
48A48TYR0-0.031-0.04231.851-0.073-0.0730.0000.0000.0000.000
49A49SER0-0.016-0.02532.029-0.380-0.3800.0000.0000.0000.000
50A50ALA00.0350.00530.413-0.099-0.0990.0000.0000.0000.000
51A51ALA00.0180.01631.557-0.114-0.1140.0000.0000.0000.000
52A52GLY00.0350.03534.2160.1760.1760.0000.0000.0000.000
53A53ALA00.017-0.00133.107-0.316-0.3160.0000.0000.0000.000
54A54LYS10.8970.93632.6738.6808.6800.0000.0000.0000.000
55A55VAL00.0040.02329.005-0.372-0.3720.0000.0000.0000.000
56A56GLN00.009-0.00528.383-0.596-0.5960.0000.0000.0000.000
57A57VAL0-0.011-0.00728.218-0.417-0.4170.0000.0000.0000.000
58A58HIS0-0.020-0.01023.994-0.154-0.1540.0000.0000.0000.000
59A59GLY00.0490.01524.357-0.595-0.5950.0000.0000.0000.000
60A60GLY00.0630.02423.373-0.609-0.6090.0000.0000.0000.000
61A61LYS10.8870.94823.18011.06911.0690.0000.0000.0000.000
62A62VAL00.0240.01819.202-0.696-0.6960.0000.0000.0000.000
63A63ILE00.0210.01418.683-1.013-1.0130.0000.0000.0000.000
64A64ARG10.8230.87618.74711.85311.8530.0000.0000.0000.000
65A65ALA0-0.0210.00017.094-0.436-0.4360.0000.0000.0000.000
66A66VAL00.0110.00813.980-1.253-1.2530.0000.0000.0000.000
67A67VAL0-0.023-0.00814.023-1.432-1.4320.0000.0000.0000.000
68A68LYS10.9740.99414.88314.81214.8120.0000.0000.0000.000
69A69ALA00.0400.01711.080-1.018-1.0180.0000.0000.0000.000
70A70ALA0-0.037-0.02710.236-2.882-2.8820.0000.0000.0000.000
71A71GLU-1-0.951-0.98210.702-19.824-19.8240.0000.0000.0000.000
72A72HIS0-0.068-0.03410.8560.6310.6310.0000.0000.0000.000
73A73VAL00.0130.0035.122-2.270-2.2700.0000.0000.0000.000
75A75ASP-1-0.871-0.9176.667-28.554-28.5540.0000.0000.0000.000
76A76LEU0-0.015-0.0085.7083.2373.2370.0000.0000.0000.000
77A77HIS0-0.009-0.0028.9594.9624.9620.0000.0000.0000.000
78A78SER00.001-0.02410.6662.7932.7930.0000.0000.0000.000
79A79HIS0-0.081-0.02912.0152.0262.0260.0000.0000.0000.000
80A80LEU0-0.008-0.01310.5501.7671.7670.0000.0000.0000.000
81A81GLU-1-0.801-0.85514.091-16.436-16.4360.0000.0000.0000.000
82A82THR00.0300.00516.2361.2541.2540.0000.0000.0000.000
83A83LEU0-0.016-0.00216.3421.0541.0540.0000.0000.0000.000
84A84ALA00.0600.03115.3550.7020.7020.0000.0000.0000.000
85A85LEU0-0.0090.00517.4920.7540.7540.0000.0000.0000.000
86A86THR0-0.069-0.04120.7360.9910.9910.0000.0000.0000.000
87A87HIS0-0.051-0.04719.3171.0181.0180.0000.0000.0000.000
88A88GLY00.0340.01620.5800.5850.5850.0000.0000.0000.000
89A89LYS10.8600.92221.82314.09914.0990.0000.0000.0000.000
90A90LYS10.9130.96624.75011.61911.6190.0000.0000.0000.000
91A91LEU0-0.065-0.04023.2560.4570.4570.0000.0000.0000.000
92A92LEU0-0.0120.00725.0490.3260.3260.0000.0000.0000.000
93A93VAL0-0.0140.00822.8010.2150.2150.0000.0000.0000.000
94A94ASP-1-0.798-0.87322.842-13.768-13.7680.0000.0000.0000.000
95A95PRO00.0620.01718.337-0.115-0.1150.0000.0000.0000.000
96A96GLN0-0.053-0.03218.913-0.765-0.7650.0000.0000.0000.000
97A97ASN0-0.057-0.05320.8450.3630.3630.0000.0000.0000.000
98A98PHE00.0090.01716.1420.0310.0310.0000.0000.0000.000
99A99PRO00.0710.02915.544-0.382-0.3820.0000.0000.0000.000
100A100MET0-0.062-0.01417.1370.4640.4640.0000.0000.0000.000
101A101LEU00.0080.00419.2280.5010.5010.0000.0000.0000.000
102A102SER00.003-0.00914.947-0.341-0.3410.0000.0000.0000.000
103A103GLU-1-0.853-0.92616.900-16.578-16.5780.0000.0000.0000.000
104A104CYS0-0.087-0.03018.9900.7570.7570.0000.0000.0000.000
105A105ILE00.0060.00216.6510.6180.6180.0000.0000.0000.000
106A106ILE00.0140.01214.4850.2290.2290.0000.0000.0000.000
107A107VAL00.003-0.01118.4930.5990.5990.0000.0000.0000.000
108A108THR0-0.059-0.04621.8390.7540.7540.0000.0000.0000.000
109A109LEU0-0.031-0.01516.7710.3380.3380.0000.0000.0000.000
110A110ALA00.0190.01521.0500.4320.4320.0000.0000.0000.000
111A111THR0-0.061-0.02923.0000.3620.3620.0000.0000.0000.000
112A112HIS10.7910.87524.18712.55812.5580.0000.0000.0000.000
113A113LEU0-0.040-0.01219.2030.2320.2320.0000.0000.0000.000
114A114THR0-0.0060.00023.7540.0150.0150.0000.0000.0000.000
115A115GLU-1-0.789-0.86819.677-16.266-16.2660.0000.0000.0000.000
116A116PHE00.015-0.00717.109-0.629-0.6290.0000.0000.0000.000
117A117SER00.002-0.00519.062-0.159-0.1590.0000.0000.0000.000
118A118PRO00.035-0.00317.263-0.786-0.7860.0000.0000.0000.000
119A119ASP-1-0.894-0.93413.785-21.217-21.2170.0000.0000.0000.000
120A120THR0-0.081-0.06513.226-2.373-2.3730.0000.0000.0000.000
121A121HIS0-0.0140.00714.322-1.820-1.8200.0000.0000.0000.000
122A122CYS00.0340.01110.309-2.149-2.1490.0000.0000.0000.000
123A123ALA0-0.003-0.0099.269-3.054-3.0540.0000.0000.0000.000
124A124VAL0-0.016-0.0119.148-2.805-2.8050.0000.0000.0000.000
125A125ASP-1-0.885-0.94010.896-25.232-25.2320.0000.0000.0000.000
127A127LEU0-0.007-0.0016.748-4.387-4.3870.0000.0000.0000.000
128A128LEU0-0.015-0.0087.9870.4780.4780.0000.0000.0000.000
129A129SER00.0320.0178.2731.6331.6330.0000.0000.0000.000
130A130ALA0-0.047-0.0225.3890.2930.2930.0000.0000.0000.000
131A131ILE00.0290.0037.3862.2402.2400.0000.0000.0000.000
132A132CYS0-0.051-0.02210.6102.5262.5260.0000.0000.0000.000
133A133GLN0-0.0180.0037.5982.9862.9860.0000.0000.0000.000
134A134GLU-1-0.805-0.8929.000-28.791-28.7910.0000.0000.0000.000
135A135LEU0-0.054-0.02111.7661.9681.9680.0000.0000.0000.000
136A136SER0-0.021-0.03514.5201.8741.8740.0000.0000.0000.000
137A137SER0-0.053-0.03413.3891.2961.2960.0000.0000.0000.000
138A138ARG10.8060.88814.68320.00320.0030.0000.0000.0000.000
139A139TYR0-0.033-0.03519.0260.6990.6990.0000.0000.0000.000
140A140ARG00.0000.02020.2980.6540.6540.0000.0000.0000.000