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: VVZ91

Calculation Name: 1FFT-C-Xray547

Preferred Name:

Target Type:

Ligand Name: heme o | protoporphyrin ix containing fe | copper (ii) ion

Ligand 3-letter code: HEO | HEM | CU

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 1FFT

Chain ID: C

ChEMBL ID:

UniProt ID: P0ABJ1

Base Structure: X-ray

Registration Date: 2025-09-02

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 185
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922
Total energy (hartree)
FMO2-HF: Electronic energy -1863556.379858
FMO2-HF: Nuclear repulsion 1790691.080869
FMO2-HF: Total energy -72865.298988
FMO2-MP2: Total energy -73073.755736


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:19:HIS)


Summations of interaction energy for fragment #1(A:19:HIS)
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.
74.40576.882-0.024-1.086-1.367-0.005
Interaction energy analysis for fragmet #1(A:19:HIS)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 1 / q_Mulliken : 0.826 / q_NPA : 0.895
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].
3A21ALA00.0540.0103.5345.9218.259-0.023-1.077-1.239-0.005
4A22GLY0-0.051-0.0024.5885.0795.218-0.001-0.009-0.1280.000
5A23GLY00.0310.0066.0754.5094.5090.0000.0000.0000.000
6A24THR00.0550.0258.0631.6101.6100.0000.0000.0000.000
7A25LYS10.9610.96810.06225.40425.4040.0000.0000.0000.000
8A26ILE00.0100.01811.6861.4631.4630.0000.0000.0000.000
9A27PHE00.0720.03013.1111.2521.2520.0000.0000.0000.000
10A28GLY0-0.002-0.00514.2561.0941.0940.0000.0000.0000.000
11A29PHE00.0080.00015.9150.6270.6270.0000.0000.0000.000
12A30TRP0-0.008-0.00617.5590.6510.6510.0000.0000.0000.000
13A31ILE00.0410.01418.9450.6970.6970.0000.0000.0000.000
14A32TYR0-0.034-0.00420.4520.4720.4720.0000.0000.0000.000
15A33LEU00.0330.00922.1070.5640.5640.0000.0000.0000.000
16A34MET0-0.036-0.01723.7970.6530.6530.0000.0000.0000.000
17A35SER0-0.0230.00126.0590.4950.4950.0000.0000.0000.000
18A36ASP-1-0.860-0.94727.172-10.634-10.6340.0000.0000.0000.000
19A37CYS0-0.041-0.00927.9710.4140.4140.0000.0000.0000.000
20A38ILE00.0090.00929.8470.3510.3510.0000.0000.0000.000
21A39LEU00.0140.02831.8120.3780.3780.0000.0000.0000.000
22A40PHE00.0460.00132.0040.2700.2700.0000.0000.0000.000
23A41SER0-0.044-0.01334.3660.2610.2610.0000.0000.0000.000
24A42ILE00.002-0.01236.1260.2720.2720.0000.0000.0000.000
25A43LEU00.0160.01737.7310.2430.2430.0000.0000.0000.000
26A44PHE00.0500.02238.8000.2520.2520.0000.0000.0000.000
27A45ALA0-0.0180.01140.3680.2110.2110.0000.0000.0000.000
28A46THR0-0.027-0.03742.3140.1730.1730.0000.0000.0000.000
29A47TYR00.0120.00243.5810.2050.2050.0000.0000.0000.000
30A48ALA00.009-0.00344.4970.1550.1550.0000.0000.0000.000
31A49VAL0-0.040-0.01246.2530.1520.1520.0000.0000.0000.000
32A50LEU0-0.083-0.02948.1470.1920.1920.0000.0000.0000.000
33A51VAL00.0250.01148.3870.0160.0160.0000.0000.0000.000
34A52ASN0-0.029-0.02150.4100.1810.1810.0000.0000.0000.000
35A53GLY0-0.034-0.00753.7550.1060.1060.0000.0000.0000.000
36A54THR0-0.009-0.00355.9810.1260.1260.0000.0000.0000.000
37A55ALA00.0510.03457.144-0.013-0.0130.0000.0000.0000.000
38A56GLY0-0.015-0.00258.2660.1090.1090.0000.0000.0000.000
39A57GLY0-0.029-0.02360.9430.0290.0290.0000.0000.0000.000
40A58PRO0-0.080-0.04859.553-0.038-0.0380.0000.0000.0000.000
41A59THR00.0290.01455.449-0.083-0.0830.0000.0000.0000.000
42A60GLY0-0.022-0.00454.3390.0700.0700.0000.0000.0000.000
43A61LYS10.9510.97853.3515.3705.3700.0000.0000.0000.000
44A62ASP-1-0.814-0.91948.553-6.481-6.4810.0000.0000.0000.000
45A63ILE0-0.0020.00551.6970.0930.0930.0000.0000.0000.000
46A64PHE00.0380.01948.734-0.117-0.1170.0000.0000.0000.000
47A65GLU-1-0.977-0.99449.288-5.954-5.9540.0000.0000.0000.000
48A66LEU00.0610.02846.885-0.159-0.1590.0000.0000.0000.000
49A67PRO0-0.028-0.00544.141-0.209-0.2090.0000.0000.0000.000
50A68PHE0-0.0250.00443.903-0.093-0.0930.0000.0000.0000.000
51A69VAL00.0360.00343.017-0.188-0.1880.0000.0000.0000.000
52A70LEU00.0130.01240.842-0.214-0.2140.0000.0000.0000.000
53A71VAL0-0.0090.00039.003-0.266-0.2660.0000.0000.0000.000
54A72GLU-1-0.874-0.93838.163-8.009-8.0090.0000.0000.0000.000
55A73THR0-0.070-0.05037.027-0.223-0.2230.0000.0000.0000.000
56A74PHE0-0.012-0.01731.723-0.366-0.3660.0000.0000.0000.000
57A75LEU00.0560.03733.487-0.383-0.3830.0000.0000.0000.000
58A76LEU0-0.021-0.02433.677-0.291-0.2910.0000.0000.0000.000
59A77LEU0-0.085-0.03130.492-0.356-0.3560.0000.0000.0000.000
60A78PHE0-0.0020.02129.226-0.525-0.5250.0000.0000.0000.000
61A79SER00.0060.00228.697-0.461-0.4610.0000.0000.0000.000
62A80SER0-0.019-0.00929.812-0.046-0.0460.0000.0000.0000.000
63A81ILE0-0.044-0.02023.700-0.413-0.4130.0000.0000.0000.000
64A82THR0-0.043-0.02324.931-0.565-0.5650.0000.0000.0000.000
65A83TYR0-0.046-0.03125.891-0.222-0.2220.0000.0000.0000.000
66A84GLY00.0500.03725.517-0.036-0.0360.0000.0000.0000.000
67A85MET00.000-0.02917.860-0.573-0.5730.0000.0000.0000.000
68A86ALA00.0290.00720.550-0.750-0.7500.0000.0000.0000.000
69A87ALA00.0340.02021.432-0.480-0.4800.0000.0000.0000.000
70A88ILE00.0160.01819.296-0.016-0.0160.0000.0000.0000.000
71A89ALA0-0.083-0.07016.136-0.677-0.6770.0000.0000.0000.000
72A90MET0-0.0050.03515.108-0.978-0.9780.0000.0000.0000.000
73A91TYR00.0310.02117.851-0.220-0.2200.0000.0000.0000.000
74A92LYS10.9520.96319.52313.23913.2390.0000.0000.0000.000
75A93ASN0-0.027-0.01018.9550.7030.7030.0000.0000.0000.000
76A94ASN00.0100.00120.8640.1610.1610.0000.0000.0000.000
77A95LYS10.9560.96821.25913.74113.7410.0000.0000.0000.000
78A96SER00.0450.01723.575-0.124-0.1240.0000.0000.0000.000
79A97GLN00.0400.03025.129-0.225-0.2250.0000.0000.0000.000
80A98VAL0-0.0250.00021.009-0.034-0.0340.0000.0000.0000.000
81A99ILE0-0.060-0.02623.704-0.126-0.1260.0000.0000.0000.000
82A100SER00.0300.01426.7620.1100.1100.0000.0000.0000.000
83A101TRP00.0680.04027.1440.2000.2000.0000.0000.0000.000
84A102LEU0-0.0020.01724.0990.0720.0720.0000.0000.0000.000
85A103ALA00.001-0.01527.5940.1540.1540.0000.0000.0000.000
86A104LEU00.0160.01731.0570.2150.2150.0000.0000.0000.000
87A105THR00.029-0.00727.7690.1420.1420.0000.0000.0000.000
88A106TRP0-0.017-0.01430.1620.1740.1740.0000.0000.0000.000
89A107LEU0-0.026-0.00931.7450.2030.2030.0000.0000.0000.000
90A108PHE00.0180.01234.1110.2250.2250.0000.0000.0000.000
91A109GLY00.0240.01233.3020.1340.1340.0000.0000.0000.000
92A110ALA0-0.014-0.01634.2900.1470.1470.0000.0000.0000.000
93A111GLY00.0010.00036.8180.2080.2080.0000.0000.0000.000
94A112PHE0-0.009-0.00736.1370.1690.1690.0000.0000.0000.000
95A113ILE00.0250.00235.4870.1360.1360.0000.0000.0000.000
96A114GLY00.0110.00839.0290.1720.1720.0000.0000.0000.000
97A115MET0-0.050-0.02241.4640.2340.2340.0000.0000.0000.000
98A116GLU-1-0.874-0.93739.158-7.643-7.6430.0000.0000.0000.000
99A117ILE0-0.061-0.02241.1570.1210.1210.0000.0000.0000.000
100A118TYR0-0.054-0.02844.5690.1930.1930.0000.0000.0000.000
101A119GLU-1-0.791-0.88846.468-6.178-6.1780.0000.0000.0000.000
102A120PHE0-0.019-0.01543.5030.1250.1250.0000.0000.0000.000
103A121HIS0-0.005-0.00547.7310.1960.1960.0000.0000.0000.000
104A122HIS0-0.051-0.03150.6150.2720.2720.0000.0000.0000.000
105A123LEU0-0.030-0.02149.1720.1550.1550.0000.0000.0000.000
106A124ILE0-0.047-0.02249.7330.0380.0380.0000.0000.0000.000
107A125VAL0-0.061-0.02453.8400.0970.0970.0000.0000.0000.000
108A126ASN0-0.073-0.02856.2730.2080.2080.0000.0000.0000.000
109A127GLY00.0200.01356.6020.1020.1020.0000.0000.0000.000
110A128MET0-0.0050.00156.559-0.050-0.0500.0000.0000.0000.000
111A129GLY0-0.013-0.01756.1690.0790.0790.0000.0000.0000.000
112A130PRO0-0.074-0.04155.417-0.098-0.0980.0000.0000.0000.000
113A131ASP-1-0.869-0.90852.780-5.967-5.9670.0000.0000.0000.000
114A132ARG10.9380.93955.0155.3065.3060.0000.0000.0000.000
115A133SER00.0130.00855.093-0.068-0.0680.0000.0000.0000.000
116A134GLY00.0680.02251.644-0.077-0.0770.0000.0000.0000.000
117A135PHE00.0300.01150.180-0.134-0.1340.0000.0000.0000.000
118A136LEU0-0.0030.00350.335-0.080-0.0800.0000.0000.0000.000
119A137SER0-0.0150.00848.940-0.075-0.0750.0000.0000.0000.000
120A138ALA00.019-0.00745.784-0.154-0.1540.0000.0000.0000.000
121A139PHE00.0240.01144.470-0.191-0.1910.0000.0000.0000.000
122A140PHE0-0.0070.01144.269-0.162-0.1620.0000.0000.0000.000
123A141ALA00.0220.01542.730-0.107-0.1070.0000.0000.0000.000
124A142LEU0-0.037-0.01339.021-0.237-0.2370.0000.0000.0000.000
125A143VAL00.0430.03339.221-0.263-0.2630.0000.0000.0000.000
126A144GLY00.0610.03739.221-0.174-0.1740.0000.0000.0000.000
127A145THR0-0.090-0.06235.962-0.250-0.2500.0000.0000.0000.000
128A146HIS00.0270.01234.120-0.365-0.3650.0000.0000.0000.000
129A147GLY00.0890.04535.078-0.216-0.2160.0000.0000.0000.000
130A148LEU0-0.046-0.00434.985-0.043-0.0430.0000.0000.0000.000
131A149HIS0-0.020-0.02330.464-0.118-0.1180.0000.0000.0000.000
132A150VAL0-0.052-0.01630.511-0.422-0.4220.0000.0000.0000.000
133A151THR00.022-0.00132.5650.1420.1420.0000.0000.0000.000
134A152SER0-0.018-0.01929.109-0.198-0.1980.0000.0000.0000.000
135A153GLY00.0270.00526.962-0.373-0.3730.0000.0000.0000.000
136A154LEU0-0.0050.01927.452-0.382-0.3820.0000.0000.0000.000
137A155ILE00.0240.00429.372-0.123-0.1230.0000.0000.0000.000
138A156TRP0-0.027-0.02119.260-0.622-0.6220.0000.0000.0000.000
139A157MET00.0070.01524.777-0.396-0.3960.0000.0000.0000.000
140A158ALA00.0530.03225.567-0.286-0.2860.0000.0000.0000.000
141A159VAL0-0.007-0.01024.739-0.102-0.1020.0000.0000.0000.000
142A160LEU0-0.049-0.03920.151-0.583-0.5830.0000.0000.0000.000
143A161MET00.0180.03222.724-0.396-0.3960.0000.0000.0000.000
144A162VAL00.0280.01524.900-0.215-0.2150.0000.0000.0000.000
145A163GLN0-0.031-0.00220.187-0.599-0.5990.0000.0000.0000.000
146A164ILE0-0.005-0.02019.543-0.665-0.6650.0000.0000.0000.000
147A165ALA0-0.0110.00821.425-0.243-0.2430.0000.0000.0000.000
148A166ARG10.9480.95823.22911.50711.5070.0000.0000.0000.000
149A167ARG10.8690.95117.45014.22214.2220.0000.0000.0000.000
150A168GLY00.0270.02018.266-0.335-0.3350.0000.0000.0000.000
151A169LEU0-0.028-0.00614.530-0.685-0.6850.0000.0000.0000.000
152A170THR00.0190.00614.2850.5270.5270.0000.0000.0000.000
153A171SER00.0550.00414.250-0.975-0.9750.0000.0000.0000.000
154A172THR00.0160.0258.087-1.072-1.0720.0000.0000.0000.000
155A173ASN0-0.016-0.0239.559-2.895-2.8950.0000.0000.0000.000
156A174ARG10.8400.93510.86216.31116.3110.0000.0000.0000.000
157A175THR00.0450.02610.548-0.025-0.0250.0000.0000.0000.000
158A176ARG10.9140.93712.64516.83916.8390.0000.0000.0000.000
159A177ILE00.0160.00916.1200.5630.5630.0000.0000.0000.000
160A178MET00.0160.01314.5970.4240.4240.0000.0000.0000.000
161A179CYS0-0.029-0.00216.0860.4180.4180.0000.0000.0000.000
162A180LEU00.0300.01117.6480.5390.5390.0000.0000.0000.000
163A181SER0-0.005-0.01419.9580.6030.6030.0000.0000.0000.000
164A182LEU0-0.0340.00118.4770.1800.1800.0000.0000.0000.000
165A183PHE0-0.004-0.00821.6590.3390.3390.0000.0000.0000.000
166A184TRP00.0430.00523.5860.2220.2220.0000.0000.0000.000
167A185HIS0-0.0130.00624.4680.4290.4290.0000.0000.0000.000
168A186PHE0-0.018-0.01925.6000.2770.2770.0000.0000.0000.000
169A187LEU00.0190.01227.2500.3060.3060.0000.0000.0000.000
170A188ASP-1-0.819-0.92529.812-8.929-8.9290.0000.0000.0000.000
171A189VAL0-0.030-0.00928.8550.2720.2720.0000.0000.0000.000
172A190VAL0-0.0020.00431.2880.2540.2540.0000.0000.0000.000
173A191TRP00.0570.01933.6610.2620.2620.0000.0000.0000.000
174A192ILE0-0.024-0.01034.3290.2670.2670.0000.0000.0000.000
175A193CYS0-0.066-0.01935.3570.1580.1580.0000.0000.0000.000
176A194VAL00.0190.00537.5970.2240.2240.0000.0000.0000.000
177A195PHE00.0760.02939.9640.2250.2250.0000.0000.0000.000
178A196THR0-0.044-0.05539.9620.2570.2570.0000.0000.0000.000
179A197VAL0-0.032-0.01341.1610.0110.0110.0000.0000.0000.000
180A198VAL0-0.044-0.01142.5560.1360.1360.0000.0000.0000.000
181A199TYR0-0.023-0.00443.2140.0770.0770.0000.0000.0000.000
182A200LEU0-0.034-0.01544.9380.1490.1490.0000.0000.0000.000
183A201MET0-0.088-0.03646.3430.0990.0990.0000.0000.0000.000
184A202GLY0-0.046-0.01148.5810.0930.0930.0000.0000.0000.000
185A203ALA-1-0.923-0.95050.294-5.759-5.7590.0000.0000.0000.000