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: 55JYZ

Calculation Name: 1X8Q-A-Xray547

Preferred Name:

Target Type:

Ligand Name: protoporphyrin ix containing fe

Ligand 3-letter code: HEM

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 1X8Q

Chain ID: A

ChEMBL ID:

UniProt ID: Q94734

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
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 182
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922
Total energy (hartree)
FMO2-HF: Electronic energy -1980579.903809
FMO2-HF: Nuclear repulsion 1909396.490537
FMO2-HF: Total energy -71183.413272
FMO2-MP2: Total energy -71391.333348


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: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.
-240.211-242.21237.698-19.102-16.594-0.224
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 : 0.765 / q_NPA : 0.868
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].
3A3THR0-0.015-0.0193.5945.4276.7970.007-0.677-0.7000.001
32A32GLU-1-0.793-0.8621.837-137.338-141.66619.075-8.918-5.829-0.104
35A35ASP0-0.087-0.0713.3885.7265.914-0.001-0.070-0.1180.000
128A129ASP-1-0.810-0.8901.950-124.543-125.34714.199-7.085-6.310-0.089
129A130LEU0-0.037-0.0252.9286.6727.6100.130-0.335-0.732-0.002
130A131GLY00.0790.0482.404-23.029-22.6024.284-1.992-2.718-0.030
131A132ASP-1-0.799-0.8773.625-34.880-34.6720.004-0.025-0.1870.000
4A4LYS10.8420.9156.15736.83536.8350.0000.0000.0000.000
5A5ASN00.0170.0069.623-0.247-0.2470.0000.0000.0000.000
6A6ALA00.0250.01912.0781.4241.4240.0000.0000.0000.000
7A7ILE00.0200.01414.5690.4840.4840.0000.0000.0000.000
8A8ALA00.0440.02018.199-0.100-0.1000.0000.0000.0000.000
9A9GLN0-0.027-0.02020.4320.2950.2950.0000.0000.0000.000
10A10THR0-0.003-0.01223.7580.3360.3360.0000.0000.0000.000
11A11GLY00.0060.00026.6700.2420.2420.0000.0000.0000.000
12A12PHE0-0.0160.00624.0540.2130.2130.0000.0000.0000.000
13A13ASN00.0100.00026.8570.1660.1660.0000.0000.0000.000
14A14LYS10.9130.92726.69410.34910.3490.0000.0000.0000.000
15A15ASP-1-0.814-0.88727.647-10.211-10.2110.0000.0000.0000.000
16A16LYS10.8300.88830.4399.6349.6340.0000.0000.0000.000
17A17TYR00.0030.00121.573-0.085-0.0850.0000.0000.0000.000
18A18PHE0-0.017-0.02121.625-0.088-0.0880.0000.0000.0000.000
19A19ASN00.0340.01727.383-0.010-0.0100.0000.0000.0000.000
20A20GLY0-0.011-0.00829.3810.3590.3590.0000.0000.0000.000
21A21ASP-1-0.872-0.93829.835-10.048-10.0480.0000.0000.0000.000
22A22VAL0-0.022-0.02626.262-0.438-0.4380.0000.0000.0000.000
23A23TRP0-0.0460.00023.2500.1910.1910.0000.0000.0000.000
24A24TYR0-0.026-0.03923.373-0.417-0.4170.0000.0000.0000.000
25A25VAL00.0000.00017.657-0.082-0.0820.0000.0000.0000.000
26A26THR0-0.0160.00020.8370.2550.2550.0000.0000.0000.000
27A27ASP-1-0.847-0.90219.850-13.871-13.8710.0000.0000.0000.000
28A28TYR0-0.054-0.05013.4340.3150.3150.0000.0000.0000.000
29A29LEU00.0050.00612.2550.5750.5750.0000.0000.0000.000
30A30ASP-1-0.813-0.9116.727-42.903-42.9030.0000.0000.0000.000
31A31LEU0-0.055-0.0357.2572.4102.4100.0000.0000.0000.000
33A33PRO0-0.016-0.0126.0541.2881.2880.0000.0000.0000.000
34A34ASP-1-0.950-0.9678.804-24.677-24.6770.0000.0000.0000.000
36A36VAL0-0.036-0.0157.8772.2942.2940.0000.0000.0000.000
37A37PRO00.0220.01811.1720.8900.8900.0000.0000.0000.000
38A38LYS10.9430.98414.82520.49620.4960.0000.0000.0000.000
39A39ARG10.9080.94816.77214.29514.2950.0000.0000.0000.000
40A40TYR00.0330.00816.381-0.538-0.5380.0000.0000.0000.000
41A41CYS0-0.0220.02119.1240.6560.6560.0000.0000.0000.000
42A42ALA00.0230.00617.829-0.464-0.4640.0000.0000.0000.000
43A43ALA0-0.0050.00219.8850.4420.4420.0000.0000.0000.000
44A44LEU0-0.0050.00819.187-0.496-0.4960.0000.0000.0000.000
45A45ALA00.0210.01622.5640.5710.5710.0000.0000.0000.000
46A46ALA00.0480.03223.672-0.455-0.4550.0000.0000.0000.000
47A47GLY00.006-0.00625.2850.4730.4730.0000.0000.0000.000
48A48THR0-0.0040.01727.539-0.280-0.2800.0000.0000.0000.000
49A49ALA00.0070.00829.5320.3920.3920.0000.0000.0000.000
50A50SER00.009-0.00130.994-0.046-0.0460.0000.0000.0000.000
51A51GLY00.0240.01532.4810.0030.0030.0000.0000.0000.000
52A52LYS10.8580.93427.55610.00410.0040.0000.0000.0000.000
53A53LEU00.0180.02223.2690.2280.2280.0000.0000.0000.000
54A54LYS10.8330.90624.11511.21511.2150.0000.0000.0000.000
55A55GLU-1-0.777-0.88719.089-16.101-16.1010.0000.0000.0000.000
56A56ALA0-0.035-0.00622.828-0.013-0.0130.0000.0000.0000.000
57A57LEU00.006-0.00116.793-0.023-0.0230.0000.0000.0000.000
58A58TYR0-0.016-0.01920.8770.4360.4360.0000.0000.0000.000
59A59HIS10.8980.94814.33018.63618.6360.0000.0000.0000.000
60A60TYR00.0580.02219.6060.4950.4950.0000.0000.0000.000
61A61ASP-1-0.768-0.85918.770-16.376-16.3760.0000.0000.0000.000
62A62PRO0-0.039-0.01420.5750.6300.6300.0000.0000.0000.000
63A63LYS10.8550.92121.88212.84512.8450.0000.0000.0000.000
64A64THR0-0.010-0.03019.7830.5700.5700.0000.0000.0000.000
65A65GLN0-0.0170.00322.7130.5690.5690.0000.0000.0000.000
66A66ASP-1-0.892-0.92818.205-16.300-16.3000.0000.0000.0000.000
67A67THR0-0.020-0.02721.021-0.109-0.1090.0000.0000.0000.000
68A68PHE0-0.159-0.08815.4400.1640.1640.0000.0000.0000.000
69A69TYR00.0700.03521.290-0.093-0.0930.0000.0000.0000.000
70A70ASP-1-0.887-0.94917.954-17.603-17.6030.0000.0000.0000.000
71A71VAL0-0.031-0.01320.8280.3770.3770.0000.0000.0000.000
72A72SER00.0270.00718.297-0.415-0.4150.0000.0000.0000.000
73A73GLU-1-0.912-0.96120.976-11.259-11.2590.0000.0000.0000.000
74A74LEU0-0.074-0.03218.955-0.644-0.6440.0000.0000.0000.000
75A75GLN0-0.016-0.00919.7830.9950.9950.0000.0000.0000.000
76A76VAL0-0.018-0.02819.820-0.646-0.6460.0000.0000.0000.000
77A77GLU-1-0.817-0.85916.355-16.532-16.5320.0000.0000.0000.000
78A78SER0-0.049-0.04919.8400.1670.1670.0000.0000.0000.000
79A79LEU0-0.048-0.00822.016-0.120-0.1200.0000.0000.0000.000
80A80GLY00.0200.00521.801-0.163-0.1630.0000.0000.0000.000
81A81LYS10.8220.89714.36019.03419.0340.0000.0000.0000.000
82A82TYR00.0460.02017.0840.9440.9440.0000.0000.0000.000
83A83THR00.003-0.02513.869-2.056-2.0560.0000.0000.0000.000
84A84ALA0-0.0140.00415.2181.3811.3810.0000.0000.0000.000
85A85ASN00.008-0.00215.444-1.643-1.6430.0000.0000.0000.000
86A86PHE0-0.0280.00212.6360.9200.9200.0000.0000.0000.000
87A87LYS10.8530.91218.09412.10912.1090.0000.0000.0000.000
88A88LYS10.9470.99717.81916.89616.8960.0000.0000.0000.000
89A89VAL0-0.016-0.01221.1580.5440.5440.0000.0000.0000.000
90A90ASP-1-0.789-0.89224.551-10.889-10.8890.0000.0000.0000.000
91A91LYS10.9070.93427.3189.7849.7840.0000.0000.0000.000
92A92ASN0-0.009-0.00428.5770.1790.1790.0000.0000.0000.000
93A93GLY00.0180.00527.9100.2450.2450.0000.0000.0000.000
94A94ASN0-0.092-0.04628.6360.0650.0650.0000.0000.0000.000
95A95VAL00.004-0.01124.702-0.415-0.4150.0000.0000.0000.000
96A96LYS10.9030.96123.80313.03013.0300.0000.0000.0000.000
97A97VAL0-0.035-0.02218.944-0.147-0.1470.0000.0000.0000.000
98A98ALA00.0360.01621.955-0.044-0.0440.0000.0000.0000.000
99A99VAL00.0380.02019.529-0.607-0.6070.0000.0000.0000.000
100A100THR0-0.001-0.01117.1920.2600.2600.0000.0000.0000.000
101A101ALA00.0260.02416.516-0.742-0.7420.0000.0000.0000.000
102A102GLY00.0240.00612.183-0.011-0.0110.0000.0000.0000.000
103A103ASN0-0.059-0.02711.684-3.242-3.2420.0000.0000.0000.000
104A104TYR00.012-0.0019.4862.1322.1320.0000.0000.0000.000
105A105TYR0-0.036-0.03510.832-2.374-2.3740.0000.0000.0000.000
106A106THR00.0190.02210.4321.4871.4870.0000.0000.0000.000
107A107PHE00.0290.01012.430-1.118-1.1180.0000.0000.0000.000
108A108THR00.0140.01114.2531.0861.0860.0000.0000.0000.000
109A109VAL00.0030.01116.561-0.426-0.4260.0000.0000.0000.000
110A110MET0-0.0150.00716.5150.0640.0640.0000.0000.0000.000
111A111TYR0-0.078-0.06420.1210.7740.7740.0000.0000.0000.000
112A112ALA00.0360.01323.172-0.414-0.4140.0000.0000.0000.000
113A113ASP-1-0.762-0.82125.875-10.521-10.5210.0000.0000.0000.000
114A114ASP-1-0.820-0.89928.929-9.806-9.8060.0000.0000.0000.000
115A115SER0-0.014-0.01030.2750.1630.1630.0000.0000.0000.000
116A116SER0-0.064-0.03326.374-0.262-0.2620.0000.0000.0000.000
117A117ALA00.028-0.00322.7920.2090.2090.0000.0000.0000.000
118A118LEU0-0.0300.00117.535-0.149-0.1490.0000.0000.0000.000
119A119ILE0-0.028-0.00814.9740.3020.3020.0000.0000.0000.000
120A120HIS00.014-0.0189.0321.8941.8940.0000.0000.0000.000
121A121THR0-0.076-0.04610.9391.2421.2420.0000.0000.0000.000
122A123LEU0-0.017-0.0117.5793.4773.4770.0000.0000.0000.000
123A124HIS00.0210.0136.532-6.689-6.6890.0000.0000.0000.000
124A125LYS10.9800.9698.28425.69825.6980.0000.0000.0000.000
125A126GLY0-0.0070.00210.573-0.404-0.4040.0000.0000.0000.000
126A127ASN0-0.028-0.0209.939-1.465-1.4650.0000.0000.0000.000
127A128LYS10.9120.9627.77925.66325.6630.0000.0000.0000.000
132A133LEU00.0190.0157.0902.2582.2580.0000.0000.0000.000
133A134TYR00.029-0.0079.7471.4341.4340.0000.0000.0000.000
134A135ALA0-0.019-0.01613.2680.1860.1860.0000.0000.0000.000
135A136VAL0-0.0030.00516.4710.4870.4870.0000.0000.0000.000
136A137LEU0-0.016-0.00519.1300.0290.0290.0000.0000.0000.000
137A138ASN00.0410.00222.2960.7510.7510.0000.0000.0000.000
138A139ARG10.9030.96126.04111.04911.0490.0000.0000.0000.000
139A140ASN0-0.015-0.01028.9600.1550.1550.0000.0000.0000.000
140A141LYS10.8780.90826.99910.17610.1760.0000.0000.0000.000
141A142ASP-1-0.845-0.89227.198-10.715-10.7150.0000.0000.0000.000
142A143ALA0-0.067-0.02229.1630.2160.2160.0000.0000.0000.000
143A144ALA00.0150.00227.409-0.444-0.4440.0000.0000.0000.000
144A145ALA00.0210.02024.2050.2190.2190.0000.0000.0000.000
145A146GLY00.0360.01126.3020.2400.2400.0000.0000.0000.000
146A147ASP-1-0.861-0.94427.506-10.898-10.8980.0000.0000.0000.000
147A148LYS10.8360.92128.23710.09210.0920.0000.0000.0000.000
148A149VAL00.0340.02022.682-0.269-0.2690.0000.0000.0000.000
149A150LYS10.9250.96923.33711.14311.1430.0000.0000.0000.000
150A151SER0-0.006-0.01323.906-0.317-0.3170.0000.0000.0000.000
151A152ALA0-0.021-0.00422.733-0.228-0.2280.0000.0000.0000.000
152A153VAL0-0.031-0.01318.527-0.653-0.6530.0000.0000.0000.000
153A154SER00.0070.00919.835-0.460-0.4600.0000.0000.0000.000
154A155ALA00.007-0.00521.718-0.239-0.2390.0000.0000.0000.000
155A156ALA0-0.054-0.02217.157-0.175-0.1750.0000.0000.0000.000
156A157THR0-0.062-0.02817.089-0.921-0.9210.0000.0000.0000.000
157A158LEU0-0.035-0.00813.594-1.198-1.1980.0000.0000.0000.000
158A159GLU-1-0.869-0.93817.337-13.638-13.6380.0000.0000.0000.000
159A160PHE00.048-0.00318.427-0.486-0.4860.0000.0000.0000.000
160A161SER0-0.048-0.02820.517-0.336-0.3360.0000.0000.0000.000
161A162LYS10.9190.95815.74617.26317.2630.0000.0000.0000.000
162A163PHE0-0.0180.00016.505-1.112-1.1120.0000.0000.0000.000
163A164ILE0-0.020-0.00215.7211.0431.0430.0000.0000.0000.000
164A165SER00.003-0.01018.2940.0860.0860.0000.0000.0000.000
165A166THR0-0.074-0.07219.6350.1040.1040.0000.0000.0000.000
166A167LYS10.9740.98822.03812.15812.1580.0000.0000.0000.000
167A168GLU-1-0.912-0.95425.079-11.297-11.2970.0000.0000.0000.000
168A169ASN0-0.075-0.04221.3850.1960.1960.0000.0000.0000.000
169A170ASN0-0.003-0.00425.2830.0560.0560.0000.0000.0000.000
170A172ALA00.0330.02326.7530.3340.3340.0000.0000.0000.000
171A173TYR00.027-0.01123.231-0.592-0.5920.0000.0000.0000.000
172A174ASP-1-0.792-0.86628.225-9.682-9.6820.0000.0000.0000.000
173A175ASN00.0680.02629.155-0.614-0.6140.0000.0000.0000.000
174A176ASP-1-0.871-0.92230.573-9.340-9.3400.0000.0000.0000.000
175A177SER0-0.034-0.01829.5170.0880.0880.0000.0000.0000.000
176A178LEU0-0.036-0.02023.973-0.153-0.1530.0000.0000.0000.000
177A179LYS10.8920.94527.8489.6439.6430.0000.0000.0000.000
178A180SER0-0.040-0.02630.5370.0180.0180.0000.0000.0000.000
179A181LEU0-0.021-0.00225.6140.0490.0490.0000.0000.0000.000
180A182LEU0-0.0040.01825.895-0.161-0.1610.0000.0000.0000.000
181A183THR0-0.077-0.05628.1430.0400.0400.0000.0000.0000.000
182A184LYS00.0720.08827.439-1.350-1.3500.0000.0000.0000.000