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: 5GLKZ

Calculation Name: 2GTL-M-Xray549

Preferred Name:

Target Type:

Ligand Name: protoporphyrin ix containing fe | carbon monoxide | calcium ion | zinc ion

Ligand 3-letter code: HEM | CMO | CA | ZN

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 2GTL

Chain ID: M

ChEMBL ID:

UniProt ID: P02218

Base Structure: X-ray

Registration Date: 2025-10-12

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 212
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922
Total energy (hartree)
FMO2-HF: Electronic energy -2309755.925222
FMO2-HF: Nuclear repulsion 2221060.386284
FMO2-HF: Total energy -88695.538938
FMO2-MP2: Total energy -88950.418913


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(M:9:ARG)


Summations of interaction energy for fragment #1(M:9:ARG)
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.
-68.427-59.5872.776-5.468-6.149-0.064
Interaction energy analysis for fragmet #1(M:9:ARG)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 2 / q_Mulliken : 1.779 / q_NPA : 1.894
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].
3M11GLN00.0790.0243.8842.6435.029-0.020-1.111-1.254-0.003
4M12TYR0-0.027-0.0102.516-18.576-12.3462.797-4.295-4.733-0.061
5M13LEU00.0500.0364.2436.1616.385-0.001-0.062-0.1620.000
6M14VAL00.0790.0317.4474.6524.6520.0000.0000.0000.000
7M15LYS10.9410.9677.40661.76261.7620.0000.0000.0000.000
8M16ASN0-0.0120.0038.5955.7025.7020.0000.0000.0000.000
9M17GLN00.0570.03111.1882.6042.6040.0000.0000.0000.000
10M18ASN00.009-0.01712.8312.3242.3240.0000.0000.0000.000
11M19LEU00.0370.02313.9231.6171.6170.0000.0000.0000.000
12M20HIS0-0.049-0.01615.4531.8851.8850.0000.0000.0000.000
13M21ILE00.0090.00217.3041.5891.5890.0000.0000.0000.000
14M22ASP-1-0.920-0.95318.549-26.918-26.9180.0000.0000.0000.000
15M23TYR00.0130.00219.7631.6181.6180.0000.0000.0000.000
16M24LEU0-0.034-0.02521.5011.1711.1710.0000.0000.0000.000
17M25ALA00.0150.01523.0951.0501.0500.0000.0000.0000.000
18M26LYS10.9430.98224.37922.44122.4410.0000.0000.0000.000
19M27LYS10.8960.94525.73323.01823.0180.0000.0000.0000.000
20M28LEU0-0.0060.00827.5270.5850.5850.0000.0000.0000.000
21M29HIS00.0210.01528.9510.2480.2480.0000.0000.0000.000
22M30ASP-1-0.900-0.97329.381-19.736-19.7360.0000.0000.0000.000
23M31ILE0-0.052-0.02131.4150.5750.5750.0000.0000.0000.000
24M32GLU-1-0.953-0.97433.334-17.567-17.5670.0000.0000.0000.000
25M33GLU-1-0.861-0.94434.787-16.440-16.4400.0000.0000.0000.000
26M34GLU-1-1.064-1.04836.473-15.718-15.7180.0000.0000.0000.000
27M35TYR0-0.0070.00337.9790.3930.3930.0000.0000.0000.000
28M36ASN00.008-0.00337.9400.6060.6060.0000.0000.0000.000
29M37LYS10.8310.93437.38216.40716.4070.0000.0000.0000.000
30M38LEU0-0.0200.00442.7940.3090.3090.0000.0000.0000.000
31M39THR0-0.059-0.02844.9050.0850.0850.0000.0000.0000.000
32M40HIS00.0360.00845.3500.1340.1340.0000.0000.0000.000
33M41ASP-1-0.928-0.95147.636-12.882-12.8820.0000.0000.0000.000
34M42VAL0-0.035-0.01950.3390.1010.1010.0000.0000.0000.000
35M43ASP-1-0.790-0.90454.065-11.207-11.2070.0000.0000.0000.000
36M44LYS10.9560.97255.47911.05611.0560.0000.0000.0000.000
37M45LYS10.8650.91657.67110.20510.2050.0000.0000.0000.000
38M46THR00.0120.01357.9500.2200.2200.0000.0000.0000.000
39M47ILE0-0.022-0.01457.1420.1650.1650.0000.0000.0000.000
40M48ARG10.7760.88260.48310.05310.0530.0000.0000.0000.000
41M49GLN00.0630.04563.4170.1910.1910.0000.0000.0000.000
42M50LEU0-0.050-0.02862.0190.1500.1500.0000.0000.0000.000
43M51LYS10.9510.96861.22410.42410.4240.0000.0000.0000.000
44M52ALA00.0300.03465.9040.1160.1160.0000.0000.0000.000
45M53ARG10.9310.95865.8069.5869.5860.0000.0000.0000.000
46M54ILE0-0.047-0.01865.3100.0770.0770.0000.0000.0000.000
47M55SER00.011-0.00569.5720.1390.1390.0000.0000.0000.000
48M56ASN0-0.050-0.03571.5890.1320.1320.0000.0000.0000.000
49M57LEU0-0.084-0.03971.9290.1190.1190.0000.0000.0000.000
50M58GLU-1-0.942-0.95270.701-9.013-9.0130.0000.0000.0000.000
51M59GLU-1-0.941-0.96475.142-7.828-7.8280.0000.0000.0000.000
52M60HIS10.8130.87674.2708.3908.3900.0000.0000.0000.000
53M61HIS0-0.003-0.00779.3730.1160.1160.0000.0000.0000.000
54M62CYS0-0.0660.00578.496-0.026-0.0260.0000.0000.0000.000
55M63ASP-1-0.842-0.90983.226-7.357-7.3570.0000.0000.0000.000
56M64GLU-1-0.925-0.97285.762-7.196-7.1960.0000.0000.0000.000
57M65HIS0-0.107-0.07386.9650.0380.0380.0000.0000.0000.000
58M66GLU-1-0.905-0.92983.939-7.580-7.5800.0000.0000.0000.000
59M67SER0-0.093-0.07179.277-0.042-0.0420.0000.0000.0000.000
60M68GLU-1-0.852-0.92674.812-8.521-8.5210.0000.0000.0000.000
61M69CYS0-0.146-0.06075.442-0.004-0.0040.0000.0000.0000.000
62M70ARG10.8450.92070.7968.5558.5550.0000.0000.0000.000
63M71GLY0-0.0180.00169.633-0.174-0.1740.0000.0000.0000.000
64M72ASP-1-1.012-1.00967.513-9.457-9.4570.0000.0000.0000.000
65M73VAL0-0.022-0.01169.7520.0530.0530.0000.0000.0000.000
66M74PRO00.0360.03573.3040.0410.0410.0000.0000.0000.000
67M75GLU-1-0.805-0.88975.582-8.044-8.0440.0000.0000.0000.000
68M77ILE00.0750.02880.3230.0580.0580.0000.0000.0000.000
69M78HIS00.0930.04282.904-0.053-0.0530.0000.0000.0000.000
70M79ASP-1-0.734-0.87883.014-7.822-7.8220.0000.0000.0000.000
71M80LEU0-0.153-0.09183.969-0.035-0.0350.0000.0000.0000.000
72M81LEU0-0.0260.01483.6600.0500.0500.0000.0000.0000.000
73M82PHE00.0130.02776.924-0.093-0.0930.0000.0000.0000.000
74M83CYS0-0.109-0.03272.5750.1410.1410.0000.0000.0000.000
75M84ASP-1-0.877-0.95179.097-7.733-7.7330.0000.0000.0000.000
76M85GLY0-0.054-0.03580.1890.0820.0820.0000.0000.0000.000
77M86GLU-1-1.014-1.00580.704-7.633-7.6330.0000.0000.0000.000
78M87LYS10.8100.90573.1408.6688.6680.0000.0000.0000.000
79M88ASP-1-0.813-0.91079.509-7.678-7.6780.0000.0000.0000.000
80M90ARG10.7910.86276.2918.0588.0580.0000.0000.0000.000
81M91ASP-1-0.849-0.91172.072-8.865-8.8650.0000.0000.0000.000
82M92GLY0-0.029-0.01773.459-0.094-0.0940.0000.0000.0000.000
83M93SER0-0.084-0.05672.116-0.035-0.0350.0000.0000.0000.000
84M94ASP-1-0.714-0.87573.386-8.370-8.3700.0000.0000.0000.000
85M95GLU-1-0.800-0.90575.402-8.220-8.2200.0000.0000.0000.000
86M96ASP-1-0.880-0.94469.275-9.311-9.3110.0000.0000.0000.000
87M97PRO0-0.056-0.04667.6120.0520.0520.0000.0000.0000.000
88M98GLU-1-0.880-0.92364.998-9.905-9.9050.0000.0000.0000.000
89M99THR0-0.0170.00168.8710.0560.0560.0000.0000.0000.000
90M101SER0-0.033-0.02070.0740.0660.0660.0000.0000.0000.000
91M102LEU0-0.001-0.01571.9290.1050.1050.0000.0000.0000.000
92M103ASN0-0.054-0.03467.4170.0780.0780.0000.0000.0000.000
93M104ILE00.0080.03971.3850.0010.0010.0000.0000.0000.000
94M105THR00.0100.00274.0140.0900.0900.0000.0000.0000.000
95M106HIS0-0.029-0.00170.9900.1910.1910.0000.0000.0000.000
96M107VAL00.006-0.01475.0910.0490.0490.0000.0000.0000.000
97M108GLY0-0.009-0.00575.048-0.105-0.1050.0000.0000.0000.000
98M109SER0-0.065-0.01973.296-0.119-0.1190.0000.0000.0000.000
99M110SER0-0.005-0.00573.2360.2190.2190.0000.0000.0000.000
100M111TYR00.0300.00572.319-0.187-0.1870.0000.0000.0000.000
101M112THR0-0.036-0.03072.8070.1280.1280.0000.0000.0000.000
102M113GLY00.0600.02573.480-0.147-0.1470.0000.0000.0000.000
103M114LEU0-0.049-0.00875.1640.0720.0720.0000.0000.0000.000
104M115ALA0-0.034-0.01477.029-0.006-0.0060.0000.0000.0000.000
105M116THR0-0.006-0.00579.7340.0310.0310.0000.0000.0000.000
106M117TRP0-0.050-0.04682.4020.0720.0720.0000.0000.0000.000
107M118THR0-0.045-0.04086.172-0.012-0.0120.0000.0000.0000.000
108M119SER0-0.075-0.04588.1940.0770.0770.0000.0000.0000.000
109M120CYS0-0.105-0.03888.6010.1320.1320.0000.0000.0000.000
110M121GLU-1-0.783-0.86589.700-6.938-6.9380.0000.0000.0000.000
111M122ASP-1-0.959-0.97490.346-6.892-6.8920.0000.0000.0000.000
112M123LEU0-0.076-0.01186.120-0.023-0.0230.0000.0000.0000.000
113M124ASN00.003-0.00584.018-0.022-0.0220.0000.0000.0000.000
114M125PRO0-0.053-0.04279.828-0.004-0.0040.0000.0000.0000.000
115M126ASP-1-0.673-0.81880.524-7.787-7.7870.0000.0000.0000.000
116M127HIS0-0.010-0.01574.894-0.174-0.1740.0000.0000.0000.000
117M128ALA00.0180.02478.7230.0920.0920.0000.0000.0000.000
118M129ILE0-0.010-0.00376.566-0.147-0.1470.0000.0000.0000.000
119M130VAL0-0.019-0.01078.1820.1400.1400.0000.0000.0000.000
120M131THR0-0.011-0.00377.012-0.099-0.0990.0000.0000.0000.000
121M132ILE00.0110.00377.7800.1600.1600.0000.0000.0000.000
122M133THR0-0.004-0.01479.138-0.059-0.0590.0000.0000.0000.000
123M134ALA0-0.028-0.02281.778-0.001-0.0010.0000.0000.0000.000
124M135ALA00.0390.02279.7950.0520.0520.0000.0000.0000.000
125M136HIS0-0.077-0.02981.4780.0600.0600.0000.0000.0000.000
126M137ARG10.9010.94277.1278.2298.2290.0000.0000.0000.000
127M138LYS10.8870.94683.1737.2317.2310.0000.0000.0000.000
128M139SER00.0080.00184.3210.0010.0010.0000.0000.0000.000
129M140PHE00.0130.00185.275-0.036-0.0360.0000.0000.0000.000
130M141PHE0-0.016-0.01286.7990.0650.0650.0000.0000.0000.000
131M142PRO0-0.0140.00681.648-0.006-0.0060.0000.0000.0000.000
132M143ASN00.0990.06981.9370.0060.0060.0000.0000.0000.000
133M144ARG10.8530.93482.8627.5407.5400.0000.0000.0000.000
134M145VAL00.0070.00279.0050.0310.0310.0000.0000.0000.000
135M146TRP0-0.001-0.00482.4450.0380.0380.0000.0000.0000.000
136M147LEU0-0.017-0.01580.702-0.036-0.0360.0000.0000.0000.000
137M148ARG10.8970.93684.0727.3407.3400.0000.0000.0000.000
138M149ALA00.0580.04182.323-0.112-0.1120.0000.0000.0000.000
139M150THR0-0.064-0.02282.1100.1220.1220.0000.0000.0000.000
140M151LEU00.0480.03082.325-0.104-0.1040.0000.0000.0000.000
141M152SER0-0.014-0.01381.7220.1390.1390.0000.0000.0000.000
142M153TYR0-0.0070.00682.051-0.080-0.0800.0000.0000.0000.000
143M154GLU-1-0.834-0.89879.923-7.911-7.9110.0000.0000.0000.000
144M155LEU0-0.051-0.02783.6270.0450.0450.0000.0000.0000.000
145M156ASP-1-0.842-0.92886.101-7.317-7.3170.0000.0000.0000.000
146M157GLU-1-0.929-0.96479.731-8.070-8.0700.0000.0000.0000.000
147M158HIS0-0.095-0.04181.503-0.155-0.1550.0000.0000.0000.000
148M159ASP-1-0.922-0.97083.098-7.375-7.3750.0000.0000.0000.000
149M160HIS10.7800.88479.7397.8857.8850.0000.0000.0000.000
150M161THR0-0.020-0.00883.566-0.003-0.0030.0000.0000.0000.000
151M162VAL0-0.003-0.00482.525-0.045-0.0450.0000.0000.0000.000
152M163SER0-0.0180.00985.6060.0930.0930.0000.0000.0000.000
153M164THR00.012-0.01884.633-0.100-0.1000.0000.0000.0000.000
154M165THR0-0.037-0.00686.8710.1270.1270.0000.0000.0000.000
155M166GLN0-0.023-0.02087.022-0.111-0.1110.0000.0000.0000.000
156M167LEU00.0130.00584.9110.1070.1070.0000.0000.0000.000
157M168ARG10.8290.89787.3626.8896.8890.0000.0000.0000.000
158M169GLY00.0250.01486.8040.0400.0400.0000.0000.0000.000
159M170PHE0-0.003-0.00684.3250.0240.0240.0000.0000.0000.000
160M171TYR00.0310.02175.044-0.002-0.0020.0000.0000.0000.000
161M172ASN0-0.063-0.03381.1720.0130.0130.0000.0000.0000.000
162M173PHE00.0280.00576.201-0.062-0.0620.0000.0000.0000.000
163M174GLY00.0440.04377.411-0.110-0.1100.0000.0000.0000.000
164M175LYS10.8670.92478.3387.6627.6620.0000.0000.0000.000
165M176ARG10.8180.91070.6928.8738.8730.0000.0000.0000.000
166M177GLU-1-0.909-0.94477.198-7.762-7.7620.0000.0000.0000.000
167M178LEU0-0.046-0.02578.4870.0420.0420.0000.0000.0000.000
168M179LEU00.0230.01780.8840.0350.0350.0000.0000.0000.000
169M180LEU0-0.041-0.02082.1580.0480.0480.0000.0000.0000.000
170M181ALA00.0680.02586.3250.0390.0390.0000.0000.0000.000
171M182PRO00.0690.03189.788-0.028-0.0280.0000.0000.0000.000
172M183LEU0-0.104-0.05990.6090.0650.0650.0000.0000.0000.000
173M184LYS10.8400.91692.8606.5576.5570.0000.0000.0000.000
174M185GLY0-0.0090.00496.5060.0170.0170.0000.0000.0000.000
175M186GLN0-0.026-0.02291.724-0.047-0.0470.0000.0000.0000.000
176M187SER00.009-0.00395.186-0.035-0.0350.0000.0000.0000.000
177M188GLU-1-0.863-0.92696.218-6.576-6.5760.0000.0000.0000.000
178M189GLY00.0750.06092.4490.0120.0120.0000.0000.0000.000
179M190TYR0-0.037-0.05288.7800.0520.0520.0000.0000.0000.000
180M191GLY0-0.038-0.02788.459-0.004-0.0040.0000.0000.0000.000
181M192VAL0-0.037-0.02682.125-0.023-0.0230.0000.0000.0000.000
182M193ILE00.0120.02082.6080.0230.0230.0000.0000.0000.000
183M194CYS0-0.057-0.01376.7140.0360.0360.0000.0000.0000.000
184M195ASP-1-0.785-0.87777.493-8.060-8.0600.0000.0000.0000.000
185M196PHE00.002-0.00572.489-0.092-0.0920.0000.0000.0000.000
186M197ASN00.0300.00973.052-0.201-0.2010.0000.0000.0000.000
187M198LEU00.0370.01669.331-0.083-0.0830.0000.0000.0000.000
188M199GLY00.0430.01767.622-0.157-0.1570.0000.0000.0000.000
189M200ASP-1-0.891-0.94565.687-9.787-9.7870.0000.0000.0000.000
190M201ASP-1-0.733-0.84267.688-9.072-9.0720.0000.0000.0000.000
191M202ASP-1-0.885-0.93865.575-9.595-9.5950.0000.0000.0000.000
192M203HIS0-0.045-0.04465.108-0.048-0.0480.0000.0000.0000.000
193M204ALA0-0.003-0.00470.5210.0290.0290.0000.0000.0000.000
194M205ASP-1-0.817-0.88374.182-8.232-8.2320.0000.0000.0000.000
195M207LYS10.8560.90679.4437.9717.9710.0000.0000.0000.000
196M208ILE00.0000.01983.0000.0310.0310.0000.0000.0000.000
197M209VAL00.0010.00185.5710.0480.0480.0000.0000.0000.000
198M210VAL00.0740.03088.9280.0380.0380.0000.0000.0000.000
199M211PRO0-0.038-0.02992.0730.0050.0050.0000.0000.0000.000
200M212SER0-0.088-0.04493.0190.0190.0190.0000.0000.0000.000
201M213SER00.005-0.01094.8860.0190.0190.0000.0000.0000.000
202M214LEU00.0150.01689.006-0.024-0.0240.0000.0000.0000.000
203M215PHE0-0.0020.01589.729-0.077-0.0770.0000.0000.0000.000
204M216VAL00.0260.00686.029-0.007-0.0070.0000.0000.0000.000
205M218ALA00.0570.01784.2900.0140.0140.0000.0000.0000.000
206M219HIS0-0.083-0.04577.2930.0230.0230.0000.0000.0000.000
207M220PHE00.0700.01477.0600.0080.0080.0000.0000.0000.000
208M221ASN0-0.050-0.01072.377-0.111-0.1110.0000.0000.0000.000
209M222ALA0-0.002-0.00173.971-0.026-0.0260.0000.0000.0000.000
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212M225TYR-1-0.957-0.96466.337-9.153-9.1530.0000.0000.0000.000