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: 1VJJZ

Calculation Name: 2GTL-N-Xray547

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: N

ChEMBL ID:

UniProt ID: P02218

Base Structure: X-ray

Registration Date: 2025-10-06

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 215
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922
Total energy (hartree)
FMO2-HF: Electronic energy -2390722.078581
FMO2-HF: Nuclear repulsion 2301623.834562
FMO2-HF: Total energy -89098.244019
FMO2-MP2: Total energy -89354.149689


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(N:10:LEU)


Summations of interaction energy for fragment #1(N:10:LEU)
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.
39.15143.5356.951-2.944-8.392-0.01
Interaction energy analysis for fragmet #1(N:10:LEU)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 1 / q_Mulliken : 0.824 / q_NPA : 0.898
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].
3N12PRO00.0350.0332.2556.5149.3331.525-1.357-2.988-0.006
4N13ARG10.9750.9782.19243.03343.5545.159-1.408-4.272-0.001
5N14LEU0-0.013-0.0072.6484.2585.3020.267-0.179-1.132-0.003
6N15GLY00.0470.0215.5245.2215.2210.0000.0000.0000.000
7N16ALA00.0070.0006.8403.6423.6420.0000.0000.0000.000
8N17ASN0-0.052-0.0267.6353.2583.2580.0000.0000.0000.000
9N18ALA00.0790.0449.2962.2402.2400.0000.0000.0000.000
10N19PHE00.0080.00011.5311.6701.6700.0000.0000.0000.000
11N20LEU0-0.057-0.02011.8181.5421.5420.0000.0000.0000.000
12N21ILE00.0490.01612.8751.2761.2760.0000.0000.0000.000
13N22ILE00.0350.01715.6931.0131.0130.0000.0000.0000.000
14N23ARG10.8970.94815.61617.10417.1040.0000.0000.0000.000
15N24LEU0-0.005-0.01317.2970.7050.7050.0000.0000.0000.000
16N25ASP-1-0.883-0.92120.204-13.333-13.3330.0000.0000.0000.000
17N26ARG10.8710.91822.13511.78011.7800.0000.0000.0000.000
18N27ILE0-0.084-0.04222.8790.6070.6070.0000.0000.0000.000
19N28ILE00.0320.01124.4370.5370.5370.0000.0000.0000.000
20N29GLU-1-0.788-0.87126.263-10.651-10.6510.0000.0000.0000.000
21N30LYS10.9350.96627.27311.20911.2090.0000.0000.0000.000
22N31LEU0-0.056-0.02627.7380.3300.3300.0000.0000.0000.000
23N32ARG10.9210.94530.2769.4319.4310.0000.0000.0000.000
24N33THR00.0200.01132.2960.2810.2810.0000.0000.0000.000
25N34LYS10.9110.93931.6339.5319.5310.0000.0000.0000.000
26N35LEU0-0.0210.00634.4570.1350.1350.0000.0000.0000.000
27N36ASP-1-0.790-0.88736.158-8.355-8.3550.0000.0000.0000.000
28N37GLU-1-0.932-0.95638.048-7.433-7.4330.0000.0000.0000.000
29N38ALA0-0.053-0.03438.2480.1910.1910.0000.0000.0000.000
30N39GLU-1-0.899-0.94240.158-7.485-7.4850.0000.0000.0000.000
31N40LYS10.8170.90342.0477.5997.5990.0000.0000.0000.000
32N41ILE0-0.116-0.05542.4740.1840.1840.0000.0000.0000.000
33N42ASP-1-0.769-0.87044.876-6.713-6.7130.0000.0000.0000.000
34N43PRO0-0.050-0.03645.0950.1550.1550.0000.0000.0000.000
35N44GLU-1-0.947-0.97448.059-6.248-6.2480.0000.0000.0000.000
36N45HIS0-0.014-0.02249.7640.1030.1030.0000.0000.0000.000
37N46PHE0-0.002-0.00550.6460.1650.1650.0000.0000.0000.000
38N47VAL0-0.038-0.03252.1050.1440.1440.0000.0000.0000.000
39N48SER00.0490.02854.0280.1710.1710.0000.0000.0000.000
40N49GLU-1-0.772-0.86555.501-5.431-5.4310.0000.0000.0000.000
41N50ILE0-0.090-0.04955.8060.1370.1370.0000.0000.0000.000
42N51ASP-1-0.894-0.93358.153-5.120-5.1200.0000.0000.0000.000
43N52ALA00.0390.01960.0530.1210.1210.0000.0000.0000.000
44N53ARG10.7570.86258.6475.3905.3900.0000.0000.0000.000
45N54VAL0-0.001-0.00261.8230.0900.0900.0000.0000.0000.000
46N55THR00.0610.03163.6300.1140.1140.0000.0000.0000.000
47N56LYS10.7560.87365.7694.7874.7870.0000.0000.0000.000
48N57ILE0-0.099-0.04965.6140.0790.0790.0000.0000.0000.000
49N58GLU-1-0.970-0.98966.680-4.687-4.6870.0000.0000.0000.000
50N59GLY0-0.0190.00569.9270.0800.0800.0000.0000.0000.000
51N60THR0-0.005-0.00569.721-0.027-0.0270.0000.0000.0000.000
52N61HIS0-0.0080.00170.7190.1070.1070.0000.0000.0000.000
53N62CYS0-0.074-0.02372.977-0.004-0.0040.0000.0000.0000.000
54N63GLU-1-0.902-0.94176.005-3.924-3.9240.0000.0000.0000.000
55N64LYS10.9400.94777.5453.9483.9480.0000.0000.0000.000
56N65ARG10.8000.87076.7864.1744.1740.0000.0000.0000.000
57N66THR0-0.0160.00576.0580.0230.0230.0000.0000.0000.000
58N67PHE0-0.0090.00266.656-0.020-0.0200.0000.0000.0000.000
59N68GLN00.0680.01769.2740.0630.0630.0000.0000.0000.000
60N69CYS0-0.113-0.03168.392-0.008-0.0080.0000.0000.0000.000
61N70GLY00.0800.03065.175-0.005-0.0050.0000.0000.0000.000
62N71GLY00.012-0.00864.9300.0490.0490.0000.0000.0000.000
63N72ASN0-0.046-0.01764.7280.0410.0410.0000.0000.0000.000
64N73GLU-1-0.967-0.99966.673-4.617-4.6170.0000.0000.0000.000
65N74GLN0-0.058-0.01168.4920.0580.0580.0000.0000.0000.000
66N75GLU-1-0.778-0.87471.299-4.234-4.2340.0000.0000.0000.000
67N77ILE00.0700.04173.6470.0660.0660.0000.0000.0000.000
68N78SER00.0240.01775.262-0.025-0.0250.0000.0000.0000.000
69N79ASP-1-0.757-0.87274.256-4.248-4.2480.0000.0000.0000.000
70N80LEU0-0.056-0.03875.318-0.028-0.0280.0000.0000.0000.000
71N81LEU0-0.011-0.00475.4470.0100.0100.0000.0000.0000.000
72N82VAL0-0.106-0.04570.316-0.053-0.0530.0000.0000.0000.000
73N83CYS0-0.0040.01963.1690.0030.0030.0000.0000.0000.000
74N84ASP-1-0.860-0.92470.048-4.333-4.3330.0000.0000.0000.000
75N85GLY0-0.058-0.03269.8450.0350.0350.0000.0000.0000.000
76N86HIS10.7110.84970.9324.3174.3170.0000.0000.0000.000
77N87LYS10.9840.99566.0624.7794.7790.0000.0000.0000.000
78N88ASP-1-0.840-0.92771.429-4.192-4.1920.0000.0000.0000.000
79N90HIS10.7780.85870.9474.2614.2610.0000.0000.0000.000
80N91ASN00.0490.02865.798-0.009-0.0090.0000.0000.0000.000
81N92ALA0-0.061-0.03165.939-0.082-0.0820.0000.0000.0000.000
82N93HIS00.0290.02263.722-0.095-0.0950.0000.0000.0000.000
83N94ASP-1-0.796-0.90766.258-4.597-4.5970.0000.0000.0000.000
84N95GLU-1-0.855-0.95366.843-4.596-4.5960.0000.0000.0000.000
85N96ASP-1-0.859-0.92560.913-5.320-5.3200.0000.0000.0000.000
86N97PRO0-0.043-0.03258.7840.0350.0350.0000.0000.0000.000
87N98ASP-1-0.873-0.93456.510-5.643-5.6430.0000.0000.0000.000
88N99VAL0-0.060-0.02059.5810.0350.0350.0000.0000.0000.000
89N101ASP-1-0.733-0.82957.937-5.505-5.5050.0000.0000.0000.000
90N102THR0-0.114-0.07561.3750.0990.0990.0000.0000.0000.000
91N103SER0-0.098-0.07757.6220.0450.0450.0000.0000.0000.000
92N104VAL00.0430.03659.748-0.017-0.0170.0000.0000.0000.000
93N105VAL0-0.009-0.01961.3540.0370.0370.0000.0000.0000.000
94N106LYS10.9490.98757.5745.5725.5720.0000.0000.0000.000
95N107ALA0-0.055-0.03662.488-0.005-0.0050.0000.0000.0000.000
96N108GLY0-0.022-0.01860.627-0.076-0.0760.0000.0000.0000.000
97N109ASN0-0.0160.01059.295-0.117-0.1170.0000.0000.0000.000
98N110VAL00.0200.00759.3100.1390.1390.0000.0000.0000.000
99N111PHE00.0010.00459.338-0.073-0.0730.0000.0000.0000.000
100N112SER0-0.027-0.02959.5380.0950.0950.0000.0000.0000.000
101N113GLY00.0570.02460.917-0.070-0.0700.0000.0000.0000.000
102N114THR0-0.005-0.00762.7350.0350.0350.0000.0000.0000.000
103N115SER0-0.015-0.01165.0320.0240.0240.0000.0000.0000.000
104N116THR0-0.0020.00267.3850.0160.0160.0000.0000.0000.000
105N117TRP0-0.039-0.03970.1320.0780.0780.0000.0000.0000.000
106N118HIS00.0090.01373.9640.0240.0240.0000.0000.0000.000
107N119GLY0-0.0330.00276.4340.0540.0540.0000.0000.0000.000
108N120CYS0-0.103-0.07177.0080.0980.0980.0000.0000.0000.000
109N121LEU0-0.004-0.00177.2920.0280.0280.0000.0000.0000.000
110N122ALA0-0.0110.00778.103-0.033-0.0330.0000.0000.0000.000
111N123ARG10.8180.91573.1944.3524.3520.0000.0000.0000.000
112N124GLU-1-0.852-0.91971.267-4.424-4.4240.0000.0000.0000.000
113N125ASP-1-0.893-0.96467.625-4.659-4.6590.0000.0000.0000.000
114N126HIS0-0.0240.00167.5100.0310.0310.0000.0000.0000.000
115N127VAL00.0300.02462.597-0.001-0.0010.0000.0000.0000.000
116N128THR0-0.082-0.05265.6790.1020.1020.0000.0000.0000.000
117N129ARG10.8350.89060.9575.1685.1680.0000.0000.0000.000
118N130ILE0-0.024-0.00664.6080.1020.1020.0000.0000.0000.000
119N131THR00.0500.03463.725-0.087-0.0870.0000.0000.0000.000
120N132ILE0-0.0050.00164.2530.1250.1250.0000.0000.0000.000
121N133THR00.0220.01265.043-0.036-0.0360.0000.0000.0000.000
122N134ALA0-0.009-0.02567.063-0.020-0.0200.0000.0000.0000.000
123N135SER00.0370.02566.1400.0280.0280.0000.0000.0000.000
124N136LYS10.8980.94468.3174.4064.4060.0000.0000.0000.000
125N137ARG10.9590.97966.1154.7954.7950.0000.0000.0000.000
126N138ARG10.9030.96171.0404.2064.2060.0000.0000.0000.000
127N139LYS11.0120.98969.4964.6204.6200.0000.0000.0000.000
128N140PHE00.0120.00973.515-0.015-0.0150.0000.0000.0000.000
129N141PHE0-0.003-0.00575.3610.0440.0440.0000.0000.0000.000
130N142THR0-0.014-0.00670.2150.0040.0040.0000.0000.0000.000
131N143ALA00.0910.06970.870-0.075-0.0750.0000.0000.0000.000
132N144ARG10.7770.87672.0824.3274.3270.0000.0000.0000.000
133N145ILE00.0010.02267.063-0.004-0.0040.0000.0000.0000.000
134N146TRP0-0.001-0.01570.5150.0450.0450.0000.0000.0000.000
135N147LEU0-0.060-0.02267.743-0.032-0.0320.0000.0000.0000.000
136N148ARG10.9120.95270.6844.3814.3810.0000.0000.0000.000
137N149ALA00.0120.01368.779-0.077-0.0770.0000.0000.0000.000
138N150LEU00.0040.03167.9000.0950.0950.0000.0000.0000.000
139N151VAL0-0.011-0.00268.340-0.078-0.0780.0000.0000.0000.000
140N152GLU-1-0.858-0.94765.752-4.843-4.8430.0000.0000.0000.000
141N153SER0-0.046-0.04368.466-0.004-0.0040.0000.0000.0000.000
142N154GLU-1-0.809-0.85463.734-5.056-5.0560.0000.0000.0000.000
143N155LEU0-0.032-0.02967.855-0.011-0.0110.0000.0000.0000.000
144N156GLU-1-0.886-0.92969.694-4.597-4.5970.0000.0000.0000.000
145N157ARG10.8940.93771.6874.2834.2830.0000.0000.0000.000
146N158HIS00.000-0.00975.210-0.041-0.0410.0000.0000.0000.000
147N159GLY0-0.0230.00075.5810.0180.0180.0000.0000.0000.000
148N160GLU-1-0.884-0.94069.813-4.681-4.6810.0000.0000.0000.000
149N161ASN0-0.014-0.01266.6690.0260.0260.0000.0000.0000.000
150N162VAL0-0.036-0.01569.9210.0370.0370.0000.0000.0000.000
151N163THR00.0220.01069.203-0.074-0.0740.0000.0000.0000.000
152N164SER0-0.086-0.03971.1800.0820.0820.0000.0000.0000.000
153N165SER00.018-0.00371.196-0.020-0.0200.0000.0000.0000.000
154N166PHE0-0.027-0.00773.1050.0690.0690.0000.0000.0000.000
155N167ASN00.0010.00373.245-0.126-0.1260.0000.0000.0000.000
156N168ALA00.0200.01572.6070.0680.0680.0000.0000.0000.000
157N169LYS10.7850.88173.9843.9653.9650.0000.0000.0000.000
158N170GLY00.0320.01774.7700.0370.0370.0000.0000.0000.000
159N171TYR0-0.065-0.04272.845-0.006-0.0060.0000.0000.0000.000
160N172TYR00.0610.03764.5740.0080.0080.0000.0000.0000.000
161N173ASN0-0.027-0.03770.4440.0170.0170.0000.0000.0000.000
162N174PHE00.0610.02765.6820.0100.0100.0000.0000.0000.000
163N175ALA00.0370.03067.576-0.038-0.0380.0000.0000.0000.000
164N176SER0-0.062-0.03469.5920.0100.0100.0000.0000.0000.000
165N177ARG10.9030.95360.1375.2085.2080.0000.0000.0000.000
166N178ARG10.9480.99166.8914.3304.3300.0000.0000.0000.000
167N179LEU00.0090.00666.4880.0180.0180.0000.0000.0000.000
168N180ILE0-0.048-0.02569.6840.0230.0230.0000.0000.0000.000
169N181LEU0-0.007-0.00969.203-0.001-0.0010.0000.0000.0000.000
170N182LEU00.0330.02673.7740.0030.0030.0000.0000.0000.000
171N183PRO00.0740.04076.677-0.055-0.0550.0000.0000.0000.000
172N184THR0-0.097-0.06976.8810.0280.0280.0000.0000.0000.000
173N185ASP-1-0.891-0.94879.398-3.896-3.8960.0000.0000.0000.000
174N186ASP-1-0.783-0.90078.010-4.145-4.1450.0000.0000.0000.000
175N187HIS10.8340.91181.3053.8573.8570.0000.0000.0000.000
176N188ASP-1-0.927-0.96681.064-3.910-3.9100.0000.0000.0000.000
177N189ASP-1-0.957-0.97181.945-3.883-3.8830.0000.0000.0000.000
178N190HIS0-0.0020.01476.591-0.051-0.0510.0000.0000.0000.000
179N191LEU0-0.013-0.00576.9710.0080.0080.0000.0000.0000.000
180N192ALA00.0590.03776.004-0.071-0.0710.0000.0000.0000.000
181N193VAL0-0.018-0.00470.032-0.008-0.0080.0000.0000.0000.000
182N194VAL0-0.028-0.01472.2950.0100.0100.0000.0000.0000.000
183N195CYS0-0.046-0.02465.8010.0210.0210.0000.0000.0000.000
184N196SER00.0260.00267.3190.0740.0740.0000.0000.0000.000
185N197PHE00.0340.03561.0350.0050.0050.0000.0000.0000.000
186N198ASN0-0.065-0.04662.8990.0000.0000.0000.0000.0000.000
187N199ARG10.8810.92158.9815.3185.3180.0000.0000.0000.000
188N200GLY00.0850.06557.807-0.072-0.0720.0000.0000.0000.000
189N201ASP-1-0.753-0.82655.447-5.717-5.7170.0000.0000.0000.000
190N202ASN00.012-0.00556.5890.1780.1780.0000.0000.0000.000
191N203GLU-1-0.837-0.91353.820-5.803-5.8030.0000.0000.0000.000
192N204ARG10.7640.85155.6995.7345.7340.0000.0000.0000.000
193N205ALA0-0.022-0.01359.3620.0560.0560.0000.0000.0000.000
194N206GLU-1-0.824-0.88963.161-4.740-4.7400.0000.0000.0000.000
195N208HIS10.8460.91868.5294.5214.5210.0000.0000.0000.000
196N209ARG10.8690.95171.5124.4384.4380.0000.0000.0000.000
197N210VAL00.003-0.01374.2840.0340.0340.0000.0000.0000.000
198N211THR00.0160.01077.7210.0240.0240.0000.0000.0000.000
199N212GLU-1-0.913-0.96580.900-3.958-3.9580.0000.0000.0000.000
200N213ALA0-0.024-0.00881.8720.0010.0010.0000.0000.0000.000
201N214THR0-0.003-0.02483.9660.0240.0240.0000.0000.0000.000
202N215LEU0-0.044-0.01877.782-0.019-0.0190.0000.0000.0000.000
203N216HIS00.0310.02179.157-0.051-0.0510.0000.0000.0000.000
204N217GLN0-0.018-0.01374.571-0.056-0.0560.0000.0000.0000.000
205N219ALA00.0630.02272.4120.0090.0090.0000.0000.0000.000
206N220ASP-1-0.851-0.91669.231-4.485-4.4850.0000.0000.0000.000
207N221LEU0-0.012-0.00265.556-0.015-0.0150.0000.0000.0000.000
208N222PHE0-0.014-0.00962.497-0.009-0.0090.0000.0000.0000.000
209N223VAL0-0.017-0.00961.998-0.037-0.0370.0000.0000.0000.000
210N224THR0-0.006-0.01655.409-0.033-0.0330.0000.0000.0000.000
211N225LEU0-0.048-0.02455.9350.0650.0650.0000.0000.0000.000
212N226GLU-1-0.831-0.90255.487-5.575-5.5750.0000.0000.0000.000
213N227GLU-1-0.944-0.96947.536-6.690-6.6900.0000.0000.0000.000
214N228HIS0-0.118-0.07351.1500.1360.1360.0000.0000.0000.000
215N229ASP-2-1.897-1.92645.227-13.911-13.9110.0000.0000.0000.000