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: 74Q2K

Calculation Name: 3CX5-E-Xray547

Preferred Name:

Target Type:

Ligand Name: protoporphyrin ix containing fe | (2r,5s,11r,14r)-5,8,11-trihydroxy-2-(nonanoyloxy)-5,11-dioxido-16-oxo-14-[(propanoyloxy)methyl]-4,6,10,12,15-pentaoxa-5,11-diphosphanonadec-1-yl undecanoate | stigmatellin a | (2r)-3-{[(s)-(2-aminoethoxy)(hydroxy)phosphoryl]oxy}-2-(tetradecanoyloxy)propyl octadecanoate | (5s,11r)-5,8,11-trihydroxy-5,11-dioxido-17-oxo-4,6,10,12,16-pentaoxa-5,11-diphosphaoctadec-1-yl pentadecanoate | undecyl-maltoside | (1r)-2-(phosphonooxy)-1-[(tridecanoyloxy)methyl]ethyl pentadecanoate | (1r)-2-{[(s)-(2-aminoethoxy)(hydroxy)phosphoryl]oxy}-1-[(heptanoyloxy)methyl]ethyl octadecanoate | (1r)-2-(dodecanoyloxy)-1-[(phosphonooxy)methyl]ethyl tetradecanoate | n-trimethyllysine | beta-d-fructofuranose | alpha-d-glucopyranose | fe2/s2 (inorganic) cluster

Ligand 3-letter code: HEM | CN3 | SMA | 8PE | CN5 | UMQ | 6PH | 9PE | 7PH | M3L | FRU | GLC | FES

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 3CX5

Chain ID: E

ChEMBL ID:

UniProt ID: P07143

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 184
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922
Total energy (hartree)
FMO2-HF: Electronic energy -1503275.301698
FMO2-HF: Nuclear repulsion 1431580.625973
FMO2-HF: Total energy -71694.675725
FMO2-MP2: Total energy -71899.377498


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(E:31:LYS)


Summations of interaction energy for fragment #1(E:31:LYS)
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.
-94.212-89.92212.13-8.206-8.214-0.101
Interaction energy analysis for fragmet #1(E:31:LYS)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 2 / q_Mulliken : 1.784 / q_NPA : 1.882
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].
3E33THR00.0700.0192.429-32.130-27.4961.513-2.877-3.270-0.034
4E34TYR00.0500.0314.7580.2630.444-0.001-0.007-0.1730.000
5E35ARG10.9070.9682.87184.39185.5680.096-0.438-0.835-0.002
6E36THR00.0610.0191.815-52.953-55.24110.521-4.710-3.523-0.064
7E37PRO0-0.054-0.0123.851-8.349-7.8170.002-0.164-0.370-0.001
8E38ASN00.0110.0014.5776.1766.230-0.001-0.010-0.0430.000
9E39PHE00.0330.0067.965-1.044-1.0440.0000.0000.0000.000
10E40ASP-1-0.882-0.93511.123-38.865-38.8650.0000.0000.0000.000
11E41ASP-1-0.928-0.96012.663-38.624-38.6240.0000.0000.0000.000
12E42VAL0-0.050-0.02814.8591.9901.9900.0000.0000.0000.000
13E43LEU0-0.083-0.03512.7121.6771.6770.0000.0000.0000.000
14E44LYS10.7980.89816.59625.18125.1810.0000.0000.0000.000
15E45GLU-1-0.827-0.91619.088-25.045-25.0450.0000.0000.0000.000
16E46ASN0-0.049-0.03719.7420.1320.1320.0000.0000.0000.000
17E47ASN0-0.041-0.01622.6260.6120.6120.0000.0000.0000.000
18E48ASP-1-0.798-0.91825.264-19.441-19.4410.0000.0000.0000.000
19E49ALA00.0230.03724.195-0.835-0.8350.0000.0000.0000.000
20E50ASP-1-0.804-0.89925.113-21.277-21.2770.0000.0000.0000.000
21E51LYS10.9080.96726.47820.22620.2260.0000.0000.0000.000
22E52GLY00.0310.01425.0980.2970.2970.0000.0000.0000.000
23E53ARG10.9140.95926.15721.24921.2490.0000.0000.0000.000
24E54SER00.000-0.01528.2190.6470.6470.0000.0000.0000.000
25E55TYR0-0.001-0.00328.9240.4960.4960.0000.0000.0000.000
26E56ALA00.0150.01327.6930.3970.3970.0000.0000.0000.000
27E57TYR00.000-0.02228.9700.3780.3780.0000.0000.0000.000
28E58PHE00.0100.01932.7960.5210.5210.0000.0000.0000.000
29E59MET0-0.0010.00131.9190.5670.5670.0000.0000.0000.000
30E60VAL00.0070.00331.6440.3390.3390.0000.0000.0000.000
31E61GLY00.0220.01734.6050.4050.4050.0000.0000.0000.000
32E62ALA0-0.007-0.00737.6260.4730.4730.0000.0000.0000.000
33E63MET00.0210.01034.0320.3110.3110.0000.0000.0000.000
34E64GLY00.0340.02938.4890.3120.3120.0000.0000.0000.000
35E65LEU0-0.0180.00740.1160.4090.4090.0000.0000.0000.000
36E66LEU00.023-0.00341.2100.3830.3830.0000.0000.0000.000
37E67SER0-0.023-0.02140.5530.2330.2330.0000.0000.0000.000
38E68SER0-0.043-0.03143.2110.2770.2770.0000.0000.0000.000
39E69ALA0-0.014-0.00345.7700.3140.3140.0000.0000.0000.000
40E70GLY00.0360.03246.6440.3020.3020.0000.0000.0000.000
41E71ALA00.0120.01246.2490.2440.2440.0000.0000.0000.000
42E72LYS10.8330.90348.21411.68511.6850.0000.0000.0000.000
43E73SER00.020-0.00651.1060.2960.2960.0000.0000.0000.000
44E74THR0-0.041-0.01449.8740.2130.2130.0000.0000.0000.000
45E75VAL0-0.005-0.00551.4460.1960.1960.0000.0000.0000.000
46E76GLU-1-0.805-0.89253.996-11.009-11.0090.0000.0000.0000.000
47E77THR0-0.0160.00655.3370.2650.2650.0000.0000.0000.000
48E78PHE0-0.015-0.01052.6290.1480.1480.0000.0000.0000.000
49E79ILE00.0080.01457.3800.1900.1900.0000.0000.0000.000
50E80SER0-0.024-0.03059.8880.2030.2030.0000.0000.0000.000
51E81SER0-0.075-0.03760.5830.1830.1830.0000.0000.0000.000
52E82MET0-0.028-0.01261.9850.0460.0460.0000.0000.0000.000
53E83THR0-0.086-0.04564.4800.1690.1690.0000.0000.0000.000
54E84ALA0-0.009-0.00866.9380.0270.0270.0000.0000.0000.000
55E85THR00.020-0.00968.372-0.041-0.0410.0000.0000.0000.000
56E86ALA00.000-0.01870.5620.1150.1150.0000.0000.0000.000
57E87ASP-1-0.885-0.91772.445-8.574-8.5740.0000.0000.0000.000
58E88VAL0-0.010-0.00673.4310.1410.1410.0000.0000.0000.000
59E89LEU0-0.048-0.01172.0860.0630.0630.0000.0000.0000.000
60E90ALA0-0.022-0.01476.4370.0660.0660.0000.0000.0000.000
61E91MET0-0.028-0.01277.6040.0600.0600.0000.0000.0000.000
62E92ALA0-0.027-0.01182.0690.0470.0470.0000.0000.0000.000
63E93LYS10.8590.92885.6627.1677.1670.0000.0000.0000.000
64E94VAL0-0.030-0.00989.0640.0030.0030.0000.0000.0000.000
65E95GLU-1-0.836-0.90591.457-6.581-6.5810.0000.0000.0000.000
66E96VAL0-0.045-0.02795.287-0.006-0.0060.0000.0000.0000.000
67E97ASN00.006-0.00197.8120.0470.0470.0000.0000.0000.000
68E98LEU00.0360.00799.690-0.015-0.0150.0000.0000.0000.000
69E99ALA00.0410.021103.0520.0320.0320.0000.0000.0000.000
70E100ALA0-0.077-0.028103.6150.0520.0520.0000.0000.0000.000
71E101ILE0-0.040-0.008100.436-0.011-0.0110.0000.0000.0000.000
72E102PRO0-0.030-0.024104.7740.0400.0400.0000.0000.0000.000
73E103LEU00.024-0.004106.016-0.046-0.0460.0000.0000.0000.000
74E104GLY00.0550.048105.715-0.051-0.0510.0000.0000.0000.000
75E105LYS10.8880.939102.2286.2596.2590.0000.0000.0000.000
76E106ASN00.0770.04697.644-0.018-0.0180.0000.0000.0000.000
77E107VAL0-0.017-0.01597.0910.0370.0370.0000.0000.0000.000
78E108VAL0-0.014-0.00291.637-0.051-0.0510.0000.0000.0000.000
79E109VAL00.0190.02091.8490.0250.0250.0000.0000.0000.000
80E110LYS10.9120.94885.2997.2737.2730.0000.0000.0000.000
81E111TRP00.0690.03484.3380.0230.0230.0000.0000.0000.000
82E112GLN00.0590.02081.320-0.009-0.0090.0000.0000.0000.000
83E113GLY00.000-0.00181.593-0.089-0.0890.0000.0000.0000.000
84E114LYS10.9050.97280.8637.7777.7770.0000.0000.0000.000
85E115PRO0-0.0200.00384.4190.0660.0660.0000.0000.0000.000
86E116VAL00.0250.00987.792-0.053-0.0530.0000.0000.0000.000
87E117PHE0-0.018-0.00290.3880.0580.0580.0000.0000.0000.000
88E118ILE00.0370.01393.313-0.004-0.0040.0000.0000.0000.000
89E119ARG10.7420.81696.6686.3626.3620.0000.0000.0000.000
90E120HIS10.8900.97099.6946.0746.0740.0000.0000.0000.000
91E121ARG10.7120.82899.0726.4786.4780.0000.0000.0000.000
92E122THR00.009-0.005103.7130.0680.0680.0000.0000.0000.000
93E123PRO00.028-0.013106.672-0.032-0.0320.0000.0000.0000.000
94E124HIS0-0.0150.002106.5930.0410.0410.0000.0000.0000.000
95E125GLU-1-0.743-0.857103.214-6.239-6.2390.0000.0000.0000.000
96E126ILE0-0.0200.002103.165-0.058-0.0580.0000.0000.0000.000
97E127GLN0-0.0130.000103.943-0.016-0.0160.0000.0000.0000.000
98E128GLU-1-0.907-0.956102.326-6.256-6.2560.0000.0000.0000.000
99E129ALA0-0.0190.00399.716-0.064-0.0640.0000.0000.0000.000
100E130ASN00.000-0.01499.734-0.053-0.0530.0000.0000.0000.000
101E131SER0-0.034-0.007101.9180.0160.0160.0000.0000.0000.000
102E132VAL0-0.040-0.02297.6240.0170.0170.0000.0000.0000.000
103E133ASP-1-0.836-0.88697.904-6.571-6.5710.0000.0000.0000.000
104E134MET00.003-0.00894.089-0.078-0.0780.0000.0000.0000.000
105E135SER0-0.058-0.05093.430-0.085-0.0850.0000.0000.0000.000
106E136ALA0-0.055-0.02293.616-0.049-0.0490.0000.0000.0000.000
107E137LEU0-0.045-0.02291.591-0.004-0.0040.0000.0000.0000.000
108E138LYS10.8560.92083.8727.5417.5410.0000.0000.0000.000
109E139ASP-1-0.814-0.89486.263-7.502-7.5020.0000.0000.0000.000
110E140PRO0-0.028-0.01587.8520.0790.0790.0000.0000.0000.000
111E141GLN00.0430.02589.835-0.041-0.0410.0000.0000.0000.000
112E142THR00.020-0.00292.2770.0850.0850.0000.0000.0000.000
113E143ASP-1-0.733-0.82795.185-6.544-6.5440.0000.0000.0000.000
114E144ALA00.010-0.00197.107-0.018-0.0180.0000.0000.0000.000
115E145ASP-1-0.913-0.93491.505-7.012-7.0120.0000.0000.0000.000
116E146ARG10.7680.87789.7006.9386.9380.0000.0000.0000.000
117E147VAL0-0.034-0.01994.049-0.024-0.0240.0000.0000.0000.000
118E148LYS10.8430.92693.1526.8636.8630.0000.0000.0000.000
119E149ASP-1-0.802-0.90698.515-6.111-6.1110.0000.0000.0000.000
120E150PRO0-0.0040.002101.004-0.043-0.0430.0000.0000.0000.000
121E151GLN0-0.016-0.013102.4960.0330.0330.0000.0000.0000.000
122E152TRP0-0.028-0.02399.666-0.013-0.0130.0000.0000.0000.000
123E153LEU00.0110.02194.743-0.046-0.0460.0000.0000.0000.000
124E154ILE0-0.007-0.00892.8550.0030.0030.0000.0000.0000.000
125E155MET00.0160.01890.517-0.045-0.0450.0000.0000.0000.000
126E156LEU0-0.013-0.00684.2940.0140.0140.0000.0000.0000.000
127E157GLY0-0.012-0.01288.0240.0180.0180.0000.0000.0000.000
128E158ILE0-0.068-0.05981.935-0.045-0.0450.0000.0000.0000.000
129E159CYS-1-0.827-0.79183.995-7.568-7.5680.0000.0000.0000.000
130E160THR00.012-0.01781.826-0.139-0.1390.0000.0000.0000.000
131E161HIS0-0.050-0.03479.400-0.153-0.1530.0000.0000.0000.000
132E162LEU0-0.012-0.02275.615-0.122-0.1220.0000.0000.0000.000
133E163GLY00.0270.02378.958-0.033-0.0330.0000.0000.0000.000
134E164CYS0-0.102-0.04780.7050.0100.0100.0000.0000.0000.000
135E165VAL00.0400.02383.3670.0360.0360.0000.0000.0000.000
136E166PRO0-0.058-0.02286.8030.0380.0380.0000.0000.0000.000
137E167ILE00.0120.00589.6130.0410.0410.0000.0000.0000.000
138E168GLY00.0340.00292.8830.0020.0020.0000.0000.0000.000
139E169GLU-1-0.913-0.94595.841-6.315-6.3150.0000.0000.0000.000
140E170ALA0-0.025-0.00395.4720.0410.0410.0000.0000.0000.000
141E171GLY0-0.011-0.00195.282-0.055-0.0550.0000.0000.0000.000
142E172ASP-1-0.858-0.93795.851-6.665-6.6650.0000.0000.0000.000
143E173PHE0-0.035-0.03294.4740.0350.0350.0000.0000.0000.000
144E174GLY00.0640.03298.197-0.003-0.0030.0000.0000.0000.000
145E175GLY00.0020.01396.6000.0360.0360.0000.0000.0000.000
146E176TRP0-0.027-0.01092.4390.0320.0320.0000.0000.0000.000
147E177PHE00.0180.01590.488-0.046-0.0460.0000.0000.0000.000
148E178CYS0-0.027-0.03684.958-0.023-0.0230.0000.0000.0000.000
149E179PRO0-0.013-0.00787.278-0.027-0.0270.0000.0000.0000.000
150E181HIS00.0550.01379.568-0.023-0.0230.0000.0000.0000.000
151E182GLY00.0170.01984.273-0.004-0.0040.0000.0000.0000.000
152E183SER0-0.023-0.02585.0270.0300.0300.0000.0000.0000.000
153E184HIS0-0.0160.00887.8140.0830.0830.0000.0000.0000.000
154E185TYR00.000-0.09185.756-0.038-0.0380.0000.0000.0000.000
155E186ASP-1-0.702-0.83592.497-6.666-6.6660.0000.0000.0000.000
156E187ILE00.0160.01595.833-0.052-0.0520.0000.0000.0000.000
157E188SER0-0.015-0.03896.0030.0170.0170.0000.0000.0000.000
158E189GLY00.0050.00192.901-0.056-0.0560.0000.0000.0000.000
159E190ARG10.7860.88091.0926.5916.5910.0000.0000.0000.000
160E191ILE0-0.033-0.01086.5870.0650.0650.0000.0000.0000.000
161E192ARG10.8090.90689.8026.7296.7290.0000.0000.0000.000
162E193LYS10.8550.91589.8036.8776.8770.0000.0000.0000.000
163E194GLY00.0560.03786.696-0.002-0.0020.0000.0000.0000.000
164E195PRO0-0.023-0.01781.2920.0030.0030.0000.0000.0000.000
165E196ALA00.0160.01382.138-0.082-0.0820.0000.0000.0000.000
166E197PRO0-0.0150.00479.5640.0820.0820.0000.0000.0000.000
167E198LEU00.0100.00780.9840.0420.0420.0000.0000.0000.000
168E199ASN00.0300.00384.6730.0520.0520.0000.0000.0000.000
169E200LEU0-0.046-0.01086.482-0.072-0.0720.0000.0000.0000.000
170E201GLU-1-0.888-0.94782.838-7.643-7.6430.0000.0000.0000.000
171E202ILE00.0110.01186.7820.0600.0600.0000.0000.0000.000
172E203PRO0-0.0300.00087.075-0.062-0.0620.0000.0000.0000.000
173E204ALA00.0430.01887.5060.0760.0760.0000.0000.0000.000
174E205TYR00.0270.00189.2400.0340.0340.0000.0000.0000.000
175E206GLU-1-0.871-0.92892.734-6.858-6.8580.0000.0000.0000.000
176E207PHE0-0.030-0.02095.770-0.005-0.0050.0000.0000.0000.000
177E208ASP-1-0.924-0.95999.431-6.355-6.3550.0000.0000.0000.000
178E209GLY00.0160.006101.2810.0190.0190.0000.0000.0000.000
179E210ASP-1-0.922-0.950104.523-5.979-5.9790.0000.0000.0000.000
180E211LYS10.8140.88399.0956.4346.4340.0000.0000.0000.000
181E212VAL00.0110.01495.6850.0030.0030.0000.0000.0000.000
182E213ILE0-0.009-0.00193.578-0.034-0.0340.0000.0000.0000.000
183E214VAL0-0.007-0.02189.473-0.002-0.0020.0000.0000.0000.000
184E215GLY-1-0.842-0.91086.763-7.332-7.3320.0000.0000.0000.000