Manual

About

FMODB

FMODB: The database of quantum mechanical data based on the FMO method

Last updated: 2024-05-02

All entries: 37386

Number of unique PDB entries: 7781

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FMODB ID: 6NRNZ

Calculation Name: 4LMQ-E-Xray372

Preferred Name: Stromal cell-derived factor 1

Target Type: SINGLE PROTEIN

Ligand Name:

ligand 3-letter code:

PDB ID: 4LMQ

Chain ID: E

ChEMBL ID: CHEMBL3286074

UniProt ID: P48061

Base Structure: X-ray

Registration Date: 2023-06-26

Reference: C. Watanabe, N. Tani, K. Kamisaka, T. Honma et al., Interaction energy analysis of Apo structure dataset on FMODB, To be published.

DOI:


IFIE MAP

IFIE Diagram


Modeling method
Optimization MOE:Amber10:EHT
Restraint OptAll
Protonation MOE:Protonate 3D
Complement MOE:Structure Preparation
Water No
Procedure Auto-FMO protocol ver. 2.20220422
FMO calculation
FMO method FMO2-MP2/6-31G(d)
Fragmentation Auto
Number of fragment 196
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -1902982.931251
FMO2-HF: Nuclear repulsion 1828866.137363
FMO2-HF: Total energy -74116.793889
FMO2-MP2: Total energy -74333.764378


3D Structure
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:1:GLU)


Summations of interaction energy for fragment #1(E:1:GLU)
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.
-69.753-70.97917.005-8.419-7.3580.077
Interaction energy analysis for fragmet #1(E:1:GLU)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : -1 / q_Mulliken : -0.896 / q_NPA : -0.944
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].
3E3GLN0-0.046-0.0271.705-33.273-34.79217.007-8.302-7.1860.077
4E4LEU0-0.027-0.0234.618-5.927-5.874-0.001-0.014-0.0380.000
5E5VAL00.0220.0108.3551.4511.4510.0000.0000.0000.000
6E6GLU-1-0.788-0.87910.76021.03621.0360.0000.0000.0000.000
7E7SER0-0.023-0.02314.467-0.187-0.1870.0000.0000.0000.000
8E8GLY00.0260.00817.180-0.435-0.4350.0000.0000.0000.000
9E9GLY00.0280.01620.465-0.575-0.5750.0000.0000.0000.000
10E10GLY0-0.018-0.01822.101-0.123-0.1230.0000.0000.0000.000
11E11LEU0-0.061-0.02525.322-0.039-0.0390.0000.0000.0000.000
12E12VAL0-0.015-0.00328.672-0.013-0.0130.0000.0000.0000.000
13E13GLN00.0270.02031.314-0.130-0.1300.0000.0000.0000.000
14E14PRO00.013-0.00434.6240.1230.1230.0000.0000.0000.000
15E15GLY0-0.009-0.00136.090-0.223-0.2230.0000.0000.0000.000
16E16GLY0-0.0010.01034.118-0.032-0.0320.0000.0000.0000.000
17E17SER0-0.067-0.05930.976-0.029-0.0290.0000.0000.0000.000
18E18LEU00.0020.01624.047-0.103-0.1030.0000.0000.0000.000
19E19ARG10.8670.94622.720-13.144-13.1440.0000.0000.0000.000
20E20LEU00.0130.03419.6660.3460.3460.0000.0000.0000.000
21E21SER0-0.026-0.03117.937-0.557-0.5570.0000.0000.0000.000
22E22CYS0-0.056-0.02013.1950.1230.1230.0000.0000.0000.000
23E23ALA00.0210.02911.988-0.690-0.6900.0000.0000.0000.000
24E24ALA00.0240.0069.1541.7751.7750.0000.0000.0000.000
25E25SER0-0.028-0.0135.152-3.385-3.3850.0000.0000.0000.000
26E26GLY00.0980.0453.9861.4491.5590.000-0.089-0.0200.000
27E27PHE0-0.031-0.0244.544-1.354-1.224-0.001-0.014-0.1140.000
28E28SER00.0540.0368.005-0.742-0.7420.0000.0000.0000.000
29E29LEU00.0290.01011.630-0.481-0.4810.0000.0000.0000.000
30E30THR0-0.022-0.00814.285-1.125-1.1250.0000.0000.0000.000
31E31VAL0-0.0230.00113.036-0.658-0.6580.0000.0000.0000.000
32E32TYR0-0.0120.00110.3920.5540.5540.0000.0000.0000.000
33E33SER00.0140.01014.533-0.308-0.3080.0000.0000.0000.000
34E34VAL0-0.028-0.01013.4531.1731.1730.0000.0000.0000.000
35E35HIS0-0.028-0.02015.921-1.582-1.5820.0000.0000.0000.000
36E36TRP00.0230.00316.7041.1041.1040.0000.0000.0000.000
37E37VAL0-0.008-0.00418.350-0.881-0.8810.0000.0000.0000.000
38E38ARG10.7550.84119.615-10.820-10.8200.0000.0000.0000.000
39E39GLN00.0110.00320.709-0.637-0.6370.0000.0000.0000.000
40E40ALA00.0520.03823.2610.0800.0800.0000.0000.0000.000
41E41PRO00.016-0.01926.1640.1900.1900.0000.0000.0000.000
42E42GLY0-0.0160.00827.278-0.039-0.0390.0000.0000.0000.000
43E43LYS10.8910.93725.038-12.073-12.0730.0000.0000.0000.000
44E44GLY00.0340.03626.048-0.101-0.1010.0000.0000.0000.000
45E45LEU0-0.018-0.01620.6010.1470.1470.0000.0000.0000.000
46E46GLU-1-0.807-0.87523.84110.61010.6100.0000.0000.0000.000
47E47TRP00.0100.01620.9600.2560.2560.0000.0000.0000.000
48E48VAL0-0.024-0.02922.485-0.660-0.6600.0000.0000.0000.000
49E49GLY00.0150.00222.772-0.587-0.5870.0000.0000.0000.000
50E50ALA0-0.0140.01320.6670.7370.7370.0000.0000.0000.000
51E51LEU0-0.024-0.01218.400-0.685-0.6850.0000.0000.0000.000
52E52TRP00.0280.00819.1541.1141.1140.0000.0000.0000.000
53E53GLY00.0190.01818.3870.0440.0440.0000.0000.0000.000
54E54SER00.009-0.00119.0600.0360.0360.0000.0000.0000.000
55E55GLY00.006-0.00722.018-0.310-0.3100.0000.0000.0000.000
56E56GLY0-0.0030.00922.923-0.066-0.0660.0000.0000.0000.000
57E57THR0-0.044-0.03723.6360.4730.4730.0000.0000.0000.000
58E58GLU-1-0.862-0.91924.99710.14710.1470.0000.0000.0000.000
59E59TYR0-0.045-0.04025.3700.5490.5490.0000.0000.0000.000
60E60ASN0-0.0050.00027.118-0.672-0.6720.0000.0000.0000.000
61E61SER00.0500.00628.813-0.082-0.0820.0000.0000.0000.000
62E62ASN00.0020.00731.553-0.424-0.4240.0000.0000.0000.000
63E63LEU0-0.037-0.00827.589-0.218-0.2180.0000.0000.0000.000
64E64LYS10.9250.93832.156-8.648-8.6480.0000.0000.0000.000
65E65SER0-0.0110.00531.114-0.365-0.3650.0000.0000.0000.000
66E66ARG10.7780.87831.249-9.786-9.7860.0000.0000.0000.000
67E67PHE00.0030.00025.8090.1350.1350.0000.0000.0000.000
68E68THR0-0.005-0.00626.884-0.334-0.3340.0000.0000.0000.000
69E69ILE0-0.0340.00721.7270.2400.2400.0000.0000.0000.000
70E70SER00.0100.00422.189-0.201-0.2010.0000.0000.0000.000
71E71ARG10.8560.90617.835-14.232-14.2320.0000.0000.0000.000
72E72ASP-1-0.751-0.84718.95514.02014.0200.0000.0000.0000.000
73E73THR00.0530.01416.6220.7410.7410.0000.0000.0000.000
74E74SER0-0.037-0.01116.4800.3760.3760.0000.0000.0000.000
75E75LYS10.8360.90216.319-14.647-14.6470.0000.0000.0000.000
76E76ASN0-0.034-0.01710.476-0.613-0.6130.0000.0000.0000.000
77E77THR00.0110.00113.1901.5601.5600.0000.0000.0000.000
78E78VAL0-0.020-0.01015.578-1.095-1.0950.0000.0000.0000.000
79E79TYR0-0.071-0.06017.5690.5160.5160.0000.0000.0000.000
80E80LEU00.0250.00920.373-0.196-0.1960.0000.0000.0000.000
81E81GLN0-0.037-0.02422.5020.1400.1400.0000.0000.0000.000
82E82MET0-0.0010.01424.7240.0670.0670.0000.0000.0000.000
83E82ASN00.0450.00927.9040.1370.1370.0000.0000.0000.000
84E82SER00.0160.00631.702-0.126-0.1260.0000.0000.0000.000
85E82LEU0-0.0090.01828.821-0.040-0.0400.0000.0000.0000.000
86E83ARG10.9010.93532.653-8.922-8.9220.0000.0000.0000.000
87E84ALA00.0690.03432.6330.2900.2900.0000.0000.0000.000
88E85GLU-1-0.818-0.91832.4669.1519.1510.0000.0000.0000.000
89E86ASP-1-0.777-0.83228.71610.48810.4880.0000.0000.0000.000
90E87THR0-0.0150.00127.5960.5230.5230.0000.0000.0000.000
91E88ALA00.0030.00124.590-0.143-0.1430.0000.0000.0000.000
92E89VAL0-0.0040.00818.9980.1090.1090.0000.0000.0000.000
93E90TYR0-0.022-0.03820.013-0.250-0.2500.0000.0000.0000.000
94E91TYR00.0300.00914.8110.1240.1240.0000.0000.0000.000
95E93ALA00.0380.01212.5121.4741.4740.0000.0000.0000.000
96E94ARG10.8320.9188.214-26.452-26.4520.0000.0000.0000.000
97E95ASP-1-0.759-0.86712.49215.58215.5820.0000.0000.0000.000
98E96GLN0-0.020-0.01313.0040.1600.1600.0000.0000.0000.000
99E97GLY0-0.052-0.03514.1350.3460.3460.0000.0000.0000.000
100E98LEU0-0.0040.00615.924-0.630-0.6300.0000.0000.0000.000
101E99ASN0-0.013-0.03018.3050.1730.1730.0000.0000.0000.000
102E100TYR0-0.022-0.00319.737-0.398-0.3980.0000.0000.0000.000
103E100GLY00.0150.02221.324-0.502-0.5020.0000.0000.0000.000
104E100SER0-0.061-0.05219.0230.2640.2640.0000.0000.0000.000
105E100LEU0-0.0160.00817.070-0.362-0.3620.0000.0000.0000.000
106E100PHE0-0.006-0.02414.5900.3150.3150.0000.0000.0000.000
107E101ASP-1-0.763-0.8529.71822.00422.0040.0000.0000.0000.000
108E102TYR0-0.018-0.0155.4741.2631.2630.0000.0000.0000.000
109E103TRP00.002-0.0179.149-2.894-2.8940.0000.0000.0000.000
110E104GLY00.0590.0448.9203.2763.2760.0000.0000.0000.000
111E105GLN0-0.047-0.03410.5420.6880.6880.0000.0000.0000.000
112E106GLY0-0.013-0.00312.332-1.583-1.5830.0000.0000.0000.000
113E107THR0-0.072-0.04015.7030.0910.0910.0000.0000.0000.000
114E108LEU0-0.0020.00718.381-0.426-0.4260.0000.0000.0000.000
115E109VAL00.0080.00722.004-0.077-0.0770.0000.0000.0000.000
116E110THR0-0.008-0.01125.057-0.174-0.1740.0000.0000.0000.000
117E111VAL0-0.018-0.00828.539-0.087-0.0870.0000.0000.0000.000
118E112SER00.0130.00031.923-0.330-0.3300.0000.0000.0000.000
119E113SER00.012-0.00135.0250.0840.0840.0000.0000.0000.000
120E114ALA00.0070.00736.381-0.095-0.0950.0000.0000.0000.000
121E115SER00.0310.00631.6920.1740.1740.0000.0000.0000.000
122E116THR00.0210.01334.1740.0370.0370.0000.0000.0000.000
123E117LYS10.8240.92936.339-8.427-8.4270.0000.0000.0000.000
124E118GLY00.0620.03933.901-0.103-0.1030.0000.0000.0000.000
125E119PRO0-0.010-0.00932.497-0.235-0.2350.0000.0000.0000.000
126E120SER0-0.072-0.02735.482-0.240-0.2400.0000.0000.0000.000
127E121VAL00.0100.01035.7680.0220.0220.0000.0000.0000.000
128E122PHE0-0.007-0.01038.764-0.189-0.1890.0000.0000.0000.000
129E123PRO00.0480.02340.8150.1720.1720.0000.0000.0000.000
130E124LEU0-0.0040.00639.942-0.113-0.1130.0000.0000.0000.000
131E137ALA0-0.019-0.00840.5440.0370.0370.0000.0000.0000.000
132E138LEU0-0.012-0.00639.280-0.207-0.2070.0000.0000.0000.000
133E139GLY00.0370.00738.1640.2570.2570.0000.0000.0000.000
134E140CYS0-0.120-0.05636.544-0.242-0.2420.0000.0000.0000.000
135E141LEU00.0200.02236.9910.2210.2210.0000.0000.0000.000
136E142VAL0-0.005-0.02132.799-0.071-0.0710.0000.0000.0000.000
137E143LYS10.8700.91435.486-7.477-7.4770.0000.0000.0000.000
138E144ASP-1-0.789-0.88037.3887.9067.9060.0000.0000.0000.000
139E145TYR0-0.045-0.04430.163-0.142-0.1420.0000.0000.0000.000
140E146PHE00.0350.01332.1280.0480.0480.0000.0000.0000.000
141E147PRO00.0210.02128.029-0.108-0.1080.0000.0000.0000.000
142E148GLU-1-0.799-0.88926.80311.38411.3840.0000.0000.0000.000
143E149PRO0-0.023-0.00422.6850.2060.2060.0000.0000.0000.000
144E150VAL00.000-0.01225.890-0.160-0.1600.0000.0000.0000.000
145E151THR0-0.035-0.00524.1460.1760.1760.0000.0000.0000.000
146E152VAL00.018-0.00126.452-0.428-0.4280.0000.0000.0000.000
147E153SER0-0.0170.00626.8880.2740.2740.0000.0000.0000.000
148E154TRP00.0420.00728.902-0.500-0.5000.0000.0000.0000.000
149E155ASN00.0170.00030.8700.1630.1630.0000.0000.0000.000
150E156SER0-0.023-0.02729.2810.0340.0340.0000.0000.0000.000
151E157GLY00.0020.00726.5920.4240.4240.0000.0000.0000.000
152E158ALA0-0.028-0.00127.2700.2480.2480.0000.0000.0000.000
153E159LEU0-0.043-0.01229.745-0.172-0.1720.0000.0000.0000.000
154E160THR00.026-0.00226.081-0.016-0.0160.0000.0000.0000.000
155E161SER00.0300.00129.3930.0890.0890.0000.0000.0000.000
156E162GLY00.0320.01931.789-0.295-0.2950.0000.0000.0000.000
157E163VAL0-0.059-0.01830.085-0.236-0.2360.0000.0000.0000.000
158E164HIS0-0.0040.00730.8350.4030.4030.0000.0000.0000.000
159E165THR00.002-0.00528.845-0.471-0.4710.0000.0000.0000.000
160E166PHE00.0000.00929.8790.2830.2830.0000.0000.0000.000
161E167PRO00.024-0.00329.4890.1590.1590.0000.0000.0000.000
162E168ALA00.0120.01829.845-0.369-0.3690.0000.0000.0000.000
163E169VAL0-0.002-0.00131.6350.0190.0190.0000.0000.0000.000
164E170LEU0-0.037-0.01534.089-0.090-0.0900.0000.0000.0000.000
165E171GLN0-0.023-0.02735.829-0.394-0.3940.0000.0000.0000.000
166E172SER00.030-0.00739.4770.0360.0360.0000.0000.0000.000
167E173SER0-0.044-0.01640.931-0.137-0.1370.0000.0000.0000.000
168E174GLY00.0150.01837.9950.0080.0080.0000.0000.0000.000
169E175LEU0-0.037-0.00936.1350.2380.2380.0000.0000.0000.000
170E176TYR00.0390.01030.576-0.140-0.1400.0000.0000.0000.000
171E177SER0-0.005-0.00434.735-0.264-0.2640.0000.0000.0000.000
172E178LEU00.0130.02130.1180.1110.1110.0000.0000.0000.000
173E179SER00.0060.00534.328-0.350-0.3500.0000.0000.0000.000
174E180SER0-0.050-0.02431.8490.1820.1820.0000.0000.0000.000
175E181VAL00.0460.01034.335-0.292-0.2920.0000.0000.0000.000
176E182VAL00.0430.03434.4780.1590.1590.0000.0000.0000.000
177E194TYR0-0.004-0.00737.402-0.027-0.0270.0000.0000.0000.000
178E195ILE00.0340.00635.708-0.174-0.1740.0000.0000.0000.000
179E196CYS00.0010.02833.6180.2210.2210.0000.0000.0000.000
180E197ASN00.0000.01929.9620.0680.0680.0000.0000.0000.000
181E198VAL00.0320.01629.8810.4130.4130.0000.0000.0000.000
182E199ASN00.005-0.02424.917-0.226-0.2260.0000.0000.0000.000
183E200HIS00.0280.00227.8690.1700.1700.0000.0000.0000.000
184E201LYS10.9720.98323.534-13.170-13.1700.0000.0000.0000.000
185E202PRO00.0120.01925.745-0.123-0.1230.0000.0000.0000.000
186E203SER0-0.016-0.00327.900-0.392-0.3920.0000.0000.0000.000
187E204ASN0-0.078-0.03529.1510.0550.0550.0000.0000.0000.000
188E205THR00.0190.01530.356-0.340-0.3400.0000.0000.0000.000
189E206LYS10.8370.88229.401-9.872-9.8720.0000.0000.0000.000
190E207VAL0-0.036-0.01331.899-0.314-0.3140.0000.0000.0000.000
191E208ASP-1-0.777-0.87033.4379.8709.8700.0000.0000.0000.000
192E209LYS10.9100.95235.880-8.025-8.0250.0000.0000.0000.000
193E210LYS10.8760.92838.347-7.074-7.0740.0000.0000.0000.000
194E211VAL0-0.034-0.01339.381-0.130-0.1300.0000.0000.0000.000
195E212GLU-1-0.820-0.90042.0717.0267.0260.0000.0000.0000.000
196E213PRO0-0.028-0.00945.564-0.187-0.1870.0000.0000.0000.000