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: 72Z2K

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 OptH
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 -1898207.14403
FMO2-HF: Nuclear repulsion 1824091.877586
FMO2-HF: Total energy -74115.266444
FMO2-MP2: Total energy -74332.148228


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.
-32.696-29.1640.35-1.499-2.382-0.001
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 : -0.958 / q_NPA : -0.991
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].
3E3GLN0-0.025-0.0172.845-0.4712.8300.350-1.372-2.279-0.001
4E4LEU0-0.022-0.0244.773-4.884-4.846-0.001-0.009-0.0280.000
5E5VAL00.0160.0118.4820.7120.7120.0000.0000.0000.000
6E6GLU-1-0.794-0.89311.03620.27820.2780.0000.0000.0000.000
7E7SER0-0.014-0.01914.654-0.171-0.1710.0000.0000.0000.000
8E8GLY00.0220.01417.731-0.443-0.4430.0000.0000.0000.000
9E9GLY00.0190.01621.274-0.480-0.4800.0000.0000.0000.000
10E10GLY00.014-0.00822.699-0.011-0.0110.0000.0000.0000.000
11E11LEU0-0.064-0.01926.152-0.024-0.0240.0000.0000.0000.000
12E12VAL0-0.014-0.00129.072-0.101-0.1010.0000.0000.0000.000
13E13GLN00.0470.03031.7660.0090.0090.0000.0000.0000.000
14E14PRO0-0.003-0.01034.8990.1210.1210.0000.0000.0000.000
15E15GLY0-0.018-0.00135.544-0.236-0.2360.0000.0000.0000.000
16E16GLY0-0.024-0.00734.220-0.026-0.0260.0000.0000.0000.000
17E17SER0-0.041-0.04330.5690.0720.0720.0000.0000.0000.000
18E18LEU00.0080.01224.143-0.049-0.0490.0000.0000.0000.000
19E19ARG10.8960.96223.103-12.584-12.5840.0000.0000.0000.000
20E20LEU0-0.0290.01419.5370.2450.2450.0000.0000.0000.000
21E21SER0-0.023-0.03217.924-0.469-0.4690.0000.0000.0000.000
22E22CYS0-0.074-0.02512.6930.3270.3270.0000.0000.0000.000
23E23ALA00.0180.02712.080-0.349-0.3490.0000.0000.0000.000
24E24ALA00.0330.0129.2731.8241.8240.0000.0000.0000.000
25E25SER0-0.016-0.0065.654-2.623-2.6230.0000.0000.0000.000
26E26GLY00.1050.0543.6402.7072.7770.002-0.1040.0330.000
27E27PHE0-0.044-0.0314.2820.2560.379-0.001-0.014-0.1080.000
28E28SER00.0420.0277.398-0.888-0.8880.0000.0000.0000.000
29E29LEU00.0400.01111.013-0.258-0.2580.0000.0000.0000.000
30E30THR0-0.013-0.00713.599-0.582-0.5820.0000.0000.0000.000
31E31VAL0-0.0220.00912.626-0.638-0.6380.0000.0000.0000.000
32E32TYR0-0.014-0.00610.4600.1760.1760.0000.0000.0000.000
33E33SER00.0110.01913.781-0.638-0.6380.0000.0000.0000.000
34E34VAL0-0.019-0.00513.5251.0381.0380.0000.0000.0000.000
35E35HIS0-0.039-0.03615.742-1.547-1.5470.0000.0000.0000.000
36E36TRP00.0180.00416.6120.9780.9780.0000.0000.0000.000
37E37VAL0-0.018-0.00818.342-0.857-0.8570.0000.0000.0000.000
38E38ARG10.8060.88419.390-10.680-10.6800.0000.0000.0000.000
39E39GLN00.003-0.00920.868-0.592-0.5920.0000.0000.0000.000
40E40ALA00.0660.04123.3110.1530.1530.0000.0000.0000.000
41E41PRO00.032-0.00226.0220.1850.1850.0000.0000.0000.000
42E42GLY0-0.023-0.00627.038-0.240-0.2400.0000.0000.0000.000
43E43LYS10.8820.93524.726-11.957-11.9570.0000.0000.0000.000
44E44GLY00.0520.03425.950-0.155-0.1550.0000.0000.0000.000
45E45LEU0-0.047-0.02520.2750.0680.0680.0000.0000.0000.000
46E46GLU-1-0.821-0.89723.72110.44610.4460.0000.0000.0000.000
47E47TRP0-0.0070.00220.9710.2170.2170.0000.0000.0000.000
48E48VAL00.002-0.00622.674-0.628-0.6280.0000.0000.0000.000
49E49GLY0-0.003-0.01122.775-0.548-0.5480.0000.0000.0000.000
50E50ALA00.0310.02120.4790.5730.5730.0000.0000.0000.000
51E51LEU00.0130.00718.303-0.567-0.5670.0000.0000.0000.000
52E52TRP00.0420.00718.9381.0571.0570.0000.0000.0000.000
53E53GLY0-0.005-0.01017.819-0.047-0.0470.0000.0000.0000.000
54E54SER0-0.0160.00218.566-0.042-0.0420.0000.0000.0000.000
55E55GLY00.026-0.00321.766-0.212-0.2120.0000.0000.0000.000
56E56GLY0-0.033-0.00222.649-0.231-0.2310.0000.0000.0000.000
57E57THR0-0.034-0.04023.7150.4050.4050.0000.0000.0000.000
58E58GLU-1-0.925-0.94124.95610.19110.1910.0000.0000.0000.000
59E59TYR0-0.015-0.02725.1640.5290.5290.0000.0000.0000.000
60E60ASN0-0.017-0.00927.041-0.586-0.5860.0000.0000.0000.000
61E61SER00.012-0.01428.837-0.091-0.0910.0000.0000.0000.000
62E62ASN00.0040.01531.789-0.332-0.3320.0000.0000.0000.000
63E63LEU0-0.034-0.00627.879-0.285-0.2850.0000.0000.0000.000
64E64LYS10.9710.96831.505-8.383-8.3830.0000.0000.0000.000
65E65SER0-0.022-0.01031.460-0.256-0.2560.0000.0000.0000.000
66E66ARG10.8760.96231.350-9.625-9.6250.0000.0000.0000.000
67E67PHE0-0.0080.00025.9940.1010.1010.0000.0000.0000.000
68E68THR00.0150.01226.840-0.227-0.2270.0000.0000.0000.000
69E69ILE0-0.045-0.00121.5250.2030.2030.0000.0000.0000.000
70E70SER00.0180.01923.074-0.027-0.0270.0000.0000.0000.000
71E71ARG10.8800.92117.451-14.170-14.1700.0000.0000.0000.000
72E72ASP-1-0.838-0.92618.83313.55013.5500.0000.0000.0000.000
73E73THR00.0410.00016.2090.5750.5750.0000.0000.0000.000
74E74SER0-0.069-0.01316.0810.7270.7270.0000.0000.0000.000
75E75LYS10.9690.97716.339-13.866-13.8660.0000.0000.0000.000
76E76ASN0-0.0020.00410.723-0.419-0.4190.0000.0000.0000.000
77E77THR0-0.036-0.01113.4631.4521.4520.0000.0000.0000.000
78E78VAL0-0.0130.00115.138-1.090-1.0900.0000.0000.0000.000
79E79TYR0-0.020-0.01817.3440.4520.4520.0000.0000.0000.000
80E80LEU00.0180.01220.285-0.158-0.1580.0000.0000.0000.000
81E81GLN0-0.035-0.03622.5320.0400.0400.0000.0000.0000.000
82E82MET00.0010.02325.282-0.120-0.1200.0000.0000.0000.000
83E82ASN00.027-0.00427.8740.0270.0270.0000.0000.0000.000
84E82SER00.005-0.01031.642-0.117-0.1170.0000.0000.0000.000
85E82LEU0-0.027-0.00228.638-0.037-0.0370.0000.0000.0000.000
86E83ARG10.9690.98632.810-8.762-8.7620.0000.0000.0000.000
87E84ALA00.0620.02432.9360.2460.2460.0000.0000.0000.000
88E85GLU-1-0.888-0.95932.7689.1319.1310.0000.0000.0000.000
89E86ASP-1-0.844-0.90428.88410.42310.4230.0000.0000.0000.000
90E87THR0-0.026-0.00927.6670.4670.4670.0000.0000.0000.000
91E88ALA0-0.006-0.00424.748-0.103-0.1030.0000.0000.0000.000
92E89VAL0-0.0060.01219.1660.1010.1010.0000.0000.0000.000
93E90TYR0-0.007-0.01219.989-0.164-0.1640.0000.0000.0000.000
94E91TYR00.003-0.00414.5940.0400.0400.0000.0000.0000.000
95E93ALA00.0300.00512.5261.3141.3140.0000.0000.0000.000
96E94ARG10.8630.9547.233-28.296-28.2960.0000.0000.0000.000
97E95ASP-1-0.776-0.85912.47115.83315.8330.0000.0000.0000.000
98E96GLN0-0.021-0.01612.701-0.028-0.0280.0000.0000.0000.000
99E97GLY0-0.043-0.01713.4720.5070.5070.0000.0000.0000.000
100E98LEU0-0.025-0.00314.974-0.620-0.6200.0000.0000.0000.000
101E99ASN00.006-0.01817.766-0.010-0.0100.0000.0000.0000.000
102E100TYR0-0.052-0.01719.974-0.553-0.5530.0000.0000.0000.000
103E100GLY00.0390.02320.639-0.606-0.6060.0000.0000.0000.000
104E100SER0-0.041-0.04518.8610.3340.3340.0000.0000.0000.000
105E100LEU0-0.0190.00716.758-0.299-0.2990.0000.0000.0000.000
106E100PHE00.000-0.02514.5430.4740.4740.0000.0000.0000.000
107E101ASP-1-0.791-0.8919.50723.49523.4950.0000.0000.0000.000
108E102TYR0-0.035-0.0195.1030.5430.5430.0000.0000.0000.000
109E103TRP0-0.001-0.0189.310-2.942-2.9420.0000.0000.0000.000
110E104GLY00.0490.0359.1602.9962.9960.0000.0000.0000.000
111E105GLN0-0.022-0.02110.8460.3680.3680.0000.0000.0000.000
112E106GLY0-0.0220.00512.774-1.365-1.3650.0000.0000.0000.000
113E107THR0-0.063-0.03216.124-0.165-0.1650.0000.0000.0000.000
114E108LEU00.0200.00518.838-0.430-0.4300.0000.0000.0000.000
115E109VAL0-0.0020.00222.493-0.147-0.1470.0000.0000.0000.000
116E110THR0-0.028-0.02425.288-0.242-0.2420.0000.0000.0000.000
117E111VAL00.0080.00628.862-0.082-0.0820.0000.0000.0000.000
118E112SER0-0.003-0.00832.001-0.304-0.3040.0000.0000.0000.000
119E113SER00.0080.00135.427-0.097-0.0970.0000.0000.0000.000
120E114ALA00.0220.00837.452-0.051-0.0510.0000.0000.0000.000
121E115SER00.032-0.01133.3180.1610.1610.0000.0000.0000.000
122E116THR0-0.0230.00235.3000.0400.0400.0000.0000.0000.000
123E117LYS10.9030.94837.190-8.120-8.1200.0000.0000.0000.000
124E118GLY00.0220.05234.3880.0880.0880.0000.0000.0000.000
125E119PRO0-0.046-0.02633.185-0.244-0.2440.0000.0000.0000.000
126E120SER0-0.052-0.03436.233-0.138-0.1380.0000.0000.0000.000
127E121VAL00.0090.00536.0280.0580.0580.0000.0000.0000.000
128E122PHE0-0.012-0.01238.882-0.172-0.1720.0000.0000.0000.000
129E123PRO00.0420.02040.8680.1860.1860.0000.0000.0000.000
130E124LEU0-0.0070.01340.024-0.097-0.0970.0000.0000.0000.000
131E137ALA00.0090.01440.7900.0310.0310.0000.0000.0000.000
132E138LEU0-0.001-0.00439.331-0.176-0.1760.0000.0000.0000.000
133E139GLY00.026-0.01038.0540.2360.2360.0000.0000.0000.000
134E140CYS0-0.114-0.08436.394-0.217-0.2170.0000.0000.0000.000
135E141LEU00.0120.01437.1140.1970.1970.0000.0000.0000.000
136E142VAL0-0.024-0.01333.179-0.091-0.0910.0000.0000.0000.000
137E143LYS10.9140.95136.086-7.570-7.5700.0000.0000.0000.000
138E144ASP-1-0.855-0.93138.2187.7977.7970.0000.0000.0000.000
139E145TYR00.0560.01230.5440.0410.0410.0000.0000.0000.000
140E146PHE00.0890.02533.3490.0180.0180.0000.0000.0000.000
141E147PRO0-0.004-0.00528.5480.1400.1400.0000.0000.0000.000
142E148GLU-1-0.896-0.97528.08811.47611.4760.0000.0000.0000.000
143E149PRO0-0.0010.06324.0680.2720.2720.0000.0000.0000.000
144E150VAL00.030-0.01226.108-0.245-0.2450.0000.0000.0000.000
145E151THR0-0.061-0.03724.5510.3590.3590.0000.0000.0000.000
146E152VAL00.0260.01226.690-0.338-0.3380.0000.0000.0000.000
147E153SER00.0150.02226.8220.1500.1500.0000.0000.0000.000
148E154TRP00.0650.02628.799-0.461-0.4610.0000.0000.0000.000
149E155ASN0-0.015-0.01030.7490.0850.0850.0000.0000.0000.000
150E156SER00.004-0.01729.1200.1230.1230.0000.0000.0000.000
151E157GLY0-0.0210.00026.2860.3600.3600.0000.0000.0000.000
152E158ALA00.0000.00926.7240.2730.2730.0000.0000.0000.000
153E159LEU0-0.041-0.01529.397-0.057-0.0570.0000.0000.0000.000
154E160THR00.028-0.00525.934-0.016-0.0160.0000.0000.0000.000
155E161SER00.0200.00029.1450.0180.0180.0000.0000.0000.000
156E162GLY00.0370.01631.454-0.295-0.2950.0000.0000.0000.000
157E163VAL0-0.067-0.01929.160-0.203-0.2030.0000.0000.0000.000
158E164HIS00.0130.01330.4760.4260.4260.0000.0000.0000.000
159E165THR0-0.029-0.03228.363-0.434-0.4340.0000.0000.0000.000
160E166PHE0-0.0090.00029.4580.2950.2950.0000.0000.0000.000
161E167PRO00.0330.00529.2640.1250.1250.0000.0000.0000.000
162E168ALA00.0170.01929.781-0.397-0.3970.0000.0000.0000.000
163E169VAL00.0020.01031.6520.0190.0190.0000.0000.0000.000
164E170LEU0-0.040-0.01534.453-0.065-0.0650.0000.0000.0000.000
165E171GLN0-0.025-0.01436.038-0.352-0.3520.0000.0000.0000.000
166E172SER00.0400.00539.6680.0800.0800.0000.0000.0000.000
167E173SER0-0.032-0.01741.4940.0050.0050.0000.0000.0000.000
168E174GLY00.0300.03038.408-0.019-0.0190.0000.0000.0000.000
169E175LEU0-0.056-0.01936.5020.2750.2750.0000.0000.0000.000
170E176TYR00.0600.01731.413-0.145-0.1450.0000.0000.0000.000
171E177SER0-0.049-0.03035.053-0.252-0.2520.0000.0000.0000.000
172E178LEU00.0040.00930.0150.1320.1320.0000.0000.0000.000
173E179SER00.0150.00534.686-0.243-0.2430.0000.0000.0000.000
174E180SER0-0.067-0.00231.8310.0640.0640.0000.0000.0000.000
175E181VAL00.0730.01934.341-0.274-0.2740.0000.0000.0000.000
176E182VAL00.0100.01933.9290.1800.1800.0000.0000.0000.000
177E194TYR00.004-0.00937.412-0.030-0.0300.0000.0000.0000.000
178E195ILE00.0220.01436.407-0.157-0.1570.0000.0000.0000.000
179E196CYS0-0.0250.04333.7620.2680.2680.0000.0000.0000.000
180E197ASN00.016-0.00330.356-0.068-0.0680.0000.0000.0000.000
181E198VAL00.0180.00930.0970.4130.4130.0000.0000.0000.000
182E199ASN00.001-0.01425.503-0.373-0.3730.0000.0000.0000.000
183E200HIS00.0390.02028.2470.1660.1660.0000.0000.0000.000
184E201LYS10.9670.96523.923-13.058-13.0580.0000.0000.0000.000
185E202PRO0-0.0140.01126.274-0.100-0.1000.0000.0000.0000.000
186E203SER00.0060.00928.451-0.211-0.2110.0000.0000.0000.000
187E204ASN0-0.088-0.03230.201-0.013-0.0130.0000.0000.0000.000
188E205THR00.0280.00830.905-0.357-0.3570.0000.0000.0000.000
189E206LYS10.9140.94629.287-9.951-9.9510.0000.0000.0000.000
190E207VAL0-0.0200.01032.503-0.242-0.2420.0000.0000.0000.000
191E208ASP-1-0.857-0.93434.3419.6039.6030.0000.0000.0000.000
192E209LYS10.8880.95136.512-7.878-7.8780.0000.0000.0000.000
193E210LYS10.9470.96739.007-7.080-7.0800.0000.0000.0000.000
194E211VAL0-0.022-0.01039.830-0.148-0.1480.0000.0000.0000.000
195E212GLU-1-0.921-0.96242.4426.8336.8330.0000.0000.0000.000
196E213PRO0-0.0040.01045.903-0.085-0.0850.0000.0000.0000.000