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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: 2J5JR

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 OptHSide
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 -1899226.810993
FMO2-HF: Nuclear repulsion 1825110.66587
FMO2-HF: Total energy -74116.145122
FMO2-MP2: Total energy -74333.038976


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.
-64.112-6414.684-7.711-7.0840.07
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 : -0.912 / q_NPA : -0.952
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].
3E3GLN0-0.071-0.0521.748-30.410-30.53114.685-7.591-6.9730.070
4E4LEU0-0.029-0.0204.811-5.897-5.866-0.001-0.009-0.0210.000
5E5VAL00.0150.0088.4070.6240.6240.0000.0000.0000.000
6E6GLU-1-0.792-0.88910.83720.72220.7220.0000.0000.0000.000
7E7SER0-0.013-0.01914.517-0.176-0.1760.0000.0000.0000.000
8E8GLY00.0230.01217.328-0.478-0.4780.0000.0000.0000.000
9E9GLY00.0160.01620.707-0.514-0.5140.0000.0000.0000.000
10E10GLY00.017-0.00822.224-0.004-0.0040.0000.0000.0000.000
11E11LEU0-0.057-0.01725.518-0.031-0.0310.0000.0000.0000.000
12E12VAL0-0.013-0.00628.711-0.095-0.0950.0000.0000.0000.000
13E13GLN00.0340.02631.431-0.029-0.0290.0000.0000.0000.000
14E14PRO00.009-0.00534.7680.1100.1100.0000.0000.0000.000
15E15GLY0-0.0150.00335.569-0.240-0.2400.0000.0000.0000.000
16E16GLY0-0.024-0.00534.147-0.024-0.0240.0000.0000.0000.000
17E17SER0-0.048-0.04530.6690.0590.0590.0000.0000.0000.000
18E18LEU00.0040.00724.132-0.041-0.0410.0000.0000.0000.000
19E19ARG10.8950.96322.928-12.933-12.9330.0000.0000.0000.000
20E20LEU0-0.0140.02319.5300.2730.2730.0000.0000.0000.000
21E21SER0-0.030-0.03817.901-0.483-0.4830.0000.0000.0000.000
22E22CYS0-0.065-0.02213.0990.3440.3440.0000.0000.0000.000
23E23ALA00.0050.02312.152-0.418-0.4180.0000.0000.0000.000
24E24ALA00.0380.0169.3162.0522.0520.0000.0000.0000.000
25E25SER0-0.0120.0055.730-2.966-2.9660.0000.0000.0000.000
26E26GLY00.1050.0523.7743.0593.1290.001-0.0980.0270.000
27E27PHE0-0.044-0.0324.406-0.223-0.091-0.001-0.013-0.1170.000
28E28SER00.0450.0287.559-0.803-0.8030.0000.0000.0000.000
29E29LEU00.0530.02011.163-0.353-0.3530.0000.0000.0000.000
30E30THR0-0.014-0.01013.748-0.553-0.5530.0000.0000.0000.000
31E31VAL0-0.0330.00512.815-0.680-0.6800.0000.0000.0000.000
32E32TYR0-0.013-0.00510.0500.3990.3990.0000.0000.0000.000
33E33SER00.0090.01613.958-0.613-0.6130.0000.0000.0000.000
34E34VAL0-0.018-0.00813.2371.0421.0420.0000.0000.0000.000
35E35HIS0-0.036-0.02415.752-1.581-1.5810.0000.0000.0000.000
36E36TRP00.013-0.00116.6251.0651.0650.0000.0000.0000.000
37E37VAL0-0.023-0.01018.356-0.903-0.9030.0000.0000.0000.000
38E38ARG10.7890.87019.402-10.741-10.7410.0000.0000.0000.000
39E39GLN00.009-0.00520.760-0.651-0.6510.0000.0000.0000.000
40E40ALA00.0620.04123.3180.1580.1580.0000.0000.0000.000
41E41PRO00.024-0.00725.8660.1710.1710.0000.0000.0000.000
42E42GLY0-0.0150.00026.871-0.245-0.2450.0000.0000.0000.000
43E43LYS10.8560.91824.943-11.998-11.9980.0000.0000.0000.000
44E44GLY00.0560.03725.955-0.184-0.1840.0000.0000.0000.000
45E45LEU0-0.035-0.01320.3170.0700.0700.0000.0000.0000.000
46E46GLU-1-0.800-0.87323.71610.61110.6110.0000.0000.0000.000
47E47TRP0-0.0050.00421.1190.2260.2260.0000.0000.0000.000
48E48VAL0-0.009-0.01622.637-0.629-0.6290.0000.0000.0000.000
49E49GLY0-0.003-0.00822.782-0.550-0.5500.0000.0000.0000.000
50E50ALA00.0320.02320.4860.5860.5860.0000.0000.0000.000
51E51LEU0-0.021-0.01718.282-0.603-0.6030.0000.0000.0000.000
52E52TRP00.0420.01418.9641.0631.0630.0000.0000.0000.000
53E53GLY00.003-0.00317.989-0.022-0.0220.0000.0000.0000.000
54E54SER0-0.0130.00418.735-0.036-0.0360.0000.0000.0000.000
55E55GLY00.023-0.00321.920-0.217-0.2170.0000.0000.0000.000
56E56GLY0-0.0250.00122.812-0.221-0.2210.0000.0000.0000.000
57E57THR0-0.048-0.04623.8320.4430.4430.0000.0000.0000.000
58E58GLU-1-0.890-0.92324.96310.22310.2230.0000.0000.0000.000
59E59TYR0-0.032-0.03925.4220.5230.5230.0000.0000.0000.000
60E60ASN00.0050.00727.150-0.621-0.6210.0000.0000.0000.000
61E61SER00.018-0.01228.845-0.076-0.0760.0000.0000.0000.000
62E62ASN0-0.0080.00531.740-0.423-0.4230.0000.0000.0000.000
63E63LEU0-0.032-0.00727.796-0.292-0.2920.0000.0000.0000.000
64E64LYS10.9650.95431.521-8.527-8.5270.0000.0000.0000.000
65E65SER0-0.030-0.00331.475-0.278-0.2780.0000.0000.0000.000
66E66ARG10.7870.88431.284-9.780-9.7800.0000.0000.0000.000
67E67PHE00.002-0.00625.7110.1150.1150.0000.0000.0000.000
68E68THR00.0070.00827.006-0.223-0.2230.0000.0000.0000.000
69E69ILE0-0.0400.00521.5400.2250.2250.0000.0000.0000.000
70E70SER00.0270.02223.116-0.019-0.0190.0000.0000.0000.000
71E71ARG10.8990.92717.329-14.580-14.5800.0000.0000.0000.000
72E72ASP-1-0.771-0.88218.93614.10014.1000.0000.0000.0000.000
73E73THR00.0550.00916.2090.6470.6470.0000.0000.0000.000
74E74SER0-0.047-0.00516.1710.3610.3610.0000.0000.0000.000
75E75LYS10.8720.91916.400-14.288-14.2880.0000.0000.0000.000
76E76ASN0-0.027-0.01710.496-0.275-0.2750.0000.0000.0000.000
77E77THR0-0.0180.00113.5571.5371.5370.0000.0000.0000.000
78E78VAL0-0.016-0.00515.556-1.168-1.1680.0000.0000.0000.000
79E79TYR0-0.049-0.02817.3780.4680.4680.0000.0000.0000.000
80E80LEU00.0160.00920.322-0.179-0.1790.0000.0000.0000.000
81E81GLN0-0.042-0.04422.5640.0880.0880.0000.0000.0000.000
82E82MET0-0.0020.02324.879-0.103-0.1030.0000.0000.0000.000
83E82ASN00.0290.00427.9050.0490.0490.0000.0000.0000.000
84E82SER00.0170.00231.674-0.119-0.1190.0000.0000.0000.000
85E82LEU0-0.0130.01328.798-0.061-0.0610.0000.0000.0000.000
86E83ARG10.9420.97232.814-8.882-8.8820.0000.0000.0000.000
87E84ALA00.0560.02532.9600.2620.2620.0000.0000.0000.000
88E85GLU-1-0.839-0.94832.7199.1949.1940.0000.0000.0000.000
89E86ASP-1-0.788-0.83928.93610.48110.4810.0000.0000.0000.000
90E87THR00.0010.02127.6890.5340.5340.0000.0000.0000.000
91E88ALA0-0.007-0.00124.755-0.120-0.1200.0000.0000.0000.000
92E89VAL0-0.0040.00818.9730.1060.1060.0000.0000.0000.000
93E90TYR0-0.032-0.04920.010-0.184-0.1840.0000.0000.0000.000
94E91TYR00.0120.00014.7350.0720.0720.0000.0000.0000.000
95E93ALA00.0340.00612.5371.3221.3220.0000.0000.0000.000
96E94ARG10.8500.9297.616-27.456-27.4560.0000.0000.0000.000
97E95ASP-1-0.778-0.87912.47015.83715.8370.0000.0000.0000.000
98E96GLN0-0.037-0.02812.723-0.129-0.1290.0000.0000.0000.000
99E97GLY0-0.045-0.02313.4950.5020.5020.0000.0000.0000.000
100E98LEU0-0.0150.00315.547-0.606-0.6060.0000.0000.0000.000
101E99ASN00.000-0.02117.7870.1160.1160.0000.0000.0000.000
102E100TYR0-0.045-0.01319.575-0.333-0.3330.0000.0000.0000.000
103E100GLY00.0400.02420.665-0.596-0.5960.0000.0000.0000.000
104E100SER0-0.043-0.03618.8880.3270.3270.0000.0000.0000.000
105E100LEU0-0.0240.00216.814-0.300-0.3000.0000.0000.0000.000
106E100PHE00.007-0.02214.5730.4740.4740.0000.0000.0000.000
107E101ASP-1-0.770-0.8529.48622.94822.9480.0000.0000.0000.000
108E102TYR0-0.022-0.0134.9540.9220.9220.0000.0000.0000.000
109E103TRP0-0.005-0.0239.315-2.975-2.9750.0000.0000.0000.000
110E104GLY00.0590.0429.1693.1673.1670.0000.0000.0000.000
111E105GLN0-0.019-0.02010.4480.4670.4670.0000.0000.0000.000
112E106GLY0-0.024-0.00212.397-1.541-1.5410.0000.0000.0000.000
113E107THR0-0.066-0.03415.841-0.124-0.1240.0000.0000.0000.000
114E108LEU00.0130.00318.410-0.474-0.4740.0000.0000.0000.000
115E109VAL0-0.0070.00021.987-0.133-0.1330.0000.0000.0000.000
116E110THR0-0.028-0.02024.971-0.267-0.2670.0000.0000.0000.000
117E111VAL00.000-0.00228.445-0.074-0.0740.0000.0000.0000.000
118E112SER0-0.007-0.01331.728-0.324-0.3240.0000.0000.0000.000
119E113SER00.0120.00835.027-0.091-0.0910.0000.0000.0000.000
120E114ALA00.0220.00736.839-0.050-0.0500.0000.0000.0000.000
121E115SER00.032-0.01632.4530.1900.1900.0000.0000.0000.000
122E116THR0-0.0170.01234.6670.0440.0440.0000.0000.0000.000
123E117LYS10.9120.95136.762-8.244-8.2440.0000.0000.0000.000
124E118GLY00.0230.05233.9020.0780.0780.0000.0000.0000.000
125E119PRO0-0.037-0.02232.871-0.245-0.2450.0000.0000.0000.000
126E120SER0-0.062-0.03835.858-0.123-0.1230.0000.0000.0000.000
127E121VAL00.0130.00735.7610.0550.0550.0000.0000.0000.000
128E122PHE0-0.005-0.00738.663-0.173-0.1730.0000.0000.0000.000
129E123PRO00.0440.01840.7760.1790.1790.0000.0000.0000.000
130E124LEU0-0.0020.01340.091-0.092-0.0920.0000.0000.0000.000
131E137ALA00.0030.01041.0750.0260.0260.0000.0000.0000.000
132E138LEU0-0.007-0.00639.414-0.177-0.1770.0000.0000.0000.000
133E139GLY00.037-0.00138.1830.2340.2340.0000.0000.0000.000
134E140CYS0-0.118-0.05736.355-0.201-0.2010.0000.0000.0000.000
135E141LEU00.0210.01737.1020.2030.2030.0000.0000.0000.000
136E142VAL0-0.024-0.01432.857-0.094-0.0940.0000.0000.0000.000
137E143LYS10.8790.91835.891-7.572-7.5720.0000.0000.0000.000
138E144ASP-1-0.807-0.88337.9027.8527.8520.0000.0000.0000.000
139E145TYR0-0.005-0.03630.037-0.196-0.1960.0000.0000.0000.000
140E146PHE00.0850.02232.6610.0100.0100.0000.0000.0000.000
141E147PRO00.006-0.00127.9220.1470.1470.0000.0000.0000.000
142E148GLU-1-0.821-0.91027.94011.40511.4050.0000.0000.0000.000
143E149PRO0-0.0130.04523.6200.2920.2920.0000.0000.0000.000
144E150VAL00.017-0.00725.766-0.231-0.2310.0000.0000.0000.000
145E151THR0-0.047-0.02124.0110.1590.1590.0000.0000.0000.000
146E152VAL00.0280.01426.511-0.340-0.3400.0000.0000.0000.000
147E153SER00.0110.01926.7710.1500.1500.0000.0000.0000.000
148E154TRP00.0600.02528.811-0.465-0.4650.0000.0000.0000.000
149E155ASN0-0.009-0.00930.8710.1290.1290.0000.0000.0000.000
150E156SER0-0.005-0.00929.1130.0170.0170.0000.0000.0000.000
151E157GLY0-0.0130.00626.3710.3670.3670.0000.0000.0000.000
152E158ALA0-0.0030.00726.9130.2670.2670.0000.0000.0000.000
153E159LEU0-0.045-0.01629.615-0.069-0.0690.0000.0000.0000.000
154E160THR00.035-0.00426.243-0.018-0.0180.0000.0000.0000.000
155E161SER00.0220.00029.4820.1300.1300.0000.0000.0000.000
156E162GLY00.0360.01731.897-0.298-0.2980.0000.0000.0000.000
157E163VAL0-0.070-0.02129.648-0.202-0.2020.0000.0000.0000.000
158E164HIS00.0080.01130.8040.4120.4120.0000.0000.0000.000
159E165THR0-0.017-0.02228.492-0.443-0.4430.0000.0000.0000.000
160E166PHE00.0020.00829.5840.2870.2870.0000.0000.0000.000
161E167PRO00.0380.00829.3400.1400.1400.0000.0000.0000.000
162E168ALA00.0180.02129.700-0.383-0.3830.0000.0000.0000.000
163E169VAL00.0000.00531.5330.0290.0290.0000.0000.0000.000
164E170LEU0-0.048-0.01834.171-0.048-0.0480.0000.0000.0000.000
165E171GLN0-0.041-0.03435.795-0.398-0.3980.0000.0000.0000.000
166E172SER00.0570.01039.4080.0150.0150.0000.0000.0000.000
167E173SER0-0.058-0.02940.880-0.056-0.0560.0000.0000.0000.000
168E174GLY00.0240.02738.008-0.013-0.0130.0000.0000.0000.000
169E175LEU0-0.053-0.01336.1090.2690.2690.0000.0000.0000.000
170E176TYR00.0580.01430.956-0.139-0.1390.0000.0000.0000.000
171E177SER0-0.032-0.02834.805-0.276-0.2760.0000.0000.0000.000
172E178LEU00.0150.01530.1400.1090.1090.0000.0000.0000.000
173E179SER00.0020.00234.592-0.277-0.2770.0000.0000.0000.000
174E180SER0-0.070-0.01631.8130.0500.0500.0000.0000.0000.000
175E181VAL00.0620.01334.413-0.272-0.2720.0000.0000.0000.000
176E182VAL00.0150.02134.0120.1890.1890.0000.0000.0000.000
177E194TYR0-0.006-0.01037.341-0.041-0.0410.0000.0000.0000.000
178E195ILE00.0330.01336.166-0.152-0.1520.0000.0000.0000.000
179E196CYS0-0.0050.01733.7490.2010.2010.0000.0000.0000.000
180E197ASN0-0.017-0.01630.1840.0750.0750.0000.0000.0000.000
181E198VAL00.0130.01029.9350.3980.3980.0000.0000.0000.000
182E199ASN00.012-0.02024.942-0.264-0.2640.0000.0000.0000.000
183E200HIS00.0130.00927.9250.1640.1640.0000.0000.0000.000
184E201LYS10.9690.97223.410-13.237-13.2370.0000.0000.0000.000
185E202PRO00.0000.01725.798-0.096-0.0960.0000.0000.0000.000
186E203SER0-0.021-0.01027.833-0.305-0.3050.0000.0000.0000.000
187E204ASN0-0.082-0.02629.594-0.006-0.0060.0000.0000.0000.000
188E205THR00.0100.00530.377-0.385-0.3850.0000.0000.0000.000
189E206LYS10.8730.89929.524-9.825-9.8250.0000.0000.0000.000
190E207VAL0-0.0300.00732.132-0.256-0.2560.0000.0000.0000.000
191E208ASP-1-0.807-0.89533.8659.7529.7520.0000.0000.0000.000
192E209LYS10.8960.95236.315-7.920-7.9200.0000.0000.0000.000
193E210LYS10.9070.93438.934-7.093-7.0930.0000.0000.0000.000
194E211VAL0-0.025-0.00839.725-0.153-0.1530.0000.0000.0000.000
195E212GLU-1-0.852-0.90842.4516.8976.8970.0000.0000.0000.000
196E213PRO0-0.023-0.00845.952-0.183-0.1830.0000.0000.0000.000