FMODB

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

Last updated: 2024-04-25

All entries: 37426

Number of unique PDB entries: 7782

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FMODB ID: N1G7Q

Calculation Name: 4LJL-B-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 4LJL

Chain ID: B

ChEMBL ID:

UniProt ID: O25100

Base Structure: X-ray

Registration Date: 2023-06-19

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 219
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2693035.265621
FMO2-HF: Nuclear repulsion 2607903.958912
FMO2-HF: Total energy -85131.306709
FMO2-MP2: Total energy -85380.688068


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(B:5:MET)


Summations of interaction energy for fragment #1(B:5:MET)
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.
-15.562-6.4219.78-5.964-12.959-0.006
Interaction energy analysis for fragmet #1(B:5:MET)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.012 / q_NPA : -0.008
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].
3B7SER0-0.036-0.0532.864-4.045-1.3940.384-1.428-1.607-0.005
4B8HIS0-0.037-0.0254.6100.6400.839-0.001-0.010-0.1880.000
5B9PHE00.0090.0017.5230.2210.2210.0000.0000.0000.000
6B10GLN00.0150.0269.668-0.009-0.0090.0000.0000.0000.000
7B11TYR0-0.078-0.06311.0420.0200.0200.0000.0000.0000.000
8B12SER00.0380.01514.8140.0090.0090.0000.0000.0000.000
9B13THR0-0.036-0.02517.961-0.005-0.0050.0000.0000.0000.000
10B14LEU0-0.033-0.03520.4990.0020.0020.0000.0000.0000.000
11B15GLU-1-0.952-0.96522.073-0.048-0.0480.0000.0000.0000.000
12B16ASN00.006-0.00325.7590.0080.0080.0000.0000.0000.000
13B17ILE0-0.010-0.00624.098-0.002-0.0020.0000.0000.0000.000
14B18PRO00.0290.01224.4900.0040.0040.0000.0000.0000.000
15B19LYS11.0791.03227.6000.0050.0050.0000.0000.0000.000
16B20ALA0-0.045-0.00227.9080.0020.0020.0000.0000.0000.000
17B21PHE0-0.011-0.02822.4000.0030.0030.0000.0000.0000.000
18B22ASP-1-0.857-0.93527.910-0.003-0.0030.0000.0000.0000.000
19B23ILE0-0.056-0.01729.8570.0020.0020.0000.0000.0000.000
20B24LEU0-0.095-0.03725.1400.0030.0030.0000.0000.0000.000
21B25LYS10.8510.90729.310-0.024-0.0240.0000.0000.0000.000
22B26ASP-1-0.872-0.92626.2000.0200.0200.0000.0000.0000.000
23B27PRO00.0560.05125.6890.0000.0000.0000.0000.0000.000
24B28PRO0-0.002-0.00121.8640.0010.0010.0000.0000.0000.000
25B29LYS10.9210.95123.639-0.002-0.0020.0000.0000.0000.000
26B30LYS10.8990.96020.2990.0640.0640.0000.0000.0000.000
27B31LEU0-0.0060.00619.3170.0000.0000.0000.0000.0000.000
28B32TYR00.0280.02815.7070.0020.0020.0000.0000.0000.000
29B33CYS0-0.011-0.01316.2520.0110.0110.0000.0000.0000.000
30B34VAL00.0420.01711.482-0.029-0.0290.0000.0000.0000.000
31B35GLY00.0630.04014.9740.0260.0260.0000.0000.0000.000
32B36ASP-1-0.803-0.89716.923-0.046-0.0460.0000.0000.0000.000
33B37THR00.035-0.00720.4840.0090.0090.0000.0000.0000.000
34B38LYS10.8940.93122.2750.0490.0490.0000.0000.0000.000
35B39LEU0-0.039-0.00320.1590.0070.0070.0000.0000.0000.000
36B40LEU0-0.006-0.00721.8370.0080.0080.0000.0000.0000.000
37B41ASP-1-0.901-0.94125.176-0.020-0.0200.0000.0000.0000.000
38B42THR0-0.114-0.06026.2520.0030.0030.0000.0000.0000.000
39B43PRO00.0220.01929.0690.0010.0010.0000.0000.0000.000
40B44LEU00.0320.02329.7890.0020.0020.0000.0000.0000.000
41B45LYS10.8180.91525.2630.0000.0000.0000.0000.0000.000
42B46VAL00.0360.00625.8470.0000.0000.0000.0000.0000.000
43B47ALA0-0.0010.01323.1960.0060.0060.0000.0000.0000.000
44B48ILE0-0.012-0.00121.787-0.001-0.0010.0000.0000.0000.000
45B49ILE00.0060.01619.5390.0150.0150.0000.0000.0000.000
46B50GLY00.023-0.01220.061-0.012-0.0120.0000.0000.0000.000
47B51THR0-0.0160.00919.6030.0220.0220.0000.0000.0000.000
48B52ARG10.9650.97013.621-0.208-0.2080.0000.0000.0000.000
49B53ARG10.9060.94217.166-0.109-0.1090.0000.0000.0000.000
50B54PRO00.0090.03318.730-0.012-0.0120.0000.0000.0000.000
51B55THR00.0530.03021.8260.0020.0020.0000.0000.0000.000
52B56PRO00.046-0.00123.8020.0040.0040.0000.0000.0000.000
53B57TYR0-0.014-0.00624.786-0.001-0.0010.0000.0000.0000.000
54B58SER00.0600.00224.553-0.004-0.0040.0000.0000.0000.000
55B59LYS10.9170.98617.470-0.131-0.1310.0000.0000.0000.000
56B60GLN00.0210.00922.9360.0030.0030.0000.0000.0000.000
57B61HIS00.0290.00825.513-0.003-0.0030.0000.0000.0000.000
58B62THR0-0.037-0.03021.259-0.002-0.0020.0000.0000.0000.000
59B63ILE0-0.025-0.00920.7820.0010.0010.0000.0000.0000.000
60B64THR0-0.035-0.00923.515-0.005-0.0050.0000.0000.0000.000
61B65LEU00.0040.00026.265-0.005-0.0050.0000.0000.0000.000
62B66ALA00.0110.01222.015-0.005-0.0050.0000.0000.0000.000
63B67ARG10.8970.92924.130-0.043-0.0430.0000.0000.0000.000
64B68GLU-1-0.808-0.88025.0460.0200.0200.0000.0000.0000.000
65B69LEU0-0.008-0.00826.810-0.005-0.0050.0000.0000.0000.000
66B70ALA00.0010.01723.892-0.005-0.0050.0000.0000.0000.000
67B71LYS10.7700.88325.897-0.025-0.0250.0000.0000.0000.000
68B72ASN0-0.032-0.02628.246-0.004-0.0040.0000.0000.0000.000
69B73GLY00.0240.01829.394-0.001-0.0010.0000.0000.0000.000
70B74ALA0-0.0200.00827.687-0.002-0.0020.0000.0000.0000.000
71B75VAL0-0.023-0.01722.5460.0010.0010.0000.0000.0000.000
72B76ILE0-0.0120.00320.1420.0010.0010.0000.0000.0000.000
73B77VAL00.0050.01820.3470.0040.0040.0000.0000.0000.000
74B78SER0-0.009-0.03217.2200.0150.0150.0000.0000.0000.000
75B79GLY00.0350.02715.302-0.022-0.0220.0000.0000.0000.000
76B80GLY00.0850.05512.1360.0000.0000.0000.0000.0000.000
77B81ALA0-0.044-0.02111.2380.1480.1480.0000.0000.0000.000
78B82LEU00.005-0.0159.9260.0010.0010.0000.0000.0000.000
79B83GLY00.0040.01113.166-0.055-0.0550.0000.0000.0000.000
80B84VAL00.0220.00116.5300.0090.0090.0000.0000.0000.000
81B85ASP-1-0.824-0.91115.5050.1590.1590.0000.0000.0000.000
82B86ILE0-0.035-0.01910.912-0.015-0.0150.0000.0000.0000.000
83B87ILE0-0.0060.00314.333-0.019-0.0190.0000.0000.0000.000
84B88ALA00.0300.01217.261-0.021-0.0210.0000.0000.0000.000
85B89GLN0-0.010-0.04015.1290.0120.0120.0000.0000.0000.000
86B90GLU-1-0.928-0.96914.4190.1790.1790.0000.0000.0000.000
87B91ASN0-0.077-0.05916.242-0.041-0.0410.0000.0000.0000.000
88B92ALA00.0110.01319.371-0.017-0.0170.0000.0000.0000.000
89B93LEU0-0.0440.03214.654-0.018-0.0180.0000.0000.0000.000
90B94PRO00.009-0.02018.978-0.006-0.0060.0000.0000.0000.000
91B95LYS10.9530.97320.062-0.005-0.0050.0000.0000.0000.000
92B96THR0-0.008-0.02316.8830.0170.0170.0000.0000.0000.000
93B97ILE00.0230.00917.986-0.009-0.0090.0000.0000.0000.000
94B98MET0-0.052-0.0129.6440.0290.0290.0000.0000.0000.000
95B99LEU00.008-0.00115.655-0.038-0.0380.0000.0000.0000.000
96B100SER00.0370.00310.3500.0530.0530.0000.0000.0000.000
97B101PRO0-0.049-0.0199.9490.0020.0020.0000.0000.0000.000
98B102CYS0-0.018-0.0027.5110.0250.0250.0000.0000.0000.000
99B103SER00.0150.0159.0580.0750.0750.0000.0000.0000.000
100B104LEU00.0330.0178.399-0.221-0.2210.0000.0000.0000.000
101B105ASP-1-0.722-0.7798.305-0.621-0.6210.0000.0000.0000.000
102B106PHE0-0.033-0.0143.662-0.848-0.2260.004-0.160-0.4660.000
103B107ILE0-0.0170.0062.487-0.9751.3732.117-1.080-3.386-0.001
104B108TYR0-0.0290.0033.236-1.603-0.3980.068-0.658-0.615-0.005
105B109PRO0-0.003-0.0175.797-0.101-0.1010.0000.0000.0000.000
106B110THR00.0980.0162.430-3.300-2.5733.668-1.253-3.1410.010
107B111ASN0-0.010-0.0193.904-0.3080.3100.0970.033-0.748-0.003
108B112ASN0-0.0130.0005.981-0.449-0.4490.0000.0000.0000.000
109B113HIS0-0.014-0.0132.798-2.967-2.4883.444-1.331-2.593-0.002
110B114LYS10.9380.9834.869-0.667-0.5680.001-0.061-0.0390.000
111B115VAL00.1200.0587.736-0.116-0.1160.0000.0000.0000.000
112B116ILE0-0.004-0.0126.793-0.147-0.1470.0000.0000.0000.000
113B117GLN0-0.023-0.0225.7640.2090.298-0.001-0.002-0.0870.000
114B118GLU-1-0.901-0.9409.2560.0000.0000.0000.0000.0000.000
115B119ILE0-0.021-0.01612.052-0.059-0.0590.0000.0000.0000.000
116B120ALA0-0.036-0.00810.458-0.049-0.0490.0000.0000.0000.000
117B121GLN0-0.057-0.02211.962-0.013-0.0130.0000.0000.0000.000
118B122ASN0-0.039-0.03014.778-0.025-0.0250.0000.0000.0000.000
119B123GLY00.0220.02816.2150.0050.0050.0000.0000.0000.000
120B124LEU0-0.036-0.00516.647-0.024-0.0240.0000.0000.0000.000
121B125ILE0-0.0240.00010.5770.0260.0260.0000.0000.0000.000
122B126LEU00.0120.00614.544-0.031-0.0310.0000.0000.0000.000
123B127SER00.007-0.03412.3330.0230.0230.0000.0000.0000.000
124B128GLU-1-0.767-0.84715.230-0.006-0.0060.0000.0000.0000.000
125B129TYR0-0.049-0.03012.6040.0320.0320.0000.0000.0000.000
126B130GLU-1-0.830-0.91713.534-0.116-0.1160.0000.0000.0000.000
127B131LYS10.8780.92911.289-0.013-0.0130.0000.0000.0000.000
128B132ASP-1-0.903-0.9609.1580.1740.1740.0000.0000.0000.000
129B133PHE0-0.061-0.0269.7280.1230.1230.0000.0000.0000.000
130B134MET00.0310.0064.141-0.199-0.095-0.001-0.014-0.0890.000
131B135PRO0-0.030-0.0037.0430.0180.0180.0000.0000.0000.000
132B136ILE00.0550.02010.0060.0620.0620.0000.0000.0000.000
133B137LYS10.9620.97613.274-0.106-0.1060.0000.0000.0000.000
134B138GLY00.019-0.00716.503-0.006-0.0060.0000.0000.0000.000
135B139SER00.0430.02312.3510.0090.0090.0000.0000.0000.000
136B140PHE0-0.015-0.01110.773-0.011-0.0110.0000.0000.0000.000
137B141LEU0-0.051-0.02615.5880.0000.0000.0000.0000.0000.000
138B142ALA00.0320.02117.982-0.002-0.0020.0000.0000.0000.000
139B143ARG10.8810.92813.306-0.101-0.1010.0000.0000.0000.000
140B144ASN0-0.0010.00217.9000.0060.0060.0000.0000.0000.000
141B145ARG10.7420.83120.164-0.005-0.0050.0000.0000.0000.000
142B146LEU0-0.0210.00018.630-0.002-0.0020.0000.0000.0000.000
143B147VAL00.0280.01518.717-0.002-0.0020.0000.0000.0000.000
144B148ILE0-0.035-0.01221.490-0.001-0.0010.0000.0000.0000.000
145B149ALA00.0030.00025.022-0.002-0.0020.0000.0000.0000.000
146B150LEU0-0.0130.00322.066-0.003-0.0030.0000.0000.0000.000
147B151SER0-0.012-0.01324.2730.0000.0000.0000.0000.0000.000
148B152ASP-1-0.832-0.89526.7900.0130.0130.0000.0000.0000.000
149B153VAL0-0.001-0.00629.2220.0000.0000.0000.0000.0000.000
150B154VAL0-0.028-0.01425.5910.0040.0040.0000.0000.0000.000
151B155ILE00.0090.00726.287-0.002-0.0020.0000.0000.0000.000
152B156ILE0-0.038-0.03224.6220.0080.0080.0000.0000.0000.000
153B157PRO00.0050.00523.828-0.004-0.0040.0000.0000.0000.000
154B158GLN00.0820.05024.6410.0000.0000.0000.0000.0000.000
155B159ALA0-0.029-0.02624.3870.0100.0100.0000.0000.0000.000
156B160ASP-1-0.857-0.90624.1160.0890.0890.0000.0000.0000.000
157B161LEU00.0850.04326.6580.0010.0010.0000.0000.0000.000
158B162LYS10.8990.94326.815-0.064-0.0640.0000.0000.0000.000
159B163SER00.0430.02122.5530.0060.0060.0000.0000.0000.000
160B164GLY00.026-0.00420.516-0.006-0.0060.0000.0000.0000.000
161B165SER00.0710.03921.590-0.005-0.0050.0000.0000.0000.000
162B166MET00.0370.05523.385-0.006-0.0060.0000.0000.0000.000
163B167SER0-0.094-0.04723.310-0.004-0.0040.0000.0000.0000.000
164B168SER0-0.009-0.02922.546-0.006-0.0060.0000.0000.0000.000
165B169ALA00.0650.03824.977-0.005-0.0050.0000.0000.0000.000
166B170ARG10.9610.97827.353-0.056-0.0560.0000.0000.0000.000
167B171LEU0-0.046-0.01524.693-0.004-0.0040.0000.0000.0000.000
168B172ALA00.0500.02028.304-0.004-0.0040.0000.0000.0000.000
169B173GLN0-0.0100.00229.781-0.005-0.0050.0000.0000.0000.000
170B174LYS10.8730.94530.470-0.028-0.0280.0000.0000.0000.000
171B175TYR0-0.014-0.02527.884-0.002-0.0020.0000.0000.0000.000
172B176GLN0-0.018-0.00132.657-0.003-0.0030.0000.0000.0000.000
173B177LYS10.8320.91729.028-0.020-0.0200.0000.0000.0000.000
174B178PRO00.0170.01032.2290.0030.0030.0000.0000.0000.000
175B179LEU00.0010.00828.8270.0030.0030.0000.0000.0000.000
176B180PHE00.008-0.00230.556-0.002-0.0020.0000.0000.0000.000
177B181VAL00.0000.00129.5920.0060.0060.0000.0000.0000.000
178B182LEU0-0.0020.00927.630-0.003-0.0030.0000.0000.0000.000
179B183PRO00.0230.01731.2860.0010.0010.0000.0000.0000.000
180B184GLN0-0.040-0.03028.2160.0010.0010.0000.0000.0000.000
181B185ARG10.8950.95033.032-0.045-0.0450.0000.0000.0000.000
182B186LEU00.0570.01234.1830.0030.0030.0000.0000.0000.000
183B187ASN0-0.030-0.01533.516-0.001-0.0010.0000.0000.0000.000
184B188GLU-1-0.859-0.90729.8960.0550.0550.0000.0000.0000.000
185B189SER0-0.014-0.03728.6190.0100.0100.0000.0000.0000.000
186B190ASP-1-0.827-0.92329.7100.0510.0510.0000.0000.0000.000
187B191GLY0-0.032-0.02628.682-0.003-0.0030.0000.0000.0000.000
188B192THR00.0560.02028.182-0.002-0.0020.0000.0000.0000.000
189B193ASN00.0140.00630.763-0.004-0.0040.0000.0000.0000.000
190B194GLU-1-0.822-0.90233.2460.0430.0430.0000.0000.0000.000
191B195LEU0-0.053-0.02929.729-0.002-0.0020.0000.0000.0000.000
192B196LEU0-0.036-0.01734.230-0.003-0.0030.0000.0000.0000.000
193B197GLU-1-0.950-0.96636.7030.0340.0340.0000.0000.0000.000
194B198LYS10.7820.89035.861-0.042-0.0420.0000.0000.0000.000
195B199GLY00.0150.01639.189-0.001-0.0010.0000.0000.0000.000
196B200GLN0-0.043-0.01734.6680.0010.0010.0000.0000.0000.000
197B201ALA0-0.026-0.01732.9550.0010.0010.0000.0000.0000.000
198B202GLN00.0150.02134.906-0.002-0.0020.0000.0000.0000.000
199B203GLY00.0270.01234.5170.0030.0030.0000.0000.0000.000
200B204ILE0-0.044-0.02830.457-0.003-0.0030.0000.0000.0000.000
201B205PHE00.027-0.00434.6070.0010.0010.0000.0000.0000.000
202B206ASN0-0.0020.00036.903-0.001-0.0010.0000.0000.0000.000
203B207ILE00.0440.02330.754-0.001-0.0010.0000.0000.0000.000
204B208GLN00.0640.03233.9800.0000.0000.0000.0000.0000.000
205B209ASN00.0270.00635.817-0.002-0.0020.0000.0000.0000.000
206B210PHE00.0020.01930.484-0.001-0.0010.0000.0000.0000.000
207B211ILE00.0340.01630.7480.0000.0000.0000.0000.0000.000
208B212ASN00.013-0.01133.891-0.001-0.0010.0000.0000.0000.000
209B213THR0-0.060-0.03937.169-0.003-0.0030.0000.0000.0000.000
210B214LEU00.0220.02831.083-0.001-0.0010.0000.0000.0000.000
211B215LEU0-0.021-0.02832.225-0.001-0.0010.0000.0000.0000.000
212B216LYS10.8570.91535.773-0.014-0.0140.0000.0000.0000.000
213B217ASP-1-0.917-0.93637.4560.0140.0140.0000.0000.0000.000
214B218TYR0-0.087-0.04533.8210.0000.0000.0000.0000.0000.000
215B219HIS0-0.048-0.02036.858-0.002-0.0020.0000.0000.0000.000
216B220LEU0-0.034-0.00132.406-0.002-0.0020.0000.0000.0000.000
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