Manual

About

FMODB

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

Last updated: 2024-04-05

All entries: 36946

Number of unique PDB entries: 7781

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FMODB ID: 6N4ZZ

Calculation Name: 4X0R-B-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 4X0R

Chain ID: B

ChEMBL ID:

UniProt ID: P20592

Base Structure: X-ray

Registration Date: 2023-06-22

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 216
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2541038.577924
FMO2-HF: Nuclear repulsion 2450559.655608
FMO2-HF: Total energy -90478.922315
FMO2-MP2: Total energy -90741.327498


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:3:GLU)


Summations of interaction energy for fragment #1(B:3: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.
-133.882-131.55521.512-12.499-11.3380.087
Interaction energy analysis for fragmet #1(B:3:GLU)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : -1 / q_Mulliken : -0.821 / q_NPA : -0.905
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].
3B5ASP-1-0.857-0.9262.35226.74030.3523.221-2.739-4.093-0.030
4B6LYS10.8510.9261.645-129.734-131.17518.292-9.743-7.1080.117
5B7MET00.003-0.0214.574-3.766-3.610-0.001-0.017-0.1370.000
6B8PHE00.0630.0186.920-3.146-3.1460.0000.0000.0000.000
7B9PHE0-0.035-0.0038.494-1.503-1.5030.0000.0000.0000.000
8B10LEU00.002-0.00610.091-2.225-2.2250.0000.0000.0000.000
9B11ILE00.0020.00210.941-1.648-1.6480.0000.0000.0000.000
10B12GLU-1-0.806-0.89012.66218.92718.9270.0000.0000.0000.000
11B13LYS10.8840.94514.542-18.429-18.4290.0000.0000.0000.000
12B14ILE00.0150.02116.625-1.093-1.0930.0000.0000.0000.000
13B15LYS10.8470.91416.153-19.350-19.3500.0000.0000.0000.000
14B16MET0-0.015-0.00718.052-0.828-0.8280.0000.0000.0000.000
15B17PHE0-0.014-0.01020.435-0.838-0.8380.0000.0000.0000.000
16B18ASN00.021-0.01722.025-0.730-0.7300.0000.0000.0000.000
17B19GLN00.0240.01721.172-0.818-0.8180.0000.0000.0000.000
18B20ASP-1-0.812-0.90824.71811.93011.9300.0000.0000.0000.000
19B21ILE0-0.053-0.01926.449-0.544-0.5440.0000.0000.0000.000
20B22GLU-1-0.741-0.83427.8349.6769.6760.0000.0000.0000.000
21B23LYS10.9330.96926.310-12.140-12.1400.0000.0000.0000.000
22B24LEU0-0.071-0.03530.849-0.420-0.4200.0000.0000.0000.000
23B25VAL0-0.037-0.01132.374-0.403-0.4030.0000.0000.0000.000
24B26GLU-1-0.913-0.94432.1269.3909.3900.0000.0000.0000.000
25B27GLY0-0.050-0.01935.360-0.189-0.1890.0000.0000.0000.000
26B28GLU-1-0.987-1.00232.8749.2939.2930.0000.0000.0000.000
27B29GLU-1-0.836-0.92431.7939.4499.4490.0000.0000.0000.000
28B30VAL0-0.034-0.02229.116-0.186-0.1860.0000.0000.0000.000
29B31VAL0-0.028-0.00232.2410.1400.1400.0000.0000.0000.000
30B32ARG10.8460.90634.640-8.776-8.7760.0000.0000.0000.000
31B33GLU-1-0.846-0.91736.2457.8727.8720.0000.0000.0000.000
32B34ASN0-0.091-0.05339.390-0.327-0.3270.0000.0000.0000.000
33B35GLU-1-0.839-0.91435.2209.0489.0480.0000.0000.0000.000
34B36THR00.0070.01239.6520.0640.0640.0000.0000.0000.000
35B37ARG10.9320.96434.962-8.690-8.6900.0000.0000.0000.000
36B38LEU0-0.024-0.01635.614-0.257-0.2570.0000.0000.0000.000
37B39TYR00.013-0.01937.795-0.364-0.3640.0000.0000.0000.000
38B40ASN0-0.014-0.00440.815-0.204-0.2040.0000.0000.0000.000
39B41LYS10.9080.96838.142-8.420-8.4200.0000.0000.0000.000
40B42ILE00.0220.01439.660-0.155-0.1550.0000.0000.0000.000
41B43ARG10.9370.96943.353-7.459-7.4590.0000.0000.0000.000
42B44GLU-1-0.888-0.95346.5996.2566.2560.0000.0000.0000.000
43B45ASP-1-0.827-0.92246.8366.4726.4720.0000.0000.0000.000
44B46PHE00.030-0.00444.397-0.137-0.1370.0000.0000.0000.000
45B47LYS10.8580.94349.698-6.303-6.3030.0000.0000.0000.000
46B48ASN0-0.032-0.01451.993-0.185-0.1850.0000.0000.0000.000
47B49TRP00.0640.02252.019-0.155-0.1550.0000.0000.0000.000
48B50VAL00.004-0.00253.356-0.133-0.1330.0000.0000.0000.000
49B51GLY00.0100.01355.884-0.129-0.1290.0000.0000.0000.000
50B52ILE00.005-0.00155.594-0.151-0.1510.0000.0000.0000.000
51B53LEU0-0.0010.01056.672-0.133-0.1330.0000.0000.0000.000
52B54ALA00.0090.02259.586-0.120-0.1200.0000.0000.0000.000
53B55THR0-0.036-0.01961.928-0.140-0.1400.0000.0000.0000.000
54B56ASN0-0.017-0.01961.754-0.136-0.1360.0000.0000.0000.000
55B57THR00.0240.00562.587-0.075-0.0750.0000.0000.0000.000
56B58GLN0-0.0010.01065.250-0.030-0.0300.0000.0000.0000.000
57B59LYS10.9270.97066.273-4.893-4.8930.0000.0000.0000.000
58B60VAL00.0360.00867.015-0.076-0.0760.0000.0000.0000.000
59B61LYS10.8860.96268.057-4.745-4.7450.0000.0000.0000.000
60B62ASN00.0440.01771.067-0.055-0.0550.0000.0000.0000.000
61B63ILE0-0.0020.01072.259-0.059-0.0590.0000.0000.0000.000
62B64ILE00.004-0.01272.300-0.062-0.0620.0000.0000.0000.000
63B65HIS0-0.049-0.02675.017-0.002-0.0020.0000.0000.0000.000
64B66GLU-1-0.906-0.95877.0233.9813.9810.0000.0000.0000.000
65B67GLU-1-0.898-0.92877.0964.0054.0050.0000.0000.0000.000
66B68VAL00.008-0.00477.956-0.055-0.0550.0000.0000.0000.000
67B69GLU-1-0.760-0.85880.5343.8393.8390.0000.0000.0000.000
68B70LYS10.7650.88080.638-4.041-4.0410.0000.0000.0000.000
69B71TYR0-0.010-0.02380.423-0.037-0.0370.0000.0000.0000.000
70B72GLU-1-0.938-0.97183.5023.8333.8330.0000.0000.0000.000
71B73LYS10.8640.91585.407-3.824-3.8240.0000.0000.0000.000
72B74GLN0-0.078-0.03286.736-0.013-0.0130.0000.0000.0000.000
73B75ALA0-0.067-0.02488.636-0.042-0.0420.0000.0000.0000.000
74B76ALA0-0.0170.00890.502-0.037-0.0370.0000.0000.0000.000
75B87LYS10.8960.91374.417-4.297-4.2970.0000.0000.0000.000
76B88THR00.0220.00174.9460.0630.0630.0000.0000.0000.000
77B89PHE00.0630.02773.9210.0400.0400.0000.0000.0000.000
78B90GLU-1-0.773-0.85871.0524.4944.4940.0000.0000.0000.000
79B91ILE0-0.0170.00070.0510.0760.0760.0000.0000.0000.000
80B92ILE00.0310.01969.9460.0690.0690.0000.0000.0000.000
81B93VAL0-0.0080.00466.5150.0680.0680.0000.0000.0000.000
82B94HIS00.0280.01364.6190.0510.0510.0000.0000.0000.000
83B95GLN00.005-0.00864.9230.0460.0460.0000.0000.0000.000
84B96TYR0-0.047-0.04662.7940.0880.0880.0000.0000.0000.000
85B97ILE0-0.0080.00360.3230.0860.0860.0000.0000.0000.000
86B98GLN00.0300.00960.0010.1070.1070.0000.0000.0000.000
87B99GLN0-0.067-0.02760.3840.0650.0650.0000.0000.0000.000
88B100LEU0-0.051-0.02357.8930.0460.0460.0000.0000.0000.000
89B101VAL00.0010.00055.0690.1100.1100.0000.0000.0000.000
90B102GLU-1-0.867-0.92754.5255.8945.8940.0000.0000.0000.000
91B103PRO0-0.024-0.02053.9840.1170.1170.0000.0000.0000.000
92B104ALA0-0.0290.00152.4730.1230.1230.0000.0000.0000.000
93B105LEU00.0300.00349.8800.1640.1640.0000.0000.0000.000
94B106SER00.0180.01849.1820.1190.1190.0000.0000.0000.000
95B107MET0-0.058-0.01148.1030.1340.1340.0000.0000.0000.000
96B108LEU0-0.015-0.00743.6420.1730.1730.0000.0000.0000.000
97B109GLN0-0.025-0.01944.3970.1940.1940.0000.0000.0000.000
98B110LYS10.9260.96944.408-6.593-6.5930.0000.0000.0000.000
99B111ALA0-0.002-0.01542.8710.1670.1670.0000.0000.0000.000
100B112MET0-0.0100.01039.8660.2700.2700.0000.0000.0000.000
101B113GLU-1-0.873-0.92439.2837.3157.3150.0000.0000.0000.000
102B114ILE0-0.055-0.02639.2570.2170.2170.0000.0000.0000.000
103B115ILE0-0.008-0.00935.6210.2420.2420.0000.0000.0000.000
104B116GLN00.0040.01135.0960.1160.1160.0000.0000.0000.000
105B117GLN0-0.037-0.02434.1710.1700.1700.0000.0000.0000.000
106B118ALA0-0.022-0.01433.8690.2840.2840.0000.0000.0000.000
107B119PHE00.0470.00130.6860.3780.3780.0000.0000.0000.000
108B120ILE0-0.0150.00129.3940.4500.4500.0000.0000.0000.000
109B121ASN0-0.006-0.00629.3270.3570.3570.0000.0000.0000.000
110B122VAL00.0130.01725.8940.3310.3310.0000.0000.0000.000
111B123ALA00.0270.01225.0030.5710.5710.0000.0000.0000.000
112B124LYS10.9260.96424.586-9.641-9.6410.0000.0000.0000.000
113B125LYS10.8920.95824.404-12.236-12.2360.0000.0000.0000.000
114B126HIS0-0.093-0.05121.1111.0131.0130.0000.0000.0000.000
115B127PHE00.001-0.01618.7561.0631.0630.0000.0000.0000.000
116B128GLY00.0130.02221.575-0.056-0.0560.0000.0000.0000.000
117B129GLU-1-0.928-0.96119.29214.02414.0240.0000.0000.0000.000
118B130PHE0-0.048-0.01115.3320.3050.3050.0000.0000.0000.000
119B131PHE00.0680.02120.036-0.271-0.2710.0000.0000.0000.000
120B132ASN0-0.009-0.01219.620-0.944-0.9440.0000.0000.0000.000
121B133LEU00.0280.01817.405-0.336-0.3360.0000.0000.0000.000
122B134ASN00.010-0.00720.924-0.365-0.3650.0000.0000.0000.000
123B135GLN0-0.014-0.00123.904-0.340-0.3400.0000.0000.0000.000
124B136THR0-0.006-0.01122.677-0.234-0.2340.0000.0000.0000.000
125B137VAL00.0360.03722.368-0.377-0.3770.0000.0000.0000.000
126B138GLN00.0340.00725.321-0.221-0.2210.0000.0000.0000.000
127B139SER0-0.070-0.02927.640-0.359-0.3590.0000.0000.0000.000
128B140THR00.005-0.01626.390-0.282-0.2820.0000.0000.0000.000
129B141ILE0-0.010-0.00727.697-0.253-0.2530.0000.0000.0000.000
130B142GLU-1-0.798-0.86830.7548.1128.1120.0000.0000.0000.000
131B143ASP-1-0.828-0.89731.6098.8748.8740.0000.0000.0000.000
132B144ILE0-0.003-0.01029.239-0.269-0.2690.0000.0000.0000.000
133B145LYS10.8380.91333.639-8.373-8.3730.0000.0000.0000.000
134B146VAL00.0110.01136.304-0.274-0.2740.0000.0000.0000.000
135B147LYS10.8100.89133.266-9.139-9.1390.0000.0000.0000.000
136B148HIS0-0.030-0.01635.403-0.073-0.0730.0000.0000.0000.000
137B149THR00.041-0.00839.006-0.155-0.1550.0000.0000.0000.000
138B150ALA00.0190.02341.597-0.203-0.2030.0000.0000.0000.000
139B151LYS10.8320.91237.767-8.246-8.2460.0000.0000.0000.000
140B152ALA00.0140.01443.016-0.160-0.1600.0000.0000.0000.000
141B153GLU-1-0.837-0.91744.7136.2286.2280.0000.0000.0000.000
142B154ASN0-0.094-0.06246.009-0.289-0.2890.0000.0000.0000.000
143B155MET00.010-0.00246.305-0.168-0.1680.0000.0000.0000.000
144B156ILE00.0150.02248.009-0.140-0.1400.0000.0000.0000.000
145B157GLN0-0.012-0.01550.826-0.257-0.2570.0000.0000.0000.000
146B158LEU0-0.089-0.04150.767-0.150-0.1500.0000.0000.0000.000
147B159GLN0-0.011-0.00652.442-0.011-0.0110.0000.0000.0000.000
148B160PHE00.0620.01754.132-0.113-0.1130.0000.0000.0000.000
149B161ARG10.9310.97852.943-5.883-5.8830.0000.0000.0000.000
150B162MET00.003-0.00454.082-0.105-0.1050.0000.0000.0000.000
151B163GLU-1-0.772-0.87057.8695.3905.3900.0000.0000.0000.000
152B164GLN0-0.046-0.02560.196-0.173-0.1730.0000.0000.0000.000
153B165MET0-0.073-0.04861.458-0.124-0.1240.0000.0000.0000.000
154B166VAL0-0.009-0.01260.534-0.077-0.0770.0000.0000.0000.000
155B167PHE0-0.0360.00463.562-0.074-0.0740.0000.0000.0000.000
156B168LYS10.8360.92365.860-4.793-4.7930.0000.0000.0000.000
157B180SER00.0090.00082.1130.0220.0220.0000.0000.0000.000
158B181VAL0-0.033-0.02483.294-0.034-0.0340.0000.0000.0000.000
159B182SER0-0.0080.00080.6520.0570.0570.0000.0000.0000.000
160B183SER00.0410.00981.445-0.042-0.0420.0000.0000.0000.000
161B184PHE00.0510.02280.8880.0540.0540.0000.0000.0000.000
162B185THR00.1020.06180.0410.0460.0460.0000.0000.0000.000
163B186GLU-1-0.908-0.94377.7054.1994.1990.0000.0000.0000.000
164B187ILE0-0.018-0.01275.8910.0710.0710.0000.0000.0000.000
165B188GLY00.0530.02875.1510.0680.0680.0000.0000.0000.000
166B189ILE0-0.0130.00074.5190.0790.0790.0000.0000.0000.000
167B190HIS0-0.019-0.01872.3300.1360.1360.0000.0000.0000.000
168B191LEU0-0.014-0.00170.6850.0950.0950.0000.0000.0000.000
169B192ASN0-0.040-0.03769.6780.1250.1250.0000.0000.0000.000
170B193ALA00.0010.00968.7470.0830.0830.0000.0000.0000.000
171B194TYR00.0820.03363.4940.0950.0950.0000.0000.0000.000
172B195PHE00.0280.01464.9770.1070.1070.0000.0000.0000.000
173B196LEU0-0.0290.00564.1430.1110.1110.0000.0000.0000.000
174B197GLU-1-0.950-0.98062.3245.1475.1470.0000.0000.0000.000
175B198THR0-0.011-0.02760.5920.1310.1310.0000.0000.0000.000
176B199SER0-0.044-0.02059.3910.1170.1170.0000.0000.0000.000
177B200LYS10.9400.96058.329-5.082-5.0820.0000.0000.0000.000
178B201ARG10.8460.92155.884-5.258-5.2580.0000.0000.0000.000
179B202LEU00.0470.01254.7230.1460.1460.0000.0000.0000.000
180B203ALA0-0.017-0.01253.8060.1210.1210.0000.0000.0000.000
181B204ASN0-0.057-0.02051.1490.1780.1780.0000.0000.0000.000
182B205GLN0-0.0070.00249.9180.1790.1790.0000.0000.0000.000
183B206ILE0-0.004-0.01449.6330.1200.1200.0000.0000.0000.000
184B207PRO00.0330.00847.4190.1410.1410.0000.0000.0000.000
185B208PHE00.0040.01145.6680.1780.1780.0000.0000.0000.000
186B209ILE00.0040.01544.4560.2140.2140.0000.0000.0000.000
187B210ILE00.0250.01643.4060.1970.1970.0000.0000.0000.000
188B211GLN0-0.028-0.02141.2810.0690.0690.0000.0000.0000.000
189B212TYR0-0.049-0.03739.6080.2480.2480.0000.0000.0000.000
190B213PHE00.021-0.00239.0390.2040.2040.0000.0000.0000.000
191B214MET00.0010.00938.3810.1810.1810.0000.0000.0000.000
192B215LEU0-0.035-0.01135.8700.1990.1990.0000.0000.0000.000
193B216ARG10.7910.83331.994-9.204-9.2040.0000.0000.0000.000
194B217GLU-1-0.772-0.86334.2658.3358.3350.0000.0000.0000.000
195B218ASN0-0.069-0.02833.8520.4060.4060.0000.0000.0000.000
196B219GLY00.0690.02131.0750.2860.2860.0000.0000.0000.000
197B220ASP-1-0.816-0.86929.55910.11510.1150.0000.0000.0000.000
198B221SER0-0.066-0.05029.1530.3980.3980.0000.0000.0000.000
199B222LEU00.0030.00626.9880.3380.3380.0000.0000.0000.000
200B223GLN0-0.012-0.01625.1280.8710.8710.0000.0000.0000.000
201B224LYS10.9580.96924.207-9.711-9.7110.0000.0000.0000.000
202B225ALA00.0020.00424.3900.3750.3750.0000.0000.0000.000
203B226MET0-0.029-0.00720.7340.3270.3270.0000.0000.0000.000
204B227MET0-0.005-0.00718.9370.8850.8850.0000.0000.0000.000
205B228GLN0-0.047-0.02619.6370.4530.4530.0000.0000.0000.000
206B229ILE00.0370.02217.4950.1940.1940.0000.0000.0000.000
207B230LEU0-0.0410.00014.2750.6530.6530.0000.0000.0000.000
208B231GLN0-0.0480.00514.8121.3311.3310.0000.0000.0000.000
209B232GLU-1-0.862-0.93615.80814.32114.3210.0000.0000.0000.000
210B233LYS10.9140.94311.239-18.391-18.3910.0000.0000.0000.000
211B234ASN0-0.044-0.01412.2550.7980.7980.0000.0000.0000.000
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