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: G68L1

Calculation Name: 4X2H-B-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 4X2H

Chain ID: B

ChEMBL ID:

UniProt ID: G0SET4

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 175
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -1858101.561586
FMO2-HF: Nuclear repulsion 1787850.630362
FMO2-HF: Total energy -70250.931224
FMO2-MP2: Total energy -70456.148527


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:2:LEU)


Summations of interaction energy for fragment #1(B:2:LEU)
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.
-14.627-9.7721.549-1.653-4.750.008
Interaction energy analysis for fragmet #1(B:2:LEU)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.037 / 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].
3B4ARG10.9870.9763.181-8.618-6.0770.130-0.803-1.8670.007
4B5ARG10.9460.9773.128-3.644-2.6240.080-0.282-0.8180.001
5B6TYR00.0350.0232.413-1.735-0.4411.339-0.568-2.0650.000
6B7ALA0-0.0050.0086.642-0.149-0.1490.0000.0000.0000.000
7B8ALA00.0240.0078.046-0.191-0.1910.0000.0000.0000.000
8B9LYS10.9190.9528.708-0.386-0.3860.0000.0000.0000.000
9B10SER0-0.038-0.01210.471-0.107-0.1070.0000.0000.0000.000
10B11PHE0-0.021-0.02112.323-0.067-0.0670.0000.0000.0000.000
11B12VAL00.0530.02613.417-0.066-0.0660.0000.0000.0000.000
12B13GLU-1-0.863-0.90914.5890.1030.1030.0000.0000.0000.000
13B14TRP0-0.047-0.01516.428-0.028-0.0280.0000.0000.0000.000
14B15TYR00.0740.02818.009-0.035-0.0350.0000.0000.0000.000
15B16TYR00.024-0.04317.721-0.010-0.0100.0000.0000.0000.000
16B17ARG10.8730.94818.130-0.157-0.1570.0000.0000.0000.000
17B18GLN0-0.040-0.02621.799-0.037-0.0370.0000.0000.0000.000
18B19ILE00.0320.03223.673-0.018-0.0180.0000.0000.0000.000
19B20ASN0-0.046-0.02423.612-0.024-0.0240.0000.0000.0000.000
20B21GLU-1-0.862-0.90925.6490.0890.0890.0000.0000.0000.000
21B22ASN0-0.082-0.04728.452-0.005-0.0050.0000.0000.0000.000
22B23LYS10.8370.90626.784-0.102-0.1020.0000.0000.0000.000
23B24PRO0-0.0120.00127.7880.0100.0100.0000.0000.0000.000
24B25VAL00.010-0.01323.2920.0030.0030.0000.0000.0000.000
25B26ALA00.0470.02424.1530.0210.0210.0000.0000.0000.000
26B27SER0-0.042-0.02223.9410.0130.0130.0000.0000.0000.000
27B28GLY0-0.036-0.02620.6380.0020.0020.0000.0000.0000.000
28B29TYR0-0.009-0.01620.5100.0450.0450.0000.0000.0000.000
29B30VAL0-0.015-0.01521.196-0.018-0.0180.0000.0000.0000.000
30B31ASN00.0420.02323.392-0.002-0.0020.0000.0000.0000.000
31B32ASN0-0.030-0.00626.167-0.020-0.0200.0000.0000.0000.000
32B33ASN00.0000.00621.413-0.011-0.0110.0000.0000.0000.000
33B34ALA00.0350.02424.845-0.001-0.0010.0000.0000.0000.000
34B35THR0-0.003-0.02722.625-0.007-0.0070.0000.0000.0000.000
35B36TYR0-0.033-0.05618.3430.0040.0040.0000.0000.0000.000
36B37THR00.0090.01124.9790.0010.0010.0000.0000.0000.000
37B38LYS10.9110.96228.261-0.077-0.0770.0000.0000.0000.000
38B39ALA0-0.049-0.03126.150-0.006-0.0060.0000.0000.0000.000
39B40GLY00.0200.02428.1710.0020.0020.0000.0000.0000.000
40B41HIS0-0.102-0.07222.5680.0310.0310.0000.0000.0000.000
41B42PRO00.0120.02125.793-0.011-0.0110.0000.0000.0000.000
42B43PRO00.0200.00626.8530.0130.0130.0000.0000.0000.000
43B44ALA00.003-0.00324.4560.0130.0130.0000.0000.0000.000
44B45ASP-1-0.873-0.91624.9720.2630.2630.0000.0000.0000.000
45B46ILE00.0200.00925.1680.0310.0310.0000.0000.0000.000
46B47THR0-0.035-0.01226.681-0.016-0.0160.0000.0000.0000.000
47B48ILE00.0480.02227.1180.0190.0190.0000.0000.0000.000
48B49ASN00.018-0.00928.892-0.005-0.0050.0000.0000.0000.000
49B50GLY0-0.045-0.02530.243-0.012-0.0120.0000.0000.0000.000
50B51ARG10.9150.95732.022-0.150-0.1500.0000.0000.0000.000
51B52VAL0-0.006-0.00831.0700.0110.0110.0000.0000.0000.000
52B53VAL0-0.044-0.01930.440-0.013-0.0130.0000.0000.0000.000
53B54ALA00.0100.01831.0030.0100.0100.0000.0000.0000.000
54B55THR0-0.027-0.04630.7140.0040.0040.0000.0000.0000.000
55B56PRO00.0310.00926.8310.0020.0020.0000.0000.0000.000
56B57GLU-1-0.782-0.87128.7660.1500.1500.0000.0000.0000.000
57B58GLU-1-0.824-0.89331.8170.1370.1370.0000.0000.0000.000
58B59TRP00.0460.00625.026-0.008-0.0080.0000.0000.0000.000
59B60ASP-1-0.730-0.88228.5010.1640.1640.0000.0000.0000.000
60B61THR0-0.116-0.06430.697-0.011-0.0110.0000.0000.0000.000
61B62MET00.0380.03532.200-0.003-0.0030.0000.0000.0000.000
62B63LEU0-0.023-0.00127.063-0.004-0.0040.0000.0000.0000.000
63B64LYS10.8290.90831.615-0.118-0.1180.0000.0000.0000.000
64B65GLU-1-0.881-0.94434.4660.1100.1100.0000.0000.0000.000
65B66GLN0-0.0230.00730.5910.0000.0000.0000.0000.0000.000
66B67ARG10.8780.94530.311-0.129-0.1290.0000.0000.0000.000
67B68ALA0-0.0140.00635.315-0.009-0.0090.0000.0000.0000.000
68B76SER00.015-0.01441.8820.0010.0010.0000.0000.0000.000
69B77THR00.0070.00943.369-0.002-0.0020.0000.0000.0000.000
70B78LEU0-0.034-0.00338.2940.0010.0010.0000.0000.0000.000
71B79PRO00.0300.02941.874-0.003-0.0030.0000.0000.0000.000
72B80ILE00.031-0.00342.0520.0030.0030.0000.0000.0000.000
73B81GLY00.0110.00439.5360.0000.0000.0000.0000.0000.000
74B82ARG10.8140.91537.213-0.073-0.0730.0000.0000.0000.000
75B83LYS10.8320.91229.243-0.121-0.1210.0000.0000.0000.000
76B84PRO00.0110.00134.7050.0050.0050.0000.0000.0000.000
77B85VAL00.0300.01729.6200.0030.0030.0000.0000.0000.000
78B86ARG10.7060.81826.930-0.135-0.1350.0000.0000.0000.000
79B87TYR0-0.0180.00723.6290.0070.0070.0000.0000.0000.000
80B88ASP-1-0.762-0.84622.8930.1580.1580.0000.0000.0000.000
81B89VAL0-0.032-0.02516.4760.0160.0160.0000.0000.0000.000
82B90ASP-1-0.853-0.93019.2370.2320.2320.0000.0000.0000.000
83B91CYS0-0.083-0.03815.3380.0190.0190.0000.0000.0000.000
84B92PHE00.024-0.0049.2730.0020.0020.0000.0000.0000.000
85B93ASP-1-0.878-0.93110.4611.5101.5100.0000.0000.0000.000
86B94VAL0-0.0010.0017.1490.0070.0070.0000.0000.0000.000
87B95HIS10.8630.9388.547-0.744-0.7440.0000.0000.0000.000
88B96VAL00.0080.0006.820-0.039-0.0390.0000.0000.0000.000
89B97ILE00.001-0.0039.713-0.106-0.1060.0000.0000.0000.000
90B98ASN00.0430.01412.539-0.137-0.1370.0000.0000.0000.000
91B99ALA00.0030.0039.7050.0750.0750.0000.0000.0000.000
92B100ASP-1-0.742-0.83611.1010.1030.1030.0000.0000.0000.000
93B101TYR0-0.016-0.00313.830-0.054-0.0540.0000.0000.0000.000
94B102ARG10.9240.91915.800-0.190-0.1900.0000.0000.0000.000
95B103PHE00.0170.02418.970-0.030-0.0300.0000.0000.0000.000
96B104ALA00.0340.00820.7820.0140.0140.0000.0000.0000.000
97B105ALA0-0.0170.00419.059-0.011-0.0110.0000.0000.0000.000
98B106PRO0-0.010-0.00719.266-0.020-0.0200.0000.0000.0000.000
99B107GLN00.0910.04220.1970.0070.0070.0000.0000.0000.000
100B108ARG11.0191.00218.9440.0150.0150.0000.0000.0000.000
101B109MET0-0.046-0.01714.081-0.033-0.0330.0000.0000.0000.000
102B110ILE0-0.047-0.03515.5780.0050.0050.0000.0000.0000.000
103B111GLU-1-0.977-0.97717.075-0.085-0.0850.0000.0000.0000.000
104B112GLN0-0.016-0.00914.938-0.009-0.0090.0000.0000.0000.000
105B113HIS10.7480.83910.7570.2250.2250.0000.0000.0000.000
106B114ALA00.1080.06512.2740.1090.1090.0000.0000.0000.000
107B115PRO00.008-0.01411.133-0.001-0.0010.0000.0000.0000.000
108B116THR0-0.005-0.0038.2570.2850.2850.0000.0000.0000.000
109B117ASP-1-0.829-0.8936.908-0.777-0.7770.0000.0000.0000.000
110B118GLY0-0.034-0.0175.390-0.147-0.1470.0000.0000.0000.000
111B119VAL00.0370.0326.4480.1210.1210.0000.0000.0000.000
112B120ARG10.7930.8979.383-0.052-0.0520.0000.0000.0000.000
113B121MET0-0.059-0.0216.5720.5180.5180.0000.0000.0000.000
114B122MET00.0270.02610.639-0.095-0.0950.0000.0000.0000.000
115B123MET0-0.075-0.0419.0200.4000.4000.0000.0000.0000.000
116B124ALA00.0490.03612.010-0.197-0.1970.0000.0000.0000.000
117B125LEU0-0.047-0.02611.6210.2100.2100.0000.0000.0000.000
118B126THR00.0030.01513.800-0.138-0.1380.0000.0000.0000.000
119B127VAL00.011-0.01914.7590.0800.0800.0000.0000.0000.000
120B128SER00.0210.01317.090-0.047-0.0470.0000.0000.0000.000
121B129GLY00.0600.03619.4260.0130.0130.0000.0000.0000.000
122B130SER0-0.0360.00322.130-0.016-0.0160.0000.0000.0000.000
123B131VAL0-0.033-0.01525.5480.0050.0050.0000.0000.0000.000
124B132TYR00.0020.00126.677-0.010-0.0100.0000.0000.0000.000
125B133PHE00.013-0.00730.883-0.001-0.0010.0000.0000.0000.000
126B134GLY00.0680.01834.172-0.004-0.0040.0000.0000.0000.000
127B135ALA00.0070.02832.767-0.006-0.0060.0000.0000.0000.000
128B136SER0-0.026-0.05934.754-0.003-0.0030.0000.0000.0000.000
129B137PRO0-0.050-0.04131.9410.0070.0070.0000.0000.0000.000
130B138ARG10.9160.95229.568-0.052-0.0520.0000.0000.0000.000
131B139SER00.0120.02830.5080.0010.0010.0000.0000.0000.000
132B140THR00.0360.00527.7110.0070.0070.0000.0000.0000.000
133B141ASP-1-0.890-0.94330.9880.0900.0900.0000.0000.0000.000
134B142ASP-1-0.745-0.82834.5070.0780.0780.0000.0000.0000.000
135B143TYR0-0.039-0.02233.2030.0000.0000.0000.0000.0000.000
136B144VAL0-0.0130.00735.891-0.004-0.0040.0000.0000.0000.000
137B145ILE0-0.005-0.01134.3160.0010.0010.0000.0000.0000.000
138B146LYS10.9360.97327.454-0.162-0.1620.0000.0000.0000.000
139B147GLN0-0.057-0.01930.0160.0030.0030.0000.0000.0000.000
140B148HIS00.0350.02423.2420.0090.0090.0000.0000.0000.000
141B149PHE0-0.033-0.02920.890-0.009-0.0090.0000.0000.0000.000
142B150ASN00.010-0.00920.5050.0450.0450.0000.0000.0000.000
143B151ASP-1-0.748-0.84719.8600.3110.3110.0000.0000.0000.000
144B152VAL0-0.037-0.01818.2180.0610.0610.0000.0000.0000.000
145B153PHE00.024-0.00816.444-0.051-0.0510.0000.0000.0000.000
146B154ILE00.0030.01116.2850.1070.1070.0000.0000.0000.000
147B155LEU0-0.047-0.02012.733-0.066-0.0660.0000.0000.0000.000
148B156VAL00.0320.02114.6140.0980.0980.0000.0000.0000.000
149B157PRO00.0090.00813.375-0.022-0.0220.0000.0000.0000.000
150B158ASN00.0330.02815.136-0.053-0.0530.0000.0000.0000.000
151B159TRP00.040-0.00515.419-0.031-0.0310.0000.0000.0000.000
152B160ASP-1-0.804-0.87518.4830.0520.0520.0000.0000.0000.000
153B161VAL0-0.072-0.03315.634-0.023-0.0230.0000.0000.0000.000
154B162LEU0-0.042-0.02211.368-0.040-0.0400.0000.0000.0000.000
155B163GLU-1-0.862-0.90211.370-0.239-0.2390.0000.0000.0000.000
156B164LYS10.8400.93015.077-0.042-0.0420.0000.0000.0000.000
157B165PRO00.0340.01518.530-0.005-0.0050.0000.0000.0000.000
158B166GLY00.0130.00019.6120.0130.0130.0000.0000.0000.000
159B167ALA0-0.026-0.00518.1340.0130.0130.0000.0000.0000.000
160B168ARG10.9320.96917.7750.0800.0800.0000.0000.0000.000
161B169SER00.0040.00917.7570.0070.0070.0000.0000.0000.000
162B170GLY00.0460.01719.044-0.006-0.0060.0000.0000.0000.000
163B171ARG10.8920.96013.331-0.377-0.3770.0000.0000.0000.000
164B172LYS10.9920.98910.760-0.032-0.0320.0000.0000.0000.000
165B173TYR0-0.020-0.0319.4630.0350.0350.0000.0000.0000.000
166B174LEU0-0.025-0.00614.598-0.021-0.0210.0000.0000.0000.000
167B175ILE0-0.003-0.00117.7980.0650.0650.0000.0000.0000.000
168B176ALA00.0150.00819.332-0.047-0.0470.0000.0000.0000.000
169B177SER00.000-0.00420.324-0.027-0.0270.0000.0000.0000.000
170B178HIS0-0.032-0.02220.5190.0370.0370.0000.0000.0000.000
171B179LYS10.8210.91022.204-0.335-0.3350.0000.0000.0000.000
172B180TYR00.0440.02122.9620.0210.0210.0000.0000.0000.000
173B181ARG10.8890.94525.065-0.239-0.2390.0000.0000.0000.000
174B182ALA00.0480.03026.0630.0140.0140.0000.0000.0000.000
175B183TYR00.0310.02626.584-0.003-0.0030.0000.0000.0000.000