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: K3153

Calculation Name: 2J92-B-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2J92

Chain ID: B

ChEMBL ID:

UniProt ID: P03306

Base Structure: X-ray

Registration Date: 2023-06-21

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 OptAll
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 185
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -1945070.616467
FMO2-HF: Nuclear repulsion 1872964.660869
FMO2-HF: Total energy -72105.955599
FMO2-MP2: Total energy -72309.254165


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:7:ASP)


Summations of interaction energy for fragment #1(B:7:ASP)
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.
-269.636-263.55413.424-8.968-10.5380.101
Interaction energy analysis for fragmet #1(B:7:ASP)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : -1 / q_Mulliken : -0.853 / q_NPA : -0.944
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].
3B9GLN00.0590.0242.873-13.573-9.9550.440-1.894-2.1650.013
4B10LYS10.9801.0001.951-97.317-95.84312.950-6.629-7.7950.083
5B11MET0-0.079-0.0293.745-16.632-15.6420.034-0.445-0.5780.005
6B12VAL00.0280.0155.909-6.024-6.0240.0000.0000.0000.000
7B13MET00.0350.0486.656-5.602-5.6020.0000.0000.0000.000
8B14GLY0-0.0200.0027.715-3.391-3.3910.0000.0000.0000.000
9B15ASN0-0.052-0.0559.686-3.124-3.1240.0000.0000.0000.000
10B16THR0-0.063-0.02210.962-2.484-2.4840.0000.0000.0000.000
11B17LYS10.8280.92813.079-21.122-21.1220.0000.0000.0000.000
12B18PRO00.0070.02516.359-0.139-0.1390.0000.0000.0000.000
13B19VAL00.0460.00219.337-0.253-0.2530.0000.0000.0000.000
14B20GLU-1-0.872-0.94922.57313.97113.9710.0000.0000.0000.000
15B21LEU00.0140.02026.059-0.173-0.1730.0000.0000.0000.000
16B22ILE0-0.040-0.02629.218-0.086-0.0860.0000.0000.0000.000
17B23LEU00.0250.00432.274-0.078-0.0780.0000.0000.0000.000
18B24ASP-1-0.892-0.94335.9547.8647.8640.0000.0000.0000.000
19B25GLY0-0.044-0.01135.910-0.051-0.0510.0000.0000.0000.000
20B26LYS10.8810.94333.194-9.375-9.3750.0000.0000.0000.000
21B27THR00.011-0.00928.239-0.052-0.0520.0000.0000.0000.000
22B28VAL0-0.032-0.01131.509-0.131-0.1310.0000.0000.0000.000
23B29ALA00.0150.01528.460-0.028-0.0280.0000.0000.0000.000
24B30ILE0-0.009-0.00523.5360.1210.1210.0000.0000.0000.000
25B31CYS0-0.078-0.03621.532-0.282-0.2820.0000.0000.0000.000
26B32CYS0-0.0370.02416.4150.7920.7920.0000.0000.0000.000
27B33ALA00.0660.03017.531-0.771-0.7710.0000.0000.0000.000
28B34THR0-0.025-0.02312.8051.8291.8290.0000.0000.0000.000
29B35GLY00.0130.01114.765-1.024-1.0240.0000.0000.0000.000
30B36VAL0-0.024-0.02213.8371.8761.8760.0000.0000.0000.000
31B37PHE00.0600.00014.6040.7740.7740.0000.0000.0000.000
32B38GLY00.0120.00916.835-0.637-0.6370.0000.0000.0000.000
33B39THR00.004-0.00418.8510.7720.7720.0000.0000.0000.000
34B40ALA00.0250.02119.885-0.517-0.5170.0000.0000.0000.000
35B41TYR0-0.005-0.01917.1091.5931.5930.0000.0000.0000.000
36B42LEU0-0.024-0.00516.722-0.829-0.8290.0000.0000.0000.000
37B43VAL0-0.006-0.00218.9430.7920.7920.0000.0000.0000.000
38B44PRO00.009-0.01121.614-0.224-0.2240.0000.0000.0000.000
39B45ARG10.8770.92524.050-10.908-10.9080.0000.0000.0000.000
40B46HIS0-0.010-0.02127.135-0.408-0.4080.0000.0000.0000.000
41B47LEU00.0220.01225.053-0.193-0.1930.0000.0000.0000.000
42B48PHE0-0.032-0.02724.735-0.056-0.0560.0000.0000.0000.000
43B49ALA0-0.019-0.00329.682-0.240-0.2400.0000.0000.0000.000
44B50GLU-1-0.940-0.95731.3309.3859.3850.0000.0000.0000.000
45B51GLN0-0.025-0.01133.657-0.068-0.0680.0000.0000.0000.000
46B52TYR0-0.057-0.04531.8020.2210.2210.0000.0000.0000.000
47B53ASP-1-0.824-0.90534.4098.4078.4070.0000.0000.0000.000
48B54LYS10.8460.91031.924-9.286-9.2860.0000.0000.0000.000
49B55ILE00.0180.02326.0380.0920.0920.0000.0000.0000.000
50B56MET0-0.041-0.00225.812-0.226-0.2260.0000.0000.0000.000
51B57LEU00.021-0.00719.8190.3500.3500.0000.0000.0000.000
52B58ASP-1-0.892-0.97418.06618.24318.2430.0000.0000.0000.000
53B59GLY00.0000.01520.653-0.031-0.0310.0000.0000.0000.000
54B60ARG10.7900.87923.934-12.740-12.7400.0000.0000.0000.000
55B61ALA00.0370.01025.9640.0940.0940.0000.0000.0000.000
56B62MET0-0.080-0.03424.8220.0600.0600.0000.0000.0000.000
57B63THR00.0430.00929.688-0.309-0.3090.0000.0000.0000.000
58B64ASP-1-0.695-0.82331.33410.28710.2870.0000.0000.0000.000
59B65SER0-0.052-0.02832.928-0.095-0.0950.0000.0000.0000.000
60B66ASP-1-0.830-0.89729.03610.52810.5280.0000.0000.0000.000
61B67TYR0-0.057-0.05427.2740.5650.5650.0000.0000.0000.000
62B68ARG10.8090.89928.299-10.463-10.4630.0000.0000.0000.000
63B69VAL00.0240.01826.8010.5430.5430.0000.0000.0000.000
64B70PHE0-0.0010.00026.857-0.489-0.4890.0000.0000.0000.000
65B71GLU-1-0.841-0.93826.90810.81110.8110.0000.0000.0000.000
66B72PHE0-0.086-0.04922.2990.0830.0830.0000.0000.0000.000
67B73GLU-1-0.904-0.94227.5049.5989.5980.0000.0000.0000.000
68B82LEU0-0.002-0.01130.7320.0700.0700.0000.0000.0000.000
69B83SER0-0.032-0.01524.2710.1080.1080.0000.0000.0000.000
70B84ASP-1-0.771-0.86225.88111.03411.0340.0000.0000.0000.000
71B85ALA0-0.080-0.02621.5570.3200.3200.0000.0000.0000.000
72B86ALA00.0250.00923.500-0.447-0.4470.0000.0000.0000.000
73B87LEU0-0.029-0.02920.5090.8420.8420.0000.0000.0000.000
74B88MET00.0460.04722.413-0.742-0.7420.0000.0000.0000.000
75B89VAL0-0.025-0.02622.7940.8330.8330.0000.0000.0000.000
76B90LEU00.0270.01122.592-0.587-0.5870.0000.0000.0000.000
77B91HIS0-0.0270.00525.6840.3720.3720.0000.0000.0000.000
78B92ARG10.9610.97826.614-10.262-10.2620.0000.0000.0000.000
79B93GLY00.0380.01923.550-0.029-0.0290.0000.0000.0000.000
80B94ASN00.0120.01417.469-0.348-0.3480.0000.0000.0000.000
81B95LYS10.9540.98716.329-16.735-16.7350.0000.0000.0000.000
82B96VAL0-0.0030.01514.4120.9760.9760.0000.0000.0000.000
83B97ARG10.9160.9567.451-31.506-31.5060.0000.0000.0000.000
84B98ASP-1-0.766-0.85812.31720.55520.5550.0000.0000.0000.000
85B99ILE0-0.044-0.0168.9632.1822.1820.0000.0000.0000.000
86B100THR00.0260.00511.0390.4030.4030.0000.0000.0000.000
87B101LYS10.7960.8718.966-23.909-23.9090.0000.0000.0000.000
88B102HIS00.0270.0025.168-2.216-2.2160.0000.0000.0000.000
89B103PHE00.0470.04310.3021.0091.0090.0000.0000.0000.000
90B104ARG10.8230.88610.041-22.930-22.9300.0000.0000.0000.000
91B105ASP-1-0.750-0.82516.21314.31714.3170.0000.0000.0000.000
92B106THR00.0100.02919.059-0.778-0.7780.0000.0000.0000.000
93B107ALA0-0.0100.01017.0870.6810.6810.0000.0000.0000.000
94B108ARG10.8690.89518.699-13.373-13.3730.0000.0000.0000.000
95B109MET0-0.0210.02416.8330.6230.6230.0000.0000.0000.000
96B110LYS10.8550.92618.390-16.427-16.4270.0000.0000.0000.000
97B111LYS10.8710.93820.276-11.928-11.9280.0000.0000.0000.000
98B112GLY00.0230.02221.225-0.157-0.1570.0000.0000.0000.000
99B113THR0-0.079-0.05516.1690.8520.8520.0000.0000.0000.000
100B114PRO00.011-0.00512.968-0.113-0.1130.0000.0000.0000.000
101B115VAL0-0.029-0.01013.8120.5910.5910.0000.0000.0000.000
102B116VAL0-0.027-0.0198.700-0.017-0.0170.0000.0000.0000.000
103B117GLY00.0120.01211.861-0.154-0.1540.0000.0000.0000.000
104B118VAL0-0.050-0.0288.5501.5541.5540.0000.0000.0000.000
105B119VAL00.013-0.00311.396-1.719-1.7190.0000.0000.0000.000
106B120ASN0-0.033-0.06113.6130.6090.6090.0000.0000.0000.000
107B121ASN00.0490.02015.762-0.830-0.8300.0000.0000.0000.000
108B122ALA00.0340.01719.6390.3220.3220.0000.0000.0000.000
109B123ASP-1-0.883-0.90822.02713.26913.2690.0000.0000.0000.000
110B124VAL0-0.046-0.03218.004-0.143-0.1430.0000.0000.0000.000
111B125GLY00.0240.03318.2250.7080.7080.0000.0000.0000.000
112B126ARG10.8650.9059.750-27.334-27.3340.0000.0000.0000.000
113B127LEU00.0180.01413.6430.2160.2160.0000.0000.0000.000
114B128ILE0-0.015-0.0138.2611.6081.6080.0000.0000.0000.000
115B129PHE00.0060.01111.720-1.567-1.5670.0000.0000.0000.000
116B130SER0-0.011-0.01612.8531.3251.3250.0000.0000.0000.000
117B131GLY00.0510.01614.722-1.326-1.3260.0000.0000.0000.000
118B132GLU-1-0.892-0.91916.72314.66514.6650.0000.0000.0000.000
119B133ALA00.0270.00318.654-0.447-0.4470.0000.0000.0000.000
120B134LEU00.0080.00620.083-0.493-0.4930.0000.0000.0000.000
121B135THR00.011-0.00123.493-0.682-0.6820.0000.0000.0000.000
122B136TYR0-0.043-0.04123.0660.7780.7780.0000.0000.0000.000
123B137LYS10.8180.90221.162-13.413-13.4130.0000.0000.0000.000
124B138ASP-1-0.730-0.82222.11912.87112.8710.0000.0000.0000.000
125B139ILE0-0.048-0.02019.082-0.179-0.1790.0000.0000.0000.000
126B140VAL0-0.001-0.02122.197-0.095-0.0950.0000.0000.0000.000
127B148MET00.0630.05327.1550.1800.1800.0000.0000.0000.000
128B149PRO0-0.032-0.02922.615-0.138-0.1380.0000.0000.0000.000
129B150GLY00.0460.01824.7580.0940.0940.0000.0000.0000.000
130B151LEU00.0530.02623.8900.5270.5270.0000.0000.0000.000
131B152PHE00.008-0.01017.208-0.194-0.1940.0000.0000.0000.000
132B153ALA00.0390.03221.8130.2180.2180.0000.0000.0000.000
133B154TYR00.032-0.02518.9430.2520.2520.0000.0000.0000.000
134B155LYS10.8540.93521.038-12.815-12.8150.0000.0000.0000.000
135B156ALA00.0410.01218.5140.6380.6380.0000.0000.0000.000
136B157ALA0-0.0090.00720.392-0.701-0.7010.0000.0000.0000.000
137B158THR0-0.041-0.02718.9790.6840.6840.0000.0000.0000.000
138B159ARG10.8860.93421.371-14.448-14.4480.0000.0000.0000.000
139B160ALA00.0610.02622.2660.5730.5730.0000.0000.0000.000
140B161GLY00.0860.04822.3530.1900.1900.0000.0000.0000.000
141B162TYR0-0.016-0.02318.2510.6230.6230.0000.0000.0000.000
142B163ALA00.0100.01518.3370.8140.8140.0000.0000.0000.000
143B164GLY00.0530.02819.1860.0310.0310.0000.0000.0000.000
144B165GLY00.0350.04015.2020.8680.8680.0000.0000.0000.000
145B166ALA0-0.017-0.01011.319-0.731-0.7310.0000.0000.0000.000
146B167VAL00.007-0.00113.1260.5200.5200.0000.0000.0000.000
147B168LEU0-0.034-0.0167.4100.6170.6170.0000.0000.0000.000
148B169ALA00.0370.01411.478-0.975-0.9750.0000.0000.0000.000
149B170LYS10.8280.8989.520-25.412-25.4120.0000.0000.0000.000
150B171ASP-1-0.807-0.89813.08114.98014.9800.0000.0000.0000.000
151B172GLY00.0110.00114.8400.0160.0160.0000.0000.0000.000
152B173ALA00.0470.01113.0220.7810.7810.0000.0000.0000.000
153B174ASP-1-0.783-0.84510.03027.05927.0590.0000.0000.0000.000
154B175THR0-0.066-0.0466.987-1.687-1.6870.0000.0000.0000.000
155B176PHE0-0.027-0.0088.9471.2561.2560.0000.0000.0000.000
156B177ILE0-0.009-0.0069.7230.7040.7040.0000.0000.0000.000
157B178VAL00.007-0.00412.111-1.450-1.4500.0000.0000.0000.000
158B179GLY00.0290.00915.298-1.386-1.3860.0000.0000.0000.000
159B180THR0-0.0230.00015.4191.4021.4020.0000.0000.0000.000
160B181HIS00.0350.03217.217-0.390-0.3900.0000.0000.0000.000
161B182SER0-0.002-0.00619.0890.0850.0850.0000.0000.0000.000
162B183ALA00.0380.03022.807-0.590-0.5900.0000.0000.0000.000
163B184GLY0-0.009-0.01423.4000.6770.6770.0000.0000.0000.000
164B185GLY00.0200.01825.097-0.388-0.3880.0000.0000.0000.000
165B186ASN00.0050.00127.6840.1330.1330.0000.0000.0000.000
166B187GLY00.0100.01625.7530.0070.0070.0000.0000.0000.000
167B188VAL0-0.022-0.00223.9930.3710.3710.0000.0000.0000.000
168B189GLY00.0250.01721.348-0.263-0.2630.0000.0000.0000.000
169B190TYR00.015-0.00522.359-0.087-0.0870.0000.0000.0000.000
170B191CYS0-0.030-0.00118.8370.3810.3810.0000.0000.0000.000
171B192SER00.0750.03120.796-0.779-0.7790.0000.0000.0000.000
172B193CYS0-0.062-0.02819.8430.9440.9440.0000.0000.0000.000
173B194VAL0-0.003-0.02118.556-0.689-0.6890.0000.0000.0000.000
174B195SER0-0.003-0.04618.0620.7650.7650.0000.0000.0000.000
175B196ARG10.9190.96113.705-18.093-18.0930.0000.0000.0000.000
176B197SER0-0.019-0.04717.679-0.460-0.4600.0000.0000.0000.000
177B198MET0-0.0330.02121.223-0.421-0.4210.0000.0000.0000.000
178B199LEU00.0410.02916.412-0.328-0.3280.0000.0000.0000.000
179B200GLN0-0.005-0.01318.489-0.109-0.1090.0000.0000.0000.000
180B201LYS10.9060.94820.990-12.457-12.4570.0000.0000.0000.000
181B202MET00.0400.04122.980-0.485-0.4850.0000.0000.0000.000
182B203LYS10.8310.90020.252-13.277-13.2770.0000.0000.0000.000
183B204ALA0-0.042-0.01622.826-0.187-0.1870.0000.0000.0000.000
184B205HIS00.0420.03625.759-0.355-0.3550.0000.0000.0000.000
185B206VAL0-0.047-0.00824.2340.2420.2420.0000.0000.0000.000