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: LNJ49

Calculation Name: 1YOX-B-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1YOX

Chain ID: B

ChEMBL ID:

UniProt ID: Q9HXU4

Base Structure: X-ray

Registration Date: 2023-09-21

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 201
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2099540.057211
FMO2-HF: Nuclear repulsion 2022875.669396
FMO2-HF: Total energy -76664.387815
FMO2-MP2: Total energy -76886.210007


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:ALA)


Summations of interaction energy for fragment #1(B:2:ALA)
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.
-13.366-8.7764.158-4.784-3.965-0.035
Interaction energy analysis for fragmet #1(B:2:ALA)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.019 / q_NPA : -0.012
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].
3B4HIS0-0.015-0.0013.880-0.8101.008-0.009-1.023-0.7860.004
4B5GLU-1-0.965-0.9805.833-1.385-1.3850.0000.0000.0000.000
5B6LEU0-0.037-0.0178.1630.3180.3180.0000.0000.0000.000
6B7ASP-1-0.758-0.85511.631-0.486-0.4860.0000.0000.0000.000
7B8TYR0-0.074-0.05514.7450.0170.0170.0000.0000.0000.000
8B9ARG10.8300.89117.5880.3490.3490.0000.0000.0000.000
9B10ILE00.0030.00120.506-0.006-0.0060.0000.0000.0000.000
10B11LEU0-0.050-0.01823.1040.0240.0240.0000.0000.0000.000
11B12GLY00.0700.04026.682-0.002-0.0020.0000.0000.0000.000
12B13GLU-1-0.889-0.95329.164-0.188-0.1880.0000.0000.0000.000
13B14SER0-0.093-0.06331.3620.0110.0110.0000.0000.0000.000
14B15MET0-0.064-0.01730.749-0.002-0.0020.0000.0000.0000.000
15B16GLN0-0.039-0.01826.388-0.005-0.0050.0000.0000.0000.000
16B17THR0-0.023-0.01424.9660.0070.0070.0000.0000.0000.000
17B18VAL0-0.0040.00218.8840.0120.0120.0000.0000.0000.000
18B19GLU-1-0.783-0.83921.461-0.337-0.3370.0000.0000.0000.000
19B20ILE00.0180.00815.155-0.008-0.0080.0000.0000.0000.000
20B21GLU-1-0.821-0.90716.430-0.372-0.3720.0000.0000.0000.000
21B22LEU0-0.024-0.00213.632-0.097-0.0970.0000.0000.0000.000
22B23ASP-1-0.817-0.91513.539-0.389-0.3890.0000.0000.0000.000
23B24PRO0-0.082-0.04514.404-0.063-0.0630.0000.0000.0000.000
24B25GLY00.0010.00813.099-0.023-0.0230.0000.0000.0000.000
25B26GLU-1-0.833-0.9139.856-1.484-1.4840.0000.0000.0000.000
26B27THR0-0.043-0.02910.9730.2590.2590.0000.0000.0000.000
27B28VAL0-0.0050.00411.201-0.242-0.2420.0000.0000.0000.000
28B29ILE0-0.041-0.02311.4810.1480.1480.0000.0000.0000.000
29B30ALA00.0790.03814.6360.0040.0040.0000.0000.0000.000
30B31GLU-1-0.905-0.96018.252-0.367-0.3670.0000.0000.0000.000
31B32ALA00.000-0.01721.311-0.001-0.0010.0000.0000.0000.000
32B33GLY0-0.047-0.02524.0900.0170.0170.0000.0000.0000.000
33B34ALA00.0360.03122.4300.0130.0130.0000.0000.0000.000
34B35MET0-0.0290.00422.698-0.003-0.0030.0000.0000.0000.000
35B36ASN0-0.060-0.03924.1150.0170.0170.0000.0000.0000.000
36B37TYR0-0.059-0.06225.5460.0310.0310.0000.0000.0000.000
37B38MET00.0030.00623.135-0.037-0.0370.0000.0000.0000.000
38B39THR0-0.005-0.00723.1760.0230.0230.0000.0000.0000.000
39B40GLY00.011-0.00224.645-0.009-0.0090.0000.0000.0000.000
40B41ASP-1-0.797-0.88121.959-0.251-0.2510.0000.0000.0000.000
41B42ILE0-0.0220.01319.261-0.030-0.0300.0000.0000.0000.000
42B43ARG10.8020.89320.1860.3490.3490.0000.0000.0000.000
43B44PHE00.0320.00619.338-0.042-0.0420.0000.0000.0000.000
44B45THR0-0.0030.00717.7810.0410.0410.0000.0000.0000.000
45B46ALA0-0.016-0.00719.031-0.032-0.0320.0000.0000.0000.000
46B47ARG10.8840.94613.3510.4550.4550.0000.0000.0000.000
47B75MET0-0.058-0.03614.5310.0170.0170.0000.0000.0000.000
48B76THR0-0.014-0.00417.6710.0010.0010.0000.0000.0000.000
49B77HIS00.0330.02113.458-0.074-0.0740.0000.0000.0000.000
50B78PHE00.015-0.00916.0080.1040.1040.0000.0000.0000.000
51B79THR00.0570.01714.209-0.087-0.0870.0000.0000.0000.000
52B80ASN0-0.039-0.02215.8870.1390.1390.0000.0000.0000.000
53B81GLU-1-0.921-0.97116.770-0.502-0.5020.0000.0000.0000.000
54B82GLY0-0.036-0.02319.1990.0530.0530.0000.0000.0000.000
55B83GLN0-0.128-0.06319.7570.0010.0010.0000.0000.0000.000
56B84GLY00.0020.00020.1840.0060.0060.0000.0000.0000.000
57B85LYS10.8500.91017.1060.4270.4270.0000.0000.0000.000
58B86GLN0-0.0390.01418.6550.0590.0590.0000.0000.0000.000
59B87HIS00.020-0.01818.915-0.046-0.0460.0000.0000.0000.000
60B88VAL0-0.023-0.02519.3060.0350.0350.0000.0000.0000.000
61B89ALA0-0.0230.01320.677-0.029-0.0290.0000.0000.0000.000
62B90PHE00.0290.00418.4460.0080.0080.0000.0000.0000.000
63B91ALA00.0280.00722.9290.0020.0020.0000.0000.0000.000
64B92ALA00.0520.03824.7230.0010.0010.0000.0000.0000.000
65B93PRO0-0.023-0.00926.0020.0150.0150.0000.0000.0000.000
66B94TYR0-0.075-0.07326.1370.0240.0240.0000.0000.0000.000
67B95PRO00.0200.01530.012-0.011-0.0110.0000.0000.0000.000
68B96GLY00.002-0.01229.3880.0110.0110.0000.0000.0000.000
69B97SER00.0430.03727.039-0.006-0.0060.0000.0000.0000.000
70B98VAL00.003-0.00221.271-0.004-0.0040.0000.0000.0000.000
71B99VAL0-0.056-0.03719.9320.0170.0170.0000.0000.0000.000
72B100ALA00.0460.03016.597-0.028-0.0280.0000.0000.0000.000
73B101VAL0-0.068-0.04414.6440.0740.0740.0000.0000.0000.000
74B102ASP-1-0.797-0.89710.207-1.055-1.0550.0000.0000.0000.000
75B103LEU0-0.033-0.0268.8620.1630.1630.0000.0000.0000.000
76B104ASP-1-0.861-0.9238.386-0.223-0.2230.0000.0000.0000.000
77B105ASP-1-0.976-0.97710.966-0.205-0.2050.0000.0000.0000.000
78B106VAL0-0.159-0.08113.3980.0650.0650.0000.0000.0000.000
79B107GLY0-0.026-0.00613.0880.0230.0230.0000.0000.0000.000
80B108GLY00.0450.0289.4840.1110.1110.0000.0000.0000.000
81B109ARG10.6820.80410.244-0.060-0.0600.0000.0000.0000.000
82B110LEU00.0190.02012.9470.0210.0210.0000.0000.0000.000
83B111PHE0-0.040-0.02115.538-0.011-0.0110.0000.0000.0000.000
84B112CYS00.0270.00118.428-0.013-0.0130.0000.0000.0000.000
85B113GLN0-0.072-0.04520.2790.0220.0220.0000.0000.0000.000
86B114LYS10.8910.93221.9540.2070.2070.0000.0000.0000.000
87B115ASP-1-0.872-0.92723.040-0.208-0.2080.0000.0000.0000.000
88B116SER0-0.035-0.00123.0930.0110.0110.0000.0000.0000.000
89B117PHE0-0.0080.00514.997-0.019-0.0190.0000.0000.0000.000
90B118LEU0-0.0150.00318.6420.0350.0350.0000.0000.0000.000
91B119CYS0-0.030-0.00416.200-0.001-0.0010.0000.0000.0000.000
92B120ALA0-0.010-0.00411.4280.0220.0220.0000.0000.0000.000
93B121ALA00.0940.0628.3330.0940.0940.0000.0000.0000.000
94B122TYR0-0.010-0.0016.9700.1260.1260.0000.0000.0000.000
95B123GLY00.0490.0294.931-0.978-0.9780.0000.0000.0000.000
96B124THR0-0.054-0.0295.4840.6770.6770.0000.0000.0000.000
97B125ARG10.8320.9107.3020.3150.3150.0000.0000.0000.000
98B126VAL00.0180.0029.7280.0630.0630.0000.0000.0000.000
99B127GLY0-0.010-0.00513.4970.0540.0540.0000.0000.0000.000
100B128ILE0-0.059-0.02716.413-0.021-0.0210.0000.0000.0000.000
101B129ALA0-0.0140.00719.5790.0240.0240.0000.0000.0000.000
102B130PHE00.0270.00620.8880.0250.0250.0000.0000.0000.000
103B131THR0-0.026-0.02524.628-0.021-0.0210.0000.0000.0000.000
104B132LYS10.8470.93627.3350.0610.0610.0000.0000.0000.000
105B133ARG10.9590.97430.4600.0770.0770.0000.0000.0000.000
106B134LEU00.0180.00034.1690.0060.0060.0000.0000.0000.000
107B135GLY00.0350.04037.4310.0020.0020.0000.0000.0000.000
108B144PHE0-0.016-0.01727.4380.0000.0000.0000.0000.0000.000
109B145ILE00.004-0.01123.3870.0100.0100.0000.0000.0000.000
110B146LEU00.0050.02022.428-0.013-0.0130.0000.0000.0000.000
111B147GLN00.0650.01317.9290.0250.0250.0000.0000.0000.000
112B148LYS10.8350.91514.9500.0710.0710.0000.0000.0000.000
113B149LEU00.0230.01812.453-0.008-0.0080.0000.0000.0000.000
114B150GLU-1-0.744-0.87210.0750.1290.1290.0000.0000.0000.000
115B151GLY0-0.042-0.0245.902-0.143-0.1430.0000.0000.0000.000
116B152ASP-1-0.786-0.8562.350-8.604-5.8324.167-3.761-3.179-0.039
117B153GLY00.1100.0555.450-0.544-0.5440.0000.0000.0000.000
118B154LEU0-0.0220.0047.4710.3890.3890.0000.0000.0000.000
119B155VAL0-0.036-0.02011.077-0.104-0.1040.0000.0000.0000.000
120B156PHE00.000-0.00813.2990.1000.1000.0000.0000.0000.000
121B157VAL0-0.006-0.00517.0650.0140.0140.0000.0000.0000.000
122B158HIS00.001-0.01019.994-0.009-0.0090.0000.0000.0000.000
123B159ALA0-0.002-0.01123.7910.0160.0160.0000.0000.0000.000
124B160GLY00.0190.01426.8510.0050.0050.0000.0000.0000.000
125B161GLY0-0.061-0.04630.2380.0120.0120.0000.0000.0000.000
126B162THR0-0.001-0.01031.333-0.007-0.0070.0000.0000.0000.000
127B163LEU00.0380.02924.6050.0070.0070.0000.0000.0000.000
128B164ILE0-0.040-0.02728.3720.0110.0110.0000.0000.0000.000
129B165ARG10.9640.99521.4550.2140.2140.0000.0000.0000.000
130B166ARG10.9300.95326.6350.0960.0960.0000.0000.0000.000
131B167GLN00.0650.05524.171-0.026-0.0260.0000.0000.0000.000
132B168LEU0-0.062-0.01527.0000.0050.0050.0000.0000.0000.000
133B169ASN0-0.053-0.05527.7290.0020.0020.0000.0000.0000.000
134B170GLY00.0340.02330.0960.0070.0070.0000.0000.0000.000
135B171GLU-1-0.892-0.92631.588-0.050-0.0500.0000.0000.0000.000
136B172THR0-0.035-0.03932.2120.0010.0010.0000.0000.0000.000
137B173LEU0-0.0110.00130.4790.0000.0000.0000.0000.0000.000
138B174ARG10.9390.96133.5280.0480.0480.0000.0000.0000.000
139B175VAL00.0050.01030.512-0.001-0.0010.0000.0000.0000.000
140B176ASP-1-0.770-0.86834.027-0.098-0.0980.0000.0000.0000.000
141B177THR00.027-0.01930.717-0.005-0.0050.0000.0000.0000.000
142B178GLY00.0190.02530.007-0.008-0.0080.0000.0000.0000.000
143B179CYS0-0.104-0.05629.725-0.009-0.0090.0000.0000.0000.000
144B180LEU0-0.0010.01625.371-0.005-0.0050.0000.0000.0000.000
145B181VAL00.0060.01922.317-0.002-0.0020.0000.0000.0000.000
146B182ALA00.0490.00919.759-0.017-0.0170.0000.0000.0000.000
147B183PHE0-0.041-0.02720.4830.0200.0200.0000.0000.0000.000
148B184THR00.0660.04418.215-0.025-0.0250.0000.0000.0000.000
149B185ASP-1-0.794-0.89416.707-0.009-0.0090.0000.0000.0000.000
150B186GLY00.0190.01519.775-0.007-0.0070.0000.0000.0000.000
151B187ILE0-0.066-0.02323.0170.0010.0010.0000.0000.0000.000
152B188ASP-1-0.875-0.93024.870-0.011-0.0110.0000.0000.0000.000
153B189TYR0-0.020-0.03823.234-0.014-0.0140.0000.0000.0000.000
154B190ASP-1-0.851-0.91228.451-0.036-0.0360.0000.0000.0000.000
155B191VAL00.0100.01829.901-0.006-0.0060.0000.0000.0000.000
156B192GLN0-0.020-0.02132.8590.0040.0040.0000.0000.0000.000
157B193LEU00.0280.01936.620-0.005-0.0050.0000.0000.0000.000
158B194ALA0-0.001-0.00239.6500.0040.0040.0000.0000.0000.000
159B195GLY00.0020.00741.1530.0030.0030.0000.0000.0000.000
160B196GLY0-0.0020.00244.7110.0000.0000.0000.0000.0000.000
161B197LEU0-0.060-0.03540.789-0.001-0.0010.0000.0000.0000.000
162B198LYS10.8730.93443.6130.0480.0480.0000.0000.0000.000
163B199SER00.0420.00443.293-0.004-0.0040.0000.0000.0000.000
164B200MET0-0.0210.00742.4900.0020.0020.0000.0000.0000.000
165B201LEU0-0.053-0.04246.0770.0030.0030.0000.0000.0000.000
166B202PHE0-0.018-0.01046.2990.0010.0010.0000.0000.0000.000
167B203GLY00.0620.04445.6710.0020.0020.0000.0000.0000.000
168B204GLY0-0.025-0.00146.7580.0020.0020.0000.0000.0000.000
169B205GLU-1-0.892-0.96443.438-0.057-0.0570.0000.0000.0000.000
170B206GLY00.0350.04941.255-0.002-0.0020.0000.0000.0000.000
171B207LEU0-0.042-0.02138.271-0.005-0.0050.0000.0000.0000.000
172B208LEU00.0270.02034.2230.0050.0050.0000.0000.0000.000
173B209LEU0-0.045-0.00235.726-0.006-0.0060.0000.0000.0000.000
174B210THR00.024-0.00729.3900.0010.0010.0000.0000.0000.000
175B211THR0-0.067-0.04532.822-0.002-0.0020.0000.0000.0000.000
176B212LEU00.0230.00527.295-0.002-0.0020.0000.0000.0000.000
177B213LYS10.9250.95729.3520.0230.0230.0000.0000.0000.000
178B214GLY00.0280.03827.9910.0000.0000.0000.0000.0000.000
179B215SER0-0.023-0.02826.404-0.004-0.0040.0000.0000.0000.000
180B216GLY00.0550.03323.2150.0080.0080.0000.0000.0000.000
181B217THR0-0.033-0.01821.346-0.002-0.0020.0000.0000.0000.000
182B218VAL0-0.024-0.02022.609-0.007-0.0070.0000.0000.0000.000
183B219TRP00.0400.00919.2980.0000.0000.0000.0000.0000.000
184B220LEU0-0.016-0.00724.7290.0020.0020.0000.0000.0000.000
185B221GLN00.0660.04127.275-0.016-0.0160.0000.0000.0000.000
186B222SER00.0240.02229.7330.0080.0080.0000.0000.0000.000
187B223LEU0-0.067-0.03932.6830.0130.0130.0000.0000.0000.000
188B224PRO00.0150.02430.959-0.008-0.0080.0000.0000.0000.000
189B225PHE00.0760.04830.0820.0100.0100.0000.0000.0000.000
190B226SER00.0260.01031.7350.0080.0080.0000.0000.0000.000
191B227ARG10.8450.89733.4840.1130.1130.0000.0000.0000.000
192B228LEU0-0.0100.00134.7060.0070.0070.0000.0000.0000.000
193B229ALA00.0320.00935.4070.0060.0060.0000.0000.0000.000
194B230GLY00.0220.01637.1850.0060.0060.0000.0000.0000.000
195B231ARG10.8360.89139.0770.0810.0810.0000.0000.0000.000
196B232ILE00.0250.01239.1020.0040.0040.0000.0000.0000.000
197B233TYR0-0.0080.01240.9990.0040.0040.0000.0000.0000.000
198B234ASP-1-0.769-0.88542.842-0.065-0.0650.0000.0000.0000.000
199B235ALA0-0.062-0.01845.0060.0040.0040.0000.0000.0000.000
200B236THR0-0.058-0.03845.2320.0010.0010.0000.0000.0000.000
201B237PHE0-0.078-0.03343.2640.0050.0050.0000.0000.0000.000