Manual

About

FMODB

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

Last updated: 2024-05-02

All entries: 37386

Number of unique PDB entries: 7781

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FMODB ID: YV6Y2

Calculation Name: 1YJE-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1YJE

Chain ID: A

ChEMBL ID:

UniProt ID: P22829

Base Structure: X-ray

Registration Date: 2023-09-20

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 226
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2787323.604837
FMO2-HF: Nuclear repulsion 2698608.713537
FMO2-HF: Total energy -88714.8913
FMO2-MP2: Total energy -88973.376042


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(A:362:ASN)


Summations of interaction energy for fragment #1(A:362:ASN)
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.
-31.573-35.26121.341-9.142-8.5110.061
Interaction energy analysis for fragmet #1(A:362:ASN)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.070 / q_NPA : 0.054
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].
3A364LEU00.1110.0472.825-2.2611.1830.692-1.861-2.2750.011
4A365THR0-0.008-0.0121.753-20.868-28.53820.609-7.113-5.8250.048
5A366SER0-0.010-0.0143.712-4.632-4.0940.040-0.168-0.4110.002
6A367LEU00.0160.0105.765-1.106-1.1060.0000.0000.0000.000
7A368ILE0-0.013-0.0065.803-0.940-0.9400.0000.0000.0000.000
8A369ARG10.8560.9307.437-1.553-1.5530.0000.0000.0000.000
9A370ALA00.0310.0229.691-0.333-0.3330.0000.0000.0000.000
10A371HIS00.0060.01311.288-0.232-0.2320.0000.0000.0000.000
11A372LEU00.0110.00311.549-0.204-0.2040.0000.0000.0000.000
12A373ASP-1-0.825-0.89413.0520.5360.5360.0000.0000.0000.000
13A374SER0-0.095-0.03815.745-0.095-0.0950.0000.0000.0000.000
14A375GLY0-0.015-0.00917.513-0.044-0.0440.0000.0000.0000.000
15A376PRO0-0.0210.00619.165-0.029-0.0290.0000.0000.0000.000
16A377ASN00.0440.00721.3120.0310.0310.0000.0000.0000.000
17A378THR00.0150.00022.074-0.027-0.0270.0000.0000.0000.000
18A379ALA00.0200.01624.352-0.020-0.0200.0000.0000.0000.000
19A380LYS10.7690.88226.002-0.185-0.1850.0000.0000.0000.000
20A381LEU00.0520.04325.7250.0160.0160.0000.0000.0000.000
21A382ASP-1-0.847-0.92828.4720.1340.1340.0000.0000.0000.000
22A383TYR00.032-0.00430.9030.0050.0050.0000.0000.0000.000
23A384SER0-0.047-0.02934.706-0.008-0.0080.0000.0000.0000.000
24A385LYS10.9580.98134.734-0.148-0.1480.0000.0000.0000.000
25A386PHE0-0.0260.00935.370-0.002-0.0020.0000.0000.0000.000
26A387GLN0-0.009-0.02037.367-0.009-0.0090.0000.0000.0000.000
27A388GLU-1-0.836-0.92538.2740.1260.1260.0000.0000.0000.000
28A389LEU0-0.035-0.00240.835-0.007-0.0070.0000.0000.0000.000
29A390VAL00.0240.00442.8700.0030.0030.0000.0000.0000.000
30A391LEU0-0.005-0.00645.5510.0000.0000.0000.0000.0000.000
31A392PRO00.015-0.00244.9480.0020.0020.0000.0000.0000.000
32A393ARG10.9630.99242.694-0.110-0.1100.0000.0000.0000.000
33A394PHE00.0200.02146.4310.0020.0020.0000.0000.0000.000
34A395GLY0-0.011-0.01749.3000.0000.0000.0000.0000.0000.000
35A396LYS10.7810.87846.510-0.092-0.0920.0000.0000.0000.000
36A397GLU-1-0.792-0.88143.3620.0990.0990.0000.0000.0000.000
37A398ASP-1-0.863-0.92546.1990.0900.0900.0000.0000.0000.000
38A399ALA00.0790.01445.0170.0050.0050.0000.0000.0000.000
39A400GLY0-0.0010.00643.5640.0040.0040.0000.0000.0000.000
40A401ASP-1-0.846-0.92741.4040.1130.1130.0000.0000.0000.000
41A402VAL00.0100.00739.8810.0090.0090.0000.0000.0000.000
42A403GLN0-0.0050.00038.3660.0020.0020.0000.0000.0000.000
43A404GLN00.0040.01236.5090.0070.0070.0000.0000.0000.000
44A405PHE0-0.019-0.01933.5890.0130.0130.0000.0000.0000.000
45A406TYR00.0600.01234.2070.0160.0160.0000.0000.0000.000
46A407ASP-1-0.828-0.90033.8620.1490.1490.0000.0000.0000.000
47A408LEU0-0.099-0.04031.1900.0130.0130.0000.0000.0000.000
48A409LEU0-0.0020.00329.5120.0230.0230.0000.0000.0000.000
49A410SER00.0300.01229.1090.0130.0130.0000.0000.0000.000
50A411GLY0-0.023-0.02128.9610.0080.0080.0000.0000.0000.000
51A412SER0-0.038-0.06225.0990.0230.0230.0000.0000.0000.000
52A413LEU00.0150.02724.0760.0350.0350.0000.0000.0000.000
53A414ASP-1-0.837-0.90424.0660.2330.2330.0000.0000.0000.000
54A415VAL0-0.109-0.06720.6010.0150.0150.0000.0000.0000.000
55A416ILE0-0.002-0.01219.8400.0490.0490.0000.0000.0000.000
56A417ARG10.9751.00019.275-0.190-0.1900.0000.0000.0000.000
57A418LYS10.9260.96518.558-0.266-0.2660.0000.0000.0000.000
58A419TRP0-0.081-0.04013.693-0.025-0.0250.0000.0000.0000.000
59A420ALA00.0360.01314.6290.0880.0880.0000.0000.0000.000
60A421GLU-1-0.879-0.94514.4470.3380.3380.0000.0000.0000.000
61A422LYS10.7350.86811.797-0.514-0.5140.0000.0000.0000.000
62A423ILE00.0130.01310.1410.2120.2120.0000.0000.0000.000
63A424PRO0-0.063-0.0546.098-0.158-0.1580.0000.0000.0000.000
64A425GLY00.0780.0538.6450.0470.0470.0000.0000.0000.000
65A426PHE0-0.016-0.01311.7500.0160.0160.0000.0000.0000.000
66A427ILE00.031-0.00113.147-0.036-0.0360.0000.0000.0000.000
67A428GLU-1-0.977-0.99311.2240.0330.0330.0000.0000.0000.000
68A429LEU0-0.057-0.00115.734-0.022-0.0220.0000.0000.0000.000
69A430SER0-0.018-0.01818.404-0.011-0.0110.0000.0000.0000.000
70A431PRO00.060-0.00222.1560.0160.0160.0000.0000.0000.000
71A432GLY0-0.0100.00923.8500.0060.0060.0000.0000.0000.000
72A433ASP-1-0.710-0.85821.7370.1800.1800.0000.0000.0000.000
73A434GLN0-0.089-0.02819.1720.0220.0220.0000.0000.0000.000
74A435ASP-1-0.840-0.93521.5360.2410.2410.0000.0000.0000.000
75A436LEU0-0.0010.01624.5760.0050.0050.0000.0000.0000.000
76A437LEU0-0.031-0.02518.7210.0090.0090.0000.0000.0000.000
77A438LEU0-0.027-0.00920.9360.0310.0310.0000.0000.0000.000
78A439GLU-1-0.827-0.90323.2430.2010.2010.0000.0000.0000.000
79A440SER00.0320.02025.212-0.011-0.0110.0000.0000.0000.000
80A441ALA0-0.060-0.01921.5000.0050.0050.0000.0000.0000.000
81A442PHE0-0.013-0.00123.5920.0160.0160.0000.0000.0000.000
82A443LEU00.0220.01325.0280.0170.0170.0000.0000.0000.000
83A444GLU-1-0.740-0.86123.1260.3440.3440.0000.0000.0000.000
84A445LEU0-0.022-0.01418.8380.0300.0300.0000.0000.0000.000
85A446PHE0-0.036-0.02022.2090.0190.0190.0000.0000.0000.000
86A447ILE00.004-0.00325.0000.0000.0000.0000.0000.0000.000
87A448LEU00.0250.02018.865-0.005-0.0050.0000.0000.0000.000
88A449ARG10.8780.92817.108-0.572-0.5720.0000.0000.0000.000
89A450LEU0-0.048-0.00721.471-0.004-0.0040.0000.0000.0000.000
90A451ALA00.0230.02824.656-0.020-0.0200.0000.0000.0000.000
91A452TYR0-0.061-0.02916.8310.0060.0060.0000.0000.0000.000
92A453ARG10.8580.92921.556-0.389-0.3890.0000.0000.0000.000
93A454SER0-0.023-0.01123.152-0.032-0.0320.0000.0000.0000.000
94A455LYS10.8680.91326.498-0.183-0.1830.0000.0000.0000.000
95A456PRO00.0340.00928.672-0.020-0.0200.0000.0000.0000.000
96A457GLY0-0.033-0.01131.618-0.012-0.0120.0000.0000.0000.000
97A458GLU-1-0.801-0.89231.8360.1490.1490.0000.0000.0000.000
98A459GLY0-0.0090.00734.070-0.007-0.0070.0000.0000.0000.000
99A460LYS10.7700.89831.686-0.142-0.1420.0000.0000.0000.000
100A461LEU00.0230.01830.0620.0150.0150.0000.0000.0000.000
101A462ILE0-0.0050.00125.998-0.010-0.0100.0000.0000.0000.000
102A463PHE00.0740.02426.3870.0290.0290.0000.0000.0000.000
103A464CYS0-0.036-0.01223.1270.0030.0030.0000.0000.0000.000
104A465SER00.0490.02923.7280.0170.0170.0000.0000.0000.000
105A466GLY00.018-0.00725.787-0.016-0.0160.0000.0000.0000.000
106A467LEU0-0.0310.00226.905-0.014-0.0140.0000.0000.0000.000
107A468VAL00.0090.01129.7140.0140.0140.0000.0000.0000.000
108A469LEU0-0.005-0.01331.793-0.013-0.0130.0000.0000.0000.000
109A470HIS00.0400.02033.9220.0100.0100.0000.0000.0000.000
110A471ARG10.9690.98235.760-0.139-0.1390.0000.0000.0000.000
111A472LEU0-0.022-0.01836.6800.0000.0000.0000.0000.0000.000
112A473GLN0-0.039-0.02638.0900.0000.0000.0000.0000.0000.000
113A474CYS0-0.046-0.00235.1790.0030.0030.0000.0000.0000.000
114A475ALA00.0050.00437.6210.0010.0010.0000.0000.0000.000
115A476ARG10.8180.91039.993-0.094-0.0940.0000.0000.0000.000
116A477GLY00.0460.02239.184-0.002-0.0020.0000.0000.0000.000
117A478PHE0-0.005-0.00631.8420.0040.0040.0000.0000.0000.000
118A479GLY00.0370.01937.3490.0010.0010.0000.0000.0000.000
119A480ASP-1-0.891-0.96838.9150.1310.1310.0000.0000.0000.000
120A481TRP00.0110.02931.1830.0050.0050.0000.0000.0000.000
121A482ILE0-0.007-0.00832.5690.0120.0120.0000.0000.0000.000
122A483ASP-1-0.851-0.94533.8500.1510.1510.0000.0000.0000.000
123A484ASN0-0.0090.00334.0890.0040.0040.0000.0000.0000.000
124A485ILE00.0370.02628.7910.0120.0120.0000.0000.0000.000
125A486LEU0-0.016-0.00529.4740.0170.0170.0000.0000.0000.000
126A487ALA0-0.047-0.02030.7090.0050.0050.0000.0000.0000.000
127A488PHE00.0350.01023.9760.0070.0070.0000.0000.0000.000
128A489SER0-0.040-0.03926.2290.0110.0110.0000.0000.0000.000
129A490ARG10.9570.96226.371-0.158-0.1580.0000.0000.0000.000
130A491SER0-0.062-0.02627.876-0.002-0.0020.0000.0000.0000.000
131A492LEU0-0.024-0.02221.5740.0080.0080.0000.0000.0000.000
132A493HIS0-0.029-0.01622.7670.0170.0170.0000.0000.0000.000
133A494SER0-0.092-0.05024.845-0.015-0.0150.0000.0000.0000.000
134A495LEU0-0.079-0.01821.388-0.012-0.0120.0000.0000.0000.000
135A496GLY00.0280.04121.367-0.006-0.0060.0000.0000.0000.000
136A497VAL00.003-0.01516.3530.0180.0180.0000.0000.0000.000
137A498ASP-1-0.821-0.88412.6270.9250.9250.0000.0000.0000.000
138A499VAL00.0680.01011.4890.0720.0720.0000.0000.0000.000
139A500PRO00.024-0.0078.3230.1510.1510.0000.0000.0000.000
140A501ALA00.0350.02510.0380.2000.2000.0000.0000.0000.000
141A502PHE00.0310.00512.755-0.046-0.0460.0000.0000.0000.000
142A503ALA0-0.038-0.0069.951-0.079-0.0790.0000.0000.0000.000
143A504CYS0-0.038-0.0118.9420.2400.2400.0000.0000.0000.000
144A505LEU0-0.028-0.01311.231-0.186-0.1860.0000.0000.0000.000
145A506SER0-0.002-0.02914.509-0.077-0.0770.0000.0000.0000.000
146A507ALA00.0390.01712.203-0.103-0.1030.0000.0000.0000.000
147A508LEU0-0.024-0.01013.738-0.108-0.1080.0000.0000.0000.000
148A509VAL0-0.0360.00515.982-0.083-0.0830.0000.0000.0000.000
149A510LEU0-0.043-0.02316.241-0.061-0.0610.0000.0000.0000.000
150A511ILE0-0.050-0.03113.583-0.059-0.0590.0000.0000.0000.000
151A512THR0-0.018-0.01417.5370.0140.0140.0000.0000.0000.000
152A513ASP-1-0.876-0.93820.3540.2080.2080.0000.0000.0000.000
153A514ARG10.8540.93422.362-0.311-0.3110.0000.0000.0000.000
154A515HIS00.000-0.01725.706-0.010-0.0100.0000.0000.0000.000
155A516GLY00.0080.01928.724-0.003-0.0030.0000.0000.0000.000
156A517LEU00.0240.01822.2580.0040.0040.0000.0000.0000.000
157A518GLN00.0170.00724.364-0.005-0.0050.0000.0000.0000.000
158A519ASP-1-0.885-0.93221.6570.0930.0930.0000.0000.0000.000
159A520PRO00.010-0.00421.0980.0170.0170.0000.0000.0000.000
160A521ARG10.9180.95617.498-0.079-0.0790.0000.0000.0000.000
161A522ARG10.8220.89517.014-0.134-0.1340.0000.0000.0000.000
162A523VAL00.0120.01315.9190.0310.0310.0000.0000.0000.000
163A524GLU-1-0.850-0.91716.4710.2240.2240.0000.0000.0000.000
164A525GLU-1-0.843-0.89613.6030.1240.1240.0000.0000.0000.000
165A526LEU0-0.051-0.03610.2130.0420.0420.0000.0000.0000.000
166A527GLN00.0450.01112.0470.1230.1230.0000.0000.0000.000
167A528ASN0-0.023-0.02713.6420.1180.1180.0000.0000.0000.000
168A529ARG10.8890.9588.468-0.207-0.2070.0000.0000.0000.000
169A530ILE00.0320.0179.2930.2710.2710.0000.0000.0000.000
170A531ALA0-0.0010.00610.4470.1620.1620.0000.0000.0000.000
171A532SER0-0.023-0.02310.250-0.038-0.0380.0000.0000.0000.000
172A533CYS0-0.0150.0026.4350.3160.3160.0000.0000.0000.000
173A534LEU0-0.0040.0188.318-0.072-0.0720.0000.0000.0000.000
174A535LYS10.9410.95611.086-0.362-0.3620.0000.0000.0000.000
175A536GLU-1-0.948-0.9828.040-0.040-0.0400.0000.0000.0000.000
176A537HIS0-0.040-0.0298.253-0.109-0.1090.0000.0000.0000.000
177A538MET0-0.027-0.0199.914-0.169-0.1690.0000.0000.0000.000
178A539ALA0-0.095-0.03513.123-0.089-0.0890.0000.0000.0000.000
179A540ALA0-0.033-0.01610.505-0.088-0.0880.0000.0000.0000.000
180A541VAL0-0.051-0.00611.913-0.081-0.0810.0000.0000.0000.000
181A549SER00.0350.00620.9530.0040.0040.0000.0000.0000.000
182A550CYS00.0220.00318.576-0.006-0.0060.0000.0000.0000.000
183A551LEU00.1000.05915.5370.0100.0100.0000.0000.0000.000
184A552SER00.023-0.00718.4250.0150.0150.0000.0000.0000.000
185A553ARG10.9160.96021.871-0.206-0.2060.0000.0000.0000.000
186A554LEU00.0370.02116.332-0.010-0.0100.0000.0000.0000.000
187A555LEU00.018-0.00618.096-0.002-0.0020.0000.0000.0000.000
188A556GLY0-0.024-0.00621.367-0.019-0.0190.0000.0000.0000.000
189A557LYS10.7930.88822.714-0.274-0.2740.0000.0000.0000.000
190A558LEU00.0370.01020.230-0.008-0.0080.0000.0000.0000.000
191A559PRO00.0000.00224.461-0.011-0.0110.0000.0000.0000.000
192A560GLU-1-0.739-0.83727.6920.2240.2240.0000.0000.0000.000
193A561LEU00.0030.01322.877-0.007-0.0070.0000.0000.0000.000
194A562ARG10.8580.89724.578-0.291-0.2910.0000.0000.0000.000
195A563THR00.002-0.00728.867-0.016-0.0160.0000.0000.0000.000
196A564LEU0-0.015-0.00728.826-0.009-0.0090.0000.0000.0000.000
197A565CYS0-0.0260.00427.8790.0010.0010.0000.0000.0000.000
198A566THR00.0050.01030.594-0.010-0.0100.0000.0000.0000.000
199A567GLN00.012-0.01733.969-0.002-0.0020.0000.0000.0000.000
200A568GLY0-0.006-0.00433.082-0.007-0.0070.0000.0000.0000.000
201A569LEU00.017-0.00732.482-0.005-0.0050.0000.0000.0000.000
202A570GLN0-0.016-0.00235.346-0.005-0.0050.0000.0000.0000.000
203A571ARG10.8120.90637.528-0.128-0.1280.0000.0000.0000.000
204A572ILE00.0260.01133.316-0.005-0.0050.0000.0000.0000.000
205A573PHE0-0.016-0.00337.857-0.006-0.0060.0000.0000.0000.000
206A574CYS0-0.038-0.03240.533-0.007-0.0070.0000.0000.0000.000
207A575LEU0-0.058-0.01738.691-0.004-0.0040.0000.0000.0000.000
208A576LYS10.8470.92040.044-0.119-0.1190.0000.0000.0000.000
209A577LEU0-0.053-0.03142.410-0.005-0.0050.0000.0000.0000.000
210A578GLU-1-0.845-0.90044.8780.0990.0990.0000.0000.0000.000
211A579ASP-1-0.943-0.96045.1780.0900.0900.0000.0000.0000.000
212A580LEU0-0.054-0.02145.428-0.004-0.0040.0000.0000.0000.000
213A581VAL0-0.044-0.03141.746-0.003-0.0030.0000.0000.0000.000
214A582PRO00.0420.02442.3560.0020.0020.0000.0000.0000.000
215A583PRO0-0.006-0.01038.6260.0050.0050.0000.0000.0000.000
216A584PRO00.0070.02234.391-0.003-0.0030.0000.0000.0000.000
217A585PRO00.0800.00933.2720.0030.0030.0000.0000.0000.000
218A586ILE0-0.035-0.01028.4990.0000.0000.0000.0000.0000.000
219A587VAL00.0200.01932.4260.0050.0050.0000.0000.0000.000
220A588ASP-1-0.829-0.90435.0240.1210.1210.0000.0000.0000.000
221A589LYS10.8180.89330.703-0.174-0.1740.0000.0000.0000.000
222A590ILE00.0280.00828.9110.0020.0020.0000.0000.0000.000
223A591PHE0-0.024-0.01332.516-0.003-0.0030.0000.0000.0000.000
224A592MET0-0.050-0.04635.816-0.007-0.0070.0000.0000.0000.000
225A593ASP-1-0.945-0.95330.8170.1740.1740.0000.0000.0000.000
226A594THR0-0.161-0.06334.001-0.003-0.0030.0000.0000.0000.000