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: 5JZ2Z

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 OptH
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 -2786978.682093
FMO2-HF: Nuclear repulsion 2698265.537769
FMO2-HF: Total energy -88713.144324
FMO2-MP2: Total energy -88971.696339


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.
-29.608-29.96814.46-6.008-8.0910.056
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 : 0.041 / q_NPA : 0.013
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].
3A364LEU00.1010.0393.060-0.8872.0860.475-1.601-1.8470.006
4A365THR0-0.0060.0121.856-15.326-18.86913.914-4.672-5.6990.047
5A366SER0-0.017-0.0193.496-5.632-5.4220.0710.265-0.5450.003
6A367LEU00.0040.0035.595-1.461-1.4610.0000.0000.0000.000
7A368ILE0-0.0080.0035.805-1.068-1.0680.0000.0000.0000.000
8A369ARG10.8920.9537.201-3.636-3.6360.0000.0000.0000.000
9A370ALA00.0150.0109.454-0.453-0.4530.0000.0000.0000.000
10A371HIS00.0000.01711.106-0.315-0.3150.0000.0000.0000.000
11A372LEU0-0.0010.00011.422-0.256-0.2560.0000.0000.0000.000
12A373ASP-1-0.913-0.94813.2841.1871.1870.0000.0000.0000.000
13A374SER0-0.117-0.05215.525-0.150-0.1500.0000.0000.0000.000
14A375GLY0-0.009-0.00917.320-0.097-0.0970.0000.0000.0000.000
15A376PRO0-0.0250.00318.986-0.015-0.0150.0000.0000.0000.000
16A377ASN00.0580.01521.1380.0320.0320.0000.0000.0000.000
17A378THR00.007-0.00422.061-0.036-0.0360.0000.0000.0000.000
18A379ALA00.0170.01624.175-0.034-0.0340.0000.0000.0000.000
19A380LYS10.8380.93125.825-0.301-0.3010.0000.0000.0000.000
20A381LEU00.0370.02925.5470.0230.0230.0000.0000.0000.000
21A382ASP-1-0.912-0.93528.3100.2350.2350.0000.0000.0000.000
22A383TYR00.015-0.01430.587-0.003-0.0030.0000.0000.0000.000
23A384SER0-0.043-0.06234.547-0.012-0.0120.0000.0000.0000.000
24A385LYS10.9880.99935.107-0.236-0.2360.0000.0000.0000.000
25A386PHE0-0.044-0.00635.198-0.006-0.0060.0000.0000.0000.000
26A387GLN0-0.007-0.02237.234-0.013-0.0130.0000.0000.0000.000
27A388GLU-1-0.924-0.95638.6390.1320.1320.0000.0000.0000.000
28A389LEU0-0.053-0.01640.753-0.007-0.0070.0000.0000.0000.000
29A390VAL00.0420.01842.8150.0000.0000.0000.0000.0000.000
30A391LEU0-0.012-0.01445.503-0.002-0.0020.0000.0000.0000.000
31A392PRO00.0190.00144.9000.0050.0050.0000.0000.0000.000
32A393ARG10.9761.00042.194-0.144-0.1440.0000.0000.0000.000
33A394PHE00.0430.03346.3570.0020.0020.0000.0000.0000.000
34A395GLY0-0.007-0.00449.2240.0030.0030.0000.0000.0000.000
35A396LYS10.7940.88546.714-0.124-0.1240.0000.0000.0000.000
36A397GLU-1-0.855-0.93243.4680.1350.1350.0000.0000.0000.000
37A398ASP-1-0.867-0.92846.0960.1330.1330.0000.0000.0000.000
38A399ALA00.0820.01544.8840.0060.0060.0000.0000.0000.000
39A400GLY0-0.0150.00143.3990.0080.0080.0000.0000.0000.000
40A401ASP-1-0.834-0.92941.2870.1560.1560.0000.0000.0000.000
41A402VAL00.0130.00339.7480.0120.0120.0000.0000.0000.000
42A403GLN00.0000.00238.0420.0030.0030.0000.0000.0000.000
43A404GLN0-0.0010.01436.3740.0150.0150.0000.0000.0000.000
44A405PHE0-0.040-0.02733.6380.0190.0190.0000.0000.0000.000
45A406TYR00.0640.01434.0670.0210.0210.0000.0000.0000.000
46A407ASP-1-0.843-0.90933.6950.2540.2540.0000.0000.0000.000
47A408LEU0-0.091-0.04230.8620.0250.0250.0000.0000.0000.000
48A409LEU00.0030.01629.3510.0340.0340.0000.0000.0000.000
49A410SER00.0140.00328.9440.0230.0230.0000.0000.0000.000
50A411GLY0-0.004-0.00428.7600.0220.0220.0000.0000.0000.000
51A412SER0-0.080-0.09624.9010.0390.0390.0000.0000.0000.000
52A413LEU00.0190.02423.8950.0540.0540.0000.0000.0000.000
53A414ASP-1-0.889-0.93423.9940.4630.4630.0000.0000.0000.000
54A415VAL0-0.070-0.05620.4260.0550.0550.0000.0000.0000.000
55A416ILE0-0.006-0.01019.6600.0870.0870.0000.0000.0000.000
56A417ARG11.0381.02619.085-0.431-0.4310.0000.0000.0000.000
57A418LYS10.9090.96418.644-0.530-0.5300.0000.0000.0000.000
58A419TRP0-0.069-0.04113.2650.0530.0530.0000.0000.0000.000
59A420ALA00.0320.01614.5930.1710.1710.0000.0000.0000.000
60A421GLU-1-0.906-0.95714.7030.9310.9310.0000.0000.0000.000
61A422LYS10.8470.93111.685-1.270-1.2700.0000.0000.0000.000
62A423ILE00.0220.02010.2440.5320.5320.0000.0000.0000.000
63A424PRO0-0.069-0.0566.359-0.140-0.1400.0000.0000.0000.000
64A425GLY00.0810.0538.999-0.151-0.1510.0000.0000.0000.000
65A426PHE0-0.015-0.00911.866-0.161-0.1610.0000.0000.0000.000
66A427ILE00.026-0.00113.922-0.111-0.1110.0000.0000.0000.000
67A428GLU-1-0.983-1.00111.5651.1601.1600.0000.0000.0000.000
68A429LEU0-0.053-0.00115.886-0.099-0.0990.0000.0000.0000.000
69A430SER00.0270.01818.4060.0050.0050.0000.0000.0000.000
70A431PRO00.045-0.00722.2120.0150.0150.0000.0000.0000.000
71A432GLY0-0.0090.00724.167-0.004-0.0040.0000.0000.0000.000
72A433ASP-1-0.758-0.91021.8690.3760.3760.0000.0000.0000.000
73A434GLN0-0.115-0.03419.4500.0030.0030.0000.0000.0000.000
74A435ASP-1-0.856-0.93821.6970.4860.4860.0000.0000.0000.000
75A436LEU00.0830.05724.711-0.011-0.0110.0000.0000.0000.000
76A437LEU0-0.0410.02618.645-0.010-0.0100.0000.0000.0000.000
77A438LEU0-0.031-0.01520.7060.0170.0170.0000.0000.0000.000
78A439GLU-1-0.915-0.96423.1350.3510.3510.0000.0000.0000.000
79A440SER0-0.023-0.07825.309-0.029-0.0290.0000.0000.0000.000
80A441ALA0-0.054-0.00721.467-0.014-0.0140.0000.0000.0000.000
81A442PHE0-0.021-0.00123.5250.0010.0010.0000.0000.0000.000
82A443LEU00.0200.01224.9360.0140.0140.0000.0000.0000.000
83A444GLU-1-0.753-0.88423.5290.3420.3420.0000.0000.0000.000
84A445LEU0-0.020-0.01418.6670.0180.0180.0000.0000.0000.000
85A446PHE0-0.041-0.02222.1440.0140.0140.0000.0000.0000.000
86A447ILE0-0.0010.00024.912-0.005-0.0050.0000.0000.0000.000
87A448LEU00.0280.02218.886-0.016-0.0160.0000.0000.0000.000
88A449ARG10.8690.92317.401-0.768-0.7680.0000.0000.0000.000
89A450LEU0-0.0390.00021.410-0.009-0.0090.0000.0000.0000.000
90A451ALA00.0300.04324.562-0.026-0.0260.0000.0000.0000.000
91A452TYR0-0.064-0.02117.0230.0030.0030.0000.0000.0000.000
92A453ARG10.8750.94021.034-0.516-0.5160.0000.0000.0000.000
93A454SER0-0.019-0.02323.101-0.023-0.0230.0000.0000.0000.000
94A455LYS10.9670.97326.479-0.228-0.2280.0000.0000.0000.000
95A456PRO00.0480.01228.640-0.016-0.0160.0000.0000.0000.000
96A457GLY0-0.052-0.02231.637-0.010-0.0100.0000.0000.0000.000
97A458GLU-1-0.895-0.95431.9950.1530.1530.0000.0000.0000.000
98A459GLY0-0.030-0.00734.034-0.003-0.0030.0000.0000.0000.000
99A460LYS10.8750.95331.327-0.171-0.1710.0000.0000.0000.000
100A461LEU00.0340.01929.9870.0110.0110.0000.0000.0000.000
101A462ILE0-0.020-0.00725.800-0.005-0.0050.0000.0000.0000.000
102A463PHE00.0640.01526.2880.0290.0290.0000.0000.0000.000
103A464CYS0-0.021-0.00422.7440.0140.0140.0000.0000.0000.000
104A465SER00.0700.04023.5400.0320.0320.0000.0000.0000.000
105A466GLY00.014-0.00825.639-0.017-0.0170.0000.0000.0000.000
106A467LEU0-0.0280.00526.734-0.026-0.0260.0000.0000.0000.000
107A468VAL00.0110.01129.5770.0100.0100.0000.0000.0000.000
108A469LEU00.005-0.00931.667-0.012-0.0120.0000.0000.0000.000
109A470HIS00.0640.04033.8360.0080.0080.0000.0000.0000.000
110A471ARG11.0151.00235.653-0.134-0.1340.0000.0000.0000.000
111A472LEU0-0.018-0.01736.6270.0010.0010.0000.0000.0000.000
112A473GLN0-0.057-0.03238.0050.0010.0010.0000.0000.0000.000
113A474CYS0-0.053-0.00735.0340.0090.0090.0000.0000.0000.000
114A475ALA00.0020.00337.5340.0030.0030.0000.0000.0000.000
115A476ARG10.8370.92139.931-0.125-0.1250.0000.0000.0000.000
116A477GLY00.0540.03139.081-0.002-0.0020.0000.0000.0000.000
117A478PHE00.001-0.00231.6890.0060.0060.0000.0000.0000.000
118A479GLY00.0220.01237.278-0.001-0.0010.0000.0000.0000.000
119A480ASP-1-0.882-0.96138.8780.1290.1290.0000.0000.0000.000
120A481TRP00.0230.02130.8670.0030.0030.0000.0000.0000.000
121A482ILE0-0.011-0.01132.6790.0090.0090.0000.0000.0000.000
122A483ASP-1-0.876-0.94033.8380.1440.1440.0000.0000.0000.000
123A484ASN0-0.0180.00734.0230.0000.0000.0000.0000.0000.000
124A485ILE00.0340.02528.7600.0040.0040.0000.0000.0000.000
125A486LEU0-0.031-0.00729.4900.0090.0090.0000.0000.0000.000
126A487ALA0-0.040-0.01530.747-0.003-0.0030.0000.0000.0000.000
127A488PHE00.0220.00224.114-0.001-0.0010.0000.0000.0000.000
128A489SER0-0.058-0.06426.1540.0000.0000.0000.0000.0000.000
129A490ARG10.9820.97126.429-0.132-0.1320.0000.0000.0000.000
130A491SER0-0.049-0.01727.828-0.019-0.0190.0000.0000.0000.000
131A492LEU0-0.021-0.02321.376-0.010-0.0100.0000.0000.0000.000
132A493HIS0-0.038-0.02222.906-0.016-0.0160.0000.0000.0000.000
133A494SER0-0.083-0.04124.600-0.023-0.0230.0000.0000.0000.000
134A495LEU0-0.080-0.02321.098-0.022-0.0220.0000.0000.0000.000
135A496GLY00.0270.04120.871-0.028-0.0280.0000.0000.0000.000
136A497VAL00.002-0.01016.514-0.009-0.0090.0000.0000.0000.000
137A498ASP-1-0.832-0.87012.4650.3720.3720.0000.0000.0000.000
138A499VAL00.0880.01811.1840.0620.0620.0000.0000.0000.000
139A500PRO00.034-0.0108.1540.2300.2300.0000.0000.0000.000
140A501ALA00.0540.03810.1110.1550.1550.0000.0000.0000.000
141A502PHE00.0240.00412.8090.0140.0140.0000.0000.0000.000
142A503ALA0-0.046-0.0199.957-0.010-0.0100.0000.0000.0000.000
143A504CYS0-0.052-0.0279.3280.2610.2610.0000.0000.0000.000
144A505LEU0-0.022-0.01611.292-0.109-0.1090.0000.0000.0000.000
145A506SER0-0.012-0.01714.483-0.020-0.0200.0000.0000.0000.000
146A507ALA00.0450.02012.156-0.057-0.0570.0000.0000.0000.000
147A508LEU0-0.014-0.00913.872-0.077-0.0770.0000.0000.0000.000
148A509VAL0-0.0480.00116.020-0.079-0.0790.0000.0000.0000.000
149A510LEU0-0.036-0.02616.029-0.048-0.0480.0000.0000.0000.000
150A511ILE0-0.074-0.03513.662-0.039-0.0390.0000.0000.0000.000
151A512THR0-0.015-0.00717.524-0.034-0.0340.0000.0000.0000.000
152A513ASP-1-0.881-0.94220.3390.2800.2800.0000.0000.0000.000
153A514ARG10.8700.93922.684-0.396-0.3960.0000.0000.0000.000
154A515HIS00.011-0.01725.6940.0040.0040.0000.0000.0000.000
155A516GLY00.0020.01928.704-0.001-0.0010.0000.0000.0000.000
156A517LEU00.0200.01722.3100.0160.0160.0000.0000.0000.000
157A518GLN00.0170.01524.2450.0040.0040.0000.0000.0000.000
158A519ASP-1-0.888-0.93121.6530.2690.2690.0000.0000.0000.000
159A520PRO00.021-0.00221.0910.0440.0440.0000.0000.0000.000
160A521ARG10.9020.93817.898-0.180-0.1800.0000.0000.0000.000
161A522ARG10.8610.91617.009-0.404-0.4040.0000.0000.0000.000
162A523VAL00.0220.02115.9100.0620.0620.0000.0000.0000.000
163A524GLU-1-0.869-0.92616.4580.2280.2280.0000.0000.0000.000
164A525GLU-1-0.868-0.91814.0620.2140.2140.0000.0000.0000.000
165A526LEU0-0.070-0.0459.955-0.010-0.0100.0000.0000.0000.000
166A527GLN00.0730.02212.0310.1110.1110.0000.0000.0000.000
167A528ASN0-0.024-0.02313.7040.0050.0050.0000.0000.0000.000
168A529ARG10.9410.9978.442-0.769-0.7690.0000.0000.0000.000
169A530ILE00.0160.0099.352-0.008-0.0080.0000.0000.0000.000
170A531ALA00.0070.00810.546-0.034-0.0340.0000.0000.0000.000
171A532SER0-0.014-0.02410.148-0.107-0.1070.0000.0000.0000.000
172A533CYS0-0.0080.0146.348-0.227-0.2270.0000.0000.0000.000
173A534LEU00.0000.0228.476-0.235-0.2350.0000.0000.0000.000
174A535LYS10.9460.95211.1630.2520.2520.0000.0000.0000.000
175A536GLU-1-0.973-0.9887.692-1.927-1.9270.0000.0000.0000.000
176A537HIS0-0.031-0.0307.522-0.282-0.2820.0000.0000.0000.000
177A538MET0-0.039-0.0259.1140.0300.0300.0000.0000.0000.000
178A539ALA0-0.101-0.03612.2950.0560.0560.0000.0000.0000.000
179A540ALA0-0.026-0.0119.815-0.017-0.0170.0000.0000.0000.000
180A541VAL0-0.052-0.00711.4800.0710.0710.0000.0000.0000.000
181A549SER00.0370.00820.489-0.009-0.0090.0000.0000.0000.000
182A550CYS00.012-0.00317.8100.0390.0390.0000.0000.0000.000
183A551LEU00.0900.05415.5180.0400.0400.0000.0000.0000.000
184A552SER00.008-0.01018.0670.0450.0450.0000.0000.0000.000
185A553ARG10.9550.97621.3890.0760.0760.0000.0000.0000.000
186A554LEU00.0240.01316.5020.0140.0140.0000.0000.0000.000
187A555LEU00.003-0.01218.0220.0310.0310.0000.0000.0000.000
188A556GLY0-0.018-0.00221.5440.0080.0080.0000.0000.0000.000
189A557LYS10.8760.94722.880-0.136-0.1360.0000.0000.0000.000
190A558LEU00.0330.00920.2380.0090.0090.0000.0000.0000.000
191A559PRO00.0010.00324.5680.0070.0070.0000.0000.0000.000
192A560GLU-1-0.810-0.89827.8140.1470.1470.0000.0000.0000.000
193A561LEU0-0.0080.00722.9060.0020.0020.0000.0000.0000.000
194A562ARG10.8690.91424.780-0.271-0.2710.0000.0000.0000.000
195A563THR0-0.012-0.00628.922-0.006-0.0060.0000.0000.0000.000
196A564LEU0-0.005-0.00328.316-0.003-0.0030.0000.0000.0000.000
197A565CYS0-0.035-0.01027.8280.0110.0110.0000.0000.0000.000
198A566THR00.0270.02530.590-0.003-0.0030.0000.0000.0000.000
199A567GLN0-0.007-0.04333.976-0.006-0.0060.0000.0000.0000.000
200A568GLY0-0.0060.00433.044-0.005-0.0050.0000.0000.0000.000
201A569LEU00.0280.00032.3730.0000.0000.0000.0000.0000.000
202A570GLN0-0.036-0.00835.303-0.007-0.0070.0000.0000.0000.000
203A571ARG10.8410.92837.467-0.162-0.1620.0000.0000.0000.000
204A572ILE00.0240.01033.402-0.002-0.0020.0000.0000.0000.000
205A573PHE0-0.0200.00237.776-0.004-0.0040.0000.0000.0000.000
206A574CYS0-0.020-0.03040.462-0.008-0.0080.0000.0000.0000.000
207A575LEU0-0.056-0.01338.610-0.004-0.0040.0000.0000.0000.000
208A576LYS10.9330.97740.365-0.166-0.1660.0000.0000.0000.000
209A577LEU0-0.067-0.04342.300-0.005-0.0050.0000.0000.0000.000
210A578GLU-1-0.879-0.91545.1560.1290.1290.0000.0000.0000.000
211A579ASP-1-0.959-0.96745.0540.1460.1460.0000.0000.0000.000
212A580LEU0-0.040-0.01445.310-0.005-0.0050.0000.0000.0000.000
213A581VAL0-0.058-0.03441.557-0.002-0.0020.0000.0000.0000.000
214A582PRO00.0330.01442.2200.0010.0010.0000.0000.0000.000
215A583PRO00.0110.00238.5070.0080.0080.0000.0000.0000.000
216A584PRO00.0020.02234.1810.0020.0020.0000.0000.0000.000
217A585PRO00.0910.01233.4030.0010.0010.0000.0000.0000.000
218A586ILE0-0.060-0.01928.2980.0010.0010.0000.0000.0000.000
219A587VAL00.0160.01832.2700.0010.0010.0000.0000.0000.000
220A588ASP-1-0.873-0.94034.8920.2020.2020.0000.0000.0000.000
221A589LYS10.8810.94930.473-0.328-0.3280.0000.0000.0000.000
222A590ILE00.0190.00528.538-0.001-0.0010.0000.0000.0000.000
223A591PHE0-0.023-0.01932.416-0.013-0.0130.0000.0000.0000.000
224A592MET0-0.046-0.04335.825-0.012-0.0120.0000.0000.0000.000
225A593ASP-1-0.946-0.95230.7710.2730.2730.0000.0000.0000.000
226A594THR0-0.140-0.05333.930-0.012-0.0120.0000.0000.0000.000