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: XVK81

Calculation Name: 4YVO-A-Xray27

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 4YVO

Chain ID: A

ChEMBL ID:

UniProt ID: Q940U6

Base Structure: X-ray

Registration Date: 2018-07-26

Reference:

DOI:


IFIE MAP

IFIE Diagram


Modeling method
Optimization MOE:Amber10:EHT
Restraint OptH
Protonation MOE:Protonate 3D
Complement Missing residues were capped by ACE, NME. Missing atoms were corrected by Structure prepareation by MOE.
Water Apo structure with with a 3 angstrom solvent shell.
Procedure Auto-FMO protocol ver. 1.20180227
FMO calculation
FMO method FMO2-MP2/6-31G(d)
Fragmentation Auto
Number of fragment 208
LigandCharge
Software MIZUHO/ABINIT-MP 3.0
Total energy (hartree)
FMO2-HF: Electronic energy -1215358.938248
FMO2-HF: Nuclear repulsion 1161810.782803
FMO2-HF: Total energy -53548.155445
FMO2-MP2: Total energy -53703.632897


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:197:ACE)


Summations of interaction energy for fragment #1(A:197:ACE)
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.
48.886-13.9159.50411.256-7.9620.035
Interaction energy analysis for fragmet #1(A:197:ACE)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.143 / q_NPA : -0.133
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].
3A199LYS10.9051.0511.50921.717-11.50137.2860.033-4.1000.024
4A200LYS10.9340.9831.8422.733-1.2254.7060.809-1.5570.015
5A201GLN00.0610.0403.8090.6650.9990.007-0.092-0.2490.000
6A202GLU-1-0.861-0.9225.7540.1570.1570.0000.0000.0000.000
7A203LEU0-0.0140.0066.4050.1280.1280.0000.0000.0000.000
8A204ILE00.0040.0047.7840.0570.0570.0000.0000.0000.000
9A205SER0-0.007-0.0079.6640.1040.1040.0000.0000.0000.000
10A206LYS10.9000.95510.9510.1100.1100.0000.0000.0000.000
11A207LEU00.0080.01711.9560.0260.0260.0000.0000.0000.000
12A208LYS10.9050.96714.0480.2080.2080.0000.0000.0000.000
13A209THR0-0.043-0.08615.5210.0130.0130.0000.0000.0000.000
14A210GLY00.0860.04516.6530.0120.0120.0000.0000.0000.000
15A211LYS10.9010.93617.9330.0470.0470.0000.0000.0000.000
16A212THR0-0.0070.00620.0560.0000.0000.0000.0000.0000.000
17A213PHE00.0340.02619.6320.0030.0030.0000.0000.0000.000
18A214LEU0-0.019-0.00322.6390.0040.0040.0000.0000.0000.000
19A215ARG10.8580.93521.6220.0710.0710.0000.0000.0000.000
20A216ASN0-0.027-0.00725.5540.0020.0020.0000.0000.0000.000
21A217GLN0-0.029-0.00927.8850.0010.0010.0000.0000.0000.000
22A218GLU-1-0.869-0.92925.838-0.032-0.0320.0000.0000.0000.000
23A219PRO00.0290.00624.9450.0000.0000.0000.0000.0000.000
24A220GLU-1-0.741-0.85024.4540.0130.0130.0000.0000.0000.000
25A221LYS10.9750.98822.5700.0270.0270.0000.0000.0000.000
26A222ALA00.0360.00920.6430.0000.0000.0000.0000.0000.000
27A223TYR00.0060.00719.5760.0110.0110.0000.0000.0000.000
28A224THR0-0.0120.01717.8830.0180.0180.0000.0000.0000.000
29A225GLU-1-0.813-0.86215.931-0.027-0.0270.0000.0000.0000.000
30A226PHE00.0110.00014.7740.0120.0120.0000.0000.0000.000
31A227LYS10.8730.95315.502-0.088-0.0880.0000.0000.0000.000
32A228ILE00.0150.00711.0580.0380.0380.0000.0000.0000.000
33A229ALA0-0.021-0.01110.8990.0770.0770.0000.0000.0000.000
34A230LEU00.013-0.00111.1930.0620.0620.0000.0000.0000.000
35A231GLU-1-0.887-0.92311.7100.3510.3510.0000.0000.0000.000
36A232LEU0-0.051-0.0376.4500.1580.1580.0000.0000.0000.000
37A233ALA0-0.005-0.0047.8270.2230.2230.0000.0000.0000.000
38A234GLN0-0.013-0.0079.7150.0460.0460.0000.0000.0000.000
39A235SER0-0.073-0.0257.9910.1510.1510.0000.0000.0000.000
40A236LEU0-0.082-0.0653.2400.0140.2500.029-0.095-0.1690.000
41A237LYS10.9380.9857.375-0.477-0.4770.0000.0000.0000.000
42A238ASP-1-0.757-0.8398.8990.1290.1290.0000.0000.0000.000
43A239PRO00.0930.04410.935-0.017-0.0170.0000.0000.0000.000
44A240THR00.0330.01913.828-0.031-0.0310.0000.0000.0000.000
45A241GLU-1-0.764-0.8819.866-0.047-0.0470.0000.0000.0000.000
46A242GLU-1-0.777-0.86612.7790.2180.2180.0000.0000.0000.000
47A243LYS10.7770.89914.236-0.086-0.0860.0000.0000.0000.000
48A244LYS10.8360.92214.0360.0090.0090.0000.0000.0000.000
49A245ALA00.0060.00614.017-0.018-0.0180.0000.0000.0000.000
50A246ALA00.0050.00916.124-0.010-0.0100.0000.0000.0000.000
51A247ARG10.8710.94619.178-0.020-0.0200.0000.0000.0000.000
52A248GLY0-0.040-0.01719.463-0.009-0.0090.0000.0000.0000.000
53A249LEU0-0.014-0.00517.961-0.007-0.0070.0000.0000.0000.000
54A250GLY00.0450.02321.430-0.005-0.0050.0000.0000.0000.000
55A251ALA00.0210.00623.928-0.005-0.0050.0000.0000.0000.000
56A252SER0-0.055-0.05022.462-0.007-0.0070.0000.0000.0000.000
57A253LEU0-0.029-0.01624.769-0.003-0.0030.0000.0000.0000.000
58A254GLN00.0550.03427.2490.0000.0000.0000.0000.0000.000
59A255ARG10.8470.92827.5830.0040.0040.0000.0000.0000.000
60A256GLN00.0260.04026.045-0.001-0.0010.0000.0000.0000.000
61A257GLY00.0710.06030.9500.0010.0010.0000.0000.0000.000
62A258LYS10.8870.95028.959-0.032-0.0320.0000.0000.0000.000
63A259TYR00.1070.03530.1660.0050.0050.0000.0000.0000.000
64A260ARG11.0111.00931.335-0.031-0.0310.0000.0000.0000.000
65A261GLU-1-0.691-0.70027.1920.0560.0560.0000.0000.0000.000
66A262ALA00.0040.00326.6780.0060.0060.0000.0000.0000.000
67A263ILE00.0400.01926.7160.0040.0040.0000.0000.0000.000
68A264GLN0-0.0130.02423.797-0.003-0.0030.0000.0000.0000.000
69A265TYR0-0.015-0.06120.1790.0130.0130.0000.0000.0000.000
70A266HIS00.0680.03122.9170.0090.0090.0000.0000.0000.000
71A267SER0-0.019-0.01125.133-0.001-0.0010.0000.0000.0000.000
72A268MET0-0.036-0.00318.3350.0000.0000.0000.0000.0000.000
73A269VAL00.0120.02720.8940.0090.0090.0000.0000.0000.000
74A270LEU0-0.0170.01322.2690.0010.0010.0000.0000.0000.000
75A271ALA00.009-0.00323.4910.0000.0000.0000.0000.0000.000
76A272ILE00.002-0.00417.5660.0020.0020.0000.0000.0000.000
77A273SER00.013-0.00221.0210.0010.0010.0000.0000.0000.000
78A274LYS10.8860.95522.805-0.058-0.0580.0000.0000.0000.000
79A275ARG10.8600.94319.386-0.145-0.1450.0000.0000.0000.000
80A276GLU-1-0.915-0.96318.1780.1630.1630.0000.0000.0000.000
81A277SER0-0.051-0.02521.266-0.008-0.0080.0000.0000.0000.000
82A278GLU-1-0.719-0.81419.4110.0500.0500.0000.0000.0000.000
83A279ASP-1-0.783-0.85622.4570.0320.0320.0000.0000.0000.000
84A280SER0-0.003-0.02619.928-0.004-0.0040.0000.0000.0000.000
85A281GLY00.0140.01322.2190.0080.0080.0000.0000.0000.000
86A282ILE0-0.017-0.00723.7170.0010.0010.0000.0000.0000.000
87A283THR00.0580.03326.3540.0020.0020.0000.0000.0000.000
88A284GLU-1-0.734-0.84725.1730.0060.0060.0000.0000.0000.000
89A285ALA00.0100.00325.3780.0000.0000.0000.0000.0000.000
90A286TYR00.0060.01527.3400.0040.0040.0000.0000.0000.000
91A287GLY00.0880.05630.9260.0000.0000.0000.0000.0000.000
92A288ALA00.001-0.00228.424-0.001-0.0010.0000.0000.0000.000
93A289ILE0-0.055-0.03028.1300.0010.0010.0000.0000.0000.000
94A290ALA00.0120.01231.4970.0000.0000.0000.0000.0000.000
95A291ASP-1-0.713-0.82333.0890.0120.0120.0000.0000.0000.000
96A292CYS0-0.076-0.03931.1610.0000.0000.0000.0000.0000.000
97A293TYR0-0.033-0.02033.6970.0010.0010.0000.0000.0000.000
98A294THR00.0040.01336.685-0.001-0.0010.0000.0000.0000.000
99A295GLU-1-0.911-0.94735.9830.0120.0120.0000.0000.0000.000
100A296LEU0-0.133-0.05534.7070.0010.0010.0000.0000.0000.000
101A297GLY00.0410.03338.9520.0000.0000.0000.0000.0000.000
102A298ASP-1-0.842-0.92939.1510.0290.0290.0000.0000.0000.000
103A299LEU00.0840.01940.4930.0010.0010.0000.0000.0000.000
104A300GLU-1-0.895-0.93242.5210.0220.0220.0000.0000.0000.000
105A301LYS10.8100.90036.898-0.033-0.0330.0000.0000.0000.000
106A302ALA00.0190.01037.6290.0010.0010.0000.0000.0000.000
107A303GLY00.0290.02038.512-0.001-0.0010.0000.0000.0000.000
108A304LYS10.9760.99938.510-0.028-0.0280.0000.0000.0000.000
109A305PHE0-0.017-0.02231.5500.0010.0010.0000.0000.0000.000
110A306TYR00.0200.01235.546-0.001-0.0010.0000.0000.0000.000
111A307ASP-1-0.858-0.92237.6160.0160.0160.0000.0000.0000.000
112A308THR0-0.061-0.03033.9460.0000.0000.0000.0000.0000.000
113A309TYR0-0.062-0.03131.951-0.001-0.0010.0000.0000.0000.000
114A310ILE00.0230.01734.751-0.002-0.0020.0000.0000.0000.000
115A311ALA00.0120.01537.686-0.001-0.0010.0000.0000.0000.000
116A312ARG10.8250.88928.160-0.024-0.0240.0000.0000.0000.000
117A313LEU0-0.0060.00532.832-0.001-0.0010.0000.0000.0000.000
118A314GLU-1-0.853-0.91335.2680.0070.0070.0000.0000.0000.000
119A315THR0-0.126-0.06234.7550.0000.0000.0000.0000.0000.000
120A316ASP-2-1.757-1.80932.1900.0030.0030.0000.0000.0000.000
121A401HOH0-0.012-0.01716.515-0.010-0.0100.0000.0000.0000.000
122A402HOH0-0.069-0.09330.8360.0000.0000.0000.0000.0000.000
123A403HOH0-0.098-0.09537.3000.0000.0000.0000.0000.0000.000
124A404HOH0-0.070-0.07930.076-0.001-0.0010.0000.0000.0000.000
125A405HOH0-0.075-0.07626.6100.0010.0010.0000.0000.0000.000
126A406HOH0-0.020-0.04028.1200.0000.0000.0000.0000.0000.000
127A407HOH00.0190.04523.6630.0050.0050.0000.0000.0000.000
128A408HOH0-0.036-0.0417.1180.0370.0370.0000.0000.0000.000
129A409HOH0-0.064-0.05121.797-0.002-0.0020.0000.0000.0000.000
130A410HOH0-0.007-0.02727.2160.0000.0000.0000.0000.0000.000
131A411HOH0-0.028-0.03233.891-0.001-0.0010.0000.0000.0000.000
132A412HOH0-0.029-0.03112.5790.0090.0090.0000.0000.0000.000
133A413HOH0-0.080-0.05229.9460.0000.0000.0000.0000.0000.000
134A414HOH0-0.050-0.03733.998-0.001-0.0010.0000.0000.0000.000
135A415HOH00.0310.02124.9360.0040.0040.0000.0000.0000.000
136A416HOH00.0330.01927.903-0.002-0.0020.0000.0000.0000.000
137A417HOH0-0.021-0.02518.060-0.010-0.0100.0000.0000.0000.000
138A418HOH00.003-0.01221.3320.0020.0020.0000.0000.0000.000
139A419HOH00.0090.00229.841-0.002-0.0020.0000.0000.0000.000
140A420HOH00.005-0.00412.699-0.011-0.0110.0000.0000.0000.000
141A421HOH0-0.019-0.02531.2830.0010.0010.0000.0000.0000.000
142A422HOH0-0.022-0.01916.076-0.010-0.0100.0000.0000.0000.000
143A423HOH0-0.034-0.03035.7910.0000.0000.0000.0000.0000.000
144A424HOH0-0.056-0.03712.8900.0040.0040.0000.0000.0000.000
145A425HOH00.0040.00532.066-0.002-0.0020.0000.0000.0000.000
146A426HOH0-0.033-0.02742.5940.0000.0000.0000.0000.0000.000
147A427HOH00.0320.00929.5510.0020.0020.0000.0000.0000.000
148A428HOH0-0.023-0.00841.7940.0010.0010.0000.0000.0000.000
149A429HOH0-0.028-0.02229.9710.0000.0000.0000.0000.0000.000
150A430HOH0-0.014-0.02124.7290.0020.0020.0000.0000.0000.000
151A431HOH0-0.042-0.03024.679-0.002-0.0020.0000.0000.0000.000
152A432HOH0-0.002-0.00127.654-0.001-0.0010.0000.0000.0000.000
153A433HOH0-0.0010.01323.364-0.004-0.0040.0000.0000.0000.000
154A434HOH0-0.014-0.01621.757-0.001-0.0010.0000.0000.0000.000
155A435HOH00.0370.02717.393-0.004-0.0040.0000.0000.0000.000
156A436HOH0-0.063-0.04432.2130.0000.0000.0000.0000.0000.000
157A437HOH0-0.048-0.02940.7530.0000.0000.0000.0000.0000.000
158A438HOH0-0.035-0.02430.631-0.001-0.0010.0000.0000.0000.000
159A439HOH00.0360.02539.6650.0000.0000.0000.0000.0000.000
160A440HOH0-0.033-0.03216.8300.0070.0070.0000.0000.0000.000
161A441HOH0-0.017-0.01523.274-0.001-0.0010.0000.0000.0000.000
162A442HOH0-0.069-0.05238.9440.0000.0000.0000.0000.0000.000
163A443HOH00.0060.0036.3790.1420.1420.0000.0000.0000.000
164A444HOH0-0.038-0.02532.611-0.001-0.0010.0000.0000.0000.000
165A445HOH0-0.014-0.01726.4990.0000.0000.0000.0000.0000.000
166A446HOH0-0.026-0.02036.9470.0000.0000.0000.0000.0000.000
167A447HOH0-0.017-0.01840.8390.0000.0000.0000.0000.0000.000
168A448HOH0-0.051-0.0419.3190.0700.0700.0000.0000.0000.000
169A449HOH0-0.003-0.00918.661-0.006-0.0060.0000.0000.0000.000
170A450HOH0-0.018-0.01534.9720.0010.0010.0000.0000.0000.000
171A451HOH0-0.029-0.03125.8530.0030.0030.0000.0000.0000.000
172A452HOH0-0.028-0.02124.9790.0000.0000.0000.0000.0000.000
173A453HOH0-0.013-0.00124.106-0.002-0.0020.0000.0000.0000.000
174A454HOH0-0.042-0.02617.005-0.006-0.0060.0000.0000.0000.000
175A455HOH00.002-0.01623.5810.0010.0010.0000.0000.0000.000
176A456HOH0-0.038-0.02740.6730.0010.0010.0000.0000.0000.000
177A457HOH0-0.065-0.04129.700-0.001-0.0010.0000.0000.0000.000
178A458HOH0-0.058-0.03423.901-0.002-0.0020.0000.0000.0000.000
179A459HOH0-0.030-0.02138.9180.0010.0010.0000.0000.0000.000
180A460HOH0-0.060-0.03723.1800.0000.0000.0000.0000.0000.000
181A461HOH0-0.051-0.03015.559-0.007-0.0070.0000.0000.0000.000
182A462HOH0-0.061-0.04640.4170.0000.0000.0000.0000.0000.000
183A463HOH0-0.022-0.01726.730-0.002-0.0020.0000.0000.0000.000
184A464HOH00.0310.02521.084-0.001-0.0010.0000.0000.0000.000
185A465HOH0-0.018-0.00818.9860.0060.0060.0000.0000.0000.000
186A466HOH0-0.023-0.01630.9380.0000.0000.0000.0000.0000.000
187A467HOH0-0.007-0.01324.9950.0010.0010.0000.0000.0000.000
188A468HOH0-0.031-0.02013.1190.0190.0190.0000.0000.0000.000
189A470HOH0-0.039-0.02244.9800.0000.0000.0000.0000.0000.000
190A471HOH00.0220.01526.3410.0000.0000.0000.0000.0000.000
191A472HOH0-0.0280.0422.18721.840-4.35017.47610.601-1.887-0.004
192A473HOH0-0.046-0.03826.543-0.001-0.0010.0000.0000.0000.000
193A474HOH00.005-0.00219.515-0.009-0.0090.0000.0000.0000.000
194A475HOH0-0.026-0.01719.2300.0010.0010.0000.0000.0000.000
195A476HOH0-0.0030.00741.5880.0000.0000.0000.0000.0000.000
196A477HOH0-0.034-0.01821.471-0.002-0.0020.0000.0000.0000.000
197A478HOH00.0050.01224.9540.0020.0020.0000.0000.0000.000
198A479HOH00.0150.01032.7740.0010.0010.0000.0000.0000.000
199A480HOH0-0.023-0.01937.0580.0010.0010.0000.0000.0000.000
200A481HOH0-0.054-0.02836.8920.0000.0000.0000.0000.0000.000
201A482HOH00.000-0.00125.5010.0020.0020.0000.0000.0000.000
202A483HOH00.0410.02419.9580.0010.0010.0000.0000.0000.000
203A484HOH0-0.012-0.01116.7780.0010.0010.0000.0000.0000.000
204A485HOH00.0070.00523.925-0.003-0.0030.0000.0000.0000.000
205A486HOH00.0120.00215.889-0.003-0.0030.0000.0000.0000.000
206A487HOH00.0350.02018.819-0.002-0.0020.0000.0000.0000.000
207A488HOH0-0.023-0.01234.6360.0000.0000.0000.0000.0000.000
208A490HOH0-0.024-0.01720.389-0.002-0.0020.0000.0000.0000.000