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: YZK22

Calculation Name: 4ATZ-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 4ATZ

Chain ID: A

ChEMBL ID:

UniProt ID: P11818

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 182
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -1869304.523224
FMO2-HF: Nuclear repulsion 1799937.179406
FMO2-HF: Total energy -69367.343818
FMO2-MP2: Total energy -69571.710465


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:400:ASN)


Summations of interaction energy for fragment #1(A:400: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.
-0.6593.2880.458-1.401-3.0040.004
Interaction energy analysis for fragmet #1(A:400:ASN)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.003 / q_NPA : -0.038
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].
3A402LYS10.9590.9892.7032.0514.3630.142-0.933-1.5220.002
4A403LEU0-0.077-0.0333.031-0.5630.9490.317-0.463-1.3660.002
5A404THR0-0.030-0.0165.0721.4141.537-0.001-0.005-0.1160.000
6A405LEU00.0050.0297.690-0.291-0.2910.0000.0000.0000.000
7A406TRP00.0350.00010.1600.2690.2690.0000.0000.0000.000
8A407THR00.0130.01413.333-0.061-0.0610.0000.0000.0000.000
9A408THR0-0.034-0.01113.4440.0140.0140.0000.0000.0000.000
10A409PRO0-0.008-0.02613.0510.0060.0060.0000.0000.0000.000
11A410ALA0-0.0050.00215.5880.0080.0080.0000.0000.0000.000
12A411PRO0-0.0510.02018.438-0.024-0.0240.0000.0000.0000.000
13A412SER00.001-0.00620.2940.0180.0180.0000.0000.0000.000
14A413PRO0-0.054-0.05223.554-0.002-0.0020.0000.0000.0000.000
15A414ASN00.0280.03520.580-0.007-0.0070.0000.0000.0000.000
16A415CYS0-0.0280.00024.556-0.013-0.0130.0000.0000.0000.000
17A416ARG10.8840.95626.4800.0070.0070.0000.0000.0000.000
18A417LEU0-0.020-0.02028.658-0.003-0.0030.0000.0000.0000.000
19A418ASN0-0.062-0.03831.679-0.007-0.0070.0000.0000.0000.000
20A419ALA0-0.068-0.03934.244-0.007-0.0070.0000.0000.0000.000
21A420GLU-1-0.902-0.96730.859-0.013-0.0130.0000.0000.0000.000
22A421LYS10.8830.94026.7130.0140.0140.0000.0000.0000.000
23A422ASP-1-0.721-0.84029.8620.0480.0480.0000.0000.0000.000
24A423ALA00.0360.02028.0160.0100.0100.0000.0000.0000.000
25A424LYS10.9170.97323.657-0.144-0.1440.0000.0000.0000.000
26A425LEU00.0440.01421.0930.0140.0140.0000.0000.0000.000
27A426THR00.0050.01017.289-0.014-0.0140.0000.0000.0000.000
28A427LEU00.0170.00116.8740.0220.0220.0000.0000.0000.000
29A428VAL0-0.012-0.01711.296-0.049-0.0490.0000.0000.0000.000
30A429LEU00.0070.00912.5530.0840.0840.0000.0000.0000.000
31A430THR00.0230.0096.931-0.058-0.0580.0000.0000.0000.000
32A431LYS10.7830.8777.6930.5400.5400.0000.0000.0000.000
33A432CYS0-0.042-0.0117.8140.4130.4130.0000.0000.0000.000
34A433GLY00.024-0.0019.071-0.118-0.1180.0000.0000.0000.000
35A434SER0-0.012-0.00710.888-0.032-0.0320.0000.0000.0000.000
36A435GLN00.0360.02913.4540.0100.0100.0000.0000.0000.000
37A436ILE0-0.0290.00911.8160.0390.0390.0000.0000.0000.000
38A437LEU0-0.0070.01011.115-0.020-0.0200.0000.0000.0000.000
39A438ALA00.029-0.00512.7970.0410.0410.0000.0000.0000.000
40A439THR0-0.063-0.03914.4520.0100.0100.0000.0000.0000.000
41A440VAL00.0440.02916.993-0.028-0.0280.0000.0000.0000.000
42A441SER0-0.018-0.00819.9390.0110.0110.0000.0000.0000.000
43A442VAL00.0180.00622.655-0.014-0.0140.0000.0000.0000.000
44A443LEU00.0030.01325.2840.0090.0090.0000.0000.0000.000
45A444ALA00.002-0.00127.690-0.010-0.0100.0000.0000.0000.000
46A445VAL0-0.059-0.04128.7050.0070.0070.0000.0000.0000.000
47A446LYS10.9420.97731.643-0.037-0.0370.0000.0000.0000.000
48A447GLY00.004-0.00734.733-0.001-0.0010.0000.0000.0000.000
49A448SER00.0030.01037.5170.0050.0050.0000.0000.0000.000
50A449LEU00.0450.01933.2760.0010.0010.0000.0000.0000.000
51A450ALA0-0.0280.00334.0440.0100.0100.0000.0000.0000.000
52A451PRO00.0290.00536.111-0.003-0.0030.0000.0000.0000.000
53A452ILE0-0.016-0.00435.551-0.007-0.0070.0000.0000.0000.000
54A453SER0-0.028-0.00938.976-0.002-0.0020.0000.0000.0000.000
55A454GLY00.004-0.01342.401-0.001-0.0010.0000.0000.0000.000
56A455THR0-0.005-0.01144.5550.0030.0030.0000.0000.0000.000
57A456VAL00.0260.03038.105-0.001-0.0010.0000.0000.0000.000
58A457GLN00.003-0.01939.1580.0060.0060.0000.0000.0000.000
59A458SER00.0320.02635.7660.0020.0020.0000.0000.0000.000
60A459ALA0-0.019-0.00132.278-0.003-0.0030.0000.0000.0000.000
61A460HIS0-0.004-0.00930.6750.0050.0050.0000.0000.0000.000
62A461LEU00.0480.03624.706-0.004-0.0040.0000.0000.0000.000
63A462ILE0-0.046-0.03126.9990.0050.0050.0000.0000.0000.000
64A463ILE00.0030.01921.009-0.005-0.0050.0000.0000.0000.000
65A464ARG10.9150.93924.0210.0550.0550.0000.0000.0000.000
66A465PHE00.009-0.00618.5170.0000.0000.0000.0000.0000.000
67A466ASP-1-0.729-0.86721.179-0.258-0.2580.0000.0000.0000.000
68A467GLU-1-0.897-0.97321.578-0.236-0.2360.0000.0000.0000.000
69A468ASN0-0.055-0.02318.305-0.041-0.0410.0000.0000.0000.000
70A469GLY0-0.033-0.03317.190-0.060-0.0600.0000.0000.0000.000
71A470VAL0-0.024-0.01117.225-0.011-0.0110.0000.0000.0000.000
72A471LEU0-0.045-0.01219.0230.0330.0330.0000.0000.0000.000
73A472LEU0-0.003-0.01721.348-0.005-0.0050.0000.0000.0000.000
74A473ASN00.012-0.00624.8870.0100.0100.0000.0000.0000.000
75A474ASN0-0.042-0.02325.1730.0030.0030.0000.0000.0000.000
76A475SER00.0200.02926.2010.0160.0160.0000.0000.0000.000
77A476PHE0-0.038-0.03627.177-0.005-0.0050.0000.0000.0000.000
78A477LEU00.0080.00519.8470.0210.0210.0000.0000.0000.000
79A478ASP-1-0.843-0.93123.526-0.057-0.0570.0000.0000.0000.000
80A479PRO00.0290.00320.4200.0030.0030.0000.0000.0000.000
81A480GLU-1-0.951-0.95619.175-0.092-0.0920.0000.0000.0000.000
82A481TYR0-0.057-0.02918.1060.0200.0200.0000.0000.0000.000
83A482TRP00.011-0.01116.0030.0440.0440.0000.0000.0000.000
84A483ASN00.0380.02312.938-0.126-0.1260.0000.0000.0000.000
85A484PHE0-0.030-0.0177.9830.0570.0570.0000.0000.0000.000
86A485ARG10.9190.9575.605-0.586-0.5860.0000.0000.0000.000
87A486ASN0-0.098-0.0607.295-0.206-0.2060.0000.0000.0000.000
88A487GLY00.0860.0629.142-0.024-0.0240.0000.0000.0000.000
89A488ASP-1-0.919-0.9599.851-0.450-0.4500.0000.0000.0000.000
90A489LEU00.007-0.02811.365-0.126-0.1260.0000.0000.0000.000
91A490THR0-0.032-0.01412.546-0.018-0.0180.0000.0000.0000.000
92A491GLU-1-0.869-0.9195.588-2.055-2.0550.0000.0000.0000.000
93A492GLY0-0.010-0.0226.926-0.637-0.6370.0000.0000.0000.000
94A493ASN00.0080.0058.6620.3310.3310.0000.0000.0000.000
95A494ALA00.0600.02111.640-0.029-0.0290.0000.0000.0000.000
96A495VAL00.0800.05013.6220.0760.0760.0000.0000.0000.000
97A496GLY0-0.046-0.01012.0160.0590.0590.0000.0000.0000.000
98A497PHE00.0340.0017.7870.0970.0970.0000.0000.0000.000
99A498MET0-0.0480.02713.5580.1150.1150.0000.0000.0000.000
100A499PRO00.006-0.00417.2930.0030.0030.0000.0000.0000.000
101A500ASN00.0410.03619.844-0.003-0.0030.0000.0000.0000.000
102A501LEU00.0440.03021.0590.0280.0280.0000.0000.0000.000
103A502SER0-0.050-0.03824.2450.0170.0170.0000.0000.0000.000
104A503ALA0-0.095-0.04723.5210.0200.0200.0000.0000.0000.000
105A504TYR0-0.015-0.01421.0350.0270.0270.0000.0000.0000.000
106A505PRO00.0310.01426.033-0.014-0.0140.0000.0000.0000.000
107A506LYS10.8480.94626.6410.1000.1000.0000.0000.0000.000
108A507SER0-0.079-0.05129.644-0.003-0.0030.0000.0000.0000.000
109A508HIS00.0370.02833.3450.0010.0010.0000.0000.0000.000
110A509GLY0-0.020-0.00136.0780.0060.0060.0000.0000.0000.000
111A510LYS10.9840.99634.391-0.013-0.0130.0000.0000.0000.000
112A511THR00.0650.01830.742-0.003-0.0030.0000.0000.0000.000
113A512ALA0-0.019-0.01231.5150.0040.0040.0000.0000.0000.000
114A513LYS10.9550.96826.7390.0090.0090.0000.0000.0000.000
115A514SER00.0290.02926.6990.0070.0070.0000.0000.0000.000
116A515ASN0-0.042-0.00926.862-0.001-0.0010.0000.0000.0000.000
117A516ILE0-0.0110.00822.1780.0080.0080.0000.0000.0000.000
118A517VAL00.002-0.00526.453-0.002-0.0020.0000.0000.0000.000
119A518SER0-0.037-0.00926.7650.0040.0040.0000.0000.0000.000
120A519GLN00.0410.02428.804-0.003-0.0030.0000.0000.0000.000
121A520VAL0-0.0230.00025.8410.0210.0210.0000.0000.0000.000
122A521TYR00.002-0.01028.718-0.010-0.0100.0000.0000.0000.000
123A522LEU00.0320.01829.9660.0120.0120.0000.0000.0000.000
124A523ASN0-0.047-0.03731.0430.0010.0010.0000.0000.0000.000
125A524GLY0-0.039-0.01729.0620.0090.0090.0000.0000.0000.000
126A525ASP-1-0.853-0.91329.7030.1540.1540.0000.0000.0000.000
127A526LYS10.9770.97733.187-0.161-0.1610.0000.0000.0000.000
128A527THR0-0.115-0.06533.964-0.009-0.0090.0000.0000.0000.000
129A528LYS10.8430.91135.172-0.130-0.1300.0000.0000.0000.000
130A529PRO00.0030.01833.4070.0080.0080.0000.0000.0000.000
131A530VAL00.0130.01731.653-0.013-0.0130.0000.0000.0000.000
132A531THR0-0.031-0.02131.5290.0150.0150.0000.0000.0000.000
133A532LEU0-0.0120.00524.583-0.007-0.0070.0000.0000.0000.000
134A533THR0-0.012-0.01628.7300.0080.0080.0000.0000.0000.000
135A534ILE00.0130.00722.500-0.007-0.0070.0000.0000.0000.000
136A535THR0-0.030-0.02626.2210.0010.0010.0000.0000.0000.000
137A536LEU0-0.035-0.00621.364-0.009-0.0090.0000.0000.0000.000
138A537ASN0-0.015-0.04822.764-0.007-0.0070.0000.0000.0000.000
139A538GLY0-0.0070.00625.944-0.002-0.0020.0000.0000.0000.000
140A539THR0-0.056-0.01428.6400.0040.0040.0000.0000.0000.000
141A540GLN00.0470.00430.398-0.002-0.0020.0000.0000.0000.000
142A541GLU-1-0.776-0.84729.848-0.073-0.0730.0000.0000.0000.000
143A542THR0-0.002-0.00234.010-0.003-0.0030.0000.0000.0000.000
144A543GLY0-0.006-0.00837.6680.0020.0020.0000.0000.0000.000
145A544ASP-1-0.871-0.94639.082-0.060-0.0600.0000.0000.0000.000
146A545THR0-0.120-0.04133.4020.0000.0000.0000.0000.0000.000
147A546THR00.0210.00430.448-0.001-0.0010.0000.0000.0000.000
148A547PRO00.0270.01230.5570.0050.0050.0000.0000.0000.000
149A548SER0-0.063-0.05125.895-0.008-0.0080.0000.0000.0000.000
150A549ALA0-0.009-0.00223.5390.0090.0090.0000.0000.0000.000
151A550TYR00.0030.00820.9580.0060.0060.0000.0000.0000.000
152A551SER0-0.038-0.04423.4420.0040.0040.0000.0000.0000.000
153A552MET00.0110.02617.9980.0160.0160.0000.0000.0000.000
154A553SER0-0.0120.00123.253-0.002-0.0020.0000.0000.0000.000
155A554PHE00.0490.02920.8910.0160.0160.0000.0000.0000.000
156A555SER00.012-0.00327.021-0.014-0.0140.0000.0000.0000.000
157A556TRP0-0.004-0.00925.6130.0040.0040.0000.0000.0000.000
158A557ASP-1-0.808-0.88831.7890.0560.0560.0000.0000.0000.000
159A558TRP0-0.043-0.01833.8180.0120.0120.0000.0000.0000.000
160A559SER0-0.032-0.04437.326-0.003-0.0030.0000.0000.0000.000
161A560GLY0-0.057-0.03140.6810.0020.0020.0000.0000.0000.000
162A561HIS0-0.0360.00339.1010.0010.0010.0000.0000.0000.000
163A562ASN00.001-0.01841.652-0.001-0.0010.0000.0000.0000.000
164A563TYR00.015-0.02536.5260.0030.0030.0000.0000.0000.000
165A564ILE00.0030.01239.9210.0020.0020.0000.0000.0000.000
166A565ASN0-0.045-0.03441.562-0.001-0.0010.0000.0000.0000.000
167A566GLU-1-0.798-0.85936.5430.1170.1170.0000.0000.0000.000
168A567ILE00.007-0.00332.454-0.008-0.0080.0000.0000.0000.000
169A568PHE00.0140.00430.0430.0090.0090.0000.0000.0000.000
170A569ALA00.0250.01129.0270.0000.0000.0000.0000.0000.000
171A570THR0-0.025-0.01725.713-0.003-0.0030.0000.0000.0000.000
172A571SER00.0480.02625.9590.0070.0070.0000.0000.0000.000
173A572SER0-0.055-0.02120.343-0.009-0.0090.0000.0000.0000.000
174A573TYR0-0.0150.00021.3960.0080.0080.0000.0000.0000.000
175A574THR00.001-0.00516.7460.0400.0400.0000.0000.0000.000
176A575PHE0-0.0040.00018.077-0.036-0.0360.0000.0000.0000.000
177A576SER0-0.005-0.01716.4950.0590.0590.0000.0000.0000.000
178A577TYR0-0.052-0.03416.037-0.009-0.0090.0000.0000.0000.000
179A578ILE00.008-0.00317.2770.0120.0120.0000.0000.0000.000
180A579ALA00.0300.00414.440-0.008-0.0080.0000.0000.0000.000
181A580GLN00.0390.00716.4990.0400.0400.0000.0000.0000.000
182A581GLU-1-0.922-0.93813.953-0.390-0.3900.0000.0000.0000.000