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: 3QRLL

Calculation Name: 2V0X-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2V0X

Chain ID: A

ChEMBL ID:

UniProt ID: Q61033

Base Structure: X-ray

Registration Date: 2023-06-20

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 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 195
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -1763245.153311
FMO2-HF: Nuclear repulsion 1687741.752947
FMO2-HF: Total energy -75503.400364
FMO2-MP2: Total energy -75719.983545


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:465:HIS)


Summations of interaction energy for fragment #1(A:465:HIS)
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.
-3.685-0.6150.895-1.486-2.4780.008
Interaction energy analysis for fragmet #1(A:465:HIS)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.048 / q_NPA : 0.030
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].
3A467LEU0-0.043-0.0093.558-3.215-0.6730.074-1.078-1.5370.007
4A468THR0-0.011-0.0155.4600.4710.4710.0000.0000.0000.000
5A469THR0-0.017-0.0369.191-0.125-0.1250.0000.0000.0000.000
6A470LEU0-0.038-0.01912.6230.0560.0560.0000.0000.0000.000
7A471GLY0-0.0040.01015.668-0.006-0.0060.0000.0000.0000.000
8A472VAL00.0130.01415.9500.0150.0150.0000.0000.0000.000
9A473GLU-1-1.003-0.99011.275-0.279-0.2790.0000.0000.0000.000
10A489PRO0-0.004-0.01331.445-0.006-0.0060.0000.0000.0000.000
11A490SER0-0.025-0.01330.2330.0150.0150.0000.0000.0000.000
12A491PHE00.0250.01324.223-0.019-0.0190.0000.0000.0000.000
13A492PRO0-0.0150.00126.4030.0180.0180.0000.0000.0000.000
14A493LEU00.007-0.00327.771-0.010-0.0100.0000.0000.0000.000
15A494HIS00.0590.02721.8460.0210.0210.0000.0000.0000.000
16A495GLU-1-0.845-0.92826.535-0.188-0.1880.0000.0000.0000.000
17A496SER00.007-0.00424.7560.0100.0100.0000.0000.0000.000
18A497ILE0-0.0040.00526.0220.0180.0180.0000.0000.0000.000
19A498LEU0-0.015-0.00629.2020.0180.0180.0000.0000.0000.000
20A499LYS10.8690.93029.5510.1340.1340.0000.0000.0000.000
21A500VAL00.0130.00328.8610.0130.0130.0000.0000.0000.000
22A501VAL0-0.004-0.00531.8000.0130.0130.0000.0000.0000.000
23A502GLU-1-0.896-0.93234.618-0.111-0.1110.0000.0000.0000.000
24A503GLU-1-0.830-0.90331.976-0.094-0.0940.0000.0000.0000.000
25A504GLU-1-0.801-0.88335.543-0.057-0.0570.0000.0000.0000.000
26A505TRP0-0.048-0.04538.0660.0050.0050.0000.0000.0000.000
27A506GLN0-0.040-0.02338.7380.0060.0060.0000.0000.0000.000
28A507GLN0-0.072-0.04541.4900.0020.0020.0000.0000.0000.000
29A508ILE00.0240.02942.7650.0010.0010.0000.0000.0000.000
30A509ASP-1-0.837-0.90744.222-0.033-0.0330.0000.0000.0000.000
31A510ARG10.7890.89737.7570.0630.0630.0000.0000.0000.000
32A511GLN0-0.016-0.01842.3010.0020.0020.0000.0000.0000.000
33A512LEU00.0210.01238.602-0.004-0.0040.0000.0000.0000.000
34A513PRO00.003-0.00834.0820.0050.0050.0000.0000.0000.000
35A514SER00.0110.01235.423-0.001-0.0010.0000.0000.0000.000
36A515VAL00.0740.03431.7130.0020.0020.0000.0000.0000.000
37A516ALA0-0.016-0.00731.4540.0040.0040.0000.0000.0000.000
38A517CYS0-0.050-0.03631.2640.0040.0040.0000.0000.0000.000
39A518ARG10.9390.98426.9360.0190.0190.0000.0000.0000.000
40A519TYR0-0.003-0.02025.0100.0010.0010.0000.0000.0000.000
41A520PRO00.0330.02828.412-0.002-0.0020.0000.0000.0000.000
42A521VAL00.0440.03431.412-0.001-0.0010.0000.0000.0000.000
43A522SER0-0.0080.00631.0970.0060.0060.0000.0000.0000.000
44A523SER0-0.008-0.01933.501-0.002-0.0020.0000.0000.0000.000
45A524ILE00.0320.00637.212-0.003-0.0030.0000.0000.0000.000
46A525GLU-1-0.827-0.89639.7730.0040.0040.0000.0000.0000.000
47A526ALA00.0240.01636.525-0.004-0.0040.0000.0000.0000.000
48A527ALA00.016-0.00238.533-0.003-0.0030.0000.0000.0000.000
49A528ARG10.8370.89940.056-0.003-0.0030.0000.0000.0000.000
50A529ILE0-0.0220.00340.772-0.002-0.0020.0000.0000.0000.000
51A530LEU0-0.016-0.00135.941-0.003-0.0030.0000.0000.0000.000
52A531SER0-0.071-0.02240.265-0.002-0.0020.0000.0000.0000.000
53A532VAL00.0330.01442.968-0.001-0.0010.0000.0000.0000.000
54A533PRO0-0.0150.00345.4580.0030.0030.0000.0000.0000.000
55A534LYS10.8980.93147.5630.0060.0060.0000.0000.0000.000
56A535VAL00.0080.00951.9480.0000.0000.0000.0000.0000.000
57A536ASP-1-0.851-0.92455.464-0.009-0.0090.0000.0000.0000.000
58A537ASP-1-0.880-0.94857.192-0.003-0.0030.0000.0000.0000.000
59A538GLU-1-0.918-0.96059.977-0.004-0.0040.0000.0000.0000.000
60A539ILE0-0.045-0.02259.245-0.001-0.0010.0000.0000.0000.000
61A540LEU0-0.003-0.00557.715-0.001-0.0010.0000.0000.0000.000
62A541GLY00.0230.02661.8630.0000.0000.0000.0000.0000.000
63A542PHE0-0.074-0.04564.8910.0000.0000.0000.0000.0000.000
64A543ILE0-0.064-0.01061.378-0.001-0.0010.0000.0000.0000.000
65A544SER0-0.125-0.06564.5590.0000.0000.0000.0000.0000.000
66A556SER00.024-0.00966.6800.0000.0000.0000.0000.0000.000
67A557THR0-0.041-0.03662.3830.0000.0000.0000.0000.0000.000
68A558GLU-1-0.742-0.83361.350-0.019-0.0190.0000.0000.0000.000
69A559SER00.0060.00160.086-0.001-0.0010.0000.0000.0000.000
70A560CYS0-0.047-0.01857.822-0.002-0.0020.0000.0000.0000.000
71A561ASP-1-0.827-0.90956.647-0.026-0.0260.0000.0000.0000.000
72A562LYS10.8680.91356.0030.0170.0170.0000.0000.0000.000
73A563HIS10.8620.94152.7780.0290.0290.0000.0000.0000.000
74A564LEU0-0.033-0.02352.015-0.002-0.0020.0000.0000.0000.000
75A565ASP-1-0.879-0.93151.535-0.022-0.0220.0000.0000.0000.000
76A566LEU00.0240.01948.335-0.001-0.0010.0000.0000.0000.000
77A567ALA0-0.019-0.01047.745-0.001-0.0010.0000.0000.0000.000
78A568LEU0-0.0040.00946.705-0.003-0.0030.0000.0000.0000.000
79A569CYS00.0120.01046.4030.0000.0000.0000.0000.0000.000
80A570ARG10.8770.92543.4930.0340.0340.0000.0000.0000.000
81A571SER0-0.031-0.03942.205-0.004-0.0040.0000.0000.0000.000
82A572TYR0-0.056-0.03141.725-0.004-0.0040.0000.0000.0000.000
83A573GLU-1-0.895-0.95240.325-0.023-0.0230.0000.0000.0000.000
84A574ALA0-0.0200.00337.9720.0000.0000.0000.0000.0000.000
85A575ALA00.0090.00136.788-0.003-0.0030.0000.0000.0000.000
86A576ALA0-0.0120.00136.793-0.001-0.0010.0000.0000.0000.000
87A577SER0-0.019-0.03834.6820.0030.0030.0000.0000.0000.000
88A578ALA00.0260.01832.5210.0000.0000.0000.0000.0000.000
89A579LEU0-0.0120.00131.828-0.001-0.0010.0000.0000.0000.000
90A580GLN0-0.065-0.04532.0780.0020.0020.0000.0000.0000.000
91A581ILE00.0300.01727.1650.0060.0060.0000.0000.0000.000
92A582ALA00.0150.02127.506-0.002-0.0020.0000.0000.0000.000
93A583ALA0-0.032-0.01627.940-0.001-0.0010.0000.0000.0000.000
94A584HIS0-0.017-0.02025.5320.0040.0040.0000.0000.0000.000
95A585THR0-0.008-0.01123.336-0.002-0.0020.0000.0000.0000.000
96A586ALA0-0.019-0.01123.249-0.006-0.0060.0000.0000.0000.000
97A587PHE0-0.040-0.01623.5040.0040.0040.0000.0000.0000.000
98A588VAL00.0520.02618.8320.0070.0070.0000.0000.0000.000
99A589ALA00.0390.03119.448-0.002-0.0020.0000.0000.0000.000
100A590LYS10.8560.91820.0580.0330.0330.0000.0000.0000.000
101A591SER0-0.043-0.02119.0440.0120.0120.0000.0000.0000.000
102A592LEU00.0660.03713.7150.0180.0180.0000.0000.0000.000
103A593GLN00.0280.02015.7810.0040.0040.0000.0000.0000.000
104A594ALA0-0.0130.00017.9310.0130.0130.0000.0000.0000.000
105A595ASP-1-0.798-0.87913.4530.1230.1230.0000.0000.0000.000
106A596ILE00.009-0.00412.5620.0410.0410.0000.0000.0000.000
107A597SER0-0.052-0.02913.8790.0320.0320.0000.0000.0000.000
108A598GLN00.0120.00714.9700.0410.0410.0000.0000.0000.000
109A599ALA00.011-0.00410.1570.0550.0550.0000.0000.0000.000
110A600ALA00.0060.00412.1610.0900.0900.0000.0000.0000.000
111A601GLN0-0.028-0.02213.9730.0240.0240.0000.0000.0000.000
112A602ILE0-0.0250.00612.3170.0050.0050.0000.0000.0000.000
113A603ILE0-0.007-0.0088.9290.0460.0460.0000.0000.0000.000
114A604ASN0-0.036-0.01412.808-0.025-0.0250.0000.0000.0000.000
115A605SER0-0.112-0.05516.220-0.049-0.0490.0000.0000.0000.000
116A606ASP-1-0.824-0.89716.9920.5330.5330.0000.0000.0000.000
117A607PRO0-0.015-0.01112.4140.0580.0580.0000.0000.0000.000
118A608SER0-0.031-0.03611.9300.2390.2390.0000.0000.0000.000
119A609ASP-1-0.863-0.91312.7760.8390.8390.0000.0000.0000.000
120A610ALA00.017-0.0027.6910.0100.0100.0000.0000.0000.000
121A611GLN00.004-0.0097.3370.0750.0750.0000.0000.0000.000
122A612GLN0-0.026-0.0088.903-0.190-0.1900.0000.0000.0000.000
123A613ALA00.0430.0208.447-0.131-0.1310.0000.0000.0000.000
124A614LEU00.006-0.0022.548-0.935-0.4070.821-0.408-0.9410.001
125A615ARG10.8780.9395.988-0.995-0.9950.0000.0000.0000.000
126A616ILE0-0.057-0.0199.053-0.125-0.1250.0000.0000.0000.000
127A617LEU00.0330.0135.844-0.085-0.0850.0000.0000.0000.000
128A618ASN00.0150.0227.084-0.216-0.2160.0000.0000.0000.000
129A619ARG10.8000.8838.024-0.150-0.1500.0000.0000.0000.000
130A620THR0-0.049-0.0479.260-0.032-0.0320.0000.0000.0000.000
131A621TYR0-0.0130.0008.113-0.006-0.0060.0000.0000.0000.000
132A622ASP-1-0.779-0.86610.2390.0660.0660.0000.0000.0000.000
133A623ALA00.0050.00213.0100.0020.0020.0000.0000.0000.000
134A624ALA0-0.026-0.01912.9100.0020.0020.0000.0000.0000.000
135A625SER00.003-0.00313.965-0.021-0.0210.0000.0000.0000.000
136A626TYR00.0160.00715.7830.0060.0060.0000.0000.0000.000
137A627LEU0-0.048-0.03117.5720.0040.0040.0000.0000.0000.000
138A628CYS0-0.027-0.00717.976-0.013-0.0130.0000.0000.0000.000
139A629ASP-1-0.875-0.94819.488-0.120-0.1200.0000.0000.0000.000
140A630ALA00.0160.00121.7760.0080.0080.0000.0000.0000.000
141A631ALA0-0.012-0.00223.3070.0070.0070.0000.0000.0000.000
142A632PHE0-0.025-0.02522.243-0.001-0.0010.0000.0000.0000.000
143A633ASP-1-0.833-0.88926.499-0.052-0.0520.0000.0000.0000.000
144A634GLU-1-0.863-0.93527.966-0.072-0.0720.0000.0000.0000.000
145A635VAL0-0.031-0.00428.5850.0030.0030.0000.0000.0000.000
146A636ARG10.8270.88730.0960.0890.0890.0000.0000.0000.000
147A637MET00.0120.00532.3810.0050.0050.0000.0000.0000.000
148A638SER00.019-0.00532.9730.0050.0050.0000.0000.0000.000
149A639ALA0-0.034-0.01334.9090.0030.0030.0000.0000.0000.000
150A640CYS0-0.005-0.00136.3710.0050.0050.0000.0000.0000.000
151A641ALA00.0400.03838.3660.0050.0050.0000.0000.0000.000
152A642MET0-0.036-0.01638.4640.0010.0010.0000.0000.0000.000
153A643GLY00.0160.01540.8750.0010.0010.0000.0000.0000.000
154A644SER00.013-0.00642.4500.0040.0040.0000.0000.0000.000
155A645SER00.0250.01244.2030.0030.0030.0000.0000.0000.000
156A646THR0-0.078-0.05244.5750.0020.0020.0000.0000.0000.000
157A647MET00.0080.01246.8180.0020.0020.0000.0000.0000.000
158A648GLY00.0340.00748.6870.0020.0020.0000.0000.0000.000
159A649ARG10.9500.96847.7920.0610.0610.0000.0000.0000.000
160A650ARG10.7620.86447.6160.0580.0580.0000.0000.0000.000
161A651TYR00.021-0.00351.3440.0020.0020.0000.0000.0000.000
162A652LEU00.0230.00954.7030.0010.0010.0000.0000.0000.000
163A653TRP0-0.038-0.02455.0150.0010.0010.0000.0000.0000.000
164A654LEU0-0.031-0.00556.2460.0000.0000.0000.0000.0000.000
165A655LYS10.8820.92959.3690.0320.0320.0000.0000.0000.000
166A656ASP-1-0.822-0.89661.264-0.030-0.0300.0000.0000.0000.000
167A657CYS0-0.0410.01461.8000.0010.0010.0000.0000.0000.000
168A658LYS10.9640.96565.0320.0270.0270.0000.0000.0000.000
169A659ILE00.0470.02661.6730.0000.0000.0000.0000.0000.000
170A660SER00.0220.00363.1670.0010.0010.0000.0000.0000.000
171A661PRO00.0720.01462.143-0.001-0.0010.0000.0000.0000.000
172A662ALA00.0370.03159.861-0.001-0.0010.0000.0000.0000.000
173A663SER00.0390.01858.530-0.001-0.0010.0000.0000.0000.000
174A664LYS10.8110.90957.9080.0300.0300.0000.0000.0000.000
175A665ASN00.0300.02654.773-0.001-0.0010.0000.0000.0000.000
176A666LYS10.8500.91152.8720.0470.0470.0000.0000.0000.000
177A667LEU00.005-0.00453.039-0.003-0.0030.0000.0000.0000.000
178A668THR0-0.023-0.03452.222-0.003-0.0030.0000.0000.0000.000
179A669VAL00.0080.01049.729-0.002-0.0020.0000.0000.0000.000
180A670ALA0-0.0190.01648.408-0.002-0.0020.0000.0000.0000.000
181A671PRO00.0370.03043.647-0.001-0.0010.0000.0000.0000.000
182A672PHE0-0.044-0.00942.577-0.001-0.0010.0000.0000.0000.000
183A673LYS10.9050.93641.3290.0740.0740.0000.0000.0000.000
184A674GLY00.0800.05641.501-0.006-0.0060.0000.0000.0000.000
185A675GLY0-0.014-0.00243.0970.0020.0020.0000.0000.0000.000
186A676THR0-0.034-0.03145.6860.0040.0040.0000.0000.0000.000
187A677LEU0-0.0110.00948.130-0.001-0.0010.0000.0000.0000.000
188A678PHE00.0540.01649.6490.0010.0010.0000.0000.0000.000
189A679GLY00.0130.02047.7150.0010.0010.0000.0000.0000.000
190A680GLY0-0.021-0.02148.528-0.003-0.0030.0000.0000.0000.000
191A681GLU-1-0.826-0.89251.433-0.050-0.0500.0000.0000.0000.000
192A682VAL00.0210.01853.7120.0030.0030.0000.0000.0000.000
193A683HIS00.0300.00456.1310.0020.0020.0000.0000.0000.000
194A684LYS10.8600.92157.5840.0520.0520.0000.0000.0000.000
195A685VAL0-0.0030.01859.5330.0010.0010.0000.0000.0000.000