FMODB

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

Last updated: 2024-07-23

All entries: 37450

Number of unique PDB entries: 7783

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FMODB ID: 6N4VZ

Calculation Name: 5NH1-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 5NH1

Chain ID: A

ChEMBL ID:

UniProt ID: P57764

Base Structure: X-ray

Registration Date: 2023-06-22

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 199
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2060490.816101
FMO2-HF: Nuclear repulsion 1984893.256669
FMO2-HF: Total energy -75597.559432
FMO2-MP2: Total energy -75815.106918


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:282:ALA)


Summations of interaction energy for fragment #1(A:282:ALA)
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.
-10.757-8.1890.216-1.201-1.583-0.002
Interaction energy analysis for fragmet #1(A:282:ALA)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.017 / q_NPA : -0.031
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].
3A284THR0-0.031-0.0142.866-1.0060.9340.163-0.823-1.2800.001
4A285GLU-1-0.891-0.9123.292-6.088-5.4600.053-0.378-0.303-0.003
5A286ASP-1-0.825-0.9105.640-1.049-1.0490.0000.0000.0000.000
6A287PHE00.0710.0157.9360.0210.0210.0000.0000.0000.000
7A288GLN0-0.052-0.02910.5130.0160.0160.0000.0000.0000.000
8A289GLY00.0480.0248.8950.1110.1110.0000.0000.0000.000
9A290LEU0-0.029-0.0179.9430.0910.0910.0000.0000.0000.000
10A291ARG10.8930.95011.9390.6600.6600.0000.0000.0000.000
11A292ALA00.003-0.00112.6610.0780.0780.0000.0000.0000.000
12A293GLU-1-0.909-0.95212.515-0.756-0.7560.0000.0000.0000.000
13A294VAL00.0070.02414.4300.1050.1050.0000.0000.0000.000
14A295GLU-1-0.947-0.98017.314-0.398-0.3980.0000.0000.0000.000
15A296THR0-0.138-0.09416.4960.0680.0680.0000.0000.0000.000
16A297ILE00.0020.01419.3790.0480.0480.0000.0000.0000.000
17A298SER00.020-0.01221.2720.0440.0440.0000.0000.0000.000
18A299LYS10.9340.98022.5060.3220.3220.0000.0000.0000.000
19A300GLU-1-0.995-1.00924.270-0.238-0.2380.0000.0000.0000.000
20A301LEU00.0010.00225.4440.0170.0170.0000.0000.0000.000
21A302GLU-1-0.952-0.97026.573-0.230-0.2300.0000.0000.0000.000
22A303LEU0-0.116-0.06729.8760.0160.0160.0000.0000.0000.000
23A304LEU0-0.0090.01330.3790.0120.0120.0000.0000.0000.000
24A305ASP-1-0.916-0.94833.311-0.131-0.1310.0000.0000.0000.000
25A306ARG10.9800.97536.2810.1370.1370.0000.0000.0000.000
26A307GLU-1-0.956-0.98837.502-0.109-0.1090.0000.0000.0000.000
27A308LEU00.0210.01535.8450.0010.0010.0000.0000.0000.000
28A309CYS0-0.0040.01833.275-0.005-0.0050.0000.0000.0000.000
29A310GLN0-0.014-0.00934.914-0.009-0.0090.0000.0000.0000.000
30A311LEU00.0350.02337.6060.0010.0010.0000.0000.0000.000
31A312LEU00.008-0.00331.0990.0000.0000.0000.0000.0000.000
32A313LEU0-0.048-0.03231.251-0.005-0.0050.0000.0000.0000.000
33A314GLU-1-0.932-0.95634.527-0.115-0.1150.0000.0000.0000.000
34A315GLY0-0.003-0.01136.9960.0030.0030.0000.0000.0000.000
35A316LEU0-0.009-0.03229.935-0.001-0.0010.0000.0000.0000.000
36A317GLU-1-0.848-0.91833.448-0.138-0.1380.0000.0000.0000.000
37A318GLY0-0.016-0.01635.1710.0020.0020.0000.0000.0000.000
38A319VAL0-0.019-0.02032.1290.0030.0030.0000.0000.0000.000
39A320LEU0-0.038-0.01028.937-0.002-0.0020.0000.0000.0000.000
40A321ARG10.7560.89032.8060.1330.1330.0000.0000.0000.000
41A322ASP-1-0.920-0.97035.487-0.110-0.1100.0000.0000.0000.000
42A323GLN00.0200.01530.432-0.009-0.0090.0000.0000.0000.000
43A324LEU0-0.033-0.02333.902-0.004-0.0040.0000.0000.0000.000
44A325ALA00.0190.01935.915-0.002-0.0020.0000.0000.0000.000
45A326LEU00.0090.00728.952-0.004-0.0040.0000.0000.0000.000
46A327ARG10.9210.95131.0350.1410.1410.0000.0000.0000.000
47A328ALA00.0070.00732.630-0.001-0.0010.0000.0000.0000.000
48A329LEU0-0.006-0.01031.8290.0020.0020.0000.0000.0000.000
49A330GLU-1-0.990-1.00027.431-0.211-0.2110.0000.0000.0000.000
50A331GLU-1-0.922-0.95529.999-0.131-0.1310.0000.0000.0000.000
51A332ALA0-0.060-0.01932.2510.0030.0030.0000.0000.0000.000
52A333LEU0-0.037-0.03029.9010.0030.0030.0000.0000.0000.000
53A334GLU-1-0.915-0.93729.364-0.158-0.1580.0000.0000.0000.000
54A335GLN0-0.069-0.04624.3570.0000.0000.0000.0000.0000.000
55A336GLY00.0120.00425.946-0.014-0.0140.0000.0000.0000.000
56A337GLN0-0.082-0.04426.003-0.003-0.0030.0000.0000.0000.000
57A338SER00.0130.01929.0820.0150.0150.0000.0000.0000.000
58A339LEU0-0.038-0.03132.6210.0020.0020.0000.0000.0000.000
59A340GLY0-0.039-0.01134.7960.0040.0040.0000.0000.0000.000
60A341PRO0-0.007-0.02836.987-0.006-0.0060.0000.0000.0000.000
61A342VAL00.0220.01235.0300.0020.0020.0000.0000.0000.000
62A343GLU-1-0.973-0.98338.317-0.084-0.0840.0000.0000.0000.000
63A344PRO0-0.019-0.00840.033-0.005-0.0050.0000.0000.0000.000
64A345LEU00.005-0.00837.4160.0030.0030.0000.0000.0000.000
65A346ASP-1-0.904-0.94941.708-0.085-0.0850.0000.0000.0000.000
66A347GLY0-0.046-0.03041.499-0.004-0.0040.0000.0000.0000.000
67A348PRO00.0390.01137.787-0.001-0.0010.0000.0000.0000.000
68A349ALA00.0470.02436.235-0.005-0.0050.0000.0000.0000.000
69A350GLY00.0030.00937.240-0.004-0.0040.0000.0000.0000.000
70A351ALA00.0200.01439.2100.0000.0000.0000.0000.0000.000
71A352VAL00.011-0.00132.895-0.002-0.0020.0000.0000.0000.000
72A353LEU0-0.022-0.00535.507-0.003-0.0030.0000.0000.0000.000
73A354GLU-1-0.966-0.98736.917-0.104-0.1040.0000.0000.0000.000
74A355CYS0-0.076-0.02336.1250.0020.0020.0000.0000.0000.000
75A356LEU0-0.023-0.01232.019-0.006-0.0060.0000.0000.0000.000
76A357VAL0-0.0340.00435.291-0.002-0.0020.0000.0000.0000.000
77A358LEU00.0070.00638.0010.0050.0050.0000.0000.0000.000
78A359SER0-0.034-0.03240.7370.0020.0020.0000.0000.0000.000
79A360SER0-0.064-0.03741.4920.0010.0010.0000.0000.0000.000
80A361GLY00.1090.05540.6310.0030.0030.0000.0000.0000.000
81A362MET0-0.099-0.02936.492-0.002-0.0020.0000.0000.0000.000
82A363LEU00.0670.03431.842-0.001-0.0010.0000.0000.0000.000
83A364VAL00.0280.01933.3800.0040.0040.0000.0000.0000.000
84A365PRO0-0.045-0.01628.673-0.010-0.0100.0000.0000.0000.000
85A366GLU-1-0.913-0.96928.584-0.174-0.1740.0000.0000.0000.000
86A367LEU00.0190.00229.295-0.013-0.0130.0000.0000.0000.000
87A368ALA00.0010.00529.908-0.009-0.0090.0000.0000.0000.000
88A369ILE00.0230.02223.651-0.011-0.0110.0000.0000.0000.000
89A370PRO00.0380.01324.387-0.027-0.0270.0000.0000.0000.000
90A371VAL00.0340.02125.021-0.016-0.0160.0000.0000.0000.000
91A372VAL00.0010.00723.616-0.007-0.0070.0000.0000.0000.000
92A373TYR0-0.024-0.01617.7500.0050.0050.0000.0000.0000.000
93A374LEU0-0.015-0.00121.757-0.025-0.0250.0000.0000.0000.000
94A375LEU00.020-0.00123.887-0.004-0.0040.0000.0000.0000.000
95A376GLY00.0260.01621.6670.0040.0040.0000.0000.0000.000
96A377ALA0-0.0450.00819.805-0.015-0.0150.0000.0000.0000.000
97A378LEU00.019-0.00120.7850.0060.0060.0000.0000.0000.000
98A379THR0-0.057-0.04122.1220.0160.0160.0000.0000.0000.000
99A380MET0-0.073-0.03417.4950.0140.0140.0000.0000.0000.000
100A381LEU0-0.073-0.02721.4470.0040.0040.0000.0000.0000.000
101A382SER0-0.032-0.05123.9730.0140.0140.0000.0000.0000.000
102A383GLU-1-0.851-0.93927.195-0.135-0.1350.0000.0000.0000.000
103A384THR0-0.040-0.02529.9660.0070.0070.0000.0000.0000.000
104A385GLN00.0310.00123.065-0.001-0.0010.0000.0000.0000.000
105A386HIS0-0.003-0.00426.1570.0130.0130.0000.0000.0000.000
106A387LYS10.9350.96229.7880.1340.1340.0000.0000.0000.000
107A388LEU0-0.036-0.01029.5590.0060.0060.0000.0000.0000.000
108A389LEU0-0.012-0.01025.690-0.001-0.0010.0000.0000.0000.000
109A390ALA00.0020.00730.0710.0020.0020.0000.0000.0000.000
110A391GLU-1-0.885-0.95333.492-0.121-0.1210.0000.0000.0000.000
111A392ALA0-0.0340.00330.7720.0040.0040.0000.0000.0000.000
112A393LEU0-0.018-0.01230.6580.0010.0010.0000.0000.0000.000
113A394GLU-1-0.946-0.94533.683-0.113-0.1130.0000.0000.0000.000
114A395SER0-0.050-0.02635.9510.0040.0040.0000.0000.0000.000
115A396GLN0-0.065-0.03934.4760.0000.0000.0000.0000.0000.000
116A397THR0-0.096-0.05533.074-0.003-0.0030.0000.0000.0000.000
117A398LEU00.0630.03228.128-0.006-0.0060.0000.0000.0000.000
118A399LEU00.015-0.01127.470-0.014-0.0140.0000.0000.0000.000
119A400GLY00.0170.02227.145-0.009-0.0090.0000.0000.0000.000
120A401PRO00.0240.01026.366-0.010-0.0100.0000.0000.0000.000
121A402LEU0-0.0010.00621.715-0.021-0.0210.0000.0000.0000.000
122A403GLU-1-0.925-0.95722.289-0.252-0.2520.0000.0000.0000.000
123A404LEU0-0.029-0.00122.695-0.011-0.0110.0000.0000.0000.000
124A405VAL00.022-0.00619.117-0.011-0.0110.0000.0000.0000.000
125A406GLY00.004-0.00418.195-0.039-0.0390.0000.0000.0000.000
126A407SER00.006-0.00317.812-0.032-0.0320.0000.0000.0000.000
127A408LEU0-0.045-0.02218.8720.0020.0020.0000.0000.0000.000
128A409LEU0-0.0050.01213.814-0.016-0.0160.0000.0000.0000.000
129A410GLU-1-0.973-0.97613.901-0.455-0.4550.0000.0000.0000.000
130A411GLN0-0.068-0.04814.8820.0090.0090.0000.0000.0000.000
131A412SER0-0.037-0.03814.5110.0200.0200.0000.0000.0000.000
132A413ALA0-0.0450.01610.552-0.017-0.0170.0000.0000.0000.000
133A414PRO0-0.044-0.0338.3750.0550.0550.0000.0000.0000.000
134A415TRP00.0790.0228.7220.0180.0180.0000.0000.0000.000
135A416GLN00.0180.0027.182-0.114-0.1140.0000.0000.0000.000
136A417GLU-1-1.000-1.0039.9820.1250.1250.0000.0000.0000.000
137A418ARG10.8470.90612.8810.0700.0700.0000.0000.0000.000
138A419SER0-0.0160.00015.8670.0270.0270.0000.0000.0000.000
139A420THR0-0.015-0.00318.145-0.011-0.0110.0000.0000.0000.000
140A421MET0-0.0300.00318.1390.0000.0000.0000.0000.0000.000
141A422SER0-0.048-0.02821.7930.0070.0070.0000.0000.0000.000
142A423LEU00.0080.01322.6280.0130.0130.0000.0000.0000.000
143A424PRO00.0360.01324.924-0.001-0.0010.0000.0000.0000.000
144A425PRO00.0540.02626.1450.0010.0010.0000.0000.0000.000
145A426GLY00.0580.02728.3590.0010.0010.0000.0000.0000.000
146A427LEU0-0.108-0.05630.5910.0060.0060.0000.0000.0000.000
147A428LEU0-0.007-0.00325.6010.0020.0020.0000.0000.0000.000
148A429GLY0-0.039-0.00430.301-0.003-0.0030.0000.0000.0000.000
149A430ASN0-0.053-0.01328.5930.0000.0000.0000.0000.0000.000
150A431SER0-0.025-0.02132.2340.0080.0080.0000.0000.0000.000
151A432TRP0-0.028-0.03226.486-0.012-0.0120.0000.0000.0000.000
152A433GLY00.0530.02232.5680.0090.0090.0000.0000.0000.000
153A434GLU-1-0.923-0.95133.045-0.102-0.1020.0000.0000.0000.000
154A435GLY0-0.051-0.02133.2310.0060.0060.0000.0000.0000.000
155A436ALA0-0.061-0.02432.670-0.001-0.0010.0000.0000.0000.000
156A437PRO00.0420.00631.928-0.007-0.0070.0000.0000.0000.000
157A438ALA00.0520.01928.114-0.011-0.0110.0000.0000.0000.000
158A439TRP00.0320.02827.372-0.015-0.0150.0000.0000.0000.000
159A440VAL00.0380.01127.734-0.009-0.0090.0000.0000.0000.000
160A441LEU0-0.010-0.00325.248-0.008-0.0080.0000.0000.0000.000
161A442LEU00.004-0.01322.031-0.023-0.0230.0000.0000.0000.000
162A443ASP-1-0.911-0.95923.332-0.166-0.1660.0000.0000.0000.000
163A444GLU-1-0.871-0.89224.980-0.177-0.1770.0000.0000.0000.000
164A445CYS0-0.134-0.06019.855-0.018-0.0180.0000.0000.0000.000
165A446GLY0-0.041-0.01819.942-0.027-0.0270.0000.0000.0000.000
166A447LEU0-0.041-0.01818.3700.0060.0060.0000.0000.0000.000
167A448GLU-1-0.910-0.94521.687-0.113-0.1130.0000.0000.0000.000
168A449LEU0-0.048-0.02724.247-0.003-0.0030.0000.0000.0000.000
169A450GLY00.0280.01026.8310.0120.0120.0000.0000.0000.000
170A451GLU-1-0.851-0.94329.811-0.105-0.1050.0000.0000.0000.000
171A452ASP-1-0.969-0.97732.642-0.079-0.0790.0000.0000.0000.000
172A453THR0-0.074-0.02028.519-0.006-0.0060.0000.0000.0000.000
173A454PRO0-0.079-0.04625.3360.0100.0100.0000.0000.0000.000
174A455HIS00.0480.01227.2840.0010.0010.0000.0000.0000.000
175A456VAL00.0830.03921.342-0.003-0.0030.0000.0000.0000.000
176A457CYS0-0.080-0.03121.4030.0140.0140.0000.0000.0000.000
177A458TRP00.0220.00412.846-0.006-0.0060.0000.0000.0000.000
178A459GLU-1-0.756-0.88017.346-0.118-0.1180.0000.0000.0000.000
179A460PRO00.0020.00812.242-0.038-0.0380.0000.0000.0000.000
180A461GLN0-0.039-0.02813.579-0.069-0.0690.0000.0000.0000.000
181A462ALA00.0190.02516.030-0.013-0.0130.0000.0000.0000.000
182A463GLN00.0090.0158.5820.0420.0420.0000.0000.0000.000
183A464GLY0-0.007-0.00513.655-0.040-0.0400.0000.0000.0000.000
184A465ARG10.9330.96614.7700.2940.2940.0000.0000.0000.000
185A466MET00.0550.03116.1410.0310.0310.0000.0000.0000.000
186A467CYS0-0.037-0.01312.796-0.038-0.0380.0000.0000.0000.000
187A468ALA00.0040.00815.4870.0100.0100.0000.0000.0000.000
188A469LEU00.0240.00718.1770.0340.0340.0000.0000.0000.000
189A470TYR00.0300.00316.9410.0170.0170.0000.0000.0000.000
190A471ALA00.0100.00317.4020.0220.0220.0000.0000.0000.000
191A472SER00.0230.00219.2730.0380.0380.0000.0000.0000.000
192A473LEU0-0.022-0.00422.5910.0290.0290.0000.0000.0000.000
193A474ALA00.0040.00320.7860.0250.0250.0000.0000.0000.000
194A475LEU0-0.0040.00421.2450.0190.0190.0000.0000.0000.000
195A476LEU00.0140.00624.1540.0240.0240.0000.0000.0000.000
196A477SER0-0.033-0.04225.8290.0240.0240.0000.0000.0000.000
197A478GLY0-0.023-0.00526.0980.0140.0140.0000.0000.0000.000
198A479LEU0-0.0190.00027.2270.0140.0140.0000.0000.0000.000
199A480SER0-0.075-0.02630.1690.0240.0240.0000.0000.0000.000