FMODB

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

Last updated: 2024-04-25

All entries: 37426

Number of unique PDB entries: 7782

tag_button

FMODB ID: R9LG8

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 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 199
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2061927.203385
FMO2-HF: Nuclear repulsion 1986328.367307
FMO2-HF: Total energy -75598.836077
FMO2-MP2: Total energy -75816.213633


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.
-9.262-4.420.469-2.629-2.682-0.004
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 : 0.024 / q_NPA : 0.008
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].
3A284THR0-0.027-0.0132.651-1.8541.8470.225-1.989-1.9370.002
4A285GLU-1-0.871-0.9162.941-4.911-3.7700.244-0.640-0.745-0.006
5A286ASP-1-0.844-0.9125.615-0.274-0.2740.0000.0000.0000.000
6A287PHE00.0520.0067.776-0.024-0.0240.0000.0000.0000.000
7A288GLN0-0.063-0.04310.841-0.018-0.0180.0000.0000.0000.000
8A289GLY00.0130.0139.1720.0610.0610.0000.0000.0000.000
9A290LEU0-0.028-0.02110.2350.0040.0040.0000.0000.0000.000
10A291ARG10.7980.90011.9030.3150.3150.0000.0000.0000.000
11A292ALA00.0290.02012.8020.0280.0280.0000.0000.0000.000
12A293GLU-1-0.860-0.92112.763-0.648-0.6480.0000.0000.0000.000
13A294VAL00.0090.00714.6490.0670.0670.0000.0000.0000.000
14A295GLU-1-0.913-0.96117.276-0.252-0.2520.0000.0000.0000.000
15A296THR0-0.117-0.06316.7180.0540.0540.0000.0000.0000.000
16A297ILE00.0050.01819.5940.0380.0380.0000.0000.0000.000
17A298SER0-0.007-0.03921.0630.0360.0360.0000.0000.0000.000
18A299LYS10.8190.90422.6400.2270.2270.0000.0000.0000.000
19A300GLU-1-0.885-0.93724.433-0.186-0.1860.0000.0000.0000.000
20A301LEU00.0010.00825.3850.0110.0110.0000.0000.0000.000
21A302GLU-1-0.945-0.97126.498-0.150-0.1500.0000.0000.0000.000
22A303LEU0-0.115-0.05929.4310.0140.0140.0000.0000.0000.000
23A304LEU0-0.0180.00630.4810.0060.0060.0000.0000.0000.000
24A305ASP-1-0.939-0.96133.628-0.102-0.1020.0000.0000.0000.000
25A306ARG10.9430.95935.2170.1040.1040.0000.0000.0000.000
26A307GLU-1-0.940-0.97637.527-0.092-0.0920.0000.0000.0000.000
27A308LEU00.0050.00336.1900.0000.0000.0000.0000.0000.000
28A309CYS0-0.0050.00633.079-0.006-0.0060.0000.0000.0000.000
29A310GLN0-0.023-0.01435.019-0.005-0.0050.0000.0000.0000.000
30A311LEU00.0230.01637.653-0.001-0.0010.0000.0000.0000.000
31A312LEU00.0300.01731.319-0.002-0.0020.0000.0000.0000.000
32A313LEU0-0.024-0.01730.802-0.008-0.0080.0000.0000.0000.000
33A314GLU-1-0.957-0.96634.350-0.102-0.1020.0000.0000.0000.000
34A315GLY00.012-0.00337.0780.0010.0010.0000.0000.0000.000
35A316LEU00.013-0.01930.050-0.003-0.0030.0000.0000.0000.000
36A317GLU-1-0.820-0.88833.131-0.121-0.1210.0000.0000.0000.000
37A318GLY0-0.018-0.01534.8970.0010.0010.0000.0000.0000.000
38A319VAL0-0.030-0.02931.9790.0020.0020.0000.0000.0000.000
39A320LEU0-0.050-0.01128.689-0.004-0.0040.0000.0000.0000.000
40A321ARG10.7060.82132.6540.1180.1180.0000.0000.0000.000
41A322ASP-1-0.882-0.94435.364-0.123-0.1230.0000.0000.0000.000
42A323GLN0-0.007-0.01230.829-0.016-0.0160.0000.0000.0000.000
43A324LEU0-0.079-0.04533.964-0.006-0.0060.0000.0000.0000.000
44A325ALA0-0.001-0.00536.138-0.004-0.0040.0000.0000.0000.000
45A326LEU00.0090.00628.623-0.004-0.0040.0000.0000.0000.000
46A327ARG10.8730.93331.0900.1780.1780.0000.0000.0000.000
47A328ALA00.0060.00432.816-0.004-0.0040.0000.0000.0000.000
48A329LEU00.0120.00831.7930.0020.0020.0000.0000.0000.000
49A330GLU-1-0.922-0.95727.131-0.268-0.2680.0000.0000.0000.000
50A331GLU-1-0.899-0.96330.484-0.178-0.1780.0000.0000.0000.000
51A332ALA0-0.051-0.01532.6020.0030.0030.0000.0000.0000.000
52A333LEU0-0.034-0.02230.3440.0050.0050.0000.0000.0000.000
53A334GLU-1-0.923-0.94629.423-0.207-0.2070.0000.0000.0000.000
54A335GLN0-0.088-0.06124.133-0.001-0.0010.0000.0000.0000.000
55A336GLY00.0220.00926.389-0.011-0.0110.0000.0000.0000.000
56A337GLN0-0.092-0.04826.5510.0080.0080.0000.0000.0000.000
57A338SER00.0340.01629.5260.0100.0100.0000.0000.0000.000
58A339LEU0-0.055-0.03932.4790.0050.0050.0000.0000.0000.000
59A340GLY0-0.048-0.02135.2530.0100.0100.0000.0000.0000.000
60A341PRO0-0.027-0.01037.279-0.007-0.0070.0000.0000.0000.000
61A342VAL00.0050.01035.355-0.001-0.0010.0000.0000.0000.000
62A343GLU-1-0.964-0.98538.706-0.100-0.1000.0000.0000.0000.000
63A344PRO0-0.019-0.00640.461-0.005-0.0050.0000.0000.0000.000
64A345LEU00.004-0.00237.3970.0010.0010.0000.0000.0000.000
65A346ASP-1-0.916-0.95741.798-0.094-0.0940.0000.0000.0000.000
66A347GLY0-0.034-0.02541.330-0.005-0.0050.0000.0000.0000.000
67A348PRO00.0140.00137.6200.0000.0000.0000.0000.0000.000
68A349ALA00.0350.02836.438-0.005-0.0050.0000.0000.0000.000
69A350GLY00.0110.01437.476-0.004-0.0040.0000.0000.0000.000
70A351ALA00.0230.01439.506-0.002-0.0020.0000.0000.0000.000
71A352VAL00.0020.00132.863-0.001-0.0010.0000.0000.0000.000
72A353LEU00.0040.00735.827-0.004-0.0040.0000.0000.0000.000
73A354GLU-1-0.954-0.99036.885-0.104-0.1040.0000.0000.0000.000
74A355CYS0-0.098-0.03436.1530.0040.0040.0000.0000.0000.000
75A356LEU0-0.011-0.00931.994-0.006-0.0060.0000.0000.0000.000
76A357VAL0-0.0260.00235.420-0.005-0.0050.0000.0000.0000.000
77A358LEU00.0090.01038.2480.0080.0080.0000.0000.0000.000
78A359SER0-0.030-0.03440.9690.0020.0020.0000.0000.0000.000
79A360SER0-0.069-0.03642.4550.0030.0030.0000.0000.0000.000
80A361GLY00.0920.04441.1620.0010.0010.0000.0000.0000.000
81A362MET0-0.077-0.02336.990-0.004-0.0040.0000.0000.0000.000
82A363LEU00.0750.03932.1440.0030.0030.0000.0000.0000.000
83A364VAL00.0050.00933.6520.0040.0040.0000.0000.0000.000
84A365PRO0-0.023-0.00729.225-0.008-0.0080.0000.0000.0000.000
85A366GLU-1-0.880-0.95528.944-0.175-0.1750.0000.0000.0000.000
86A367LEU0-0.0090.00329.509-0.005-0.0050.0000.0000.0000.000
87A368ALA00.012-0.00229.723-0.010-0.0100.0000.0000.0000.000
88A369ILE00.0050.00623.977-0.013-0.0130.0000.0000.0000.000
89A370PRO00.0330.00424.377-0.028-0.0280.0000.0000.0000.000
90A371VAL00.0210.01924.954-0.014-0.0140.0000.0000.0000.000
91A372VAL0-0.0030.00623.767-0.008-0.0080.0000.0000.0000.000
92A373TYR0-0.080-0.04817.2730.0020.0020.0000.0000.0000.000
93A374LEU0-0.0190.00321.705-0.023-0.0230.0000.0000.0000.000
94A375LEU00.010-0.00123.957-0.002-0.0020.0000.0000.0000.000
95A376GLY00.0320.01721.586-0.001-0.0010.0000.0000.0000.000
96A377ALA0-0.048-0.01019.833-0.021-0.0210.0000.0000.0000.000
97A378LEU00.0390.00420.7980.0050.0050.0000.0000.0000.000
98A379THR0-0.073-0.03721.9590.0120.0120.0000.0000.0000.000
99A380MET0-0.083-0.03516.881-0.001-0.0010.0000.0000.0000.000
100A381LEU0-0.059-0.02221.0040.0050.0050.0000.0000.0000.000
101A382SER0-0.026-0.04923.7750.0100.0100.0000.0000.0000.000
102A383GLU-1-0.788-0.88427.086-0.142-0.1420.0000.0000.0000.000
103A384THR0-0.069-0.05129.5150.0080.0080.0000.0000.0000.000
104A385GLN00.011-0.00722.885-0.003-0.0030.0000.0000.0000.000
105A386HIS00.0020.00026.3770.0170.0170.0000.0000.0000.000
106A387LYS10.8960.93429.5820.1360.1360.0000.0000.0000.000
107A388LEU0-0.041-0.01829.3630.0080.0080.0000.0000.0000.000
108A389LEU0-0.002-0.00425.4840.0040.0040.0000.0000.0000.000
109A390ALA00.0130.01629.9420.0030.0030.0000.0000.0000.000
110A391GLU-1-0.855-0.91433.523-0.101-0.1010.0000.0000.0000.000
111A392ALA0-0.032-0.00330.6250.0070.0070.0000.0000.0000.000
112A393LEU0-0.011-0.00231.1800.0000.0000.0000.0000.0000.000
113A394GLU-1-0.927-0.95133.752-0.087-0.0870.0000.0000.0000.000
114A395SER0-0.053-0.03635.7720.0040.0040.0000.0000.0000.000
115A396GLN0-0.068-0.03734.3660.0050.0050.0000.0000.0000.000
116A397THR0-0.058-0.03533.074-0.002-0.0020.0000.0000.0000.000
117A398LEU00.0160.00828.245-0.001-0.0010.0000.0000.0000.000
118A399LEU00.0330.00127.519-0.009-0.0090.0000.0000.0000.000
119A400GLY00.0120.02727.184-0.002-0.0020.0000.0000.0000.000
120A401PRO00.014-0.00426.115-0.002-0.0020.0000.0000.0000.000
121A402LEU0-0.0020.01321.877-0.015-0.0150.0000.0000.0000.000
122A403GLU-1-0.911-0.95222.312-0.123-0.1230.0000.0000.0000.000
123A404LEU0-0.0300.00222.6940.0000.0000.0000.0000.0000.000
124A405VAL00.019-0.00519.167-0.001-0.0010.0000.0000.0000.000
125A406GLY00.0220.01118.271-0.026-0.0260.0000.0000.0000.000
126A407SER0-0.044-0.03317.870-0.003-0.0030.0000.0000.0000.000
127A408LEU0-0.020-0.01818.7590.0130.0130.0000.0000.0000.000
128A409LEU0-0.0030.03013.644-0.005-0.0050.0000.0000.0000.000
129A410GLU-1-0.829-0.89713.874-0.202-0.2020.0000.0000.0000.000
130A411GLN0-0.067-0.05114.9530.0300.0300.0000.0000.0000.000
131A412SER0-0.012-0.03214.3410.0170.0170.0000.0000.0000.000
132A413ALA0-0.0270.02210.304-0.022-0.0220.0000.0000.0000.000
133A414PRO0-0.066-0.0357.7810.0650.0650.0000.0000.0000.000
134A415TRP00.0780.0148.223-0.027-0.0270.0000.0000.0000.000
135A416GLN0-0.025-0.0186.655-0.186-0.1860.0000.0000.0000.000
136A417GLU-1-0.944-0.9709.5950.3970.3970.0000.0000.0000.000
137A418ARG10.7510.86312.6350.0410.0410.0000.0000.0000.000
138A419SER0-0.008-0.00615.2470.0310.0310.0000.0000.0000.000
139A420THR0-0.029-0.01617.948-0.019-0.0190.0000.0000.0000.000
140A421MET0-0.047-0.00917.8390.0100.0100.0000.0000.0000.000
141A422SER0-0.034-0.02621.742-0.002-0.0020.0000.0000.0000.000
142A423LEU0-0.0010.01022.2570.0050.0050.0000.0000.0000.000
143A424PRO00.0350.02324.853-0.006-0.0060.0000.0000.0000.000
144A425PRO00.0470.01526.1740.0010.0010.0000.0000.0000.000
145A426GLY00.0550.03128.312-0.002-0.0020.0000.0000.0000.000
146A427LEU0-0.109-0.05830.5650.0040.0040.0000.0000.0000.000
147A428LEU0-0.0080.00625.5440.0050.0050.0000.0000.0000.000
148A429GLY0-0.034-0.00930.206-0.005-0.0050.0000.0000.0000.000
149A430ASN0-0.052-0.02028.298-0.007-0.0070.0000.0000.0000.000
150A431SER0-0.026-0.02231.7920.0070.0070.0000.0000.0000.000
151A432TRP0-0.035-0.03726.319-0.010-0.0100.0000.0000.0000.000
152A433GLY00.0720.03732.2860.0070.0070.0000.0000.0000.000
153A434GLU-1-0.964-0.98832.914-0.078-0.0780.0000.0000.0000.000
154A435GLY0-0.036-0.01432.9680.0040.0040.0000.0000.0000.000
155A436ALA0-0.042-0.00932.740-0.002-0.0020.0000.0000.0000.000
156A437PRO00.018-0.01131.828-0.007-0.0070.0000.0000.0000.000
157A438ALA00.0390.01328.460-0.010-0.0100.0000.0000.0000.000
158A439TRP0-0.0020.00727.301-0.007-0.0070.0000.0000.0000.000
159A440VAL00.0230.00327.386-0.010-0.0100.0000.0000.0000.000
160A441LEU00.0140.00925.077-0.010-0.0100.0000.0000.0000.000
161A442LEU00.0350.00821.812-0.024-0.0240.0000.0000.0000.000
162A443ASP-1-0.884-0.93423.149-0.134-0.1340.0000.0000.0000.000
163A444GLU-1-0.809-0.84924.736-0.176-0.1760.0000.0000.0000.000
164A445CYS0-0.091-0.03219.903-0.030-0.0300.0000.0000.0000.000
165A446GLY0-0.048-0.02219.903-0.026-0.0260.0000.0000.0000.000
166A447LEU0-0.016-0.01318.0430.0020.0020.0000.0000.0000.000
167A448GLU-1-0.858-0.90721.356-0.066-0.0660.0000.0000.0000.000
168A449LEU0-0.029-0.01723.7790.0030.0030.0000.0000.0000.000
169A450GLY00.0240.00826.6160.0070.0070.0000.0000.0000.000
170A451GLU-1-0.841-0.91129.742-0.064-0.0640.0000.0000.0000.000
171A452ASP-1-0.963-0.97332.537-0.030-0.0300.0000.0000.0000.000
172A453THR0-0.077-0.04028.328-0.002-0.0020.0000.0000.0000.000
173A454PRO0-0.086-0.04424.8840.0080.0080.0000.0000.0000.000
174A455HIS00.0320.00526.9610.0020.0020.0000.0000.0000.000
175A456VAL00.0680.03721.382-0.009-0.0090.0000.0000.0000.000
176A457CYS0-0.061-0.02620.9480.0250.0250.0000.0000.0000.000
177A458TRP00.0400.01412.408-0.017-0.0170.0000.0000.0000.000
178A459GLU-1-0.769-0.89416.826-0.097-0.0970.0000.0000.0000.000
179A460PRO00.0010.01011.888-0.041-0.0410.0000.0000.0000.000
180A461GLN0-0.072-0.04213.509-0.079-0.0790.0000.0000.0000.000
181A462ALA00.0400.03516.026-0.009-0.0090.0000.0000.0000.000
182A463GLN0-0.038-0.0057.8150.1020.1020.0000.0000.0000.000
183A464GLY00.0110.00213.452-0.034-0.0340.0000.0000.0000.000
184A465ARG10.8810.94314.5450.2850.2850.0000.0000.0000.000
185A466MET00.0470.01815.8050.0260.0260.0000.0000.0000.000
186A467CYS0-0.043-0.02012.628-0.017-0.0170.0000.0000.0000.000
187A468ALA00.0180.01615.2570.0120.0120.0000.0000.0000.000
188A469LEU00.0360.02318.1200.0350.0350.0000.0000.0000.000
189A470TYR00.0290.00416.8030.0400.0400.0000.0000.0000.000
190A471ALA00.0040.00117.4680.0250.0250.0000.0000.0000.000
191A472SER00.003-0.01619.3210.0310.0310.0000.0000.0000.000
192A473LEU0-0.021-0.01322.4960.0250.0250.0000.0000.0000.000
193A474ALA00.0090.02120.8890.0250.0250.0000.0000.0000.000
194A475LEU00.0140.00821.2610.0210.0210.0000.0000.0000.000
195A476LEU00.0260.01624.3790.0190.0190.0000.0000.0000.000
196A477SER0-0.014-0.02325.9200.0240.0240.0000.0000.0000.000
197A478GLY0-0.026-0.00626.2760.0150.0150.0000.0000.0000.000
198A479LEU00.0030.00927.2660.0100.0100.0000.0000.0000.000
199A480SER0-0.094-0.05430.1990.0290.0290.0000.0000.0000.000