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: Z6Z5N

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 OptHSide
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 -2061128.980502
FMO2-HF: Nuclear repulsion 1985530.572928
FMO2-HF: Total energy -75598.407574
FMO2-MP2: Total energy -75815.929842


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.
-9.697-6.4680.127-1.625-1.7310.001
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 : 0.005 / q_NPA : -0.004
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].
3A284THR0-0.015-0.0033.005-1.7620.8640.079-1.263-1.4420.004
4A285GLU-1-0.892-0.9273.316-5.137-4.5340.048-0.362-0.289-0.003
5A286ASP-1-0.857-0.9245.657-0.275-0.2750.0000.0000.0000.000
6A287PHE00.0400.0057.949-0.052-0.0520.0000.0000.0000.000
7A288GLN0-0.065-0.03610.785-0.013-0.0130.0000.0000.0000.000
8A289GLY00.0440.0318.8860.0590.0590.0000.0000.0000.000
9A290LEU0-0.026-0.0179.9370.0200.0200.0000.0000.0000.000
10A291ARG10.8300.92311.9460.3820.3820.0000.0000.0000.000
11A292ALA00.0150.00712.6410.0500.0500.0000.0000.0000.000
12A293GLU-1-0.900-0.95512.523-0.746-0.7460.0000.0000.0000.000
13A294VAL00.0070.00114.4250.0790.0790.0000.0000.0000.000
14A295GLU-1-0.925-0.96717.303-0.284-0.2840.0000.0000.0000.000
15A296THR0-0.113-0.05716.5270.0610.0610.0000.0000.0000.000
16A297ILE0-0.0090.00719.3320.0390.0390.0000.0000.0000.000
17A298SER00.001-0.02621.1130.0380.0380.0000.0000.0000.000
18A299LYS10.8350.92022.5020.2520.2520.0000.0000.0000.000
19A300GLU-1-0.906-0.95424.261-0.207-0.2070.0000.0000.0000.000
20A301LEU00.0130.00725.5310.0120.0120.0000.0000.0000.000
21A302GLU-1-0.953-0.97026.618-0.170-0.1700.0000.0000.0000.000
22A303LEU0-0.111-0.06229.5430.0150.0150.0000.0000.0000.000
23A304LEU0-0.0190.00630.2530.0080.0080.0000.0000.0000.000
24A305ASP-1-0.929-0.95133.306-0.114-0.1140.0000.0000.0000.000
25A306ARG10.9520.96135.3490.1150.1150.0000.0000.0000.000
26A307GLU-1-0.943-0.97937.502-0.100-0.1000.0000.0000.0000.000
27A308LEU00.0180.00835.9340.0000.0000.0000.0000.0000.000
28A309CYS00.0060.02132.836-0.005-0.0050.0000.0000.0000.000
29A310GLN0-0.015-0.00334.918-0.006-0.0060.0000.0000.0000.000
30A311LEU00.0280.02037.6140.0000.0000.0000.0000.0000.000
31A312LEU00.008-0.00231.144-0.002-0.0020.0000.0000.0000.000
32A313LEU0-0.038-0.02631.050-0.007-0.0070.0000.0000.0000.000
33A314GLU-1-0.958-0.96934.539-0.110-0.1100.0000.0000.0000.000
34A315GLY00.000-0.00737.0090.0020.0020.0000.0000.0000.000
35A316LEU00.003-0.02730.039-0.004-0.0040.0000.0000.0000.000
36A317GLU-1-0.813-0.88233.468-0.130-0.1300.0000.0000.0000.000
37A318GLY0-0.006-0.00935.1900.0010.0010.0000.0000.0000.000
38A319VAL0-0.026-0.02332.3020.0010.0010.0000.0000.0000.000
39A320LEU0-0.035-0.00628.826-0.004-0.0040.0000.0000.0000.000
40A321ARG10.6830.81432.8300.1260.1260.0000.0000.0000.000
41A322ASP-1-0.891-0.95635.503-0.128-0.1280.0000.0000.0000.000
42A323GLN0-0.016-0.00230.824-0.016-0.0160.0000.0000.0000.000
43A324LEU0-0.053-0.03733.929-0.007-0.0070.0000.0000.0000.000
44A325ALA00.0140.01235.939-0.004-0.0040.0000.0000.0000.000
45A326LEU00.0110.00428.843-0.005-0.0050.0000.0000.0000.000
46A327ARG10.9160.95431.2270.1810.1810.0000.0000.0000.000
47A328ALA00.0040.00332.654-0.003-0.0030.0000.0000.0000.000
48A329LEU0-0.007-0.00931.8030.0010.0010.0000.0000.0000.000
49A330GLU-1-0.954-0.97627.015-0.283-0.2830.0000.0000.0000.000
50A331GLU-1-0.941-0.96830.290-0.182-0.1820.0000.0000.0000.000
51A332ALA0-0.054-0.01932.5680.0010.0010.0000.0000.0000.000
52A333LEU0-0.028-0.02330.1800.0040.0040.0000.0000.0000.000
53A334GLU-1-0.932-0.94729.638-0.220-0.2200.0000.0000.0000.000
54A335GLN0-0.079-0.05224.326-0.004-0.0040.0000.0000.0000.000
55A336GLY00.0160.00226.218-0.013-0.0130.0000.0000.0000.000
56A337GLN0-0.087-0.04626.2670.0040.0040.0000.0000.0000.000
57A338SER00.0160.02229.4040.0120.0120.0000.0000.0000.000
58A339LEU0-0.038-0.03132.6450.0050.0050.0000.0000.0000.000
59A340GLY0-0.038-0.01235.1250.0070.0070.0000.0000.0000.000
60A341PRO0-0.013-0.02637.281-0.006-0.0060.0000.0000.0000.000
61A342VAL00.0100.00535.2650.0000.0000.0000.0000.0000.000
62A343GLU-1-0.965-0.97838.591-0.105-0.1050.0000.0000.0000.000
63A344PRO0-0.019-0.00940.290-0.006-0.0060.0000.0000.0000.000
64A345LEU00.0150.00037.5890.0020.0020.0000.0000.0000.000
65A346ASP-1-0.916-0.95541.765-0.098-0.0980.0000.0000.0000.000
66A347GLY0-0.039-0.02641.518-0.005-0.0050.0000.0000.0000.000
67A348PRO00.0360.01037.773-0.001-0.0010.0000.0000.0000.000
68A349ALA00.0410.02436.241-0.004-0.0040.0000.0000.0000.000
69A350GLY00.0070.00737.257-0.005-0.0050.0000.0000.0000.000
70A351ALA00.0120.01239.3210.0010.0010.0000.0000.0000.000
71A352VAL00.0190.00432.875-0.001-0.0010.0000.0000.0000.000
72A353LEU0-0.023-0.00735.765-0.003-0.0030.0000.0000.0000.000
73A354GLU-1-0.956-0.98236.927-0.110-0.1100.0000.0000.0000.000
74A355CYS0-0.085-0.02936.1280.0040.0040.0000.0000.0000.000
75A356LEU0-0.025-0.01531.963-0.005-0.0050.0000.0000.0000.000
76A357VAL0-0.0320.00435.429-0.004-0.0040.0000.0000.0000.000
77A358LEU00.0040.01038.1500.0080.0080.0000.0000.0000.000
78A359SER0-0.017-0.02540.8740.0030.0030.0000.0000.0000.000
79A360SER0-0.084-0.05141.8580.0010.0010.0000.0000.0000.000
80A361GLY00.1070.05640.8320.0020.0020.0000.0000.0000.000
81A362MET0-0.091-0.02636.485-0.003-0.0030.0000.0000.0000.000
82A363LEU00.0640.03031.9900.0020.0020.0000.0000.0000.000
83A364VAL00.0150.01433.4370.0030.0030.0000.0000.0000.000
84A365PRO0-0.032-0.00728.805-0.008-0.0080.0000.0000.0000.000
85A366GLU-1-0.887-0.95928.690-0.185-0.1850.0000.0000.0000.000
86A367LEU0-0.009-0.01229.330-0.009-0.0090.0000.0000.0000.000
87A368ALA00.0000.00229.976-0.008-0.0080.0000.0000.0000.000
88A369ILE00.0240.02223.741-0.013-0.0130.0000.0000.0000.000
89A370PRO00.0420.01424.387-0.028-0.0280.0000.0000.0000.000
90A371VAL00.0290.01925.028-0.014-0.0140.0000.0000.0000.000
91A372VAL00.0020.00823.836-0.009-0.0090.0000.0000.0000.000
92A373TYR0-0.038-0.01717.4910.0020.0020.0000.0000.0000.000
93A374LEU0-0.021-0.00121.772-0.025-0.0250.0000.0000.0000.000
94A375LEU00.018-0.00223.905-0.004-0.0040.0000.0000.0000.000
95A376GLY00.0260.01521.685-0.001-0.0010.0000.0000.0000.000
96A377ALA0-0.045-0.01019.848-0.022-0.0220.0000.0000.0000.000
97A378LEU00.0380.00420.8070.0080.0080.0000.0000.0000.000
98A379THR0-0.063-0.02322.1370.0150.0150.0000.0000.0000.000
99A380MET0-0.075-0.03517.3660.0020.0020.0000.0000.0000.000
100A381LEU0-0.075-0.02821.3680.0090.0090.0000.0000.0000.000
101A382SER0-0.026-0.04724.0320.0100.0100.0000.0000.0000.000
102A383GLU-1-0.792-0.89927.257-0.150-0.1500.0000.0000.0000.000
103A384THR0-0.074-0.04429.8410.0080.0080.0000.0000.0000.000
104A385GLN00.004-0.01823.209-0.005-0.0050.0000.0000.0000.000
105A386HIS00.0140.00626.3820.0180.0180.0000.0000.0000.000
106A387LYS10.9120.94329.8160.1450.1450.0000.0000.0000.000
107A388LEU0-0.035-0.00829.6400.0080.0080.0000.0000.0000.000
108A389LEU0-0.006-0.01025.6520.0030.0030.0000.0000.0000.000
109A390ALA0-0.0040.00730.0960.0030.0030.0000.0000.0000.000
110A391GLU-1-0.844-0.90833.515-0.109-0.1090.0000.0000.0000.000
111A392ALA0-0.0290.00430.7760.0060.0060.0000.0000.0000.000
112A393LEU0-0.001-0.00531.0840.0030.0030.0000.0000.0000.000
113A394GLU-1-0.955-0.95233.701-0.097-0.0970.0000.0000.0000.000
114A395SER0-0.050-0.03235.9690.0060.0060.0000.0000.0000.000
115A396GLN0-0.072-0.04134.4650.0030.0030.0000.0000.0000.000
116A397THR0-0.097-0.05233.0910.0010.0010.0000.0000.0000.000
117A398LEU00.0560.02728.149-0.004-0.0040.0000.0000.0000.000
118A399LEU00.010-0.01127.480-0.010-0.0100.0000.0000.0000.000
119A400GLY00.0170.02127.160-0.003-0.0030.0000.0000.0000.000
120A401PRO00.0290.00826.378-0.004-0.0040.0000.0000.0000.000
121A402LEU0-0.0020.01221.717-0.015-0.0150.0000.0000.0000.000
122A403GLU-1-0.920-0.95622.305-0.154-0.1540.0000.0000.0000.000
123A404LEU0-0.0250.00322.713-0.001-0.0010.0000.0000.0000.000
124A405VAL00.021-0.00719.143-0.003-0.0030.0000.0000.0000.000
125A406GLY00.0190.00618.212-0.027-0.0270.0000.0000.0000.000
126A407SER0-0.017-0.01717.829-0.007-0.0070.0000.0000.0000.000
127A408LEU0-0.037-0.02018.8770.0150.0150.0000.0000.0000.000
128A409LEU00.0030.02313.7600.0000.0000.0000.0000.0000.000
129A410GLU-1-0.856-0.92113.903-0.261-0.2610.0000.0000.0000.000
130A411GLN0-0.058-0.04614.8910.0290.0290.0000.0000.0000.000
131A412SER0-0.030-0.03914.5850.0200.0200.0000.0000.0000.000
132A413ALA0-0.0490.01610.565-0.011-0.0110.0000.0000.0000.000
133A414PRO0-0.049-0.0348.2290.0580.0580.0000.0000.0000.000
134A415TRP00.0810.0188.781-0.034-0.0340.0000.0000.0000.000
135A416GLN0-0.031-0.0226.983-0.146-0.1460.0000.0000.0000.000
136A417GLU-1-0.944-0.97310.0210.3520.3520.0000.0000.0000.000
137A418ARG10.8610.91312.9050.0280.0280.0000.0000.0000.000
138A419SER0-0.012-0.00115.5700.0310.0310.0000.0000.0000.000
139A420THR0-0.021-0.00118.159-0.019-0.0190.0000.0000.0000.000
140A421MET0-0.041-0.00318.0250.0080.0080.0000.0000.0000.000
141A422SER0-0.034-0.02521.7980.0000.0000.0000.0000.0000.000
142A423LEU0-0.0040.01222.4590.0060.0060.0000.0000.0000.000
143A424PRO00.0380.01724.923-0.005-0.0050.0000.0000.0000.000
144A425PRO00.0600.02226.1490.0020.0020.0000.0000.0000.000
145A426GLY00.0550.02728.369-0.001-0.0010.0000.0000.0000.000
146A427LEU0-0.106-0.05430.7090.0040.0040.0000.0000.0000.000
147A428LEU0-0.005-0.00325.6540.0040.0040.0000.0000.0000.000
148A429GLY0-0.040-0.00430.319-0.004-0.0040.0000.0000.0000.000
149A430ASN0-0.059-0.01728.678-0.007-0.0070.0000.0000.0000.000
150A431SER0-0.023-0.02032.2480.0080.0080.0000.0000.0000.000
151A432TRP0-0.024-0.03026.494-0.011-0.0110.0000.0000.0000.000
152A433GLY00.0510.02232.5840.0080.0080.0000.0000.0000.000
153A434GLU-1-0.941-0.96633.077-0.088-0.0880.0000.0000.0000.000
154A435GLY0-0.044-0.01933.2760.0050.0050.0000.0000.0000.000
155A436ALA0-0.064-0.02532.737-0.002-0.0020.0000.0000.0000.000
156A437PRO00.0400.00631.965-0.007-0.0070.0000.0000.0000.000
157A438ALA00.0450.01728.209-0.011-0.0110.0000.0000.0000.000
158A439TRP00.0070.00827.405-0.009-0.0090.0000.0000.0000.000
159A440VAL00.0320.00927.774-0.009-0.0090.0000.0000.0000.000
160A441LEU00.0010.00525.280-0.011-0.0110.0000.0000.0000.000
161A442LEU00.0320.00021.982-0.023-0.0230.0000.0000.0000.000
162A443ASP-1-0.881-0.94123.376-0.147-0.1470.0000.0000.0000.000
163A444GLU-1-0.830-0.87325.032-0.186-0.1860.0000.0000.0000.000
164A445CYS0-0.099-0.03119.878-0.029-0.0290.0000.0000.0000.000
165A446GLY0-0.053-0.02919.997-0.029-0.0290.0000.0000.0000.000
166A447LEU0-0.040-0.01718.3160.0110.0110.0000.0000.0000.000
167A448GLU-1-0.936-0.95821.729-0.088-0.0880.0000.0000.0000.000
168A449LEU0-0.034-0.02224.2860.0050.0050.0000.0000.0000.000
169A450GLY00.0340.01426.8640.0080.0080.0000.0000.0000.000
170A451GLU-1-0.818-0.91729.839-0.075-0.0750.0000.0000.0000.000
171A452ASP-1-0.990-0.98832.678-0.040-0.0400.0000.0000.0000.000
172A453THR0-0.083-0.02628.618-0.001-0.0010.0000.0000.0000.000
173A454PRO0-0.074-0.04125.3290.0080.0080.0000.0000.0000.000
174A455HIS00.0310.00527.3200.0020.0020.0000.0000.0000.000
175A456VAL00.0780.04021.512-0.008-0.0080.0000.0000.0000.000
176A457CYS0-0.067-0.03021.4170.0230.0230.0000.0000.0000.000
177A458TRP00.0240.00312.944-0.019-0.0190.0000.0000.0000.000
178A459GLU-1-0.764-0.88617.388-0.091-0.0910.0000.0000.0000.000
179A460PRO0-0.0030.00612.291-0.042-0.0420.0000.0000.0000.000
180A461GLN0-0.045-0.03213.636-0.082-0.0820.0000.0000.0000.000
181A462ALA00.0130.01316.092-0.025-0.0250.0000.0000.0000.000
182A463GLN0-0.0110.0058.0290.1130.1130.0000.0000.0000.000
183A464GLY00.0140.00713.708-0.034-0.0340.0000.0000.0000.000
184A465ARG10.9240.96914.8310.2980.2980.0000.0000.0000.000
185A466MET00.0350.02416.1320.0330.0330.0000.0000.0000.000
186A467CYS0-0.052-0.02312.917-0.019-0.0190.0000.0000.0000.000
187A468ALA00.0090.00915.5150.0120.0120.0000.0000.0000.000
188A469LEU00.0360.02318.2030.0350.0350.0000.0000.0000.000
189A470TYR00.0190.00116.8580.0410.0410.0000.0000.0000.000
190A471ALA00.0100.00317.3890.0240.0240.0000.0000.0000.000
191A472SER00.008-0.01319.2890.0310.0310.0000.0000.0000.000
192A473LEU0-0.017-0.00522.6130.0280.0280.0000.0000.0000.000
193A474ALA00.0010.01620.8080.0260.0260.0000.0000.0000.000
194A475LEU00.0070.00621.1750.0180.0180.0000.0000.0000.000
195A476LEU00.0130.00624.1630.0220.0220.0000.0000.0000.000
196A477SER0-0.036-0.05425.8900.0240.0240.0000.0000.0000.000
197A478GLY0-0.028-0.01026.1060.0150.0150.0000.0000.0000.000
198A479LEU0-0.0120.00227.2300.0120.0120.0000.0000.0000.000
199A480SER0-0.060-0.02230.1800.0230.0230.0000.0000.0000.000