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: QYLGY

Calculation Name: 5NGO-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 5NGO

Chain ID: A

ChEMBL ID:

UniProt ID: Q8RY59

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 180
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -1925427.494683
FMO2-HF: Nuclear repulsion 1853819.202695
FMO2-HF: Total energy -71608.291988
FMO2-MP2: Total energy -71813.375531


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:273:LEU)


Summations of interaction energy for fragment #1(A:273:LEU)
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.
-4.5372.25211.383-5.224-12.944-0.01
Interaction energy analysis for fragmet #1(A:273:LEU)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.026 / q_NPA : 0.020
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].
3A275LYS10.9740.9583.046-0.9242.7320.189-2.068-1.7760.005
4A276ASP-1-0.884-0.9435.780-0.093-0.0930.0000.0000.0000.000
5A277ALA0-0.0020.0012.310-0.4570.0661.309-0.500-1.332-0.001
6A278VAL0-0.0010.0152.672-0.7600.2610.397-0.244-1.1740.000
7A279LYS10.9730.9824.2530.2680.3920.000-0.019-0.1040.000
8A280LYS10.9310.9636.7660.0080.0080.0000.0000.0000.000
9A281MET00.0330.0172.2091.113-1.7155.621-0.516-2.2770.004
10A282PHE00.0220.0117.038-0.045-0.0450.0000.0000.0000.000
11A283ALA0-0.0230.0049.266-0.015-0.0150.0000.0000.0000.000
12A284VAL0-0.021-0.0159.783-0.010-0.0100.0000.0000.0000.000
13A285GLY00.0400.02110.999-0.012-0.0120.0000.0000.0000.000
14A286THR0-0.049-0.05212.310-0.025-0.0250.0000.0000.0000.000
15A287ALA00.0340.02114.927-0.020-0.0200.0000.0000.0000.000
16A288SER0-0.020-0.01117.166-0.012-0.0120.0000.0000.0000.000
17A289LEU0-0.061-0.02517.503-0.009-0.0090.0000.0000.0000.000
18A290GLY0-0.0110.00720.326-0.011-0.0110.0000.0000.0000.000
19A291HIS0-0.029-0.01919.7250.0090.0090.0000.0000.0000.000
20A292VAL00.0160.01315.387-0.010-0.0100.0000.0000.0000.000
21A293PRO0-0.053-0.01416.307-0.006-0.0060.0000.0000.0000.000
22A294VAL00.015-0.00711.473-0.007-0.0070.0000.0000.0000.000
23A295LEU0-0.064-0.04214.781-0.007-0.0070.0000.0000.0000.000
24A296ASP-1-0.893-0.95313.940-0.483-0.4830.0000.0000.0000.000
25A297VAL0-0.030-0.0097.1600.0210.0210.0000.0000.0000.000
26A298GLY00.0080.01510.306-0.071-0.0710.0000.0000.0000.000
27A299ARG10.9270.9525.6781.7661.7660.0000.0000.0000.000
28A300PHE00.0000.0139.2920.1320.1320.0000.0000.0000.000
29A301SER0-0.001-0.00610.705-0.137-0.1370.0000.0000.0000.000
30A302SER0-0.012-0.01312.8200.0840.0840.0000.0000.0000.000
31A303GLU-1-0.799-0.90215.295-0.253-0.2530.0000.0000.0000.000
32A304ILE00.0120.00717.5510.0150.0150.0000.0000.0000.000
33A305ALA0-0.029-0.02612.3830.0200.0200.0000.0000.0000.000
34A306GLU-1-0.933-0.96012.921-0.461-0.4610.0000.0000.0000.000
35A307ALA00.0130.00714.0160.0460.0460.0000.0000.0000.000
36A308ARG10.8770.92414.4050.2030.2030.0000.0000.0000.000
37A309LEU0-0.0090.0058.7630.0440.0440.0000.0000.0000.000
38A310ALA0-0.003-0.00812.4470.0830.0830.0000.0000.0000.000
39A311LEU0-0.031-0.00315.0870.0470.0470.0000.0000.0000.000
40A312PHE00.0150.00410.3380.0370.0370.0000.0000.0000.000
41A313GLN00.002-0.02510.0590.1150.1150.0000.0000.0000.000
42A314LYS10.9350.97314.007-0.003-0.0030.0000.0000.0000.000
43A315GLN00.0350.02016.8360.0280.0280.0000.0000.0000.000
44A316VAL0-0.0060.00012.5010.0230.0230.0000.0000.0000.000
45A317GLU-1-0.948-0.97815.9070.1220.1220.0000.0000.0000.000
46A318ILE0-0.020-0.00818.5030.0010.0010.0000.0000.0000.000
47A319THR00.0360.01117.962-0.002-0.0020.0000.0000.0000.000
48A320LYS10.9490.98016.728-0.299-0.2990.0000.0000.0000.000
49A321LYS10.8720.93119.256-0.130-0.1300.0000.0000.0000.000
50A322HIS0-0.0040.01622.695-0.002-0.0020.0000.0000.0000.000
51A323ARG10.8270.91020.733-0.123-0.1230.0000.0000.0000.000
52A324GLY0-0.0230.00421.7570.0010.0010.0000.0000.0000.000
53A325ASP-1-0.909-0.97315.6020.4140.4140.0000.0000.0000.000
54A326ALA0-0.029-0.01414.354-0.023-0.0230.0000.0000.0000.000
55A327ASN00.0000.02313.4000.0280.0280.0000.0000.0000.000
56A328VAL0-0.009-0.0128.260-0.045-0.0450.0000.0000.0000.000
57A329ARG10.8950.9327.875-0.240-0.2400.0000.0000.0000.000
58A330TYR00.000-0.0032.828-1.7560.4483.526-1.290-4.440-0.015
59A331ALA00.006-0.0035.9530.0220.0220.0000.0000.0000.000
60A332TRP0-0.045-0.0336.545-0.100-0.1000.0000.0000.0000.000
61A333LEU00.0230.01310.4300.0180.0180.0000.0000.0000.000
62A334PRO00.018-0.00613.245-0.037-0.0370.0000.0000.0000.000
63A335ALA00.0020.00415.433-0.005-0.0050.0000.0000.0000.000
64A336LYS11.0050.99817.2040.0960.0960.0000.0000.0000.000
65A337ARG10.9830.97919.4340.1270.1270.0000.0000.0000.000
66A338GLU-1-0.968-0.98720.736-0.115-0.1150.0000.0000.0000.000
67A339VAL0-0.0170.00818.3590.0000.0000.0000.0000.0000.000
68A340LEU0-0.041-0.02415.223-0.012-0.0120.0000.0000.0000.000
69A341SER0-0.029-0.01517.974-0.023-0.0230.0000.0000.0000.000
70A342ALA00.0550.02620.581-0.006-0.0060.0000.0000.0000.000
71A343VAL0-0.055-0.02515.1600.0000.0000.0000.0000.0000.000
72A344MET00.0270.03912.6450.0110.0110.0000.0000.0000.000
73A345MET00.0100.01717.5460.0150.0150.0000.0000.0000.000
74A346GLN0-0.011-0.01721.0040.0080.0080.0000.0000.0000.000
75A347GLY00.0010.02019.0570.0170.0170.0000.0000.0000.000
76A348LEU00.0460.00714.985-0.013-0.0130.0000.0000.0000.000
77A349GLY00.0260.01318.9270.0090.0090.0000.0000.0000.000
78A350VAL0-0.0060.01821.0860.0020.0020.0000.0000.0000.000
79A351GLY00.000-0.02723.5960.0040.0040.0000.0000.0000.000
80A352GLY00.0160.00525.2530.0060.0060.0000.0000.0000.000
81A353ALA0-0.066-0.02823.2210.0020.0020.0000.0000.0000.000
82A354PHE00.004-0.00416.743-0.010-0.0100.0000.0000.0000.000
83A355ILE0-0.077-0.00920.5240.0100.0100.0000.0000.0000.000
84A356ARG10.9670.98720.750-0.015-0.0150.0000.0000.0000.000
85A357LYS10.9750.98924.254-0.004-0.0040.0000.0000.0000.000
86A358SER0-0.063-0.04423.7240.0000.0000.0000.0000.0000.000
87A359ILE0-0.056-0.05525.706-0.003-0.0030.0000.0000.0000.000
88A360TYR00.0500.01423.0040.0010.0010.0000.0000.0000.000
89A361GLY00.0850.08125.5860.0030.0030.0000.0000.0000.000
90A362VAL0-0.110-0.07425.392-0.004-0.0040.0000.0000.0000.000
91A363GLY00.0730.03022.1720.0050.0050.0000.0000.0000.000
92A364ILE0-0.024-0.02116.383-0.011-0.0110.0000.0000.0000.000
93A365HIS0-0.0200.01518.1830.0190.0190.0000.0000.0000.000
94A366LEU0-0.021-0.01211.936-0.019-0.0190.0000.0000.0000.000
95A367THR0-0.0020.01912.6520.0030.0030.0000.0000.0000.000
96A368ALA00.0540.03711.0060.0080.0080.0000.0000.0000.000
97A369ALA00.012-0.0166.326-0.021-0.0210.0000.0000.0000.000
98A370ASP-1-0.859-0.9118.1470.2980.2980.0000.0000.0000.000
99A371CYS0-0.033-0.01110.600-0.042-0.0420.0000.0000.0000.000
100A372PRO0-0.0020.00810.215-0.035-0.0350.0000.0000.0000.000
101A373TYR00.016-0.01312.935-0.039-0.0390.0000.0000.0000.000
102A374PHE0-0.043-0.01116.170-0.016-0.0160.0000.0000.0000.000
103A375SER0-0.010-0.01915.226-0.015-0.0150.0000.0000.0000.000
104A376ALA00.0390.02215.874-0.019-0.0190.0000.0000.0000.000
105A377ARG10.9340.94917.074-0.004-0.0040.0000.0000.0000.000
106A378TYR0-0.042-0.01719.751-0.003-0.0030.0000.0000.0000.000
107A379CYS0-0.0480.01116.433-0.010-0.0100.0000.0000.0000.000
108A380ASP-1-0.877-0.93519.242-0.063-0.0630.0000.0000.0000.000
109A381VAL0-0.075-0.02621.451-0.012-0.0120.0000.0000.0000.000
110A382ASP-1-0.800-0.88622.581-0.139-0.1390.0000.0000.0000.000
111A383GLU-1-0.920-0.98024.588-0.103-0.1030.0000.0000.0000.000
112A384ASN0-0.0090.00924.5080.0110.0110.0000.0000.0000.000
113A385GLY0-0.034-0.03524.6020.0010.0010.0000.0000.0000.000
114A386VAL0-0.077-0.03718.7250.0030.0030.0000.0000.0000.000
115A387ARG10.8930.96218.0400.0640.0640.0000.0000.0000.000
116A388TYR0-0.017-0.05015.186-0.033-0.0330.0000.0000.0000.000
117A389MET00.0260.03211.2420.0260.0260.0000.0000.0000.000
118A390VAL0-0.031-0.01310.038-0.059-0.0590.0000.0000.0000.000
119A391LEU0-0.0170.0063.108-0.4400.0600.191-0.114-0.5760.000
120A392CYS0-0.026-0.0177.074-0.218-0.2180.0000.0000.0000.000
121A393ARG10.8620.9314.6750.3580.476-0.001-0.001-0.1150.000
122A394VAL00.0280.0017.764-0.082-0.0820.0000.0000.0000.000
123A395ILE0-0.045-0.00511.0820.0820.0820.0000.0000.0000.000
124A396MET0-0.027-0.01512.747-0.051-0.0510.0000.0000.0000.000
125A397GLY00.0300.02815.128-0.025-0.0250.0000.0000.0000.000
126A398ASN0-0.014-0.01217.5630.0160.0160.0000.0000.0000.000
127A399MET0-0.048-0.01915.250-0.003-0.0030.0000.0000.0000.000
128A400GLU-1-0.748-0.85519.6510.0750.0750.0000.0000.0000.000
129A401LEU0-0.004-0.00221.7760.0020.0020.0000.0000.0000.000
130A402LEU0-0.031-0.01321.592-0.010-0.0100.0000.0000.0000.000
131A403ARG10.9640.97424.882-0.068-0.0680.0000.0000.0000.000
132A404GLY0-0.027-0.01027.331-0.003-0.0030.0000.0000.0000.000
133A405ASP-1-0.861-0.91928.7400.0330.0330.0000.0000.0000.000
134A406LYS10.9230.94529.077-0.023-0.0230.0000.0000.0000.000
135A407ALA0-0.062-0.03330.261-0.004-0.0040.0000.0000.0000.000
136A408GLN0-0.0190.01126.802-0.003-0.0030.0000.0000.0000.000
137A409PHE0-0.026-0.03026.839-0.002-0.0020.0000.0000.0000.000
138A410PHE0-0.059-0.03725.882-0.004-0.0040.0000.0000.0000.000
139A411SER00.0170.01224.9200.0020.0020.0000.0000.0000.000
140A412GLY00.0250.00126.066-0.006-0.0060.0000.0000.0000.000
141A413GLY0-0.013-0.00527.581-0.003-0.0030.0000.0000.0000.000
142A414GLU-1-0.950-0.96527.2360.0640.0640.0000.0000.0000.000
143A415GLU-1-0.915-0.96226.9670.0870.0870.0000.0000.0000.000
144A416TYR0-0.034-0.01123.4490.0160.0160.0000.0000.0000.000
145A417ASP-1-0.829-0.88919.6490.1250.1250.0000.0000.0000.000
146A418ASN0-0.029-0.03016.756-0.034-0.0340.0000.0000.0000.000
147A419GLY00.0430.01819.5790.0100.0100.0000.0000.0000.000
148A420VAL0-0.041-0.03816.8160.0060.0060.0000.0000.0000.000
149A421ASP-1-0.765-0.88418.8570.1140.1140.0000.0000.0000.000
150A422ASP-1-0.860-0.91519.3950.1390.1390.0000.0000.0000.000
151A423ILE0-0.009-0.02518.5120.0120.0120.0000.0000.0000.000
152A424GLU-1-0.981-0.97617.9690.1990.1990.0000.0000.0000.000
153A425SER0-0.029-0.02016.5700.0300.0300.0000.0000.0000.000
154A426PRO0-0.049-0.01314.055-0.018-0.0180.0000.0000.0000.000
155A427LYS10.9520.96914.896-0.115-0.1150.0000.0000.0000.000
156A428ASN0-0.150-0.09715.411-0.019-0.0190.0000.0000.0000.000
157A429TYR00.0550.01910.7310.0190.0190.0000.0000.0000.000
158A430ILE0-0.013-0.00716.181-0.020-0.0200.0000.0000.0000.000
159A431VAL0-0.0050.00315.3870.0120.0120.0000.0000.0000.000
160A432TRP00.0580.03818.598-0.022-0.0220.0000.0000.0000.000
161A433ASN00.055-0.00121.404-0.003-0.0030.0000.0000.0000.000
162A434ILE0-0.004-0.00322.836-0.009-0.0090.0000.0000.0000.000
163A435ASN00.0410.02119.199-0.009-0.0090.0000.0000.0000.000
164A436MET0-0.065-0.00318.167-0.005-0.0050.0000.0000.0000.000
165A437ASN0-0.015-0.02617.197-0.025-0.0250.0000.0000.0000.000
166A438THR0-0.039-0.01817.795-0.021-0.0210.0000.0000.0000.000
167A439HIS00.0820.03615.445-0.009-0.0090.0000.0000.0000.000
168A440ILE00.0100.00511.9800.0340.0340.0000.0000.0000.000
169A441PHE00.0120.0047.750-0.018-0.0180.0000.0000.0000.000
170A442PRO0-0.018-0.0129.018-0.028-0.0280.0000.0000.0000.000
171A443GLU-1-0.813-0.8914.514-2.344-2.181-0.001-0.018-0.1440.000
172A444PHE0-0.009-0.0303.063-0.9300.3780.152-0.454-1.006-0.003
173A445VAL0-0.0070.0097.7490.2230.2230.0000.0000.0000.000
174A446VAL00.0050.0098.432-0.080-0.0800.0000.0000.0000.000
175A447ARG10.9480.97711.0990.3680.3680.0000.0000.0000.000
176A448PHE0-0.001-0.01114.2780.0060.0060.0000.0000.0000.000
177A449LYS10.9510.99016.3600.1040.1040.0000.0000.0000.000
178A450LEU00.0240.00718.0870.0100.0100.0000.0000.0000.000
179A451SER00.0370.02621.450-0.005-0.0050.0000.0000.0000.000
180A452ASN00.0020.00125.0610.0000.0000.0000.0000.0000.000