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: NN77Q

Calculation Name: 1YK9-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1YK9

Chain ID: A

ChEMBL ID:

UniProt ID: P9WQ35

Base Structure: X-ray

Registration Date: 2023-09-23

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 184
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -1833761.206525
FMO2-HF: Nuclear repulsion 1762791.273497
FMO2-HF: Total energy -70969.933027
FMO2-MP2: Total energy -71177.656343


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:245:ASP)


Summations of interaction energy for fragment #1(A:245:ASP)
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.
30.28637.6563.19-4.962-5.5940.035
Interaction energy analysis for fragmet #1(A:245:ASP)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : -1 / q_Mulliken : -0.931 / q_NPA : -0.964
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].
3A247TYR0-0.034-0.0183.811-0.8611.605-0.029-1.298-1.1380.006
4A248ASP-1-0.888-0.9626.49128.82428.8240.0000.0000.0000.000
5A249GLU-1-0.940-0.97310.04717.58117.5810.0000.0000.0000.000
6A250ALA00.0080.01710.6090.2560.2560.0000.0000.0000.000
7A251SER00.0200.00912.571-1.036-1.0360.0000.0000.0000.000
8A252VAL0-0.057-0.04214.3701.0701.0700.0000.0000.0000.000
9A253LEU00.0190.01616.034-0.996-0.9960.0000.0000.0000.000
10A254PHE0-0.011-0.02018.6860.8980.8980.0000.0000.0000.000
11A255ALA00.0070.00021.073-0.680-0.6800.0000.0000.0000.000
12A256ASP-1-0.825-0.92023.99812.31312.3130.0000.0000.0000.000
13A257ILE0-0.0360.01426.730-0.469-0.4690.0000.0000.0000.000
14A258VAL00.0080.01430.440-0.020-0.0200.0000.0000.0000.000
15A259GLY0-0.081-0.05732.942-0.263-0.2630.0000.0000.0000.000
16A260PHE00.0360.01630.991-0.208-0.2080.0000.0000.0000.000
17A261THR0-0.051-0.03333.870-0.069-0.0690.0000.0000.0000.000
18A262GLU-1-0.851-0.92034.9679.2009.2000.0000.0000.0000.000
19A263ARG10.8700.93837.175-8.594-8.5940.0000.0000.0000.000
20A264ALA00.0390.01240.220-0.111-0.1110.0000.0000.0000.000
21A265SER0-0.029-0.00940.790-0.113-0.1130.0000.0000.0000.000
22A266SER00.0280.00942.6590.0040.0040.0000.0000.0000.000
23A267THR0-0.0070.00438.5760.1010.1010.0000.0000.0000.000
24A268ALA0-0.012-0.00640.819-0.165-0.1650.0000.0000.0000.000
25A269PRO00.0130.00839.5400.1820.1820.0000.0000.0000.000
26A270ALA00.0030.00439.7050.1510.1510.0000.0000.0000.000
27A271ASP-1-0.906-0.93741.0507.3687.3680.0000.0000.0000.000
28A272LEU00.002-0.03537.5280.1660.1660.0000.0000.0000.000
29A273VAL0-0.019-0.01534.0700.0290.0290.0000.0000.0000.000
30A274ARG10.9770.99734.389-8.598-8.5980.0000.0000.0000.000
31A275PHE0-0.040-0.02735.1450.0970.0970.0000.0000.0000.000
32A276LEU00.0080.00233.0200.0310.0310.0000.0000.0000.000
33A277ASP-1-0.847-0.93130.49310.65610.6560.0000.0000.0000.000
34A278ARG10.9110.95530.490-8.454-8.4540.0000.0000.0000.000
35A279LEU0-0.0220.00732.0350.0230.0230.0000.0000.0000.000
36A280TYR0-0.005-0.02225.6940.2180.2180.0000.0000.0000.000
37A281SER0-0.059-0.01526.7530.3150.3150.0000.0000.0000.000
38A282ALA00.0590.03628.6240.0090.0090.0000.0000.0000.000
39A283PHE0-0.062-0.03525.079-0.012-0.0120.0000.0000.0000.000
40A284ASP-1-0.904-0.96523.20312.90812.9080.0000.0000.0000.000
41A285GLU-1-0.931-0.96223.81410.96110.9610.0000.0000.0000.000
42A286LEU0-0.099-0.04326.405-0.118-0.1180.0000.0000.0000.000
43A287VAL0-0.034-0.00519.7030.1480.1480.0000.0000.0000.000
44A288ASP-1-0.912-0.96421.77514.25714.2570.0000.0000.0000.000
45A289GLN0-0.036-0.01021.780-0.294-0.2940.0000.0000.0000.000
46A290HIS0-0.018-0.01319.3500.3080.3080.0000.0000.0000.000
47A291GLY0-0.078-0.04115.5500.4080.4080.0000.0000.0000.000
48A292LEU0-0.040-0.00615.3140.9050.9050.0000.0000.0000.000
49A293GLU-1-0.859-0.93913.43718.97918.9790.0000.0000.0000.000
50A294LYS10.9470.99414.887-14.931-14.9310.0000.0000.0000.000
51A295ILE0-0.056-0.02310.6911.3251.3250.0000.0000.0000.000
52A296GLU-1-0.825-0.90613.22123.02323.0230.0000.0000.0000.000
53A297VAL0-0.002-0.01215.279-0.810-0.8100.0000.0000.0000.000
54A298SER0-0.072-0.03019.003-0.080-0.0800.0000.0000.0000.000
55A299GLY00.016-0.00521.231-0.319-0.3190.0000.0000.0000.000
56A300ASP-1-0.931-0.94924.57111.77911.7790.0000.0000.0000.000
57A301SER0-0.0360.00621.9840.2560.2560.0000.0000.0000.000
58A302TYR00.033-0.01021.2200.7300.7300.0000.0000.0000.000
59A303MET0-0.0160.00314.6970.2500.2500.0000.0000.0000.000
60A304VAL00.0400.01916.4160.8420.8420.0000.0000.0000.000
61A305VAL0-0.012-0.00210.827-0.385-0.3850.0000.0000.0000.000
62A306SER00.0660.02113.833-0.433-0.4330.0000.0000.0000.000
63A307GLY0-0.047-0.0229.654-0.244-0.2440.0000.0000.0000.000
64A308VAL00.0100.0198.1763.7073.7070.0000.0000.0000.000
65A309PRO00.0270.0006.9680.0650.0650.0000.0000.0000.000
66A310ARG10.8720.9478.047-19.397-19.3970.0000.0000.0000.000
67A311PRO00.0850.0499.493-1.312-1.3120.0000.0000.0000.000
68A312ARG10.9540.95011.982-18.523-18.5230.0000.0000.0000.000
69A313PRO00.0390.00315.6950.3250.3250.0000.0000.0000.000
70A314ASP-1-0.943-0.96017.79014.29114.2910.0000.0000.0000.000
71A315HIS00.0340.02815.106-0.106-0.1060.0000.0000.0000.000
72A316THR0-0.016-0.01517.067-0.019-0.0190.0000.0000.0000.000
73A317GLN0-0.053-0.04519.510-0.061-0.0610.0000.0000.0000.000
74A318ALA00.0230.03318.573-0.444-0.4440.0000.0000.0000.000
75A319LEU00.0320.01016.917-0.110-0.1100.0000.0000.0000.000
76A320ALA0-0.053-0.01621.024-0.452-0.4520.0000.0000.0000.000
77A321ASP-1-0.912-0.97823.97811.92811.9280.0000.0000.0000.000
78A322PHE00.0660.05021.716-0.208-0.2080.0000.0000.0000.000
79A323ALA0-0.001-0.01224.474-0.174-0.1740.0000.0000.0000.000
80A324LEU0-0.102-0.03825.890-0.472-0.4720.0000.0000.0000.000
81A325ASP-1-0.881-0.94727.73310.15110.1510.0000.0000.0000.000
82A326MET0-0.029-0.01325.112-0.074-0.0740.0000.0000.0000.000
83A327THR0-0.016-0.01328.343-0.135-0.1350.0000.0000.0000.000
84A328ASN0-0.052-0.01631.872-0.517-0.5170.0000.0000.0000.000
85A329VAL00.0640.03630.023-0.334-0.3340.0000.0000.0000.000
86A330ALA0-0.0050.01431.702-0.256-0.2560.0000.0000.0000.000
87A331ALA0-0.063-0.04433.541-0.158-0.1580.0000.0000.0000.000
88A332GLN0-0.045-0.02336.823-0.420-0.4200.0000.0000.0000.000
89A333LEU0-0.0020.01035.498-0.235-0.2350.0000.0000.0000.000
90A334LYS10.9010.95238.996-7.753-7.7530.0000.0000.0000.000
91A335ASP-1-0.905-0.91641.9296.7826.7820.0000.0000.0000.000
92A336PRO00.017-0.01242.9280.0910.0910.0000.0000.0000.000
93A337ARG10.9200.93442.913-7.070-7.0700.0000.0000.0000.000
94A338GLY00.0720.04842.9250.1400.1400.0000.0000.0000.000
95A339ASN0-0.069-0.03438.3480.1360.1360.0000.0000.0000.000
96A340PRO0-0.038-0.02139.3910.0050.0050.0000.0000.0000.000
97A341VAL00.0800.02934.2980.0960.0960.0000.0000.0000.000
98A342PRO0-0.078-0.01935.322-0.002-0.0020.0000.0000.0000.000
99A343LEU00.025-0.00828.2030.1250.1250.0000.0000.0000.000
100A344ARG10.8270.90028.491-11.042-11.0420.0000.0000.0000.000
101A345VAL00.0130.01024.5660.4350.4350.0000.0000.0000.000
102A346GLY00.0350.03124.294-0.432-0.4320.0000.0000.0000.000
103A347LEU0-0.012-0.01720.2920.6840.6840.0000.0000.0000.000
104A348ALA0-0.007-0.02118.710-0.374-0.3740.0000.0000.0000.000
105A349THR0-0.021-0.01816.3571.0061.0060.0000.0000.0000.000
106A350GLY00.0290.01614.881-0.929-0.9290.0000.0000.0000.000
107A351PRO00.0070.02010.7980.8930.8930.0000.0000.0000.000
108A352VAL0-0.028-0.0307.987-0.635-0.6350.0000.0000.0000.000
109A353VAL00.0090.0133.2270.9361.1110.021-0.059-0.1370.000
110A354ALA0-0.037-0.0182.485-7.167-5.6032.817-2.020-2.3600.019
111A355GLY0-0.003-0.0033.7783.6154.2770.043-0.388-0.317-0.001
112A356VAL0-0.021-0.0163.074-1.0531.3380.339-1.197-1.5330.011
113A357VAL0-0.0110.0175.2201.0171.129-0.0010.000-0.1090.000
114A358GLY00.0260.0187.953-2.699-2.6990.0000.0000.0000.000
115A359SER00.009-0.0119.798-2.862-2.8620.0000.0000.0000.000
116A360ARG11.0051.01710.991-23.883-23.8830.0000.0000.0000.000
117A361ARG10.8590.89013.754-18.847-18.8470.0000.0000.0000.000
118A362PHE00.0380.03612.8091.8251.8250.0000.0000.0000.000
119A363ARG10.8750.93010.857-25.202-25.2020.0000.0000.0000.000
120A364TYR00.0450.0267.5672.7032.7030.0000.0000.0000.000
121A365CYS0-0.084-0.0507.3084.0534.0530.0000.0000.0000.000
122A366VAL00.0790.0358.2153.2913.2910.0000.0000.0000.000
123A367TRP0-0.0080.0008.388-3.436-3.4360.0000.0000.0000.000
124A368GLY00.0500.0208.6932.3112.3110.0000.0000.0000.000
125A369ASP-1-0.950-0.97010.81116.04916.0490.0000.0000.0000.000
126A370ALA00.0260.01313.461-1.245-1.2450.0000.0000.0000.000
127A371VAL00.0360.00711.597-1.056-1.0560.0000.0000.0000.000
128A372ASN0-0.0160.00414.729-1.081-1.0810.0000.0000.0000.000
129A373VAL0-0.092-0.06117.017-1.244-1.2440.0000.0000.0000.000
130A374ALA00.0600.03318.057-0.782-0.7820.0000.0000.0000.000
131A375SER00.0310.03419.843-0.693-0.6930.0000.0000.0000.000
132A376ARG10.9010.96220.906-14.580-14.5800.0000.0000.0000.000
133A377MET0-0.0390.04423.159-0.842-0.8420.0000.0000.0000.000
134A378GLU-1-0.751-0.84324.47311.98011.9800.0000.0000.0000.000
135A379SER0-0.003-0.01325.516-0.555-0.5550.0000.0000.0000.000
136A380THR0-0.161-0.11427.923-0.498-0.4980.0000.0000.0000.000
137A381ASP-1-0.822-0.90529.44910.42510.4250.0000.0000.0000.000
138A382SER0-0.081-0.05431.526-0.308-0.3080.0000.0000.0000.000
139A383VAL0-0.054-0.04134.6050.1300.1300.0000.0000.0000.000
140A384GLY0-0.0100.01733.609-0.102-0.1020.0000.0000.0000.000
141A385GLN0-0.022-0.01932.491-0.112-0.1120.0000.0000.0000.000
142A386ILE00.0520.02626.4940.1850.1850.0000.0000.0000.000
143A387GLN00.001-0.01527.017-0.499-0.4990.0000.0000.0000.000
144A388VAL0-0.032-0.03824.8400.6600.6600.0000.0000.0000.000
145A389PRO0-0.033-0.01522.177-0.472-0.4720.0000.0000.0000.000
146A390ASP-1-0.805-0.94225.25910.75710.7570.0000.0000.0000.000
147A391GLU-1-0.953-0.97219.99414.01614.0160.0000.0000.0000.000
148A392VAL0-0.017-0.02920.9050.1270.1270.0000.0000.0000.000
149A393TYR0-0.044-0.00623.112-0.223-0.2230.0000.0000.0000.000
150A394GLU-1-0.906-0.94524.45210.54910.5490.0000.0000.0000.000
151A395ARG10.8380.93319.864-14.293-14.2930.0000.0000.0000.000
152A396LEU0-0.006-0.00224.0980.1880.1880.0000.0000.0000.000
153A397LYS10.9420.94322.862-12.494-12.4940.0000.0000.0000.000
154A398ASP-1-0.879-0.92828.5279.2089.2080.0000.0000.0000.000
155A399ASP-1-0.868-0.92029.1179.7349.7340.0000.0000.0000.000
156A400PHE0-0.052-0.04326.1620.0970.0970.0000.0000.0000.000
157A401VAL0-0.024-0.00130.904-0.196-0.1960.0000.0000.0000.000
158A402LEU00.0160.00528.0920.1530.1530.0000.0000.0000.000
159A403ARG10.8890.94432.667-8.387-8.3870.0000.0000.0000.000
160A404GLU-1-0.904-0.95333.9478.6948.6940.0000.0000.0000.000
161A405ARG10.9370.98932.642-9.463-9.4630.0000.0000.0000.000
162A406GLY00.011-0.00733.777-0.294-0.2940.0000.0000.0000.000
163A407HIS00.0070.00232.5420.4320.4320.0000.0000.0000.000
164A408ILE0-0.014-0.05932.357-0.194-0.1940.0000.0000.0000.000
165A409ASN00.010-0.00733.030-0.191-0.1910.0000.0000.0000.000
166A410VAL0-0.0010.01226.4590.2900.2900.0000.0000.0000.000
167A411LYS10.9700.97028.246-10.149-10.1490.0000.0000.0000.000
168A412GLY00.0110.01024.2230.0750.0750.0000.0000.0000.000
169A413LYS10.9650.97520.696-13.539-13.5390.0000.0000.0000.000
170A414GLY00.0180.02725.184-0.039-0.0390.0000.0000.0000.000
171A415VAL0-0.008-0.00627.716-0.385-0.3850.0000.0000.0000.000
172A416MET0-0.0590.03528.3660.2930.2930.0000.0000.0000.000
173A417ARG10.9660.97023.068-12.019-12.0190.0000.0000.0000.000
174A418THR00.0180.02029.520-0.070-0.0700.0000.0000.0000.000
175A419TRP00.0220.02225.2760.5630.5630.0000.0000.0000.000
176A420TYR00.0330.00129.149-0.547-0.5470.0000.0000.0000.000
177A421LEU00.0080.01529.8100.2510.2510.0000.0000.0000.000
178A422ILE00.0300.02527.601-0.297-0.2970.0000.0000.0000.000
179A423GLY0-0.021-0.00130.568-0.104-0.1040.0000.0000.0000.000
180A424ARG10.9250.93132.724-8.527-8.5270.0000.0000.0000.000
181A425LYS11.0061.00527.250-10.805-10.8050.0000.0000.0000.000
182A426VAL0-0.070-0.02431.874-0.303-0.3030.0000.0000.0000.000
183A427ALA00.0230.01033.2370.2020.2020.0000.0000.0000.000
184A428ALA0-0.0150.00335.354-0.310-0.3100.0000.0000.0000.000