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

tag_button

FMODB ID: 94QY2

Calculation Name: 1KCV-L-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1KCV

Chain ID: L

ChEMBL ID:

UniProt ID: P18532

Base Structure: X-ray

Registration Date: 2023-06-26

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 212
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2075799.622673
FMO2-HF: Nuclear repulsion 1993732.276651
FMO2-HF: Total energy -82067.346022
FMO2-MP2: Total energy -82302.504701


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(L:1:ASP)


Summations of interaction energy for fragment #1(L:1: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.
2.1217.6541.977-2.834-4.6730.027
Interaction energy analysis for fragmet #1(L:1:ASP)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : -1 / q_Mulliken : -0.936 / q_NPA : -0.975
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].
3L3VAL00.0050.0063.7860.3452.337-0.009-0.879-1.1040.006
4L4MET0-0.0020.0085.558-3.072-3.0720.0000.0000.0000.000
5L5THR0-0.011-0.0218.723-0.236-0.2360.0000.0000.0000.000
6L6GLN0-0.019-0.03411.6900.2090.2090.0000.0000.0000.000
7L7SER0-0.035-0.00914.879-0.390-0.3900.0000.0000.0000.000
8L8PRO00.0590.04517.966-0.002-0.0020.0000.0000.0000.000
9L9LYS10.8910.94316.338-16.577-16.5770.0000.0000.0000.000
10L10SER0-0.022-0.02119.8130.0470.0470.0000.0000.0000.000
11L11MET00.0040.00823.271-0.184-0.1840.0000.0000.0000.000
12L12GLY00.0280.03626.111-0.010-0.0100.0000.0000.0000.000
13L13MET0-0.065-0.03628.976-0.106-0.1060.0000.0000.0000.000
14L14SER0-0.050-0.05731.767-0.091-0.0910.0000.0000.0000.000
15L15VAL0-0.001-0.01334.5040.1210.1210.0000.0000.0000.000
16L16GLY0-0.0130.00735.251-0.235-0.2350.0000.0000.0000.000
17L17GLU-1-0.793-0.85933.3128.8228.8220.0000.0000.0000.000
18L18ALA00.0200.02031.2610.1780.1780.0000.0000.0000.000
19L19VAL0-0.018-0.02126.1990.0520.0520.0000.0000.0000.000
20L20THR00.0000.00023.505-0.004-0.0040.0000.0000.0000.000
21L21LEU0-0.0090.00320.0690.0940.0940.0000.0000.0000.000
22L22ASN0-0.072-0.06818.5010.2420.2420.0000.0000.0000.000
23L23CYS0-0.0210.00113.0990.3360.3360.0000.0000.0000.000
24L24LYS10.8190.91613.521-16.155-16.1550.0000.0000.0000.000
25L25ALA00.0350.0259.3891.2571.2570.0000.0000.0000.000
26L26SER00.0100.0016.457-0.743-0.7430.0000.0000.0000.000
27L27GLU-1-0.936-0.9715.59335.40035.4000.0000.0000.0000.000
28L28ASN00.001-0.0169.432-0.642-0.6420.0000.0000.0000.000
29L29VAL00.0410.0238.3051.7121.7120.0000.0000.0000.000
30L30GLY0-0.0080.00310.955-0.730-0.7300.0000.0000.0000.000
31L31THR00.035-0.00614.612-0.089-0.0890.0000.0000.0000.000
32L32TYR0-0.042-0.00812.468-0.814-0.8140.0000.0000.0000.000
33L33VAL00.0210.01312.3351.7371.7370.0000.0000.0000.000
34L34SER0-0.024-0.01514.262-1.459-1.4590.0000.0000.0000.000
35L35TRP0-0.010-0.00915.3611.0851.0850.0000.0000.0000.000
36L36TYR00.003-0.01614.446-0.876-0.8760.0000.0000.0000.000
37L37GLN00.0000.00018.875-0.013-0.0130.0000.0000.0000.000
38L38GLN0-0.014-0.02619.3010.6110.6110.0000.0000.0000.000
39L39LYS10.8950.96122.202-10.673-10.6730.0000.0000.0000.000
40L40PRO00.0720.01925.1820.3280.3280.0000.0000.0000.000
41L41GLY0-0.015-0.00326.278-0.305-0.3050.0000.0000.0000.000
42L42GLN0-0.037-0.01025.378-0.321-0.3210.0000.0000.0000.000
43L43SER00.0180.02321.7670.3580.3580.0000.0000.0000.000
44L44PRO0-0.013-0.02117.725-0.420-0.4200.0000.0000.0000.000
45L45VAL0-0.0030.01420.607-0.178-0.1780.0000.0000.0000.000
46L46LEU0-0.021-0.00818.7720.3500.3500.0000.0000.0000.000
47L47LEU0-0.020-0.00320.953-0.657-0.6570.0000.0000.0000.000
48L48ILE0-0.008-0.01320.518-0.562-0.5620.0000.0000.0000.000
49L49TYR00.0530.02818.4090.9860.9860.0000.0000.0000.000
50L50GLY00.0300.01217.612-0.747-0.7470.0000.0000.0000.000
51L51ALA0-0.012-0.00117.471-0.593-0.5930.0000.0000.0000.000
52L52SER0-0.009-0.02018.913-0.191-0.1910.0000.0000.0000.000
53L53ASN0-0.096-0.02721.522-1.106-1.1060.0000.0000.0000.000
54L54ARG10.8690.93723.246-9.843-9.8430.0000.0000.0000.000
55L55TYR0-0.0010.00023.691-0.114-0.1140.0000.0000.0000.000
56L56THR00.042-0.00125.664-0.342-0.3420.0000.0000.0000.000
57L57GLY0-0.018-0.00628.7750.1690.1690.0000.0000.0000.000
58L58VAL0-0.0450.00225.660-0.127-0.1270.0000.0000.0000.000
59L59PRO00.0080.00229.004-0.220-0.2200.0000.0000.0000.000
60L60ASP-1-0.816-0.93029.9349.6399.6390.0000.0000.0000.000
61L61ARG10.7910.90329.799-9.649-9.6490.0000.0000.0000.000
62L62PHE00.0310.02525.3890.1710.1710.0000.0000.0000.000
63L63THR0-0.018-0.01026.286-0.086-0.0860.0000.0000.0000.000
64L64GLY00.0260.02022.3040.2580.2580.0000.0000.0000.000
65L65SER0-0.021-0.00921.850-0.439-0.4390.0000.0000.0000.000
66L66GLY00.0510.01519.3230.4860.4860.0000.0000.0000.000
67L67SER0-0.010-0.02217.3760.2730.2730.0000.0000.0000.000
68L68ALA00.0090.01514.754-0.197-0.1970.0000.0000.0000.000
69L69THR00.0170.00611.8791.0041.0040.0000.0000.0000.000
70L70ASP-1-0.779-0.87014.09715.69515.6950.0000.0000.0000.000
71L71PHE00.0060.01513.429-0.695-0.6950.0000.0000.0000.000
72L72THR0-0.026-0.02017.907-0.110-0.1100.0000.0000.0000.000
73L73LEU0-0.0030.02520.363-0.161-0.1610.0000.0000.0000.000
74L74THR00.013-0.01322.045-0.217-0.2170.0000.0000.0000.000
75L75ILE0-0.0070.00425.415-0.051-0.0510.0000.0000.0000.000
76L76SER0-0.004-0.02228.251-0.170-0.1700.0000.0000.0000.000
77L77SER00.0250.01031.673-0.294-0.2940.0000.0000.0000.000
78L78VAL0-0.048-0.00829.3190.0530.0530.0000.0000.0000.000
79L79GLN00.022-0.00331.841-0.420-0.4200.0000.0000.0000.000
80L80ALA00.0440.01632.2430.2500.2500.0000.0000.0000.000
81L81ASP-1-0.866-0.94231.9319.8259.8250.0000.0000.0000.000
82L82ASP-1-0.802-0.88128.29810.56510.5650.0000.0000.0000.000
83L83ASP-1-0.830-0.89927.27511.32711.3270.0000.0000.0000.000
84L84ALA0-0.027-0.02223.9390.0350.0350.0000.0000.0000.000
85L85ASP-1-0.837-0.90019.58214.33414.3340.0000.0000.0000.000
86L86TYR0-0.044-0.04619.4520.0600.0600.0000.0000.0000.000
87L87TYR0-0.046-0.01314.0040.7250.7250.0000.0000.0000.000
88L89GLY00.0350.01110.5071.4121.4120.0000.0000.0000.000
89L90GLN00.000-0.0035.426-6.000-6.0000.0000.0000.0000.000
90L91SER00.018-0.0158.9151.7841.7840.0000.0000.0000.000
91L92TYR0-0.062-0.0038.530-2.202-2.2020.0000.0000.0000.000
92L93SER00.0100.0005.250-1.566-1.5660.0000.0000.0000.000
93L94SER0-0.0500.0046.2090.8520.8520.0000.0000.0000.000
94L95PRO00.0370.0122.679-5.904-3.1771.911-1.760-2.8780.020
95L96LEU00.014-0.0074.6220.7580.843-0.001-0.008-0.0750.000
96L97THR0-0.033-0.0102.9280.4501.1790.076-0.187-0.6160.001
97L98PHE0-0.006-0.0226.406-4.522-4.5220.0000.0000.0000.000
98L99GLY00.0230.0278.3501.7541.7540.0000.0000.0000.000
99L100GLY0-0.003-0.01810.619-0.304-0.3040.0000.0000.0000.000
100L101GLY00.0100.00612.721-1.076-1.0760.0000.0000.0000.000
101L102THR0-0.076-0.03715.9260.1210.1210.0000.0000.0000.000
102L103LYS10.8610.94419.253-11.726-11.7260.0000.0000.0000.000
103L104LEU0-0.049-0.02322.438-0.238-0.2380.0000.0000.0000.000
104L105GLU-1-0.803-0.88025.49510.27210.2720.0000.0000.0000.000
105L106LEU00.0200.00228.828-0.112-0.1120.0000.0000.0000.000
106L107LYS10.8230.93132.305-8.937-8.9370.0000.0000.0000.000
107L108ARG10.8400.90035.034-7.768-7.7680.0000.0000.0000.000
108L109ALA00.0180.01338.660-0.023-0.0230.0000.0000.0000.000
109L110ASP-1-0.779-0.87641.6777.4727.4720.0000.0000.0000.000
110L111ALA0-0.020-0.01542.709-0.155-0.1550.0000.0000.0000.000
111L112ALA00.0360.01643.6590.1250.1250.0000.0000.0000.000
112L113PRO00.0000.01343.7410.0060.0060.0000.0000.0000.000
113L114THR0-0.0140.00845.474-0.222-0.2220.0000.0000.0000.000
114L115SER0-0.011-0.01746.5050.1370.1370.0000.0000.0000.000
115L116SER0-0.013-0.00547.722-0.200-0.2000.0000.0000.0000.000
116L117ILE0-0.029-0.01248.1130.1360.1360.0000.0000.0000.000
117L118PHE0-0.002-0.00646.665-0.094-0.0940.0000.0000.0000.000
118L119PRO00.0060.00450.0830.0970.0970.0000.0000.0000.000
119L120PRO0-0.0050.00850.4520.0750.0750.0000.0000.0000.000
120L121SER0-0.002-0.01450.639-0.103-0.1030.0000.0000.0000.000
121L122SER00.027-0.01052.300-0.027-0.0270.0000.0000.0000.000
122L123GLU-1-0.815-0.90350.7656.1586.1580.0000.0000.0000.000
123L124GLN00.0290.02046.499-0.041-0.0410.0000.0000.0000.000
124L125LEU00.0200.02550.424-0.001-0.0010.0000.0000.0000.000
125L126SER0-0.022-0.00353.511-0.098-0.0980.0000.0000.0000.000
126L127SER0-0.106-0.06349.3560.0210.0210.0000.0000.0000.000
127L128GLY00.0320.01750.7600.0600.0600.0000.0000.0000.000
128L129GLY0-0.048-0.02348.9070.0220.0220.0000.0000.0000.000
129L130ALA0-0.002-0.01549.437-0.095-0.0950.0000.0000.0000.000
130L131SER0-0.019-0.00645.2140.0570.0570.0000.0000.0000.000
131L132VAL0-0.0160.00447.549-0.091-0.0910.0000.0000.0000.000
132L133VAL00.0110.00743.6380.1450.1450.0000.0000.0000.000
133L134CYS0-0.050-0.01245.081-0.051-0.0510.0000.0000.0000.000
134L135PHE00.009-0.00840.2970.1770.1770.0000.0000.0000.000
135L136LEU0-0.010-0.00842.195-0.206-0.2060.0000.0000.0000.000
136L137ASN00.0300.00041.7720.3850.3850.0000.0000.0000.000
137L138SER00.0470.01741.104-0.209-0.2090.0000.0000.0000.000
138L139PHE0-0.0230.00538.658-0.150-0.1500.0000.0000.0000.000
139L140TYR00.0520.03134.3840.1920.1920.0000.0000.0000.000
140L141PRO00.005-0.00536.913-0.218-0.2180.0000.0000.0000.000
141L142LYS10.9150.94529.498-10.371-10.3710.0000.0000.0000.000
142L143SER0-0.045-0.01236.101-0.048-0.0480.0000.0000.0000.000
143L144ILE00.0220.01437.425-0.219-0.2190.0000.0000.0000.000
144L145ALA0-0.0130.00539.6360.1510.1510.0000.0000.0000.000
145L146VAL00.0300.00842.150-0.184-0.1840.0000.0000.0000.000
146L147LYS10.8430.90844.167-6.593-6.5930.0000.0000.0000.000
147L148TRP00.0400.01544.670-0.184-0.1840.0000.0000.0000.000
148L149LYS10.7880.86748.943-5.985-5.9850.0000.0000.0000.000
149L150VAL00.000-0.00352.1360.0010.0010.0000.0000.0000.000
150L151ASP-1-0.776-0.87054.8015.3485.3480.0000.0000.0000.000
151L152GLY00.0190.01057.199-0.065-0.0650.0000.0000.0000.000
152L153SER0-0.0140.00355.3850.0020.0020.0000.0000.0000.000
153L154LYN00.0340.03247.6860.1010.1010.0000.0000.0000.000
154L155ARG10.8020.90247.363-6.636-6.6360.0000.0000.0000.000
155L156ALA00.0260.00444.6620.0740.0740.0000.0000.0000.000
156L157ASN00.0080.01643.8810.2840.2840.0000.0000.0000.000
157L158GLY00.0640.02643.248-0.172-0.1720.0000.0000.0000.000
158L159THR00.0100.00441.749-0.107-0.1070.0000.0000.0000.000
159L160ALA00.0070.01837.9360.1710.1710.0000.0000.0000.000
160L161ASN00.0180.01837.275-0.322-0.3220.0000.0000.0000.000
161L162SER00.0150.01133.9580.3240.3240.0000.0000.0000.000
162L163TRP0-0.013-0.01833.034-0.267-0.2670.0000.0000.0000.000
163L164THR00.0000.01633.0800.1020.1020.0000.0000.0000.000
164L165ASP-1-0.904-0.95528.44810.85710.8570.0000.0000.0000.000
165L166GLN0-0.063-0.04631.045-0.086-0.0860.0000.0000.0000.000
166L167ASP-1-0.780-0.86432.6168.4598.4590.0000.0000.0000.000
167L168SER00.000-0.00832.1060.0370.0370.0000.0000.0000.000
168L169ALA0-0.0160.00534.236-0.018-0.0180.0000.0000.0000.000
169L170SER0-0.064-0.06037.778-0.116-0.1160.0000.0000.0000.000
170L171SER00.0250.00934.891-0.155-0.1550.0000.0000.0000.000
171L172THR0-0.075-0.03036.3110.0240.0240.0000.0000.0000.000
172L173TYR0-0.013-0.03731.4440.0840.0840.0000.0000.0000.000
173L174SER00.0350.00536.895-0.282-0.2820.0000.0000.0000.000
174L175MET0-0.056-0.00537.0990.2400.2400.0000.0000.0000.000
175L176SER00.0120.01538.637-0.232-0.2320.0000.0000.0000.000
176L177SER0-0.016-0.02039.5110.1280.1280.0000.0000.0000.000
177L178THR00.016-0.00841.156-0.226-0.2260.0000.0000.0000.000
178L179LEU0-0.0100.01342.9340.0900.0900.0000.0000.0000.000
179L180THR00.0280.01643.867-0.109-0.1090.0000.0000.0000.000
180L181LEU0-0.080-0.04346.258-0.026-0.0260.0000.0000.0000.000
181L182THR00.0540.01949.4760.0480.0480.0000.0000.0000.000
182L183LYS10.8970.93151.488-5.656-5.6560.0000.0000.0000.000
183L184ASP-1-0.822-0.91554.3965.5875.5870.0000.0000.0000.000
184L185LYS10.8260.92450.009-6.454-6.4540.0000.0000.0000.000
185L186TYR00.0670.02253.419-0.046-0.0460.0000.0000.0000.000
186L187GLU-1-0.796-0.89655.2575.4635.4630.0000.0000.0000.000
187L188ARG10.8490.94457.962-5.637-5.6370.0000.0000.0000.000
188L189HIS10.8120.89856.366-5.611-5.6110.0000.0000.0000.000
189L190ASN00.0450.02859.3610.0470.0470.0000.0000.0000.000
190L191SER00.0120.02258.2820.0140.0140.0000.0000.0000.000
191L192TYR0-0.013-0.00552.5960.1120.1120.0000.0000.0000.000
192L193THR0-0.025-0.01153.031-0.037-0.0370.0000.0000.0000.000
193L195GLU-1-0.802-0.89548.9835.9985.9980.0000.0000.0000.000
194L196ALA00.0420.02145.3780.1560.1560.0000.0000.0000.000
195L197THR0-0.030-0.00544.660-0.144-0.1440.0000.0000.0000.000
196L198HIS00.0800.03240.6160.0060.0060.0000.0000.0000.000
197L199LYS10.8330.90741.130-7.537-7.5370.0000.0000.0000.000
198L200THR0-0.029-0.03544.552-0.142-0.1420.0000.0000.0000.000
199L201SER0-0.034-0.01246.801-0.111-0.1110.0000.0000.0000.000
200L202SER00.0100.01249.1190.0380.0380.0000.0000.0000.000
201L203SER0-0.016-0.00151.358-0.014-0.0140.0000.0000.0000.000
202L204PRO0-0.017-0.01749.7570.0600.0600.0000.0000.0000.000
203L205VAL00.0270.01849.029-0.141-0.1410.0000.0000.0000.000
204L206VAL0-0.012-0.01250.2300.1050.1050.0000.0000.0000.000
205L207LYS10.9440.97550.979-6.033-6.0330.0000.0000.0000.000
206L208SER0-0.043-0.04452.7120.0480.0480.0000.0000.0000.000
207L209PHE00.0400.02052.371-0.022-0.0220.0000.0000.0000.000
208L210ASN00.0580.01957.0120.0530.0530.0000.0000.0000.000
209L211ARG10.9320.93658.064-5.344-5.3440.0000.0000.0000.000
210L212ASN0-0.066-0.02959.8490.0350.0350.0000.0000.0000.000
211L213GLU-1-0.915-0.95561.7265.0245.0240.0000.0000.0000.000
212L214CYS0-0.069-0.01157.6420.0300.0300.0000.0000.0000.000