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: LZRL9

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 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 212
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2074116.423376
FMO2-HF: Nuclear repulsion 1992050.099636
FMO2-HF: Total energy -82066.32374
FMO2-MP2: Total energy -82301.461238


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.
2.9138.8170.885-2.639-4.1520.021
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 : -0.938 / q_NPA : -0.974
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].
3L3VAL00.0070.0073.7860.2592.289-0.008-0.916-1.1070.006
4L4MET0-0.0080.0035.517-3.111-3.1110.0000.0000.0000.000
5L5THR0-0.008-0.0208.664-0.181-0.1810.0000.0000.0000.000
6L6GLN0-0.021-0.03611.6470.2320.2320.0000.0000.0000.000
7L7SER0-0.0130.00214.830-0.369-0.3690.0000.0000.0000.000
8L8PRO00.0260.02417.9230.0580.0580.0000.0000.0000.000
9L9LYS10.9951.03016.676-16.158-16.1580.0000.0000.0000.000
10L10SER0-0.031-0.02519.7790.0490.0490.0000.0000.0000.000
11L11MET00.0090.00523.234-0.142-0.1420.0000.0000.0000.000
12L12GLY00.0310.04026.067-0.009-0.0090.0000.0000.0000.000
13L13MET0-0.067-0.03529.018-0.141-0.1410.0000.0000.0000.000
14L14SER0-0.0050.00031.713-0.076-0.0760.0000.0000.0000.000
15L15VAL00.013-0.00634.4430.1230.1230.0000.0000.0000.000
16L16GLY0-0.039-0.01335.189-0.232-0.2320.0000.0000.0000.000
17L17GLU-1-0.895-0.93933.3268.8188.8180.0000.0000.0000.000
18L18ALA00.0130.01831.1430.1850.1850.0000.0000.0000.000
19L19VAL0-0.009-0.01026.5470.0480.0480.0000.0000.0000.000
20L20THR00.0100.00023.390-0.005-0.0050.0000.0000.0000.000
21L21LEU0-0.019-0.00220.0710.1020.1020.0000.0000.0000.000
22L22ASN0-0.047-0.04418.0330.5150.5150.0000.0000.0000.000
23L23CYS0-0.023-0.00312.9760.3370.3370.0000.0000.0000.000
24L24LYS10.9110.97513.463-16.375-16.3750.0000.0000.0000.000
25L25ALA00.0350.0279.3681.2631.2630.0000.0000.0000.000
26L26SER00.008-0.0016.474-0.786-0.7860.0000.0000.0000.000
27L27GLU-1-0.941-0.9715.51435.60935.6090.0000.0000.0000.000
28L28ASN00.021-0.0099.432-0.810-0.8100.0000.0000.0000.000
29L29VAL00.0300.0238.3281.7001.7000.0000.0000.0000.000
30L30GLY0-0.019-0.00210.933-0.742-0.7420.0000.0000.0000.000
31L31THR00.039-0.00414.590-0.092-0.0920.0000.0000.0000.000
32L32TYR0-0.035-0.00512.458-0.852-0.8520.0000.0000.0000.000
33L33VAL00.0210.01312.4321.7701.7700.0000.0000.0000.000
34L34SER0-0.029-0.01614.255-1.766-1.7660.0000.0000.0000.000
35L35TRP0-0.005-0.00915.2771.1231.1230.0000.0000.0000.000
36L36TYR00.001-0.01914.544-0.206-0.2060.0000.0000.0000.000
37L37GLN00.0050.00518.8000.0560.0560.0000.0000.0000.000
38L38GLN0-0.023-0.02419.4780.5210.5210.0000.0000.0000.000
39L39LYS10.9650.99722.142-10.678-10.6780.0000.0000.0000.000
40L40PRO00.0600.01425.1310.3340.3340.0000.0000.0000.000
41L41GLY0-0.014-0.00426.240-0.300-0.3000.0000.0000.0000.000
42L42GLN0-0.029-0.00525.319-0.227-0.2270.0000.0000.0000.000
43L43SER00.0140.01621.6420.3700.3700.0000.0000.0000.000
44L44PRO0-0.012-0.02017.688-0.410-0.4100.0000.0000.0000.000
45L45VAL00.0120.02220.543-0.158-0.1580.0000.0000.0000.000
46L46LEU0-0.025-0.01018.7090.3560.3560.0000.0000.0000.000
47L47LEU0-0.026-0.00720.873-0.664-0.6640.0000.0000.0000.000
48L48ILE00.006-0.00320.288-0.557-0.5570.0000.0000.0000.000
49L49TYR00.0440.02318.3950.8490.8490.0000.0000.0000.000
50L50GLY00.0120.00117.596-0.706-0.7060.0000.0000.0000.000
51L51ALA0-0.017-0.00317.680-0.591-0.5910.0000.0000.0000.000
52L52SER0-0.044-0.03718.893-0.469-0.4690.0000.0000.0000.000
53L53ASN0-0.0390.00521.708-1.053-1.0530.0000.0000.0000.000
54L54ARG10.9410.97523.229-9.911-9.9110.0000.0000.0000.000
55L55TYR00.0020.00423.729-0.205-0.2050.0000.0000.0000.000
56L56THR00.040-0.00225.649-0.331-0.3310.0000.0000.0000.000
57L57GLY0-0.022-0.00728.6920.1660.1660.0000.0000.0000.000
58L58VAL0-0.0450.00225.575-0.120-0.1200.0000.0000.0000.000
59L59PRO0-0.013-0.00228.921-0.227-0.2270.0000.0000.0000.000
60L60ASP-1-0.844-0.94929.8519.5779.5770.0000.0000.0000.000
61L61ARG10.8540.94229.820-9.580-9.5800.0000.0000.0000.000
62L62PHE00.0050.01525.3010.1260.1260.0000.0000.0000.000
63L63THR0-0.022-0.01726.181-0.090-0.0900.0000.0000.0000.000
64L64GLY00.0380.02422.2580.2590.2590.0000.0000.0000.000
65L65SER0-0.011-0.00421.805-0.461-0.4610.0000.0000.0000.000
66L66GLY00.0420.01219.2980.4810.4810.0000.0000.0000.000
67L67SER0-0.021-0.02517.3610.2600.2600.0000.0000.0000.000
68L68ALA00.0230.02414.798-0.190-0.1900.0000.0000.0000.000
69L69THR0-0.006-0.00912.0450.9950.9950.0000.0000.0000.000
70L70ASP-1-0.869-0.93014.09715.44315.4430.0000.0000.0000.000
71L71PHE00.0020.00613.624-0.636-0.6360.0000.0000.0000.000
72L72THR0-0.028-0.02317.833-0.085-0.0850.0000.0000.0000.000
73L73LEU0-0.0020.02320.343-0.148-0.1480.0000.0000.0000.000
74L74THR00.006-0.01621.968-0.206-0.2060.0000.0000.0000.000
75L75ILE0-0.024-0.00125.421-0.041-0.0410.0000.0000.0000.000
76L76SER0-0.017-0.02928.176-0.261-0.2610.0000.0000.0000.000
77L77SER00.0300.01331.598-0.289-0.2890.0000.0000.0000.000
78L78VAL0-0.066-0.02029.3550.0540.0540.0000.0000.0000.000
79L79GLN00.0350.00931.774-0.409-0.4090.0000.0000.0000.000
80L80ALA00.0190.00532.1790.2460.2460.0000.0000.0000.000
81L81ASP-1-0.914-0.96332.2929.5189.5180.0000.0000.0000.000
82L82ASP-1-0.853-0.93228.27610.52410.5240.0000.0000.0000.000
83L83ASP-1-0.912-0.93827.21211.18711.1870.0000.0000.0000.000
84L84ALA0-0.018-0.03023.8470.0510.0510.0000.0000.0000.000
85L85ASP-1-0.898-0.92519.51914.08414.0840.0000.0000.0000.000
86L86TYR0-0.044-0.05119.3880.0850.0850.0000.0000.0000.000
87L87TYR0-0.0040.01313.9350.6630.6630.0000.0000.0000.000
88L89GLY00.0340.01210.4251.4341.4340.0000.0000.0000.000
89L90GLN00.0080.0055.547-6.020-6.0200.0000.0000.0000.000
90L91SER0-0.012-0.0258.9011.5931.5930.0000.0000.0000.000
91L92TYR0-0.0400.0018.645-1.483-1.4830.0000.0000.0000.000
92L93SER00.002-0.0024.836-1.116-1.1160.0000.0000.0000.000
93L94SER0-0.0420.0046.2110.4200.4200.0000.0000.0000.000
94L95PRO00.0380.0122.804-5.119-2.0270.796-1.534-2.3540.014
95L96LEU00.022-0.0054.6180.6390.705-0.001-0.007-0.0580.000
96L97THR0-0.038-0.0132.8540.3551.0710.098-0.182-0.6330.001
97L98PHE00.002-0.0186.329-4.481-4.4810.0000.0000.0000.000
98L99GLY00.0110.0198.2931.8271.8270.0000.0000.0000.000
99L100GLY0-0.027-0.03010.561-0.243-0.2430.0000.0000.0000.000
100L101GLY0-0.023-0.00812.683-1.000-1.0000.0000.0000.0000.000
101L102THR0-0.098-0.07315.8770.0980.0980.0000.0000.0000.000
102L103LYS10.9500.98919.204-12.002-12.0020.0000.0000.0000.000
103L104LEU0-0.060-0.02922.392-0.201-0.2010.0000.0000.0000.000
104L105GLU-1-0.894-0.95625.44310.49510.4950.0000.0000.0000.000
105L106LEU00.0260.00428.780-0.122-0.1220.0000.0000.0000.000
106L107LYS10.8900.95732.254-8.958-8.9580.0000.0000.0000.000
107L108ARG10.8530.90334.986-7.757-7.7570.0000.0000.0000.000
108L109ALA0-0.0030.00338.611-0.025-0.0250.0000.0000.0000.000
109L110ASP-1-0.869-0.94041.4667.5077.5070.0000.0000.0000.000
110L111ALA0-0.034-0.02242.715-0.157-0.1570.0000.0000.0000.000
111L112ALA00.0330.01443.6240.1260.1260.0000.0000.0000.000
112L113PRO0-0.0220.00543.6470.0060.0060.0000.0000.0000.000
113L114THR00.0120.01845.443-0.220-0.2200.0000.0000.0000.000
114L115SER0-0.018-0.01746.4760.1400.1400.0000.0000.0000.000
115L116SER0-0.015-0.00847.700-0.195-0.1950.0000.0000.0000.000
116L117ILE0-0.024-0.00848.0920.1390.1390.0000.0000.0000.000
117L118PHE0-0.006-0.00846.655-0.095-0.0950.0000.0000.0000.000
118L119PRO0-0.0030.00049.9590.0980.0980.0000.0000.0000.000
119L120PRO00.0000.00750.1520.0740.0740.0000.0000.0000.000
120L121SER00.0510.03449.826-0.119-0.1190.0000.0000.0000.000
121L122SER00.009-0.00952.010-0.028-0.0280.0000.0000.0000.000
122L123GLU-1-0.836-0.94450.5836.1816.1810.0000.0000.0000.000
123L124GLN00.0220.01146.151-0.044-0.0440.0000.0000.0000.000
124L125LEU00.0220.03050.1190.0010.0010.0000.0000.0000.000
125L126SER0-0.0060.00453.195-0.099-0.0990.0000.0000.0000.000
126L127SER0-0.101-0.06549.0120.0190.0190.0000.0000.0000.000
127L128GLY0-0.032-0.01850.4310.0460.0460.0000.0000.0000.000
128L129GLY0-0.023-0.00748.5750.0190.0190.0000.0000.0000.000
129L130ALA00.016-0.00849.109-0.092-0.0920.0000.0000.0000.000
130L131SER0-0.0220.00944.8920.0580.0580.0000.0000.0000.000
131L132VAL0-0.0080.01047.233-0.090-0.0900.0000.0000.0000.000
132L133VAL00.0160.01043.8060.1420.1420.0000.0000.0000.000
133L134CYS0-0.055-0.01445.068-0.055-0.0550.0000.0000.0000.000
134L135PHE00.013-0.00940.2580.1750.1750.0000.0000.0000.000
135L136LEU0-0.008-0.01242.111-0.202-0.2020.0000.0000.0000.000
136L137ASN00.0670.02441.7440.4300.4300.0000.0000.0000.000
137L138SER00.0530.02341.095-0.216-0.2160.0000.0000.0000.000
138L139PHE0-0.0390.00338.346-0.146-0.1460.0000.0000.0000.000
139L140TYR00.0510.02634.4880.2120.2120.0000.0000.0000.000
140L141PRO00.0140.00236.904-0.208-0.2080.0000.0000.0000.000
141L142LYS11.0091.00930.110-10.215-10.2150.0000.0000.0000.000
142L143SER0-0.061-0.02136.073-0.065-0.0650.0000.0000.0000.000
143L144ILE00.0510.02237.404-0.208-0.2080.0000.0000.0000.000
144L145ALA0-0.0060.00539.6230.1590.1590.0000.0000.0000.000
145L146VAL00.0350.01642.139-0.185-0.1850.0000.0000.0000.000
146L147LYS10.8600.93344.163-6.616-6.6160.0000.0000.0000.000
147L148TRP00.0370.01644.613-0.201-0.2010.0000.0000.0000.000
148L149LYS10.8360.91448.941-6.086-6.0860.0000.0000.0000.000
149L150VAL00.002-0.00252.2200.0030.0030.0000.0000.0000.000
150L151ASP-1-0.774-0.88954.8035.3685.3680.0000.0000.0000.000
151L152GLY00.0060.00457.198-0.064-0.0640.0000.0000.0000.000
152L153SER0-0.0110.00555.3930.0050.0050.0000.0000.0000.000
153L154LYN00.006-0.00547.4210.0980.0980.0000.0000.0000.000
154L155ARG10.8630.94947.844-6.629-6.6290.0000.0000.0000.000
155L156ALA00.0430.01244.6110.0710.0710.0000.0000.0000.000
156L157ASN0-0.024-0.00743.8910.2770.2770.0000.0000.0000.000
157L158GLY00.0360.00443.104-0.153-0.1530.0000.0000.0000.000
158L159THR00.0050.00641.443-0.122-0.1220.0000.0000.0000.000
159L160ALA0-0.0020.00937.7990.1670.1670.0000.0000.0000.000
160L161ASN00.0240.01537.287-0.319-0.3190.0000.0000.0000.000
161L162SER00.0110.00833.9010.3340.3340.0000.0000.0000.000
162L163TRP0-0.025-0.02332.954-0.225-0.2250.0000.0000.0000.000
163L164THR00.0050.01933.0570.1090.1090.0000.0000.0000.000
164L165ASP-1-0.932-0.97228.26410.85010.8500.0000.0000.0000.000
165L166GLN0-0.061-0.03731.004-0.108-0.1080.0000.0000.0000.000
166L167ASP-1-0.809-0.90732.5698.4928.4920.0000.0000.0000.000
167L168SER00.005-0.01731.9140.0500.0500.0000.0000.0000.000
168L169ALA0-0.0140.01334.181-0.021-0.0210.0000.0000.0000.000
169L170SER0-0.053-0.02737.721-0.117-0.1170.0000.0000.0000.000
170L171SER00.0440.02435.157-0.178-0.1780.0000.0000.0000.000
171L172THR0-0.075-0.02336.2610.0300.0300.0000.0000.0000.000
172L173TYR00.001-0.00731.1100.1060.1060.0000.0000.0000.000
173L174SER00.021-0.00636.865-0.261-0.2610.0000.0000.0000.000
174L175MET0-0.0780.00237.0720.2740.2740.0000.0000.0000.000
175L176SER00.016-0.00638.620-0.247-0.2470.0000.0000.0000.000
176L177SER0-0.002-0.01139.4980.1260.1260.0000.0000.0000.000
177L178THR00.022-0.00341.121-0.227-0.2270.0000.0000.0000.000
178L179LEU0-0.0080.01442.8550.0920.0920.0000.0000.0000.000
179L180THR00.0350.01343.460-0.107-0.1070.0000.0000.0000.000
180L181LEU0-0.086-0.05845.975-0.032-0.0320.0000.0000.0000.000
181L182THR00.0510.02549.1360.0450.0450.0000.0000.0000.000
182L183LYS10.9960.98851.139-5.838-5.8380.0000.0000.0000.000
183L184ASP-1-0.834-0.91254.0585.5775.5770.0000.0000.0000.000
184L185LYS10.8040.90549.480-6.476-6.4760.0000.0000.0000.000
185L186TYR00.0450.00653.157-0.039-0.0390.0000.0000.0000.000
186L187GLU-1-0.858-0.94954.9665.4425.4420.0000.0000.0000.000
187L188ARG10.8690.96657.089-5.670-5.6700.0000.0000.0000.000
188L189HIS10.7840.90556.111-5.646-5.6460.0000.0000.0000.000
189L190ASN00.0600.02459.2440.0470.0470.0000.0000.0000.000
190L191SER0-0.0130.00658.2770.0190.0190.0000.0000.0000.000
191L192TYR0-0.034-0.01252.3720.1160.1160.0000.0000.0000.000
192L193THR0-0.017-0.01152.891-0.051-0.0510.0000.0000.0000.000
193L195GLU-1-0.860-0.94448.9546.0036.0030.0000.0000.0000.000
194L196ALA00.0350.01445.3480.1580.1580.0000.0000.0000.000
195L197THR0-0.039-0.00344.302-0.138-0.1380.0000.0000.0000.000
196L198HIS00.0780.01440.4980.0060.0060.0000.0000.0000.000
197L199LYS10.9610.98140.824-7.582-7.5820.0000.0000.0000.000
198L200THR0-0.030-0.02244.449-0.148-0.1480.0000.0000.0000.000
199L201SER0-0.026-0.00646.771-0.108-0.1080.0000.0000.0000.000
200L202SER0-0.0120.00249.0970.0780.0780.0000.0000.0000.000
201L203SER00.0050.00751.341-0.016-0.0160.0000.0000.0000.000
202L204PRO0-0.024-0.01749.7390.0690.0690.0000.0000.0000.000
203L205VAL00.0360.02049.048-0.139-0.1390.0000.0000.0000.000
204L206VAL0-0.007-0.00750.2120.1100.1100.0000.0000.0000.000
205L207LYS10.9420.96950.964-6.019-6.0190.0000.0000.0000.000
206L208SER0-0.033-0.02652.6980.0410.0410.0000.0000.0000.000
207L209PHE00.0340.01852.458-0.013-0.0130.0000.0000.0000.000
208L210ASN00.0620.02556.9980.0260.0260.0000.0000.0000.000
209L211ARG10.9710.96457.833-5.349-5.3490.0000.0000.0000.000
210L212ASN0-0.077-0.03659.7220.0370.0370.0000.0000.0000.000
211L213GLU-1-0.909-0.95561.6355.0375.0370.0000.0000.0000.000
212L214CYS0-0.074-0.01057.4680.0280.0280.0000.0000.0000.000