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: VK281

Calculation Name: 15C8-L-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 15C8

Chain ID: L

ChEMBL ID:

UniProt ID: P01869

Base Structure: X-ray

Registration Date: 2023-09-26

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 OptAll
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 211
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2145458.636516
FMO2-HF: Nuclear repulsion 2062789.641183
FMO2-HF: Total energy -82668.995333
FMO2-MP2: Total energy -82907.406745


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.
-112.673-112.78414.8-6.7-7.9870.049
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 : -0.900 / q_NPA : -0.945
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].
3L3VAL00.0430.0343.796-5.676-3.692-0.006-0.809-1.1680.002
4L4LEU00.0060.0055.807-4.213-4.2130.0000.0000.0000.000
5L5THR00.0100.0058.962-0.833-0.8330.0000.0000.0000.000
6L6GLN00.016-0.01311.7600.1990.1990.0000.0000.0000.000
7L7SER0-0.0310.01115.097-0.308-0.3080.0000.0000.0000.000
8L8PRO00.0840.03118.568-0.233-0.2330.0000.0000.0000.000
9L9ALA00.0540.03817.9010.3190.3190.0000.0000.0000.000
10L10ILE0-0.063-0.03219.374-0.157-0.1570.0000.0000.0000.000
11L11MET0-0.047-0.00823.0790.0880.0880.0000.0000.0000.000
12L12SER00.021-0.01826.0090.0620.0620.0000.0000.0000.000
13L13ALA0-0.046-0.01229.658-0.116-0.1160.0000.0000.0000.000
14L14SER00.015-0.00731.707-0.120-0.1200.0000.0000.0000.000
15L15LEU00.010-0.00434.6780.1360.1360.0000.0000.0000.000
16L16GLY00.0080.01136.196-0.208-0.2080.0000.0000.0000.000
17L17GLU-1-0.792-0.84333.2089.4489.4480.0000.0000.0000.000
18L18ARG10.9470.98630.140-9.897-9.8970.0000.0000.0000.000
19L19VAL00.002-0.00426.1900.0950.0950.0000.0000.0000.000
20L20THR0-0.001-0.00124.098-0.040-0.0400.0000.0000.0000.000
21L21MET0-0.0150.02520.6090.1730.1730.0000.0000.0000.000
22L22THR0-0.024-0.02718.7610.1760.1760.0000.0000.0000.000
23L23CYS0-0.040-0.00913.1150.8120.8120.0000.0000.0000.000
24L24THR0-0.016-0.00213.003-1.133-1.1330.0000.0000.0000.000
25L25ALA00.0030.0058.8801.4451.4450.0000.0000.0000.000
26L26SER0-0.014-0.0055.694-2.173-2.1730.0000.0000.0000.000
27L27SER00.0200.0006.7250.6390.6390.0000.0000.0000.000
28L27SER0-0.023-0.0108.691-1.223-1.2230.0000.0000.0000.000
29L28VAL0-0.026-0.0168.4952.2382.2380.0000.0000.0000.000
30L29SER00.0140.01611.167-1.871-1.8710.0000.0000.0000.000
31L30SER00.0650.02913.9320.5920.5920.0000.0000.0000.000
32L31SER0-0.020-0.00716.386-0.061-0.0610.0000.0000.0000.000
33L32ASN00.006-0.00411.914-1.256-1.2560.0000.0000.0000.000
34L33LEU0-0.0100.01011.6191.6651.6650.0000.0000.0000.000
35L34HIS0-0.0010.01113.484-2.104-2.1040.0000.0000.0000.000
36L35TRP00.0310.01015.0971.2771.2770.0000.0000.0000.000
37L36TYR00.0150.00515.099-1.014-1.0140.0000.0000.0000.000
38L37GLN00.0360.03319.157-0.040-0.0400.0000.0000.0000.000
39L38GLN0-0.002-0.00119.2200.0350.0350.0000.0000.0000.000
40L39LYS10.8660.89822.420-10.958-10.9580.0000.0000.0000.000
41L40PRO00.0280.00625.5920.1720.1720.0000.0000.0000.000
42L41GLY00.0210.02226.382-0.349-0.3490.0000.0000.0000.000
43L42SER0-0.026-0.00926.172-0.101-0.1010.0000.0000.0000.000
44L43SER00.0480.03022.0800.2690.2690.0000.0000.0000.000
45L44PRO00.0260.00817.949-0.446-0.4460.0000.0000.0000.000
46L45LYS10.8420.92620.844-12.259-12.2590.0000.0000.0000.000
47L46LEU00.008-0.00118.1900.3840.3840.0000.0000.0000.000
48L47TRP0-0.037-0.02320.634-0.548-0.5480.0000.0000.0000.000
49L48ILE00.0140.00320.650-0.521-0.5210.0000.0000.0000.000
50L49TYR00.0090.00518.7090.8100.8100.0000.0000.0000.000
51L50SER00.004-0.02917.667-0.653-0.6530.0000.0000.0000.000
52L51THR0-0.076-0.04416.966-0.304-0.3040.0000.0000.0000.000
53L52SER0-0.066-0.03218.800-0.366-0.3660.0000.0000.0000.000
54L53ASN0-0.0140.00722.277-0.213-0.2130.0000.0000.0000.000
55L54LEU00.0100.00923.3400.4690.4690.0000.0000.0000.000
56L55ALA00.0050.00823.399-0.153-0.1530.0000.0000.0000.000
57L56SER0-0.014-0.02025.359-0.429-0.4290.0000.0000.0000.000
58L57GLY00.0220.01128.6560.0980.0980.0000.0000.0000.000
59L58VAL0-0.044-0.00825.590-0.119-0.1190.0000.0000.0000.000
60L59PRO00.0110.00829.011-0.140-0.1400.0000.0000.0000.000
61L60ALA00.031-0.00130.3820.2780.2780.0000.0000.0000.000
62L61ARG10.7000.81831.185-9.461-9.4610.0000.0000.0000.000
63L62PHE00.0040.00725.7390.2780.2780.0000.0000.0000.000
64L63SER0-0.015-0.01226.407-0.213-0.2130.0000.0000.0000.000
65L64GLY00.0460.02122.2070.3410.3410.0000.0000.0000.000
66L65SER0-0.041-0.02721.328-0.670-0.6700.0000.0000.0000.000
67L66GLY00.0550.01818.7020.6240.6240.0000.0000.0000.000
68L67SER0-0.033-0.01917.354-0.517-0.5170.0000.0000.0000.000
69L68GLY00.0740.04514.9410.1370.1370.0000.0000.0000.000
70L69THR00.0120.01011.7570.9680.9680.0000.0000.0000.000
71L70SER0-0.0120.00213.6450.5710.5710.0000.0000.0000.000
72L71TYR00.0260.00413.302-1.211-1.2110.0000.0000.0000.000
73L72SER0-0.001-0.00617.5730.1960.1960.0000.0000.0000.000
74L73LEU0-0.030-0.00120.270-0.120-0.1200.0000.0000.0000.000
75L74THR0-0.018-0.03722.2100.0910.0910.0000.0000.0000.000
76L75ILE00.0130.02325.987-0.104-0.1040.0000.0000.0000.000
77L76SER0-0.031-0.03728.942-0.104-0.1040.0000.0000.0000.000
78L77SER0-0.026-0.03532.228-0.245-0.2450.0000.0000.0000.000
79L78MET0-0.0080.02129.6690.1050.1050.0000.0000.0000.000
80L79GLU-1-0.807-0.90032.7838.2798.2790.0000.0000.0000.000
81L80ALA00.033-0.00132.8550.2700.2700.0000.0000.0000.000
82L81GLU-1-0.826-0.89232.4299.3589.3580.0000.0000.0000.000
83L82ASP-1-0.769-0.85528.83810.45210.4520.0000.0000.0000.000
84L83ALA00.0150.02827.5900.5070.5070.0000.0000.0000.000
85L84ALA0-0.042-0.01524.534-0.108-0.1080.0000.0000.0000.000
86L85THR0-0.018-0.00419.196-0.133-0.1330.0000.0000.0000.000
87L86TYR0-0.008-0.01119.8660.0390.0390.0000.0000.0000.000
88L87TYR00.0050.00414.4790.0270.0270.0000.0000.0000.000
89L89HIS0-0.003-0.02310.2450.0910.0910.0000.0000.0000.000
90L90GLN00.0160.0034.731-4.011-3.937-0.001-0.002-0.0710.000
91L91TYR00.018-0.0018.4711.5811.5810.0000.0000.0000.000
92L92HIS00.0210.0228.559-2.319-2.3190.0000.0000.0000.000
93L93ARG10.8750.9191.964-80.120-84.48613.091-4.670-4.0550.047
94L94SER00.0230.0384.7780.6430.747-0.001-0.008-0.0940.000
95L95PRO0-0.010-0.0192.4021.3192.6581.703-0.929-2.1130.002
96L96TYR00.0140.0113.6113.1653.7000.011-0.240-0.306-0.002
97L97THR0-0.021-0.0163.698-1.332-1.1130.003-0.042-0.1800.000
98L98PHE0-0.001-0.0116.877-2.843-2.8430.0000.0000.0000.000
99L99GLY00.0440.0198.9752.3092.3090.0000.0000.0000.000
100L100GLY0-0.044-0.02611.327-0.691-0.6910.0000.0000.0000.000
101L101GLY0-0.010-0.00413.082-1.055-1.0550.0000.0000.0000.000
102L102THR0-0.036-0.03816.2210.3460.3460.0000.0000.0000.000
103L103LYS10.8370.92119.631-11.876-11.8760.0000.0000.0000.000
104L104LEU00.001-0.01022.7070.0100.0100.0000.0000.0000.000
105L105GLU-1-0.815-0.84625.83710.31810.3180.0000.0000.0000.000
106L106ILE00.018-0.00229.205-0.001-0.0010.0000.0000.0000.000
107L107LYS10.7890.87432.346-9.615-9.6150.0000.0000.0000.000
108L108ARG10.8070.90034.223-8.218-8.2180.0000.0000.0000.000
109L109ALA00.0270.01237.5390.1190.1190.0000.0000.0000.000
110L110ASP-1-0.872-0.94338.0678.4688.4680.0000.0000.0000.000
111L111ALA0-0.033-0.01739.614-0.221-0.2210.0000.0000.0000.000
112L112ALA00.0310.02140.0680.2030.2030.0000.0000.0000.000
113L113PRO00.0030.01539.627-0.069-0.0690.0000.0000.0000.000
114L114THR00.0210.00841.621-0.125-0.1250.0000.0000.0000.000
115L115VAL0-0.043-0.02242.025-0.036-0.0360.0000.0000.0000.000
116L116SER0-0.029-0.01144.279-0.293-0.2930.0000.0000.0000.000
117L117ILE0-0.019-0.00844.6660.1840.1840.0000.0000.0000.000
118L118PHE0-0.006-0.00645.279-0.173-0.1730.0000.0000.0000.000
119L119PRO00.0150.00546.9960.1320.1320.0000.0000.0000.000
120L120PRO00.0160.02247.2640.0220.0220.0000.0000.0000.000
121L121SER00.0220.02048.832-0.152-0.1520.0000.0000.0000.000
122L122SER00.023-0.00150.9970.0640.0640.0000.0000.0000.000
123L123GLU-1-0.903-0.93150.8816.1556.1550.0000.0000.0000.000
124L124GLN00.0660.02544.289-0.055-0.0550.0000.0000.0000.000
125L125LEU00.0210.01349.7430.0210.0210.0000.0000.0000.000
126L126THR0-0.071-0.04851.776-0.083-0.0830.0000.0000.0000.000
127L127SER0-0.084-0.04749.1540.0130.0130.0000.0000.0000.000
128L128GLY00.0430.02649.8960.0650.0650.0000.0000.0000.000
129L129GLY0-0.033-0.01046.4590.1000.1000.0000.0000.0000.000
130L130ALA0-0.016-0.02445.728-0.149-0.1490.0000.0000.0000.000
131L131SER0-0.017-0.01741.8860.1020.1020.0000.0000.0000.000
132L132VAL0-0.0110.00843.926-0.139-0.1390.0000.0000.0000.000
133L133VAL00.0070.00741.3980.2290.2290.0000.0000.0000.000
134L134CYS0-0.0350.00540.8660.0240.0240.0000.0000.0000.000
135L135PHE0-0.0040.00340.3780.2470.2470.0000.0000.0000.000
136L136LEU00.019-0.01037.900-0.182-0.1820.0000.0000.0000.000
137L137ASN00.0330.00038.7600.4010.4010.0000.0000.0000.000
138L138ASN0-0.010-0.02039.853-0.152-0.1520.0000.0000.0000.000
139L139PHE0-0.0060.01534.241-0.105-0.1050.0000.0000.0000.000
140L140TYR00.036-0.02032.0490.1520.1520.0000.0000.0000.000
141L141PRO00.0430.01732.395-0.187-0.1870.0000.0000.0000.000
142L142LYS10.9330.95826.448-11.536-11.5360.0000.0000.0000.000
143L143ASP-1-0.860-0.89529.62410.71210.7120.0000.0000.0000.000
144L144ILE0-0.0010.00331.791-0.338-0.3380.0000.0000.0000.000
145L145ASN0-0.047-0.01731.9030.1080.1080.0000.0000.0000.000
146L146VAL00.0350.00634.244-0.296-0.2960.0000.0000.0000.000
147L147LYS10.7980.89935.662-7.971-7.9710.0000.0000.0000.000
148L148TRP00.0420.00238.157-0.308-0.3080.0000.0000.0000.000
149L149LYS10.8090.88340.911-7.314-7.3140.0000.0000.0000.000
150L150ILE0-0.006-0.00443.768-0.084-0.0840.0000.0000.0000.000
151L151ASP-1-0.787-0.90146.6946.2226.2220.0000.0000.0000.000
152L152GLY0-0.0140.00147.880-0.049-0.0490.0000.0000.0000.000
153L153SER0-0.0060.00245.1250.1740.1740.0000.0000.0000.000
154L154GLU-1-0.807-0.89737.9628.2358.2350.0000.0000.0000.000
155L155ARG10.7440.83240.093-7.562-7.5620.0000.0000.0000.000
156L156GLN0-0.004-0.01634.1980.2140.2140.0000.0000.0000.000
157L157ASN00.0190.01535.4870.0190.0190.0000.0000.0000.000
158L158GLY00.0730.03636.070-0.222-0.2220.0000.0000.0000.000
159L159VAL0-0.0390.00135.176-0.150-0.1500.0000.0000.0000.000
160L160LEU0-0.0160.00232.6700.3270.3270.0000.0000.0000.000
161L161ASN00.0130.01331.548-0.531-0.5310.0000.0000.0000.000
162L162SER00.0050.00331.4190.3950.3950.0000.0000.0000.000
163L163TRP00.0350.00129.405-0.179-0.1790.0000.0000.0000.000
164L164THR0-0.011-0.00231.5770.0580.0580.0000.0000.0000.000
165L165ASP-1-0.813-0.89927.77711.28511.2850.0000.0000.0000.000
166L166GLN0-0.054-0.03230.526-0.112-0.1120.0000.0000.0000.000
167L167ASP-1-0.751-0.84832.5208.0198.0190.0000.0000.0000.000
168L168SER0-0.039-0.03434.750-0.048-0.0480.0000.0000.0000.000
169L169LYS10.7840.87236.564-7.891-7.8910.0000.0000.0000.000
170L170ASP-1-0.760-0.84939.5227.7907.7900.0000.0000.0000.000
171L171SER0-0.022-0.00635.6080.0550.0550.0000.0000.0000.000
172L172THR0-0.094-0.05435.6080.2250.2250.0000.0000.0000.000
173L173TYR0-0.039-0.04629.3290.3270.3270.0000.0000.0000.000
174L174SER00.0220.01535.051-0.385-0.3850.0000.0000.0000.000
175L175MET0-0.052-0.00433.4340.2860.2860.0000.0000.0000.000
176L176SER0-0.0080.00235.679-0.307-0.3070.0000.0000.0000.000
177L177SER0-0.012-0.01835.7280.2280.2280.0000.0000.0000.000
178L178THR00.010-0.00937.286-0.335-0.3350.0000.0000.0000.000
179L179LEU00.0170.03138.2040.2060.2060.0000.0000.0000.000
180L180THR0-0.010-0.00939.592-0.268-0.2680.0000.0000.0000.000
181L181LEU0-0.0320.00141.0390.1040.1040.0000.0000.0000.000
182L182THR00.0530.01943.900-0.042-0.0420.0000.0000.0000.000
183L183LYS10.8420.89546.705-5.862-5.8620.0000.0000.0000.000
184L184ASP-1-0.822-0.88650.2446.0896.0890.0000.0000.0000.000
185L185GLU-1-0.797-0.89644.1507.1147.1140.0000.0000.0000.000
186L186TYR00.0270.02148.023-0.001-0.0010.0000.0000.0000.000
187L187GLU-1-0.819-0.90149.3095.7805.7800.0000.0000.0000.000
188L188ARG10.7740.88350.150-6.220-6.2200.0000.0000.0000.000
189L189HIS10.8660.93547.251-6.539-6.5390.0000.0000.0000.000
190L190ASN0-0.048-0.01851.798-0.105-0.1050.0000.0000.0000.000
191L191SER00.009-0.00851.265-0.029-0.0290.0000.0000.0000.000
192L192TYR0-0.043-0.02646.2310.1890.1890.0000.0000.0000.000
193L193THR00.0170.01844.710-0.146-0.1460.0000.0000.0000.000
194L195GLU-1-0.803-0.89041.4237.3327.3320.0000.0000.0000.000
195L196ALA00.0190.01438.9930.2500.2500.0000.0000.0000.000
196L197THR0-0.032-0.01437.208-0.127-0.1270.0000.0000.0000.000
197L198HIS00.0390.00436.0140.0610.0610.0000.0000.0000.000
198L199LYS10.8910.92031.645-9.890-9.8900.0000.0000.0000.000
199L200THR00.0040.01237.686-0.156-0.1560.0000.0000.0000.000
200L201SER0-0.052-0.03640.815-0.271-0.2710.0000.0000.0000.000
201L202THR00.0010.00341.2560.1400.1400.0000.0000.0000.000
202L203SER0-0.0190.00342.767-0.051-0.0510.0000.0000.0000.000
203L204PRO0-0.003-0.00841.9730.0280.0280.0000.0000.0000.000
204L205ILE00.0290.02242.065-0.200-0.2000.0000.0000.0000.000
205L206VAL0-0.0080.00043.7090.1480.1480.0000.0000.0000.000
206L207LYS10.8510.92345.845-6.721-6.7210.0000.0000.0000.000
207L208SER00.033-0.01646.6460.1400.1400.0000.0000.0000.000
208L209PHE0-0.026-0.00647.808-0.105-0.1050.0000.0000.0000.000
209L210ASN00.0690.03151.6700.1210.1210.0000.0000.0000.000
210L211ARG10.8840.94252.531-5.891-5.8910.0000.0000.0000.000
211L212ASN0-0.0120.01555.170-0.094-0.0940.0000.0000.0000.000