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: YNQ62

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 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 211
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2144616.062432
FMO2-HF: Nuclear repulsion 2061947.755168
FMO2-HF: Total energy -82668.307264
FMO2-MP2: Total energy -82906.774697


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.
-100.685-98.2027.009-3.654-5.8360.037
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 : -0.911 / q_NPA : -0.971
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].
3L3VAL00.0350.0243.801-4.032-2.128-0.010-0.773-1.1210.005
4L4LEU0-0.002-0.0035.295-3.442-3.385-0.001-0.004-0.0520.000
5L5THR0-0.001-0.0048.6330.0170.0170.0000.0000.0000.000
6L6GLN00.009-0.00911.444-0.004-0.0040.0000.0000.0000.000
7L7SER0-0.0440.02114.681-0.241-0.2410.0000.0000.0000.000
8L8PRO00.0720.01117.995-0.265-0.2650.0000.0000.0000.000
9L9ALA00.0620.03017.9380.2100.2100.0000.0000.0000.000
10L10ILE0-0.056-0.01719.163-0.118-0.1180.0000.0000.0000.000
11L11MET0-0.026-0.00622.7870.0380.0380.0000.0000.0000.000
12L12SER00.017-0.02025.4840.0460.0460.0000.0000.0000.000
13L13ALA0-0.051-0.01829.117-0.024-0.0240.0000.0000.0000.000
14L14SER0-0.008-0.02031.419-0.096-0.0960.0000.0000.0000.000
15L15LEU00.021-0.00534.2210.1320.1320.0000.0000.0000.000
16L16GLY0-0.032-0.01135.449-0.192-0.1920.0000.0000.0000.000
17L17GLU-1-0.821-0.86732.8259.1999.1990.0000.0000.0000.000
18L18ARG10.9931.00229.944-9.772-9.7720.0000.0000.0000.000
19L19VAL0-0.029-0.03125.7680.1080.1080.0000.0000.0000.000
20L20THR00.0070.00923.550-0.032-0.0320.0000.0000.0000.000
21L21MET0-0.0010.03520.2120.2260.2260.0000.0000.0000.000
22L22THR0-0.005-0.01418.1730.2300.2300.0000.0000.0000.000
23L23CYS0-0.038-0.00312.9590.5900.5900.0000.0000.0000.000
24L24THR0-0.0010.01212.684-0.783-0.7830.0000.0000.0000.000
25L25ALA0-0.011-0.0078.9481.3221.3220.0000.0000.0000.000
26L26SER0-0.0010.0055.803-1.865-1.8650.0000.0000.0000.000
27L27SER00.0250.0007.137-0.479-0.4790.0000.0000.0000.000
28L27SER0-0.024-0.0219.135-0.432-0.4320.0000.0000.0000.000
29L28VAL0-0.033-0.0108.7361.8541.8540.0000.0000.0000.000
30L29SER00.0280.03011.475-1.757-1.7570.0000.0000.0000.000
31L30SER00.0540.02914.2430.5390.5390.0000.0000.0000.000
32L31SER00.0000.00216.678-0.223-0.2230.0000.0000.0000.000
33L32ASN0-0.027-0.02112.007-1.149-1.1490.0000.0000.0000.000
34L33LEU00.0110.01411.7721.6101.6100.0000.0000.0000.000
35L34HIS00.0010.01313.863-1.920-1.9200.0000.0000.0000.000
36L35TRP00.0420.01115.1581.1581.1580.0000.0000.0000.000
37L36TYR0-0.006-0.01215.234-0.862-0.8620.0000.0000.0000.000
38L37GLN00.0380.03219.057-0.016-0.0160.0000.0000.0000.000
39L38GLN00.019-0.00219.3000.0070.0070.0000.0000.0000.000
40L39LYS10.8780.92422.432-10.717-10.7170.0000.0000.0000.000
41L40PRO00.0520.00325.4790.1860.1860.0000.0000.0000.000
42L41GLY0-0.0020.01325.853-0.371-0.3710.0000.0000.0000.000
43L42SER0-0.0190.00026.143-0.025-0.0250.0000.0000.0000.000
44L43SER00.0250.02522.7010.3320.3320.0000.0000.0000.000
45L44PRO00.019-0.00318.355-0.394-0.3940.0000.0000.0000.000
46L45LYS10.8530.92120.900-12.091-12.0910.0000.0000.0000.000
47L46LEU00.0070.02018.7120.3410.3410.0000.0000.0000.000
48L47TRP0-0.015-0.00720.856-0.491-0.4910.0000.0000.0000.000
49L48ILE00.0190.00420.702-0.462-0.4620.0000.0000.0000.000
50L49TYR0-0.013-0.01218.9390.7380.7380.0000.0000.0000.000
51L50SER0-0.021-0.03717.783-0.641-0.6410.0000.0000.0000.000
52L51THR0-0.050-0.04117.201-0.288-0.2880.0000.0000.0000.000
53L52SER0-0.077-0.04619.012-0.341-0.3410.0000.0000.0000.000
54L53ASN0-0.0020.02022.392-0.217-0.2170.0000.0000.0000.000
55L54LEU0-0.0040.01123.4150.4960.4960.0000.0000.0000.000
56L55ALA00.0090.00823.652-0.157-0.1570.0000.0000.0000.000
57L56SER00.014-0.01125.657-0.425-0.4250.0000.0000.0000.000
58L57GLY0-0.013-0.01028.5780.1460.1460.0000.0000.0000.000
59L58VAL0-0.0320.00425.759-0.032-0.0320.0000.0000.0000.000
60L59PRO0-0.004-0.00129.161-0.169-0.1690.0000.0000.0000.000
61L60ALA00.0670.01630.2810.2590.2590.0000.0000.0000.000
62L61ARG10.6650.80831.126-9.227-9.2270.0000.0000.0000.000
63L62PHE00.0380.02525.8390.2610.2610.0000.0000.0000.000
64L63SER00.000-0.00126.411-0.149-0.1490.0000.0000.0000.000
65L64GLY00.0430.02722.2570.2890.2890.0000.0000.0000.000
66L65SER0-0.049-0.03321.721-0.569-0.5690.0000.0000.0000.000
67L66GLY00.0580.01919.0620.5930.5930.0000.0000.0000.000
68L67SER0-0.016-0.01217.481-0.444-0.4440.0000.0000.0000.000
69L68GLY00.0450.04015.433-0.033-0.0330.0000.0000.0000.000
70L69THR0-0.001-0.00111.6810.7830.7830.0000.0000.0000.000
71L70SER00.0030.00613.7830.7490.7490.0000.0000.0000.000
72L71TYR00.0160.01213.406-1.013-1.0130.0000.0000.0000.000
73L72SER00.006-0.00917.6330.1810.1810.0000.0000.0000.000
74L73LEU0-0.0330.00720.294-0.216-0.2160.0000.0000.0000.000
75L74THR0-0.023-0.05622.2430.0270.0270.0000.0000.0000.000
76L75ILE00.0120.00825.887-0.067-0.0670.0000.0000.0000.000
77L76SER0-0.054-0.02728.734-0.093-0.0930.0000.0000.0000.000
78L77SER00.0370.00132.132-0.219-0.2190.0000.0000.0000.000
79L78MET0-0.0340.01229.2750.0720.0720.0000.0000.0000.000
80L79GLU-1-0.799-0.89432.3958.2338.2330.0000.0000.0000.000
81L80ALA00.0620.01232.4240.2650.2650.0000.0000.0000.000
82L81GLU-1-0.873-0.90732.1099.2749.2740.0000.0000.0000.000
83L82ASP-1-0.751-0.84828.64710.23910.2390.0000.0000.0000.000
84L83ALA0-0.0130.01627.3150.5070.5070.0000.0000.0000.000
85L84ALA0-0.040-0.02324.559-0.131-0.1310.0000.0000.0000.000
86L85THR0-0.0190.00218.861-0.111-0.1110.0000.0000.0000.000
87L86TYR0-0.015-0.02019.5500.0030.0030.0000.0000.0000.000
88L87TYR00.0120.02014.2180.1070.1070.0000.0000.0000.000
89L89HIS0-0.002-0.02710.3170.2650.2650.0000.0000.0000.000
90L90GLN00.0540.0264.793-4.035-3.970-0.001-0.001-0.0630.000
91L91TYR0-0.021-0.0178.5111.6631.6630.0000.0000.0000.000
92L92HIS00.0160.0138.502-2.403-2.4030.0000.0000.0000.000
93L93ARG10.9310.9602.310-72.536-73.8406.596-2.335-2.9570.032
94L94SER0-0.0060.0264.7812.2822.352-0.001-0.004-0.0640.000
95L95PRO00.016-0.0162.7090.8972.0960.417-0.415-1.2000.000
96L96TYR00.0020.0074.0352.8983.1330.000-0.060-0.1750.000
97L97THR0-0.012-0.0093.498-1.592-1.3350.009-0.062-0.2040.000
98L98PHE0-0.004-0.0136.771-2.925-2.9250.0000.0000.0000.000
99L99GLY00.0420.0328.7541.8561.8560.0000.0000.0000.000
100L100GLY0-0.041-0.03010.915-0.500-0.5000.0000.0000.0000.000
101L101GLY0-0.024-0.02112.925-1.025-1.0250.0000.0000.0000.000
102L102THR0-0.050-0.03315.8720.2450.2450.0000.0000.0000.000
103L103LYS10.8500.90419.170-11.812-11.8120.0000.0000.0000.000
104L104LEU0-0.010-0.01222.215-0.104-0.1040.0000.0000.0000.000
105L105GLU-1-0.829-0.85225.28810.16010.1600.0000.0000.0000.000
106L106ILE00.0430.01028.531-0.019-0.0190.0000.0000.0000.000
107L107LYS10.8260.91032.174-9.267-9.2670.0000.0000.0000.000
108L108ARG10.8240.91233.758-8.116-8.1160.0000.0000.0000.000
109L109ALA00.0030.00437.2430.0980.0980.0000.0000.0000.000
110L110ASP-1-0.857-0.93237.3158.4228.4220.0000.0000.0000.000
111L111ALA0-0.043-0.02839.218-0.224-0.2240.0000.0000.0000.000
112L112ALA00.0290.01939.7510.1960.1960.0000.0000.0000.000
113L113PRO00.0040.01539.350-0.042-0.0420.0000.0000.0000.000
114L114THR0-0.023-0.01641.370-0.163-0.1630.0000.0000.0000.000
115L115VAL00.000-0.01142.1940.0470.0470.0000.0000.0000.000
116L116SER0-0.055-0.02944.178-0.265-0.2650.0000.0000.0000.000
117L117ILE0-0.0200.01044.6930.1700.1700.0000.0000.0000.000
118L118PHE0-0.012-0.00945.047-0.169-0.1690.0000.0000.0000.000
119L119PRO00.0040.00046.8620.1290.1290.0000.0000.0000.000
120L120PRO00.0140.01447.6570.0200.0200.0000.0000.0000.000
121L121SER00.0310.02949.048-0.126-0.1260.0000.0000.0000.000
122L122SER00.0410.01950.9480.0500.0500.0000.0000.0000.000
123L123GLU-1-0.893-0.94350.9556.1976.1970.0000.0000.0000.000
124L124GLN00.0650.00544.417-0.053-0.0530.0000.0000.0000.000
125L125LEU0-0.0010.00449.6270.0470.0470.0000.0000.0000.000
126L126THR0-0.078-0.04051.588-0.063-0.0630.0000.0000.0000.000
127L127SER0-0.083-0.03848.6240.0060.0060.0000.0000.0000.000
128L128GLY00.012-0.00249.3190.0710.0710.0000.0000.0000.000
129L129GLY0-0.018-0.00446.2240.1160.1160.0000.0000.0000.000
130L130ALA0-0.031-0.02345.698-0.142-0.1420.0000.0000.0000.000
131L131SER0-0.009-0.01141.9820.1160.1160.0000.0000.0000.000
132L132VAL0-0.0320.00143.641-0.143-0.1430.0000.0000.0000.000
133L133VAL00.0160.01240.8840.2290.2290.0000.0000.0000.000
134L134CYS0-0.0270.00140.8700.0070.0070.0000.0000.0000.000
135L135PHE0-0.009-0.00440.1560.2580.2580.0000.0000.0000.000
136L136LEU00.009-0.00837.644-0.171-0.1710.0000.0000.0000.000
137L137ASN00.022-0.00838.4890.3760.3760.0000.0000.0000.000
138L138ASN0-0.010-0.02039.121-0.122-0.1220.0000.0000.0000.000
139L139PHE0-0.0220.01534.215-0.130-0.1300.0000.0000.0000.000
140L140TYR00.020-0.02531.5630.1720.1720.0000.0000.0000.000
141L141PRO00.0320.00732.151-0.183-0.1830.0000.0000.0000.000
142L142LYS10.9730.98826.092-11.407-11.4070.0000.0000.0000.000
143L143ASP-1-0.875-0.91029.42610.52910.5290.0000.0000.0000.000
144L144ILE00.0080.00331.595-0.339-0.3390.0000.0000.0000.000
145L145ASN0-0.056-0.02032.6210.1570.1570.0000.0000.0000.000
146L146VAL00.0460.01534.739-0.278-0.2780.0000.0000.0000.000
147L147LYS10.8020.89136.158-7.943-7.9430.0000.0000.0000.000
148L148TRP00.0410.01338.302-0.336-0.3360.0000.0000.0000.000
149L149LYS10.8340.87641.149-7.276-7.2760.0000.0000.0000.000
150L150ILE0-0.016-0.00543.507-0.122-0.1220.0000.0000.0000.000
151L151ASP-1-0.765-0.88346.4686.2366.2360.0000.0000.0000.000
152L152GLY0-0.028-0.01047.869-0.021-0.0210.0000.0000.0000.000
153L153SER0-0.0070.00145.0010.1550.1550.0000.0000.0000.000
154L154GLU-1-0.818-0.89638.0248.2738.2730.0000.0000.0000.000
155L155ARG10.7310.82240.086-7.615-7.6150.0000.0000.0000.000
156L156GLN0-0.008-0.01834.2440.2640.2640.0000.0000.0000.000
157L157ASN0-0.0170.00935.0920.0510.0510.0000.0000.0000.000
158L158GLY00.0950.04435.677-0.252-0.2520.0000.0000.0000.000
159L159VAL0-0.032-0.01035.110-0.161-0.1610.0000.0000.0000.000
160L160LEU0-0.0090.00132.1720.3330.3330.0000.0000.0000.000
161L161ASN00.0230.01731.521-0.536-0.5360.0000.0000.0000.000
162L162SER00.0010.00631.1490.3880.3880.0000.0000.0000.000
163L163TRP00.0340.00428.975-0.187-0.1870.0000.0000.0000.000
164L164THR00.0130.01730.9150.1100.1100.0000.0000.0000.000
165L165ASP-1-0.848-0.93027.94011.07311.0730.0000.0000.0000.000
166L166GLN0-0.055-0.02130.474-0.088-0.0880.0000.0000.0000.000
167L167ASP-1-0.767-0.85932.4507.9737.9730.0000.0000.0000.000
168L168SER0-0.024-0.02834.8280.0000.0000.0000.0000.0000.000
169L169LYS10.7790.86436.326-7.844-7.8440.0000.0000.0000.000
170L170ASP-1-0.766-0.86839.4667.7417.7410.0000.0000.0000.000
171L171SER0-0.020-0.00835.2650.0750.0750.0000.0000.0000.000
172L172THR0-0.102-0.05835.6450.1600.1600.0000.0000.0000.000
173L173TYR0-0.046-0.04329.2270.2400.2400.0000.0000.0000.000
174L174SER00.0480.02034.553-0.369-0.3690.0000.0000.0000.000
175L175MET0-0.053-0.01033.0670.3100.3100.0000.0000.0000.000
176L176SER0-0.0050.00935.364-0.303-0.3030.0000.0000.0000.000
177L177SER0-0.027-0.02435.6320.2180.2180.0000.0000.0000.000
178L178THR00.021-0.00137.075-0.344-0.3440.0000.0000.0000.000
179L179LEU00.0050.01937.9880.2220.2220.0000.0000.0000.000
180L180THR0-0.011-0.00339.576-0.258-0.2580.0000.0000.0000.000
181L181LEU0-0.025-0.00541.0680.0980.0980.0000.0000.0000.000
182L182THR00.0690.02543.820-0.089-0.0890.0000.0000.0000.000
183L183LYS10.8840.91646.587-5.892-5.8920.0000.0000.0000.000
184L184ASP-1-0.781-0.89649.8076.0486.0480.0000.0000.0000.000
185L185GLU-1-0.885-0.91743.7167.1957.1950.0000.0000.0000.000
186L186TYR00.0530.03647.6900.0430.0430.0000.0000.0000.000
187L187GLU-1-0.834-0.90549.0755.7945.7940.0000.0000.0000.000
188L188ARG10.7880.90949.912-6.284-6.2840.0000.0000.0000.000
189L189HIS10.8630.93347.311-6.574-6.5740.0000.0000.0000.000
190L190ASN0-0.049-0.01751.677-0.085-0.0850.0000.0000.0000.000
191L191SER00.0130.00050.969-0.020-0.0200.0000.0000.0000.000
192L192TYR0-0.042-0.01946.0410.1970.1970.0000.0000.0000.000
193L193THR0-0.011-0.00545.176-0.128-0.1280.0000.0000.0000.000
194L195GLU-1-0.828-0.89741.5397.3597.3590.0000.0000.0000.000
195L196ALA00.0460.02039.0120.2500.2500.0000.0000.0000.000
196L197THR0-0.0150.00737.655-0.114-0.1140.0000.0000.0000.000
197L198HIS00.025-0.00535.7230.0610.0610.0000.0000.0000.000
198L199LYS10.9540.95931.773-9.746-9.7460.0000.0000.0000.000
199L200THR0-0.009-0.00637.687-0.176-0.1760.0000.0000.0000.000
200L201SER0-0.106-0.05040.632-0.265-0.2650.0000.0000.0000.000
201L202THR00.0260.01841.1890.1400.1400.0000.0000.0000.000
202L203SER0-0.023-0.00742.940-0.054-0.0540.0000.0000.0000.000
203L204PRO0-0.019-0.02042.2190.0140.0140.0000.0000.0000.000
204L205ILE00.0230.02542.323-0.195-0.1950.0000.0000.0000.000
205L206VAL00.014-0.00343.8940.1450.1450.0000.0000.0000.000
206L207LYS10.8980.96346.087-6.666-6.6660.0000.0000.0000.000
207L208SER00.018-0.01846.9610.1450.1450.0000.0000.0000.000
208L209PHE0-0.008-0.00647.868-0.088-0.0880.0000.0000.0000.000
209L210ASN00.0530.02451.8490.1260.1260.0000.0000.0000.000
210L211ARG10.8950.94552.646-5.894-5.8940.0000.0000.0000.000
211L212ASN00.0110.02355.319-0.092-0.0920.0000.0000.0000.000