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: 5N99Z

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 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 211
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2144009.324172
FMO2-HF: Nuclear repulsion 2061342.411481
FMO2-HF: Total energy -82666.912691
FMO2-MP2: Total energy -82905.466795


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.
-89.691-83.7281.453-2.851-4.5640.026
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 : -0.902 / q_NPA : -0.969
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].
3L3VAL00.0320.0123.786-4.020-2.137-0.008-0.793-1.0820.006
4L4LEU0-0.003-0.0035.148-3.066-3.005-0.001-0.004-0.0560.000
5L5THR00.006-0.0018.613-0.104-0.1040.0000.0000.0000.000
6L6GLN0-0.003-0.00411.342-0.016-0.0160.0000.0000.0000.000
7L7SER0-0.0420.02114.653-0.254-0.2540.0000.0000.0000.000
8L8PRO00.0810.02017.913-0.238-0.2380.0000.0000.0000.000
9L9ALA00.0740.03017.9100.2100.2100.0000.0000.0000.000
10L10ILE0-0.042-0.01419.152-0.085-0.0850.0000.0000.0000.000
11L11MET0-0.022-0.00322.8000.0000.0000.0000.0000.0000.000
12L12SER00.0160.00625.4890.0140.0140.0000.0000.0000.000
13L13ALA0-0.038-0.00629.140-0.001-0.0010.0000.0000.0000.000
14L14SER0-0.028-0.03031.451-0.117-0.1170.0000.0000.0000.000
15L15LEU00.019-0.00534.2810.1280.1280.0000.0000.0000.000
16L16GLY0-0.043-0.02035.543-0.191-0.1910.0000.0000.0000.000
17L17GLU-1-0.863-0.91632.6509.1679.1670.0000.0000.0000.000
18L18ARG10.9660.99829.860-9.732-9.7320.0000.0000.0000.000
19L19VAL0-0.028-0.02625.8380.1090.1090.0000.0000.0000.000
20L20THR0-0.016-0.01723.623-0.058-0.0580.0000.0000.0000.000
21L21MET0-0.0120.02020.1420.2020.2020.0000.0000.0000.000
22L22THR0-0.020-0.02718.1930.2710.2710.0000.0000.0000.000
23L23CYS0-0.039-0.00613.1980.5190.5190.0000.0000.0000.000
24L24THR0-0.0010.00412.188-0.592-0.5920.0000.0000.0000.000
25L25ALA0-0.007-0.0018.9071.1821.1820.0000.0000.0000.000
26L26SER0-0.007-0.0025.703-1.815-1.8150.0000.0000.0000.000
27L27SER00.023-0.0036.913-0.089-0.0890.0000.0000.0000.000
28L27SER0-0.072-0.0369.0400.0570.0570.0000.0000.0000.000
29L28VAL00.0130.0068.8711.9671.9670.0000.0000.0000.000
30L29SER0-0.007-0.00611.532-1.719-1.7190.0000.0000.0000.000
31L30SER00.0590.02814.2870.5240.5240.0000.0000.0000.000
32L31SER00.0630.07316.721-0.149-0.1490.0000.0000.0000.000
33L32ASN0-0.069-0.05112.036-1.283-1.2830.0000.0000.0000.000
34L33LEU00.0210.02011.7271.6211.6210.0000.0000.0000.000
35L34HIS00.0060.00313.711-1.951-1.9510.0000.0000.0000.000
36L35TRP00.0310.01215.1481.1121.1120.0000.0000.0000.000
37L36TYR0-0.014-0.01615.000-0.355-0.3550.0000.0000.0000.000
38L37GLN00.0020.00319.0620.1150.1150.0000.0000.0000.000
39L38GLN00.0330.00419.594-0.237-0.2370.0000.0000.0000.000
40L39LYS10.9320.97322.732-10.422-10.4220.0000.0000.0000.000
41L40PRO00.0550.00525.7930.1930.1930.0000.0000.0000.000
42L41GLY00.0040.01726.174-0.359-0.3590.0000.0000.0000.000
43L42SER0-0.018-0.00326.472-0.040-0.0400.0000.0000.0000.000
44L43SER00.0040.02922.9480.3090.3090.0000.0000.0000.000
45L44PRO00.0420.00918.694-0.357-0.3570.0000.0000.0000.000
46L45LYS10.8370.90521.128-12.106-12.1060.0000.0000.0000.000
47L46LEU00.0160.01718.7560.3460.3460.0000.0000.0000.000
48L47TRP0-0.008-0.00220.840-0.459-0.4590.0000.0000.0000.000
49L48ILE00.0240.00720.532-0.454-0.4540.0000.0000.0000.000
50L49TYR0-0.023-0.01718.9430.6990.6990.0000.0000.0000.000
51L50SER0-0.023-0.02017.836-0.628-0.6280.0000.0000.0000.000
52L51THR0-0.045-0.06317.404-0.233-0.2330.0000.0000.0000.000
53L52SER0-0.072-0.05119.033-0.355-0.3550.0000.0000.0000.000
54L53ASN0-0.0020.02022.415-0.103-0.1030.0000.0000.0000.000
55L54LEU00.0000.01323.4230.4960.4960.0000.0000.0000.000
56L55ALA00.0120.01023.690-0.143-0.1430.0000.0000.0000.000
57L56SER0-0.023-0.02425.655-0.406-0.4060.0000.0000.0000.000
58L57GLY00.0280.00528.5660.1430.1430.0000.0000.0000.000
59L58VAL0-0.0460.00025.817-0.039-0.0390.0000.0000.0000.000
60L59PRO00.0090.00229.149-0.191-0.1910.0000.0000.0000.000
61L60ALA00.0670.01430.2740.2520.2520.0000.0000.0000.000
62L61ARG10.7040.83531.193-9.169-9.1690.0000.0000.0000.000
63L62PHE00.0370.02925.8170.2420.2420.0000.0000.0000.000
64L63SER0-0.009-0.00526.409-0.119-0.1190.0000.0000.0000.000
65L64GLY00.0410.02522.2650.2740.2740.0000.0000.0000.000
66L65SER0-0.008-0.01621.747-0.485-0.4850.0000.0000.0000.000
67L66GLY00.0230.00919.0870.5850.5850.0000.0000.0000.000
68L67SER0-0.015-0.00617.540-0.354-0.3540.0000.0000.0000.000
69L68GLY00.0530.03515.477-0.020-0.0200.0000.0000.0000.000
70L69THR0-0.010-0.00511.9930.7140.7140.0000.0000.0000.000
71L70SER00.0030.01313.7830.6410.6410.0000.0000.0000.000
72L71TYR00.0270.01613.684-0.978-0.9780.0000.0000.0000.000
73L72SER0-0.034-0.02517.6470.0920.0920.0000.0000.0000.000
74L73LEU00.0250.03420.309-0.188-0.1880.0000.0000.0000.000
75L74THR00.001-0.02522.298-0.138-0.1380.0000.0000.0000.000
76L75ILE00.0110.01125.956-0.047-0.0470.0000.0000.0000.000
77L76SER0-0.052-0.02928.833-0.076-0.0760.0000.0000.0000.000
78L77SER00.0590.02032.210-0.131-0.1310.0000.0000.0000.000
79L78MET0-0.0140.00830.1200.1260.1260.0000.0000.0000.000
80L79GLU-1-0.873-0.93332.5438.1268.1260.0000.0000.0000.000
81L80ALA00.0590.00932.5870.2600.2600.0000.0000.0000.000
82L81GLU-1-0.896-0.93132.3029.2049.2040.0000.0000.0000.000
83L82ASP-1-0.740-0.84428.92310.10510.1050.0000.0000.0000.000
84L83ALA0-0.0230.03127.5000.5020.5020.0000.0000.0000.000
85L84ALA0-0.060-0.04224.869-0.133-0.1330.0000.0000.0000.000
86L85THR0-0.0160.00819.042-0.105-0.1050.0000.0000.0000.000
87L86TYR0-0.007-0.03519.7460.0090.0090.0000.0000.0000.000
88L87TYR00.0100.01414.4390.0630.0630.0000.0000.0000.000
89L89HIS0-0.021-0.04310.0900.3820.3820.0000.0000.0000.000
90L90GLN00.0640.0414.809-4.299-4.2990.0000.0000.0000.000
91L91TYR0-0.031-0.0258.5141.5441.5440.0000.0000.0000.000
92L92HIS00.0180.0198.461-2.210-2.2100.0000.0000.0000.000
93L93ARG10.9300.9572.900-66.271-63.9251.152-1.585-1.9130.020
94L94SER0-0.0480.0104.8204.6304.717-0.001-0.005-0.0800.000
95L95PRO00.0730.0152.7231.4002.5440.308-0.358-1.0940.000
96L96TYR00.0050.0044.0142.4342.6890.000-0.065-0.1900.000
97L97THR0-0.0050.0013.889-1.595-1.4080.003-0.041-0.1490.000
98L98PHE0-0.007-0.0056.747-2.757-2.7570.0000.0000.0000.000
99L99GLY00.0380.0258.9581.6611.6610.0000.0000.0000.000
100L100GLY0-0.038-0.02911.049-0.486-0.4860.0000.0000.0000.000
101L101GLY0-0.024-0.02313.026-0.977-0.9770.0000.0000.0000.000
102L102THR0-0.055-0.03216.0070.2420.2420.0000.0000.0000.000
103L103LYS10.9290.95519.253-11.839-11.8390.0000.0000.0000.000
104L104LEU0-0.004-0.00622.327-0.097-0.0970.0000.0000.0000.000
105L105GLU-1-0.829-0.87525.39210.12710.1270.0000.0000.0000.000
106L106ILE00.0410.01228.632-0.015-0.0150.0000.0000.0000.000
107L107LYS10.9590.98432.270-8.977-8.9770.0000.0000.0000.000
108L108ARG10.8280.91733.801-7.983-7.9830.0000.0000.0000.000
109L109ALA00.0020.00337.2560.0960.0960.0000.0000.0000.000
110L110ASP-1-0.879-0.93837.4158.2528.2520.0000.0000.0000.000
111L111ALA0-0.041-0.03239.212-0.214-0.2140.0000.0000.0000.000
112L112ALA00.0640.02439.7630.1990.1990.0000.0000.0000.000
113L113PRO0-0.0110.00839.350-0.042-0.0420.0000.0000.0000.000
114L114THR0-0.014-0.02541.401-0.162-0.1620.0000.0000.0000.000
115L115VAL00.0000.00542.3590.0480.0480.0000.0000.0000.000
116L116SER0-0.067-0.03644.238-0.245-0.2450.0000.0000.0000.000
117L117ILE0-0.0200.01344.7680.1640.1640.0000.0000.0000.000
118L118PHE0-0.027-0.01845.305-0.166-0.1660.0000.0000.0000.000
119L119PRO00.004-0.00246.9520.1260.1260.0000.0000.0000.000
120L120PRO00.0220.01548.0100.0290.0290.0000.0000.0000.000
121L121SER00.0630.03649.161-0.142-0.1420.0000.0000.0000.000
122L122SER00.0440.02051.0930.0470.0470.0000.0000.0000.000
123L123GLU-1-0.898-0.93251.0066.1406.1400.0000.0000.0000.000
124L124GLN00.0240.00344.665-0.002-0.0020.0000.0000.0000.000
125L125LEU0-0.023-0.00349.9260.0460.0460.0000.0000.0000.000
126L126THR0-0.066-0.04051.928-0.060-0.0600.0000.0000.0000.000
127L127SER0-0.072-0.04349.259-0.006-0.0060.0000.0000.0000.000
128L128GLY00.014-0.00349.8300.0770.0770.0000.0000.0000.000
129L129GLY0-0.010-0.00146.6890.1180.1180.0000.0000.0000.000
130L130ALA0-0.025-0.02846.142-0.143-0.1430.0000.0000.0000.000
131L131SER00.0230.01242.4100.1540.1540.0000.0000.0000.000
132L132VAL0-0.0110.01343.779-0.146-0.1460.0000.0000.0000.000
133L133VAL00.0260.01841.2580.2130.2130.0000.0000.0000.000
134L134CYS0-0.045-0.01540.834-0.002-0.0020.0000.0000.0000.000
135L135PHE00.0070.00140.2300.2450.2450.0000.0000.0000.000
136L136LEU0-0.003-0.01137.884-0.167-0.1670.0000.0000.0000.000
137L137ASN00.0440.00638.5690.4150.4150.0000.0000.0000.000
138L138ASN00.014-0.01539.239-0.128-0.1280.0000.0000.0000.000
139L139PHE0-0.0140.02234.174-0.127-0.1270.0000.0000.0000.000
140L140TYR0-0.024-0.04131.6260.1780.1780.0000.0000.0000.000
141L141PRO00.0540.01332.352-0.184-0.1840.0000.0000.0000.000
142L142LYS10.9850.99426.496-11.097-11.0970.0000.0000.0000.000
143L143ASP-1-0.972-0.97529.38810.44410.4440.0000.0000.0000.000
144L144ILE00.0420.01031.565-0.342-0.3420.0000.0000.0000.000
145L145ASN0-0.042-0.01232.6090.1810.1810.0000.0000.0000.000
146L146VAL00.0450.01934.688-0.280-0.2800.0000.0000.0000.000
147L147LYS10.9080.96436.120-7.853-7.8530.0000.0000.0000.000
148L148TRP00.0360.02038.474-0.319-0.3190.0000.0000.0000.000
149L149LYS10.8620.90641.217-7.095-7.0950.0000.0000.0000.000
150L150ILE0-0.026-0.00443.689-0.113-0.1130.0000.0000.0000.000
151L151ASP-1-0.794-0.89946.7526.1916.1910.0000.0000.0000.000
152L152GLY0-0.042-0.01848.034-0.020-0.0200.0000.0000.0000.000
153L153SER00.0170.00145.6070.1470.1470.0000.0000.0000.000
154L154GLU-1-0.904-0.95538.3708.1588.1580.0000.0000.0000.000
155L155ARG10.8060.91240.227-7.614-7.6140.0000.0000.0000.000
156L156GLN00.021-0.00534.7830.2680.2680.0000.0000.0000.000
157L157ASN0-0.047-0.01235.5570.0730.0730.0000.0000.0000.000
158L158GLY00.1260.05836.217-0.248-0.2480.0000.0000.0000.000
159L159VAL0-0.028-0.00935.224-0.157-0.1570.0000.0000.0000.000
160L160LEU0-0.0010.00832.3150.3370.3370.0000.0000.0000.000
161L161ASN00.0150.02631.648-0.529-0.5290.0000.0000.0000.000
162L162SER0-0.0030.00531.2770.3460.3460.0000.0000.0000.000
163L163TRP00.0440.00829.023-0.197-0.1970.0000.0000.0000.000
164L164THR00.0200.02031.0750.0970.0970.0000.0000.0000.000
165L165ASP-1-0.942-0.97028.52510.70010.7000.0000.0000.0000.000
166L166GLN0-0.076-0.04630.643-0.026-0.0260.0000.0000.0000.000
167L167ASP-1-0.764-0.85932.5957.9067.9060.0000.0000.0000.000
168L168SER0-0.034-0.03835.385-0.020-0.0200.0000.0000.0000.000
169L169LYS10.8090.89436.527-7.876-7.8760.0000.0000.0000.000
170L170ASP-1-0.790-0.85039.9067.6687.6680.0000.0000.0000.000
171L171SER0-0.043-0.01235.3730.0750.0750.0000.0000.0000.000
172L172THR0-0.094-0.09835.7420.1540.1540.0000.0000.0000.000
173L173TYR0-0.090-0.06729.7430.2190.2190.0000.0000.0000.000
174L174SER00.0490.02134.663-0.357-0.3570.0000.0000.0000.000
175L175MET0-0.037-0.00832.8340.3120.3120.0000.0000.0000.000
176L176SER0-0.052-0.00435.466-0.347-0.3470.0000.0000.0000.000
177L177SER0-0.020-0.04335.7300.2240.2240.0000.0000.0000.000
178L178THR00.0200.00037.162-0.340-0.3400.0000.0000.0000.000
179L179LEU0-0.0010.01538.1110.2130.2130.0000.0000.0000.000
180L180THR0-0.036-0.02639.932-0.145-0.1450.0000.0000.0000.000
181L181LEU0-0.023-0.01841.5540.0890.0890.0000.0000.0000.000
182L182THR00.0590.03044.328-0.096-0.0960.0000.0000.0000.000
183L183LYS10.9120.94147.123-5.827-5.8270.0000.0000.0000.000
184L184ASP-1-0.833-0.92350.1156.0866.0860.0000.0000.0000.000
185L185GLU-1-0.999-1.01344.5687.1147.1140.0000.0000.0000.000
186L186TYR00.0650.04448.0890.0400.0400.0000.0000.0000.000
187L187GLU-1-0.894-0.92749.5535.7175.7170.0000.0000.0000.000
188L188ARG10.9020.97950.079-6.273-6.2730.0000.0000.0000.000
189L189HIS10.8620.93348.330-6.496-6.4960.0000.0000.0000.000
190L190ASN0-0.032-0.01752.120-0.080-0.0800.0000.0000.0000.000
191L191SER00.022-0.00150.941-0.016-0.0160.0000.0000.0000.000
192L192TYR0-0.049-0.03046.4220.1880.1880.0000.0000.0000.000
193L193THR0-0.021-0.03645.353-0.092-0.0920.0000.0000.0000.000
194L195GLU-1-0.877-0.95041.4637.2347.2340.0000.0000.0000.000
195L196ALA00.0530.02538.9400.2440.2440.0000.0000.0000.000
196L197THR0-0.0100.01237.644-0.105-0.1050.0000.0000.0000.000
197L198HIS0-0.003-0.02535.5490.0640.0640.0000.0000.0000.000
198L199LYS10.9350.96832.455-9.321-9.3210.0000.0000.0000.000
199L200THR0-0.0090.00837.602-0.204-0.2040.0000.0000.0000.000
200L201SER0-0.053-0.02740.553-0.231-0.2310.0000.0000.0000.000
201L202THR00.0100.01641.0880.1370.1370.0000.0000.0000.000
202L203SER0-0.020-0.01242.814-0.014-0.0140.0000.0000.0000.000
203L204PRO0-0.028-0.01841.9880.0080.0080.0000.0000.0000.000
204L205ILE00.0380.03442.529-0.191-0.1910.0000.0000.0000.000
205L206VAL00.017-0.00143.8560.1320.1320.0000.0000.0000.000
206L207LYS10.9100.96546.117-6.563-6.5630.0000.0000.0000.000
207L208SER00.0200.01446.9670.1640.1640.0000.0000.0000.000
208L209PHE0-0.010-0.00547.859-0.084-0.0840.0000.0000.0000.000
209L210ASN00.0580.03451.8650.1090.1090.0000.0000.0000.000
210L211ARG10.8730.93252.741-5.860-5.8600.0000.0000.0000.000
211L212ASN00.0060.02055.462-0.096-0.0960.0000.0000.0000.000