Manual

About

FMODB

FMODB: The database of quantum mechanical data based on the FMO method

Last updated: 2024-05-02

All entries: 37386

Number of unique PDB entries: 7781

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FMODB ID: YZ782

Calculation Name: 3MLR-L-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3MLR

Chain ID: L

ChEMBL ID:

UniProt ID: P12490

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 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 217
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2120972.710917
FMO2-HF: Nuclear repulsion 2039133.252755
FMO2-HF: Total energy -81839.458162
FMO2-MP2: Total energy -82078.80554


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:SER)


Summations of interaction energy for fragment #1(L:1:SER)
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.
-19.541-23.89424.357-9.824-10.181-0.037
Interaction energy analysis for fragmet #1(L:1:SER)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.059 / q_NPA : -0.071
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].
3L3ASP-1-0.855-0.9253.867-2.296-0.907-0.016-0.633-0.7410.000
4L4LEU0-0.048-0.0376.3630.4870.4870.0000.0000.0000.000
5L5THR00.0510.0388.8480.0710.0710.0000.0000.0000.000
6L6GLN00.028-0.00912.3450.0690.0690.0000.0000.0000.000
7L7PRO00.0000.00915.229-0.014-0.0140.0000.0000.0000.000
8L8PRO00.0650.05618.7840.0160.0160.0000.0000.0000.000
9L9SER0-0.037-0.02319.6690.0160.0160.0000.0000.0000.000
10L11VAL0-0.022-0.00622.358-0.003-0.0030.0000.0000.0000.000
11L12SER0-0.004-0.00624.9630.0080.0080.0000.0000.0000.000
12L13VAL00.0020.00628.754-0.001-0.0010.0000.0000.0000.000
13L14SER00.0300.00231.1350.0010.0010.0000.0000.0000.000
14L15PRO00.0350.01133.9200.0000.0000.0000.0000.0000.000
15L16GLY0-0.0230.00035.0040.0010.0010.0000.0000.0000.000
16L17GLN0-0.013-0.00133.3530.0020.0020.0000.0000.0000.000
17L18THR0-0.010-0.00828.4190.0020.0020.0000.0000.0000.000
18L19ALA0-0.0050.01926.430-0.004-0.0040.0000.0000.0000.000
19L20SER0-0.030-0.03823.5650.0040.0040.0000.0000.0000.000
20L21ILE00.0170.01118.186-0.008-0.0080.0000.0000.0000.000
21L22SER00.0180.01717.7320.0110.0110.0000.0000.0000.000
22L23CYS0-0.025-0.00911.8260.0050.0050.0000.0000.0000.000
23L24SER0-0.028-0.01812.7210.0600.0600.0000.0000.0000.000
24L25GLY00.0770.0318.748-0.110-0.1100.0000.0000.0000.000
25L26ASP-1-0.900-0.9516.956-0.803-0.8030.0000.0000.0000.000
26L27LYS10.8360.9163.4501.5471.9900.003-0.153-0.2930.000
27L28LEU00.0010.0128.7360.1060.1060.0000.0000.0000.000
28L29ASP-1-0.835-0.90210.952-0.103-0.1030.0000.0000.0000.000
29L30ASP-1-0.843-0.90110.5020.1380.1380.0000.0000.0000.000
30L31LYS10.7320.8676.866-0.193-0.1930.0000.0000.0000.000
31L32TYR0-0.051-0.03010.703-0.063-0.0630.0000.0000.0000.000
32L33VAL0-0.0020.00510.9520.0620.0620.0000.0000.0000.000
33L34SER0-0.052-0.02712.435-0.007-0.0070.0000.0000.0000.000
34L35TRP0-0.013-0.00913.677-0.025-0.0250.0000.0000.0000.000
35L36TYR0-0.006-0.01013.6070.0160.0160.0000.0000.0000.000
36L37TYR0-0.018-0.02017.771-0.015-0.0150.0000.0000.0000.000
37L38GLN00.0180.00719.581-0.002-0.0020.0000.0000.0000.000
38L39ARG10.9070.96422.0060.0360.0360.0000.0000.0000.000
39L40PRO00.029-0.01125.0500.0030.0030.0000.0000.0000.000
40L41GLY00.0020.00525.3280.0060.0060.0000.0000.0000.000
41L42GLN0-0.043-0.00125.2990.0110.0110.0000.0000.0000.000
42L43SER00.0270.01122.192-0.005-0.0050.0000.0000.0000.000
43L44PRO0-0.017-0.01417.6540.0000.0000.0000.0000.0000.000
44L45VAL0-0.0140.00420.1780.0130.0130.0000.0000.0000.000
45L46LEU0-0.021-0.00317.148-0.010-0.0100.0000.0000.0000.000
46L47LEU0-0.028-0.02219.333-0.001-0.0010.0000.0000.0000.000
47L48MET0-0.025-0.01318.2350.0010.0010.0000.0000.0000.000
48L49TYR00.0260.00916.5680.0080.0080.0000.0000.0000.000
49L50GLN00.0320.01916.152-0.016-0.0160.0000.0000.0000.000
50L51ASP-1-0.750-0.87014.9680.0690.0690.0000.0000.0000.000
51L52PHE0-0.048-0.03217.202-0.017-0.0170.0000.0000.0000.000
52L53LYS10.8720.95020.386-0.068-0.0680.0000.0000.0000.000
53L54ARG10.8800.91421.3120.0030.0030.0000.0000.0000.000
54L55PRO0-0.0230.00021.8240.0060.0060.0000.0000.0000.000
55L56SER00.001-0.01524.278-0.004-0.0040.0000.0000.0000.000
56L57GLY00.0140.00727.9950.0000.0000.0000.0000.0000.000
57L58ILE0-0.0170.01024.211-0.005-0.0050.0000.0000.0000.000
58L59PRO00.0130.00927.5610.0020.0020.0000.0000.0000.000
59L60GLU-1-0.793-0.90228.743-0.001-0.0010.0000.0000.0000.000
60L61ARG10.7500.87629.8940.0310.0310.0000.0000.0000.000
61L62LEU0-0.0070.01423.015-0.006-0.0060.0000.0000.0000.000
62L63SER0-0.007-0.01024.6320.0050.0050.0000.0000.0000.000
63L64GLY00.0440.01720.466-0.008-0.0080.0000.0000.0000.000
64L65SER0-0.026-0.01719.5960.0030.0030.0000.0000.0000.000
65L66LYS10.8200.90013.436-0.083-0.0830.0000.0000.0000.000
66L67SER0-0.0100.00217.9870.0080.0080.0000.0000.0000.000
67L68GLY00.0500.02517.426-0.019-0.0190.0000.0000.0000.000
68L69LYS10.7910.86511.1440.2490.2490.0000.0000.0000.000
69L70THR00.0510.02813.237-0.054-0.0540.0000.0000.0000.000
70L71ALA00.0070.02214.1320.0310.0310.0000.0000.0000.000
71L72THR0-0.005-0.02815.830-0.034-0.0340.0000.0000.0000.000
72L73LEU0-0.0100.02918.8060.0190.0190.0000.0000.0000.000
73L74THR00.016-0.00520.392-0.015-0.0150.0000.0000.0000.000
74L75ILE00.0070.01123.5460.0100.0100.0000.0000.0000.000
75L76SER00.009-0.00426.838-0.003-0.0030.0000.0000.0000.000
76L77GLY00.027-0.00230.5360.0020.0020.0000.0000.0000.000
77L78THR0-0.055-0.02729.1720.0020.0020.0000.0000.0000.000
78L79GLN00.0250.00531.5850.0040.0040.0000.0000.0000.000
79L80SER00.0340.01231.682-0.001-0.0010.0000.0000.0000.000
80L81LEU0-0.010-0.00631.961-0.002-0.0020.0000.0000.0000.000
81L82ASP-1-0.722-0.81027.662-0.041-0.0410.0000.0000.0000.000
82L83GLU-1-0.863-0.91326.727-0.070-0.0700.0000.0000.0000.000
83L84GLY0-0.025-0.00725.1410.0080.0080.0000.0000.0000.000
84L85ASP-1-0.799-0.85119.915-0.120-0.1200.0000.0000.0000.000
85L86TYR0-0.035-0.04419.0460.0180.0180.0000.0000.0000.000
86L87TYR00.0100.00913.700-0.022-0.0220.0000.0000.0000.000
87L89GLN00.021-0.0078.877-0.067-0.0670.0000.0000.0000.000
88L90ALA00.0410.0236.9910.0280.0280.0000.0000.0000.000
89L91TRP00.0160.0075.856-0.117-0.1170.0000.0000.0000.000
90L92ASP-1-0.751-0.8451.716-14.496-20.30317.171-6.480-4.885-0.043
91L93ALA0-0.033-0.0214.271-0.353-0.239-0.001-0.022-0.0910.000
92L94SER0-0.0050.0093.9210.0130.093-0.001-0.016-0.0630.000
93L95THR0-0.009-0.0226.2440.0390.0390.0000.0000.0000.000
94L95GLY00.0330.0309.3530.0530.0530.0000.0000.0000.000
95L95VAL00.0240.00310.626-0.121-0.1210.0000.0000.0000.000
96L95SER00.0010.00513.138-0.056-0.0560.0000.0000.0000.000
97L95GLY0-0.0050.00514.240-0.044-0.0440.0000.0000.0000.000
98L95GLY0-0.006-0.01513.1520.0950.0950.0000.0000.0000.000
99L95GLY00.0190.01713.407-0.017-0.0170.0000.0000.0000.000
100L96THR0-0.014-0.0129.0220.1080.1080.0000.0000.0000.000
101L97LYS10.9190.9634.771-3.386-3.327-0.001-0.003-0.0550.000
102L98LEU0-0.003-0.0036.0510.4130.4130.0000.0000.0000.000
103L99THR0-0.022-0.0112.659-0.2791.1840.695-0.786-1.3720.004
104L100VAL00.0090.0194.732-0.0360.037-0.001-0.002-0.0690.000
105L101LEU0-0.0180.0031.731-0.053-2.2206.508-1.729-2.6120.002
106L102PHE00.016-0.0185.4470.2810.2810.0000.0000.0000.000
107L103GLY00.0750.0328.338-0.173-0.1730.0000.0000.0000.000
108L104ASP-1-0.943-0.97310.712-0.540-0.5400.0000.0000.0000.000
109L105GLY0-0.027-0.00713.3330.0460.0460.0000.0000.0000.000
110L106THR0-0.050-0.04216.033-0.011-0.0110.0000.0000.0000.000
111L106ARG10.7920.86919.3660.1250.1250.0000.0000.0000.000
112L107LEU0-0.029-0.00822.799-0.002-0.0020.0000.0000.0000.000
113L108THR0-0.030-0.02825.1530.0030.0030.0000.0000.0000.000
114L109VAL0-0.021-0.02628.8430.0000.0000.0000.0000.0000.000
115L110LEU00.004-0.00531.7940.0040.0040.0000.0000.0000.000
116L111GLY0-0.017-0.01335.0160.0030.0030.0000.0000.0000.000
117L112GLN0-0.081-0.04437.5480.0040.0040.0000.0000.0000.000
118L113PRO00.0250.00339.285-0.003-0.0030.0000.0000.0000.000
119L114LYS10.8690.93437.3890.0680.0680.0000.0000.0000.000
120L115ALA0-0.043-0.02740.1020.0030.0030.0000.0000.0000.000
121L116ALA00.0570.02940.379-0.003-0.0030.0000.0000.0000.000
122L117PRO0-0.034-0.00139.4030.0020.0020.0000.0000.0000.000
123L118SER00.0270.02041.7390.0010.0010.0000.0000.0000.000
124L119VAL0-0.001-0.00941.774-0.002-0.0020.0000.0000.0000.000
125L120THR0-0.023-0.00744.2330.0030.0030.0000.0000.0000.000
126L121LEU0-0.0300.00043.464-0.002-0.0020.0000.0000.0000.000
127L122PHE0-0.010-0.00645.6780.0020.0020.0000.0000.0000.000
128L123PRO00.000-0.00146.387-0.002-0.0020.0000.0000.0000.000
129L124PRO00.0210.01646.8680.0000.0000.0000.0000.0000.000
130L125SER0-0.033-0.02948.5750.0010.0010.0000.0000.0000.000
131L126SER00.007-0.02851.3510.0000.0000.0000.0000.0000.000
132L127GLU-1-0.819-0.88252.114-0.025-0.0250.0000.0000.0000.000
133L128GLU-1-0.764-0.86345.176-0.037-0.0370.0000.0000.0000.000
134L129LEU0-0.014-0.00949.8510.0000.0000.0000.0000.0000.000
135L130GLN0-0.055-0.02951.6420.0010.0010.0000.0000.0000.000
136L131ALA0-0.0340.00449.6450.0010.0010.0000.0000.0000.000
137L132ASN0-0.051-0.02749.2350.0000.0000.0000.0000.0000.000
138L133LYS10.8230.91441.6890.0390.0390.0000.0000.0000.000
139L134ALA00.000-0.00645.2740.0010.0010.0000.0000.0000.000
140L135THR0-0.034-0.05240.954-0.004-0.0040.0000.0000.0000.000
141L136LEU0-0.0200.01542.4430.0020.0020.0000.0000.0000.000
142L137VAL00.0190.00841.661-0.003-0.0030.0000.0000.0000.000
143L138CYS0-0.063-0.02340.056-0.002-0.0020.0000.0000.0000.000
144L139LEU00.0130.01140.173-0.003-0.0030.0000.0000.0000.000
145L140ILE0-0.001-0.00537.0520.0000.0000.0000.0000.0000.000
146L141SER00.014-0.01840.2460.0000.0000.0000.0000.0000.000
147L142ASP-1-0.803-0.88941.987-0.041-0.0410.0000.0000.0000.000
148L143PHE00.0290.03134.8370.0000.0000.0000.0000.0000.000
149L144TYR00.0160.00534.1420.0010.0010.0000.0000.0000.000
150L145PRO00.0840.02033.0120.0020.0020.0000.0000.0000.000
151L146GLY0-0.0080.00833.3710.0000.0000.0000.0000.0000.000
152L147ALA0-0.022-0.02030.088-0.004-0.0040.0000.0000.0000.000
153L148VAL0-0.0030.00031.7520.0030.0030.0000.0000.0000.000
154L149THR0-0.020-0.00130.119-0.004-0.0040.0000.0000.0000.000
155L150VAL00.0400.01132.8060.0060.0060.0000.0000.0000.000
156L151ALA0-0.043-0.02134.172-0.006-0.0060.0000.0000.0000.000
157L152TRP00.0540.02136.2860.0060.0060.0000.0000.0000.000
158L153LYS10.7980.86638.6670.0590.0590.0000.0000.0000.000
159L154ALA00.0560.03841.4760.0030.0030.0000.0000.0000.000
160L155ASP-1-0.738-0.87543.969-0.045-0.0450.0000.0000.0000.000
161L156SER0-0.094-0.05144.8230.0010.0010.0000.0000.0000.000
162L157SER0-0.057-0.00341.213-0.003-0.0030.0000.0000.0000.000
163L158PRO00.022-0.00736.8470.0010.0010.0000.0000.0000.000
164L159VAL0-0.0090.00437.0730.0000.0000.0000.0000.0000.000
165L160LYS10.9280.94531.7220.0990.0990.0000.0000.0000.000
166L161ALA00.0340.02433.281-0.002-0.0020.0000.0000.0000.000
167L162GLY00.0440.01934.4560.0030.0030.0000.0000.0000.000
168L163VAL0-0.062-0.01633.2830.0040.0040.0000.0000.0000.000
169L164GLU-1-0.838-0.89830.944-0.087-0.0870.0000.0000.0000.000
170L165THR0-0.111-0.07031.6510.0040.0040.0000.0000.0000.000
171L166THR0-0.0030.01831.062-0.004-0.0040.0000.0000.0000.000
172L167THR00.008-0.00627.923-0.003-0.0030.0000.0000.0000.000
173L168PRO0-0.021-0.00230.1140.0060.0060.0000.0000.0000.000
174L169SER0-0.024-0.00631.9940.0000.0000.0000.0000.0000.000
175L170LYS10.8850.95434.5710.0490.0490.0000.0000.0000.000
176L171GLN00.0340.00036.9180.0010.0010.0000.0000.0000.000
177L172SER00.024-0.00340.6930.0000.0000.0000.0000.0000.000
178L173ASN0-0.0030.00943.3410.0000.0000.0000.0000.0000.000
179L174ASN0-0.013-0.01939.962-0.001-0.0010.0000.0000.0000.000
180L175LYS10.8720.97438.9580.0410.0410.0000.0000.0000.000
181L176TYR0-0.001-0.00732.6790.0020.0020.0000.0000.0000.000
182L177ALA00.0140.01337.3660.0010.0010.0000.0000.0000.000
183L178ALA0-0.020-0.02335.123-0.003-0.0030.0000.0000.0000.000
184L179SER0-0.0050.00836.0820.0040.0040.0000.0000.0000.000
185L180SER00.0220.00035.236-0.004-0.0040.0000.0000.0000.000
186L181TYR00.0210.00736.3610.0050.0050.0000.0000.0000.000
187L182LEU00.0120.00837.143-0.005-0.0050.0000.0000.0000.000
188L183SER0-0.025-0.00838.0940.0050.0050.0000.0000.0000.000
189L184LEU0-0.039-0.01939.956-0.002-0.0020.0000.0000.0000.000
190L185THR00.002-0.02142.7460.0010.0010.0000.0000.0000.000
191L186PRO00.0490.01845.638-0.001-0.0010.0000.0000.0000.000
192L187GLU-1-0.843-0.90248.611-0.033-0.0330.0000.0000.0000.000
193L188GLN00.0040.01641.5910.0000.0000.0000.0000.0000.000
194L189TRP00.0400.02247.003-0.001-0.0010.0000.0000.0000.000
195L190LYS10.9490.96748.3220.0280.0280.0000.0000.0000.000
196L191SER0-0.061-0.04149.1260.0010.0010.0000.0000.0000.000
197L192HIS0-0.091-0.03545.646-0.003-0.0030.0000.0000.0000.000
198L193LYS10.8880.93149.9680.0420.0420.0000.0000.0000.000
199L194SER0-0.046-0.02649.2430.0010.0010.0000.0000.0000.000
200L195TYR00.0570.01942.936-0.001-0.0010.0000.0000.0000.000
201L196SER0-0.024-0.02843.8830.0030.0030.0000.0000.0000.000
202L198GLN00.0370.01639.7110.0020.0020.0000.0000.0000.000
203L199VAL00.0210.01137.199-0.005-0.0050.0000.0000.0000.000
204L200THR0-0.019-0.01435.0150.0020.0020.0000.0000.0000.000
205L201HIS0-0.006-0.02335.338-0.002-0.0020.0000.0000.0000.000
206L202GLU-1-0.847-0.91233.979-0.077-0.0770.0000.0000.0000.000
207L203GLY00.0000.00835.4370.0020.0020.0000.0000.0000.000
208L204SER0-0.0250.00136.6310.0030.0030.0000.0000.0000.000
209L205THR0-0.023-0.02038.691-0.003-0.0030.0000.0000.0000.000
210L206VAL0-0.0160.00040.8270.0030.0030.0000.0000.0000.000
211L207GLU-1-0.776-0.84842.115-0.061-0.0610.0000.0000.0000.000
212L208LYS10.8360.92044.2950.0460.0460.0000.0000.0000.000
213L209THR00.019-0.00745.570-0.002-0.0020.0000.0000.0000.000
214L210VAL0-0.019-0.00647.2680.0020.0020.0000.0000.0000.000
215L211ALA00.0560.01349.536-0.002-0.0020.0000.0000.0000.000
216L212PRO0-0.019-0.00151.2180.0010.0010.0000.0000.0000.000
217L213THR0-0.0040.01253.6110.0010.0010.0000.0000.0000.000