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: 49G1N

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 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 217
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2120271.770759
FMO2-HF: Nuclear repulsion 2038433.310073
FMO2-HF: Total energy -81838.460686
FMO2-MP2: Total energy -82077.795595


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.
-18.38-26.71831.783-11.853-11.591-0.033
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 : -0.064 / q_NPA : -0.064
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-1-0.833-0.9123.807-3.995-2.615-0.005-0.638-0.7370.001
4L4LEU0-0.055-0.0396.0220.6530.6530.0000.0000.0000.000
5L5THR00.0250.0078.2670.0900.0900.0000.0000.0000.000
6L6GLN00.026-0.01711.9180.0260.0260.0000.0000.0000.000
7L7PRO0-0.0210.01114.821-0.003-0.0030.0000.0000.0000.000
8L8PRO00.0920.06618.4840.0080.0080.0000.0000.0000.000
9L9SER0-0.056-0.02819.5260.0230.0230.0000.0000.0000.000
10L11VAL00.0340.02321.8670.0000.0000.0000.0000.0000.000
11L12SER0-0.0090.00124.5210.0070.0070.0000.0000.0000.000
12L13VAL00.003-0.00128.2640.0000.0000.0000.0000.0000.000
13L14SER00.0030.01430.3680.0030.0030.0000.0000.0000.000
14L15PRO00.035-0.00233.500-0.001-0.0010.0000.0000.0000.000
15L16GLY0-0.0180.00034.1710.0040.0040.0000.0000.0000.000
16L17GLN0-0.032-0.01432.8110.0050.0050.0000.0000.0000.000
17L18THR0-0.010-0.01927.745-0.001-0.0010.0000.0000.0000.000
18L19ALA0-0.0090.01725.851-0.001-0.0010.0000.0000.0000.000
19L20SER0-0.019-0.01022.592-0.002-0.0020.0000.0000.0000.000
20L21ILE00.0250.01317.628-0.005-0.0050.0000.0000.0000.000
21L22SER00.0210.01317.217-0.004-0.0040.0000.0000.0000.000
22L23CYS0-0.0010.00611.457-0.025-0.0250.0000.0000.0000.000
23L24SER0-0.0110.00712.2800.0880.0880.0000.0000.0000.000
24L25GLY00.0880.0378.350-0.183-0.1830.0000.0000.0000.000
25L26ASP-1-0.933-0.9687.052-0.438-0.4380.0000.0000.0000.000
26L27LYS10.8700.9314.032-0.772-0.623-0.001-0.011-0.1370.000
27L28LEU00.0110.0218.0950.0270.0270.0000.0000.0000.000
28L29ASP-1-0.921-0.95310.235-0.006-0.0060.0000.0000.0000.000
29L30ASP-1-0.884-0.94510.7640.2070.2070.0000.0000.0000.000
30L31LYS10.8140.9227.229-0.315-0.3150.0000.0000.0000.000
31L32TYR0-0.071-0.03810.599-0.052-0.0520.0000.0000.0000.000
32L33VAL00.0170.00810.685-0.019-0.0190.0000.0000.0000.000
33L34SER0-0.051-0.02412.1190.0530.0530.0000.0000.0000.000
34L35TRP00.006-0.00413.347-0.061-0.0610.0000.0000.0000.000
35L36TYR0-0.018-0.02312.9850.0480.0480.0000.0000.0000.000
36L37TYR0-0.007-0.00317.443-0.013-0.0130.0000.0000.0000.000
37L38GLN00.016-0.00119.550-0.011-0.0110.0000.0000.0000.000
38L39ARG10.9420.99121.6800.1060.1060.0000.0000.0000.000
39L40PRO00.036-0.00624.8560.0000.0000.0000.0000.0000.000
40L41GLY00.0030.00525.0720.0100.0100.0000.0000.0000.000
41L42GLN0-0.048-0.00925.3550.0110.0110.0000.0000.0000.000
42L43SER00.0160.00522.166-0.011-0.0110.0000.0000.0000.000
43L44PRO0-0.008-0.01117.6830.0050.0050.0000.0000.0000.000
44L45VAL0-0.0010.01120.1140.0160.0160.0000.0000.0000.000
45L46LEU0-0.0130.00017.104-0.015-0.0150.0000.0000.0000.000
46L47LEU0-0.020-0.01419.0520.0170.0170.0000.0000.0000.000
47L48MET0-0.033-0.01518.1650.0180.0180.0000.0000.0000.000
48L49TYR00.0420.02216.198-0.018-0.0180.0000.0000.0000.000
49L50GLN00.0270.00715.6670.0130.0130.0000.0000.0000.000
50L51ASP-1-0.796-0.89714.827-0.083-0.0830.0000.0000.0000.000
51L52PHE0-0.043-0.03816.882-0.010-0.0100.0000.0000.0000.000
52L53LYS10.8590.95119.9760.0560.0560.0000.0000.0000.000
53L54ARG10.9770.99020.9880.0680.0680.0000.0000.0000.000
54L55PRO0-0.0310.00521.4800.0100.0100.0000.0000.0000.000
55L56SER00.026-0.00924.1080.0010.0010.0000.0000.0000.000
56L57GLY0-0.007-0.00427.332-0.003-0.0030.0000.0000.0000.000
57L58ILE0-0.0220.01523.730-0.002-0.0020.0000.0000.0000.000
58L59PRO00.0080.00027.0850.0050.0050.0000.0000.0000.000
59L60GLU-1-0.898-0.97627.900-0.064-0.0640.0000.0000.0000.000
60L61ARG10.7670.89429.0340.0920.0920.0000.0000.0000.000
61L62LEU00.0040.01522.598-0.005-0.0050.0000.0000.0000.000
62L63SER0-0.005-0.01424.1360.0060.0060.0000.0000.0000.000
63L64GLY00.0410.02019.997-0.014-0.0140.0000.0000.0000.000
64L65SER0-0.020-0.01319.4720.0160.0160.0000.0000.0000.000
65L66LYS10.8540.92012.9090.0560.0560.0000.0000.0000.000
66L67SER0-0.0100.01217.7680.0240.0240.0000.0000.0000.000
67L68GLY00.0370.02217.359-0.018-0.0180.0000.0000.0000.000
68L69LYS10.9080.95711.7520.1270.1270.0000.0000.0000.000
69L70THR00.0200.00712.828-0.051-0.0510.0000.0000.0000.000
70L71ALA0-0.0040.00613.7340.0430.0430.0000.0000.0000.000
71L72THR0-0.044-0.04515.432-0.028-0.0280.0000.0000.0000.000
72L73LEU0-0.0330.00518.4580.0210.0210.0000.0000.0000.000
73L74THR00.001-0.02120.057-0.003-0.0030.0000.0000.0000.000
74L75ILE00.0040.01023.3510.0080.0080.0000.0000.0000.000
75L76SER00.0090.00126.3210.0040.0040.0000.0000.0000.000
76L77GLY00.016-0.01029.9130.0000.0000.0000.0000.0000.000
77L78THR0-0.064-0.02228.5210.0020.0020.0000.0000.0000.000
78L79GLN00.0420.01231.1060.0050.0050.0000.0000.0000.000
79L80SER00.0540.00531.293-0.006-0.0060.0000.0000.0000.000
80L81LEU0-0.034-0.01731.295-0.005-0.0050.0000.0000.0000.000
81L82ASP-1-0.725-0.82627.356-0.109-0.1090.0000.0000.0000.000
82L83GLU-1-0.875-0.90926.289-0.126-0.1260.0000.0000.0000.000
83L84GLY0-0.023-0.01024.6280.0070.0070.0000.0000.0000.000
84L85ASP-1-0.795-0.86219.247-0.221-0.2210.0000.0000.0000.000
85L86TYR0-0.040-0.05418.5440.0150.0150.0000.0000.0000.000
86L87TYR00.0120.03113.315-0.020-0.0200.0000.0000.0000.000
87L89GLN00.0230.0018.371-0.020-0.0200.0000.0000.0000.000
88L90ALA00.0340.0206.7300.1460.1460.0000.0000.0000.000
89L91TRP00.0240.0145.598-0.273-0.2730.0000.0000.0000.000
90L92ASP-1-0.795-0.8821.885-14.471-15.11312.369-6.175-5.552-0.037
91L93ALA0-0.014-0.0164.148-0.912-0.7700.000-0.049-0.0920.000
92L94SER0-0.0160.0004.2980.4380.464-0.001-0.001-0.0230.000
93L95THR00.0300.0146.7280.0530.0530.0000.0000.0000.000
94L95GLY00.0320.0319.6000.0920.0920.0000.0000.0000.000
95L95VAL00.0410.00910.410-0.119-0.1190.0000.0000.0000.000
96L95SER0-0.010-0.00512.953-0.053-0.0530.0000.0000.0000.000
97L95GLY0-0.0200.00214.104-0.050-0.0500.0000.0000.0000.000
98L95GLY0-0.004-0.01213.5340.0600.0600.0000.0000.0000.000
99L95GLY0-0.021-0.00213.797-0.009-0.0090.0000.0000.0000.000
100L96THR0-0.024-0.0189.0080.0590.0590.0000.0000.0000.000
101L97LYS10.9760.9935.270-2.357-2.3570.0000.0000.0000.000
102L98LEU0-0.009-0.0206.488-0.177-0.1770.0000.0000.0000.000
103L99THR0-0.016-0.0082.688-0.0131.1330.340-0.499-0.9870.002
104L100VAL0-0.0190.0034.782-0.106-0.036-0.001-0.002-0.0670.000
105L101LEU0-0.031-0.0031.6194.145-6.49619.083-4.474-3.9680.001
106L102PHE00.014-0.0145.0970.4610.493-0.001-0.004-0.0280.000
107L103GLY00.0380.0218.350-0.190-0.1900.0000.0000.0000.000
108L104ASP-1-0.924-0.97210.426-0.752-0.7520.0000.0000.0000.000
109L105GLY0-0.040-0.01412.9870.0750.0750.0000.0000.0000.000
110L106THR0-0.061-0.05215.673-0.001-0.0010.0000.0000.0000.000
111L106ARG10.8160.88018.8350.2010.2010.0000.0000.0000.000
112L107LEU0-0.051-0.03122.2950.0050.0050.0000.0000.0000.000
113L108THR0-0.040-0.02624.7740.0090.0090.0000.0000.0000.000
114L109VAL0-0.029-0.02928.3850.0000.0000.0000.0000.0000.000
115L110LEU0-0.002-0.01831.2540.0050.0050.0000.0000.0000.000
116L111GLY0-0.004-0.00334.3720.0040.0040.0000.0000.0000.000
117L112GLN0-0.091-0.04037.0380.0080.0080.0000.0000.0000.000
118L113PRO00.0230.00238.788-0.003-0.0030.0000.0000.0000.000
119L114LYS10.9741.00738.0050.0760.0760.0000.0000.0000.000
120L115ALA0-0.051-0.03039.6960.0040.0040.0000.0000.0000.000
121L116ALA00.0340.01240.266-0.004-0.0040.0000.0000.0000.000
122L117PRO0-0.0160.00739.3230.0020.0020.0000.0000.0000.000
123L118SER00.0300.02041.6920.0030.0030.0000.0000.0000.000
124L119VAL00.0160.00141.693-0.002-0.0020.0000.0000.0000.000
125L120THR0-0.0100.01044.2050.0030.0030.0000.0000.0000.000
126L121LEU0-0.028-0.00843.165-0.002-0.0020.0000.0000.0000.000
127L122PHE0-0.007-0.00745.2600.0020.0020.0000.0000.0000.000
128L123PRO0-0.006-0.00246.081-0.002-0.0020.0000.0000.0000.000
129L124PRO00.0420.01946.4640.0000.0000.0000.0000.0000.000
130L125SER00.0280.03448.3480.0010.0010.0000.0000.0000.000
131L126SER00.008-0.01250.9100.0010.0010.0000.0000.0000.000
132L127GLU-1-0.853-0.94751.957-0.027-0.0270.0000.0000.0000.000
133L128GLU-1-0.846-0.90044.738-0.038-0.0380.0000.0000.0000.000
134L129LEU0-0.010-0.01249.3620.0010.0010.0000.0000.0000.000
135L130GLN0-0.074-0.02751.0510.0010.0010.0000.0000.0000.000
136L131ALA0-0.0160.01049.2180.0010.0010.0000.0000.0000.000
137L132ASN0-0.053-0.03448.9930.0000.0000.0000.0000.0000.000
138L133LYS10.8780.93542.0390.0320.0320.0000.0000.0000.000
139L134ALA00.0280.00044.7440.0010.0010.0000.0000.0000.000
140L135THR0-0.017-0.02040.857-0.003-0.0030.0000.0000.0000.000
141L136LEU0-0.053-0.00442.1700.0010.0010.0000.0000.0000.000
142L137VAL00.0170.00141.225-0.003-0.0030.0000.0000.0000.000
143L138CYS0-0.066-0.01439.538-0.002-0.0020.0000.0000.0000.000
144L139LEU0-0.007-0.00339.914-0.004-0.0040.0000.0000.0000.000
145L140ILE00.0080.00236.8970.0020.0020.0000.0000.0000.000
146L141SER00.0200.00239.941-0.001-0.0010.0000.0000.0000.000
147L142ASP-1-0.836-0.91841.699-0.055-0.0550.0000.0000.0000.000
148L143PHE0-0.0090.01334.6480.0000.0000.0000.0000.0000.000
149L144TYR00.0220.01634.208-0.002-0.0020.0000.0000.0000.000
150L145PRO00.0690.01232.8860.0040.0040.0000.0000.0000.000
151L146GLY00.0270.01232.9530.0030.0030.0000.0000.0000.000
152L147ALA0-0.010-0.01129.856-0.007-0.0070.0000.0000.0000.000
153L148VAL0-0.0040.00231.5780.0060.0060.0000.0000.0000.000
154L149THR0-0.0250.00229.854-0.005-0.0050.0000.0000.0000.000
155L150VAL00.0300.00132.4580.0060.0060.0000.0000.0000.000
156L151ALA0-0.051-0.01433.762-0.004-0.0040.0000.0000.0000.000
157L152TRP00.0560.01435.9160.0060.0060.0000.0000.0000.000
158L153LYS10.8890.94038.3530.0560.0560.0000.0000.0000.000
159L154ALA00.0650.04741.1000.0010.0010.0000.0000.0000.000
160L155ASP-1-0.811-0.92343.416-0.037-0.0370.0000.0000.0000.000
161L156SER0-0.067-0.04944.660-0.001-0.0010.0000.0000.0000.000
162L157SER0-0.071-0.01540.911-0.002-0.0020.0000.0000.0000.000
163L158PRO00.019-0.00336.3870.0000.0000.0000.0000.0000.000
164L159VAL00.0210.02537.0580.0020.0020.0000.0000.0000.000
165L160LYS10.9530.95730.4530.0980.0980.0000.0000.0000.000
166L161ALA00.0070.00732.876-0.003-0.0030.0000.0000.0000.000
167L162GLY00.0500.01833.7500.0020.0020.0000.0000.0000.000
168L163VAL0-0.033-0.00932.9500.0020.0020.0000.0000.0000.000
169L164GLU-1-0.885-0.93029.964-0.095-0.0950.0000.0000.0000.000
170L165THR0-0.045-0.02731.3200.0070.0070.0000.0000.0000.000
171L166THR0-0.0140.00630.778-0.007-0.0070.0000.0000.0000.000
172L167THR0-0.012-0.01027.886-0.007-0.0070.0000.0000.0000.000
173L168PRO0-0.033-0.01430.2690.0060.0060.0000.0000.0000.000
174L169SER00.0220.01532.153-0.003-0.0030.0000.0000.0000.000
175L170LYS10.8910.95534.6190.0830.0830.0000.0000.0000.000
176L171GLN0-0.018-0.01936.8080.0020.0020.0000.0000.0000.000
177L172SER00.039-0.00440.545-0.001-0.0010.0000.0000.0000.000
178L173ASN00.0000.01442.903-0.002-0.0020.0000.0000.0000.000
179L174ASN0-0.008-0.02139.813-0.001-0.0010.0000.0000.0000.000
180L175LYS10.9130.99238.8330.0540.0540.0000.0000.0000.000
181L176TYR0-0.008-0.01232.4610.0000.0000.0000.0000.0000.000
182L177ALA00.0230.00637.1390.0040.0040.0000.0000.0000.000
183L178ALA0-0.011-0.01135.016-0.006-0.0060.0000.0000.0000.000
184L179SER00.0140.02435.8020.0030.0030.0000.0000.0000.000
185L180SER00.0100.00034.909-0.004-0.0040.0000.0000.0000.000
186L181TYR00.0090.00036.0290.0040.0040.0000.0000.0000.000
187L182LEU00.0180.02536.592-0.004-0.0040.0000.0000.0000.000
188L183SER0-0.026-0.01138.0740.0040.0040.0000.0000.0000.000
189L184LEU0-0.039-0.02339.727-0.001-0.0010.0000.0000.0000.000
190L185THR00.0080.00642.4850.0010.0010.0000.0000.0000.000
191L186PRO00.0690.02345.183-0.001-0.0010.0000.0000.0000.000
192L187GLU-1-0.904-0.95648.134-0.026-0.0260.0000.0000.0000.000
193L188GLN0-0.0110.00741.3340.0000.0000.0000.0000.0000.000
194L189TRP00.0400.02346.816-0.001-0.0010.0000.0000.0000.000
195L190LYS10.9580.97148.0800.0230.0230.0000.0000.0000.000
196L191SER0-0.066-0.04249.2830.0010.0010.0000.0000.0000.000
197L192HIS0-0.071-0.01445.316-0.001-0.0010.0000.0000.0000.000
198L193LYS10.9260.95449.3910.0310.0310.0000.0000.0000.000
199L194SER0-0.047-0.02248.6280.0000.0000.0000.0000.0000.000
200L195TYR00.0850.04042.3590.0000.0000.0000.0000.0000.000
201L196SER00.0020.01543.4790.0020.0020.0000.0000.0000.000
202L198GLN00.019-0.00339.3540.0010.0010.0000.0000.0000.000
203L199VAL00.009-0.00336.820-0.005-0.0050.0000.0000.0000.000
204L200THR00.0000.00534.8500.0050.0050.0000.0000.0000.000
205L201HIS0-0.031-0.03135.095-0.004-0.0040.0000.0000.0000.000
206L202GLU-1-0.908-0.96233.392-0.101-0.1010.0000.0000.0000.000
207L203GLY0-0.023-0.01334.9700.0040.0040.0000.0000.0000.000
208L204SER0-0.040-0.01036.3160.0050.0050.0000.0000.0000.000
209L205THR0-0.027-0.02038.615-0.001-0.0010.0000.0000.0000.000
210L206VAL0-0.0030.01340.7370.0040.0040.0000.0000.0000.000
211L207GLU-1-0.914-0.96941.960-0.057-0.0570.0000.0000.0000.000
212L208LYS10.8330.90543.9950.0510.0510.0000.0000.0000.000
213L209THR00.030-0.00345.246-0.002-0.0020.0000.0000.0000.000
214L210VAL0-0.036-0.01146.8060.0020.0020.0000.0000.0000.000
215L211ALA00.0470.00149.127-0.001-0.0010.0000.0000.0000.000
216L212PRO0-0.0220.00250.9240.0000.0000.0000.0000.0000.000
217L213THR0-0.0020.01053.2120.0010.0010.0000.0000.0000.000