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: 3952L

Calculation Name: 4ALN-L-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 4ALN

Chain ID: L

ChEMBL ID:

UniProt ID: A0A0H3

Base Structure: X-ray

Registration Date: 2023-09-20

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 193
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2091401.095347
FMO2-HF: Nuclear repulsion 2018082.532666
FMO2-HF: Total energy -73318.562682
FMO2-MP2: Total energy -73535.392222


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:3:ASN)


Summations of interaction energy for fragment #1(L:3:ASN)
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.
-24.84-23.49415.509-8.656-8.198-0.051
Interaction energy analysis for fragmet #1(L:3:ASN)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.055 / q_NPA : -0.028
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].
3L5GLU-1-0.794-0.8871.842-20.170-20.41413.884-7.709-5.930-0.049
4L6ASN0-0.126-0.0704.9050.9701.029-0.001-0.005-0.0530.000
5L7LYS10.8550.9376.0021.6841.6840.0000.0000.0000.000
6L8THR00.0240.0158.678-0.151-0.1510.0000.0000.0000.000
7L9TYR0-0.0160.0046.7570.0780.0780.0000.0000.0000.000
8L10VAL00.0350.03012.386-0.029-0.0290.0000.0000.0000.000
9L11ILE0-0.046-0.02012.3680.0840.0840.0000.0000.0000.000
10L12MET00.0070.00816.4080.0120.0120.0000.0000.0000.000
11L13GLY00.0640.02819.7810.0220.0220.0000.0000.0000.000
12L14ILE0-0.100-0.04317.3880.0200.0200.0000.0000.0000.000
13L15ALA0-0.040-0.01621.6860.0170.0170.0000.0000.0000.000
14L16ASN00.007-0.01824.302-0.003-0.0030.0000.0000.0000.000
15L17LYS10.8890.92721.8950.2930.2930.0000.0000.0000.000
16L18ARG10.9250.96321.3850.1600.1600.0000.0000.0000.000
17L19SER00.0490.05421.3200.0210.0210.0000.0000.0000.000
18L20ILE00.0890.02717.950-0.041-0.0410.0000.0000.0000.000
19L21ALA00.0590.03617.032-0.036-0.0360.0000.0000.0000.000
20L22PHE00.0290.00516.115-0.063-0.0630.0000.0000.0000.000
21L23GLY0-0.047-0.02515.571-0.084-0.0840.0000.0000.0000.000
22L24VAL00.0100.00011.837-0.099-0.0990.0000.0000.0000.000
23L25ALA00.0230.01411.440-0.147-0.1470.0000.0000.0000.000
24L26LYS10.9120.97111.4850.3520.3520.0000.0000.0000.000
25L27VAL00.0060.0097.814-0.173-0.1730.0000.0000.0000.000
26L28LEU00.0440.0186.866-0.440-0.4400.0000.0000.0000.000
27L29ASP-1-0.772-0.8687.259-2.125-2.1250.0000.0000.0000.000
28L30GLN0-0.079-0.0428.055-0.349-0.3490.0000.0000.0000.000
29L31LEU0-0.057-0.0252.341-1.602-0.7671.617-0.611-1.8420.000
30L32GLY0-0.0010.0013.556-3.278-2.7910.011-0.311-0.187-0.002
31L33ALA0-0.0020.0165.8990.1090.1090.0000.0000.0000.000
32L34LYS10.8640.9307.6721.5271.5270.0000.0000.0000.000
33L35LEU0-0.043-0.03610.2690.1580.1580.0000.0000.0000.000
34L36VAL00.0320.02513.6650.0820.0820.0000.0000.0000.000
35L37PHE00.001-0.00815.1370.0220.0220.0000.0000.0000.000
36L38THR00.0580.02219.2670.0280.0280.0000.0000.0000.000
37L39TYR0-0.094-0.06422.4130.0030.0030.0000.0000.0000.000
38L40ARG10.8920.93425.2750.1590.1590.0000.0000.0000.000
39L41LYS10.9600.96728.6140.1530.1530.0000.0000.0000.000
40L42GLU-1-0.710-0.84230.138-0.256-0.2560.0000.0000.0000.000
41L43ARG10.8770.92531.5690.1490.1490.0000.0000.0000.000
42L44SER0-0.023-0.01827.2600.0020.0020.0000.0000.0000.000
43L45ARG10.9100.98526.3200.3300.3300.0000.0000.0000.000
44L46LYS10.9720.97626.4850.2240.2240.0000.0000.0000.000
45L47GLU-1-0.819-0.89925.158-0.329-0.3290.0000.0000.0000.000
46L48LEU00.0410.01420.711-0.019-0.0190.0000.0000.0000.000
47L49GLU-1-0.814-0.89522.109-0.403-0.4030.0000.0000.0000.000
48L50LYS10.7650.87423.2670.3470.3470.0000.0000.0000.000
49L51LEU0-0.068-0.03119.985-0.010-0.0100.0000.0000.0000.000
50L52LEU0-0.017-0.02017.938-0.045-0.0450.0000.0000.0000.000
51L53GLU-1-0.810-0.87918.929-0.447-0.4470.0000.0000.0000.000
52L54GLN0-0.112-0.06318.422-0.023-0.0230.0000.0000.0000.000
53L55LEU0-0.069-0.01413.673-0.025-0.0250.0000.0000.0000.000
54L56ASN0-0.051-0.01711.9710.2110.2110.0000.0000.0000.000
55L57GLN0-0.002-0.02811.126-0.070-0.0700.0000.0000.0000.000
56L58PRO0-0.042-0.00512.8620.1260.1260.0000.0000.0000.000
57L59GLU-1-0.823-0.90215.877-0.778-0.7780.0000.0000.0000.000
58L60ALA0-0.017-0.01717.780-0.053-0.0530.0000.0000.0000.000
59L61HIS0-0.015-0.01017.3330.1130.1130.0000.0000.0000.000
60L62LEU0-0.078-0.04620.404-0.003-0.0030.0000.0000.0000.000
61L63TYR00.019-0.03221.2950.0120.0120.0000.0000.0000.000
62L64GLN0-0.107-0.05124.7560.0070.0070.0000.0000.0000.000
63L65ILE00.0530.02523.8040.0070.0070.0000.0000.0000.000
64L66ASP-1-0.849-0.92027.167-0.143-0.1430.0000.0000.0000.000
65L67VAL0-0.009-0.02225.1380.0100.0100.0000.0000.0000.000
66L68GLN0-0.093-0.02428.3940.0190.0190.0000.0000.0000.000
67L69SER0-0.082-0.07331.4900.0120.0120.0000.0000.0000.000
68L70ASP-1-0.840-0.93131.536-0.089-0.0890.0000.0000.0000.000
69L71GLU-1-0.972-0.98931.240-0.134-0.1340.0000.0000.0000.000
70L72GLU-1-0.789-0.86429.949-0.175-0.1750.0000.0000.0000.000
71L73VAL0-0.021-0.01025.628-0.024-0.0240.0000.0000.0000.000
72L74ILE00.0250.02326.670-0.016-0.0160.0000.0000.0000.000
73L75ASN0-0.029-0.01627.795-0.010-0.0100.0000.0000.0000.000
74L76GLY00.017-0.00326.252-0.018-0.0180.0000.0000.0000.000
75L77PHE00.017-0.01419.486-0.037-0.0370.0000.0000.0000.000
76L78GLU-1-0.796-0.86223.605-0.228-0.2280.0000.0000.0000.000
77L79GLN0-0.085-0.03925.7240.0090.0090.0000.0000.0000.000
78L80ILE00.0090.02619.421-0.029-0.0290.0000.0000.0000.000
79L81GLY00.0390.00921.651-0.039-0.0390.0000.0000.0000.000
80L82LYS10.7230.84222.7050.2080.2080.0000.0000.0000.000
81L83ASP-1-0.861-0.91222.923-0.382-0.3820.0000.0000.0000.000
82L84VAL0-0.116-0.05616.875-0.055-0.0550.0000.0000.0000.000
83L85GLY0-0.0010.00818.284-0.059-0.0590.0000.0000.0000.000
84L86ASN0-0.039-0.03417.4430.0160.0160.0000.0000.0000.000
85L87ILE0-0.039-0.02214.691-0.111-0.1110.0000.0000.0000.000
86L88ASP-1-0.760-0.86610.416-0.937-0.9370.0000.0000.0000.000
87L89GLY00.025-0.02812.3410.1940.1940.0000.0000.0000.000
88L90VAL0-0.033-0.01113.208-0.113-0.1130.0000.0000.0000.000
89L91TYR00.004-0.01713.6620.0620.0620.0000.0000.0000.000
90L92HIS00.024-0.01315.638-0.060-0.0600.0000.0000.0000.000
91L93SER0-0.050-0.01719.0900.0400.0400.0000.0000.0000.000
92L94ILE00.009-0.00120.817-0.009-0.0090.0000.0000.0000.000
93L108GLU-1-0.860-0.95237.722-0.021-0.0210.0000.0000.0000.000
94L109THR0-0.018-0.02041.5730.0040.0040.0000.0000.0000.000
95L110SER0-0.044-0.02743.7930.0020.0020.0000.0000.0000.000
96L111ARG11.0030.99843.0950.0120.0120.0000.0000.0000.000
97L112GLU-1-0.825-0.90241.843-0.028-0.0280.0000.0000.0000.000
98L113GLY00.0330.02339.757-0.003-0.0030.0000.0000.0000.000
99L114PHE0-0.002-0.00838.145-0.002-0.0020.0000.0000.0000.000
100L115LEU00.006-0.01237.0650.0010.0010.0000.0000.0000.000
101L116LEU00.0190.02835.678-0.002-0.0020.0000.0000.0000.000
102L117ALA00.0000.00033.764-0.006-0.0060.0000.0000.0000.000
103L118GLN0-0.0020.00232.2660.0010.0010.0000.0000.0000.000
104L119ASP-1-0.872-0.93531.720-0.065-0.0650.0000.0000.0000.000
105L120ILE00.0190.00229.213-0.006-0.0060.0000.0000.0000.000
106L121SER0-0.112-0.03728.032-0.009-0.0090.0000.0000.0000.000
107L122SER0-0.014-0.01627.0010.0050.0050.0000.0000.0000.000
108L123TYR00.0110.00927.5910.0060.0060.0000.0000.0000.000
109L124SER00.024-0.01726.524-0.002-0.0020.0000.0000.0000.000
110L125LEU00.0170.02520.951-0.014-0.0140.0000.0000.0000.000
111L126THR00.0130.01224.438-0.005-0.0050.0000.0000.0000.000
112L127ILE0-0.0060.01626.432-0.001-0.0010.0000.0000.0000.000
113L128VAL00.022-0.00421.170-0.012-0.0120.0000.0000.0000.000
114L129ALA0-0.020-0.01221.669-0.017-0.0170.0000.0000.0000.000
115L130HIS0-0.066-0.03222.7390.0010.0010.0000.0000.0000.000
116L131GLU-1-0.801-0.89824.985-0.123-0.1230.0000.0000.0000.000
117L132ALA00.0370.01819.231-0.020-0.0200.0000.0000.0000.000
118L133LYS10.8430.92520.561-0.039-0.0390.0000.0000.0000.000
119L134LYS10.7530.86921.8950.1280.1280.0000.0000.0000.000
120L135LEU0-0.070-0.02119.199-0.011-0.0110.0000.0000.0000.000
121L136MET0-0.0400.00415.612-0.037-0.0370.0000.0000.0000.000
122L137PRO00.0060.00818.5180.0580.0580.0000.0000.0000.000
123L138GLU-1-0.966-0.98616.949-0.134-0.1340.0000.0000.0000.000
124L139GLY00.0150.02016.6370.0740.0740.0000.0000.0000.000
125L140GLY00.015-0.00613.302-0.096-0.0960.0000.0000.0000.000
126L141SER0-0.123-0.05611.8160.0830.0830.0000.0000.0000.000
127L142ILE00.0330.01113.840-0.131-0.1310.0000.0000.0000.000
128L143VAL00.0120.00312.9560.0740.0740.0000.0000.0000.000
129L144ALA00.0260.03316.211-0.074-0.0740.0000.0000.0000.000
130L145THR0-0.048-0.01317.5570.0300.0300.0000.0000.0000.000
131L146THR0-0.0100.00419.792-0.029-0.0290.0000.0000.0000.000
132L159VAL0-0.015-0.00936.7600.0030.0030.0000.0000.0000.000
133L160MET00.0560.01532.5490.0040.0040.0000.0000.0000.000
134L161GLY00.0110.01132.4190.0030.0030.0000.0000.0000.000
135L162VAL0-0.006-0.00632.5340.0070.0070.0000.0000.0000.000
136L163ALA00.0110.00431.8880.0050.0050.0000.0000.0000.000
137L164LYS10.9050.94826.4350.0240.0240.0000.0000.0000.000
138L165ALA00.0240.02228.5340.0100.0100.0000.0000.0000.000
139L166SER0-0.003-0.00929.9280.0110.0110.0000.0000.0000.000
140L167LEU00.0290.02623.8180.0070.0070.0000.0000.0000.000
141L168GLU-1-0.880-0.94725.0410.1470.1470.0000.0000.0000.000
142L169ALA0-0.060-0.03125.9150.0210.0210.0000.0000.0000.000
143L170ASN00.000-0.01526.4900.0170.0170.0000.0000.0000.000
144L171VAL0-0.006-0.00121.1580.0050.0050.0000.0000.0000.000
145L172LYS10.9240.98423.436-0.157-0.1570.0000.0000.0000.000
146L173TYR0-0.009-0.02025.2850.0130.0130.0000.0000.0000.000
147L174LEU00.0420.03323.393-0.004-0.0040.0000.0000.0000.000
148L175ALA0-0.025-0.00721.3750.0030.0030.0000.0000.0000.000
149L176LEU0-0.117-0.05422.3270.0210.0210.0000.0000.0000.000
150L177ASP-1-0.964-1.00325.4790.0690.0690.0000.0000.0000.000
151L178LEU00.0120.00421.793-0.012-0.0120.0000.0000.0000.000
152L179GLY00.0290.03521.3650.0090.0090.0000.0000.0000.000
153L180PRO0-0.061-0.04321.7590.0260.0260.0000.0000.0000.000
154L181ASP-1-0.858-0.91622.3410.0490.0490.0000.0000.0000.000
155L182ASN0-0.066-0.03615.9770.0400.0400.0000.0000.0000.000
156L183ILE00.0160.01117.189-0.006-0.0060.0000.0000.0000.000
157L184ARG10.8000.92310.722-0.831-0.8310.0000.0000.0000.000
158L185VAL00.0200.01616.542-0.055-0.0550.0000.0000.0000.000
159L186ASN00.0200.01515.1720.0570.0570.0000.0000.0000.000
160L187ALA0-0.035-0.02818.018-0.066-0.0660.0000.0000.0000.000
161L188ILE0-0.0060.01114.1280.0440.0440.0000.0000.0000.000
162L189SER00.0110.00318.664-0.056-0.0560.0000.0000.0000.000
163L222ASP-1-0.787-0.91017.720-0.217-0.2170.0000.0000.0000.000
164L223GLN0-0.092-0.07217.7210.0170.0170.0000.0000.0000.000
165L224VAL00.0020.00612.597-0.020-0.0200.0000.0000.0000.000
166L225GLU-1-0.850-0.90613.170-0.001-0.0010.0000.0000.0000.000
167L226VAL00.0160.01013.6380.0700.0700.0000.0000.0000.000
168L227GLY00.0690.02812.3360.0540.0540.0000.0000.0000.000
169L228LYS10.8400.9229.3740.1170.1170.0000.0000.0000.000
170L229THR00.0050.0089.4130.2450.2450.0000.0000.0000.000
171L230ALA00.006-0.02010.9730.1610.1610.0000.0000.0000.000
172L231ALA00.0080.0075.9090.0010.0010.0000.0000.0000.000
173L232TYR0-0.023-0.0167.0190.2100.2100.0000.0000.0000.000
174L233LEU0-0.0050.0008.3740.2810.2810.0000.0000.0000.000
175L234LEU0-0.026-0.0028.5320.0390.0390.0000.0000.0000.000
176L235SER0-0.0240.0024.6800.4310.437-0.001-0.0070.0020.000
177L236ASP-1-0.874-0.9586.4072.1292.1290.0000.0000.0000.000
178L237LEU0-0.011-0.0144.451-0.611-0.408-0.001-0.013-0.1880.000
179L238SER0-0.064-0.0247.565-0.550-0.5500.0000.0000.0000.000
180L239SER00.0430.02110.698-0.427-0.4270.0000.0000.0000.000
181L240GLY0-0.037-0.01012.511-0.184-0.1840.0000.0000.0000.000
182L241VAL0-0.076-0.02814.634-0.110-0.1100.0000.0000.0000.000
183L242THR00.0660.02116.025-0.024-0.0240.0000.0000.0000.000
184L243GLY00.010-0.01018.624-0.012-0.0120.0000.0000.0000.000
185L244GLU-1-0.938-0.96318.1610.3670.3670.0000.0000.0000.000
186L245ASN0-0.080-0.04719.279-0.034-0.0340.0000.0000.0000.000
187L246ILE00.0200.01515.0940.0230.0230.0000.0000.0000.000
188L247HIS00.0230.00519.141-0.031-0.0310.0000.0000.0000.000
189L248VAL0-0.033-0.00816.3580.0290.0290.0000.0000.0000.000
190L249ASP-1-0.817-0.89719.3840.0920.0920.0000.0000.0000.000
191L250SER0-0.059-0.03521.149-0.015-0.0150.0000.0000.0000.000
192L251GLY0-0.0050.00822.3560.0030.0030.0000.0000.0000.000
193L252PHE0-0.118-0.07423.866-0.006-0.0060.0000.0000.0000.000