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: LZ259

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 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 193
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2093162.266836
FMO2-HF: Nuclear repulsion 2019842.644971
FMO2-HF: Total energy -73319.621865
FMO2-MP2: Total energy -73536.242421


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.
-30.931-28.85714.613-8.635-8.053-0.065
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 : -0.082 / q_NPA : -0.045
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-1-0.808-0.8971.854-26.226-26.19513.644-7.736-5.939-0.064
4L6ASN0-0.108-0.0595.1261.1191.182-0.001-0.004-0.0590.000
5L7LYS10.8580.9406.2032.6482.6480.0000.0000.0000.000
6L8THR00.0020.0028.970-0.033-0.0330.0000.0000.0000.000
7L9TYR0-0.028-0.0187.1250.0040.0040.0000.0000.0000.000
8L10VAL00.0260.01712.684-0.021-0.0210.0000.0000.0000.000
9L11ILE0-0.045-0.02112.8960.1180.1180.0000.0000.0000.000
10L12MET00.0160.01416.896-0.016-0.0160.0000.0000.0000.000
11L13GLY00.0830.03720.0990.0520.0520.0000.0000.0000.000
12L14ILE0-0.117-0.05317.3810.0320.0320.0000.0000.0000.000
13L15ALA0-0.023-0.01121.839-0.012-0.0120.0000.0000.0000.000
14L16ASN0-0.020-0.02824.0650.0060.0060.0000.0000.0000.000
15L17LYS10.8900.92622.1660.1570.1570.0000.0000.0000.000
16L18ARG10.9250.97021.774-0.055-0.0550.0000.0000.0000.000
17L19SER00.0430.03621.3350.0350.0350.0000.0000.0000.000
18L20ILE00.0640.01718.010-0.027-0.0270.0000.0000.0000.000
19L21ALA00.0730.03917.0320.0210.0210.0000.0000.0000.000
20L22PHE00.0290.00416.116-0.039-0.0390.0000.0000.0000.000
21L23GLY0-0.058-0.02815.506-0.063-0.0630.0000.0000.0000.000
22L24VAL00.0280.01411.7900.0100.0100.0000.0000.0000.000
23L25ALA00.0090.00511.259-0.085-0.0850.0000.0000.0000.000
24L26LYS10.9000.96711.516-0.102-0.1020.0000.0000.0000.000
25L27VAL0-0.0020.0047.658-0.179-0.1790.0000.0000.0000.000
26L28LEU00.0340.0126.925-0.103-0.1030.0000.0000.0000.000
27L29ASP-1-0.783-0.8587.062-2.154-2.1540.0000.0000.0000.000
28L30GLN0-0.080-0.0498.066-0.338-0.3380.0000.0000.0000.000
29L31LEU0-0.042-0.0162.318-0.5320.4000.944-0.404-1.4720.000
30L32GLY00.0250.0113.676-4.154-3.7450.006-0.286-0.129-0.002
31L33ALA00.0080.0215.8780.1690.1690.0000.0000.0000.000
32L34LYS10.8690.9397.9361.7291.7290.0000.0000.0000.000
33L35LEU0-0.047-0.03210.4450.1490.1490.0000.0000.0000.000
34L36VAL00.0390.02413.8900.0470.0470.0000.0000.0000.000
35L37PHE0-0.006-0.01015.1220.0860.0860.0000.0000.0000.000
36L38THR00.0490.02319.6680.0140.0140.0000.0000.0000.000
37L39TYR0-0.090-0.06222.8460.0300.0300.0000.0000.0000.000
38L40ARG10.9350.95125.8030.0390.0390.0000.0000.0000.000
39L41LYS10.9410.95229.1500.0770.0770.0000.0000.0000.000
40L42GLU-1-0.710-0.81030.577-0.202-0.2020.0000.0000.0000.000
41L43ARG10.8900.93431.3230.0690.0690.0000.0000.0000.000
42L44SER0-0.044-0.03727.461-0.004-0.0040.0000.0000.0000.000
43L45ARG10.8790.95526.2700.3090.3090.0000.0000.0000.000
44L46LYS10.9730.98126.3210.1800.1800.0000.0000.0000.000
45L47GLU-1-0.798-0.87925.205-0.167-0.1670.0000.0000.0000.000
46L48LEU00.0320.00920.395-0.009-0.0090.0000.0000.0000.000
47L49GLU-1-0.811-0.89622.059-0.352-0.3520.0000.0000.0000.000
48L50LYS10.7440.84423.0920.2780.2780.0000.0000.0000.000
49L51LEU0-0.059-0.02619.9330.0220.0220.0000.0000.0000.000
50L52LEU00.0470.01117.787-0.027-0.0270.0000.0000.0000.000
51L53GLU-1-0.814-0.87418.712-0.408-0.4080.0000.0000.0000.000
52L54GLN0-0.144-0.06518.7660.0310.0310.0000.0000.0000.000
53L55LEU0-0.070-0.02113.5020.0310.0310.0000.0000.0000.000
54L56ASN0-0.060-0.04311.7380.1110.1110.0000.0000.0000.000
55L57GLN0-0.032-0.04311.233-0.084-0.0840.0000.0000.0000.000
56L58PRO0-0.0200.00013.1250.1400.1400.0000.0000.0000.000
57L59GLU-1-0.805-0.88316.227-0.931-0.9310.0000.0000.0000.000
58L60ALA0-0.017-0.01318.292-0.032-0.0320.0000.0000.0000.000
59L61HIS0-0.010-0.01017.5830.1330.1330.0000.0000.0000.000
60L62LEU0-0.061-0.02420.4300.0250.0250.0000.0000.0000.000
61L63TYR0-0.005-0.04221.8080.0110.0110.0000.0000.0000.000
62L64GLN0-0.087-0.05525.3480.0260.0260.0000.0000.0000.000
63L65ILE00.0500.01724.268-0.006-0.0060.0000.0000.0000.000
64L66ASP-1-0.868-0.92027.544-0.032-0.0320.0000.0000.0000.000
65L67VAL00.008-0.01325.4000.0000.0000.0000.0000.0000.000
66L68GLN0-0.111-0.03828.5870.0160.0160.0000.0000.0000.000
67L69SER0-0.046-0.03831.4910.0060.0060.0000.0000.0000.000
68L70ASP-1-0.807-0.91131.512-0.041-0.0410.0000.0000.0000.000
69L71GLU-1-0.961-0.97331.342-0.112-0.1120.0000.0000.0000.000
70L72GLU-1-0.812-0.88530.196-0.119-0.1190.0000.0000.0000.000
71L73VAL0-0.022-0.01325.702-0.024-0.0240.0000.0000.0000.000
72L74ILE00.0100.01326.794-0.023-0.0230.0000.0000.0000.000
73L75ASN0-0.031-0.02528.034-0.013-0.0130.0000.0000.0000.000
74L76GLY00.0200.01126.444-0.025-0.0250.0000.0000.0000.000
75L77PHE00.002-0.01219.631-0.037-0.0370.0000.0000.0000.000
76L78GLU-1-0.817-0.88223.955-0.289-0.2890.0000.0000.0000.000
77L79GLN0-0.069-0.05226.2400.0000.0000.0000.0000.0000.000
78L80ILE0-0.0080.00619.708-0.037-0.0370.0000.0000.0000.000
79L81GLY00.0510.01821.721-0.062-0.0620.0000.0000.0000.000
80L82LYS10.7040.83623.2600.2460.2460.0000.0000.0000.000
81L83ASP-1-0.842-0.89223.222-0.433-0.4330.0000.0000.0000.000
82L84VAL0-0.108-0.05517.134-0.071-0.0710.0000.0000.0000.000
83L85GLY00.0020.02118.537-0.094-0.0940.0000.0000.0000.000
84L86ASN0-0.032-0.02717.4530.0640.0640.0000.0000.0000.000
85L87ILE0-0.044-0.02614.663-0.123-0.1230.0000.0000.0000.000
86L88ASP-1-0.762-0.86010.206-1.409-1.4090.0000.0000.0000.000
87L89GLY00.033-0.02412.2660.2500.2500.0000.0000.0000.000
88L90VAL0-0.026-0.00513.428-0.125-0.1250.0000.0000.0000.000
89L91TYR00.006-0.00913.9640.0950.0950.0000.0000.0000.000
90L92HIS00.0440.00615.910-0.090-0.0900.0000.0000.0000.000
91L93SER0-0.039-0.01319.3060.0480.0480.0000.0000.0000.000
92L94ILE0-0.012-0.00821.092-0.027-0.0270.0000.0000.0000.000
93L108GLU-1-0.804-0.91137.8320.0970.0970.0000.0000.0000.000
94L109THR0-0.027-0.03441.1930.0050.0050.0000.0000.0000.000
95L110SER0-0.027-0.02143.934-0.001-0.0010.0000.0000.0000.000
96L111ARG10.9840.99042.917-0.042-0.0420.0000.0000.0000.000
97L112GLU-1-0.805-0.88841.9010.0410.0410.0000.0000.0000.000
98L113GLY00.0200.01439.822-0.001-0.0010.0000.0000.0000.000
99L114PHE00.004-0.00938.1920.0050.0050.0000.0000.0000.000
100L115LEU0-0.005-0.01637.1850.0060.0060.0000.0000.0000.000
101L116LEU00.0260.02935.6390.0010.0010.0000.0000.0000.000
102L117ALA0-0.0020.00033.8180.0000.0000.0000.0000.0000.000
103L118GLN0-0.009-0.00832.3990.0130.0130.0000.0000.0000.000
104L119ASP-1-0.859-0.93631.8620.0280.0280.0000.0000.0000.000
105L120ILE00.0320.01429.6410.0020.0020.0000.0000.0000.000
106L121SER0-0.115-0.04528.0740.0050.0050.0000.0000.0000.000
107L122SER0-0.016-0.00927.1830.0250.0250.0000.0000.0000.000
108L123TYR0-0.021-0.01527.7680.0110.0110.0000.0000.0000.000
109L124SER00.021-0.01726.795-0.004-0.0040.0000.0000.0000.000
110L125LEU0-0.0060.00520.874-0.015-0.0150.0000.0000.0000.000
111L126THR00.0080.00524.194-0.007-0.0070.0000.0000.0000.000
112L127ILE00.0050.01626.348-0.011-0.0110.0000.0000.0000.000
113L128VAL00.004-0.00421.215-0.024-0.0240.0000.0000.0000.000
114L129ALA00.001-0.00221.573-0.028-0.0280.0000.0000.0000.000
115L130HIS0-0.057-0.02722.610-0.012-0.0120.0000.0000.0000.000
116L131GLU-1-0.782-0.88424.829-0.126-0.1260.0000.0000.0000.000
117L132ALA00.0020.00119.170-0.032-0.0320.0000.0000.0000.000
118L133LYS10.8660.93120.345-0.062-0.0620.0000.0000.0000.000
119L134LYS10.7400.85621.9690.1010.1010.0000.0000.0000.000
120L135LEU0-0.059-0.00519.380-0.024-0.0240.0000.0000.0000.000
121L136MET0-0.0220.01115.632-0.042-0.0420.0000.0000.0000.000
122L137PRO00.0050.00618.7210.0640.0640.0000.0000.0000.000
123L138GLU-1-0.927-0.96716.667-0.377-0.3770.0000.0000.0000.000
124L139GLY00.0050.01816.7460.0700.0700.0000.0000.0000.000
125L140GLY00.002-0.01313.476-0.134-0.1340.0000.0000.0000.000
126L141SER0-0.120-0.06111.7720.1400.1400.0000.0000.0000.000
127L142ILE00.0280.02013.797-0.127-0.1270.0000.0000.0000.000
128L143VAL0-0.015-0.00812.7680.1080.1080.0000.0000.0000.000
129L144ALA00.0560.03516.076-0.080-0.0800.0000.0000.0000.000
130L145THR0-0.079-0.04617.9820.0870.0870.0000.0000.0000.000
131L146THR0-0.0140.00420.229-0.065-0.0650.0000.0000.0000.000
132L159VAL0-0.043-0.02737.0050.0030.0030.0000.0000.0000.000
133L160MET00.0170.00032.8220.0100.0100.0000.0000.0000.000
134L161GLY00.0120.01232.5610.0110.0110.0000.0000.0000.000
135L162VAL0-0.002-0.00632.8270.0130.0130.0000.0000.0000.000
136L163ALA00.0150.01132.1380.0030.0030.0000.0000.0000.000
137L164LYS10.8990.95126.245-0.177-0.1770.0000.0000.0000.000
138L165ALA00.0210.01128.5580.0190.0190.0000.0000.0000.000
139L166SER0-0.021-0.00330.3290.0110.0110.0000.0000.0000.000
140L167LEU00.0090.01223.8060.0060.0060.0000.0000.0000.000
141L168GLU-1-0.827-0.90825.2440.4140.4140.0000.0000.0000.000
142L169ALA0-0.0060.00826.0600.0260.0260.0000.0000.0000.000
143L170ASN0-0.031-0.02926.9020.0070.0070.0000.0000.0000.000
144L171VAL00.0240.01320.988-0.007-0.0070.0000.0000.0000.000
145L172LYS10.8370.92523.079-0.393-0.3930.0000.0000.0000.000
146L173TYR0-0.035-0.02624.9910.0010.0010.0000.0000.0000.000
147L174LEU00.0190.01323.217-0.014-0.0140.0000.0000.0000.000
148L175ALA0-0.0110.00421.349-0.010-0.0100.0000.0000.0000.000
149L176LEU0-0.095-0.04222.3480.0080.0080.0000.0000.0000.000
150L177ASP-1-0.955-0.99425.5170.0900.0900.0000.0000.0000.000
151L178LEU00.0150.00821.647-0.024-0.0240.0000.0000.0000.000
152L179GLY00.0180.02620.777-0.002-0.0020.0000.0000.0000.000
153L180PRO0-0.065-0.04721.5120.0020.0020.0000.0000.0000.000
154L181ASP-1-0.834-0.90521.6880.0240.0240.0000.0000.0000.000
155L182ASN0-0.058-0.03815.7020.0490.0490.0000.0000.0000.000
156L183ILE0-0.0030.01116.8080.0010.0010.0000.0000.0000.000
157L184ARG10.8320.93210.485-1.084-1.0840.0000.0000.0000.000
158L185VAL00.0130.00016.697-0.052-0.0520.0000.0000.0000.000
159L186ASN0-0.014-0.01715.0530.0500.0500.0000.0000.0000.000
160L187ALA0-0.021-0.01017.920-0.086-0.0860.0000.0000.0000.000
161L188ILE00.0150.01914.2730.1010.1010.0000.0000.0000.000
162L189SER00.0030.00518.780-0.096-0.0960.0000.0000.0000.000
163L222ASP-1-0.751-0.87717.9070.4000.4000.0000.0000.0000.000
164L223GLN0-0.077-0.05317.9880.0850.0850.0000.0000.0000.000
165L224VAL00.018-0.00113.1510.0130.0130.0000.0000.0000.000
166L225GLU-1-0.878-0.91113.5101.1381.1380.0000.0000.0000.000
167L226VAL00.0150.00714.3490.1710.1710.0000.0000.0000.000
168L227GLY00.0180.00112.5280.0680.0680.0000.0000.0000.000
169L228LYS10.8230.8869.609-0.918-0.9180.0000.0000.0000.000
170L229THR0-0.0050.0059.5820.5450.5450.0000.0000.0000.000
171L230ALA00.006-0.00611.4080.1150.1150.0000.0000.0000.000
172L231ALA00.0310.0176.193-0.092-0.0920.0000.0000.0000.000
173L232TYR0-0.028-0.0076.7620.1830.1830.0000.0000.0000.000
174L233LEU00.0040.0078.2320.0330.0330.0000.0000.0000.000
175L234LEU0-0.0210.0108.651-0.192-0.1920.0000.0000.0000.000
176L235SER0-0.0260.0064.3690.2460.265-0.001-0.010-0.0080.000
177L236ASP-1-0.861-0.9555.9511.3721.3720.0000.0000.0000.000
178L237LEU0-0.032-0.0093.432-1.294-0.6740.021-0.195-0.4460.001
179L238SER0-0.027-0.0227.446-0.699-0.6990.0000.0000.0000.000
180L239SER00.0210.01110.718-0.427-0.4270.0000.0000.0000.000
181L240GLY0-0.032-0.00912.518-0.242-0.2420.0000.0000.0000.000
182L241VAL0-0.048-0.02214.102-0.096-0.0960.0000.0000.0000.000
183L242THR00.0580.02515.567-0.021-0.0210.0000.0000.0000.000
184L243GLY00.0140.00418.386-0.010-0.0100.0000.0000.0000.000
185L244GLU-1-0.907-0.94618.0100.6740.6740.0000.0000.0000.000
186L245ASN0-0.088-0.07719.467-0.002-0.0020.0000.0000.0000.000
187L246ILE00.0190.01914.6380.0270.0270.0000.0000.0000.000
188L247HIS00.0170.00118.748-0.010-0.0100.0000.0000.0000.000
189L248VAL0-0.037-0.02016.6200.0760.0760.0000.0000.0000.000
190L249ASP-1-0.799-0.87219.5500.4550.4550.0000.0000.0000.000
191L250SER0-0.059-0.03621.704-0.044-0.0440.0000.0000.0000.000
192L251GLY0-0.0200.00523.115-0.002-0.0020.0000.0000.0000.000
193L252PHE0-0.119-0.08824.194-0.068-0.0680.0000.0000.0000.000