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: R93J8

Calculation Name: 1L0B-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1L0B

Chain ID: A

ChEMBL ID:

UniProt ID: O54952

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 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 192
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2172695.335417
FMO2-HF: Nuclear repulsion 2094393.251643
FMO2-HF: Total energy -78302.083774
FMO2-MP2: Total energy -78527.708873


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(A:1591:ARG)


Summations of interaction energy for fragment #1(A:1591:ARG)
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.
-74.205-71.0540.015-1.349-1.817-0.004
Interaction energy analysis for fragmet #1(A:1591:ARG)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 1 / q_Mulliken : 0.946 / q_NPA : 0.963
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].
3A1593GLU-1-0.966-1.0013.533-71.752-68.6010.015-1.349-1.817-0.004
4A1594ARG10.9120.9506.23028.13028.1300.0000.0000.0000.000
5A1595ASP-1-0.866-0.8949.515-21.630-21.6300.0000.0000.0000.000
6A1596ILE0-0.053-0.03811.3850.1570.1570.0000.0000.0000.000
7A1597SER00.0200.02513.3731.7621.7620.0000.0000.0000.000
8A1598MET0-0.045-0.03116.469-0.465-0.4650.0000.0000.0000.000
9A1599VAL00.0350.05118.3120.8060.8060.0000.0000.0000.000
10A1600VAL00.0190.00220.405-0.427-0.4270.0000.0000.0000.000
11A1601SER00.026-0.01422.6720.4950.4950.0000.0000.0000.000
12A1602GLY00.0240.00624.335-0.132-0.1320.0000.0000.0000.000
13A1603LEU0-0.0380.00424.4320.0870.0870.0000.0000.0000.000
14A1604THR00.0130.00228.2610.3200.3200.0000.0000.0000.000
15A1605PRO00.1060.03130.936-0.250-0.2500.0000.0000.0000.000
16A1606LYS10.9710.98632.1298.6538.6530.0000.0000.0000.000
17A1607GLU-1-0.812-0.89928.101-10.778-10.7780.0000.0000.0000.000
18A1608VAL00.0280.01427.544-0.443-0.4430.0000.0000.0000.000
19A1609MET0-0.021-0.01727.620-0.205-0.2050.0000.0000.0000.000
20A1610ILE0-0.076-0.03126.258-0.083-0.0830.0000.0000.0000.000
21A1611VAL00.0060.00322.283-0.302-0.3020.0000.0000.0000.000
22A1612GLN00.016-0.00623.884-0.060-0.0600.0000.0000.0000.000
23A1613LYS11.0030.99925.5609.5109.5100.0000.0000.0000.000
24A1614PHE0-0.027-0.00618.5640.0060.0060.0000.0000.0000.000
25A1615ALA00.0310.00920.724-0.419-0.4190.0000.0000.0000.000
26A1616GLU-1-0.921-0.95421.358-11.207-11.2070.0000.0000.0000.000
27A1617LYS10.8830.94922.69612.04212.0420.0000.0000.0000.000
28A1618TYR0-0.062-0.03717.9530.1220.1220.0000.0000.0000.000
29A1619ARG10.9390.97717.33714.22414.2240.0000.0000.0000.000
30A1620LEU0-0.027-0.00415.368-0.788-0.7880.0000.0000.0000.000
31A1621ALA00.0470.02617.5830.8620.8620.0000.0000.0000.000
32A1622LEU0-0.038-0.02619.090-0.532-0.5320.0000.0000.0000.000
33A1623THR0-0.030-0.02421.6440.4580.4580.0000.0000.0000.000
34A1624ASP-1-0.911-0.96023.767-11.301-11.3010.0000.0000.0000.000
35A1625VAL00.0160.00224.747-0.040-0.0400.0000.0000.0000.000
36A1626ILE0-0.041-0.00618.906-0.399-0.3990.0000.0000.0000.000
37A1627THR00.0260.01020.3190.2780.2780.0000.0000.0000.000
38A1628GLU-1-0.930-0.96918.441-16.078-16.0780.0000.0000.0000.000
39A1629GLU-1-0.899-0.96916.466-17.492-17.4920.0000.0000.0000.000
40A1630THR0-0.056-0.00415.594-0.840-0.8400.0000.0000.0000.000
41A1631THR00.019-0.04611.585-0.671-0.6710.0000.0000.0000.000
42A1632HIS00.0230.04810.893-0.709-0.7090.0000.0000.0000.000
43A1633VAL00.0280.01114.6251.2191.2190.0000.0000.0000.000
44A1634ILE0-0.041-0.01317.047-0.346-0.3460.0000.0000.0000.000
45A1635ILE00.013-0.01119.4800.7820.7820.0000.0000.0000.000
46A1636LYS10.9060.96021.88510.58310.5830.0000.0000.0000.000
47A1637THR0-0.0230.01720.964-0.333-0.3330.0000.0000.0000.000
48A1638ASP-1-0.838-0.90624.380-11.527-11.5270.0000.0000.0000.000
49A1639ALA0-0.018-0.03824.952-0.471-0.4710.0000.0000.0000.000
50A1640GLU-1-0.936-0.95524.191-12.229-12.2290.0000.0000.0000.000
51A1641PHE0-0.083-0.04719.536-0.690-0.6900.0000.0000.0000.000
52A1642VAL00.0560.04120.787-0.718-0.7180.0000.0000.0000.000
53A1643CYS0-0.052-0.03022.1250.1550.1550.0000.0000.0000.000
54A1644GLU-1-0.875-0.92824.092-10.225-10.2250.0000.0000.0000.000
55A1645ARG10.8420.91524.87311.20111.2010.0000.0000.0000.000
56A1646THR00.007-0.00724.1070.2790.2790.0000.0000.0000.000
57A1647LEU00.0770.03524.103-0.432-0.4320.0000.0000.0000.000
58A1648LYS10.9120.95121.43712.11312.1130.0000.0000.0000.000
59A1649TYR0-0.027-0.00919.375-1.191-1.1910.0000.0000.0000.000
60A1650PHE00.0460.00719.119-0.785-0.7850.0000.0000.0000.000
61A1651LEU00.0170.00119.517-0.687-0.6870.0000.0000.0000.000
62A1652GLY0-0.011-0.01816.633-0.834-0.8340.0000.0000.0000.000
63A1653ILE0-0.024-0.01315.017-1.541-1.5410.0000.0000.0000.000
64A1654ALA00.0280.02815.034-1.173-1.1730.0000.0000.0000.000
65A1655GLY0-0.029-0.01414.828-0.366-0.3660.0000.0000.0000.000
66A1656GLY00.0240.01811.093-1.485-1.4850.0000.0000.0000.000
67A1657LYS10.7800.8999.92018.30718.3070.0000.0000.0000.000
68A1658TRP00.0350.0186.7940.5510.5510.0000.0000.0000.000
69A1659ILE00.0070.01511.6571.5961.5960.0000.0000.0000.000
70A1660VAL0-0.009-0.01513.825-0.465-0.4650.0000.0000.0000.000
71A1661SER00.0540.01916.4111.0291.0290.0000.0000.0000.000
72A1662TYR00.0470.00719.819-0.127-0.1270.0000.0000.0000.000
73A1663SER00.018-0.03221.444-0.035-0.0350.0000.0000.0000.000
74A1664TRP00.0370.00115.2850.2820.2820.0000.0000.0000.000
75A1665VAL0-0.039-0.01819.703-0.025-0.0250.0000.0000.0000.000
76A1666ILE0-0.0310.01721.5840.3230.3230.0000.0000.0000.000
77A1667LYS10.9840.98721.53414.00814.0080.0000.0000.0000.000
78A1668SER0-0.039-0.01919.0600.1800.1800.0000.0000.0000.000
79A1669ILE0-0.0010.00521.0070.2710.2710.0000.0000.0000.000
80A1670GLN0-0.093-0.04324.2880.5880.5880.0000.0000.0000.000
81A1671GLU-1-0.899-0.94221.596-12.383-12.3830.0000.0000.0000.000
82A1672ARG10.8340.91923.16010.60710.6070.0000.0000.0000.000
83A1673LYS10.9350.97918.07114.72014.7200.0000.0000.0000.000
84A1674LEU00.0690.04214.6670.1430.1430.0000.0000.0000.000
85A1675LEU0-0.017-0.00915.154-0.854-0.8540.0000.0000.0000.000
86A1676SER00.0510.04610.124-1.384-1.3840.0000.0000.0000.000
87A1677VAL00.0550.02010.5590.9460.9460.0000.0000.0000.000
88A1678HIS10.9140.9256.64534.38634.3860.0000.0000.0000.000
89A1679GLU-1-0.932-0.96111.873-18.306-18.3060.0000.0000.0000.000
90A1680PHE0-0.047-0.00914.9661.3171.3170.0000.0000.0000.000
91A1681GLU-1-0.821-0.88511.274-25.431-25.4310.0000.0000.0000.000
92A1682VAL0-0.043-0.02514.6750.7660.7660.0000.0000.0000.000
93A1683LYS10.9170.95416.17114.90914.9090.0000.0000.0000.000
94A1684GLY00.0170.01018.261-0.073-0.0730.0000.0000.0000.000
95A1685ASP-1-0.745-0.85220.725-12.734-12.7340.0000.0000.0000.000
96A1686VAL00.018-0.01523.8120.0930.0930.0000.0000.0000.000
97A1687VAL0-0.057-0.00926.6680.3710.3710.0000.0000.0000.000
98A1688THR0-0.052-0.03422.687-0.028-0.0280.0000.0000.0000.000
99A1689GLY00.0030.02025.2380.0910.0910.0000.0000.0000.000
100A1690SER00.031-0.00521.709-0.411-0.4110.0000.0000.0000.000
101A1691ASN0-0.002-0.01520.701-0.913-0.9130.0000.0000.0000.000
102A1692HIS0-0.010-0.00520.124-0.725-0.7250.0000.0000.0000.000
103A1693GLN0-0.0170.01515.182-1.783-1.7830.0000.0000.0000.000
104A1694GLY00.0670.04315.203-1.107-1.1070.0000.0000.0000.000
105A1695PRO00.000-0.00814.459-0.989-0.9890.0000.0000.0000.000
106A1696ARG10.9340.96910.25722.42522.4250.0000.0000.0000.000
107A1697ARG10.8780.95710.32216.04016.0400.0000.0000.0000.000
108A1698SER0-0.020-0.00111.449-1.648-1.6480.0000.0000.0000.000
109A1699ARG10.8230.8896.38632.04532.0450.0000.0000.0000.000
110A1700GLU-1-0.984-1.0046.340-34.858-34.8580.0000.0000.0000.000
111A1701SER0-0.104-0.0736.821-1.500-1.5000.0000.0000.0000.000
112A1702GLN0-0.104-0.0238.9880.6860.6860.0000.0000.0000.000
113A1703GLU-1-0.702-0.7596.734-27.446-27.4460.0000.0000.0000.000
114A1704LYS10.8320.88710.84622.06322.0630.0000.0000.0000.000
115A1705LEU0-0.158-0.16815.6280.6690.6690.0000.0000.0000.000
116A1706PHE0-0.041-0.03319.5240.6300.6300.0000.0000.0000.000
117A1707GLU-1-0.917-0.95118.959-15.145-15.1450.0000.0000.0000.000
118A1708GLY00.0080.01122.5190.2500.2500.0000.0000.0000.000
119A1709LEU0-0.030-0.00325.7690.5500.5500.0000.0000.0000.000
120A1710GLN00.0070.01127.849-0.162-0.1620.0000.0000.0000.000
121A1711ILE00.0100.00327.0550.2370.2370.0000.0000.0000.000
122A1712TYR0-0.065-0.03630.947-0.107-0.1070.0000.0000.0000.000
123A1713CYS0-0.040-0.01231.085-0.045-0.0450.0000.0000.0000.000
124A1714CYS00.0310.01334.0180.1930.1930.0000.0000.0000.000
125A1715GLU-1-0.876-0.94037.744-7.921-7.9210.0000.0000.0000.000
126A1716PRO0-0.039-0.00338.371-0.078-0.0780.0000.0000.0000.000
127A1717PHE00.006-0.01032.920-0.192-0.1920.0000.0000.0000.000
128A1718THR0-0.029-0.01136.199-0.004-0.0040.0000.0000.0000.000
129A1719ASN0-0.069-0.01731.808-0.072-0.0720.0000.0000.0000.000
130A1720MET00.0270.01627.563-0.159-0.1590.0000.0000.0000.000
131A1721PRO00.0200.01330.7810.2020.2020.0000.0000.0000.000
132A1722LYS10.9970.98631.3818.7958.7950.0000.0000.0000.000
133A1723ASP-1-0.937-0.97630.595-10.497-10.4970.0000.0000.0000.000
134A1724GLU-1-0.858-0.94126.465-12.121-12.1210.0000.0000.0000.000
135A1725LEU0-0.0320.00326.449-0.547-0.5470.0000.0000.0000.000
136A1726GLU-1-0.841-0.94526.865-10.231-10.2310.0000.0000.0000.000
137A1727ARG10.9621.00120.92513.60313.6030.0000.0000.0000.000
138A1728MET0-0.019-0.02222.419-0.617-0.6170.0000.0000.0000.000
139A1729LEU00.0070.00022.080-0.598-0.5980.0000.0000.0000.000
140A1730GLN00.0080.01420.837-0.336-0.3360.0000.0000.0000.000
141A1731LEU0-0.027-0.00717.639-0.544-0.5440.0000.0000.0000.000
142A1732CYS0-0.068-0.03318.160-1.152-1.1520.0000.0000.0000.000
143A1733GLY00.0410.01119.702-0.013-0.0130.0000.0000.0000.000
144A1734ALA0-0.0140.01121.1000.3470.3470.0000.0000.0000.000
145A1735SER0-0.0250.00024.721-0.033-0.0330.0000.0000.0000.000
146A1736VAL0-0.041-0.03926.6830.2940.2940.0000.0000.0000.000
147A1737VAL0-0.022-0.01729.2840.1630.1630.0000.0000.0000.000
148A1738LYS10.8860.92930.38110.18810.1880.0000.0000.0000.000
149A1739GLU-1-0.924-0.96035.077-7.529-7.5290.0000.0000.0000.000
150A1740LEU0-0.0360.00737.707-0.104-0.1040.0000.0000.0000.000
151A1741PRO0-0.010-0.01740.3980.1340.1340.0000.0000.0000.000
152A1742LEU00.0900.03434.978-0.027-0.0270.0000.0000.0000.000
153A1743LEU00.0070.00738.839-0.036-0.0360.0000.0000.0000.000
154A1744THR00.004-0.01339.536-0.189-0.1890.0000.0000.0000.000
155A1745ARG10.8620.92934.7278.5818.5810.0000.0000.0000.000
156A1746ASP-1-0.871-0.93034.421-8.848-8.8480.0000.0000.0000.000
157A1747THR0-0.031-0.02130.131-0.028-0.0280.0000.0000.0000.000
158A1748GLY0-0.0020.00133.195-0.066-0.0660.0000.0000.0000.000
159A1749ALA0-0.037-0.00230.9170.1140.1140.0000.0000.0000.000
160A1750HIS00.0340.00333.0130.2820.2820.0000.0000.0000.000
161A1751PRO0-0.014-0.00333.700-0.172-0.1720.0000.0000.0000.000
162A1752ILE00.0040.01329.8130.1660.1660.0000.0000.0000.000
163A1753VAL0-0.041-0.02633.442-0.117-0.1170.0000.0000.0000.000
164A1754LEU00.0140.01029.5430.0570.0570.0000.0000.0000.000
165A1755VAL00.014-0.00434.1450.1730.1730.0000.0000.0000.000
166A1756GLN00.0220.01135.335-0.087-0.0870.0000.0000.0000.000
167A1776ARG10.9310.96636.1448.0278.0270.0000.0000.0000.000
168A1777LEU0-0.0100.00736.680-0.128-0.1280.0000.0000.0000.000
169A1778VAL0-0.006-0.01131.8480.0400.0400.0000.0000.0000.000
170A1779MET00.0430.01934.3880.0350.0350.0000.0000.0000.000
171A1780TRP00.1000.02729.852-0.442-0.4420.0000.0000.0000.000
172A1781ASP-1-0.888-0.93429.617-10.007-10.0070.0000.0000.0000.000
173A1782TRP00.006-0.01426.679-0.375-0.3750.0000.0000.0000.000
174A1783VAL0-0.0090.02824.941-0.541-0.5410.0000.0000.0000.000
175A1784LEU0-0.012-0.01124.472-0.650-0.6500.0000.0000.0000.000
176A1785ASP-1-0.732-0.83023.997-11.641-11.6410.0000.0000.0000.000
177A1786SER0-0.058-0.06522.992-0.423-0.4230.0000.0000.0000.000
178A1787ILE00.0090.00519.049-0.799-0.7990.0000.0000.0000.000
179A1788SER0-0.073-0.02519.193-0.705-0.7050.0000.0000.0000.000
180A1789VAL0-0.018-0.01419.489-0.541-0.5410.0000.0000.0000.000
181A1790TYR0-0.018-0.00814.131-0.415-0.4150.0000.0000.0000.000
182A1791ARG10.9180.94617.59514.32114.3210.0000.0000.0000.000
183A1792CYS00.0220.03120.2320.5710.5710.0000.0000.0000.000
184A1793ARG10.8800.93123.03311.52811.5280.0000.0000.0000.000
185A1794ASP-1-0.856-0.91626.027-9.773-9.7730.0000.0000.0000.000
186A1795LEU00.038-0.01229.3090.1170.1170.0000.0000.0000.000
187A1796ASP-1-0.882-0.91631.680-8.506-8.5060.0000.0000.0000.000
188A1797ALA0-0.061-0.03232.5880.2220.2220.0000.0000.0000.000
189A1798TYR0-0.063-0.06629.307-0.084-0.0840.0000.0000.0000.000
190A1799LEU0-0.0280.01134.3990.0460.0460.0000.0000.0000.000
191A1800VAL00.0130.00537.1120.1420.1420.0000.0000.0000.000
192A1801GLN0-0.047-0.01740.0280.1990.1990.0000.0000.0000.000