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: Z6NZN

Calculation Name: 3THF-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3THF

Chain ID: A

ChEMBL ID:

UniProt ID: A1Z9P3

Base Structure: X-ray

Registration Date: 2023-06-22

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 175
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -1183031.342115
FMO2-HF: Nuclear repulsion 1113415.474541
FMO2-HF: Total energy -69615.867574
FMO2-MP2: Total energy -69817.191962


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:1396:THR)


Summations of interaction energy for fragment #1(A:1396:THR)
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.
-17.295-11.5542.2-3.425-4.515-0.02
Interaction energy analysis for fragmet #1(A:1396:THR)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.009 / q_NPA : 0.000
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].
3A1398LEU00.0640.0153.850-0.4151.396-0.003-0.760-1.0470.004
4A1399ILE00.0240.0144.900-0.407-0.270-0.001-0.009-0.1270.000
5A1400LYS10.9370.9724.568-2.698-2.575-0.001-0.011-0.1100.000
6A1401GLN00.0230.0102.193-14.184-10.6322.206-2.626-3.133-0.024
7A1402LYS10.9990.9944.3300.4580.576-0.001-0.019-0.0980.000
8A1403MET0-0.0140.0058.001-0.061-0.0610.0000.0000.0000.000
9A1404ASP-1-0.898-0.9506.0610.7270.7270.0000.0000.0000.000
10A1405GLU-1-0.911-0.9566.831-2.406-2.4060.0000.0000.0000.000
11A1406LEU00.0000.0039.7990.0920.0920.0000.0000.0000.000
12A1407ILE00.0280.00811.6330.0140.0140.0000.0000.0000.000
13A1408LYS10.9541.00211.4280.8810.8810.0000.0000.0000.000
14A1409HIS0-0.029-0.03413.494-0.021-0.0210.0000.0000.0000.000
15A1410LEU00.005-0.00215.8930.0330.0330.0000.0000.0000.000
16A1411ASN0-0.024-0.02116.3160.0340.0340.0000.0000.0000.000
17A1412GLN0-0.009-0.00115.672-0.030-0.0300.0000.0000.0000.000
18A1413LYS10.9941.00019.5220.1720.1720.0000.0000.0000.000
19A1414ILE00.0070.01221.5760.0200.0200.0000.0000.0000.000
20A1415VAL0-0.013-0.00821.9540.0140.0140.0000.0000.0000.000
21A1416SER0-0.037-0.02723.9750.0030.0030.0000.0000.0000.000
22A1417LEU00.0250.01525.3660.0100.0100.0000.0000.0000.000
23A1418LYS10.9440.97426.7820.0750.0750.0000.0000.0000.000
24A1419ARG10.9280.97525.9590.1740.1740.0000.0000.0000.000
25A1420GLU-1-0.901-0.94830.163-0.115-0.1150.0000.0000.0000.000
26A1421GLN00.009-0.00631.5610.0040.0040.0000.0000.0000.000
27A1422GLN0-0.085-0.05033.0200.0100.0100.0000.0000.0000.000
28A1423THR00.0060.00034.5920.0020.0020.0000.0000.0000.000
29A1424ILE00.0590.03235.7370.0040.0040.0000.0000.0000.000
30A1425SER00.0300.02137.6760.0070.0070.0000.0000.0000.000
31A1426GLU-1-0.922-0.94037.741-0.078-0.0780.0000.0000.0000.000
32A1427GLU-1-0.926-0.96939.950-0.073-0.0730.0000.0000.0000.000
33A1428CYS0-0.047-0.02541.6760.0040.0040.0000.0000.0000.000
34A1429SER0-0.024-0.02242.9280.0040.0040.0000.0000.0000.000
35A1430ALA0-0.059-0.02445.2580.0020.0020.0000.0000.0000.000
36A1431ASN0-0.038-0.03146.7140.0010.0010.0000.0000.0000.000
37A1432ASP-1-0.826-0.91647.433-0.035-0.0350.0000.0000.0000.000
38A1433ARG10.8810.94848.7300.0460.0460.0000.0000.0000.000
39A1434LEU00.0560.03651.3970.0020.0020.0000.0000.0000.000
40A1435GLY00.0250.00852.6160.0020.0020.0000.0000.0000.000
41A1436GLN0-0.069-0.03951.1060.0030.0030.0000.0000.0000.000
42A1437ASP-1-0.891-0.94055.800-0.034-0.0340.0000.0000.0000.000
43A1438LEU0-0.044-0.02856.4770.0020.0020.0000.0000.0000.000
44A1439PHE0-0.035-0.01658.3780.0020.0020.0000.0000.0000.000
45A1440ALA00.0080.00959.9660.0020.0020.0000.0000.0000.000
46A1441LYS10.8760.91861.5440.0290.0290.0000.0000.0000.000
47A1442LEU0-0.042-0.00562.9960.0010.0010.0000.0000.0000.000
48A1443ALA00.006-0.00564.1520.0010.0010.0000.0000.0000.000
49A1444GLU-1-0.909-0.95164.980-0.023-0.0230.0000.0000.0000.000
50A1445LYS10.8770.94267.5900.0260.0260.0000.0000.0000.000
51A1446VAL0-0.032-0.00367.1740.0000.0000.0000.0000.0000.000
52A1447ARG10.8830.92569.7540.0140.0140.0000.0000.0000.000
53A1448PRO00.0790.01567.6400.0000.0000.0000.0000.0000.000
54A1449SER0-0.024-0.02266.6930.0000.0000.0000.0000.0000.000
55A1450GLU-1-0.775-0.85566.594-0.015-0.0150.0000.0000.0000.000
56A1451ALA00.0550.03864.225-0.001-0.0010.0000.0000.0000.000
57A1452SER0-0.006-0.01162.450-0.001-0.0010.0000.0000.0000.000
58A1453LYS10.9200.97761.7440.0120.0120.0000.0000.0000.000
59A1454PHE00.0290.01958.4290.0000.0000.0000.0000.0000.000
60A1455ARG10.9540.98257.2480.0160.0160.0000.0000.0000.000
61A1456THR0-0.003-0.02057.0310.0000.0000.0000.0000.0000.000
62A1457HIS0-0.021-0.00257.1530.0020.0020.0000.0000.0000.000
63A1458VAL00.0110.00453.284-0.001-0.0010.0000.0000.0000.000
64A1459ASP-1-0.863-0.94052.805-0.020-0.0200.0000.0000.0000.000
65A1460ALA0-0.030-0.01252.2650.0000.0000.0000.0000.0000.000
66A1461VAL00.0090.00651.0560.0000.0000.0000.0000.0000.000
67A1462GLY00.0550.04448.614-0.001-0.0010.0000.0000.0000.000
68A1463ASN0-0.044-0.03047.8090.0010.0010.0000.0000.0000.000
69A1464ILE0-0.004-0.00548.6350.0010.0010.0000.0000.0000.000
70A1465THR0-0.001-0.00745.2450.0000.0000.0000.0000.0000.000
71A1466SER00.009-0.00644.193-0.001-0.0010.0000.0000.0000.000
72A1467LEU0-0.045-0.00844.2860.0020.0020.0000.0000.0000.000
73A1468LEU0-0.002-0.01045.8430.0020.0020.0000.0000.0000.000
74A1469LEU00.0120.02340.9120.0010.0010.0000.0000.0000.000
75A1470SER00.1060.06240.8120.0030.0030.0000.0000.0000.000
76A1471LEU0-0.073-0.02341.7710.0050.0050.0000.0000.0000.000
77A1472SER0-0.044-0.03041.9330.0010.0010.0000.0000.0000.000
78A1473GLU-1-0.902-0.96337.396-0.018-0.0180.0000.0000.0000.000
79A1474ARG10.8840.91338.3950.0020.0020.0000.0000.0000.000
80A1475LEU00.0010.02240.4130.0040.0040.0000.0000.0000.000
81A1476ALA00.0370.01737.3480.0020.0020.0000.0000.0000.000
82A1477GLN0-0.0040.00632.4990.0070.0070.0000.0000.0000.000
83A1478THR0-0.040-0.00636.9840.0070.0070.0000.0000.0000.000
84A1479GLU-1-0.894-0.96339.7190.0140.0140.0000.0000.0000.000
85A1480SER0-0.002-0.00534.2900.0040.0040.0000.0000.0000.000
86A1481SER0-0.034-0.01835.4800.0090.0090.0000.0000.0000.000
87A1482LEU0-0.015-0.01836.9690.0060.0060.0000.0000.0000.000
88A1483GLU-1-0.909-0.95635.1450.0090.0090.0000.0000.0000.000
89A1484THR0-0.048-0.01432.9780.0040.0040.0000.0000.0000.000
90A1485ARG10.8100.86434.310-0.055-0.0550.0000.0000.0000.000
91A1486GLN00.0190.01138.3170.0060.0060.0000.0000.0000.000
92A1487GLN0-0.027-0.02333.8060.0020.0020.0000.0000.0000.000
93A1488GLU-1-0.828-0.87633.8590.0750.0750.0000.0000.0000.000
94A1489ARG10.8050.86936.188-0.035-0.0350.0000.0000.0000.000
95A1490GLY00.0440.02839.2810.0010.0010.0000.0000.0000.000
96A1491ALA00.0010.01134.9660.0010.0010.0000.0000.0000.000
97A1492LEU0-0.043-0.03636.6740.0060.0060.0000.0000.0000.000
98A1493GLU-1-0.838-0.88438.9260.0450.0450.0000.0000.0000.000
99A1494SER00.0270.00338.474-0.001-0.0010.0000.0000.0000.000
100A1495LYS10.9160.96135.664-0.100-0.1000.0000.0000.0000.000
101A1496ARG10.7890.86639.482-0.050-0.0500.0000.0000.0000.000
102A1497ASP-1-0.788-0.86243.0680.0480.0480.0000.0000.0000.000
103A1498LEU00.0360.02338.7300.0010.0010.0000.0000.0000.000
104A1499LEU0-0.039-0.02140.1860.0020.0020.0000.0000.0000.000
105A1500TYR0-0.020-0.01543.423-0.001-0.0010.0000.0000.0000.000
106A1501GLU-1-0.870-0.93144.2850.0540.0540.0000.0000.0000.000
107A1502GLN0-0.045-0.03040.2420.0010.0010.0000.0000.0000.000
108A1503MET0-0.022-0.01445.3510.0020.0020.0000.0000.0000.000
109A1504GLU-1-0.854-0.90548.1680.0450.0450.0000.0000.0000.000
110A1505GLU-1-0.840-0.89947.5110.0530.0530.0000.0000.0000.000
111A1506ALA0-0.024-0.01447.4510.0000.0000.0000.0000.0000.000
112A1507GLN0-0.032-0.02549.3650.0020.0020.0000.0000.0000.000
113A1508ARG10.7890.86850.520-0.052-0.0520.0000.0000.0000.000
114A1509LEU00.018-0.00149.079-0.001-0.0010.0000.0000.0000.000
115A1510LYS10.8540.93352.400-0.058-0.0580.0000.0000.0000.000
116A1511SER00.047-0.00454.197-0.001-0.0010.0000.0000.0000.000
117A1512ASP-1-0.896-0.92554.9900.0470.0470.0000.0000.0000.000
118A1513ILE0-0.072-0.03951.6200.0000.0000.0000.0000.0000.000
119A1514GLU-1-0.821-0.88856.2780.0520.0520.0000.0000.0000.000
120A1515ARG10.8530.91258.192-0.047-0.0470.0000.0000.0000.000
121A1516ARG10.9590.99253.194-0.062-0.0620.0000.0000.0000.000
122A1517GLY00.0330.01459.8690.0000.0000.0000.0000.0000.000
123A1518VAL00.0130.00460.969-0.001-0.0010.0000.0000.0000.000
124A1519SER0-0.045-0.02862.847-0.002-0.0020.0000.0000.0000.000
125A1520ILE0-0.029-0.01359.884-0.001-0.0010.0000.0000.0000.000
126A1521ALA00.0490.02963.3730.0000.0000.0000.0000.0000.000
127A1522GLY0-0.0010.00066.044-0.001-0.0010.0000.0000.0000.000
128A1523LEU0-0.072-0.03163.574-0.001-0.0010.0000.0000.0000.000
129A1524LEU00.0370.00663.395-0.001-0.0010.0000.0000.0000.000
130A1525ALA00.0360.01367.433-0.001-0.0010.0000.0000.0000.000
131A1526LYS10.8560.94070.552-0.039-0.0390.0000.0000.0000.000
132A1527ASN0-0.086-0.05468.800-0.001-0.0010.0000.0000.0000.000
133A1528LEU0-0.0130.00966.0020.0010.0010.0000.0000.0000.000
134A1529SER0-0.007-0.02870.757-0.001-0.0010.0000.0000.0000.000
135A1530ALA00.0320.00471.3730.0010.0010.0000.0000.0000.000
136A1531ASP-1-0.813-0.87971.3060.0440.0440.0000.0000.0000.000
137A1532MET00.0460.01867.9350.0020.0020.0000.0000.0000.000
138A1533CYS0-0.074-0.02466.7390.0020.0020.0000.0000.0000.000
139A1534ALA00.0270.01466.6280.0010.0010.0000.0000.0000.000
140A1535ASP-1-0.882-0.94064.9630.0540.0540.0000.0000.0000.000
141A1536TYR0-0.052-0.02459.9980.0040.0040.0000.0000.0000.000
142A1537ASP-1-0.887-0.95261.8930.0520.0520.0000.0000.0000.000
143A1538TYR0-0.021-0.00861.1850.0020.0020.0000.0000.0000.000
144A1539PHE00.001-0.00355.5350.0030.0030.0000.0000.0000.000
145A1540ILE0-0.020-0.01055.9930.0040.0040.0000.0000.0000.000
146A1541ASN0-0.030-0.02957.1570.0020.0020.0000.0000.0000.000
147A1542MET0-0.0070.01057.1470.0010.0010.0000.0000.0000.000
148A1543LYS10.9540.97650.350-0.080-0.0800.0000.0000.0000.000
149A1544ALA0-0.018-0.01153.0730.0040.0040.0000.0000.0000.000
150A1545LYS10.8410.89853.254-0.068-0.0680.0000.0000.0000.000
151A1546LEU00.0310.00952.0980.0020.0020.0000.0000.0000.000
152A1547ILE0-0.035-0.01647.9800.0050.0050.0000.0000.0000.000
153A1548ALA0-0.014-0.00548.6520.0040.0040.0000.0000.0000.000
154A1549ASP-1-0.796-0.87649.6970.0780.0780.0000.0000.0000.000
155A1550ALA0-0.001-0.00346.5480.0030.0030.0000.0000.0000.000
156A1551ARG10.9030.94842.304-0.100-0.1000.0000.0000.0000.000
157A1552ASP-1-0.785-0.86145.1390.0920.0920.0000.0000.0000.000
158A1553LEU00.0130.01246.0340.0030.0030.0000.0000.0000.000
159A1554ALA0-0.009-0.00441.6090.0050.0050.0000.0000.0000.000
160A1555VAL0-0.043-0.01141.0590.0080.0080.0000.0000.0000.000
161A1556ARG10.8610.88341.926-0.087-0.0870.0000.0000.0000.000
162A1557ILE0-0.0170.01339.6610.0000.0000.0000.0000.0000.000
163A1558LYS10.9210.97336.852-0.141-0.1410.0000.0000.0000.000
164A1559GLY00.0700.04238.0580.0040.0040.0000.0000.0000.000
165A1560SER0-0.038-0.03439.963-0.002-0.0020.0000.0000.0000.000
166A1561GLU-1-0.930-0.97335.6760.1670.1670.0000.0000.0000.000
167A1562GLU-1-0.932-0.95634.8950.1510.1510.0000.0000.0000.000
168A1563GLN0-0.0270.00635.7470.0000.0000.0000.0000.0000.000
169A1564LEU0-0.0110.00235.7780.0000.0000.0000.0000.0000.000
170A1565SER0-0.037-0.03731.8670.0040.0040.0000.0000.0000.000
171A1566SER0-0.011-0.02333.1200.0000.0000.0000.0000.0000.000
172A1567LEU0-0.031-0.01934.147-0.006-0.0060.0000.0000.0000.000
173A1568SER0-0.086-0.05532.850-0.003-0.0030.0000.0000.0000.000
174A1569ASP-1-0.940-0.95529.6640.2120.2120.0000.0000.0000.000
175A1570ALA0-0.110-0.04532.096-0.005-0.0050.0000.0000.0000.000