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: MN2ZZ

Calculation Name: 1WWM-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1WWM

Chain ID: A

ChEMBL ID:

UniProt ID: Q5SLX4

Base Structure: X-ray

Registration Date: 2023-09-23

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 180
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2063431.070305
FMO2-HF: Nuclear repulsion 1991653.00634
FMO2-HF: Total energy -71778.063966
FMO2-MP2: Total energy -71993.697627


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:11:GLU)


Summations of interaction energy for fragment #1(A:11:GLU)
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.
136.501143.1020.856-2.706-4.7470.035
Interaction energy analysis for fragmet #1(A:11:GLU)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : -1 / q_Mulliken : -0.913 / q_NPA : -0.968
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].
3A13PRO0-0.084-0.0173.6973.3334.793-0.002-0.332-1.1250.006
4A14GLY00.0470.0145.326-6.850-6.8500.0000.0000.0000.000
5A15LEU0-0.016-0.0126.368-2.378-2.3780.0000.0000.0000.000
6A16LEU00.0480.0353.541-9.883-8.2250.051-0.684-1.0240.005
7A17GLU-1-0.827-0.9405.43242.35642.384-0.0010.000-0.0270.000
8A18GLU-1-0.849-0.9038.04920.73520.7350.0000.0000.0000.000
9A19ILE00.0220.0087.817-3.353-3.3530.0000.0000.0000.000
10A20LYS10.8460.9357.518-38.755-38.7550.0000.0000.0000.000
11A21ALA0-0.033-0.01011.487-2.528-2.5280.0000.0000.0000.000
12A22LEU0-0.049-0.00613.580-2.053-2.0530.0000.0000.0000.000
13A23PRO0-0.037-0.01915.960-0.455-0.4550.0000.0000.0000.000
14A24LEU0-0.012-0.00916.982-0.839-0.8390.0000.0000.0000.000
15A25ARG10.8670.93320.259-13.687-13.6870.0000.0000.0000.000
16A26LEU00.0120.01718.987-0.225-0.2250.0000.0000.0000.000
17A27ASP-1-0.844-0.92823.13810.75010.7500.0000.0000.0000.000
18A28GLU-1-0.823-0.89525.86111.86811.8680.0000.0000.0000.000
19A29GLU-1-0.910-0.94926.92110.13310.1330.0000.0000.0000.000
20A30ARG10.8310.88923.792-12.855-12.8550.0000.0000.0000.000
21A31PHE0-0.026-0.01418.5750.3270.3270.0000.0000.0000.000
22A32ARG10.8920.91123.517-11.015-11.0150.0000.0000.0000.000
23A33PHE0-0.0010.00825.6850.1740.1740.0000.0000.0000.000
24A34TRP0-0.055-0.04516.009-0.205-0.2050.0000.0000.0000.000
25A35LEU00.0170.01719.9100.5250.5250.0000.0000.0000.000
26A36GLN0-0.038-0.02822.4930.1550.1550.0000.0000.0000.000
27A37GLN0-0.132-0.07023.791-0.443-0.4430.0000.0000.0000.000
28A38ASP-1-0.806-0.90418.30317.68017.6800.0000.0000.0000.000
29A39TYR00.0230.02421.4570.2020.2020.0000.0000.0000.000
30A40PRO0-0.014-0.02223.7290.0890.0890.0000.0000.0000.000
31A41PHE0-0.014-0.01214.339-0.183-0.1830.0000.0000.0000.000
32A42VAL00.0750.04419.1530.4090.4090.0000.0000.0000.000
33A43GLU-1-0.896-0.94520.70912.00012.0000.0000.0000.0000.000
34A44ALA0-0.027-0.01920.529-0.155-0.1550.0000.0000.0000.000
35A45LEU00.0330.00915.0460.1720.1720.0000.0000.0000.000
36A46TYR00.0090.01819.205-0.009-0.0090.0000.0000.0000.000
37A47ARG10.8990.95122.257-12.048-12.0480.0000.0000.0000.000
38A48TYR0-0.036-0.03214.480-0.317-0.3170.0000.0000.0000.000
39A49GLN00.016-0.02218.555-0.087-0.0870.0000.0000.0000.000
40A50VAL0-0.009-0.00120.657-0.358-0.3580.0000.0000.0000.000
41A51GLY0-0.023-0.00723.004-0.457-0.4570.0000.0000.0000.000
42A52LEU0-0.031-0.00817.267-0.185-0.1850.0000.0000.0000.000
43A53LEU00.006-0.00921.159-0.376-0.3760.0000.0000.0000.000
44A54LEU0-0.066-0.01524.198-0.558-0.5580.0000.0000.0000.000
45A55GLU-1-0.834-0.90722.67313.16913.1690.0000.0000.0000.000
46A56ALA0-0.0260.00721.978-0.029-0.0290.0000.0000.0000.000
47A57PRO00.0030.00721.749-0.788-0.7880.0000.0000.0000.000
48A58GLN00.0430.00624.4700.2260.2260.0000.0000.0000.000
49A59ALA0-0.046-0.03923.7740.1120.1120.0000.0000.0000.000
50A60HIS00.0510.04019.0170.4050.4050.0000.0000.0000.000
51A61ARG10.8780.94321.448-10.945-10.9450.0000.0000.0000.000
52A62ALA00.0100.01223.6830.1360.1360.0000.0000.0000.000
53A63PRO00.0760.02918.892-0.160-0.1600.0000.0000.0000.000
54A64LEU00.0330.01517.8890.2500.2500.0000.0000.0000.000
55A65VAL0-0.028-0.01020.987-0.080-0.0800.0000.0000.0000.000
56A66GLN0-0.0080.00121.900-0.204-0.2040.0000.0000.0000.000
57A67ALA00.0150.01718.1360.0600.0600.0000.0000.0000.000
58A68LEU0-0.012-0.00319.985-0.045-0.0450.0000.0000.0000.000
59A69MET0-0.035-0.01822.529-0.371-0.3710.0000.0000.0000.000
60A70ALA00.0500.03620.194-0.246-0.2460.0000.0000.0000.000
61A71THR00.0170.01819.9350.2240.2240.0000.0000.0000.000
62A72VAL0-0.032-0.02521.637-0.284-0.2840.0000.0000.0000.000
63A73GLU-1-0.915-0.96324.86111.64811.6480.0000.0000.0000.000
64A74GLU-1-0.918-0.95119.31016.09816.0980.0000.0000.0000.000
65A75LEU0-0.049-0.03423.652-0.213-0.2130.0000.0000.0000.000
66A76ASP-1-0.891-0.95025.74010.00610.0060.0000.0000.0000.000
67A77TRP0-0.042-0.02324.488-0.262-0.2620.0000.0000.0000.000
68A78LEU00.008-0.00322.691-0.342-0.3420.0000.0000.0000.000
69A79LEU0-0.061-0.02026.950-0.361-0.3610.0000.0000.0000.000
70A80LEU0-0.062-0.02530.415-0.380-0.3800.0000.0000.0000.000
71A81GLN0-0.0090.01827.531-0.217-0.2170.0000.0000.0000.000
72A82GLY0-0.007-0.00329.9690.1640.1640.0000.0000.0000.000
73A83ALA00.0030.02227.685-0.100-0.1000.0000.0000.0000.000
74A84SER00.004-0.01429.671-0.406-0.4060.0000.0000.0000.000
75A85PRO00.0010.00629.3290.1470.1470.0000.0000.0000.000
76A86SER0-0.078-0.02630.1120.1130.1130.0000.0000.0000.000
77A87ALA00.0450.01130.348-0.323-0.3230.0000.0000.0000.000
78A88PRO0-0.053-0.01829.9380.2540.2540.0000.0000.0000.000
79A89VAL00.0620.03224.2690.1620.1620.0000.0000.0000.000
80A90HIS00.0360.02523.7150.1250.1250.0000.0000.0000.000
81A91PRO00.042-0.00123.8720.4360.4360.0000.0000.0000.000
82A92VAL0-0.018-0.00318.8090.3010.3010.0000.0000.0000.000
83A93ARG10.8910.93119.532-15.031-15.0310.0000.0000.0000.000
84A94ALA0-0.021-0.00320.5430.2570.2570.0000.0000.0000.000
85A95GLY0-0.010-0.00620.593-0.035-0.0350.0000.0000.0000.000
86A96TYR0-0.037-0.04912.2030.6980.6980.0000.0000.0000.000
87A97ILE00.0340.01317.5220.5140.5140.0000.0000.0000.000
88A98ALA0-0.008-0.00120.056-0.079-0.0790.0000.0000.0000.000
89A99LEU0-0.0080.00313.713-0.057-0.0570.0000.0000.0000.000
90A100LEU00.0370.03414.9230.2360.2360.0000.0000.0000.000
91A101GLU-1-0.906-0.96617.61913.18213.1820.0000.0000.0000.000
92A102GLU-1-0.874-0.88018.18317.26017.2600.0000.0000.0000.000
93A103MET0-0.006-0.00111.150-0.162-0.1620.0000.0000.0000.000
94A104GLY0-0.024-0.00816.925-0.141-0.1410.0000.0000.0000.000
95A105ARG10.8430.92619.845-14.697-14.6970.0000.0000.0000.000
96A106LEU0-0.0330.01014.818-0.546-0.5460.0000.0000.0000.000
97A107PRO00.0470.01217.302-0.406-0.4060.0000.0000.0000.000
98A108TYR00.0400.00417.1821.0191.0190.0000.0000.0000.000
99A109ALA00.0300.00015.3380.7110.7110.0000.0000.0000.000
100A110TYR00.0300.01512.0650.4250.4250.0000.0000.0000.000
101A111ARG10.7740.88212.409-13.545-13.5450.0000.0000.0000.000
102A112VAL00.0080.00513.8280.9810.9810.0000.0000.0000.000
103A113VAL00.0100.0178.0921.1271.1270.0000.0000.0000.000
104A114PHE0-0.001-0.0198.8072.6292.6290.0000.0000.0000.000
105A115PHE00.0060.01310.4371.5651.5650.0000.0000.0000.000
106A116TYR0-0.025-0.0186.3361.9001.9000.0000.0000.0000.000
107A117PHE0-0.010-0.0092.554-6.685-4.1150.776-1.501-1.8450.023
108A118LEU0-0.014-0.0136.9872.6172.6170.0000.0000.0000.000
109A119ASN00.005-0.0049.419-0.712-0.7120.0000.0000.0000.000
110A120GLY00.0110.0116.987-0.969-0.9690.0000.0000.0000.000
111A121LEU0-0.020-0.0124.8710.9751.134-0.001-0.004-0.1540.000
112A122PHE00.004-0.0026.751-1.986-1.9860.0000.0000.0000.000
113A123LEU00.0010.0029.920-1.445-1.4450.0000.0000.0000.000
114A124GLU-1-0.839-0.9075.54236.39836.3980.0000.0000.0000.000
115A125ALA0-0.049-0.0258.644-1.886-1.8860.0000.0000.0000.000
116A126TRP00.023-0.00910.431-2.257-2.2570.0000.0000.0000.000
117A127ALA00.0110.00712.040-1.564-1.5640.0000.0000.0000.000
118A128HIS0-0.050-0.01411.5360.0720.0720.0000.0000.0000.000
119A129HIS10.7830.87213.550-23.347-23.3470.0000.0000.0000.000
120A130VAL0-0.0160.00116.042-1.217-1.2170.0000.0000.0000.000
121A131PRO0-0.0260.00218.2820.2560.2560.0000.0000.0000.000
122A132GLU-1-0.914-0.96319.46515.92615.9260.0000.0000.0000.000
123A133GLU-1-0.960-1.00721.85113.00613.0060.0000.0000.0000.000
124A134GLY0-0.0020.00925.533-0.267-0.2670.0000.0000.0000.000
125A135PRO00.0130.00326.9980.1150.1150.0000.0000.0000.000
126A136TRP00.0270.01322.4300.1520.1520.0000.0000.0000.000
127A137ALA00.0750.05422.8280.5360.5360.0000.0000.0000.000
128A138GLU-1-0.970-0.98223.72510.73710.7370.0000.0000.0000.000
129A139LEU0-0.042-0.01522.3160.1400.1400.0000.0000.0000.000
130A140SER00.031-0.00719.1430.3350.3350.0000.0000.0000.000
131A141GLN0-0.089-0.03620.5620.3430.3430.0000.0000.0000.000
132A142HIS0-0.036-0.02922.611-0.642-0.6420.0000.0000.0000.000
133A143TRP0-0.0140.00616.974-0.742-0.7420.0000.0000.0000.000
134A144PHE0-0.027-0.00214.0650.7680.7680.0000.0000.0000.000
135A145ALA00.0520.02919.224-0.588-0.5880.0000.0000.0000.000
136A146PRO00.0320.00920.1120.6860.6860.0000.0000.0000.000
137A147GLU-1-0.921-0.96520.87013.34213.3420.0000.0000.0000.000
138A148PHE00.0180.01912.6380.5540.5540.0000.0000.0000.000
139A149GLN00.039-0.00713.7540.5390.5390.0000.0000.0000.000
140A150ALA0-0.050-0.00615.7380.4440.4440.0000.0000.0000.000
141A151VAL00.0500.00617.0660.1320.1320.0000.0000.0000.000
142A152LEU00.003-0.00110.0840.3420.3420.0000.0000.0000.000
143A153TYR0-0.036-0.01013.1111.1381.1380.0000.0000.0000.000
144A154ASP-1-0.879-0.94814.45315.73115.7310.0000.0000.0000.000
145A155LEU0-0.048-0.03113.039-0.252-0.2520.0000.0000.0000.000
146A156GLU-1-0.855-0.8838.95628.35728.3570.0000.0000.0000.000
147A157VAL0-0.032-0.02311.4990.1270.1270.0000.0000.0000.000
148A158LEU0-0.039-0.00814.410-0.747-0.7470.0000.0000.0000.000
149A159ALA00.003-0.0059.830-0.368-0.3680.0000.0000.0000.000
150A160ARG10.8700.9099.987-23.350-23.3500.0000.0000.0000.000
151A161GLY0-0.0230.00711.308-0.342-0.3420.0000.0000.0000.000
152A162LEU0-0.040-0.03813.583-0.569-0.5690.0000.0000.0000.000
153A163TRP0-0.051-0.0195.321-0.700-0.7000.0000.0000.0000.000
154A164GLU-1-0.990-1.00311.00215.87815.8780.0000.0000.0000.000
155A165ASP-1-0.971-0.97312.82415.77815.7780.0000.0000.0000.000
156A166LEU0-0.0080.00210.416-0.548-0.5480.0000.0000.0000.000
157A167ASP-1-0.863-0.93311.90520.08220.0820.0000.0000.0000.000
158A168PRO00.0700.0158.9061.1901.1900.0000.0000.0000.000
159A169GLU-1-0.883-0.9298.91526.87826.8780.0000.0000.0000.000
160A170VAL0-0.039-0.02011.3680.7380.7380.0000.0000.0000.000
161A171VAL00.0360.0156.2820.7190.7190.0000.0000.0000.000
162A172ARG10.8930.9416.660-24.987-24.9870.0000.0000.0000.000
163A173THR0-0.064-0.0248.0901.1451.1450.0000.0000.0000.000
164A174TYR0-0.039-0.05510.830-0.539-0.5390.0000.0000.0000.000
165A175LEU00.0450.0293.592-1.285-0.7830.034-0.165-0.3700.001
166A176ARG10.7580.8487.474-23.012-23.0120.0000.0000.0000.000
167A177ARG10.8090.8588.345-21.502-21.5020.0000.0000.0000.000
168A178ILE00.0300.0268.308-1.757-1.7570.0000.0000.0000.000
169A179LEU00.0210.0154.602-2.194-1.970-0.001-0.020-0.2020.000
170A180GLU-1-0.821-0.8858.62122.86322.8630.0000.0000.0000.000
171A181ALA0-0.012-0.00112.006-1.856-1.8560.0000.0000.0000.000
172A182GLU-1-0.742-0.8529.30324.81224.8120.0000.0000.0000.000
173A183LYS10.7790.87611.531-25.884-25.8840.0000.0000.0000.000
174A184ALA0-0.035-0.01813.116-1.793-1.7930.0000.0000.0000.000
175A185THR00.0540.01815.405-1.867-1.8670.0000.0000.0000.000
176A186TRP00.0370.02312.241-2.235-2.2350.0000.0000.0000.000
177A187SER0-0.037-0.01916.244-1.352-1.3520.0000.0000.0000.000
178A188LEU0-0.062-0.01818.468-1.144-1.1440.0000.0000.0000.000
179A189LEU00.0370.02118.399-0.907-0.9070.0000.0000.0000.000
180A190LEU0-0.109-0.02719.223-0.589-0.5890.0000.0000.0000.000