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: R91G8

Calculation Name: 1MW7-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1MW7

Chain ID: A

ChEMBL ID:

UniProt ID: O24970

Base Structure: X-ray

Registration Date: 2023-06-21

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 220
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2527263.518592
FMO2-HF: Nuclear repulsion 2440700.601079
FMO2-HF: Total energy -86562.917513
FMO2-MP2: Total energy -86814.99892


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:21:LYS)


Summations of interaction energy for fragment #1(A:21:LYS)
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.
-315.069-311.10113.839-9.641-8.17-0.09
Interaction energy analysis for fragmet #1(A:21:LYS)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 1 / q_Mulliken : 0.931 / q_NPA : 0.948
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].
3A23PHE00.0200.0033.8340.0913.089-0.036-1.577-1.386-0.001
4A24PRO00.0460.0132.755-0.0921.2890.557-0.735-1.2040.006
5A25LYS10.9060.9473.78754.69355.0420.000-0.043-0.3070.000
6A26LEU00.0380.0266.4052.4402.4400.0000.0000.0000.000
7A27ALA0-0.030-0.0157.9362.0982.0980.0000.0000.0000.000
8A28LYS10.8060.8998.18226.90526.9050.0000.0000.0000.000
9A29ALA00.0450.02110.6091.2171.2170.0000.0000.0000.000
10A30ILE0-0.034-0.01912.3571.2311.2310.0000.0000.0000.000
11A31THR0-0.053-0.03013.0250.9180.9180.0000.0000.0000.000
12A32LEU00.0150.00314.7010.6750.6750.0000.0000.0000.000
13A33ALA00.0080.00916.5590.6830.6830.0000.0000.0000.000
14A34ALA0-0.0020.01218.2170.6690.6690.0000.0000.0000.000
15A35LYS10.8300.91519.22912.90912.9090.0000.0000.0000.000
16A36ASP-1-0.973-0.98220.781-12.610-12.6100.0000.0000.0000.000
17A37GLY00.0380.01023.210-0.020-0.0200.0000.0000.0000.000
18A38GLY0-0.0190.01123.7530.3870.3870.0000.0000.0000.000
19A39SER0-0.045-0.04722.492-0.485-0.4850.0000.0000.0000.000
20A40GLU-1-0.814-0.90223.510-9.963-9.9630.0000.0000.0000.000
21A41PRO0-0.004-0.00822.292-0.033-0.0330.0000.0000.0000.000
22A42ASP-1-0.904-0.94424.443-9.724-9.7240.0000.0000.0000.000
23A43THR0-0.032-0.02927.4670.1750.1750.0000.0000.0000.000
24A44ASN0-0.057-0.00522.011-0.146-0.1460.0000.0000.0000.000
25A45ALA00.0320.00123.648-0.323-0.3230.0000.0000.0000.000
26A46LYS10.9991.00319.23713.68513.6850.0000.0000.0000.000
27A47LEU00.0130.01118.240-0.765-0.7650.0000.0000.0000.000
28A48ARG10.8860.93819.05910.28510.2850.0000.0000.0000.000
29A49THR00.0040.00718.203-0.226-0.2260.0000.0000.0000.000
30A50ALA0-0.0070.00014.989-0.716-0.7160.0000.0000.0000.000
31A51ILE0-0.037-0.03214.976-0.700-0.7000.0000.0000.0000.000
32A52LEU0-0.023-0.00616.694-0.304-0.3040.0000.0000.0000.000
33A53ASN00.0270.00713.480-0.247-0.2470.0000.0000.0000.000
34A54ALA00.003-0.00711.940-0.831-0.8310.0000.0000.0000.000
35A55LYS10.8780.93212.59912.70212.7020.0000.0000.0000.000
36A56ALA0-0.0050.00914.7620.0050.0050.0000.0000.0000.000
37A57GLN00.1760.1218.727-1.798-1.7980.0000.0000.0000.000
38A58ASN0-0.189-0.09210.0480.0410.0410.0000.0000.0000.000
39A59MET0-0.065-0.0268.8930.6580.6580.0000.0000.0000.000
40A60PRO00.0100.00911.6741.0471.0470.0000.0000.0000.000
41A61LYS10.8780.91614.57111.73511.7350.0000.0000.0000.000
42A62ASP-1-0.832-0.92417.393-12.315-12.3150.0000.0000.0000.000
43A63ASN0-0.028-0.01011.772-0.098-0.0980.0000.0000.0000.000
44A64ILE00.0920.04213.8850.0170.0170.0000.0000.0000.000
45A65ASP-1-0.845-0.88915.049-11.666-11.6660.0000.0000.0000.000
46A66ALA00.0310.00014.4640.2990.2990.0000.0000.0000.000
47A67ALA0-0.074-0.04512.735-0.090-0.0900.0000.0000.0000.000
48A68ILE00.0090.00514.6250.1460.1460.0000.0000.0000.000
49A69LYS10.8390.89518.14411.87311.8730.0000.0000.0000.000
50A70ARG10.9250.99511.82416.90016.9000.0000.0000.0000.000
51A71ALA00.0780.05417.5780.0450.0450.0000.0000.0000.000
52A72SER0-0.034-0.01119.2450.2160.2160.0000.0000.0000.000
53A73SER0-0.012-0.02418.9350.2750.2750.0000.0000.0000.000
54A74LYS10.8970.94920.29311.43611.4360.0000.0000.0000.000
55A75GLU-1-0.885-0.95415.548-14.307-14.3070.0000.0000.0000.000
56A76GLY00.0200.01515.809-0.799-0.7990.0000.0000.0000.000
57A77ASN0-0.091-0.04317.9410.5590.5590.0000.0000.0000.000
58A78LEU00.0240.01912.350-0.234-0.2340.0000.0000.0000.000
59A79SER0-0.019-0.00516.0330.7670.7670.0000.0000.0000.000
60A80GLU-1-0.872-0.94615.810-17.315-17.3150.0000.0000.0000.000
61A81ILE0-0.055-0.02916.3541.0111.0110.0000.0000.0000.000
62A82THR00.0020.00216.624-1.161-1.1610.0000.0000.0000.000
63A83TYR00.0030.00015.5781.4721.4720.0000.0000.0000.000
64A84GLU-1-0.737-0.86317.386-14.634-14.6340.0000.0000.0000.000
65A85GLY00.0110.00117.9420.2580.2580.0000.0000.0000.000
66A86LYS10.9300.99218.83412.90512.9050.0000.0000.0000.000
67A87ALA00.0290.00217.534-0.434-0.4340.0000.0000.0000.000
68A88ASN0-0.012-0.01519.6121.0461.0460.0000.0000.0000.000
69A89PHE00.0330.00319.029-0.193-0.1930.0000.0000.0000.000
70A90GLY00.0250.03322.5160.0460.0460.0000.0000.0000.000
71A91VAL00.0390.04116.533-0.033-0.0330.0000.0000.0000.000
72A92LEU0-0.073-0.04519.2060.3950.3950.0000.0000.0000.000
73A93ILE00.012-0.01313.537-0.681-0.6810.0000.0000.0000.000
74A94ILE0-0.006-0.00315.5650.9280.9280.0000.0000.0000.000
75A95MET0-0.0290.00011.924-1.539-1.5390.0000.0000.0000.000
76A96GLU-1-0.760-0.85312.898-16.405-16.4050.0000.0000.0000.000
77A97CYS0-0.025-0.00712.053-2.529-2.5290.0000.0000.0000.000
78A98MET00.0220.02611.2181.7161.7160.0000.0000.0000.000
79A99THR0-0.006-0.01011.330-1.241-1.2410.0000.0000.0000.000
80A100ASP-1-0.818-0.86713.006-17.577-17.5770.0000.0000.0000.000
81A101ASN00.004-0.02215.6521.0551.0550.0000.0000.0000.000
82A102PRO00.0780.03716.811-0.641-0.6410.0000.0000.0000.000
83A103THR0-0.015-0.00418.382-0.261-0.2610.0000.0000.0000.000
84A104ARG10.7910.85412.15920.26720.2670.0000.0000.0000.000
85A105THR00.000-0.00313.403-0.071-0.0710.0000.0000.0000.000
86A106ILE0-0.0020.00015.445-0.589-0.5890.0000.0000.0000.000
87A107ALA0-0.022-0.01318.2630.1230.1230.0000.0000.0000.000
88A108ASN0-0.0080.00012.3131.7821.7820.0000.0000.0000.000
89A109LEU00.0530.03712.021-0.484-0.4840.0000.0000.0000.000
90A110LYS10.9210.97114.59815.26415.2640.0000.0000.0000.000
91A111SER0-0.051-0.02214.7380.5030.5030.0000.0000.0000.000
92A112TYR0-0.048-0.04810.5410.2620.2620.0000.0000.0000.000
93A113PHE00.1110.03814.1240.0820.0820.0000.0000.0000.000
94A114ASN0-0.049-0.02616.8011.4181.4180.0000.0000.0000.000
95A115LYS10.8820.94313.56422.29122.2910.0000.0000.0000.000
96A116THR0-0.063-0.02615.747-0.404-0.4040.0000.0000.0000.000
97A117GLN00.0250.00617.897-0.144-0.1440.0000.0000.0000.000
98A118GLY00.0240.01820.917-0.208-0.2080.0000.0000.0000.000
99A119ALA0-0.0240.00917.9320.0300.0300.0000.0000.0000.000
100A120SER0-0.063-0.02719.9290.4370.4370.0000.0000.0000.000
101A121ILE0-0.0110.00118.013-0.137-0.1370.0000.0000.0000.000
102A122VAL0-0.052-0.03720.0960.7950.7950.0000.0000.0000.000
103A123PRO0-0.009-0.00622.455-0.372-0.3720.0000.0000.0000.000
104A124ASN0-0.002-0.00821.438-0.085-0.0850.0000.0000.0000.000
105A125GLY00.0280.01024.2320.5600.5600.0000.0000.0000.000
106A126SER0-0.071-0.05224.3740.4770.4770.0000.0000.0000.000
107A127LEU0-0.077-0.05020.2860.2370.2370.0000.0000.0000.000
108A128GLU-1-0.919-0.95724.334-11.003-11.0030.0000.0000.0000.000
109A129PHE0-0.045-0.02926.7820.2380.2380.0000.0000.0000.000
110A130MET0-0.0230.00324.1510.2840.2840.0000.0000.0000.000
111A131PHE0-0.029-0.01418.140-0.410-0.4100.0000.0000.0000.000
112A132ASN00.0120.01822.9120.8310.8310.0000.0000.0000.000
113A133ARG10.8060.89317.93915.45015.4500.0000.0000.0000.000
114A134LYS10.8390.88221.72312.43012.4300.0000.0000.0000.000
115A135SER0-0.074-0.04821.454-0.898-0.8980.0000.0000.0000.000
116A136VAL0-0.030-0.01718.2970.3330.3330.0000.0000.0000.000
117A137PHE0-0.002-0.01719.114-0.675-0.6750.0000.0000.0000.000
118A138GLU-1-0.834-0.89314.730-19.582-19.5820.0000.0000.0000.000
119A139CYS0-0.031-0.02219.0290.2290.2290.0000.0000.0000.000
120A140LEU00.0580.04018.695-0.275-0.2750.0000.0000.0000.000
121A141LYS10.8660.92621.57011.22911.2290.0000.0000.0000.000
122A142ASN0-0.030-0.04122.8400.7740.7740.0000.0000.0000.000
123A143GLU-1-0.901-0.96223.413-10.862-10.8620.0000.0000.0000.000
124A144VAL0-0.006-0.00925.8280.3840.3840.0000.0000.0000.000
125A145GLU-1-0.863-0.92428.165-9.839-9.8390.0000.0000.0000.000
126A146ASN0-0.073-0.01427.9570.6940.6940.0000.0000.0000.000
127A147LEU0-0.110-0.04128.8290.3490.3490.0000.0000.0000.000
128A148LYS10.8560.91432.6528.1418.1410.0000.0000.0000.000
129A149LEU0-0.0170.00530.8720.2710.2710.0000.0000.0000.000
130A150SER0-0.037-0.03432.213-0.308-0.3080.0000.0000.0000.000
131A151LEU00.0310.00228.200-0.112-0.1120.0000.0000.0000.000
132A152GLU-1-0.854-0.94131.420-8.995-8.9950.0000.0000.0000.000
133A153ASP-1-0.881-0.91134.671-8.237-8.2370.0000.0000.0000.000
134A154LEU0-0.046-0.02727.1260.0040.0040.0000.0000.0000.000
135A155GLU-1-0.915-0.96631.248-9.890-9.8900.0000.0000.0000.000
136A156PHE0-0.044-0.02532.2330.1340.1340.0000.0000.0000.000
137A157ALA0-0.019-0.00633.5170.1060.1060.0000.0000.0000.000
138A158LEU0-0.004-0.01627.9830.0370.0370.0000.0000.0000.000
139A159ILE0-0.0020.02131.885-0.182-0.1820.0000.0000.0000.000
140A160ASP-1-0.930-0.95133.998-8.162-8.1620.0000.0000.0000.000
141A161TYR0-0.134-0.08331.1550.0980.0980.0000.0000.0000.000
142A162GLY0-0.010-0.02430.409-0.336-0.3360.0000.0000.0000.000
143A163LEU0-0.0490.00428.353-0.327-0.3270.0000.0000.0000.000
144A164GLU-1-0.856-0.92827.868-11.025-11.0250.0000.0000.0000.000
145A165GLU-1-0.888-0.94224.726-12.714-12.7140.0000.0000.0000.000
146A166LEU00.0200.00926.144-0.404-0.4040.0000.0000.0000.000
147A167GLU-1-0.843-0.89821.328-14.319-14.3190.0000.0000.0000.000
148A168GLU-1-0.879-0.96823.740-11.467-11.4670.0000.0000.0000.000
149A169VAL0-0.052-0.03417.549-0.328-0.3280.0000.0000.0000.000
150A170GLU-1-0.906-0.97020.056-13.076-13.0760.0000.0000.0000.000
151A171ASP-1-0.866-0.90719.632-14.319-14.3190.0000.0000.0000.000
152A172LYS10.8500.91914.48918.73418.7340.0000.0000.0000.000
153A173ILE00.0040.00720.8860.1320.1320.0000.0000.0000.000
154A174ILE0-0.020-0.01417.844-0.529-0.5290.0000.0000.0000.000
155A175ILE00.0310.02021.5270.4550.4550.0000.0000.0000.000
156A176ARG10.7840.86419.07114.18414.1840.0000.0000.0000.000
157A177GLY00.1230.06624.2630.6320.6320.0000.0000.0000.000
158A178ASP-1-0.798-0.88925.472-11.825-11.8250.0000.0000.0000.000
159A179TYR00.0070.02323.509-0.307-0.3070.0000.0000.0000.000
160A180ASN0-0.069-0.05025.700-0.054-0.0540.0000.0000.0000.000
161A181SER0-0.0140.00128.2270.3650.3650.0000.0000.0000.000
162A182PHE00.0150.02420.7550.0710.0710.0000.0000.0000.000
163A183LYS10.8930.93925.8349.6269.6260.0000.0000.0000.000
164A184LEU0-0.0090.00927.8600.0680.0680.0000.0000.0000.000
165A185LEU00.1120.05625.4550.1150.1150.0000.0000.0000.000
166A186ASN0-0.088-0.05823.831-0.409-0.4090.0000.0000.0000.000
167A187GLU-1-0.890-0.94926.654-9.049-9.0490.0000.0000.0000.000
168A188GLY00.0520.04030.1150.2440.2440.0000.0000.0000.000
169A189PHE00.028-0.00924.3920.1510.1510.0000.0000.0000.000
170A190GLU-1-0.932-0.94927.008-10.604-10.6040.0000.0000.0000.000
171A191SER0-0.103-0.05829.5030.4000.4000.0000.0000.0000.000
172A192LEU0-0.018-0.01330.4110.3160.3160.0000.0000.0000.000
173A193LYS10.8020.90429.8738.7958.7950.0000.0000.0000.000
174A194LEU00.0310.02925.721-0.023-0.0230.0000.0000.0000.000
175A195PRO0-0.010-0.01023.226-0.305-0.3050.0000.0000.0000.000
176A196ILE0-0.0120.00919.385-0.188-0.1880.0000.0000.0000.000
177A197LEU0-0.033-0.01115.493-0.227-0.2270.0000.0000.0000.000
178A198LYS10.8770.91611.98621.18621.1860.0000.0000.0000.000
179A199ALA00.0400.04716.3750.5520.5520.0000.0000.0000.000
180A200SER0-0.060-0.02815.548-1.132-1.1320.0000.0000.0000.000
181A201LEU00.0210.01717.6640.7850.7850.0000.0000.0000.000
182A202GLN0-0.013-0.00615.719-1.029-1.0290.0000.0000.0000.000
183A203ARG10.8310.90917.12117.62617.6260.0000.0000.0000.000
184A204ILE00.0490.01617.892-0.940-0.9400.0000.0000.0000.000
185A205ALA00.0070.01419.9850.7300.7300.0000.0000.0000.000
186A206THR0-0.014-0.01621.7950.1180.1180.0000.0000.0000.000
187A207THR0-0.051-0.02725.0420.5370.5370.0000.0000.0000.000
188A208PRO00.0060.01521.670-0.140-0.1400.0000.0000.0000.000
189A209ILE0-0.058-0.01620.7060.6880.6880.0000.0000.0000.000
190A210GLU-1-0.898-0.94620.972-13.517-13.5170.0000.0000.0000.000
191A211LEU0-0.070-0.03217.3080.4810.4810.0000.0000.0000.000
192A212ASN00.0220.00820.725-0.593-0.5930.0000.0000.0000.000
193A213ASP-1-0.832-0.94019.129-15.652-15.6520.0000.0000.0000.000
194A214GLU-1-0.976-0.97818.479-13.982-13.9820.0000.0000.0000.000
195A215GLN0-0.011-0.01818.954-0.720-0.7200.0000.0000.0000.000
196A216MET00.0470.04514.376-1.007-1.0070.0000.0000.0000.000
197A217GLU-1-0.896-0.93114.364-19.796-19.7960.0000.0000.0000.000
198A218LEU0-0.087-0.05314.200-1.195-1.1950.0000.0000.0000.000
199A219THR0-0.075-0.06014.121-0.269-0.2690.0000.0000.0000.000
200A220GLU-1-0.861-0.94010.432-26.671-26.6710.0000.0000.0000.000
201A221LYS10.9250.9739.51319.35619.3560.0000.0000.0000.000
202A222LEU0-0.096-0.05710.045-2.005-2.0050.0000.0000.0000.000
203A223LEU00.033-0.0019.568-1.099-1.0990.0000.0000.0000.000
204A224ASP-1-0.838-0.9075.691-49.810-49.8100.0000.0000.0000.000
205A225ARG10.7280.8585.38919.48819.4880.0000.0000.0000.000
206A226ILE0-0.035-0.0197.449-0.766-0.7660.0000.0000.0000.000
207A227GLU-1-0.883-0.9343.780-44.426-44.231-0.001-0.042-0.1530.000
208A228ASP-1-0.938-0.9631.719-134.647-135.81513.321-7.217-4.936-0.095
209A229ASP-1-0.785-0.8604.111-24.518-24.405-0.001-0.017-0.0960.000
210A230ASP-1-0.881-0.9514.447-40.378-40.278-0.001-0.010-0.0880.000
211A231ASP-1-0.863-0.9176.313-20.531-20.5310.0000.0000.0000.000
212A232VAL00.0170.0047.9873.1463.1460.0000.0000.0000.000
213A233VAL0-0.059-0.0297.828-4.571-4.5710.0000.0000.0000.000
214A234ALA00.0100.0049.331-0.122-0.1220.0000.0000.0000.000
215A235LEU00.0240.0207.9851.8641.8640.0000.0000.0000.000
216A236TYR00.0130.01510.912-0.164-0.1640.0000.0000.0000.000
217A237THR00.0340.00612.8960.8300.8300.0000.0000.0000.000
218A238ASN00.013-0.00715.653-0.520-0.5200.0000.0000.0000.000
219A239ILE0-0.014-0.01414.8320.8860.8860.0000.0000.0000.000
220A240GLU-1-0.940-0.95817.737-15.693-15.6930.0000.0000.0000.000