FMODB

FMODB: The database of quantum mechanical data based on the FMO method

Last updated: 2025-07-23

All entries: 44592

Number of unique PDB entries: 7794

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FMODB ID: YZ3M2

Calculation Name: 5CWB-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 5CWB

Chain ID: A

ChEMBL ID:

UniProt ID:

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:

Apendix: None


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 194
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2257248.253715
FMO2-HF: Nuclear repulsion 2179659.392518
FMO2-HF: Total energy -77588.861197
FMO2-MP2: Total energy -77814.107104


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:5:ASP)


Summations of interaction energy for fragment #1(A:5:ASP)
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.
106.23109.627-0.021-1.654-1.7220.005
Interaction energy analysis for fragmet #1(A:5:ASP)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : -1 / q_Mulliken : -0.932 / q_NPA : -0.971
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].
3A7CYS0-0.062-0.0253.473-9.598-6.201-0.021-1.654-1.7220.005
4A8GLU-1-0.801-0.8625.21521.72621.7260.0000.0000.0000.000
5A9GLU-1-0.781-0.8696.50421.02621.0260.0000.0000.0000.000
6A10LYS10.7900.8817.614-24.581-24.5810.0000.0000.0000.000
7A11ALA00.0130.0099.317-2.417-2.4170.0000.0000.0000.000
8A12ARG10.8440.90210.692-24.076-24.0760.0000.0000.0000.000
9A13ARG10.8240.89310.159-25.431-25.4310.0000.0000.0000.000
10A14VAL00.0050.00313.277-1.296-1.2960.0000.0000.0000.000
11A15ALA00.0390.02115.300-1.260-1.2600.0000.0000.0000.000
12A16GLU-1-0.886-0.93616.65815.63215.6320.0000.0000.0000.000
13A17LYS10.7520.87018.101-15.391-15.3910.0000.0000.0000.000
14A18VAL00.0570.03419.646-0.757-0.7570.0000.0000.0000.000
15A19GLU-1-0.819-0.88621.31711.80811.8080.0000.0000.0000.000
16A20ARG10.7740.87118.145-15.456-15.4560.0000.0000.0000.000
17A21LEU00.0030.01522.974-0.453-0.4530.0000.0000.0000.000
18A22LYS10.8920.93825.672-10.989-10.9890.0000.0000.0000.000
19A23ARG10.7660.86724.941-11.799-11.7990.0000.0000.0000.000
20A24SER0-0.081-0.04128.711-0.241-0.2410.0000.0000.0000.000
21A25GLY0-0.024-0.01230.637-0.234-0.2340.0000.0000.0000.000
22A26THR0-0.080-0.03827.434-0.183-0.1830.0000.0000.0000.000
23A27SER0-0.036-0.04730.2010.0480.0480.0000.0000.0000.000
24A28GLU-1-0.846-0.94628.5079.8989.8980.0000.0000.0000.000
25A29ASP-1-0.927-0.96327.70510.37210.3720.0000.0000.0000.000
26A30GLU-1-0.859-0.89827.64210.16010.1600.0000.0000.0000.000
27A31ILE0-0.056-0.03423.4660.5670.5670.0000.0000.0000.000
28A32ALA00.0120.00723.1680.6780.6780.0000.0000.0000.000
29A33GLU-1-0.959-0.96622.90711.66311.6630.0000.0000.0000.000
30A34GLU-1-0.750-0.84420.57014.63914.6390.0000.0000.0000.000
31A35VAL0-0.001-0.00717.7600.8680.8680.0000.0000.0000.000
32A36ALA00.0010.00517.9570.9900.9900.0000.0000.0000.000
33A37ARG10.7970.87417.570-14.532-14.5320.0000.0000.0000.000
34A38GLU-1-0.838-0.92615.04818.58118.5810.0000.0000.0000.000
35A39ILE0-0.001-0.00613.8851.5221.5220.0000.0000.0000.000
36A40SER0-0.006-0.00814.2650.9440.9440.0000.0000.0000.000
37A41GLU-1-0.858-0.92413.12819.52719.5270.0000.0000.0000.000
38A42VAL0-0.0090.0038.8801.2521.2520.0000.0000.0000.000
39A43ILE0-0.001-0.00210.4431.8271.8270.0000.0000.0000.000
40A44ARG10.8160.88712.510-14.881-14.8810.0000.0000.0000.000
41A45THR00.0170.0079.063-0.043-0.0430.0000.0000.0000.000
42A46LEU0-0.006-0.0035.4761.3811.3810.0000.0000.0000.000
43A47LYS10.9000.9409.093-17.396-17.3960.0000.0000.0000.000
44A48GLU-1-0.973-0.98612.44318.51718.5170.0000.0000.0000.000
45A49SER0-0.086-0.0458.4720.0370.0370.0000.0000.0000.000
46A50GLY0-0.044-0.01510.2061.5101.5100.0000.0000.0000.000
47A51SER0-0.060-0.0277.5582.4242.4240.0000.0000.0000.000
48A52SER0-0.039-0.0499.213-1.623-1.6230.0000.0000.0000.000
49A53TYR00.0690.00410.6681.1451.1450.0000.0000.0000.000
50A54GLU-1-0.828-0.88411.69321.87621.8760.0000.0000.0000.000
51A55VAL0-0.027-0.0095.5800.5690.5690.0000.0000.0000.000
52A56ILE00.0020.0008.3770.9900.9900.0000.0000.0000.000
53A57CYS0-0.094-0.05010.0460.0810.0810.0000.0000.0000.000
54A58GLH0-0.048-0.0579.474-1.290-1.2900.0000.0000.0000.000
55A60VAL00.0350.0058.644-1.287-1.2870.0000.0000.0000.000
56A61ALA0-0.0010.00912.052-1.249-1.2490.0000.0000.0000.000
57A62ARG10.9290.9586.738-30.907-30.9070.0000.0000.0000.000
58A63ILE0-0.019-0.0189.492-1.026-1.0260.0000.0000.0000.000
59A64VAL00.0170.00412.745-1.216-1.2160.0000.0000.0000.000
60A65ALA00.0050.00914.635-1.068-1.0680.0000.0000.0000.000
61A66GLU-1-0.842-0.93212.76117.94717.9470.0000.0000.0000.000
62A67ILE0-0.028-0.01015.812-0.960-0.9600.0000.0000.0000.000
63A68VAL00.0120.00618.443-0.850-0.8500.0000.0000.0000.000
64A69GLU-1-0.820-0.89717.81415.02215.0220.0000.0000.0000.000
65A70ALA0-0.058-0.03719.436-0.610-0.6100.0000.0000.0000.000
66A71LEU0-0.003-0.00121.238-0.609-0.6090.0000.0000.0000.000
67A72LYS10.8470.91423.697-11.353-11.3530.0000.0000.0000.000
68A73ARG10.9090.97118.678-14.775-14.7750.0000.0000.0000.000
69A74SER0-0.081-0.03425.504-0.382-0.3820.0000.0000.0000.000
70A75GLY0-0.038-0.01727.895-0.327-0.3270.0000.0000.0000.000
71A76THR0-0.067-0.03127.230-0.314-0.3140.0000.0000.0000.000
72A77SER00.0050.00429.3840.1010.1010.0000.0000.0000.000
73A78GLU-1-0.868-0.96329.8349.7689.7680.0000.0000.0000.000
74A79ASP-1-0.892-0.94029.9079.2549.2540.0000.0000.0000.000
75A80GLU-1-0.753-0.85328.04610.55010.5500.0000.0000.0000.000
76A81ILE0-0.059-0.03924.3680.4740.4740.0000.0000.0000.000
77A82ALA00.0090.00125.5860.4910.4910.0000.0000.0000.000
78A83GLU-1-0.743-0.83927.03010.12710.1270.0000.0000.0000.000
79A84ILE0-0.029-0.00622.4570.3730.3730.0000.0000.0000.000
80A85VAL0-0.033-0.03021.2770.5270.5270.0000.0000.0000.000
81A86ALA00.0020.00622.7850.3850.3850.0000.0000.0000.000
82A87ARG10.8820.93424.054-11.778-11.7780.0000.0000.0000.000
83A88VAL0-0.013-0.00818.2810.3470.3470.0000.0000.0000.000
84A89ILE00.0240.00319.6060.5180.5180.0000.0000.0000.000
85A90SER00.0470.02921.6820.1770.1770.0000.0000.0000.000
86A91GLU-1-0.828-0.90820.37112.67612.6760.0000.0000.0000.000
87A92VAL0-0.046-0.00416.7810.5090.5090.0000.0000.0000.000
88A93ILE0-0.019-0.01319.1960.2100.2100.0000.0000.0000.000
89A94ARG10.8340.89822.070-11.667-11.6670.0000.0000.0000.000
90A95THR0-0.0110.00317.151-0.086-0.0860.0000.0000.0000.000
91A96LEU00.0230.00715.7340.1880.1880.0000.0000.0000.000
92A97LYS10.9410.99019.427-11.618-11.6180.0000.0000.0000.000
93A98GLU-1-0.893-0.91520.85013.97213.9720.0000.0000.0000.000
94A99SER0-0.075-0.04318.3170.2310.2310.0000.0000.0000.000
95A100GLY0-0.001-0.00820.3810.2670.2670.0000.0000.0000.000
96A101SER0-0.054-0.01219.2850.2940.2940.0000.0000.0000.000
97A102SER00.0160.01321.345-0.477-0.4770.0000.0000.0000.000
98A103TYR00.062-0.02022.7200.3600.3600.0000.0000.0000.000
99A104GLU-1-0.932-0.94822.71213.04013.0400.0000.0000.0000.000
100A105VAL00.0190.00817.5530.3090.3090.0000.0000.0000.000
101A106ILE0-0.010-0.00119.3710.4960.4960.0000.0000.0000.000
102A107CYS0-0.064-0.03020.7330.4870.4870.0000.0000.0000.000
103A108GLU-1-0.813-0.88218.47014.63414.6340.0000.0000.0000.000
104A110VAL00.026-0.00117.6750.3420.3420.0000.0000.0000.000
105A111ALA00.0010.00920.219-0.146-0.1460.0000.0000.0000.000
106A112ARG10.8220.91214.843-17.907-17.9070.0000.0000.0000.000
107A113ILE0-0.015-0.01315.5440.1700.1700.0000.0000.0000.000
108A114VAL00.0160.00117.676-0.240-0.2400.0000.0000.0000.000
109A115ALA0-0.0060.00319.532-0.400-0.4000.0000.0000.0000.000
110A116GLU-1-0.809-0.87613.67520.80620.8060.0000.0000.0000.000
111A117ILE0-0.019-0.00218.029-0.077-0.0770.0000.0000.0000.000
112A118VAL00.0160.00920.385-0.455-0.4550.0000.0000.0000.000
113A119GLU-1-0.847-0.92818.29415.09615.0960.0000.0000.0000.000
114A120ALA0-0.011-0.00418.412-0.175-0.1750.0000.0000.0000.000
115A121LEU0-0.010-0.00220.152-0.337-0.3370.0000.0000.0000.000
116A122LYS10.8370.89923.644-10.964-10.9640.0000.0000.0000.000
117A123ARG10.7870.89316.768-16.258-16.2580.0000.0000.0000.000
118A124SER0-0.043-0.02522.404-0.164-0.1640.0000.0000.0000.000
119A125GLY0-0.0430.00724.454-0.403-0.4030.0000.0000.0000.000
120A126THR0-0.037-0.06626.916-0.058-0.0580.0000.0000.0000.000
121A127SER0-0.075-0.07129.279-0.188-0.1880.0000.0000.0000.000
122A128GLU-1-0.875-0.95131.1158.9608.9600.0000.0000.0000.000
123A129ASP-1-0.786-0.87832.8198.5748.5740.0000.0000.0000.000
124A130GLU-1-0.799-0.84628.37110.57410.5740.0000.0000.0000.000
125A131ILE0-0.016-0.01026.9900.2960.2960.0000.0000.0000.000
126A132ALA0-0.0040.00029.1420.2070.2070.0000.0000.0000.000
127A133GLU-1-0.792-0.85331.8248.6838.6830.0000.0000.0000.000
128A134ILE00.0430.02425.6410.1570.1570.0000.0000.0000.000
129A135VAL0-0.023-0.01626.2140.2140.2140.0000.0000.0000.000
130A136ALA0-0.028-0.01028.1790.0690.0690.0000.0000.0000.000
131A137ARG10.7550.83429.387-10.112-10.1120.0000.0000.0000.000
132A138VAL00.0220.00524.0240.0570.0570.0000.0000.0000.000
133A139ILE0-0.010-0.01527.2930.0600.0600.0000.0000.0000.000
134A140SER0-0.015-0.03528.857-0.133-0.1330.0000.0000.0000.000
135A141GLU-1-0.798-0.86226.54110.42510.4250.0000.0000.0000.000
136A142VAL0-0.0050.01124.8880.0490.0490.0000.0000.0000.000
137A143ILE0-0.037-0.01427.612-0.102-0.1020.0000.0000.0000.000
138A144ARG10.9400.97131.126-9.037-9.0370.0000.0000.0000.000
139A145THR00.0250.00325.853-0.063-0.0630.0000.0000.0000.000
140A146LEU0-0.012-0.01726.3210.0210.0210.0000.0000.0000.000
141A147LYS10.8710.94829.385-8.509-8.5090.0000.0000.0000.000
142A148GLU-1-0.874-0.91529.11710.14710.1470.0000.0000.0000.000
143A149SER0-0.099-0.05028.3650.0820.0820.0000.0000.0000.000
144A150GLY0-0.012-0.01230.3190.0650.0650.0000.0000.0000.000
145A151SER0-0.047-0.01030.1720.0330.0330.0000.0000.0000.000
146A152SER0-0.027-0.03832.100-0.175-0.1750.0000.0000.0000.000
147A153TYR00.0480.00133.6640.2120.2120.0000.0000.0000.000
148A154GLU-1-0.860-0.92434.8228.5478.5470.0000.0000.0000.000
149A155VAL00.0390.03228.7770.1810.1810.0000.0000.0000.000
150A156ILE0-0.020-0.00430.0890.2610.2610.0000.0000.0000.000
151A157LYS10.8150.90231.120-8.255-8.2550.0000.0000.0000.000
152A158GLU-1-0.928-0.95629.35810.14010.1400.0000.0000.0000.000
153A160VAL00.010-0.00427.1790.2740.2740.0000.0000.0000.000
154A161GLN0-0.087-0.04629.215-0.129-0.1290.0000.0000.0000.000
155A162ARG10.8220.88922.495-12.795-12.7950.0000.0000.0000.000
156A163ILE00.0270.00123.8910.3120.3120.0000.0000.0000.000
157A164VAL0-0.013-0.01125.6310.0860.0860.0000.0000.0000.000
158A165GLU-1-0.834-0.89826.98010.97910.9790.0000.0000.0000.000
159A166GLU-1-0.763-0.88819.90614.97114.9710.0000.0000.0000.000
160A167ILE0-0.0170.00723.6460.2200.2200.0000.0000.0000.000
161A168VAL00.000-0.00425.462-0.101-0.1010.0000.0000.0000.000
162A169GLU-1-0.856-0.91824.14911.02111.0210.0000.0000.0000.000
163A170ALA00.0050.00222.1670.0780.0780.0000.0000.0000.000
164A171LEU0-0.006-0.00223.416-0.085-0.0850.0000.0000.0000.000
165A172LYS10.8680.91626.750-10.604-10.6040.0000.0000.0000.000
166A173ARG10.7540.89320.231-14.402-14.4020.0000.0000.0000.000
167A174SER0-0.061-0.02124.4860.1940.1940.0000.0000.0000.000
168A175GLY0-0.055-0.01325.979-0.261-0.2610.0000.0000.0000.000
169A176THR0-0.070-0.03628.434-0.307-0.3070.0000.0000.0000.000
170A177SER0-0.0020.00131.032-0.174-0.1740.0000.0000.0000.000
171A178GLU-1-0.810-0.92734.2568.9288.9280.0000.0000.0000.000
172A179ASP-1-0.923-0.96735.9177.6877.6870.0000.0000.0000.000
173A180GLU-1-0.860-0.91231.5629.5349.5340.0000.0000.0000.000
174A181ILE00.0230.00630.7530.1530.1530.0000.0000.0000.000
175A182ASN0-0.094-0.06933.2110.0050.0050.0000.0000.0000.000
176A183GLU-1-0.860-0.89936.3447.6547.6540.0000.0000.0000.000
177A184ILE00.0680.04030.2070.0270.0270.0000.0000.0000.000
178A185VAL0-0.039-0.02431.9900.0280.0280.0000.0000.0000.000
179A186ARG10.7750.88134.052-7.852-7.8520.0000.0000.0000.000
180A187ARG10.7440.83635.067-8.736-8.7360.0000.0000.0000.000
181A188VAL00.0520.01930.966-0.070-0.0700.0000.0000.0000.000
182A189LYS10.9390.96034.032-8.786-8.7860.0000.0000.0000.000
183A190SER0-0.053-0.02336.320-0.168-0.1680.0000.0000.0000.000
184A191GLU-1-0.786-0.85133.6218.5178.5170.0000.0000.0000.000
185A192VAL00.0200.01632.856-0.059-0.0590.0000.0000.0000.000
186A193GLU-1-0.832-0.93135.5248.0828.0820.0000.0000.0000.000
187A194ARG10.8480.94038.978-7.778-7.7780.0000.0000.0000.000
188A195THR00.0440.02334.060-0.224-0.2240.0000.0000.0000.000
189A196LEU0-0.040-0.01035.458-0.057-0.0570.0000.0000.0000.000
190A197LYS10.8340.89938.328-7.484-7.4840.0000.0000.0000.000
191A198GLU-1-0.904-0.94139.2617.6897.6890.0000.0000.0000.000
192A199SER0-0.062-0.04536.9570.0210.0210.0000.0000.0000.000
193A200GLY00.0050.02839.313-0.062-0.0620.0000.0000.0000.000
194A201SER0-0.027-0.02240.5010.1280.1280.0000.0000.0000.000