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

tag_button

FMODB ID: ZYR6N

Calculation Name: 3MTV-A-Xray317

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3MTV

Chain ID: A

ChEMBL ID:

UniProt ID: B2ZAB4

Base Structure: X-ray

Registration Date: 2021-09-07

Reference: C. Watanabe, S. Koyama, K. Kamisaka, D. Takaya, T. Honma et. al., Interaction energy analysis of Apo structure dataset on FMODB, To be pubulished.

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. 1.20200129
FMO calculation
FMO method FMO2-MP2/6-31G(d)
Fragmentation Auto
Number of fragment 203
LigandCharge
Software ABINIT-MP - Open Ver.1 Rev. 15 / 20190524
Total energy (hartree)
FMO2-HF: Electronic energy -2245205.346084
FMO2-HF: Nuclear repulsion 2165410.191261
FMO2-HF: Total energy -79795.154823
FMO2-MP2: Total energy -80032.006551


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:1:ALA )


Summations of interaction energy for fragment #1(A:1:ALA )
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.
72.91373.9354.936-3.708-2.249-0.019
Interaction energy analysis for fragmet #1(A:1:ALA )
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 1 / q_Mulliken : 0.763 / q_NPA : 0.864
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].
3A3VAL 0-0.058-0.0273.8942.5173.722-0.003-0.663-0.539-0.002
4A4TYR 00.0420.0286.1862.5062.5060.0000.0000.0000.000
5A5ASP -1-0.826-0.9029.982-17.349-17.3490.0000.0000.0000.000
6A6ILE 0-0.023-0.03212.2280.4180.4180.0000.0000.0000.000
7A7GLY 0-0.0020.00214.9960.9980.9980.0000.0000.0000.000
8A8ARG 10.8740.92117.18015.29315.2930.0000.0000.0000.000
9A9GLY 00.0210.01918.4810.0970.0970.0000.0000.0000.000
10A10ALA 0-0.0130.00614.116-0.313-0.3130.0000.0000.0000.000
11A11VAL 0-0.010-0.0029.8700.1510.1510.0000.0000.0000.000
12A12MET 00.002-0.0148.7270.8070.8070.0000.0000.0000.000
13A13TYR 0-0.050-0.0154.010-2.573-2.4880.000-0.016-0.0690.000
14A14VAL 00.046-0.0014.4934.3574.4770.000-0.015-0.1040.000
15A15ALA 0-0.020-0.0111.836-16.507-17.0414.930-2.973-1.423-0.017
16A16GLY 00.0370.0373.7205.9816.1270.009-0.041-0.1140.000
17A17GLY 00.0210.0117.2370.2660.2660.0000.0000.0000.000
18A18LYS 10.8780.9337.68328.08128.0810.0000.0000.0000.000
19A19VAL 00.0540.0266.852-4.137-4.1370.0000.0000.0000.000
20A20SER 0-0.0030.0007.6282.9862.9860.0000.0000.0000.000
21A21TRP 00.0290.0069.333-0.728-0.7280.0000.0000.0000.000
22A22ALA 00.0390.02110.6000.5770.5770.0000.0000.0000.000
23A23PRO 00.0310.00112.2890.0010.0010.0000.0000.0000.000
24A24ARG 10.8620.96713.51515.39215.3920.0000.0000.0000.000
25A25GLY 00.0760.02414.147-0.897-0.8970.0000.0000.0000.000
26A26GLY 00.0860.03316.9010.6320.6320.0000.0000.0000.000
27A27ASN 0-0.083-0.04118.262-0.850-0.8500.0000.0000.0000.000
28A28GLU -1-0.869-0.95016.975-15.329-15.3290.0000.0000.0000.000
29A29VAL 0-0.056-0.02513.121-0.798-0.7980.0000.0000.0000.000
30A30LYS 10.8560.92914.65314.85714.8570.0000.0000.0000.000
31A31PHE 00.0480.0348.637-0.295-0.2950.0000.0000.0000.000
32A32GLU -1-0.886-0.95111.699-22.951-22.9510.0000.0000.0000.000
33A33PRO 0-0.030-0.01412.606-0.854-0.8540.0000.0000.0000.000
34A34VAL 00.0270.02612.439-0.772-0.7720.0000.0000.0000.000
35A35PRO 00.0750.03711.6752.0332.0330.0000.0000.0000.000
36A36LYS 10.8400.91714.90215.26115.2610.0000.0000.0000.000
37A37GLU -1-0.895-0.95014.764-17.845-17.8450.0000.0000.0000.000
38A38LEU 00.0360.00110.298-0.532-0.5320.0000.0000.0000.000
39A39LYS 10.9320.97514.59415.84015.8400.0000.0000.0000.000
40A40LEU 0-0.0150.00717.0320.3910.3910.0000.0000.0000.000
41A41VAL 00.081-0.00812.4620.6150.6150.0000.0000.0000.000
42A42ALA 00.0360.05514.282-0.260-0.2600.0000.0000.0000.000
43A43ASN 0-0.006-0.01915.215-0.266-0.2660.0000.0000.0000.000
44A44ARG 10.9610.99717.42915.18415.1840.0000.0000.0000.000
45A45LEU 00.0860.03911.7960.7670.7670.0000.0000.0000.000
46A46HIS 0-0.0330.00115.7831.1521.1520.0000.0000.0000.000
47A47THR 00.0150.02216.9490.8610.8610.0000.0000.0000.000
48A48SER 0-0.045-0.04219.4270.5650.5650.0000.0000.0000.000
49A49PHE 00.0210.02016.3830.2950.2950.0000.0000.0000.000
50A50PRO 00.0320.01717.7110.1760.1760.0000.0000.0000.000
51A51PRO 00.0090.00014.302-0.814-0.8140.0000.0000.0000.000
52A52HIS 0-0.0130.00711.535-0.436-0.4360.0000.0000.0000.000
53A53HIS 0-0.051-0.02512.5910.4410.4410.0000.0000.0000.000
54A54VAL 00.0150.0168.731-0.851-0.8510.0000.0000.0000.000
55A55VAL 00.0100.00611.3241.7121.7120.0000.0000.0000.000
56A56ASP -1-0.802-0.87311.633-22.668-22.6680.0000.0000.0000.000
57A57MET 0-0.077-0.03913.0451.7781.7780.0000.0000.0000.000
58A58SER 0-0.022-0.04215.1241.4991.4990.0000.0000.0000.000
59A59LYS 10.8510.92416.79618.54418.5440.0000.0000.0000.000
60A60PHE 00.0280.02716.9630.5210.5210.0000.0000.0000.000
61A61THR 00.002-0.00320.4570.0810.0810.0000.0000.0000.000
62A62PHE 00.015-0.00917.9940.0320.0320.0000.0000.0000.000
63A63ILE 00.0540.02823.5530.2480.2480.0000.0000.0000.000
64A64THR 0-0.048-0.01426.225-0.293-0.2930.0000.0000.0000.000
65A65PRO 00.034-0.00924.8060.0670.0670.0000.0000.0000.000
66A66GLY 00.0230.02627.1300.3320.3320.0000.0000.0000.000
67A67SER 0-0.052-0.02829.2880.4090.4090.0000.0000.0000.000
68A68GLY 00.0590.03027.9760.0780.0780.0000.0000.0000.000
69A69VAL 0-0.0010.00126.8970.1860.1860.0000.0000.0000.000
70A70SER 00.019-0.00823.176-0.657-0.6570.0000.0000.0000.000
71A71MET 0-0.036-0.02721.5370.2910.2910.0000.0000.0000.000
72A72ARG 10.8080.92519.89314.29114.2910.0000.0000.0000.000
73A73VAL 00.0300.01823.3080.3720.3720.0000.0000.0000.000
74A74GLU -1-0.895-0.95223.134-12.310-12.3100.0000.0000.0000.000
75A75TYR 0-0.071-0.02822.7060.2280.2280.0000.0000.0000.000
76A76GLN 00.008-0.00626.773-0.025-0.0250.0000.0000.0000.000
77A77TYR 00.0170.01828.9630.0080.0080.0000.0000.0000.000
78A78GLY 0-0.033-0.03025.307-0.316-0.3160.0000.0000.0000.000
79A79CYS 0-0.082-0.05322.3070.0920.0920.0000.0000.0000.000
80A80LEU 0-0.0050.01121.304-0.370-0.3700.0000.0000.0000.000
81A81PRO 00.0850.08025.1140.5060.5060.0000.0000.0000.000
82A82ALA 00.0290.01627.526-0.273-0.2730.0000.0000.0000.000
83A83ASP -1-0.894-0.92229.652-9.949-9.9490.0000.0000.0000.000
84A84THR 0-0.109-0.11525.192-0.311-0.3110.0000.0000.0000.000
85A85VAL 00.0170.00524.283-0.594-0.5940.0000.0000.0000.000
86A86PRO 0-0.038-0.01425.5470.3960.3960.0000.0000.0000.000
87A87GLU -1-0.866-0.93328.778-8.923-8.9230.0000.0000.0000.000
88A88GLY 0-0.036-0.01931.2700.1480.1480.0000.0000.0000.000
89A89ASN 00.010-0.00732.149-0.043-0.0430.0000.0000.0000.000
90A90CYS 0-0.0350.01531.6950.0380.0380.0000.0000.0000.000
91A91TRP 0-0.010-0.02534.0090.1630.1630.0000.0000.0000.000
92A92TRP 00.0370.00735.7270.1530.1530.0000.0000.0000.000
93A93ARG 11.0231.04234.1448.9678.9670.0000.0000.0000.000
94A94LEU 0-0.021-0.03035.8110.1300.1300.0000.0000.0000.000
95A95LEU 0-0.086-0.04539.4810.1490.1490.0000.0000.0000.000
96A96ASP -1-0.852-0.93342.117-7.388-7.3880.0000.0000.0000.000
97A97SER 0-0.096-0.02644.1650.2050.2050.0000.0000.0000.000
98A98LEU 0-0.034-0.02745.7750.1510.1510.0000.0000.0000.000
99A99PRO 00.0600.05048.549-0.031-0.0310.0000.0000.0000.000
100A100PRO 00.1180.05749.399-0.111-0.1110.0000.0000.0000.000
101A101GLU -1-0.886-0.96149.454-6.038-6.0380.0000.0000.0000.000
102A102VAL 0-0.009-0.01448.201-0.083-0.0830.0000.0000.0000.000
103A103GLN 00.0000.01845.084-0.221-0.2210.0000.0000.0000.000
104A104TYR 00.029-0.00945.529-0.046-0.0460.0000.0000.0000.000
105A105LYS 10.8730.93546.6195.8975.8970.0000.0000.0000.000
106A106GLU -1-0.799-0.89643.425-7.111-7.1110.0000.0000.0000.000
107A107ILE 0-0.0260.00041.453-0.148-0.1480.0000.0000.0000.000
108A108ARG 10.9640.97442.3916.2516.2510.0000.0000.0000.000
109A109HIS 0-0.033-0.00743.806-0.024-0.0240.0000.0000.0000.000
110A110ALA 0-0.028-0.03438.883-0.079-0.0790.0000.0000.0000.000
111A111ASN 00.023-0.01739.776-0.334-0.3340.0000.0000.0000.000
112A112GLN 0-0.0790.00841.1880.1280.1280.0000.0000.0000.000
113A113PHE 0-0.071-0.01738.9140.0030.0030.0000.0000.0000.000
114A114GLY 00.0300.01436.429-0.008-0.0080.0000.0000.0000.000
115A115TYR 00.022-0.02734.1640.1020.1020.0000.0000.0000.000
116A116GLN 00.0110.05435.279-0.015-0.0150.0000.0000.0000.000
117A117THR 0-0.044-0.02331.543-0.079-0.0790.0000.0000.0000.000
118A118LYS 10.9590.98626.51611.16311.1630.0000.0000.0000.000
119A119HIS 0-0.042-0.03025.989-0.527-0.5270.0000.0000.0000.000
120A120GLY 00.0680.04229.109-0.107-0.1070.0000.0000.0000.000
121A121VAL 0-0.068-0.04132.1140.1500.1500.0000.0000.0000.000
122A122PRO 0-0.001-0.00631.401-0.188-0.1880.0000.0000.0000.000
123A123GLY 00.0810.04231.355-0.241-0.2410.0000.0000.0000.000
124A124LYS 10.9330.96331.8149.5939.5930.0000.0000.0000.000
125A125TYR 0-0.0220.00235.4910.2650.2650.0000.0000.0000.000
126A126LEU 00.0380.01333.7960.1840.1840.0000.0000.0000.000
127A127GLN 0-0.021-0.02036.499-0.013-0.0130.0000.0000.0000.000
128A128ARG 10.9771.00438.1038.0288.0280.0000.0000.0000.000
129A129ARG 10.8800.95440.3647.2957.2950.0000.0000.0000.000
130A130LEU 00.1010.01739.235-0.070-0.0700.0000.0000.0000.000
131A131GLN 0-0.0140.01842.1770.0280.0280.0000.0000.0000.000
132A132VAL 0-0.073-0.03143.9090.1440.1440.0000.0000.0000.000
133A133ASN 0-0.088-0.06845.1900.2610.2610.0000.0000.0000.000
134A134GLY 00.0170.03747.2850.0860.0860.0000.0000.0000.000
135A135LEU 0-0.0090.00143.348-0.030-0.0300.0000.0000.0000.000
136A136ARG 10.7660.85442.0046.9416.9410.0000.0000.0000.000
137A137ALA 0-0.0140.01837.2690.0020.0020.0000.0000.0000.000
138A138VAL 00.020-0.00638.206-0.114-0.1140.0000.0000.0000.000
139A139THR 0-0.071-0.04133.356-0.126-0.1260.0000.0000.0000.000
140A140ASP -1-0.582-0.81035.343-8.061-8.0610.0000.0000.0000.000
141A141THR 00.0860.00634.072-0.260-0.2600.0000.0000.0000.000
142A142HIS 0-0.127-0.10634.600-0.296-0.2960.0000.0000.0000.000
143A143GLY 0-0.169-0.08036.6240.1600.1600.0000.0000.0000.000
144A144PRO 0-0.006-0.01435.941-0.211-0.2110.0000.0000.0000.000
145A145ILE 00.0320.01133.580-0.164-0.1640.0000.0000.0000.000
146A146VAL 00.0020.03028.507-0.060-0.0600.0000.0000.0000.000
147A147ILE 0-0.058-0.02727.501-0.010-0.0100.0000.0000.0000.000
148A148GLN 0-0.025-0.04324.541-0.229-0.2290.0000.0000.0000.000
149A149TYR 0-0.0060.00617.9710.0790.0790.0000.0000.0000.000
150A150PHE 00.0620.01517.985-0.434-0.4340.0000.0000.0000.000
151A151SER 0-0.043-0.00614.571-0.643-0.6430.0000.0000.0000.000
152A152VAL 0-0.019-0.02213.580-1.166-1.1660.0000.0000.0000.000
153A153LYS 10.9850.99914.23919.95319.9530.0000.0000.0000.000
154A154GLU -1-0.953-0.97916.483-16.158-16.1580.0000.0000.0000.000
155A155SER 0-0.016-0.00118.5750.7670.7670.0000.0000.0000.000
156A156TRP 0-0.064-0.04718.8260.4710.4710.0000.0000.0000.000
157A157ILE 0-0.0030.00520.8000.6640.6640.0000.0000.0000.000
158A158ARG 10.9160.92222.99511.27911.2790.0000.0000.0000.000
159A159HIS 00.020-0.01025.8490.4530.4530.0000.0000.0000.000
160A160LEU 0-0.030-0.00228.117-0.103-0.1030.0000.0000.0000.000
161A161LYS 10.8790.95228.13510.91910.9190.0000.0000.0000.000
162A162LEU 00.0350.00532.250-0.054-0.0540.0000.0000.0000.000
163A163VAL 0-0.070-0.05032.453-0.264-0.2640.0000.0000.0000.000
164A164GLU -1-0.899-0.95432.323-8.677-8.6770.0000.0000.0000.000
165A165GLU -1-0.871-0.90132.522-9.163-9.1630.0000.0000.0000.000
166A166PRO 00.0470.02129.255-0.277-0.2770.0000.0000.0000.000
167A167SER 0-0.050-0.03624.6690.2700.2700.0000.0000.0000.000
168A168LEU 00.0640.04624.875-0.108-0.1080.0000.0000.0000.000
169A169PRO 00.0170.00321.271-0.489-0.4890.0000.0000.0000.000
170A170GLY 0-0.006-0.00518.277-0.186-0.1860.0000.0000.0000.000
171A171PHE 0-0.034-0.02919.146-0.187-0.1870.0000.0000.0000.000
172A172GLU -1-0.947-0.97118.318-16.513-16.5130.0000.0000.0000.000
173A173ASP -1-0.884-0.93121.956-11.611-11.6110.0000.0000.0000.000
174A174LEU 0-0.074-0.03523.629-0.308-0.3080.0000.0000.0000.000
175A175LEU 0-0.016-0.01825.0310.1200.1200.0000.0000.0000.000
176A176ARG 10.8761.04628.7259.3619.3610.0000.0000.0000.000
177A177ILE 0-0.0270.00932.2390.1040.1040.0000.0000.0000.000
178A178ARG 10.8860.92735.2777.6087.6080.0000.0000.0000.000
179A179VAL 0-0.045-0.02938.858-0.050-0.0500.0000.0000.0000.000
180A180GLU -1-0.805-0.88141.061-7.037-7.0370.0000.0000.0000.000
181A181PRO 00.0740.02444.578-0.034-0.0340.0000.0000.0000.000
182A182ASN 0-0.042-0.01845.630-0.042-0.0420.0000.0000.0000.000
183A183THR 00.015-0.01547.0830.0710.0710.0000.0000.0000.000
184A184SER 00.0000.01149.6020.1700.1700.0000.0000.0000.000
185A185PRO 00.006-0.00148.886-0.163-0.1630.0000.0000.0000.000
186A186LEU 00.0020.00041.997-0.017-0.0170.0000.0000.0000.000
187A187ALA 00.0490.02945.7750.0930.0930.0000.0000.0000.000
188A188GLY 00.0580.04445.043-0.122-0.1220.0000.0000.0000.000
189A189LYS 10.8840.91843.2707.0277.0270.0000.0000.0000.000
190A190ASP -1-0.880-0.93839.667-7.646-7.6460.0000.0000.0000.000
191A191GLU -1-0.866-0.90238.516-7.951-7.9510.0000.0000.0000.000
192A192LYS 10.8630.90736.1298.3288.3280.0000.0000.0000.000
193A193ILE 00.0650.04037.573-0.127-0.1270.0000.0000.0000.000
194A194PHE 00.0240.00330.233-0.226-0.2260.0000.0000.0000.000
195A195ARG 10.9480.98731.8739.3859.3850.0000.0000.0000.000
196A196PHE 00.0750.02631.761-0.347-0.3470.0000.0000.0000.000
197A197GLY 00.0160.02528.955-0.289-0.2890.0000.0000.0000.000
198A198SER 0-0.023-0.03029.4150.3540.3540.0000.0000.0000.000
199A199HIS 0-0.039-0.04126.556-0.297-0.2970.0000.0000.0000.000
200A200LYS 10.9130.98922.75712.25312.2530.0000.0000.0000.000
201A201TRP 0-0.012-0.00426.9790.4740.4740.0000.0000.0000.000
202A202TYR 0-0.042-0.04027.748-0.453-0.4530.0000.0000.0000.000
203A203NME 00.0770.07629.1260.4100.4100.0000.0000.0000.000