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: 1412Z

Calculation Name: 3MTV-A-Xray372

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: 2023-06-20

Reference: C. Watanabe, N. Tani, K. Kamisaka, T. Honma et al., Interaction energy analysis of Apo structure dataset on FMODB, To be published.

DOI:


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 202
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2241700.034886
FMO2-HF: Nuclear repulsion 2161917.013418
FMO2-HF: Total energy -79783.021468
FMO2-MP2: Total energy -80018.764613


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.
-3.5110.1782.361-3.02-3.029-0.012
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 : 0 / q_Mulliken : -0.020 / q_NPA : -0.015
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].
3A3VAL0-0.056-0.0383.8820.2882.239-0.010-1.073-0.8670.003
4A4TYR0-0.010-0.0276.2620.3500.3500.0000.0000.0000.000
5A5ASP-1-0.820-0.89710.002-0.214-0.2140.0000.0000.0000.000
6A6ILE0-0.032-0.02212.444-0.010-0.0100.0000.0000.0000.000
7A7GLY00.0430.02515.2080.0570.0570.0000.0000.0000.000
8A8ARG10.7940.86417.4870.1940.1940.0000.0000.0000.000
9A9GLY00.0430.03618.9860.0200.0200.0000.0000.0000.000
10A10ALA0-0.0280.00114.8630.0230.0230.0000.0000.0000.000
11A11VAL00.0090.00710.396-0.050-0.0500.0000.0000.0000.000
12A12MET0-0.042-0.0178.9840.1820.1820.0000.0000.0000.000
13A13TYR00.0140.0074.081-0.268-0.200-0.001-0.012-0.0550.000
14A14VAL0-0.001-0.0134.2880.4690.626-0.001-0.035-0.1210.000
15A15ALA00.0610.0192.390-2.938-1.4702.355-1.910-1.913-0.015
16A16GLY00.0120.0183.566-0.258-0.2130.0180.010-0.0730.000
17A17GLY00.0070.0026.903-0.377-0.3770.0000.0000.0000.000
18A18LYS10.8910.9497.759-1.082-1.0820.0000.0000.0000.000
19A19VAL00.0180.0046.8760.0240.0240.0000.0000.0000.000
20A20SER00.0070.0097.6980.0770.0770.0000.0000.0000.000
21A21TRP00.028-0.0058.981-0.196-0.1960.0000.0000.0000.000
22A22ALA00.0330.03410.8600.0950.0950.0000.0000.0000.000
23A23PRO00.023-0.00712.527-0.056-0.0560.0000.0000.0000.000
24A24ARG10.8160.90413.9130.3140.3140.0000.0000.0000.000
25A25GLY00.0330.02214.341-0.029-0.0290.0000.0000.0000.000
26A26GLY00.0130.00816.9820.0170.0170.0000.0000.0000.000
27A27ASN0-0.027-0.02719.034-0.034-0.0340.0000.0000.0000.000
28A28GLU-1-0.849-0.92418.248-0.229-0.2290.0000.0000.0000.000
29A29VAL0-0.0180.01213.503-0.044-0.0440.0000.0000.0000.000
30A30LYS10.8560.90215.3550.3410.3410.0000.0000.0000.000
31A31PHE00.0470.0329.379-0.020-0.0200.0000.0000.0000.000
32A32GLU-1-0.874-0.92912.298-0.894-0.8940.0000.0000.0000.000
33A33PRO0-0.008-0.01612.769-0.036-0.0360.0000.0000.0000.000
34A34VAL00.0010.00711.738-0.042-0.0420.0000.0000.0000.000
35A35PRO00.0760.05011.7170.1450.1450.0000.0000.0000.000
36A36LYS10.7760.88814.7540.3780.3780.0000.0000.0000.000
37A37GLU-1-0.834-0.92514.912-0.357-0.3570.0000.0000.0000.000
38A38LEU00.0370.0199.6850.0690.0690.0000.0000.0000.000
39A39LYS10.9240.96713.8380.3760.3760.0000.0000.0000.000
40A40LEU00.0220.01116.6750.0330.0330.0000.0000.0000.000
41A41VAL00.0310.01412.1490.0370.0370.0000.0000.0000.000
42A42ALA00.0750.02413.7650.0490.0490.0000.0000.0000.000
43A43ASN00.0000.00814.7940.0250.0250.0000.0000.0000.000
44A44ARG10.9631.00017.4980.0370.0370.0000.0000.0000.000
45A45LEU00.0310.03411.8180.0210.0210.0000.0000.0000.000
46A46HIS00.0310.01215.7740.0250.0250.0000.0000.0000.000
47A47THR0-0.041-0.01916.8090.0110.0110.0000.0000.0000.000
48A48SER0-0.017-0.01819.0920.0170.0170.0000.0000.0000.000
49A49PHE00.0520.02716.1750.0230.0230.0000.0000.0000.000
50A50PRO00.0190.00917.572-0.031-0.0310.0000.0000.0000.000
51A51PRO00.0100.00814.1960.0280.0280.0000.0000.0000.000
52A52HIS00.014-0.00111.2730.0440.0440.0000.0000.0000.000
53A53HIS0-0.0650.00211.7190.1080.1080.0000.0000.0000.000
54A54VAL00.0130.0138.455-0.029-0.0290.0000.0000.0000.000
55A55VAL00.0310.02410.912-0.015-0.0150.0000.0000.0000.000
56A56ASP-1-0.770-0.85311.4030.4500.4500.0000.0000.0000.000
57A57MET0-0.010-0.00712.573-0.055-0.0550.0000.0000.0000.000
58A58SER0-0.041-0.03314.575-0.049-0.0490.0000.0000.0000.000
59A59LYS10.7940.88016.145-0.340-0.3400.0000.0000.0000.000
60A60PHE00.0250.01416.515-0.006-0.0060.0000.0000.0000.000
61A61THR00.0220.02320.224-0.013-0.0130.0000.0000.0000.000
62A62PHE0-0.025-0.04717.881-0.006-0.0060.0000.0000.0000.000
63A63ILE00.0090.01023.451-0.005-0.0050.0000.0000.0000.000
64A64THR00.016-0.00725.707-0.006-0.0060.0000.0000.0000.000
65A65PRO0-0.033-0.02324.5020.0060.0060.0000.0000.0000.000
66A66GLY0-0.0040.01326.935-0.004-0.0040.0000.0000.0000.000
67A67SER0-0.040-0.01629.4240.0020.0020.0000.0000.0000.000
68A68GLY00.0580.03527.9490.0050.0050.0000.0000.0000.000
69A69VAL0-0.0030.00726.401-0.006-0.0060.0000.0000.0000.000
70A70SER0-0.006-0.04022.6270.0050.0050.0000.0000.0000.000
71A71MET00.0020.00821.1040.0020.0020.0000.0000.0000.000
72A72ARG10.7590.88719.4370.0140.0140.0000.0000.0000.000
73A73VAL00.0180.01922.796-0.007-0.0070.0000.0000.0000.000
74A74GLU-1-0.854-0.92122.6130.0210.0210.0000.0000.0000.000
75A75TYR0-0.046-0.01322.706-0.012-0.0120.0000.0000.0000.000
76A76GLN00.0150.00726.6300.0050.0050.0000.0000.0000.000
77A77TYR00.004-0.00128.6100.0050.0050.0000.0000.0000.000
78A78GLY0-0.007-0.02925.107-0.002-0.0020.0000.0000.0000.000
79A79CYS0-0.066-0.01322.074-0.011-0.0110.0000.0000.0000.000
80A80LEU00.0340.03521.0170.0010.0010.0000.0000.0000.000
81A81PRO00.0330.02924.898-0.009-0.0090.0000.0000.0000.000
82A82ALA00.0300.00127.4410.0110.0110.0000.0000.0000.000
83A83ASP-1-0.866-0.93029.5120.0740.0740.0000.0000.0000.000
84A84THR0-0.091-0.05124.5710.0120.0120.0000.0000.0000.000
85A85VAL0-0.029-0.02324.0770.0190.0190.0000.0000.0000.000
86A86PRO0-0.012-0.00225.655-0.008-0.0080.0000.0000.0000.000
87A87GLU-1-0.826-0.89428.5910.0710.0710.0000.0000.0000.000
88A88GLY0-0.0030.00331.252-0.007-0.0070.0000.0000.0000.000
89A89ASN0-0.054-0.05032.1980.0060.0060.0000.0000.0000.000
90A90CYS0-0.0380.01531.1380.0030.0030.0000.0000.0000.000
91A91TRP00.013-0.01733.5010.0000.0000.0000.0000.0000.000
92A92TRP0-0.003-0.01235.134-0.002-0.0020.0000.0000.0000.000
93A93ARG10.9410.95633.082-0.117-0.1170.0000.0000.0000.000
94A94LEU0-0.084-0.03935.1570.0000.0000.0000.0000.0000.000
95A95LEU0-0.041-0.03839.173-0.003-0.0030.0000.0000.0000.000
96A96ASP-1-0.840-0.90741.2530.0780.0780.0000.0000.0000.000
97A97SER0-0.054-0.02643.888-0.003-0.0030.0000.0000.0000.000
98A98LEU0-0.045-0.01345.355-0.003-0.0030.0000.0000.0000.000
99A99PRO00.0440.01948.0960.0000.0000.0000.0000.0000.000
100A100PRO00.0870.03948.9380.0010.0010.0000.0000.0000.000
101A101GLU-1-0.800-0.90649.0140.0450.0450.0000.0000.0000.000
102A102VAL0-0.037-0.01547.989-0.001-0.0010.0000.0000.0000.000
103A103GLN0-0.011-0.00145.0380.0010.0010.0000.0000.0000.000
104A104TYR00.0540.02645.077-0.001-0.0010.0000.0000.0000.000
105A105LYS10.8310.90946.349-0.043-0.0430.0000.0000.0000.000
106A106GLU-1-0.718-0.83743.2880.0580.0580.0000.0000.0000.000
107A107ILE0-0.023-0.00341.1330.0010.0010.0000.0000.0000.000
108A108ARG10.9230.95642.093-0.039-0.0390.0000.0000.0000.000
109A109HIS00.0070.00943.887-0.003-0.0030.0000.0000.0000.000
110A110ALA0-0.020-0.01838.4680.0000.0000.0000.0000.0000.000
111A111ASN0-0.005-0.00239.1170.0020.0020.0000.0000.0000.000
112A112GLN0-0.058-0.01541.232-0.005-0.0050.0000.0000.0000.000
113A113PHE0-0.048-0.02138.640-0.001-0.0010.0000.0000.0000.000
114A114GLY00.0210.00436.694-0.002-0.0020.0000.0000.0000.000
115A115TYR0-0.045-0.04634.3200.0020.0020.0000.0000.0000.000
116A116GLN0-0.0210.01135.0930.0080.0080.0000.0000.0000.000
117A117THR0-0.002-0.00331.479-0.003-0.0030.0000.0000.0000.000
118A118LYS10.8960.93326.362-0.052-0.0520.0000.0000.0000.000
119A119HIS00.006-0.00426.0330.0080.0080.0000.0000.0000.000
120A120GLY00.0460.04328.7100.0100.0100.0000.0000.0000.000
121A121VAL0-0.007-0.00631.848-0.006-0.0060.0000.0000.0000.000
122A122PRO00.0040.00630.8360.0100.0100.0000.0000.0000.000
123A123GLY00.0260.02131.8320.0030.0030.0000.0000.0000.000
124A124LYS10.8220.88831.315-0.100-0.1000.0000.0000.0000.000
125A125TYR0-0.0120.00735.218-0.005-0.0050.0000.0000.0000.000
126A126LEU00.0300.01633.754-0.004-0.0040.0000.0000.0000.000
127A127GLN0-0.019-0.01735.7190.0040.0040.0000.0000.0000.000
128A128ARG10.9730.99638.112-0.070-0.0700.0000.0000.0000.000
129A129ARG10.8180.90040.433-0.065-0.0650.0000.0000.0000.000
130A130LEU00.0610.03438.8920.0030.0030.0000.0000.0000.000
131A131GLN00.0120.01442.247-0.003-0.0030.0000.0000.0000.000
132A132VAL0-0.075-0.04644.009-0.002-0.0020.0000.0000.0000.000
133A133ASN0-0.070-0.04444.994-0.005-0.0050.0000.0000.0000.000
134A134GLY00.0380.03147.618-0.001-0.0010.0000.0000.0000.000
135A135LEU0-0.0160.01043.5100.0010.0010.0000.0000.0000.000
136A136ARG10.7490.83941.763-0.081-0.0810.0000.0000.0000.000
137A137ALA00.0220.02436.9320.0010.0010.0000.0000.0000.000
138A138VAL0-0.027-0.00738.2630.0000.0000.0000.0000.0000.000
139A139THR0-0.025-0.02032.9140.0070.0070.0000.0000.0000.000
140A140ASP-1-0.799-0.89534.6540.1180.1180.0000.0000.0000.000
141A141THR00.013-0.00233.4690.0080.0080.0000.0000.0000.000
142A142HIS0-0.040-0.02834.2450.0110.0110.0000.0000.0000.000
143A143GLY0-0.0120.01635.788-0.004-0.0040.0000.0000.0000.000
144A144PRO00.0180.00635.3840.0070.0070.0000.0000.0000.000
145A145ILE00.0080.01033.2720.0000.0000.0000.0000.0000.000
146A146VAL00.0000.00027.9310.0060.0060.0000.0000.0000.000
147A147ILE0-0.037-0.01726.792-0.006-0.0060.0000.0000.0000.000
148A148GLN00.014-0.00424.348-0.001-0.0010.0000.0000.0000.000
149A149TYR0-0.042-0.02717.343-0.006-0.0060.0000.0000.0000.000
150A150PHE00.0270.02117.4200.0200.0200.0000.0000.0000.000
151A151SER0-0.012-0.01313.8020.0070.0070.0000.0000.0000.000
152A152VAL0-0.049-0.03313.1560.0800.0800.0000.0000.0000.000
153A153LYS10.9090.94715.624-0.591-0.5910.0000.0000.0000.000
154A154GLU-1-0.818-0.91816.3810.4250.4250.0000.0000.0000.000
155A155SER00.0250.00718.455-0.052-0.0520.0000.0000.0000.000
156A156TRP0-0.026-0.00418.567-0.006-0.0060.0000.0000.0000.000
157A157ILE00.0110.00820.434-0.020-0.0200.0000.0000.0000.000
158A158ARG10.9180.95322.600-0.189-0.1890.0000.0000.0000.000
159A159HIS00.003-0.01125.344-0.028-0.0280.0000.0000.0000.000
160A160LEU0-0.045-0.02727.5880.0100.0100.0000.0000.0000.000
161A161LYS10.8430.94427.053-0.210-0.2100.0000.0000.0000.000
162A162LEU00.0380.01031.9090.0030.0030.0000.0000.0000.000
163A163VAL0-0.038-0.03732.3380.0090.0090.0000.0000.0000.000
164A164GLU-1-0.893-0.94732.5460.1260.1260.0000.0000.0000.000
165A165GLU-1-0.825-0.86932.3400.1170.1170.0000.0000.0000.000
166A166PRO00.0040.00128.7430.0120.0120.0000.0000.0000.000
167A167SER0-0.009-0.01224.460-0.012-0.0120.0000.0000.0000.000
168A168LEU00.0380.03124.9970.0010.0010.0000.0000.0000.000
169A169PRO00.006-0.00720.8580.0260.0260.0000.0000.0000.000
170A170GLY00.0120.01218.394-0.007-0.0070.0000.0000.0000.000
171A171PHE0-0.034-0.02719.1300.0110.0110.0000.0000.0000.000
172A172GLU-1-0.889-0.94317.6480.4120.4120.0000.0000.0000.000
173A173ASP-1-0.783-0.90621.1430.2140.2140.0000.0000.0000.000
174A174LEU0-0.095-0.03922.8710.0240.0240.0000.0000.0000.000
175A175LEU0-0.030-0.01524.5920.0020.0020.0000.0000.0000.000
176A176ARG10.9270.97228.236-0.164-0.1640.0000.0000.0000.000
177A177ILE0-0.021-0.01231.802-0.002-0.0020.0000.0000.0000.000
178A178ARG10.7560.83634.840-0.107-0.1070.0000.0000.0000.000
179A179VAL0-0.014-0.01638.5610.0010.0010.0000.0000.0000.000
180A180GLU-1-0.772-0.86540.8700.0880.0880.0000.0000.0000.000
181A181PRO00.0680.01644.4560.0000.0000.0000.0000.0000.000
182A182ASN0-0.037-0.01545.5840.0030.0030.0000.0000.0000.000
183A183THR00.001-0.00247.167-0.002-0.0020.0000.0000.0000.000
184A184SER0-0.004-0.00549.553-0.003-0.0030.0000.0000.0000.000
185A185PRO00.0170.00748.6250.0030.0030.0000.0000.0000.000
186A186LEU00.0110.00541.8500.0010.0010.0000.0000.0000.000
187A187ALA00.0130.01745.071-0.003-0.0030.0000.0000.0000.000
188A188GLY00.0350.01744.3080.0010.0010.0000.0000.0000.000
189A189LYS10.8650.92042.880-0.090-0.0900.0000.0000.0000.000
190A190ASP-1-0.818-0.89739.1860.1100.1100.0000.0000.0000.000
191A191GLU-1-0.706-0.81438.1730.1140.1140.0000.0000.0000.000
192A192LYS10.7850.87236.270-0.123-0.1230.0000.0000.0000.000
193A193ILE00.0370.03237.6940.0030.0030.0000.0000.0000.000
194A194PHE00.0130.00729.9820.0050.0050.0000.0000.0000.000
195A195ARG10.9300.95432.583-0.135-0.1350.0000.0000.0000.000
196A196PHE00.0470.03731.4500.0100.0100.0000.0000.0000.000
197A197GLY00.0330.04629.4580.0100.0100.0000.0000.0000.000
198A198SER0-0.010-0.02329.849-0.014-0.0140.0000.0000.0000.000
199A199HIS00.0330.00726.3280.0100.0100.0000.0000.0000.000
200A200LYS10.8250.90222.555-0.192-0.1920.0000.0000.0000.000
201A201TRP0-0.047-0.01326.531-0.016-0.0160.0000.0000.0000.000
202A202TYR00.029-0.02027.2450.0070.0070.0000.0000.0000.000