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: MVRVZ

Calculation Name: 5CRB-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 5CRB

Chain ID: A

ChEMBL ID:

UniProt ID: Q5ZTK4

Base Structure: X-ray

Registration Date: 2023-06-22

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 192
LigandCharge CYM=-1
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2068270.386134
FMO2-HF: Nuclear repulsion 1994449.162117
FMO2-HF: Total energy -73821.224018
FMO2-MP2: Total energy -74034.574708


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:9:PRO)


Summations of interaction energy for fragment #1(A:9:PRO)
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.
-12.114-3.6194.536-5.505-7.525-0.04
Interaction energy analysis for fragmet #1(A:9:PRO)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.004 / q_NPA : -0.016
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].
3A11TYR0-0.0030.0153.668-0.6640.912-0.016-0.643-0.9170.003
4A12VAL0-0.015-0.0062.7830.3901.0810.050-0.213-0.5280.001
5A13GLU-1-0.872-0.9332.464-9.401-7.1732.030-1.718-2.539-0.023
6A14GLY0-0.021-0.0064.2840.9351.023-0.001-0.010-0.0770.000
7A15VAL0-0.073-0.0496.5750.1070.1070.0000.0000.0000.000
8A16GLU-1-0.782-0.8947.787-0.753-0.7530.0000.0000.0000.000
9A17LEU0-0.038-0.0127.030-0.492-0.4920.0000.0000.0000.000
10A18THR00.0530.0155.5680.6200.6200.0000.0000.0000.000
11A19GLN00.002-0.0128.3240.3330.3330.0000.0000.0000.000
12A20GLU-1-0.880-0.9498.013-1.094-1.0940.0000.0000.0000.000
13A21GLY00.0440.0167.7620.1500.1500.0000.0000.0000.000
14A22MET0-0.089-0.0208.3960.2640.2640.0000.0000.0000.000
15A23HIS00.0270.02211.9490.1100.1100.0000.0000.0000.000
16A24ALA00.0070.0149.8450.1090.1090.0000.0000.0000.000
17A25ILE00.0090.01311.4280.1070.1070.0000.0000.0000.000
18A26PHE0-0.016-0.03012.9450.0960.0960.0000.0000.0000.000
19A27ALA0-0.0040.00715.1170.0580.0580.0000.0000.0000.000
20A28ARG10.8030.89514.0970.2320.2320.0000.0000.0000.000
21A29MET0-0.081-0.02116.0870.0440.0440.0000.0000.0000.000
22A30GLY00.0460.02918.5350.0300.0300.0000.0000.0000.000
23A31TYR0-0.094-0.06519.8920.0260.0260.0000.0000.0000.000
24A32GLY0-0.022-0.00320.8370.0080.0080.0000.0000.0000.000
25A33ASP-1-0.939-0.97618.471-0.268-0.2680.0000.0000.0000.000
26A34ILE0-0.055-0.01316.7910.0160.0160.0000.0000.0000.000
27A35THR0-0.019-0.02118.728-0.011-0.0110.0000.0000.0000.000
28A36SER0-0.020-0.02816.5130.0020.0020.0000.0000.0000.000
29A37GLY00.0390.00518.9130.0360.0360.0000.0000.0000.000
30A38SER0-0.043-0.01918.629-0.039-0.0390.0000.0000.0000.000
31A39ILE0-0.020-0.01120.3610.0450.0450.0000.0000.0000.000
32A40TYR00.0660.04618.376-0.006-0.0060.0000.0000.0000.000
33A41ASN0-0.024-0.02922.0430.0160.0160.0000.0000.0000.000
34A42GLY0-0.023-0.00824.3130.0200.0200.0000.0000.0000.000
35A43VAL0-0.014-0.01725.6050.0140.0140.0000.0000.0000.000
36A44PRO0-0.031-0.02024.814-0.020-0.0200.0000.0000.0000.000
37A45THR0-0.0290.01622.5260.0260.0260.0000.0000.0000.000
38A46ILE00.029-0.01623.385-0.030-0.0300.0000.0000.0000.000
39A47ASP-1-0.820-0.89424.917-0.153-0.1530.0000.0000.0000.000
40A48THR00.039-0.00426.735-0.003-0.0030.0000.0000.0000.000
41A49GLY0-0.0040.00629.4890.0040.0040.0000.0000.0000.000
42A50ALA0-0.006-0.02124.6340.0060.0060.0000.0000.0000.000
43A51LEU00.0100.02525.761-0.005-0.0050.0000.0000.0000.000
44A52ASN0-0.007-0.00726.936-0.004-0.0040.0000.0000.0000.000
45A53ARG10.9040.97225.5140.1640.1640.0000.0000.0000.000
46A54GLN0-0.0180.00522.0410.0110.0110.0000.0000.0000.000
47A55GLY00.0170.02126.1210.0010.0010.0000.0000.0000.000
48A56PHE0-0.027-0.02620.377-0.002-0.0020.0000.0000.0000.000
49A57MET0-0.022-0.00821.4620.0070.0070.0000.0000.0000.000
50A58PRO00.0320.03816.8950.0090.0090.0000.0000.0000.000
51A59VAL0-0.012-0.01519.0840.0060.0060.0000.0000.0000.000
52A60LEU00.0290.02713.5470.0050.0050.0000.0000.0000.000
53A61THR0-0.041-0.04517.3680.0520.0520.0000.0000.0000.000
54A62GLY00.005-0.00918.169-0.045-0.0450.0000.0000.0000.000
55A63VAL00.0440.03215.5630.0010.0010.0000.0000.0000.000
56A64GLY00.010-0.02117.8950.0590.0590.0000.0000.0000.000
57A65PRO0-0.073-0.02517.937-0.032-0.0320.0000.0000.0000.000
58A66HIS0-0.008-0.00417.538-0.010-0.0100.0000.0000.0000.000
59A67ARG10.8800.94815.4630.3210.3210.0000.0000.0000.000
60A68ASP-1-0.811-0.89611.276-0.611-0.6110.0000.0000.0000.000
61A69SER0-0.015-0.0119.870-0.056-0.0560.0000.0000.0000.000
62A70GLY00.021-0.00712.3830.1200.1200.0000.0000.0000.000
63A71HIS10.7040.78215.2400.4190.4190.0000.0000.0000.000
64A72TRP00.0200.02511.5500.1660.1660.0000.0000.0000.000
65A73ILE0-0.040-0.01916.9800.0380.0380.0000.0000.0000.000
66A74MET0-0.0220.00619.755-0.028-0.0280.0000.0000.0000.000
67A75LEU0-0.0200.00221.8580.0270.0270.0000.0000.0000.000
68A76ILE00.011-0.00224.691-0.005-0.0050.0000.0000.0000.000
69A77LYS10.8600.93027.1460.1430.1430.0000.0000.0000.000
70A78GLY00.0150.01630.285-0.001-0.0010.0000.0000.0000.000
71A79PRO00.0460.01733.0920.0040.0040.0000.0000.0000.000
72A80GLY0-0.023-0.00936.4340.0010.0010.0000.0000.0000.000
73A81ASN00.018-0.00236.682-0.010-0.0100.0000.0000.0000.000
74A82GLN00.0050.01835.6620.0020.0020.0000.0000.0000.000
75A83TYR00.018-0.00730.043-0.001-0.0010.0000.0000.0000.000
76A84TYR0-0.002-0.01829.4480.0090.0090.0000.0000.0000.000
77A85LEU00.0190.02825.445-0.010-0.0100.0000.0000.0000.000
78A86PHE00.0180.00120.7500.0150.0150.0000.0000.0000.000
79A87ASP-1-0.665-0.80822.670-0.355-0.3550.0000.0000.0000.000
80A88PRO00.0170.03018.7450.0280.0280.0000.0000.0000.000
81A89LEU0-0.044-0.02820.3990.0100.0100.0000.0000.0000.000
82A90GLY0-0.015-0.00623.2580.0230.0230.0000.0000.0000.000
83A91LYS10.8380.91126.6630.1490.1490.0000.0000.0000.000
84A92THR00.0210.00129.674-0.001-0.0010.0000.0000.0000.000
85A93SER0-0.037-0.03824.1230.0000.0000.0000.0000.0000.000
86A94GLY00.0570.02126.317-0.005-0.0050.0000.0000.0000.000
87A95GLU-1-0.868-0.93527.205-0.156-0.1560.0000.0000.0000.000
88A96GLY0-0.0260.00228.1360.0100.0100.0000.0000.0000.000
89A97TYR0-0.021-0.02222.849-0.006-0.0060.0000.0000.0000.000
90A98GLN0-0.024-0.01527.7850.0040.0040.0000.0000.0000.000
91A99ASN00.007-0.00530.6820.0060.0060.0000.0000.0000.000
92A100ILE0-0.016-0.00127.8740.0060.0060.0000.0000.0000.000
93A101LEU00.0520.01224.8850.0000.0000.0000.0000.0000.000
94A102ALA00.0160.00729.1830.0040.0040.0000.0000.0000.000
95A103ALA0-0.060-0.02832.5890.0070.0070.0000.0000.0000.000
96A104GLN0-0.030-0.00928.6690.0030.0030.0000.0000.0000.000
97A105LEU0-0.0280.00229.676-0.002-0.0020.0000.0000.0000.000
98A106PRO00.0090.00332.9250.0080.0080.0000.0000.0000.000
99A107MET00.0400.02536.0440.0010.0010.0000.0000.0000.000
100A108GLY0-0.026-0.01639.4820.0020.0020.0000.0000.0000.000
101A109SER0-0.073-0.03335.407-0.001-0.0010.0000.0000.0000.000
102A110THR0-0.017-0.01136.6110.0000.0000.0000.0000.0000.000
103A111LEU00.0180.01729.409-0.004-0.0040.0000.0000.0000.000
104A112SER0-0.053-0.01532.9340.0050.0050.0000.0000.0000.000
105A113VAL00.0190.00628.712-0.008-0.0080.0000.0000.0000.000
106A114ILE00.0110.00027.4010.0140.0140.0000.0000.0000.000
107A115PRO0-0.072-0.02529.414-0.009-0.0090.0000.0000.0000.000
108A116ASN0-0.001-0.01025.2190.0130.0130.0000.0000.0000.000
109A117GLY0-0.004-0.01628.9390.0010.0010.0000.0000.0000.000
110A118SER00.0050.00126.501-0.012-0.0120.0000.0000.0000.000
111A119GLY0-0.020-0.01925.1780.0090.0090.0000.0000.0000.000
112A120LEU00.007-0.00723.5230.0040.0040.0000.0000.0000.000
113A121ASN00.007-0.05217.666-0.014-0.0140.0000.0000.0000.000
114A122MET0-0.030-0.01818.151-0.030-0.0300.0000.0000.0000.000
115A123GLY00.0130.01214.999-0.019-0.0190.0000.0000.0000.000
116A124LEU0-0.0050.00412.600-0.086-0.0860.0000.0000.0000.000
117A125CYM-1-0.710-0.73214.673-0.521-0.5210.0000.0000.0000.000
118A126GLY00.0490.00812.5320.0600.0600.0000.0000.0000.000
119A127TYR00.005-0.01812.7390.0470.0470.0000.0000.0000.000
120A128TRP00.0080.00614.0890.0790.0790.0000.0000.0000.000
121A129VAL0-0.034-0.02016.4950.0610.0610.0000.0000.0000.000
122A130ALA00.0340.01514.8110.0440.0440.0000.0000.0000.000
123A131SER0-0.013-0.01016.8270.0460.0460.0000.0000.0000.000
124A132ALA00.0110.00419.2890.0320.0320.0000.0000.0000.000
125A133GLY00.006-0.00120.7010.0240.0240.0000.0000.0000.000
126A134LEU00.0060.00919.5570.0270.0270.0000.0000.0000.000
127A135ARG10.8090.88021.4620.2720.2720.0000.0000.0000.000
128A136ALA00.0030.00125.1170.0210.0210.0000.0000.0000.000
129A137HIS0-0.020-0.01625.2970.0240.0240.0000.0000.0000.000
130A138GLN0-0.016-0.01624.3410.0220.0220.0000.0000.0000.000
131A139ALA0-0.0030.00528.8250.0130.0130.0000.0000.0000.000
132A140LEU0-0.061-0.04429.5270.0120.0120.0000.0000.0000.000
133A141ASN0-0.079-0.05030.0410.0160.0160.0000.0000.0000.000
134A142GLN0-0.0350.00933.1610.0020.0020.0000.0000.0000.000
135A143HIS00.000-0.02434.9220.0000.0000.0000.0000.0000.000
136A144ASN0-0.027-0.01338.5930.0040.0040.0000.0000.0000.000
137A145PRO0-0.0010.03335.858-0.002-0.0020.0000.0000.0000.000
138A146PRO00.0140.01234.0740.0060.0060.0000.0000.0000.000
139A147THR00.014-0.00136.540-0.004-0.0040.0000.0000.0000.000
140A148LEU00.0800.03332.485-0.004-0.0040.0000.0000.0000.000
141A149LEU0-0.007-0.01433.851-0.008-0.0080.0000.0000.0000.000
142A150ASN00.0060.00734.691-0.009-0.0090.0000.0000.0000.000
143A151VAL00.0800.05130.020-0.004-0.0040.0000.0000.0000.000
144A152GLY00.0440.02030.089-0.011-0.0110.0000.0000.0000.000
145A153GLN0-0.030-0.00830.183-0.008-0.0080.0000.0000.0000.000
146A154THR00.003-0.01129.759-0.001-0.0010.0000.0000.0000.000
147A155ILE00.0160.02125.032-0.005-0.0050.0000.0000.0000.000
148A156THR00.002-0.01626.392-0.014-0.0140.0000.0000.0000.000
149A157ASN0-0.042-0.02827.549-0.005-0.0050.0000.0000.0000.000
150A158GLU-1-0.839-0.88925.348-0.203-0.2030.0000.0000.0000.000
151A159MET0-0.044-0.01321.152-0.001-0.0010.0000.0000.0000.000
152A160ARG10.8260.89123.6440.1830.1830.0000.0000.0000.000
153A161ASN0-0.006-0.01725.9830.0060.0060.0000.0000.0000.000
154A162GLU-1-0.788-0.84419.466-0.287-0.2870.0000.0000.0000.000
155A163LEU0-0.018-0.01219.604-0.008-0.0080.0000.0000.0000.000
156A164ASP-1-0.850-0.88822.509-0.159-0.1590.0000.0000.0000.000
157A165HIS0-0.018-0.01224.2930.0000.0000.0000.0000.0000.000
158A166ASP-1-0.786-0.88920.996-0.162-0.1620.0000.0000.0000.000
159A167GLY00.0500.04220.087-0.010-0.0100.0000.0000.0000.000
160A168TYR00.0200.00914.541-0.010-0.0100.0000.0000.0000.000
161A169ARG10.8570.92715.8120.1170.1170.0000.0000.0000.000
162A170LYS10.8710.93115.2330.1560.1560.0000.0000.0000.000
163A171ILE00.0230.01513.510-0.014-0.0140.0000.0000.0000.000
164A172THR0-0.002-0.02111.557-0.047-0.0470.0000.0000.0000.000
165A173GLY0-0.042-0.01810.349-0.070-0.0700.0000.0000.0000.000
166A174TRP00.0440.01610.827-0.055-0.0550.0000.0000.0000.000
167A175LEU0-0.008-0.0118.1680.0030.0030.0000.0000.0000.000
168A176ARG10.9380.9666.041-0.052-0.0520.0000.0000.0000.000
169A177ALA0-0.038-0.0176.1520.1060.1060.0000.0000.0000.000
170A178VAL0-0.027-0.0027.7790.1350.1350.0000.0000.0000.000
171A179ALA00.0000.0082.394-0.533-0.5151.498-0.563-0.9520.003
172A180ASP-1-0.822-0.9132.725-2.7441.1530.976-2.353-2.520-0.024
173A181GLU-1-0.948-0.9744.8590.2690.266-0.001-0.0050.0080.000
174A182PHE00.012-0.0038.615-0.047-0.0470.0000.0000.0000.000
175A183PRO00.0260.02211.4570.0630.0630.0000.0000.0000.000
176A184GLU-1-0.884-0.92414.409-0.119-0.1190.0000.0000.0000.000
177A185GLY00.061-0.01817.9630.0050.0050.0000.0000.0000.000
178A186ASP-1-1.021-0.97820.095-0.086-0.0860.0000.0000.0000.000
179A187PRO0-0.0090.00520.814-0.021-0.0210.0000.0000.0000.000
180A188GLN0-0.043-0.03419.8690.0040.0040.0000.0000.0000.000
181A189LEU00.0240.01621.815-0.010-0.0100.0000.0000.0000.000
182A190ASP-1-0.756-0.88520.266-0.279-0.2790.0000.0000.0000.000
183A191GLY00.0960.02516.5620.0070.0070.0000.0000.0000.000
184A192LYS10.7570.88516.8390.2120.2120.0000.0000.0000.000
185A193ALA00.0010.01019.0760.0140.0140.0000.0000.0000.000
186A194LEU00.0400.02514.2450.0180.0180.0000.0000.0000.000
187A195ARG10.8030.90315.0450.3180.3180.0000.0000.0000.000
188A196GLU-1-0.885-0.95016.366-0.180-0.1800.0000.0000.0000.000
189A197ASN0-0.086-0.05019.4220.0390.0390.0000.0000.0000.000
190A198THR0-0.063-0.05015.3850.0030.0030.0000.0000.0000.000
191A199GLU-1-0.946-0.95715.032-0.092-0.0920.0000.0000.0000.000
192A200LYN0-0.062-0.01915.831-0.028-0.0280.0000.0000.0000.000