Manual

About

FMODB

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

Last updated: 2024-05-02

All entries: 37386

Number of unique PDB entries: 7781

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FMODB ID: 2NV2R

Calculation Name: 4P5P-A-Xray372

Preferred Name:

Target Type:

Ligand Name: 3-sulfinoalanine

ligand 3-letter code: CSD

PDB ID: 4P5P

Chain ID: A

ChEMBL ID:

UniProt ID: A0Q664

Base Structure: X-ray

Registration Date: 2023-09-23

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 OptH
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 225
LigandCharge CSD=-1
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2795098.963341
FMO2-HF: Nuclear repulsion 2707596.599338
FMO2-HF: Total energy -87502.364002
FMO2-MP2: Total energy -87757.228886


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:MET)


Summations of interaction energy for fragment #1(A:1:MET)
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.
-10.871-3.5835.006-4.145-8.147-0.035
Interaction energy analysis for fragmet #1(A:1:MET)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.059 / q_NPA : -0.030
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].
3A3ASN00.0400.0192.950-2.5901.0250.385-1.598-2.403-0.008
4A4VAL0-0.006-0.0024.8220.3410.396-0.001-0.007-0.0460.000
5A5LEU00.0200.0258.3720.0590.0590.0000.0000.0000.000
6A6MET0-0.055-0.02211.4200.1050.1050.0000.0000.0000.000
7A7VAL00.0080.00414.352-0.034-0.0340.0000.0000.0000.000
8A8THR0-0.006-0.01717.7250.0300.0300.0000.0000.0000.000
9A9THR0-0.033-0.03720.982-0.018-0.0180.0000.0000.0000.000
10A10SER00.010-0.00824.320-0.008-0.0080.0000.0000.0000.000
11A11HIS0-0.0280.00526.436-0.005-0.0050.0000.0000.0000.000
12A12ASP-1-0.846-0.93929.840-0.045-0.0450.0000.0000.0000.000
13A13VAL0-0.032-0.00531.8670.0060.0060.0000.0000.0000.000
14A14MET0-0.0130.00334.382-0.003-0.0030.0000.0000.0000.000
15A15GLY00.0320.01336.3690.0030.0030.0000.0000.0000.000
16A16ASN0-0.028-0.02138.371-0.006-0.0060.0000.0000.0000.000
17A17SER0-0.055-0.01739.9460.0010.0010.0000.0000.0000.000
18A18ASN00.006-0.01440.728-0.005-0.0050.0000.0000.0000.000
19A19GLU-1-0.955-0.96837.285-0.001-0.0010.0000.0000.0000.000
20A20LYS10.9460.97234.3570.0320.0320.0000.0000.0000.000
21A21THR0-0.011-0.02931.7410.0050.0050.0000.0000.0000.000
22A22GLY00.0280.00728.680-0.007-0.0070.0000.0000.0000.000
23A23LEU0-0.043-0.03121.8510.0050.0050.0000.0000.0000.000
24A24TRP00.0320.01925.3960.0010.0010.0000.0000.0000.000
25A25LEU00.0420.02522.2700.0100.0100.0000.0000.0000.000
26A26SER00.0480.02022.0790.0050.0050.0000.0000.0000.000
27A27GLH0-0.054-0.07021.4560.0210.0210.0000.0000.0000.000
28A28LEU00.0020.01616.5130.0030.0030.0000.0000.0000.000
29A29THR00.013-0.02517.3160.0420.0420.0000.0000.0000.000
30A30HIS10.7840.86717.509-0.123-0.1230.0000.0000.0000.000
31A31PRO00.002-0.00916.2670.0550.0550.0000.0000.0000.000
32A32TYR00.0550.03311.3360.1060.1060.0000.0000.0000.000
33A33TYR00.015-0.01912.5670.0910.0910.0000.0000.0000.000
34A34SER0-0.069-0.01214.0810.0860.0860.0000.0000.0000.000
35A35ILE0-0.009-0.0129.5800.0960.0960.0000.0000.0000.000
36A36ILE0-0.0040.0217.7990.2770.2770.0000.0000.0000.000
37A37ASP-1-0.818-0.9236.6282.6272.6270.0000.0000.0000.000
38A38LYS10.9170.9444.756-0.327-0.123-0.001-0.015-0.1880.000
39A39ASN0-0.051-0.0172.979-2.951-1.5101.532-1.020-1.953-0.004
40A40ILE0-0.021-0.0012.491-2.118-0.9622.847-1.274-2.728-0.023
41A41ASN00.0120.0083.745-0.3060.4970.242-0.218-0.8270.000
42A42ILE0-0.047-0.0285.080-0.857-0.8430.002-0.013-0.0020.000
43A43ASP-1-0.800-0.8568.520-0.824-0.8240.0000.0000.0000.000
44A44ILE0-0.032-0.02910.6160.0430.0430.0000.0000.0000.000
45A45VAL0-0.027-0.00614.318-0.036-0.0360.0000.0000.0000.000
46A46SER00.0130.01117.0720.0340.0340.0000.0000.0000.000
47A47ILE00.007-0.00120.703-0.029-0.0290.0000.0000.0000.000
48A48MET0-0.046-0.04023.109-0.018-0.0180.0000.0000.0000.000
49A49GLY00.0010.01022.079-0.012-0.0120.0000.0000.0000.000
50A50GLY0-0.042-0.01423.0760.0170.0170.0000.0000.0000.000
51A51GLU-1-0.929-0.95223.731-0.069-0.0690.0000.0000.0000.000
52A52ILE0-0.050-0.03620.0540.0000.0000.0000.0000.0000.000
53A53PRO0-0.0040.02724.6500.0110.0110.0000.0000.0000.000
54A54ILE00.008-0.01025.1420.0040.0040.0000.0000.0000.000
55A55ASP-1-0.833-0.90127.9580.0040.0040.0000.0000.0000.000
56A56PRO00.0590.02530.5260.0070.0070.0000.0000.0000.000
57A57ASN00.014-0.00332.8680.0080.0080.0000.0000.0000.000
58A58SER0-0.132-0.06027.9830.0080.0080.0000.0000.0000.000
59A59VAL0-0.011-0.01727.6270.0090.0090.0000.0000.0000.000
60A60ALA0-0.0200.01330.1870.0000.0000.0000.0000.0000.000
61A61GLN0-0.074-0.03030.737-0.002-0.0020.0000.0000.0000.000
62A62GLU-1-0.875-0.93529.7110.0550.0550.0000.0000.0000.000
63A63ASP-1-0.810-0.89924.4930.1380.1380.0000.0000.0000.000
64A64TYR00.0070.01120.9230.0060.0060.0000.0000.0000.000
65A65TYR0-0.012-0.02218.4180.0120.0120.0000.0000.0000.000
66A66ASN00.0820.03221.0430.0050.0050.0000.0000.0000.000
67A67ASP-1-0.833-0.90823.1140.0530.0530.0000.0000.0000.000
68A68LYS10.8470.92616.466-0.213-0.2130.0000.0000.0000.000
69A69PHE00.000-0.01815.983-0.007-0.0070.0000.0000.0000.000
70A70LEU00.0080.00419.535-0.023-0.0230.0000.0000.0000.000
71A71ALA0-0.038-0.02121.873-0.018-0.0180.0000.0000.0000.000
72A72ASP-1-0.889-0.93215.2830.0040.0040.0000.0000.0000.000
73A73ASP-1-0.889-0.95718.902-0.062-0.0620.0000.0000.0000.000
74A74ASN0-0.026-0.01512.877-0.061-0.0610.0000.0000.0000.000
75A75LEU0-0.024-0.00713.810-0.021-0.0210.0000.0000.0000.000
76A76LYS10.9260.96517.3960.0180.0180.0000.0000.0000.000
77A77ASN0-0.034-0.02818.8450.0080.0080.0000.0000.0000.000
78A78ILE00.0190.02314.248-0.011-0.0110.0000.0000.0000.000
79A79MET0-0.020-0.00318.788-0.005-0.0050.0000.0000.0000.000
80A80LYS10.9380.98821.9300.0890.0890.0000.0000.0000.000
81A81ASN0-0.073-0.03521.7150.0030.0030.0000.0000.0000.000
82A82SER00.0080.02119.490-0.030-0.0300.0000.0000.0000.000
83A83THR00.0370.01216.731-0.013-0.0130.0000.0000.0000.000
84A84SER0-0.006-0.00318.9740.0120.0120.0000.0000.0000.000
85A85LEU00.0330.00117.208-0.039-0.0390.0000.0000.0000.000
86A86ARG10.8430.91518.7020.1650.1650.0000.0000.0000.000
87A87ASP-1-0.910-0.94919.221-0.297-0.2970.0000.0000.0000.000
88A88VAL0-0.0290.00913.785-0.048-0.0480.0000.0000.0000.000
89A89ASN0-0.003-0.01913.5640.0530.0530.0000.0000.0000.000
90A90ILE00.0350.00512.539-0.104-0.1040.0000.0000.0000.000
91A91LYS10.8080.88312.1900.4160.4160.0000.0000.0000.000
92A92GLU-1-0.962-0.9708.431-1.722-1.7220.0000.0000.0000.000
93A93TYR0-0.096-0.0527.221-0.481-0.4810.0000.0000.0000.000
94A94ASP-1-0.882-0.9395.896-2.307-2.3070.0000.0000.0000.000
95A95ALA0-0.032-0.0339.1300.2980.2980.0000.0000.0000.000
96A96ILE0-0.0150.01411.199-0.102-0.1020.0000.0000.0000.000
97A97ILE0-0.038-0.01813.1720.0760.0760.0000.0000.0000.000
98A98PHE00.012-0.00515.787-0.025-0.0250.0000.0000.0000.000
99A99ALA00.0200.00519.2470.0300.0300.0000.0000.0000.000
100A100GLY00.0560.01720.778-0.015-0.0150.0000.0000.0000.000
101A101GLY00.0220.00824.585-0.005-0.0050.0000.0000.0000.000
102A102HIS10.8590.90327.630-0.015-0.0150.0000.0000.0000.000
103A103GLY00.0620.05529.120-0.004-0.0040.0000.0000.0000.000
104A104THR00.007-0.01524.904-0.006-0.0060.0000.0000.0000.000
105A105MET0-0.027-0.00127.581-0.006-0.0060.0000.0000.0000.000
106A106TRP0-0.010-0.00630.7270.0000.0000.0000.0000.0000.000
107A107ASP-1-0.790-0.88227.087-0.086-0.0860.0000.0000.0000.000
108A108PHE0-0.017-0.02621.971-0.015-0.0150.0000.0000.0000.000
109A109PRO00.0300.03126.538-0.010-0.0100.0000.0000.0000.000
110A110ASN00.001-0.00728.942-0.002-0.0020.0000.0000.0000.000
111A111ASN00.0270.03224.008-0.022-0.0220.0000.0000.0000.000
112A112ALA00.0940.03325.613-0.005-0.0050.0000.0000.0000.000
113A113ASN00.001-0.00221.159-0.035-0.0350.0000.0000.0000.000
114A114ILE00.0300.03220.907-0.026-0.0260.0000.0000.0000.000
115A115HIS0-0.029-0.01221.467-0.013-0.0130.0000.0000.0000.000
116A116SER0-0.018-0.01322.251-0.012-0.0120.0000.0000.0000.000
117A117LYS10.8800.93617.0530.3280.3280.0000.0000.0000.000
118A118VAL00.0430.02117.530-0.027-0.0270.0000.0000.0000.000
119A119LEU0-0.013-0.00619.1470.0050.0050.0000.0000.0000.000
120A120ASP-1-0.863-0.90615.778-0.451-0.4510.0000.0000.0000.000
121A121ILE00.0290.00912.650-0.013-0.0130.0000.0000.0000.000
122A122TYR00.000-0.01015.8820.0370.0370.0000.0000.0000.000
123A123ALA0-0.0150.00518.9650.0310.0310.0000.0000.0000.000
124A124LYS10.8440.92510.8690.8320.8320.0000.0000.0000.000
125A125ASN0-0.042-0.02214.7070.0250.0250.0000.0000.0000.000
126A126GLY00.0170.00013.2700.0540.0540.0000.0000.0000.000
127A127VAL0-0.049-0.02513.0150.0550.0550.0000.0000.0000.000
128A128ILE00.0150.01014.400-0.073-0.0730.0000.0000.0000.000
129A129GLY00.0310.01316.7810.0450.0450.0000.0000.0000.000
130A130ALA0-0.027-0.00618.073-0.033-0.0330.0000.0000.0000.000
131A131ILE00.0040.01221.0030.0210.0210.0000.0000.0000.000
132A132CSD-1-0.777-0.80923.1500.0210.0210.0000.0000.0000.000
133A133HIS10.7740.79126.773-0.019-0.0190.0000.0000.0000.000
134A134GLY00.0470.04223.523-0.011-0.0110.0000.0000.0000.000
135A135VAL0-0.041-0.02223.945-0.015-0.0150.0000.0000.0000.000
136A136ALA00.0370.00125.408-0.006-0.0060.0000.0000.0000.000
137A137ALA0-0.078-0.02922.613-0.008-0.0080.0000.0000.0000.000
138A138LEU0-0.015-0.03121.291-0.014-0.0140.0000.0000.0000.000
139A139ILE0-0.0100.02625.1890.0000.0000.0000.0000.0000.000
140A140ASN0-0.016-0.01928.4170.0080.0080.0000.0000.0000.000
141A141VAL0-0.0090.01223.344-0.010-0.0100.0000.0000.0000.000
142A142LYS10.8850.95326.5720.0660.0660.0000.0000.0000.000
143A143ASP-1-0.792-0.89727.102-0.076-0.0760.0000.0000.0000.000
144A144ASN0-0.022-0.02728.108-0.006-0.0060.0000.0000.0000.000
145A145ASN0-0.061-0.02430.086-0.001-0.0010.0000.0000.0000.000
146A146GLY0-0.006-0.00131.8070.0070.0070.0000.0000.0000.000
147A147GLN0-0.028-0.01931.9160.0100.0100.0000.0000.0000.000
148A148ASN00.0270.01029.687-0.009-0.0090.0000.0000.0000.000
149A149ILE00.0190.00423.0070.0080.0080.0000.0000.0000.000
150A150ILE00.0040.00325.4620.0090.0090.0000.0000.0000.000
151A151ARG10.9140.97627.7740.0340.0340.0000.0000.0000.000
152A152ASP-1-0.953-0.99630.4570.0140.0140.0000.0000.0000.000
153A153LYS10.8200.92424.7840.0000.0000.0000.0000.0000.000
154A154GLU-1-0.938-0.97028.2240.0880.0880.0000.0000.0000.000
155A155VAL0-0.049-0.02026.3190.0050.0050.0000.0000.0000.000
156A156THR0-0.008-0.02526.7840.0020.0020.0000.0000.0000.000
157A157GLY00.018-0.00427.590-0.008-0.0080.0000.0000.0000.000
158A158PHE0-0.027-0.01428.6600.0050.0050.0000.0000.0000.000
159A159SER0-0.010-0.01030.978-0.007-0.0070.0000.0000.0000.000
160A160ASN00.0660.02434.378-0.004-0.0040.0000.0000.0000.000
161A161ASN0-0.073-0.03437.716-0.006-0.0060.0000.0000.0000.000
162A162GLU-1-0.721-0.82933.0990.0630.0630.0000.0000.0000.000
163A163GLU-1-0.729-0.84034.7250.0110.0110.0000.0000.0000.000
164A164LYS10.9470.97537.206-0.026-0.0260.0000.0000.0000.000
165A165ILE0-0.063-0.01938.665-0.002-0.0020.0000.0000.0000.000
166A166VAL0-0.055-0.03235.6510.0000.0000.0000.0000.0000.000
167A167GLY0-0.0100.00538.999-0.003-0.0030.0000.0000.0000.000
168A168LEU00.013-0.00236.084-0.003-0.0030.0000.0000.0000.000
169A169THR0-0.020-0.01739.128-0.002-0.0020.0000.0000.0000.000
170A170ASP-1-0.953-0.97940.574-0.006-0.0060.0000.0000.0000.000
171A171VAL0-0.0250.00738.477-0.003-0.0030.0000.0000.0000.000
172A172VAL0-0.056-0.03135.038-0.005-0.0050.0000.0000.0000.000
173A173PRO0-0.032-0.00934.9430.0010.0010.0000.0000.0000.000
174A174PHE0-0.004-0.01431.459-0.002-0.0020.0000.0000.0000.000
175A175SER00.0180.01736.1600.0010.0010.0000.0000.0000.000
176A176LEU00.014-0.00528.964-0.003-0.0030.0000.0000.0000.000
177A177GLU-1-0.850-0.93333.0320.0320.0320.0000.0000.0000.000
178A178ASP-1-0.847-0.93234.4270.0110.0110.0000.0000.0000.000
179A179SER00.006-0.00833.396-0.001-0.0010.0000.0000.0000.000
180A180LEU0-0.055-0.02328.754-0.004-0.0040.0000.0000.0000.000
181A181VAL0-0.0070.00132.4740.0000.0000.0000.0000.0000.000
182A182GLU-1-0.968-0.97635.634-0.018-0.0180.0000.0000.0000.000
183A183ALA0-0.077-0.03331.733-0.003-0.0030.0000.0000.0000.000
184A184GLY0-0.004-0.00733.175-0.003-0.0030.0000.0000.0000.000
185A185ALA0-0.044-0.00430.2890.0040.0040.0000.0000.0000.000
186A186LYS10.9110.95731.573-0.046-0.0460.0000.0000.0000.000
187A187TYR00.0340.01031.2220.0080.0080.0000.0000.0000.000
188A188SER0-0.0210.01731.5890.0060.0060.0000.0000.0000.000
189A189SER00.0140.00031.9360.0020.0020.0000.0000.0000.000
190A190ALA0-0.0040.01132.2470.0010.0010.0000.0000.0000.000
191A191SER00.030-0.00133.966-0.007-0.0070.0000.0000.0000.000
192A192GLU-1-0.901-0.95334.7270.0630.0630.0000.0000.0000.000
193A193TRP0-0.050-0.03732.5730.0030.0030.0000.0000.0000.000
194A194GLN0-0.0350.00232.1510.0060.0060.0000.0000.0000.000
195A195SER0-0.041-0.00726.021-0.004-0.0040.0000.0000.0000.000
196A196TYR0-0.032-0.04727.5050.0070.0070.0000.0000.0000.000
197A197VAL00.013-0.00621.629-0.007-0.0070.0000.0000.0000.000
198A198LYS10.8400.94324.764-0.102-0.1020.0000.0000.0000.000
199A199SER00.001-0.02020.181-0.006-0.0060.0000.0000.0000.000
200A200ASP-1-0.766-0.86822.9080.0800.0800.0000.0000.0000.000
201A201SER0-0.018-0.02121.840-0.017-0.0170.0000.0000.0000.000
202A202LYS10.8550.94513.578-0.200-0.2000.0000.0000.0000.000
203A203ILE00.0140.01818.228-0.024-0.0240.0000.0000.0000.000
204A204ILE0-0.036-0.02116.8620.0220.0220.0000.0000.0000.000
205A205THR00.0360.01720.683-0.019-0.0190.0000.0000.0000.000
206A206ALA00.019-0.00422.9510.0210.0210.0000.0000.0000.000
207A207GLN00.0450.02724.656-0.009-0.0090.0000.0000.0000.000
208A208ASN00.0090.00027.239-0.003-0.0030.0000.0000.0000.000
209A209PRO00.0440.02025.8900.0140.0140.0000.0000.0000.000
210A210GLN00.0190.00625.8510.0150.0150.0000.0000.0000.000
211A211SER00.017-0.01025.1640.0140.0140.0000.0000.0000.000
212A212ALA0-0.016-0.00221.4590.0190.0190.0000.0000.0000.000
213A213THR0-0.021-0.01820.3200.0260.0260.0000.0000.0000.000
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