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: P7MRK

Calculation Name: 4XIN-A-Xray40

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 4XIN

Chain ID: A

ChEMBL ID:

UniProt ID: A0A0J9

Base Structure: X-ray

Registration Date: 2019-02-15

Reference:

DOI:


IFIE MAP

IFIE Diagram


Modeling method
Optimization MOE:Amber10:EHT
Restraint OptH
Protonation MOE:Protonate 3D
Complement Missing residues were capped by ACE, NME. Missing atoms were corrected by Structure prepareation by MOE.
Water Apo structure with with a 3 angstrom solvent shell.
Procedure Auto-FMO protocol ver. 1.20180227
FMO calculation
FMO method FMO2-MP2/6-31G(d)
Fragmentation Auto
Number of fragment 190
LigandCharge NA+=1
Software MIZUHO/ABINIT-MP 3.0
Total energy (hartree)
FMO2-HF: Electronic energy -1026755.348046
FMO2-HF: Nuclear repulsion 977304.314436
FMO2-HF: Total energy -49451.03361
FMO2-MP2: Total energy -49589.352506


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:12:ACE)


Summations of interaction energy for fragment #1(A:12:ACE)
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.
-1.4161.160.242-1.292-1.527-0.003
Interaction energy analysis for fragmet #1(A:12:ACE)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.005 / q_NPA : -0.012
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].
3A14GLN0-0.0180.0163.6460.4951.660-0.002-0.577-0.5860.000
4A15LEU00.0140.0054.2900.0660.201-0.001-0.017-0.1170.000
5A16SER00.0630.0336.032-0.442-0.4420.0000.0000.0000.000
6A17SER0-0.019-0.0307.8730.0550.0550.0000.0000.0000.000
7A18THR0-0.075-0.0273.802-0.929-0.7180.008-0.082-0.1380.000
8A19ALA00.016-0.0084.8690.0260.0260.0000.0000.0000.000
9A20SER0-0.042-0.0142.8320.2130.7230.186-0.273-0.423-0.001
10A21VAL0-0.021-0.0055.1830.2720.295-0.001-0.005-0.0170.000
11A22THR0-0.032-0.0738.8240.0730.0730.0000.0000.0000.000
12A23VAL00.010-0.00210.956-0.010-0.0100.0000.0000.0000.000
13A24ASP-1-0.772-0.88014.545-0.075-0.0750.0000.0000.0000.000
14A25GLY0-0.025-0.01614.4970.0230.0230.0000.0000.0000.000
15A26LYS10.9030.94613.0560.0600.0600.0000.0000.0000.000
16A27ASP-1-0.813-0.8447.513-0.132-0.1320.0000.0000.0000.000
17A28ARG10.8360.9288.1140.3250.3250.0000.0000.0000.000
18A29ASN00.0250.0173.303-1.118-0.6390.053-0.332-0.200-0.002
19A30PHE0-0.031-0.0284.6700.6010.654-0.001-0.006-0.0460.000
20A31HIS00.0850.0245.547-0.760-0.7600.0000.0000.0000.000
21A32ILE0-0.0360.0047.5480.0640.0640.0000.0000.0000.000
22A33VAL00.0300.0128.325-0.069-0.0690.0000.0000.0000.000
23A34THR0-0.002-0.00411.3970.0800.0800.0000.0000.0000.000
24A126CYS-1-0.828-0.8889.139-0.639-0.6390.0000.0000.0000.000
25A36ARG10.9420.97316.3320.2590.2590.0000.0000.0000.000
26A37GLN00.001-0.01820.114-0.004-0.0040.0000.0000.0000.000
27A38LEU0-0.061-0.02522.8740.0160.0160.0000.0000.0000.000
28A39GLU-1-0.880-0.90825.438-0.137-0.1370.0000.0000.0000.000
29A40TRP0-0.055-0.02927.7410.0070.0070.0000.0000.0000.000
30A41ARG10.9580.98123.4560.1650.1650.0000.0000.0000.000
31A42ARG10.9330.97317.3000.2870.2870.0000.0000.0000.000
32A43MET0-0.075-0.03019.395-0.005-0.0050.0000.0000.0000.000
33A44ILE00.0290.00512.716-0.013-0.0130.0000.0000.0000.000
34A45ASP-1-0.810-0.90515.256-0.280-0.2800.0000.0000.0000.000
35A46ILE00.0110.0049.298-0.044-0.0440.0000.0000.0000.000
36A47GLY00.0180.01111.4040.0720.0720.0000.0000.0000.000
37A48ALA00.0080.00512.5520.0340.0340.0000.0000.0000.000
38A49ASP-1-0.803-0.90916.290-0.190-0.1900.0000.0000.0000.000
39A50PHE0-0.039-0.01918.3930.0000.0000.0000.0000.0000.000
40A51SER0-0.031-0.03115.1040.0090.0090.0000.0000.0000.000
41A52GLY00.0510.04713.079-0.022-0.0220.0000.0000.0000.000
42A53ALA0-0.017-0.00212.8000.0340.0340.0000.0000.0000.000
43A54LYS10.8130.90414.4750.1790.1790.0000.0000.0000.000
44A55VAL00.0200.01314.8190.0280.0280.0000.0000.0000.000
45A56ALA0-0.0050.00717.572-0.001-0.0010.0000.0000.0000.000
46A57VAL00.014-0.00617.5880.0050.0050.0000.0000.0000.000
47A58ASP-1-0.785-0.89320.850-0.139-0.1390.0000.0000.0000.000
48A59GLU-1-0.767-0.91019.435-0.257-0.2570.0000.0000.0000.000
49A60ASN0-0.025-0.00523.2680.0070.0070.0000.0000.0000.000
50A61ALA0-0.0250.01626.1290.0140.0140.0000.0000.0000.000
51A62GLN0-0.0240.00125.564-0.009-0.0090.0000.0000.0000.000
52A63PRO0-0.012-0.03123.9170.0110.0110.0000.0000.0000.000
53A64PRO00.0610.04821.0610.0050.0050.0000.0000.0000.000
54A65VAL00.0300.01822.740-0.004-0.0040.0000.0000.0000.000
55A66VAL0-0.021-0.00918.799-0.014-0.0140.0000.0000.0000.000
56A67GLU-1-0.812-0.89821.570-0.127-0.1270.0000.0000.0000.000
57A68SER0-0.029-0.00921.9310.0140.0140.0000.0000.0000.000
58A69VAL0-0.009-0.00516.859-0.032-0.0320.0000.0000.0000.000
59A70HIS00.0110.00518.6840.0230.0230.0000.0000.0000.000
60A71ILE0-0.027-0.00515.108-0.036-0.0360.0000.0000.0000.000
61A72GLN00.0350.02916.7060.0310.0310.0000.0000.0000.000
62A73ASN0-0.042-0.04016.814-0.009-0.0090.0000.0000.0000.000
63A74LEU00.0260.01710.9350.0000.0000.0000.0000.0000.000
64A75SER0-0.020-0.02212.1830.0100.0100.0000.0000.0000.000
65A76GLY00.0090.01214.6660.0170.0170.0000.0000.0000.000
66A77PHE00.0200.02117.5020.0130.0130.0000.0000.0000.000
67A78SER00.0040.00718.151-0.026-0.0260.0000.0000.0000.000
68A79GLY00.0170.00920.0430.0180.0180.0000.0000.0000.000
69A80MET0-0.0110.00120.858-0.026-0.0260.0000.0000.0000.000
70A81TYR0-0.024-0.00621.5930.0150.0150.0000.0000.0000.000
71A82SER00.0550.04523.426-0.014-0.0140.0000.0000.0000.000
72A83ARG10.8990.96725.8570.1390.1390.0000.0000.0000.000
73A84GLY0-0.020-0.00727.1220.0060.0060.0000.0000.0000.000
74A85GLY0-0.036-0.00528.7440.0090.0090.0000.0000.0000.000
75A86SER0-0.036-0.02328.565-0.001-0.0010.0000.0000.0000.000
76A87GLY00.0650.04424.749-0.010-0.0100.0000.0000.0000.000
77A88SER0-0.034-0.00822.2780.0110.0110.0000.0000.0000.000
78A89ALA00.0020.00019.403-0.019-0.0190.0000.0000.0000.000
79A90ASP-1-0.790-0.85119.285-0.154-0.1540.0000.0000.0000.000
80A91MET0-0.034-0.02816.812-0.044-0.0440.0000.0000.0000.000
81A92SER0-0.0040.00815.3720.0310.0310.0000.0000.0000.000
82A93MET00.0000.01314.704-0.067-0.0670.0000.0000.0000.000
83A94THR0-0.031-0.02511.8450.0710.0710.0000.0000.0000.000
84A95GLY00.0260.01912.622-0.045-0.0450.0000.0000.0000.000
85A96ASP-1-0.848-0.92312.107-0.295-0.2950.0000.0000.0000.000
86A97LYS10.8630.9636.9310.5550.5550.0000.0000.0000.000
87A98PHE00.0570.02010.9250.1350.1350.0000.0000.0000.000
88A99THR0-0.059-0.03610.590-0.214-0.2140.0000.0000.0000.000
89A100ILE00.0130.01412.3660.0910.0910.0000.0000.0000.000
90A101SER0-0.014-0.02314.099-0.041-0.0410.0000.0000.0000.000
91A102GLY00.0300.01816.1340.0210.0210.0000.0000.0000.000
92A103THR00.0010.01818.8780.0010.0010.0000.0000.0000.000
93A104ALA00.013-0.00120.373-0.004-0.0040.0000.0000.0000.000
94A105ASP-1-0.775-0.84722.134-0.096-0.0960.0000.0000.0000.000
95A106GLY0-0.003-0.02323.588-0.012-0.0120.0000.0000.0000.000
96A107TYR0-0.0200.00223.5000.0100.0100.0000.0000.0000.000
97A108LYS10.8360.88819.8180.0720.0720.0000.0000.0000.000
98A109THR00.0150.00421.0810.0010.0010.0000.0000.0000.000
99A110ASP-1-0.919-0.94223.200-0.026-0.0260.0000.0000.0000.000
100A111LYS10.8850.95225.2480.0370.0370.0000.0000.0000.000
101A112PRO00.0290.03027.060-0.004-0.0040.0000.0000.0000.000
102A113GLY00.0250.01327.992-0.003-0.0030.0000.0000.0000.000
103A114GLU-1-0.887-0.87929.304-0.034-0.0340.0000.0000.0000.000
104A115PRO00.0060.02228.398-0.005-0.0050.0000.0000.0000.000
105A116ALA0-0.028-0.01423.9940.0050.0050.0000.0000.0000.000
106A117THR00.021-0.01424.044-0.004-0.0040.0000.0000.0000.000
107A118ALA0-0.0430.01918.9560.0090.0090.0000.0000.0000.000
108A119THR00.0130.00317.564-0.009-0.0090.0000.0000.0000.000
109A120PHE0-0.029-0.02214.537-0.007-0.0070.0000.0000.0000.000
110A121LYS10.9290.95910.7940.3200.3200.0000.0000.0000.000
111A122ILE0-0.0030.0019.962-0.071-0.0710.0000.0000.0000.000
112A123VAL0-0.0060.0046.4900.1520.1520.0000.0000.0000.000
113A124VAL00.005-0.0126.731-0.714-0.7140.0000.0000.0000.000
114A125THR0-0.028-0.0107.3520.4390.4390.0000.0000.0000.000
115B201NA+10.7920.96824.6580.1480.1480.0000.0000.0000.000
116A203HOH0-0.014-0.02623.4580.0020.0020.0000.0000.0000.000
117A204HOH0-0.057-0.06721.8610.0050.0050.0000.0000.0000.000
118A205HOH00.0150.00922.502-0.002-0.0020.0000.0000.0000.000
119A206HOH00.0410.03313.296-0.003-0.0030.0000.0000.0000.000
120A207HOH0-0.037-0.03626.7120.0010.0010.0000.0000.0000.000
121A208HOH0-0.037-0.04113.740-0.001-0.0010.0000.0000.0000.000
122A209HOH0-0.034-0.03220.1950.0060.0060.0000.0000.0000.000
123A210HOH0-0.032-0.03123.844-0.004-0.0040.0000.0000.0000.000
124A211HOH0-0.048-0.04411.327-0.031-0.0310.0000.0000.0000.000
125A212HOH0-0.032-0.03010.6660.0040.0040.0000.0000.0000.000
126A213HOH00.0170.02123.6790.0000.0000.0000.0000.0000.000
127A214HOH0-0.047-0.03413.6530.0210.0210.0000.0000.0000.000
128A215HOH0-0.040-0.02618.1900.0130.0130.0000.0000.0000.000
129A216HOH00.0320.0209.432-0.004-0.0040.0000.0000.0000.000
130A217HOH0-0.015-0.02512.885-0.012-0.0120.0000.0000.0000.000
131A218HOH0-0.047-0.0327.1530.0110.0110.0000.0000.0000.000
132A219HOH00.0210.02518.0560.0080.0080.0000.0000.0000.000
133A220HOH00.0330.01822.170-0.007-0.0070.0000.0000.0000.000
134A221HOH0-0.020-0.02218.924-0.004-0.0040.0000.0000.0000.000
135A222HOH0-0.027-0.01510.2570.0240.0240.0000.0000.0000.000
136A223HOH0-0.009-0.00327.9210.0040.0040.0000.0000.0000.000
137A224HOH00.0310.01822.240-0.004-0.0040.0000.0000.0000.000
138A225HOH0-0.017-0.01825.0220.0030.0030.0000.0000.0000.000
139A226HOH0-0.022-0.02015.6870.0130.0130.0000.0000.0000.000
140A227HOH0-0.034-0.02120.5190.0040.0040.0000.0000.0000.000
141A228HOH0-0.003-0.00312.4490.0000.0000.0000.0000.0000.000
142A229HOH0-0.023-0.01117.1740.0020.0020.0000.0000.0000.000
143A230HOH00.0070.01912.942-0.013-0.0130.0000.0000.0000.000
144A231HOH00.0190.00427.3040.0010.0010.0000.0000.0000.000
145A232HOH00.0330.02314.3830.0100.0100.0000.0000.0000.000
146A233HOH0-0.035-0.02817.7090.0100.0100.0000.0000.0000.000
147A234HOH00.0300.01321.605-0.005-0.0050.0000.0000.0000.000
148A235HOH00.0260.01925.281-0.002-0.0020.0000.0000.0000.000
149A236HOH00.0220.01518.153-0.010-0.0100.0000.0000.0000.000
150A237HOH0-0.019-0.01624.0680.0030.0030.0000.0000.0000.000
151A238HOH0-0.030-0.01516.9750.0080.0080.0000.0000.0000.000
152A239HOH0-0.026-0.01321.714-0.004-0.0040.0000.0000.0000.000
153A240HOH00.0090.0098.7120.0070.0070.0000.0000.0000.000
154A241HOH0-0.010-0.00828.840-0.002-0.0020.0000.0000.0000.000
155A242HOH0-0.051-0.0288.0250.0750.0750.0000.0000.0000.000
156A243HOH00.0400.02324.4030.0000.0000.0000.0000.0000.000
157A254HOH0-0.0040.00421.419-0.003-0.0030.0000.0000.0000.000
158A255HOH0-0.009-0.01426.467-0.002-0.0020.0000.0000.0000.000
159A256HOH0-0.026-0.02024.8990.0000.0000.0000.0000.0000.000
160A257HOH0-0.0020.00026.741-0.004-0.0040.0000.0000.0000.000
161A258HOH0-0.030-0.00823.2100.0080.0080.0000.0000.0000.000
162A259HOH0-0.056-0.03727.3720.0000.0000.0000.0000.0000.000
163A260HOH0-0.044-0.04425.873-0.002-0.0020.0000.0000.0000.000
164A261HOH0-0.020-0.01527.8650.0000.0000.0000.0000.0000.000
165A262HOH00.0150.01422.2650.0040.0040.0000.0000.0000.000
166A263HOH00.0330.01931.050-0.002-0.0020.0000.0000.0000.000
167A264HOH00.0140.01429.700-0.002-0.0020.0000.0000.0000.000
168A265HOH0-0.037-0.0228.266-0.088-0.0880.0000.0000.0000.000
169A267HOH0-0.025-0.01613.9020.0150.0150.0000.0000.0000.000
170A269HOH0-0.0040.00816.4760.0090.0090.0000.0000.0000.000
171A270HOH0-0.004-0.02118.5630.0030.0030.0000.0000.0000.000
172A271HOH00.0080.01423.514-0.002-0.0020.0000.0000.0000.000
173A272HOH0-0.045-0.03320.0140.0050.0050.0000.0000.0000.000
174A273HOH0-0.015-0.01616.827-0.007-0.0070.0000.0000.0000.000
175A275HOH00.005-0.00928.390-0.002-0.0020.0000.0000.0000.000
176A279HOH0-0.022-0.02026.1570.0040.0040.0000.0000.0000.000
177A280HOH0-0.097-0.07227.6110.0020.0020.0000.0000.0000.000
178A282HOH00.0980.02421.9180.0050.0050.0000.0000.0000.000
179A283HOH00.0380.0289.200-0.057-0.0570.0000.0000.0000.000
180A285HOH0-0.049-0.06925.3170.0020.0020.0000.0000.0000.000
181A287HOH0-0.0040.00620.3270.0070.0070.0000.0000.0000.000
182A289HOH0-0.0060.00114.6560.0000.0000.0000.0000.0000.000
183A291HOH0-0.027-0.02118.5440.0150.0150.0000.0000.0000.000
184A293HOH0-0.039-0.02534.1510.0010.0010.0000.0000.0000.000
185A294HOH00.004-0.0048.9450.0470.0470.0000.0000.0000.000
186A295HOH0-0.094-0.10029.0850.0010.0010.0000.0000.0000.000
187A296HOH0-0.019-0.0097.8590.0520.0520.0000.0000.0000.000
188B347HOH0-0.014-0.01931.4010.0000.0000.0000.0000.0000.000
189B350HOH0-0.051-0.03426.0180.0020.0020.0000.0000.0000.000
190B370HOH00.0660.00623.305-0.001-0.0010.0000.0000.0000.000