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: 1NZKZ

Calculation Name: 4P9F-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 4P9F

Chain ID: A

ChEMBL ID:

UniProt ID: T9SVH4

Base Structure: X-ray

Registration Date: 2023-09-24

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 212
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2555086.305656
FMO2-HF: Nuclear repulsion 2469549.363089
FMO2-HF: Total energy -85536.942567
FMO2-MP2: Total energy -85783.226616


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:MET)


Summations of interaction energy for fragment #1(A:9: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.
-0.5811.5050.002-1.042-1.0450.005
Interaction energy analysis for fragmet #1(A:9:MET)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.031 / q_NPA : 0.011
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].
3A11SER00.002-0.0033.683-0.9591.1270.002-1.042-1.0450.005
4A12LEU00.0460.0145.9500.2070.2070.0000.0000.0000.000
5A13THR0-0.026-0.0279.4410.0630.0630.0000.0000.0000.000
6A14LEU0-0.0050.0055.3830.0930.0930.0000.0000.0000.000
7A15GLN0-0.050-0.0259.164-0.130-0.1300.0000.0000.0000.000
8A16VAL00.0590.02110.8100.1930.1930.0000.0000.0000.000
9A17GLU-1-0.849-0.91311.254-0.919-0.9190.0000.0000.0000.000
10A18ASN00.020-0.0029.5180.3160.3160.0000.0000.0000.000
11A19ASP-1-0.812-0.88513.537-0.828-0.8280.0000.0000.0000.000
12A20LEU0-0.040-0.02616.0580.1050.1050.0000.0000.0000.000
13A21LYS10.8750.93312.5440.9170.9170.0000.0000.0000.000
14A22HIS00.0380.04417.2630.0460.0460.0000.0000.0000.000
15A23GLN00.016-0.01218.8920.0800.0800.0000.0000.0000.000
16A24LEU0-0.032-0.01620.5960.0440.0440.0000.0000.0000.000
17A25SER0-0.022-0.02820.2330.0400.0400.0000.0000.0000.000
18A26ILE0-0.040-0.01322.3430.0270.0270.0000.0000.0000.000
19A27GLY00.0290.03224.9110.0240.0240.0000.0000.0000.000
20A28ALA00.0190.02024.8450.0180.0180.0000.0000.0000.000
21A29LEU0-0.083-0.04522.7400.0140.0140.0000.0000.0000.000
22A30LYS10.8100.89527.0530.1800.1800.0000.0000.0000.000
23A31PRO00.0340.00030.097-0.007-0.0070.0000.0000.0000.000
24A32GLY00.0620.05431.4120.0050.0050.0000.0000.0000.000
25A33ALA0-0.064-0.02529.5390.0040.0040.0000.0000.0000.000
26A34ARG10.8530.90929.2110.1670.1670.0000.0000.0000.000
27A35LEU00.0260.02023.587-0.006-0.0060.0000.0000.0000.000
28A36ILE0-0.029-0.02726.3350.0100.0100.0000.0000.0000.000
29A37THR00.015-0.01120.660-0.022-0.0220.0000.0000.0000.000
30A38LYS10.7890.87122.3500.2020.2020.0000.0000.0000.000
31A39ASN00.0440.02124.002-0.010-0.0100.0000.0000.0000.000
32A40LEU00.0600.03319.986-0.008-0.0080.0000.0000.0000.000
33A41ALA0-0.003-0.00619.425-0.037-0.0370.0000.0000.0000.000
34A42GLU-1-0.802-0.88020.310-0.268-0.2680.0000.0000.0000.000
35A43GLN0-0.045-0.03223.0270.0160.0160.0000.0000.0000.000
36A44LEU0-0.0040.00917.016-0.016-0.0160.0000.0000.0000.000
37A45GLY0-0.0110.01418.045-0.043-0.0430.0000.0000.0000.000
38A46MET0-0.046-0.02113.567-0.051-0.0510.0000.0000.0000.000
39A47SER00.015-0.00415.8820.0560.0560.0000.0000.0000.000
40A48ILE00.0310.00517.197-0.039-0.0390.0000.0000.0000.000
41A49THR0-0.028-0.02013.8730.0040.0040.0000.0000.0000.000
42A50PRO00.0630.04111.9100.0290.0290.0000.0000.0000.000
43A51VAL00.0660.03013.751-0.037-0.0370.0000.0000.0000.000
44A52ARG10.8850.93816.1730.3200.3200.0000.0000.0000.000
45A53GLU-1-0.849-0.92312.444-0.469-0.4690.0000.0000.0000.000
46A54ALA00.0220.02514.1740.0120.0120.0000.0000.0000.000
47A55LEU00.0000.00315.2850.0310.0310.0000.0000.0000.000
48A56LEU0-0.008-0.01317.7400.0350.0350.0000.0000.0000.000
49A57ARG10.8810.9389.0680.9920.9920.0000.0000.0000.000
50A58LEU00.0530.03916.6860.0370.0370.0000.0000.0000.000
51A59VAL0-0.030-0.00618.9870.0380.0380.0000.0000.0000.000
52A60SER0-0.089-0.05018.0940.0300.0300.0000.0000.0000.000
53A61VAL00.0360.02117.7580.0310.0310.0000.0000.0000.000
54A62ASN0-0.095-0.05220.7350.0220.0220.0000.0000.0000.000
55A63ALA00.0130.00720.6600.0110.0110.0000.0000.0000.000
56A64LEU0-0.022-0.00621.200-0.011-0.0110.0000.0000.0000.000
57A65SER0-0.012-0.00224.1470.0240.0240.0000.0000.0000.000
58A66VAL00.0210.00924.969-0.015-0.0150.0000.0000.0000.000
59A67ALA00.0140.01127.1980.0140.0140.0000.0000.0000.000
60A68PRO00.0190.00029.250-0.003-0.0030.0000.0000.0000.000
61A69ALA00.002-0.00130.518-0.008-0.0080.0000.0000.0000.000
62A70GLN00.008-0.00325.455-0.021-0.0210.0000.0000.0000.000
63A71ALA00.0010.02125.678-0.022-0.0220.0000.0000.0000.000
64A72PHE00.0130.01121.8600.0070.0070.0000.0000.0000.000
65A73THR0-0.002-0.00526.3310.0030.0030.0000.0000.0000.000
66A74VAL00.0250.02626.083-0.013-0.0130.0000.0000.0000.000
67A75PRO0-0.012-0.00226.0020.0190.0190.0000.0000.0000.000
68A76GLU-1-0.858-0.93528.976-0.159-0.1590.0000.0000.0000.000
69A77VAL0-0.040-0.00629.1450.0110.0110.0000.0000.0000.000
70A78GLY00.0430.02932.2220.0040.0040.0000.0000.0000.000
71A79LYS10.9240.97835.0660.0960.0960.0000.0000.0000.000
72A80ARG10.9570.98936.4980.0830.0830.0000.0000.0000.000
73A81GLN00.0600.01731.6670.0040.0040.0000.0000.0000.000
74A82LEU00.0390.03031.697-0.006-0.0060.0000.0000.0000.000
75A83ASP-1-0.854-0.91233.121-0.101-0.1010.0000.0000.0000.000
76A84GLU-1-1.022-1.00830.852-0.116-0.1160.0000.0000.0000.000
77A85ILE00.0280.00527.3350.0020.0020.0000.0000.0000.000
78A86ASN00.0220.01429.407-0.014-0.0140.0000.0000.0000.000
79A87ARG10.9270.95631.6930.0830.0830.0000.0000.0000.000
80A88ILE0-0.0170.00527.3860.0060.0060.0000.0000.0000.000
81A89ARG10.8950.92626.5870.1720.1720.0000.0000.0000.000
82A90TYR00.0130.01328.015-0.002-0.0020.0000.0000.0000.000
83A91GLU-1-0.781-0.87430.669-0.070-0.0700.0000.0000.0000.000
84A92LEU0-0.0170.00324.5940.0040.0040.0000.0000.0000.000
85A93GLU-1-0.690-0.81025.328-0.191-0.1910.0000.0000.0000.000
86A94LEU0-0.0100.00626.9980.0030.0030.0000.0000.0000.000
87A95MET0-0.040-0.01127.1710.0120.0120.0000.0000.0000.000
88A96ALA00.0170.00223.6390.0080.0080.0000.0000.0000.000
89A97VAL00.0320.01125.4630.0050.0050.0000.0000.0000.000
90A98ALA0-0.0050.00327.8140.0080.0080.0000.0000.0000.000
91A99LEU0-0.011-0.00325.0780.0110.0110.0000.0000.0000.000
92A100ALA00.0370.02524.7110.0090.0090.0000.0000.0000.000
93A101VAL00.0060.01325.9210.0060.0060.0000.0000.0000.000
94A102GLU-1-0.901-0.93128.545-0.016-0.0160.0000.0000.0000.000
95A103ASN0-0.036-0.02224.0130.0200.0200.0000.0000.0000.000
96A104LEU0-0.0310.00524.358-0.002-0.0020.0000.0000.0000.000
97A105THR0-0.040-0.05524.5980.0130.0130.0000.0000.0000.000
98A106PRO00.015-0.02826.977-0.010-0.0100.0000.0000.0000.000
99A107GLN0-0.026-0.00823.0690.0100.0100.0000.0000.0000.000
100A108ASP-1-0.717-0.81821.976-0.117-0.1170.0000.0000.0000.000
101A109LEU0-0.058-0.02824.479-0.012-0.0120.0000.0000.0000.000
102A110ALA0-0.032-0.00627.0880.0030.0030.0000.0000.0000.000
103A111GLU-1-0.829-0.90720.680-0.193-0.1930.0000.0000.0000.000
104A112LEU0-0.024-0.02024.002-0.014-0.0140.0000.0000.0000.000
105A113GLN0-0.051-0.03326.3680.0030.0030.0000.0000.0000.000
106A114GLU-1-0.843-0.90326.122-0.174-0.1740.0000.0000.0000.000
107A115LEU0-0.032-0.02622.136-0.007-0.0070.0000.0000.0000.000
108A116LEU00.0160.00726.444-0.005-0.0050.0000.0000.0000.000
109A117GLU-1-0.837-0.90630.058-0.131-0.1310.0000.0000.0000.000
110A118LYS10.7570.86326.1950.1750.1750.0000.0000.0000.000
111A119LEU0-0.0120.01028.660-0.006-0.0060.0000.0000.0000.000
112A120GLN0-0.001-0.02230.0230.0010.0010.0000.0000.0000.000
113A121GLN0-0.028-0.02030.765-0.007-0.0070.0000.0000.0000.000
114A122ALA0-0.051-0.02229.4300.0010.0010.0000.0000.0000.000
115A123GLN00.024-0.01031.5640.0050.0050.0000.0000.0000.000
116A124GLU-1-0.876-0.93134.624-0.115-0.1150.0000.0000.0000.000
117A125LYS10.7760.88129.8500.2130.2130.0000.0000.0000.000
118A126GLY00.0140.01735.5370.0000.0000.0000.0000.0000.000
119A127ASP-1-0.864-0.93429.294-0.242-0.2420.0000.0000.0000.000
120A128MET00.0370.01330.569-0.010-0.0100.0000.0000.0000.000
121A129GLU-1-0.891-0.93924.108-0.344-0.3440.0000.0000.0000.000
122A130GLN00.011-0.00423.912-0.033-0.0330.0000.0000.0000.000
123A131ILE0-0.0010.01427.025-0.001-0.0010.0000.0000.0000.000
124A132ILE00.0060.01525.7820.0000.0000.0000.0000.0000.000
125A133ASN00.013-0.01020.875-0.030-0.0300.0000.0000.0000.000
126A134VAL0-0.003-0.00122.974-0.017-0.0170.0000.0000.0000.000
127A135ASN00.0310.03324.9020.0220.0220.0000.0000.0000.000
128A136ARG10.8140.90917.1000.4740.4740.0000.0000.0000.000
129A137LEU0-0.005-0.00818.292-0.008-0.0080.0000.0000.0000.000
130A138PHE00.0280.00821.3290.0060.0060.0000.0000.0000.000
131A139ARG10.8620.92223.9310.1910.1910.0000.0000.0000.000
132A140LEU0-0.005-0.00116.2920.0130.0130.0000.0000.0000.000
133A141ALA0-0.0060.00519.5030.0010.0010.0000.0000.0000.000
134A142ILE0-0.018-0.00520.5130.0250.0250.0000.0000.0000.000
135A143TYR0-0.021-0.05820.9060.0210.0210.0000.0000.0000.000
136A144HIS00.0460.02815.1000.0590.0590.0000.0000.0000.000
137A145ARG10.8370.91618.6270.1170.1170.0000.0000.0000.000
138A146SER0-0.030-0.03721.2480.0270.0270.0000.0000.0000.000
139A147ASN0-0.052-0.02419.1130.0120.0120.0000.0000.0000.000
140A148MET00.0100.01119.6330.0330.0330.0000.0000.0000.000
141A149PRO00.0470.01414.151-0.028-0.0280.0000.0000.0000.000
142A150ILE00.0060.00016.267-0.046-0.0460.0000.0000.0000.000
143A151LEU0-0.0140.01117.623-0.016-0.0160.0000.0000.0000.000
144A152CYS0-0.023-0.00717.069-0.006-0.0060.0000.0000.0000.000
145A153GLU-1-0.886-0.92713.942-0.459-0.4590.0000.0000.0000.000
146A154MET00.0350.01516.832-0.003-0.0030.0000.0000.0000.000
147A155ILE0-0.010-0.00120.1520.0080.0080.0000.0000.0000.000
148A156GLU-1-0.807-0.89716.265-0.512-0.5120.0000.0000.0000.000
149A157GLN0-0.090-0.06417.5420.0170.0170.0000.0000.0000.000
150A158LEU0-0.040-0.01820.1700.0160.0160.0000.0000.0000.000
151A159TRP0-0.049-0.04620.2810.0080.0080.0000.0000.0000.000
152A160VAL0-0.010-0.00318.7280.0060.0060.0000.0000.0000.000
153A161ARG10.8660.93222.2000.2160.2160.0000.0000.0000.000
154A162MET0-0.029-0.01124.8930.0190.0190.0000.0000.0000.000
155A163GLY00.0440.03125.2760.0120.0120.0000.0000.0000.000
156A164PRO00.009-0.00125.8110.0090.0090.0000.0000.0000.000
157A165GLY00.0110.00928.6930.0110.0110.0000.0000.0000.000
158A166LEU00.003-0.00127.2340.0140.0140.0000.0000.0000.000
159A167HIS0-0.025-0.00129.9410.0170.0170.0000.0000.0000.000
160A168TYR00.004-0.01731.6410.0050.0050.0000.0000.0000.000
161A169LEU0-0.004-0.01131.2170.0080.0080.0000.0000.0000.000
162A170TYR0-0.039-0.04427.6180.0050.0050.0000.0000.0000.000
163A171GLU-1-0.852-0.90934.283-0.158-0.1580.0000.0000.0000.000
164A172ALA0-0.028-0.00937.4840.0080.0080.0000.0000.0000.000
165A173ILE0-0.055-0.01636.8590.0080.0080.0000.0000.0000.000
166A174ASN0-0.003-0.01437.748-0.012-0.0120.0000.0000.0000.000
167A175PRO00.0370.01335.6660.0030.0030.0000.0000.0000.000
168A176ALA00.0020.01337.5700.0010.0010.0000.0000.0000.000
169A177GLU-1-0.882-0.92840.675-0.098-0.0980.0000.0000.0000.000
170A178LEU0-0.064-0.03535.0600.0010.0010.0000.0000.0000.000
171A179ARG10.8040.89937.4330.1040.1040.0000.0000.0000.000
172A180GLU-1-0.925-0.96038.815-0.085-0.0850.0000.0000.0000.000
173A181HIS00.0500.02536.1600.0020.0020.0000.0000.0000.000
174A182ILE00.0070.01532.977-0.003-0.0030.0000.0000.0000.000
175A183GLU-1-0.791-0.88735.416-0.098-0.0980.0000.0000.0000.000
176A184ASN00.009-0.01236.2740.0070.0070.0000.0000.0000.000
177A185TYR0-0.043-0.04129.0110.0010.0010.0000.0000.0000.000
178A186HIS00.0280.01632.9390.0000.0000.0000.0000.0000.000
179A187LEU0-0.009-0.00135.1170.0050.0050.0000.0000.0000.000
180A188LEU00.0060.01229.8830.0050.0050.0000.0000.0000.000
181A189LEU0-0.019-0.00529.5590.0040.0040.0000.0000.0000.000
182A190ALA0-0.029-0.01932.3080.0060.0060.0000.0000.0000.000
183A191ALA00.0210.01034.6780.0060.0060.0000.0000.0000.000
184A192LEU00.003-0.02228.4240.0060.0060.0000.0000.0000.000
185A193LYS10.8670.93631.8560.0910.0910.0000.0000.0000.000
186A194ALA0-0.034-0.01733.4350.0070.0070.0000.0000.0000.000
187A195LYS10.8010.90729.7560.0590.0590.0000.0000.0000.000
188A196ASP-1-0.808-0.89134.623-0.047-0.0470.0000.0000.0000.000
189A197LYS10.8400.88631.0850.0280.0280.0000.0000.0000.000
190A198GLU-1-0.941-0.94534.819-0.050-0.0500.0000.0000.0000.000
191A199GLY00.0520.02137.293-0.005-0.0050.0000.0000.0000.000
192A200CYS0-0.061-0.03531.931-0.008-0.0080.0000.0000.0000.000
193A201ARG10.7890.85131.5160.0620.0620.0000.0000.0000.000
194A202HIS0-0.010-0.00534.369-0.004-0.0040.0000.0000.0000.000
195A203CYS00.000-0.00934.870-0.004-0.0040.0000.0000.0000.000
196A204LEU0-0.013-0.00528.493-0.006-0.0060.0000.0000.0000.000
197A205ALA00.0460.01632.684-0.009-0.0090.0000.0000.0000.000
198A206GLU-1-0.877-0.92235.051-0.083-0.0830.0000.0000.0000.000
199A207ILE0-0.028-0.01131.333-0.005-0.0050.0000.0000.0000.000
200A208MET0-0.106-0.04030.836-0.012-0.0120.0000.0000.0000.000
201A209GLN0-0.039-0.02433.4100.0000.0000.0000.0000.0000.000
202A210GLN0-0.0090.00734.9150.0060.0060.0000.0000.0000.000
203A211ASN00.017-0.00531.1750.0060.0060.0000.0000.0000.000
204A212ILE0-0.033-0.01833.231-0.004-0.0040.0000.0000.0000.000
205A213ALA0-0.012-0.01135.6280.0010.0010.0000.0000.0000.000
206A214ILE0-0.0090.00435.5930.0040.0040.0000.0000.0000.000
207A215LEU00.0030.00631.7370.0010.0010.0000.0000.0000.000
208A216TYR0-0.043-0.07535.6880.0000.0000.0000.0000.0000.000
209A217GLN00.0200.02539.0280.0040.0040.0000.0000.0000.000
210A218GLN0-0.076-0.04334.3990.0010.0010.0000.0000.0000.000
211A219TYR0-0.068-0.04734.7320.0030.0030.0000.0000.0000.000
212A220ASN0-0.050-0.00941.4750.0060.0060.0000.0000.0000.000