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: M34NZ

Calculation Name: 2Z9O-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2Z9O

Chain ID: A

ChEMBL ID:

UniProt ID: P03856

Base Structure: X-ray

Registration Date: 2023-06-19

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 222
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2773202.89618
FMO2-HF: Nuclear repulsion 2681818.112911
FMO2-HF: Total energy -91384.783269
FMO2-MP2: Total energy -91652.472546


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:21:SER)


Summations of interaction energy for fragment #1(A:21:SER)
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.
-17.624-12.2351.258-2.767-3.880.007
Interaction energy analysis for fragmet #1(A:21:SER)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.018 / q_NPA : -0.010
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].
3A23ASP-1-0.704-0.8623.821-4.037-2.333-0.011-0.700-0.9920.001
4A24LEU00.001-0.0035.5951.3661.3660.0000.0000.0000.000
5A25THR0-0.028-0.0355.3540.4650.4650.0000.0000.0000.000
6A26GLU-1-0.903-0.9413.086-0.7580.7080.063-0.740-0.789-0.006
7A27ALA0-0.0050.0137.008-0.281-0.2810.0000.0000.0000.000
8A28ALA00.0500.02110.192-0.006-0.0060.0000.0000.0000.000
9A29TYR0-0.041-0.0567.839-0.513-0.5130.0000.0000.0000.000
10A30SER0-0.011-0.01611.591-0.163-0.1630.0000.0000.0000.000
11A31LEU0-0.105-0.00713.285-0.131-0.1310.0000.0000.0000.000
12A32SER00.0470.00816.2610.0520.0520.0000.0000.0000.000
13A33ARG10.9450.96319.113-0.351-0.3510.0000.0000.0000.000
14A34ASP-1-0.837-0.96420.2060.2830.2830.0000.0000.0000.000
15A35GLN0-0.040-0.01519.2440.0120.0120.0000.0000.0000.000
16A36LYS10.8670.97314.082-0.844-0.8440.0000.0000.0000.000
17A37ARG10.8550.97917.812-0.347-0.3470.0000.0000.0000.000
18A38MET0-0.033-0.00520.806-0.021-0.0210.0000.0000.0000.000
19A39LEU00.005-0.01415.164-0.003-0.0030.0000.0000.0000.000
20A40TYR00.0280.02718.3290.0110.0110.0000.0000.0000.000
21A41LEU00.0740.02819.803-0.027-0.0270.0000.0000.0000.000
22A42PHE0-0.025-0.00720.127-0.011-0.0110.0000.0000.0000.000
23A43VAL00.009-0.00916.189-0.027-0.0270.0000.0000.0000.000
24A44ASP-1-1.057-1.00819.2590.2600.2600.0000.0000.0000.000
25A45GLN00.000-0.02921.962-0.016-0.0160.0000.0000.0000.000
26A46ILE0-0.0920.01219.171-0.025-0.0250.0000.0000.0000.000
27A47ARG10.9360.95818.859-0.262-0.2620.0000.0000.0000.000
28A57ASP-1-0.913-0.96623.523-0.073-0.0730.0000.0000.0000.000
29A58GLY0-0.014-0.01724.708-0.029-0.0290.0000.0000.0000.000
30A59ILE0-0.063-0.02325.3050.0090.0090.0000.0000.0000.000
31A60CYS00.0240.01925.7930.0160.0160.0000.0000.0000.000
32A61GLU-1-0.820-0.89227.858-0.002-0.0020.0000.0000.0000.000
33A62ILE0-0.039-0.03226.0830.0120.0120.0000.0000.0000.000
34A63HIS00.0060.00428.870-0.002-0.0020.0000.0000.0000.000
35A64VAL00.0030.00330.3660.0150.0150.0000.0000.0000.000
36A65ALA00.0160.01131.5190.0140.0140.0000.0000.0000.000
37A66LYS10.9711.00127.872-0.174-0.1740.0000.0000.0000.000
38A67TYR00.008-0.01324.7130.0250.0250.0000.0000.0000.000
39A68ALA0-0.013-0.03928.5990.0170.0170.0000.0000.0000.000
40A69GLU-1-0.871-0.93031.2800.1900.1900.0000.0000.0000.000
41A70ILE0-0.0180.01724.6910.0110.0110.0000.0000.0000.000
42A71PHE0-0.105-0.06722.4310.0440.0440.0000.0000.0000.000
43A72GLY0-0.0060.01527.860-0.001-0.0010.0000.0000.0000.000
44A73LEU0-0.012-0.01429.636-0.001-0.0010.0000.0000.0000.000
45A74THR00.0440.02933.009-0.012-0.0120.0000.0000.0000.000
46A75SER00.065-0.00234.1210.0030.0030.0000.0000.0000.000
47A76ALA0-0.029-0.00235.055-0.003-0.0030.0000.0000.0000.000
48A77GLU-1-0.820-0.92232.7930.1570.1570.0000.0000.0000.000
49A78ALA00.0370.03130.4640.0020.0020.0000.0000.0000.000
50A79SER0-0.058-0.03230.554-0.003-0.0030.0000.0000.0000.000
51A80LYS10.9450.96631.458-0.132-0.1320.0000.0000.0000.000
52A81ASP-1-0.856-0.92327.4000.1980.1980.0000.0000.0000.000
53A82ILE00.0200.02226.850-0.009-0.0090.0000.0000.0000.000
54A83ARG10.8920.94427.642-0.091-0.0910.0000.0000.0000.000
55A84GLN00.005-0.01127.609-0.018-0.0180.0000.0000.0000.000
56A85ALA00.0480.04223.680-0.010-0.0100.0000.0000.0000.000
57A86LEU00.0730.02724.184-0.014-0.0140.0000.0000.0000.000
58A87LYS10.9100.95425.259-0.066-0.0660.0000.0000.0000.000
59A88SER0-0.003-0.01523.067-0.017-0.0170.0000.0000.0000.000
60A89PHE0-0.068-0.03717.904-0.003-0.0030.0000.0000.0000.000
61A90ALA0-0.085-0.04322.139-0.034-0.0340.0000.0000.0000.000
62A91GLY00.016-0.01322.2200.0090.0090.0000.0000.0000.000
63A92LYS10.8930.98517.686-0.029-0.0290.0000.0000.0000.000
64A93GLU-1-0.881-0.97615.967-0.416-0.4160.0000.0000.0000.000
65A94VAL0-0.094-0.01910.4090.0710.0710.0000.0000.0000.000
66A95VAL00.0210.0029.906-0.003-0.0030.0000.0000.0000.000
67A96PHE0-0.039-0.0127.903-0.286-0.2860.0000.0000.0000.000
68A97TYR00.013-0.0186.8460.7000.7000.0000.0000.0000.000
69A98ARG10.8190.8988.5111.1551.1550.0000.0000.0000.000
70A99PRO0-0.0660.0009.5130.0650.0650.0000.0000.0000.000
71A100GLU-1-0.786-0.89311.790-1.379-1.3790.0000.0000.0000.000
72A101GLU-1-0.969-1.00714.653-0.763-0.7630.0000.0000.0000.000
73A102ASP-1-1.071-1.01613.697-1.082-1.0820.0000.0000.0000.000
74A103ALA00.0350.00416.4730.0380.0380.0000.0000.0000.000
75A104GLY0-0.0010.01619.0730.0390.0390.0000.0000.0000.000
76A105ASP-1-0.995-0.97818.136-0.486-0.4860.0000.0000.0000.000
77A106GLU-1-1.025-1.03417.722-0.471-0.4710.0000.0000.0000.000
78A107LYS10.9150.96910.6981.0171.0170.0000.0000.0000.000
79A108GLY00.0940.04313.7860.0970.0970.0000.0000.0000.000
80A109TYR0-0.100-0.05412.054-0.237-0.2370.0000.0000.0000.000
81A110GLU-1-0.784-0.90012.627-0.899-0.8990.0000.0000.0000.000
82A111SER0-0.060-0.01912.618-0.155-0.1550.0000.0000.0000.000
83A112PHE00.0410.01713.3630.1140.1140.0000.0000.0000.000
84A113PRO00.0310.04615.9670.0330.0330.0000.0000.0000.000
85A114TRP00.023-0.01012.782-0.008-0.0080.0000.0000.0000.000
86A115PHE0-0.054-0.04118.5120.0130.0130.0000.0000.0000.000
87A116ILE00.0340.05022.144-0.009-0.0090.0000.0000.0000.000
88A117LYS10.9680.98024.1190.0630.0630.0000.0000.0000.000
89A118ARG10.9500.98224.4930.0370.0370.0000.0000.0000.000
90A119ALA0-0.028-0.01728.051-0.007-0.0070.0000.0000.0000.000
91A120HIS10.9070.97031.371-0.035-0.0350.0000.0000.0000.000
92A121SER00.0060.00333.572-0.009-0.0090.0000.0000.0000.000
93A122PRO0-0.0100.00637.2800.0050.0050.0000.0000.0000.000
94A123SER00.0600.04039.0270.0020.0020.0000.0000.0000.000
95A124ARG10.9590.97134.514-0.007-0.0070.0000.0000.0000.000
96A125GLY0-0.001-0.01638.1180.0020.0020.0000.0000.0000.000
97A126LEU00.0020.01033.5110.0080.0080.0000.0000.0000.000
98A127TYR0-0.068-0.04630.120-0.011-0.0110.0000.0000.0000.000
99A128SER00.009-0.02230.4420.0070.0070.0000.0000.0000.000
100A129VAL0-0.038-0.03424.908-0.002-0.0020.0000.0000.0000.000
101A130HIS0-0.0230.00226.2050.0140.0140.0000.0000.0000.000
102A131ILE00.0940.03219.917-0.010-0.0100.0000.0000.0000.000
103A132ASN00.0310.02819.260-0.031-0.0310.0000.0000.0000.000
104A133PRO00.039-0.01419.706-0.008-0.0080.0000.0000.0000.000
105A134TYR00.0160.00016.7450.0300.0300.0000.0000.0000.000
106A135LEU00.0620.02913.798-0.055-0.0550.0000.0000.0000.000
107A136ILE00.0030.02714.8030.0230.0230.0000.0000.0000.000
108A137PRO0-0.025-0.01514.7610.0840.0840.0000.0000.0000.000
109A138PHE00.0300.0198.9860.0010.0010.0000.0000.0000.000
110A139PHE00.000-0.00411.5070.2220.2220.0000.0000.0000.000
111A140ILE00.0330.02712.9980.1620.1620.0000.0000.0000.000
112A141GLY00.0120.0089.9550.0910.0910.0000.0000.0000.000
113A142LEU0-0.007-0.01710.4610.3540.3540.0000.0000.0000.000
114A143GLN00.0220.04111.9840.1030.1030.0000.0000.0000.000
115A144ASN0-0.016-0.02010.790-0.044-0.0440.0000.0000.0000.000
116A145ARG10.8810.9104.806-4.088-4.0880.0000.0000.0000.000
117A146PHE0-0.069-0.05311.915-0.030-0.0300.0000.0000.0000.000
118A147THR0-0.0080.01715.242-0.077-0.0770.0000.0000.0000.000
119A148GLN0-0.0100.00712.3380.1120.1120.0000.0000.0000.000
120A149PHE0-0.034-0.0249.819-0.002-0.0020.0000.0000.0000.000
121A150ARG10.8050.89313.936-0.675-0.6750.0000.0000.0000.000
122A151LEU00.0500.02611.868-0.061-0.0610.0000.0000.0000.000
123A152SER00.011-0.01815.011-0.049-0.0490.0000.0000.0000.000
124A153GLU-1-0.912-0.94018.1460.4980.4980.0000.0000.0000.000
125A154THR0-0.020-0.01014.4070.0680.0680.0000.0000.0000.000
126A155LYS10.8610.93717.423-0.447-0.4470.0000.0000.0000.000
127A156GLU-1-0.815-0.90316.4480.4850.4850.0000.0000.0000.000
128A157ILE0-0.048-0.03111.485-0.004-0.0040.0000.0000.0000.000
129A158THR00.0460.00412.1780.1050.1050.0000.0000.0000.000
130A159ASN00.0780.04411.6690.0750.0750.0000.0000.0000.000
131A160PRO00.1230.0406.9110.3050.3050.0000.0000.0000.000
132A161TYR00.007-0.0116.8850.8790.8790.0000.0000.0000.000
133A162ALA0-0.062-0.0289.3830.1800.1800.0000.0000.0000.000
134A163MET0-0.0670.0007.3610.2760.2760.0000.0000.0000.000
135A164ARG10.9060.9472.032-8.143-6.1131.207-1.315-1.9220.012
136A165LEU00.019-0.0027.215-0.198-0.1980.0000.0000.0000.000
137A166TYR0-0.007-0.03410.849-0.233-0.2330.0000.0000.0000.000
138A167GLU-1-0.799-0.8857.2034.4344.4340.0000.0000.0000.000
139A168SER0-0.0250.0049.181-0.376-0.3760.0000.0000.0000.000
140A169LEU0-0.032-0.02311.173-0.291-0.2910.0000.0000.0000.000
141A170CYS0-0.0160.00613.033-0.216-0.2160.0000.0000.0000.000
142A171GLN00.0060.01012.308-0.079-0.0790.0000.0000.0000.000
143A172TYR0-0.051-0.03313.688-0.168-0.1680.0000.0000.0000.000
144A173ARG10.8930.96417.175-0.992-0.9920.0000.0000.0000.000
145A174LYS10.9530.99919.643-0.467-0.4670.0000.0000.0000.000
146A175PRO00.0110.00223.0330.0230.0230.0000.0000.0000.000
147A176ASP-1-0.821-0.91824.9920.3960.3960.0000.0000.0000.000
148A177GLY0-0.064-0.03122.443-0.001-0.0010.0000.0000.0000.000
149A178SER0-0.022-0.02923.171-0.011-0.0110.0000.0000.0000.000
150A179GLY00.003-0.00321.8180.0140.0140.0000.0000.0000.000
151A180ILE0-0.0230.00422.5490.0020.0020.0000.0000.0000.000
152A181VAL00.0180.02217.057-0.004-0.0040.0000.0000.0000.000
153A182SER0-0.030-0.01520.174-0.012-0.0120.0000.0000.0000.000
154A183LEU00.0110.01814.2100.0000.0000.0000.0000.0000.000
155A184LYS10.9470.94817.352-0.375-0.3750.0000.0000.0000.000
156A185ILE00.0800.03716.6840.0640.0640.0000.0000.0000.000
157A186ASP-1-0.842-0.92316.2550.3020.3020.0000.0000.0000.000
158A187TRP0-0.051-0.02510.915-0.065-0.0650.0000.0000.0000.000
159A188ILE0-0.026-0.02412.3100.1070.1070.0000.0000.0000.000
160A189ILE0-0.019-0.01511.6200.1570.1570.0000.0000.0000.000
161A190GLU-1-0.854-0.90010.3170.0090.0090.0000.0000.0000.000
162A191ARG10.9100.9737.194-0.537-0.5370.0000.0000.0000.000
163A192TYR0-0.063-0.0536.7500.7930.7930.0000.0000.0000.000
164A193GLN00.003-0.0184.513-0.362-0.173-0.001-0.012-0.1770.000
165A194LEU0-0.055-0.0178.343-0.112-0.1120.0000.0000.0000.000
166A195PRO00.0080.01411.511-0.134-0.1340.0000.0000.0000.000
167A196GLN00.1260.05114.0060.0730.0730.0000.0000.0000.000
168A197SER00.0300.01416.7340.0550.0550.0000.0000.0000.000
169A198TYR0-0.047-0.03415.625-0.002-0.0020.0000.0000.0000.000
170A199GLN00.041-0.00917.4750.0720.0720.0000.0000.0000.000
171A200ARG10.8920.98219.480-0.097-0.0970.0000.0000.0000.000
172A201MET00.010-0.01722.1100.0180.0180.0000.0000.0000.000
173A202PRO0-0.030-0.03023.0250.0300.0300.0000.0000.0000.000
174A203ASP-1-0.854-0.92421.1750.1380.1380.0000.0000.0000.000
175A204PHE00.0450.01316.8860.0400.0400.0000.0000.0000.000
176A205ARG10.7840.86319.261-0.210-0.2100.0000.0000.0000.000
177A206ARG10.9941.00521.240-0.123-0.1230.0000.0000.0000.000
178A207ARG10.8840.94618.093-0.203-0.2030.0000.0000.0000.000
179A208PHE00.0560.03311.8410.0130.0130.0000.0000.0000.000
180A209LEU0-0.014-0.00916.6180.0330.0330.0000.0000.0000.000
181A210GLN0-0.011-0.00118.5860.0220.0220.0000.0000.0000.000
182A211VAL00.0230.01716.1540.0180.0180.0000.0000.0000.000
183A212CYS00.0380.02713.4260.0170.0170.0000.0000.0000.000
184A213VAL00.0280.03316.1510.0370.0370.0000.0000.0000.000
185A214ASN0-0.062-0.03818.6350.0160.0160.0000.0000.0000.000
186A215GLU-1-0.872-0.93915.6930.5200.5200.0000.0000.0000.000
187A216ILE0-0.075-0.05113.8970.0550.0550.0000.0000.0000.000
188A217ASN0-0.019-0.02117.349-0.035-0.0350.0000.0000.0000.000
189A218SER00.0150.01120.220-0.057-0.0570.0000.0000.0000.000
190A219ARG10.8530.94316.983-0.535-0.5350.0000.0000.0000.000
191A220THR00.0490.07115.231-0.015-0.0150.0000.0000.0000.000
192A221PRO00.0290.01517.581-0.077-0.0770.0000.0000.0000.000
193A222MET0-0.0020.01116.223-0.031-0.0310.0000.0000.0000.000
194A223ARG10.8910.94719.973-0.550-0.5500.0000.0000.0000.000
195A224LEU0-0.063-0.03017.3170.0140.0140.0000.0000.0000.000
196A225SER00.0410.03021.494-0.039-0.0390.0000.0000.0000.000
197A226TYR00.005-0.02321.5400.0470.0470.0000.0000.0000.000
198A227ILE00.0460.03623.566-0.040-0.0400.0000.0000.0000.000
199A228GLU-1-0.803-0.86924.4200.3230.3230.0000.0000.0000.000
200A229LYS10.9840.99525.163-0.331-0.3310.0000.0000.0000.000
201A230LYS10.9230.95326.219-0.235-0.2350.0000.0000.0000.000
202A231LYS10.9681.00128.523-0.171-0.1710.0000.0000.0000.000
203A232GLY00.0720.03430.250-0.012-0.0120.0000.0000.0000.000
204A233ARG10.9110.94232.303-0.139-0.1390.0000.0000.0000.000
205A234GLN00.0890.05624.2170.0050.0050.0000.0000.0000.000
206A235THR0-0.014-0.04425.337-0.006-0.0060.0000.0000.0000.000
207A236THR00.0040.01423.6280.0020.0020.0000.0000.0000.000
208A237HIS0-0.0340.00521.1860.0080.0080.0000.0000.0000.000
209A238ILE00.0200.03319.293-0.048-0.0480.0000.0000.0000.000
210A239VAL0-0.028-0.01920.2990.0520.0520.0000.0000.0000.000
211A240PHE00.0710.02517.046-0.027-0.0270.0000.0000.0000.000
212A241SER0-0.003-0.02621.099-0.030-0.0300.0000.0000.0000.000
213A242PHE00.029-0.00117.546-0.022-0.0220.0000.0000.0000.000
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