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: N9QQQ

Calculation Name: 1DOV-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1DOV

Chain ID: A

ChEMBL ID:

UniProt ID: P26231

Base Structure: X-ray

Registration Date: 2023-09-20

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 181
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -1600999.062677
FMO2-HF: Nuclear repulsion 1531033.130947
FMO2-HF: Total energy -69965.93173
FMO2-MP2: Total energy -70168.716053


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:82:GLU)


Summations of interaction energy for fragment #1(A:82:GLU)
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.
-140.601-141.27820.797-10.62-9.4960.092
Interaction energy analysis for fragmet #1(A:82:GLU)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : -1 / q_Mulliken : -0.840 / q_NPA : -0.911
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].
3A84GLN00.0040.0071.781-38.448-40.63520.321-10.016-8.1170.091
4A85PHE00.1090.0594.944-4.139-4.004-0.001-0.010-0.1230.000
5A86LEU00.0360.0227.146-2.766-2.7660.0000.0000.0000.000
6A87LYS10.8720.9354.959-59.198-59.101-0.001-0.007-0.0880.000
7A88GLU-1-0.928-0.9698.46928.70528.7050.0000.0000.0000.000
8A89GLU-1-0.842-0.90410.87817.69517.6950.0000.0000.0000.000
9A90LEU0-0.005-0.01711.317-1.803-1.8030.0000.0000.0000.000
10A91VAL00.0010.00912.617-1.490-1.4900.0000.0000.0000.000
11A92VAL00.0140.00414.973-1.564-1.5640.0000.0000.0000.000
12A93ALA0-0.021-0.00516.354-1.249-1.2490.0000.0000.0000.000
13A94VAL00.005-0.01116.877-1.073-1.0730.0000.0000.0000.000
14A95GLU-1-0.788-0.86219.05213.13713.1370.0000.0000.0000.000
15A96ASP-1-0.872-0.90521.33613.18213.1820.0000.0000.0000.000
16A97VAL0-0.025-0.02221.689-0.758-0.7580.0000.0000.0000.000
17A98ARG10.7700.85723.269-13.429-13.4290.0000.0000.0000.000
18A99LYS10.8440.91122.911-14.179-14.1790.0000.0000.0000.000
19A100GLN0-0.018-0.01826.809-0.837-0.8370.0000.0000.0000.000
20A101GLY00.0310.01527.554-0.434-0.4340.0000.0000.0000.000
21A102ASP-1-0.891-0.93529.13210.74310.7430.0000.0000.0000.000
22A103LEU0-0.019-0.02231.304-0.402-0.4020.0000.0000.0000.000
23A104MET0-0.051-0.00532.078-0.396-0.3960.0000.0000.0000.000
24A105LYS10.9680.98233.352-9.978-9.9780.0000.0000.0000.000
25A106SER00.0260.01435.124-0.175-0.1750.0000.0000.0000.000
26A107ALA00.0000.00637.225-0.262-0.2620.0000.0000.0000.000
27A108ALA0-0.040-0.02837.208-0.244-0.2440.0000.0000.0000.000
28A109GLY0-0.0050.00139.110-0.189-0.1890.0000.0000.0000.000
29A110GLU-1-0.869-0.95741.1667.3067.3060.0000.0000.0000.000
30A111PHE0-0.067-0.03642.321-0.219-0.2190.0000.0000.0000.000
31A112ALA0-0.017-0.01243.035-0.167-0.1670.0000.0000.0000.000
32A113ASP-1-0.906-0.93744.9256.9996.9990.0000.0000.0000.000
33A114ASP-1-0.889-0.94147.2066.2616.2610.0000.0000.0000.000
34A115PRO00.0480.03247.3360.0020.0020.0000.0000.0000.000
35A116CYS0-0.074-0.03848.347-0.025-0.0250.0000.0000.0000.000
36A117SER0-0.0070.00548.206-0.061-0.0610.0000.0000.0000.000
37A118SER0-0.020-0.01948.0050.1900.1900.0000.0000.0000.000
38A119VAL00.037-0.00545.8890.1540.1540.0000.0000.0000.000
39A120LYS10.8630.92844.447-6.637-6.6370.0000.0000.0000.000
40A121ARG11.0171.03443.067-6.748-6.7480.0000.0000.0000.000
41A122GLY00.0130.00442.0790.2000.2000.0000.0000.0000.000
42A123ASN0-0.015-0.01740.2910.1720.1720.0000.0000.0000.000
43A124MET00.0700.04638.3520.2400.2400.0000.0000.0000.000
44A125VAL0-0.030-0.01037.3800.2540.2540.0000.0000.0000.000
45A126ARG10.8630.90736.370-7.576-7.5760.0000.0000.0000.000
46A127ALA00.0390.04634.3000.2570.2570.0000.0000.0000.000
47A128ALA00.0670.01332.7110.3500.3500.0000.0000.0000.000
48A129ARG10.8890.94831.974-8.156-8.1560.0000.0000.0000.000
49A130ALA00.0350.02130.1310.3270.3270.0000.0000.0000.000
50A131LEU00.0240.01027.2320.4310.4310.0000.0000.0000.000
51A132LEU00.0120.01027.1380.4840.4840.0000.0000.0000.000
52A133SER0-0.029-0.01126.4440.3310.3310.0000.0000.0000.000
53A134ALA00.0170.01623.7000.5120.5120.0000.0000.0000.000
54A135VAL00.0270.00722.3180.7270.7270.0000.0000.0000.000
55A136THR0-0.032-0.02222.0840.5700.5700.0000.0000.0000.000
56A137ARG10.8480.90816.475-16.529-16.5290.0000.0000.0000.000
57A138LEU00.0040.00016.7720.8780.8780.0000.0000.0000.000
58A139LEU0-0.005-0.01017.2100.9720.9720.0000.0000.0000.000
59A140ILE00.0020.00817.7240.5570.5570.0000.0000.0000.000
60A141LEU00.0050.01312.2980.7040.7040.0000.0000.0000.000
61A142ALA0-0.016-0.02213.0921.7421.7420.0000.0000.0000.000
62A143ASP-1-0.837-0.89912.99819.25019.2500.0000.0000.0000.000
63A144MET0-0.0100.00012.0110.4860.4860.0000.0000.0000.000
64A145ALA0-0.0020.0118.9071.7481.7480.0000.0000.0000.000
65A146ASP-1-0.836-0.9138.62028.41528.4150.0000.0000.0000.000
66A147VAL00.0750.02910.0471.5481.5480.0000.0000.0000.000
67A148TYR0-0.022-0.0323.870-0.822-0.6320.001-0.029-0.1620.000
68A149LYS10.8110.8945.496-28.249-28.2490.0000.0000.0000.000
69A150LEU0-0.046-0.0306.5851.3181.3180.0000.0000.0000.000
70A151LEU00.011-0.0048.608-0.402-0.4020.0000.0000.0000.000
71A152VAL0-0.0050.0092.641-2.153-1.0650.477-0.558-1.0060.001
72A153GLN0-0.044-0.0225.9022.7182.7180.0000.0000.0000.000
73A154LEU0-0.035-0.0168.067-2.184-2.1840.0000.0000.0000.000
74A155LYS10.9230.9457.449-21.531-21.5310.0000.0000.0000.000
75A156VAL0-0.0250.0106.541-1.508-1.5080.0000.0000.0000.000
76A157VAL00.000-0.0129.197-2.003-2.0030.0000.0000.0000.000
77A158GLU-1-0.856-0.90912.03016.77916.7790.0000.0000.0000.000
78A159ASP-1-0.798-0.90511.52817.36417.3640.0000.0000.0000.000
79A160GLY0-0.0180.00313.394-0.850-0.8500.0000.0000.0000.000
80A161ILE00.021-0.00215.097-1.178-1.1780.0000.0000.0000.000
81A162LEU0-0.027-0.01116.979-0.958-0.9580.0000.0000.0000.000
82A163LYS10.8650.92412.341-19.637-19.6370.0000.0000.0000.000
83A164LEU0-0.066-0.02418.576-0.515-0.5150.0000.0000.0000.000
84A165ARG10.7890.86220.912-11.548-11.5480.0000.0000.0000.000
85A166ASN0-0.054-0.03220.683-0.854-0.8540.0000.0000.0000.000
86A167ALA00.0120.03323.215-0.112-0.1120.0000.0000.0000.000
87A168GLY00.0430.01624.293-0.330-0.3300.0000.0000.0000.000
88A169ASN0-0.024-0.01327.012-0.697-0.6970.0000.0000.0000.000
89A170GLU-1-0.814-0.91127.4099.6629.6620.0000.0000.0000.000
90A171GLN0-0.012-0.01227.5730.3570.3570.0000.0000.0000.000
91A172ASP-1-0.808-0.91322.79812.18512.1850.0000.0000.0000.000
92A173LEU0-0.0150.02322.7470.6700.6700.0000.0000.0000.000
93A174GLY00.0200.00523.4340.4090.4090.0000.0000.0000.000
94A175ILE0-0.051-0.02920.0060.4430.4430.0000.0000.0000.000
95A176GLN00.008-0.00517.6041.4061.4060.0000.0000.0000.000
96A177TYR00.0230.01318.7520.8830.8830.0000.0000.0000.000
97A178LYS10.9090.96120.012-12.217-12.2170.0000.0000.0000.000
98A179ALA00.0190.01015.2330.6230.6230.0000.0000.0000.000
99A180LEU0-0.022-0.00714.8091.3111.3110.0000.0000.0000.000
100A181LYS10.8520.91215.938-14.565-14.5650.0000.0000.0000.000
101A182PRO00.0470.02414.4070.1600.1600.0000.0000.0000.000
102A183GLU-1-0.804-0.8809.73930.37630.3760.0000.0000.0000.000
103A184VAL0-0.001-0.00512.8940.6800.6800.0000.0000.0000.000
104A185ASP-1-0.807-0.89215.65016.19116.1910.0000.0000.0000.000
105A186LYS10.8090.8858.361-32.674-32.6740.0000.0000.0000.000
106A187LEU00.0390.00911.3380.2970.2970.0000.0000.0000.000
107A188ASN00.0310.03112.622-0.753-0.7530.0000.0000.0000.000
108A189ILE0-0.0070.00013.848-0.653-0.6530.0000.0000.0000.000
109A190MET0-0.071-0.0357.521-0.596-0.5960.0000.0000.0000.000
110A191ALA00.0300.01712.947-0.653-0.6530.0000.0000.0000.000
111A192ALA0-0.015-0.01115.595-0.799-0.7990.0000.0000.0000.000
112A193LYS10.9710.98512.856-23.191-23.1910.0000.0000.0000.000
113A194ARG10.8590.92714.205-19.480-19.4800.0000.0000.0000.000
114A195GLN00.0040.01917.016-0.468-0.4680.0000.0000.0000.000
115A196GLN0-0.053-0.04220.080-0.238-0.2380.0000.0000.0000.000
116A197GLU-1-0.860-0.91716.86017.40217.4020.0000.0000.0000.000
117A198LEU0-0.039-0.01318.775-0.486-0.4860.0000.0000.0000.000
118A199LYS10.9680.96922.117-12.654-12.6540.0000.0000.0000.000
119A200ASP-1-0.855-0.93625.60110.16110.1610.0000.0000.0000.000
120A201VAL00.009-0.02226.4800.4170.4170.0000.0000.0000.000
121A202GLY00.1000.07127.7960.1360.1360.0000.0000.0000.000
122A203ASN0-0.018-0.02323.0010.1750.1750.0000.0000.0000.000
123A204ARG10.8330.92323.579-11.713-11.7130.0000.0000.0000.000
124A205ASP-1-0.868-0.92624.65910.82710.8270.0000.0000.0000.000
125A206GLN0-0.043-0.01523.6600.1960.1960.0000.0000.0000.000
126A207MET0-0.0150.00916.9430.2530.2530.0000.0000.0000.000
127A208ALA0-0.0090.00921.7270.3720.3720.0000.0000.0000.000
128A209ALA00.008-0.00723.9200.0440.0440.0000.0000.0000.000
129A210ALA0-0.035-0.01821.147-0.047-0.0470.0000.0000.0000.000
130A211ARG10.8740.91218.653-14.852-14.8520.0000.0000.0000.000
131A212GLY00.0050.01921.1920.1040.1040.0000.0000.0000.000
132A213ILE0-0.038-0.02124.324-0.111-0.1110.0000.0000.0000.000
133A214LEU00.0010.00116.982-0.090-0.0900.0000.0000.0000.000
134A215GLN0-0.022-0.01220.8670.3230.3230.0000.0000.0000.000
135A216LYS10.9340.96222.622-10.435-10.4350.0000.0000.0000.000
136A217ASN00.024-0.01624.437-0.434-0.4340.0000.0000.0000.000
137A218VAL00.0370.04319.642-0.187-0.1870.0000.0000.0000.000
138A219PRO0-0.008-0.00822.700-0.076-0.0760.0000.0000.0000.000
139A220ILE00.0280.02125.625-0.259-0.2590.0000.0000.0000.000
140A221LEU00.0200.01022.140-0.326-0.3260.0000.0000.0000.000
141A222TYR00.0130.02024.459-0.085-0.0850.0000.0000.0000.000
142A223THR0-0.002-0.00626.051-0.338-0.3380.0000.0000.0000.000
143A224ALA0-0.008-0.00428.611-0.329-0.3290.0000.0000.0000.000
144A225SER0-0.045-0.06926.161-0.189-0.1890.0000.0000.0000.000
145A226GLN0-0.019-0.00528.3130.0990.0990.0000.0000.0000.000
146A227ALA00.0500.03030.195-0.221-0.2210.0000.0000.0000.000
147A228CYS0-0.103-0.04330.875-0.232-0.2320.0000.0000.0000.000
148A229LEU0-0.036-0.01428.000-0.184-0.1840.0000.0000.0000.000
149A230GLN0-0.053-0.01632.520-0.319-0.3190.0000.0000.0000.000
150A231HIS0-0.030-0.01835.901-0.197-0.1970.0000.0000.0000.000
151A232PRO00.0520.02435.3560.0120.0120.0000.0000.0000.000
152A233ASP-1-0.912-0.95536.4017.5347.5340.0000.0000.0000.000
153A234VAL0-0.0070.01038.033-0.173-0.1730.0000.0000.0000.000
154A235ALA0-0.010-0.01436.4420.2290.2290.0000.0000.0000.000
155A236ALA00.0200.00435.8400.1970.1970.0000.0000.0000.000
156A237TYR00.0370.00734.2660.1420.1420.0000.0000.0000.000
157A238LYS10.9350.96631.618-8.091-8.0910.0000.0000.0000.000
158A239ALA00.0020.00731.0550.2800.2800.0000.0000.0000.000
159A240ASN00.0160.00431.6390.2190.2190.0000.0000.0000.000
160A241ARG10.8980.93526.894-10.001-10.0010.0000.0000.0000.000
161A242ASP-1-0.763-0.85226.77910.60810.6080.0000.0000.0000.000
162A243LEU00.0000.00426.9590.2940.2940.0000.0000.0000.000
163A244ILE00.0040.01025.7700.2320.2320.0000.0000.0000.000
164A245TYR00.0060.00019.1460.1610.1610.0000.0000.0000.000
165A246LYS10.9400.96322.726-9.926-9.9260.0000.0000.0000.000
166A247GLN0-0.0050.00123.6080.3740.3740.0000.0000.0000.000
167A248LEU0-0.0260.00720.1090.2620.2620.0000.0000.0000.000
168A249GLN00.003-0.01116.1050.6730.6730.0000.0000.0000.000
169A250GLN0-0.021-0.01419.2890.3660.3660.0000.0000.0000.000
170A251ALA0-0.0110.00121.2070.1740.1740.0000.0000.0000.000
171A252VAL00.0350.01714.8350.4240.4240.0000.0000.0000.000
172A253THR0-0.004-0.01016.7720.7130.7130.0000.0000.0000.000
173A254GLY00.0100.01217.9960.0340.0340.0000.0000.0000.000
174A255ILE0-0.009-0.01115.421-0.002-0.0020.0000.0000.0000.000
175A256SER0-0.015-0.01214.5790.4180.4180.0000.0000.0000.000
176A257ASN0-0.023-0.00715.7270.0590.0590.0000.0000.0000.000
177A258ALA0-0.020-0.00818.912-0.185-0.1850.0000.0000.0000.000
178A259ALA00.0350.00414.872-0.065-0.0650.0000.0000.0000.000
179A260GLN0-0.106-0.05915.1740.5500.5500.0000.0000.0000.000
180A261ALA0-0.0190.00617.519-0.518-0.5180.0000.0000.0000.000
181A262THR0-0.0320.00620.034-0.752-0.7520.0000.0000.0000.000