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: 6GG4Z

Calculation Name: 4O7H-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 4O7H

Chain ID: A

ChEMBL ID:

UniProt ID:

Base Structure: X-ray

Registration Date: 2023-09-27

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 222
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2888482.990844
FMO2-HF: Nuclear repulsion 2799493.528187
FMO2-HF: Total energy -88989.462657
FMO2-MP2: Total energy -89252.055581


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.
-15.033-8.0734.872-3.619-8.213-0.026
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 : -0.003 / q_NPA : 0.005
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].
3A3ARG10.8240.8822.610-3.5930.1471.579-2.545-2.774-0.019
4A4LEU0-0.027-0.0164.7270.7690.881-0.001-0.016-0.0950.000
5A5TYR00.0430.0338.0810.1160.1160.0000.0000.0000.000
6A6HIS0-0.035-0.04210.2820.1240.1240.0000.0000.0000.000
7A7HIS00.0980.04513.2150.0860.0860.0000.0000.0000.000
8A8GLY00.0380.01616.082-0.003-0.0030.0000.0000.0000.000
9A9LEU0-0.012-0.01717.8600.0420.0420.0000.0000.0000.000
10A10SER00.0240.03017.7950.0280.0280.0000.0000.0000.000
11A11PRO00.0130.00318.505-0.029-0.0290.0000.0000.0000.000
12A12ALA00.0310.00718.787-0.018-0.0180.0000.0000.0000.000
13A13ALA00.0350.01714.366-0.065-0.0650.0000.0000.0000.000
14A14ARG10.8320.90214.0770.2640.2640.0000.0000.0000.000
15A15LYS10.8620.88615.2900.4670.4670.0000.0000.0000.000
16A16VAL00.0290.00511.1450.0050.0050.0000.0000.0000.000
17A17ARG10.7900.86010.2240.5670.5670.0000.0000.0000.000
18A18VAL0-0.0060.00111.4130.0010.0010.0000.0000.0000.000
19A19ALA0-0.007-0.00913.8440.0340.0340.0000.0000.0000.000
20A20LEU00.0050.0147.4400.0430.0430.0000.0000.0000.000
21A21ALA00.0190.02010.3220.0520.0520.0000.0000.0000.000
22A22GLU-1-0.807-0.86111.194-0.218-0.2180.0000.0000.0000.000
23A23LYS10.7740.87912.8130.6570.6570.0000.0000.0000.000
24A24ARG10.7700.87810.8500.3620.3620.0000.0000.0000.000
25A25LEU0-0.0060.0157.8630.0470.0470.0000.0000.0000.000
26A26ASP-1-0.888-0.9473.239-1.367-0.9370.047-0.086-0.3900.000
27A27TYR0-0.043-0.0192.467-1.374-0.7680.756-0.372-0.990-0.001
28A28GLU-1-0.801-0.8732.493-3.224-2.0081.978-0.256-2.938-0.005
29A29ALA00.001-0.0053.731-0.764-0.6360.0130.004-0.1450.000
30A30VAL00.0130.0126.8080.4240.4240.0000.0000.0000.000
31A31ILE0-0.023-0.0129.352-0.075-0.0750.0000.0000.0000.000
32A32GLU-1-0.824-0.90513.176-0.706-0.7060.0000.0000.0000.000
33A33GLU-1-0.880-0.94315.329-0.240-0.2400.0000.0000.0000.000
34A34THR0-0.019-0.02618.0580.0380.0380.0000.0000.0000.000
35A35TRP0-0.091-0.05120.4290.0090.0090.0000.0000.0000.000
36A36ILE0-0.054-0.02921.7370.0430.0430.0000.0000.0000.000
37A37ARG10.8070.86621.8190.2770.2770.0000.0000.0000.000
38A38ASN00.015-0.01116.2480.0530.0530.0000.0000.0000.000
39A39GLU-1-0.771-0.86320.003-0.367-0.3670.0000.0000.0000.000
40A40SER0-0.011-0.01015.616-0.004-0.0040.0000.0000.0000.000
41A41PHE0-0.0060.01213.790-0.093-0.0930.0000.0000.0000.000
42A42LEU0-0.009-0.00316.822-0.037-0.0370.0000.0000.0000.000
43A43ALA0-0.054-0.02417.5240.0130.0130.0000.0000.0000.000
44A44MET0-0.053-0.00912.197-0.106-0.1060.0000.0000.0000.000
45A45ASN0-0.021-0.03215.984-0.006-0.0060.0000.0000.0000.000
46A46PRO00.0100.01318.5780.0440.0440.0000.0000.0000.000
47A47GLU-1-0.977-0.98521.697-0.487-0.4870.0000.0000.0000.000
48A48GLY0-0.018-0.01720.8010.0370.0370.0000.0000.0000.000
49A49GLU-1-0.849-0.91819.877-0.480-0.4800.0000.0000.0000.000
50A50VAL0-0.0110.02214.745-0.099-0.0990.0000.0000.0000.000
51A51PRO0-0.077-0.04913.6760.1000.1000.0000.0000.0000.000
52A52VAL00.002-0.00112.1620.0860.0860.0000.0000.0000.000
53A53LEU0-0.034-0.0098.065-0.196-0.1960.0000.0000.0000.000
54A54VAL00.0110.0046.7080.3700.3700.0000.0000.0000.000
55A55GLU-1-0.706-0.7916.243-3.869-3.8690.0000.0000.0000.000
56A56ALA0-0.033-0.0292.703-1.218-0.7150.497-0.351-0.650-0.001
57A57ASP-1-0.877-0.9353.867-1.055-0.8300.0030.003-0.2310.000
58A58GLY0-0.0030.0056.4740.3500.3500.0000.0000.0000.000
59A59LEU0-0.031-0.0167.8860.2350.2350.0000.0000.0000.000
60A60THR0-0.017-0.00910.135-0.374-0.3740.0000.0000.0000.000
61A61ILE0-0.042-0.01511.9150.2630.2630.0000.0000.0000.000
62A62THR00.0610.01113.827-0.173-0.1730.0000.0000.0000.000
63A63ASP-1-0.721-0.85816.577-0.523-0.5230.0000.0000.0000.000
64A64GLY00.0020.00517.228-0.064-0.0640.0000.0000.0000.000
65A65TRP0-0.126-0.08218.1930.0150.0150.0000.0000.0000.000
66A66ALA00.0420.01619.4750.0010.0010.0000.0000.0000.000
67A67ILE0-0.0010.01012.894-0.040-0.0400.0000.0000.0000.000
68A68CYS0-0.062-0.03215.534-0.015-0.0150.0000.0000.0000.000
69A69GLU-1-0.793-0.86817.338-0.402-0.4020.0000.0000.0000.000
70A70TYR00.035-0.00210.9500.0950.0950.0000.0000.0000.000
71A71LEU0-0.009-0.01511.002-0.009-0.0090.0000.0000.0000.000
72A72GLU-1-0.740-0.84814.983-0.364-0.3640.0000.0000.0000.000
73A73GLU-1-0.983-0.98718.446-0.467-0.4670.0000.0000.0000.000
74A74VAL0-0.021-0.01112.7570.0650.0650.0000.0000.0000.000
75A75TYR0-0.056-0.0499.5930.0460.0460.0000.0000.0000.000
76A76PRO00.0030.01915.2000.0150.0150.0000.0000.0000.000
77A77GLU-1-0.898-0.94717.905-0.227-0.2270.0000.0000.0000.000
78A78PRO0-0.042-0.01515.824-0.014-0.0140.0000.0000.0000.000
79A79SER0-0.007-0.01318.326-0.050-0.0500.0000.0000.0000.000
80A80LEU0-0.034-0.02916.8090.0150.0150.0000.0000.0000.000
81A81LEU0-0.054-0.02720.9430.0130.0130.0000.0000.0000.000
82A82GLY00.0690.02424.0010.0260.0260.0000.0000.0000.000
83A83GLY00.0150.00926.262-0.012-0.0120.0000.0000.0000.000
84A84PRO00.018-0.01028.612-0.006-0.0060.0000.0000.0000.000
85A85ALA00.0540.02430.901-0.010-0.0100.0000.0000.0000.000
86A86ALA00.0130.00131.666-0.009-0.0090.0000.0000.0000.000
87A87MET0-0.0130.02528.175-0.001-0.0010.0000.0000.0000.000
88A88ARG10.9020.94223.1020.3250.3250.0000.0000.0000.000
89A89ALA0-0.021-0.00828.095-0.017-0.0170.0000.0000.0000.000
90A90GLU-1-0.736-0.82430.761-0.195-0.1950.0000.0000.0000.000
91A91VAL0-0.0010.00124.551-0.003-0.0030.0000.0000.0000.000
92A92ARG10.8450.89324.5020.3490.3490.0000.0000.0000.000
93A93ARG10.7980.88027.5340.1890.1890.0000.0000.0000.000
94A94LEU0-0.023-0.01328.5750.0040.0040.0000.0000.0000.000
95A95VAL0-0.004-0.00323.4910.0010.0010.0000.0000.0000.000
96A96ALA00.0050.00426.173-0.003-0.0030.0000.0000.0000.000
97A97TRP0-0.062-0.03228.5850.0140.0140.0000.0000.0000.000
98A98PHE00.002-0.02126.6440.0110.0110.0000.0000.0000.000
99A99ASP-1-0.693-0.82823.443-0.413-0.4130.0000.0000.0000.000
100A100ARG10.9340.98126.3650.2510.2510.0000.0000.0000.000
101A101LYS10.8030.89929.9120.1790.1790.0000.0000.0000.000
102A102PHE00.0290.00728.3870.0110.0110.0000.0000.0000.000
103A103ASN00.021-0.00226.061-0.005-0.0050.0000.0000.0000.000
104A104ARG10.8350.87828.9230.2390.2390.0000.0000.0000.000
105A105GLU-1-0.839-0.87632.278-0.162-0.1620.0000.0000.0000.000
106A106VAL0-0.008-0.01030.9140.0170.0170.0000.0000.0000.000
107A107THR00.010-0.01225.1920.0150.0150.0000.0000.0000.000
108A108GLU-1-0.770-0.84128.582-0.254-0.2540.0000.0000.0000.000
109A109PRO0-0.057-0.01729.7890.0060.0060.0000.0000.0000.000
110A110LEU0-0.020-0.01030.4520.0070.0070.0000.0000.0000.000
111A111VAL00.0490.02524.5170.0110.0110.0000.0000.0000.000
112A112ARG10.8500.91327.7810.1940.1940.0000.0000.0000.000
113A113GLU-1-0.757-0.85629.538-0.146-0.1460.0000.0000.0000.000
114A114LYS10.8050.88431.0450.1430.1430.0000.0000.0000.000
115A115LEU0-0.024-0.00524.8270.0100.0100.0000.0000.0000.000
116A116LEU00.0820.03724.7590.0120.0120.0000.0000.0000.000
117A117LYS10.7490.85527.2720.1490.1490.0000.0000.0000.000
118A118ARG10.8820.95229.4270.1240.1240.0000.0000.0000.000
119A119VAL0-0.0130.00923.4290.0120.0120.0000.0000.0000.000
120A120ILE00.0340.03226.3570.0070.0070.0000.0000.0000.000
121A121SER00.004-0.00828.7720.0060.0060.0000.0000.0000.000
122A122GLY0-0.028-0.01331.8540.0050.0050.0000.0000.0000.000
123A123GLY00.0250.01533.2070.0010.0010.0000.0000.0000.000
124A124ALA00.005-0.00835.941-0.002-0.0020.0000.0000.0000.000
125A125PRO00.0270.01835.165-0.006-0.0060.0000.0000.0000.000
126A126ASP-1-0.778-0.88836.913-0.117-0.1170.0000.0000.0000.000
127A127SER0-0.001-0.01238.382-0.002-0.0020.0000.0000.0000.000
128A128ARG10.8040.90240.7190.1020.1020.0000.0000.0000.000
129A129GLN00.0740.04736.047-0.011-0.0110.0000.0000.0000.000
130A130ILE00.0500.02935.036-0.004-0.0040.0000.0000.0000.000
131A131ARG10.8650.92436.9920.1040.1040.0000.0000.0000.000
132A132ALA00.0390.03038.3040.0020.0020.0000.0000.0000.000
133A133GLY00.0740.04234.817-0.001-0.0010.0000.0000.0000.000
134A134ARG10.8840.91835.5060.1090.1090.0000.0000.0000.000
135A135ALA0-0.081-0.02436.9940.0070.0070.0000.0000.0000.000
136A136ASN0-0.006-0.01936.1040.0080.0080.0000.0000.0000.000
137A137VAL00.0130.00532.220-0.003-0.0030.0000.0000.0000.000
138A138HIS0-0.0010.00034.825-0.004-0.0040.0000.0000.0000.000
139A139THR0-0.017-0.02037.8720.0060.0060.0000.0000.0000.000
140A140HIS0-0.020-0.01832.698-0.003-0.0030.0000.0000.0000.000
141A141LEU00.0190.02631.970-0.005-0.0050.0000.0000.0000.000
142A142ARG10.9721.00434.7200.1170.1170.0000.0000.0000.000
143A143TYR0-0.0100.00833.4720.0000.0000.0000.0000.0000.000
144A144ILE00.013-0.00229.9070.0000.0000.0000.0000.0000.000
145A145SER00.017-0.00533.3440.0030.0030.0000.0000.0000.000
146A146TRP00.000-0.00736.0460.0060.0060.0000.0000.0000.000
147A147LEU0-0.062-0.03332.1970.0030.0030.0000.0000.0000.000
148A148ILE0-0.016-0.00230.7610.0000.0000.0000.0000.0000.000
149A149ASP-1-0.912-0.93534.277-0.091-0.0910.0000.0000.0000.000
150A150ARG10.8500.94337.0090.1170.1170.0000.0000.0000.000
151A151ARG10.7410.85432.6670.1680.1680.0000.0000.0000.000
152A152ARG10.9310.98429.4990.1220.1220.0000.0000.0000.000
153A153TRP00.0070.00025.579-0.004-0.0040.0000.0000.0000.000
154A154LEU00.003-0.00427.7860.0050.0050.0000.0000.0000.000
155A155ALA00.0080.00428.0300.0060.0060.0000.0000.0000.000
156A156GLY0-0.026-0.01429.9210.0060.0060.0000.0000.0000.000
157A157ASP-1-0.857-0.93329.905-0.168-0.1680.0000.0000.0000.000
158A158MET0-0.010-0.00523.7580.0130.0130.0000.0000.0000.000
159A159LEU0-0.023-0.00320.753-0.004-0.0040.0000.0000.0000.000
160A160THR0-0.016-0.01322.543-0.016-0.0160.0000.0000.0000.000
161A161TYR00.065-0.01516.8830.0010.0010.0000.0000.0000.000
162A162ALA0-0.0140.02721.636-0.005-0.0050.0000.0000.0000.000
163A163ASP-1-0.754-0.87423.575-0.236-0.2360.0000.0000.0000.000
164A164ILE00.0590.02917.5770.0090.0090.0000.0000.0000.000
165A165THR0-0.013-0.01520.999-0.020-0.0200.0000.0000.0000.000
166A166ALA00.0000.00822.5320.0060.0060.0000.0000.0000.000
167A167ALA00.0270.01822.3310.0140.0140.0000.0000.0000.000
168A168CYS0-0.0400.00718.895-0.001-0.0010.0000.0000.0000.000
169A169HIS0-0.004-0.00721.2820.0240.0240.0000.0000.0000.000
170A170LEU0-0.007-0.00424.4010.0170.0170.0000.0000.0000.000
171A171SER00.0100.01121.4980.0100.0100.0000.0000.0000.000
172A172LEU0-0.0020.00721.3380.0160.0160.0000.0000.0000.000
173A173ILE0-0.024-0.01724.4790.0200.0200.0000.0000.0000.000
174A174ASP-1-0.793-0.86126.065-0.129-0.1290.0000.0000.0000.000
175A175TYR0-0.015-0.01821.9850.0140.0140.0000.0000.0000.000
176A176ALA0-0.010-0.00826.0630.0140.0140.0000.0000.0000.000
177A177GLY0-0.026-0.00529.0950.0130.0130.0000.0000.0000.000
178A178ASP-1-0.837-0.91931.226-0.126-0.1260.0000.0000.0000.000
179A179VAL00.0160.01229.5070.0000.0000.0000.0000.0000.000
180A180PRO0-0.048-0.00632.8070.0060.0060.0000.0000.0000.000
181A181TRP00.025-0.03028.2320.0000.0000.0000.0000.0000.000
182A182GLU-1-0.803-0.89934.660-0.084-0.0840.0000.0000.0000.000
183A183ASP-1-0.900-0.93437.955-0.086-0.0860.0000.0000.0000.000
184A184HIS0-0.083-0.04935.867-0.003-0.0030.0000.0000.0000.000
185A185PRO00.0670.03735.734-0.007-0.0070.0000.0000.0000.000
186A186GLN0-0.010-0.02135.212-0.003-0.0030.0000.0000.0000.000
187A187ALA0-0.012-0.01132.474-0.007-0.0070.0000.0000.0000.000
188A188LYS10.8100.90031.0460.0720.0720.0000.0000.0000.000
189A189GLU-1-0.858-0.93730.509-0.096-0.0960.0000.0000.0000.000
190A190TRP0-0.067-0.03525.803-0.006-0.0060.0000.0000.0000.000
191A191TYR0-0.042-0.05324.280-0.022-0.0220.0000.0000.0000.000
192A192ALA00.0410.02825.781-0.010-0.0100.0000.0000.0000.000
193A193LEU0-0.022-0.00425.743-0.001-0.0010.0000.0000.0000.000
194A194VAL0-0.050-0.02821.742-0.011-0.0110.0000.0000.0000.000
195A195LYS10.8020.90321.3970.1100.1100.0000.0000.0000.000
196A196SER00.021-0.00221.0750.0070.0070.0000.0000.0000.000
197A197ARG10.7980.89418.6970.2730.2730.0000.0000.0000.000
198A198PRO0-0.041-0.04315.359-0.011-0.0110.0000.0000.0000.000
199A199SER0-0.028-0.04113.4740.0090.0090.0000.0000.0000.000
200A200PHE00.0480.01814.299-0.065-0.0650.0000.0000.0000.000
201A201ARG10.9891.00315.4120.0820.0820.0000.0000.0000.000
202A202PRO00.0370.01411.9020.0340.0340.0000.0000.0000.000
203A203LEU0-0.0020.00514.4450.0180.0180.0000.0000.0000.000
204A204LEU0-0.0490.00717.2630.0200.0200.0000.0000.0000.000
205A205THR0-0.003-0.00315.8370.0260.0260.0000.0000.0000.000
206A206GLU-1-0.844-0.87012.812-0.327-0.3270.0000.0000.0000.000
207A207THR0-0.037-0.02617.4240.0020.0020.0000.0000.0000.000
208A208ILE00.0120.01319.775-0.003-0.0030.0000.0000.0000.000
209A209SER0-0.0080.01521.6010.0240.0240.0000.0000.0000.000
210A210PRO00.0760.02724.042-0.017-0.0170.0000.0000.0000.000
211A211ILE0-0.043-0.02025.9780.0160.0160.0000.0000.0000.000
212A212ARG10.8560.92923.2200.0740.0740.0000.0000.0000.000
213A213PRO00.0390.03823.939-0.003-0.0030.0000.0000.0000.000
214A214PRO0-0.011-0.00127.0210.0160.0160.0000.0000.0000.000
215A215ARG10.9700.95928.4380.0300.0300.0000.0000.0000.000
216A216HIS00.0020.00029.4790.0170.0170.0000.0000.0000.000
217A217TYR0-0.073-0.04320.776-0.010-0.0100.0000.0000.0000.000
218A218ALA00.038-0.00522.942-0.011-0.0110.0000.0000.0000.000
219A219ASP-1-0.907-0.94224.071-0.054-0.0540.0000.0000.0000.000
220A220LEU00.005-0.00122.353-0.015-0.0150.0000.0000.0000.000
221A221ASP-1-0.880-0.92526.447-0.054-0.0540.0000.0000.0000.000
222A222PHE0-0.096-0.04028.584-0.005-0.0050.0000.0000.0000.000