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: 7G1MK

Calculation Name: 3QC1-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3QC1

Chain ID: A

ChEMBL ID:

UniProt ID: Q61249

Base Structure: X-ray

Registration Date: 2023-06-20

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 189
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2054025.623366
FMO2-HF: Nuclear repulsion 1977024.755829
FMO2-HF: Total energy -77000.867538
FMO2-MP2: Total energy -77226.019378


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:10:LEU)


Summations of interaction energy for fragment #1(A:10:LEU)
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.
-1.2630.654-0.001-0.786-1.130.004
Interaction energy analysis for fragmet #1(A:10:LEU)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.022 / q_NPA : 0.007
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].
3A12ARG10.9770.9923.5522.0994.016-0.001-0.786-1.1300.004
4A13LEU00.0760.0455.7190.2230.2230.0000.0000.0000.000
5A14PRO0-0.019-0.0098.6540.0620.0620.0000.0000.0000.000
6A15GLU-1-0.850-0.9285.214-4.408-4.4080.0000.0000.0000.000
7A16LEU0-0.0080.0048.0210.2210.2210.0000.0000.0000.000
8A17PHE00.0370.01710.6140.1740.1740.0000.0000.0000.000
9A18GLU-1-0.776-0.86512.854-0.474-0.4740.0000.0000.0000.000
10A19THR0-0.034-0.01510.6490.1170.1170.0000.0000.0000.000
11A20SER0-0.004-0.01513.3780.1180.1180.0000.0000.0000.000
12A21LYS10.8390.92215.7540.4120.4120.0000.0000.0000.000
13A22LYS10.8130.88516.2210.5720.5720.0000.0000.0000.000
14A23LEU0-0.008-0.00815.2790.0440.0440.0000.0000.0000.000
15A24LEU0-0.022-0.00218.6000.0400.0400.0000.0000.0000.000
16A25GLU-1-0.840-0.92721.477-0.292-0.2920.0000.0000.0000.000
17A26ASP-1-0.833-0.90020.248-0.255-0.2550.0000.0000.0000.000
18A27VAL0-0.037-0.02322.3170.0290.0290.0000.0000.0000.000
19A28GLU-1-0.985-1.01024.714-0.183-0.1830.0000.0000.0000.000
20A29VAL0-0.045-0.00925.9220.0150.0150.0000.0000.0000.000
21A30ALA0-0.042-0.00626.3120.0120.0120.0000.0000.0000.000
22A31THR0-0.014-0.00328.3200.0070.0070.0000.0000.0000.000
23A32GLU-1-0.928-0.96527.531-0.125-0.1250.0000.0000.0000.000
24A33PRO00.0520.01731.541-0.004-0.0040.0000.0000.0000.000
25A34THR00.0850.04229.3360.0000.0000.0000.0000.0000.000
26A35GLY0-0.0020.00428.707-0.007-0.0070.0000.0000.0000.000
27A36SER0-0.046-0.03328.3620.0090.0090.0000.0000.0000.000
28A37ARG10.8420.89422.9980.0970.0970.0000.0000.0000.000
29A38THR00.0490.02523.382-0.005-0.0050.0000.0000.0000.000
30A39ILE00.0180.01922.664-0.021-0.0210.0000.0000.0000.000
31A40GLN00.008-0.02423.321-0.018-0.0180.0000.0000.0000.000
32A41ASP-1-0.828-0.86319.970-0.141-0.1410.0000.0000.0000.000
33A42LYS10.8310.89518.6980.2200.2200.0000.0000.0000.000
34A43VAL0-0.0040.00218.973-0.037-0.0370.0000.0000.0000.000
35A44SER0-0.004-0.02220.079-0.010-0.0100.0000.0000.0000.000
36A45LYS10.9630.99311.1040.5440.5440.0000.0000.0000.000
37A46GLY00.011-0.00215.398-0.060-0.0600.0000.0000.0000.000
38A47LEU00.002-0.00316.900-0.030-0.0300.0000.0000.0000.000
39A48GLU-1-0.940-0.95412.860-0.321-0.3210.0000.0000.0000.000
40A49LEU0-0.028-0.03310.607-0.058-0.0580.0000.0000.0000.000
41A50LEU0-0.0060.00012.982-0.074-0.0740.0000.0000.0000.000
42A51GLU-1-0.948-0.94715.674-0.206-0.2060.0000.0000.0000.000
43A52LYS10.9320.9698.0680.3840.3840.0000.0000.0000.000
44A53ALA00.001-0.01811.680-0.017-0.0170.0000.0000.0000.000
45A54ALA00.0380.01412.6320.0250.0250.0000.0000.0000.000
46A55GLY00.0200.01114.0620.0340.0340.0000.0000.0000.000
47A56MET0-0.081-0.0516.3080.0050.0050.0000.0000.0000.000
48A57LEU0-0.013-0.01312.1660.0200.0200.0000.0000.0000.000
49A58SER0-0.039-0.01315.1160.0420.0420.0000.0000.0000.000
50A59GLN0-0.080-0.02912.5440.0350.0350.0000.0000.0000.000
51A60LEU0-0.079-0.04511.6120.0150.0150.0000.0000.0000.000
52A61ASP-1-0.842-0.88615.417-0.134-0.1340.0000.0000.0000.000
53A62LEU0-0.009-0.01715.4470.0070.0070.0000.0000.0000.000
54A63PHE0-0.048-0.04119.3080.0050.0050.0000.0000.0000.000
55A64SER0-0.012-0.00322.7050.0150.0150.0000.0000.0000.000
56A65ARG10.8060.87824.4050.1150.1150.0000.0000.0000.000
57A66ASN0-0.0040.02927.545-0.005-0.0050.0000.0000.0000.000
58A67GLU-1-0.973-1.02029.403-0.083-0.0830.0000.0000.0000.000
59A68ASP-1-0.842-0.89228.367-0.126-0.1260.0000.0000.0000.000
60A69LEU0-0.025-0.00827.0880.0000.0000.0000.0000.0000.000
61A70GLU-1-0.935-0.99327.603-0.144-0.1440.0000.0000.0000.000
62A71GLU-1-0.950-0.97927.568-0.121-0.1210.0000.0000.0000.000
63A72ILE0-0.0320.01421.867-0.008-0.0080.0000.0000.0000.000
64A73ALA00.0490.03419.9220.0020.0020.0000.0000.0000.000
65A74SER00.044-0.02321.591-0.016-0.0160.0000.0000.0000.000
66A75THR0-0.056-0.03516.833-0.014-0.0140.0000.0000.0000.000
67A76ASP-1-0.880-0.94716.818-0.415-0.4150.0000.0000.0000.000
68A77LEU0-0.007-0.00618.760-0.007-0.0070.0000.0000.0000.000
69A78LYS10.8350.90914.5600.6300.6300.0000.0000.0000.000
70A79TYR0-0.001-0.01513.508-0.069-0.0690.0000.0000.0000.000
71A80LEU00.0370.03818.3240.0090.0090.0000.0000.0000.000
72A81MET0-0.058-0.01621.4430.0230.0230.0000.0000.0000.000
73A82VAL0-0.0140.00116.756-0.003-0.0030.0000.0000.0000.000
74A83PRO00.0680.03219.9350.0030.0030.0000.0000.0000.000
75A84ALA00.0330.02222.7170.0160.0160.0000.0000.0000.000
76A85LEU0-0.025-0.00619.1880.0100.0100.0000.0000.0000.000
77A86GLN00.0240.00519.2700.0060.0060.0000.0000.0000.000
78A87GLY00.0230.03222.2970.0170.0170.0000.0000.0000.000
79A88ALA00.009-0.00124.9330.0130.0130.0000.0000.0000.000
80A89LEU0-0.013-0.00819.6360.0110.0110.0000.0000.0000.000
81A90THR0-0.021-0.01824.0950.0150.0150.0000.0000.0000.000
82A91MET0-0.064-0.02225.7600.0180.0180.0000.0000.0000.000
83A92LYS10.8540.93825.8080.1710.1710.0000.0000.0000.000
84A93GLN0-0.0180.00725.158-0.001-0.0010.0000.0000.0000.000
85A94VAL0-0.036-0.01627.6220.0100.0100.0000.0000.0000.000
86A95ASN00.0420.00829.4230.0100.0100.0000.0000.0000.000
87A96PRO00.0680.03431.8590.0010.0010.0000.0000.0000.000
88A97SER0-0.030-0.00534.0000.0010.0010.0000.0000.0000.000
89A98LYS10.8690.92530.8380.0650.0650.0000.0000.0000.000
90A99ARG10.8840.92132.4220.0960.0960.0000.0000.0000.000
91A100LEU00.0360.01733.492-0.005-0.0050.0000.0000.0000.000
92A101ASP-1-0.854-0.92129.233-0.102-0.1020.0000.0000.0000.000
93A102HIS0-0.012-0.01128.811-0.005-0.0050.0000.0000.0000.000
94A103LEU00.0410.02429.937-0.007-0.0070.0000.0000.0000.000
95A104GLN0-0.007-0.00432.1280.0020.0020.0000.0000.0000.000
96A105ARG10.8270.88326.0330.1030.1030.0000.0000.0000.000
97A106ALA00.001-0.00427.735-0.010-0.0100.0000.0000.0000.000
98A107ARG10.7860.84328.7800.0840.0840.0000.0000.0000.000
99A108GLU-1-0.839-0.90128.022-0.110-0.1100.0000.0000.0000.000
100A109HIS00.0280.02622.655-0.008-0.0080.0000.0000.0000.000
101A110PHE00.0560.02326.463-0.008-0.0080.0000.0000.0000.000
102A111VAL0-0.014-0.00328.9730.0010.0010.0000.0000.0000.000
103A112HIS00.0370.03922.3660.0120.0120.0000.0000.0000.000
104A113PHE0-0.011-0.01524.893-0.006-0.0060.0000.0000.0000.000
105A114LEU0-0.004-0.00726.6450.0010.0010.0000.0000.0000.000
106A115THR0-0.129-0.06328.7760.0060.0060.0000.0000.0000.000
107A116GLN00.007-0.01923.973-0.011-0.0110.0000.0000.0000.000
108A117CYS0-0.102-0.02426.4750.0090.0090.0000.0000.0000.000
109A118HIS00.0410.02526.2730.0050.0050.0000.0000.0000.000
110A120TYR00.0260.01431.1020.0080.0080.0000.0000.0000.000
111A121HIS10.9090.95633.8440.1160.1160.0000.0000.0000.000
112A145ALA00.011-0.00769.9160.0000.0000.0000.0000.0000.000
113A146TYR00.0640.01267.338-0.001-0.0010.0000.0000.0000.000
114A147PRO00.0560.05565.355-0.001-0.0010.0000.0000.0000.000
115A148ASN00.0340.00263.809-0.001-0.0010.0000.0000.0000.000
116A149LEU00.0610.02462.910-0.001-0.0010.0000.0000.0000.000
117A150VAL00.0450.03261.000-0.002-0.0020.0000.0000.0000.000
118A151ALA00.0340.03559.311-0.002-0.0020.0000.0000.0000.000
119A152MET0-0.050-0.03358.179-0.002-0.0020.0000.0000.0000.000
120A153ALA0-0.004-0.00157.697-0.002-0.0020.0000.0000.0000.000
121A154SER00.004-0.01855.796-0.002-0.0020.0000.0000.0000.000
122A155GLN0-0.012-0.01453.994-0.003-0.0030.0000.0000.0000.000
123A156ARG10.8600.94253.2460.0490.0490.0000.0000.0000.000
124A157GLN0-0.021-0.03251.6690.0000.0000.0000.0000.0000.000
125A158ALA00.0770.05849.754-0.003-0.0030.0000.0000.0000.000
126A159LYS10.9390.95547.7220.0600.0600.0000.0000.0000.000
127A160ILE00.0010.00546.857-0.003-0.0030.0000.0000.0000.000
128A161GLU-1-0.806-0.89646.054-0.072-0.0720.0000.0000.0000.000
129A162ARG10.9670.99142.7000.0760.0760.0000.0000.0000.000
130A163TYR00.0060.00641.976-0.006-0.0060.0000.0000.0000.000
131A164LYS10.8770.93741.3470.0710.0710.0000.0000.0000.000
132A165GLN00.0230.02539.843-0.005-0.0050.0000.0000.0000.000
133A166LYS10.9110.96435.2120.1200.1200.0000.0000.0000.000
134A167LYS10.8690.91536.5250.0880.0880.0000.0000.0000.000
135A168GLU-1-0.825-0.92136.686-0.103-0.1030.0000.0000.0000.000
136A169VAL0-0.012-0.00932.906-0.006-0.0060.0000.0000.0000.000
137A170GLU-1-0.796-0.87532.116-0.161-0.1610.0000.0000.0000.000
138A171HIS0-0.0020.00431.919-0.010-0.0100.0000.0000.0000.000
139A172ARG10.8230.88532.0700.1290.1290.0000.0000.0000.000
140A173LEU00.018-0.00627.503-0.006-0.0060.0000.0000.0000.000
141A174SER0-0.064-0.02927.640-0.013-0.0130.0000.0000.0000.000
142A175ALA0-0.015-0.00428.541-0.005-0.0050.0000.0000.0000.000
143A176LEU0-0.016-0.01126.957-0.001-0.0010.0000.0000.0000.000
144A177LYS10.8510.93521.2400.3120.3120.0000.0000.0000.000
145A178SER00.0180.00522.582-0.028-0.0280.0000.0000.0000.000
146A179ALA00.0620.03521.830-0.025-0.0250.0000.0000.0000.000
147A180VAL00.000-0.00221.243-0.012-0.0120.0000.0000.0000.000
148A181GLU-1-0.825-0.90518.154-0.422-0.4220.0000.0000.0000.000
149A182SER0-0.078-0.03917.230-0.050-0.0500.0000.0000.0000.000
150A183GLY0-0.0260.00018.440-0.008-0.0080.0000.0000.0000.000
151A184GLN0-0.055-0.04119.5300.0230.0230.0000.0000.0000.000
152A185ALA0-0.0440.00023.0080.0230.0230.0000.0000.0000.000
153A186ASP-1-0.773-0.86424.401-0.163-0.1630.0000.0000.0000.000
154A187ASP-1-0.802-0.90424.503-0.208-0.2080.0000.0000.0000.000
155A188GLU-1-0.833-0.89626.185-0.129-0.1290.0000.0000.0000.000
156A189ARG10.7740.84027.5240.1400.1400.0000.0000.0000.000
157A190VAL0-0.0230.00021.906-0.010-0.0100.0000.0000.0000.000
158A191ARG10.9000.94225.0050.1680.1680.0000.0000.0000.000
159A192GLU-1-0.829-0.88926.546-0.143-0.1430.0000.0000.0000.000
160A193TYR0-0.045-0.03722.4060.0100.0100.0000.0000.0000.000
161A194HIS00.0340.00620.6490.0010.0010.0000.0000.0000.000
162A195LEU00.0280.02525.4150.0030.0030.0000.0000.0000.000
163A196LEU0-0.060-0.02428.5290.0120.0120.0000.0000.0000.000
164A197HIS00.022-0.00424.771-0.002-0.0020.0000.0000.0000.000
165A198LEU00.0220.01524.7760.0050.0050.0000.0000.0000.000
166A199ARG10.9340.97028.0050.1360.1360.0000.0000.0000.000
167A200ARG10.8380.91028.7890.1850.1850.0000.0000.0000.000
168A201TRP00.0810.01624.7140.0080.0080.0000.0000.0000.000
169A202ILE00.0070.02529.4450.0040.0040.0000.0000.0000.000
170A203ALA0-0.046-0.01832.1080.0060.0060.0000.0000.0000.000
171A204VAL00.0500.02930.0510.0040.0040.0000.0000.0000.000
172A205SER00.008-0.01929.7890.0000.0000.0000.0000.0000.000
173A206LEU0-0.061-0.02431.9450.0070.0070.0000.0000.0000.000
174A207GLU-1-0.950-0.97335.566-0.113-0.1130.0000.0000.0000.000
175A208GLU-1-0.855-0.94031.382-0.127-0.1270.0000.0000.0000.000
176A209LEU0-0.045-0.02232.6640.0060.0060.0000.0000.0000.000
177A210GLU-1-0.973-0.97235.489-0.076-0.0760.0000.0000.0000.000
178A211SER0-0.014-0.01936.5800.0070.0070.0000.0000.0000.000
179A212ILE0-0.014-0.01832.0720.0050.0050.0000.0000.0000.000
180A213ASP-1-0.768-0.84636.508-0.081-0.0810.0000.0000.0000.000
181A214GLN0-0.060-0.02839.2690.0040.0040.0000.0000.0000.000
182A215GLU-1-0.796-0.85837.337-0.083-0.0830.0000.0000.0000.000
183A216ILE00.005-0.01235.2610.0050.0050.0000.0000.0000.000
184A217LYS10.8870.94539.3810.0590.0590.0000.0000.0000.000
185A218ILE00.0400.02543.0320.0030.0030.0000.0000.0000.000
186A219LEU0-0.0250.00138.0150.0030.0030.0000.0000.0000.000
187A220LYS10.8240.90938.0020.0660.0660.0000.0000.0000.000
188A221GLU-1-0.934-0.94843.066-0.045-0.0450.0000.0000.0000.000
189A222LYS10.8680.93343.6110.0480.0480.0000.0000.0000.000