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: KG883

Calculation Name: 1CQ3-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1CQ3

Chain ID: A

ChEMBL ID:

UniProt ID: Q85307

Base Structure: X-ray

Registration Date: 2023-09-23

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 224
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2564494.357374
FMO2-HF: Nuclear repulsion 2476675.989616
FMO2-HF: Total energy -87818.367758
FMO2-MP2: Total energy -88066.078003


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:SER)


Summations of interaction energy for fragment #1(A:1: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.
-9.808-4.161-0.051-2.84-2.756-0.006
Interaction energy analysis for fragmet #1(A:1:SER)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.054 / q_NPA : -0.043
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].
3A3SER00.0140.0393.627-6.143-0.897-0.056-2.765-2.425-0.006
4A4SER00.0910.0375.754-0.467-0.436-0.001-0.001-0.0290.000
5A5SER00.0580.0228.6520.0380.0380.0000.0000.0000.000
6A6SER0-0.110-0.0514.103-0.144-0.0160.000-0.023-0.1050.000
7A7SER0-0.024-0.0113.606-0.1960.0460.006-0.051-0.1970.000
8A8CYS00.0650.0395.6480.2930.2930.0000.0000.0000.000
9A9THR0-0.017-0.0137.079-0.655-0.6550.0000.0000.0000.000
10A10GLU-1-0.959-0.9805.334-2.296-2.2960.0000.0000.0000.000
11A11GLU-1-0.987-0.9989.187-0.366-0.3660.0000.0000.0000.000
12A12GLU-1-0.925-0.96811.799-0.265-0.2650.0000.0000.0000.000
13A13ASN0-0.072-0.04415.2210.0280.0280.0000.0000.0000.000
14A14LYS10.8890.95613.8410.3810.3810.0000.0000.0000.000
15A15HIS0-0.025-0.03514.799-0.053-0.0530.0000.0000.0000.000
16A16HIS0-0.0040.01310.407-0.180-0.1800.0000.0000.0000.000
17A17MET0-0.0160.00915.2250.0070.0070.0000.0000.0000.000
18A18GLY0-0.007-0.01318.5490.0180.0180.0000.0000.0000.000
19A19ILE00.0930.04520.101-0.010-0.0100.0000.0000.0000.000
20A20ASP-1-0.820-0.88222.7830.0130.0130.0000.0000.0000.000
21A21VAL00.0640.03124.747-0.005-0.0050.0000.0000.0000.000
22A22ILE0-0.051-0.02228.0510.0070.0070.0000.0000.0000.000
23A23ILE00.0450.01530.387-0.003-0.0030.0000.0000.0000.000
24A24LYS10.9170.96833.681-0.006-0.0060.0000.0000.0000.000
25A25VAL00.0500.02936.536-0.002-0.0020.0000.0000.0000.000
26A26THR0-0.070-0.02839.6750.0010.0010.0000.0000.0000.000
27A27LYS10.9120.95041.960-0.020-0.0200.0000.0000.0000.000
28A28GLN0-0.060-0.03445.108-0.001-0.0010.0000.0000.0000.000
29A29ASP-1-0.919-0.96548.8980.0090.0090.0000.0000.0000.000
30A30GLN0-0.104-0.05951.2230.0010.0010.0000.0000.0000.000
31A31THR0-0.0040.01546.4210.0000.0000.0000.0000.0000.000
32A32PRO0-0.024-0.01548.5620.0000.0000.0000.0000.0000.000
33A33THR0-0.001-0.01545.5480.0000.0000.0000.0000.0000.000
34A34ASN00.021-0.00141.8940.0020.0020.0000.0000.0000.000
35A35ASP-1-0.959-0.97440.0070.0270.0270.0000.0000.0000.000
36A36LYS10.8200.91738.391-0.026-0.0260.0000.0000.0000.000
37A37ILE0-0.020-0.00532.723-0.001-0.0010.0000.0000.0000.000
38A38CYS-1-0.743-0.84230.8270.0510.0510.0000.0000.0000.000
39A39GLN0-0.179-0.10933.0120.0020.0020.0000.0000.0000.000
40A40SER0-0.083-0.06933.3420.0020.0020.0000.0000.0000.000
41A41VAL00.0770.04728.241-0.003-0.0030.0000.0000.0000.000
42A42THR0-0.069-0.02831.1800.0040.0040.0000.0000.0000.000
43A43GLU-1-0.908-0.95925.6350.0660.0660.0000.0000.0000.000
44A44VAL0-0.020-0.00630.1170.0020.0020.0000.0000.0000.000
45A45THR0-0.0260.00227.976-0.004-0.0040.0000.0000.0000.000
46A46GLU-1-0.815-0.89030.5810.0090.0090.0000.0000.0000.000
47A47SER0-0.072-0.06631.520-0.002-0.0020.0000.0000.0000.000
48A48GLU-1-0.923-0.93129.7380.0440.0440.0000.0000.0000.000
49A49ASP-1-0.951-0.97730.8520.0330.0330.0000.0000.0000.000
50A50GLU-1-0.983-0.99233.8640.0260.0260.0000.0000.0000.000
51A51SER0-0.114-0.07234.702-0.003-0.0030.0000.0000.0000.000
52A52GLU-1-0.918-0.94035.8000.0150.0150.0000.0000.0000.000
53A53GLU-1-0.918-0.96235.4390.0060.0060.0000.0000.0000.000
54A54VAL00.0180.02333.884-0.002-0.0020.0000.0000.0000.000
55A55VAL0-0.048-0.01735.943-0.002-0.0020.0000.0000.0000.000
56A56LYS10.8740.90738.2090.0100.0100.0000.0000.0000.000
57A57GLY0-0.0060.01236.5540.0020.0020.0000.0000.0000.000
58A58ASP-1-0.881-0.95630.983-0.019-0.0190.0000.0000.0000.000
59A59PRO0-0.0080.00029.1280.0010.0010.0000.0000.0000.000
60A60THR00.001-0.00830.286-0.001-0.0010.0000.0000.0000.000
61A61THR0-0.045-0.02927.0650.0030.0030.0000.0000.0000.000
62A62TYR0-0.105-0.08430.037-0.004-0.0040.0000.0000.0000.000
63A63TYR0-0.010-0.01225.1800.0040.0040.0000.0000.0000.000
64A64THR0-0.042-0.04231.560-0.003-0.0030.0000.0000.0000.000
65A65VAL0-0.007-0.02131.1010.0040.0040.0000.0000.0000.000
66A66VAL0-0.053-0.00833.882-0.003-0.0030.0000.0000.0000.000
67A67GLY00.0750.02135.8250.0040.0040.0000.0000.0000.000
68A68GLY00.0070.00637.371-0.002-0.0020.0000.0000.0000.000
69A69GLY0-0.010-0.01039.709-0.002-0.0020.0000.0000.0000.000
70A70LEU0-0.053-0.03239.205-0.002-0.0020.0000.0000.0000.000
71A71THR00.0390.02538.4230.0030.0030.0000.0000.0000.000
72A72MET0-0.080-0.02933.477-0.004-0.0040.0000.0000.0000.000
73A73ASP-1-0.823-0.88835.2820.0230.0230.0000.0000.0000.000
74A74PHE0-0.012-0.02931.641-0.003-0.0030.0000.0000.0000.000
75A75GLY00.0250.01332.9300.0030.0030.0000.0000.0000.000
76A76PHE0-0.012-0.00428.209-0.001-0.0010.0000.0000.0000.000
77A77THR00.0650.04730.1030.0060.0060.0000.0000.0000.000
78A78LYS10.8940.95527.9340.0270.0270.0000.0000.0000.000
79A79CYS-1-0.740-0.85626.029-0.022-0.0220.0000.0000.0000.000
80A80PRO0-0.139-0.06420.6330.0070.0070.0000.0000.0000.000
81A81LYS10.9570.98019.646-0.077-0.0770.0000.0000.0000.000
82A82ILE00.0520.06020.801-0.001-0.0010.0000.0000.0000.000
83A83SER0-0.132-0.08918.5190.0220.0220.0000.0000.0000.000
84A84SER0-0.120-0.06120.3140.0180.0180.0000.0000.0000.000
85A85ILE00.0960.05122.105-0.010-0.0100.0000.0000.0000.000
86A86SER0-0.033-0.01125.8480.0050.0050.0000.0000.0000.000
87A87GLU-1-0.682-0.88127.6280.0250.0250.0000.0000.0000.000
88A88TYR0-0.016-0.00131.1420.0020.0020.0000.0000.0000.000
89A89SER00.0500.03033.499-0.003-0.0030.0000.0000.0000.000
90A90ASP-1-0.942-0.98537.2400.0220.0220.0000.0000.0000.000
91A91GLY00.0170.03239.130-0.002-0.0020.0000.0000.0000.000
92A92ASN0-0.023-0.01042.8500.0010.0010.0000.0000.0000.000
93A93THR0-0.027-0.04239.232-0.001-0.0010.0000.0000.0000.000
94A94VAL00.0180.01336.2020.0020.0020.0000.0000.0000.000
95A95ASN0-0.081-0.04933.494-0.005-0.0050.0000.0000.0000.000
96A96ALA00.0630.03730.9730.0040.0040.0000.0000.0000.000
97A97ARG10.8520.92024.100-0.014-0.0140.0000.0000.0000.000
98A98LEU00.0180.02425.7980.0080.0080.0000.0000.0000.000
99A99SER00.001-0.00220.869-0.007-0.0070.0000.0000.0000.000
100A100SER00.0560.02518.5470.0090.0090.0000.0000.0000.000
101A101VAL0-0.067-0.04014.3120.0010.0010.0000.0000.0000.000
102A102SER00.0200.00313.6670.0130.0130.0000.0000.0000.000
103A103PRO0-0.022-0.0298.7790.0690.0690.0000.0000.0000.000
104A104GLY0-0.024-0.0047.739-0.049-0.0490.0000.0000.0000.000
105A105GLN0-0.042-0.0348.6880.0350.0350.0000.0000.0000.000
106A106GLY0-0.038-0.01310.207-0.019-0.0190.0000.0000.0000.000
107A107LYS10.9290.97111.599-0.191-0.1910.0000.0000.0000.000
108A108ASP-1-0.917-0.96811.5030.5110.5110.0000.0000.0000.000
109A109SER00.0240.02711.844-0.083-0.0830.0000.0000.0000.000
110A110PRO00.0150.00012.489-0.062-0.0620.0000.0000.0000.000
111A111ALA00.0090.00912.798-0.029-0.0290.0000.0000.0000.000
112A112ILE00.0130.01714.7110.0030.0030.0000.0000.0000.000
113A113THR0-0.0010.00117.762-0.033-0.0330.0000.0000.0000.000
114A114ARG11.0291.01619.6210.1650.1650.0000.0000.0000.000
115A115GLU-1-0.924-0.97421.776-0.148-0.1480.0000.0000.0000.000
116A116GLU-1-0.900-0.96121.987-0.075-0.0750.0000.0000.0000.000
117A117ALA00.0210.01021.3900.0130.0130.0000.0000.0000.000
118A118LEU0-0.059-0.03723.3660.0130.0130.0000.0000.0000.000
119A119SER0-0.086-0.04026.7560.0100.0100.0000.0000.0000.000
120A120MET00.0150.03122.6180.0060.0060.0000.0000.0000.000
121A121ILE0-0.038-0.01824.7900.0040.0040.0000.0000.0000.000
122A122LYS10.8710.93427.9420.0690.0690.0000.0000.0000.000
123A123ASP-1-0.964-0.98230.032-0.040-0.0400.0000.0000.0000.000
124A124CYS-1-0.938-0.93827.642-0.018-0.0180.0000.0000.0000.000
125A125GLU-1-0.866-0.92729.783-0.012-0.0120.0000.0000.0000.000
126A126MET00.000-0.00330.8960.0050.0050.0000.0000.0000.000
127A127SER0-0.070-0.01232.808-0.001-0.0010.0000.0000.0000.000
128A128ILE00.023-0.01134.7040.0030.0030.0000.0000.0000.000
129A129ASN0-0.026-0.02237.063-0.001-0.0010.0000.0000.0000.000
130A130ILE00.0270.02638.1050.0020.0020.0000.0000.0000.000
131A131LYS10.9530.96640.702-0.014-0.0140.0000.0000.0000.000
132A132CYS0-0.0080.00542.5250.0010.0010.0000.0000.0000.000
133A133SER0-0.0230.01241.8330.0010.0010.0000.0000.0000.000
134A134GLU-1-0.969-0.99943.8990.0190.0190.0000.0000.0000.000
135A135GLU-1-0.867-0.93040.2360.0290.0290.0000.0000.0000.000
136A136GLU-1-0.842-0.92143.0260.0240.0240.0000.0000.0000.000
137A137LYS10.7890.92935.798-0.041-0.0410.0000.0000.0000.000
138A138ASP-1-0.915-0.94338.1580.0360.0360.0000.0000.0000.000
139A139SER0-0.029-0.04734.2120.0000.0000.0000.0000.0000.000
140A140ASN0-0.089-0.03831.3640.0040.0040.0000.0000.0000.000
141A141ILE00.0510.02829.2940.0020.0020.0000.0000.0000.000
142A142LYS10.8440.92922.474-0.093-0.0930.0000.0000.0000.000
143A143THR0-0.026-0.02225.989-0.002-0.0020.0000.0000.0000.000
144A144HIS0-0.040-0.02620.638-0.005-0.0050.0000.0000.0000.000
145A145PRO00.0060.00719.988-0.006-0.0060.0000.0000.0000.000
146A146VAL00.0310.02020.7210.0100.0100.0000.0000.0000.000
147A147LEU0-0.044-0.01115.9510.0010.0010.0000.0000.0000.000
148A148GLY00.0390.02317.731-0.010-0.0100.0000.0000.0000.000
149A149SER00.0650.00417.1210.0030.0030.0000.0000.0000.000
150A150ASN0-0.092-0.06116.4570.0010.0010.0000.0000.0000.000
151A151ILE00.0410.03918.582-0.017-0.0170.0000.0000.0000.000
152A152SER0-0.031-0.00821.6160.0130.0130.0000.0000.0000.000
153A153HIS00.0320.02624.729-0.009-0.0090.0000.0000.0000.000
154A154LYS10.8570.93225.2400.0660.0660.0000.0000.0000.000
155A155LYS10.9270.94929.7800.0220.0220.0000.0000.0000.000
156A156VAL0-0.039-0.01527.239-0.004-0.0040.0000.0000.0000.000
157A157SER0-0.039-0.02230.1230.0060.0060.0000.0000.0000.000
158A158TYR0-0.037-0.01231.521-0.003-0.0030.0000.0000.0000.000
159A159GLU-1-0.929-0.98031.265-0.046-0.0460.0000.0000.0000.000
160A160ASP-1-1.008-0.97633.843-0.018-0.0180.0000.0000.0000.000
161A161ILE00.024-0.00429.442-0.001-0.0010.0000.0000.0000.000
162A162ILE0-0.073-0.04633.3100.0040.0040.0000.0000.0000.000
163A163GLY00.1300.07535.306-0.001-0.0010.0000.0000.0000.000
164A164SER0-0.128-0.07837.7400.0010.0010.0000.0000.0000.000
165A165THR00.0790.03439.0040.0020.0020.0000.0000.0000.000
166A166ILE0-0.111-0.05040.7900.0000.0000.0000.0000.0000.000
167A167VAL00.0390.01941.9760.0010.0010.0000.0000.0000.000
168A168ASP-1-0.849-0.91944.2880.0090.0090.0000.0000.0000.000
169A169THR00.013-0.01046.8400.0010.0010.0000.0000.0000.000
170A170LYS10.9330.97949.020-0.011-0.0110.0000.0000.0000.000
171A171CYS0-0.021-0.03744.6460.0010.0010.0000.0000.0000.000
172A172VAL0-0.0200.00942.9590.0010.0010.0000.0000.0000.000
173A173LYS10.8810.95545.317-0.007-0.0070.0000.0000.0000.000
174A174ASN00.022-0.01343.306-0.002-0.0020.0000.0000.0000.000
175A175LEU00.0030.00537.8450.0020.0020.0000.0000.0000.000
176A176GLU-1-0.962-0.98337.9200.0010.0010.0000.0000.0000.000
177A177ILE00.0160.01332.5910.0030.0030.0000.0000.0000.000
178A178SER0-0.014-0.01230.624-0.004-0.0040.0000.0000.0000.000
179A179VAL00.0350.02128.4920.0040.0040.0000.0000.0000.000
180A180ARG10.7290.84824.2530.0520.0520.0000.0000.0000.000
181A181ILE00.1120.04623.9060.0030.0030.0000.0000.0000.000
182A182GLY00.009-0.00922.366-0.002-0.0020.0000.0000.0000.000
183A183ASP-1-0.766-0.86716.265-0.279-0.2790.0000.0000.0000.000
184A184MET0-0.048-0.00515.5880.0170.0170.0000.0000.0000.000
185A185CYS0-0.147-0.06112.367-0.045-0.0450.0000.0000.0000.000
186A186LYS10.7770.86714.3830.3530.3530.0000.0000.0000.000
187A187GLU-1-0.815-0.88716.871-0.081-0.0810.0000.0000.0000.000
188A188SER0-0.059-0.01519.193-0.020-0.0200.0000.0000.0000.000
189A189SER0-0.018-0.02021.5950.0110.0110.0000.0000.0000.000
190A190GLU-1-0.923-0.97823.668-0.134-0.1340.0000.0000.0000.000
191A191LEU0-0.039-0.02720.6700.0040.0040.0000.0000.0000.000
192A192GLU-1-0.779-0.86821.928-0.103-0.1030.0000.0000.0000.000
193A193VAL00.0310.01825.6180.0030.0030.0000.0000.0000.000
194A194LYS10.7650.85528.0980.0210.0210.0000.0000.0000.000
195A195ASP-1-0.655-0.78430.718-0.020-0.0200.0000.0000.0000.000
196A196GLY0-0.058-0.05833.0560.0020.0020.0000.0000.0000.000
197A197PHE00.0010.01735.6410.0000.0000.0000.0000.0000.000
198A198LYS10.9300.96938.7370.0060.0060.0000.0000.0000.000
199A199TYR00.0060.01941.337-0.001-0.0010.0000.0000.0000.000
200A200VAL0-0.062-0.05344.0080.0020.0020.0000.0000.0000.000
201A201ASP-1-0.921-0.97346.5050.0030.0030.0000.0000.0000.000
202A202GLY0-0.011-0.00448.2080.0000.0000.0000.0000.0000.000
203A203SER0-0.098-0.04349.020-0.001-0.0010.0000.0000.0000.000
204A204ALA00.0460.01944.3740.0010.0010.0000.0000.0000.000
205A205SER0-0.046-0.02843.1470.0000.0000.0000.0000.0000.000
206A206GLU-1-0.874-0.95240.010-0.015-0.0150.0000.0000.0000.000
207A207ASP-1-1.000-0.97440.375-0.014-0.0140.0000.0000.0000.000
208A208ALA00.0450.02736.5410.0000.0000.0000.0000.0000.000
209A209ALA0-0.058-0.05236.1150.0010.0010.0000.0000.0000.000
210A210ASP-1-0.922-0.95432.348-0.019-0.0190.0000.0000.0000.000
211A211ASP-1-0.770-0.89332.029-0.007-0.0070.0000.0000.0000.000
212A212THR0-0.068-0.04128.1470.0020.0020.0000.0000.0000.000
213A213SER0-0.101-0.06729.8520.0040.0040.0000.0000.0000.000
214A214LEU0-0.0020.03732.5630.0020.0020.0000.0000.0000.000
215A215ILE00.0160.00629.3800.0020.0020.0000.0000.0000.000
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