FMODB

FMODB: The database of quantum mechanical data based on the FMO method

Last updated: 2024-07-23

All entries: 37450

Number of unique PDB entries: 7783

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FMODB ID: NN29Q

Calculation Name: 1C4X-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1C4X

Chain ID: A

ChEMBL ID:

UniProt ID: Q75WN8

Base Structure: X-ray

Registration Date: 2023-09-22

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 281
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -4061740.71606
FMO2-HF: Nuclear repulsion 3951269.08722
FMO2-HF: Total energy -110471.62884
FMO2-MP2: Total energy -110791.016571


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:3:THR)


Summations of interaction energy for fragment #1(A:3:THR)
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.
-10.126-6.8950.023-1.656-1.5960.001
Interaction energy analysis for fragmet #1(A:3:THR)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.011 / 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].
3A5GLU-1-0.949-0.9763.291-2.8910.1820.025-1.616-1.4810.001
4A6ILE0-0.027-0.0245.6520.2100.2100.0000.0000.0000.000
5A7ILE0-0.032-0.0048.8330.3480.3480.0000.0000.0000.000
6A8GLU-1-0.799-0.90611.945-0.463-0.4630.0000.0000.0000.000
7A9LYS10.9090.96614.7050.6320.6320.0000.0000.0000.000
8A10ARG10.9670.98018.1550.2310.2310.0000.0000.0000.000
9A11PHE0-0.024-0.00616.796-0.021-0.0210.0000.0000.0000.000
10A12PRO0-0.0100.00622.8290.0250.0250.0000.0000.0000.000
11A13SER00.0160.03825.505-0.026-0.0260.0000.0000.0000.000
12A14GLY00.007-0.00127.2850.0120.0120.0000.0000.0000.000
13A15THR0-0.024-0.02531.0170.0020.0020.0000.0000.0000.000
14A16LEU00.0160.02930.0630.0090.0090.0000.0000.0000.000
15A17ALA0-0.0020.01226.200-0.021-0.0210.0000.0000.0000.000
16A18SER00.007-0.05723.4500.0030.0030.0000.0000.0000.000
17A19HIS0-0.071-0.03817.763-0.012-0.0120.0000.0000.0000.000
18A20ALA0-0.020-0.02018.5440.0090.0090.0000.0000.0000.000
19A21LEU0-0.0170.00113.322-0.010-0.0100.0000.0000.0000.000
20A22VAL0-0.011-0.00613.4720.0110.0110.0000.0000.0000.000
21A23ALA0-0.003-0.0098.964-0.104-0.1040.0000.0000.0000.000
22A24GLY00.0880.0569.2820.1670.1670.0000.0000.0000.000
23A25ASP-1-0.877-0.94610.280-1.196-1.1960.0000.0000.0000.000
24A26PRO0-0.044-0.03112.0600.1150.1150.0000.0000.0000.000
25A27GLN0-0.0090.01415.0630.1910.1910.0000.0000.0000.000
26A28SER0-0.075-0.02613.2690.0560.0560.0000.0000.0000.000
27A29PRO0-0.004-0.00415.6180.0480.0480.0000.0000.0000.000
28A30ALA00.0570.03816.257-0.116-0.1160.0000.0000.0000.000
29A31VAL0-0.0030.00115.9050.0770.0770.0000.0000.0000.000
30A32VAL0-0.0150.00617.609-0.053-0.0530.0000.0000.0000.000
31A33LEU0-0.002-0.00915.2340.0350.0350.0000.0000.0000.000
32A34LEU0-0.013-0.01619.6680.0230.0230.0000.0000.0000.000
33A35HIS0-0.007-0.00421.3640.0050.0050.0000.0000.0000.000
34A36GLY00.0550.03722.9130.0150.0150.0000.0000.0000.000
35A37ALA0-0.028-0.00426.155-0.002-0.0020.0000.0000.0000.000
36A38GLY00.0340.01228.0460.0010.0010.0000.0000.0000.000
37A39PRO00.0260.00128.904-0.011-0.0110.0000.0000.0000.000
38A40GLY00.0270.05526.7070.0070.0070.0000.0000.0000.000
39A41ALA0-0.0080.02224.531-0.012-0.0120.0000.0000.0000.000
40A42HIS00.014-0.02118.6330.0210.0210.0000.0000.0000.000
41A43ALA00.0650.04718.6000.0000.0000.0000.0000.0000.000
42A44ALA0-0.011-0.02015.626-0.025-0.0250.0000.0000.0000.000
43A45SER0-0.045-0.02816.214-0.006-0.0060.0000.0000.0000.000
44A46ASN0-0.019-0.01518.6330.0170.0170.0000.0000.0000.000
45A47TRP00.056-0.01215.281-0.007-0.0070.0000.0000.0000.000
46A48ARG10.9090.97510.6250.4710.4710.0000.0000.0000.000
47A49PRO0-0.029-0.03810.770-0.166-0.1660.0000.0000.0000.000
48A50ILE00.0510.04210.373-0.015-0.0150.0000.0000.0000.000
49A51ILE0-0.0350.0029.418-0.120-0.1200.0000.0000.0000.000
50A52PRO0-0.020-0.0104.789-0.319-0.287-0.001-0.003-0.0280.000
51A53ASP-1-0.819-0.9186.506-2.003-2.0030.0000.0000.0000.000
52A54LEU0-0.045-0.0148.2440.0480.0480.0000.0000.0000.000
53A55ALA0-0.011-0.0267.4320.0870.0870.0000.0000.0000.000
54A56GLU-1-0.988-0.9784.189-5.542-5.416-0.001-0.037-0.0870.000
55A57ASN0-0.111-0.0527.4460.3800.3800.0000.0000.0000.000
56A58PHE0-0.035-0.03111.1480.3180.3180.0000.0000.0000.000
57A59PHE00.0070.02811.834-0.233-0.2330.0000.0000.0000.000
58A60VAL00.015-0.01411.8160.2080.2080.0000.0000.0000.000
59A61VAL00.023-0.00214.420-0.013-0.0130.0000.0000.0000.000
60A62ALA00.0080.00416.2030.0840.0840.0000.0000.0000.000
61A63PRO00.0010.00117.8660.0120.0120.0000.0000.0000.000
62A64ASP-1-0.797-0.89020.715-0.345-0.3450.0000.0000.0000.000
63A65LEU0-0.027-0.00922.6880.0180.0180.0000.0000.0000.000
64A66ILE00.0460.02326.0330.0210.0210.0000.0000.0000.000
65A67GLY0-0.001-0.00729.0150.0060.0060.0000.0000.0000.000
66A68PHE0-0.074-0.03525.7680.0150.0150.0000.0000.0000.000
67A69GLY00.0330.00623.606-0.015-0.0150.0000.0000.0000.000
68A70GLN0-0.039-0.00819.7190.0260.0260.0000.0000.0000.000
69A71SER0-0.012-0.01724.233-0.018-0.0180.0000.0000.0000.000
70A72GLU-1-0.975-0.98125.556-0.192-0.1920.0000.0000.0000.000
71A73TYR0-0.007-0.00628.070-0.001-0.0010.0000.0000.0000.000
72A74PRO0-0.037-0.01231.9850.0010.0010.0000.0000.0000.000
73A75GLU-1-0.901-0.95335.292-0.119-0.1190.0000.0000.0000.000
74A76THR0-0.027-0.01138.3970.0050.0050.0000.0000.0000.000
75A77TYR00.025-0.01035.017-0.009-0.0090.0000.0000.0000.000
76A78PRO00.0170.00237.5810.0080.0080.0000.0000.0000.000
77A79GLY00.0290.02040.2170.0010.0010.0000.0000.0000.000
78A80HIS00.0180.01141.896-0.002-0.0020.0000.0000.0000.000
79A81ILE00.0700.02835.191-0.008-0.0080.0000.0000.0000.000
80A82MET00.0330.00236.997-0.012-0.0120.0000.0000.0000.000
81A83SER0-0.051-0.01837.927-0.006-0.0060.0000.0000.0000.000
82A84TRP00.0320.01133.484-0.013-0.0130.0000.0000.0000.000
83A85VAL0-0.035-0.01833.239-0.015-0.0150.0000.0000.0000.000
84A86GLY00.0560.03433.386-0.014-0.0140.0000.0000.0000.000
85A87MET0-0.009-0.00332.923-0.005-0.0050.0000.0000.0000.000
86A88ARG10.8840.93628.9860.2130.2130.0000.0000.0000.000
87A89VAL0-0.0080.00629.265-0.028-0.0280.0000.0000.0000.000
88A90GLU-1-0.884-0.95230.768-0.252-0.2520.0000.0000.0000.000
89A91GLN00.0050.00225.0810.0060.0060.0000.0000.0000.000
90A92ILE0-0.021-0.01524.291-0.028-0.0280.0000.0000.0000.000
91A93LEU00.0530.02626.336-0.031-0.0310.0000.0000.0000.000
92A94GLY00.003-0.00128.521-0.010-0.0100.0000.0000.0000.000
93A95LEU0-0.015-0.03321.691-0.009-0.0090.0000.0000.0000.000
94A96MET0-0.058-0.01523.970-0.032-0.0320.0000.0000.0000.000
95A97ASN0-0.011-0.00825.054-0.022-0.0220.0000.0000.0000.000
96A98HIS0-0.0350.00021.7040.0260.0260.0000.0000.0000.000
97A99PHE0-0.058-0.04818.447-0.008-0.0080.0000.0000.0000.000
98A100GLY00.0130.02222.651-0.032-0.0320.0000.0000.0000.000
99A101ILE0-0.0160.00520.105-0.008-0.0080.0000.0000.0000.000
100A102GLU-1-0.925-0.96123.868-0.384-0.3840.0000.0000.0000.000
101A103LYS10.9250.95725.1280.4060.4060.0000.0000.0000.000
102A104SER00.004-0.00921.696-0.066-0.0660.0000.0000.0000.000
103A105HIS00.0390.03218.6460.0980.0980.0000.0000.0000.000
104A106ILE0-0.030-0.00621.194-0.031-0.0310.0000.0000.0000.000
105A107VAL00.0330.01219.5810.0280.0280.0000.0000.0000.000
106A108GLY00.0100.02222.179-0.013-0.0130.0000.0000.0000.000
107A109ASN0-0.035-0.02722.8080.0310.0310.0000.0000.0000.000
108A110SER00.0210.01124.8700.0100.0100.0000.0000.0000.000
109A111MET0-0.003-0.02628.368-0.003-0.0030.0000.0000.0000.000
110A112GLY00.0670.04625.8480.0020.0020.0000.0000.0000.000
111A113GLY0-0.0100.00126.917-0.020-0.0200.0000.0000.0000.000
112A114ALA0-0.010-0.00428.4660.0040.0040.0000.0000.0000.000
113A115VAL0-0.002-0.00628.4830.0050.0050.0000.0000.0000.000
114A116THR00.015-0.01026.431-0.014-0.0140.0000.0000.0000.000
115A117LEU0-0.056-0.03528.6350.0000.0000.0000.0000.0000.000
116A118GLN0-0.022-0.01031.9490.0140.0140.0000.0000.0000.000
117A119LEU00.0280.02627.3650.0040.0040.0000.0000.0000.000
118A120VAL0-0.026-0.00328.7550.0020.0020.0000.0000.0000.000
119A121VAL0-0.055-0.03131.4470.0110.0110.0000.0000.0000.000
120A122GLU-1-0.938-0.98234.604-0.211-0.2110.0000.0000.0000.000
121A123ALA0-0.0020.01031.6230.0070.0070.0000.0000.0000.000
122A124PRO0-0.014-0.00231.414-0.023-0.0230.0000.0000.0000.000
123A125GLU-1-0.915-0.97830.981-0.285-0.2850.0000.0000.0000.000
124A126ARG10.8330.91827.3860.3570.3570.0000.0000.0000.000
125A127PHE0-0.013-0.01225.185-0.039-0.0390.0000.0000.0000.000
126A128ASP-1-0.947-0.96823.926-0.420-0.4200.0000.0000.0000.000
127A129LYS10.8830.96222.7290.4370.4370.0000.0000.0000.000
128A130VAL0-0.002-0.00423.708-0.026-0.0260.0000.0000.0000.000
129A131ALA00.0240.01622.1730.0150.0150.0000.0000.0000.000
130A132LEU0-0.027-0.01124.256-0.004-0.0040.0000.0000.0000.000
131A133MET00.0210.02720.4430.0140.0140.0000.0000.0000.000
132A134GLY00.0110.00025.9880.0030.0030.0000.0000.0000.000
133A135SER00.0130.00228.9020.0050.0050.0000.0000.0000.000
134A136VAL00.0420.01130.0790.0170.0170.0000.0000.0000.000
135A137GLY00.0160.03033.0250.0090.0090.0000.0000.0000.000
136A138ALA0-0.064-0.03634.9240.0030.0030.0000.0000.0000.000
137A139PRO00.0000.00537.5570.0030.0030.0000.0000.0000.000
138A140MET0-0.002-0.00236.4240.0000.0000.0000.0000.0000.000
139A141ASN0-0.071-0.00840.3860.0080.0080.0000.0000.0000.000
140A142ALA00.0630.01541.9940.0040.0040.0000.0000.0000.000
141A143ARG10.9270.95939.2850.0940.0940.0000.0000.0000.000
142A144PRO00.0450.04636.7730.0070.0070.0000.0000.0000.000
143A145PRO00.0230.00039.511-0.002-0.0020.0000.0000.0000.000
144A146GLU-1-0.764-0.87134.904-0.067-0.0670.0000.0000.0000.000
145A147LEU00.0190.02034.455-0.002-0.0020.0000.0000.0000.000
146A148ALA0-0.056-0.03336.552-0.002-0.0020.0000.0000.0000.000
147A149ARG10.9230.94637.9250.0480.0480.0000.0000.0000.000
148A150LEU00.0370.02432.0870.0020.0020.0000.0000.0000.000
149A151LEU0-0.048-0.02735.710-0.002-0.0020.0000.0000.0000.000
150A152ALA0-0.0110.00037.6140.0000.0000.0000.0000.0000.000
151A153PHE00.0490.03533.9300.0070.0070.0000.0000.0000.000
152A154TYR0-0.028-0.03933.0270.0020.0020.0000.0000.0000.000
153A155ALA0-0.0300.00038.8180.0040.0040.0000.0000.0000.000
154A156ASP-1-0.851-0.91840.379-0.025-0.0250.0000.0000.0000.000
155A157PRO00.0060.02436.6210.0010.0010.0000.0000.0000.000
156A158ARG10.8240.88536.6290.0250.0250.0000.0000.0000.000
157A159LEU00.0470.01430.668-0.003-0.0030.0000.0000.0000.000
158A160THR0-0.010-0.01533.460-0.003-0.0030.0000.0000.0000.000
159A161PRO0-0.004-0.00734.846-0.002-0.0020.0000.0000.0000.000
160A162TYR00.013-0.00727.973-0.004-0.0040.0000.0000.0000.000
161A163ARG10.8900.93929.836-0.021-0.0210.0000.0000.0000.000
162A164GLU-1-0.956-0.96730.909-0.019-0.0190.0000.0000.0000.000
163A165LEU0-0.054-0.01231.713-0.007-0.0070.0000.0000.0000.000
164A166ILE00.0100.00725.937-0.011-0.0110.0000.0000.0000.000
165A167HIS00.023-0.00228.0330.0010.0010.0000.0000.0000.000
166A168SER0-0.091-0.04229.483-0.004-0.0040.0000.0000.0000.000
167A169PHE00.012-0.00826.278-0.010-0.0100.0000.0000.0000.000
168A170VAL0-0.051-0.01023.608-0.021-0.0210.0000.0000.0000.000
169A171TYR0-0.059-0.04026.3210.0140.0140.0000.0000.0000.000
170A172ASP-1-0.861-0.93626.4320.0280.0280.0000.0000.0000.000
171A173PRO0-0.036-0.02025.9420.0030.0030.0000.0000.0000.000
172A174GLU-1-0.901-0.94425.8650.0230.0230.0000.0000.0000.000
173A175ASN0-0.090-0.05124.0540.0370.0370.0000.0000.0000.000
174A176PHE00.0060.00719.8270.0070.0070.0000.0000.0000.000
175A177PRO00.001-0.00617.1560.0170.0170.0000.0000.0000.000
176A178GLY00.0370.00718.585-0.028-0.0280.0000.0000.0000.000
177A179MET00.0050.02019.623-0.026-0.0260.0000.0000.0000.000
178A180GLU-1-0.780-0.88323.2440.0110.0110.0000.0000.0000.000
179A181GLU-1-0.936-0.97020.2380.0780.0780.0000.0000.0000.000
180A182ILE0-0.019-0.00819.345-0.020-0.0200.0000.0000.0000.000
181A183VAL0-0.041-0.02622.494-0.017-0.0170.0000.0000.0000.000
182A184LYS10.9190.94725.653-0.067-0.0670.0000.0000.0000.000
183A185SER00.0030.00922.221-0.015-0.0150.0000.0000.0000.000
184A186ARG10.9060.93721.9080.1550.1550.0000.0000.0000.000
185A187PHE0-0.013-0.00625.491-0.008-0.0080.0000.0000.0000.000
186A188GLU-1-0.919-0.96027.273-0.020-0.0200.0000.0000.0000.000
187A189VAL0-0.034-0.01324.466-0.006-0.0060.0000.0000.0000.000
188A190ALA0-0.027-0.00927.890-0.004-0.0040.0000.0000.0000.000
189A191ASN00.009-0.01130.277-0.005-0.0050.0000.0000.0000.000
190A192ASP-1-0.865-0.90830.354-0.084-0.0840.0000.0000.0000.000
191A193PRO0-0.025-0.02132.452-0.006-0.0060.0000.0000.0000.000
192A194GLU-1-0.921-0.96932.795-0.119-0.1190.0000.0000.0000.000
193A195VAL00.0090.01929.160-0.009-0.0090.0000.0000.0000.000
194A196ARG10.8580.90332.1740.0620.0620.0000.0000.0000.000
195A197ARG10.9020.96334.9820.0920.0920.0000.0000.0000.000
196A198ILE00.0060.01732.0950.0000.0000.0000.0000.0000.000
197A199GLN0-0.002-0.01930.265-0.008-0.0080.0000.0000.0000.000
198A200GLU-1-0.878-0.90434.352-0.075-0.0750.0000.0000.0000.000
199A201VAL00.0120.00937.9680.0020.0020.0000.0000.0000.000
200A202MET00.0070.02331.008-0.006-0.0060.0000.0000.0000.000
201A203PHE0-0.0040.01531.949-0.004-0.0040.0000.0000.0000.000
202A204GLU-1-0.887-0.93037.324-0.083-0.0830.0000.0000.0000.000
203A205SER0-0.085-0.07138.259-0.002-0.0020.0000.0000.0000.000
204A206MET0-0.031-0.02733.361-0.004-0.0040.0000.0000.0000.000
205A207LYS10.8230.92338.4110.0900.0900.0000.0000.0000.000
206A208ALA0-0.096-0.05341.0580.0030.0030.0000.0000.0000.000
207A209GLY00.1160.05142.5090.0010.0010.0000.0000.0000.000
208A210MET00.008-0.00536.446-0.006-0.0060.0000.0000.0000.000
209A211GLU-1-0.910-0.94039.876-0.114-0.1140.0000.0000.0000.000
210A212SER0-0.025-0.01641.226-0.001-0.0010.0000.0000.0000.000
211A213LEU0-0.022-0.02835.348-0.005-0.0050.0000.0000.0000.000
212A214VAL0-0.076-0.01637.409-0.010-0.0100.0000.0000.0000.000
213A215ILE00.0420.03535.6390.0030.0030.0000.0000.0000.000
214A216PRO00.0460.01639.0010.0060.0060.0000.0000.0000.000
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