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: NN4QQ

Calculation Name: 3CYG-A-Xray372

Preferred Name:
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Target Type:
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Ligand Name:
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ligand 3-letter code:
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PDB ID: 3CYG

Chain ID: A

ChEMBL ID:
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UniProt ID: A7HM60

Base Structure: X-ray

Registration Date: 2023-09-24

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 215
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2626291.992347
FMO2-HF: Nuclear repulsion 2538726.578356
FMO2-HF: Total energy -87565.413991
FMO2-MP2: Total energy -87825.30479


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:36:LEU)


Summations of interaction energy for fragment #1(A:36: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.
-3.797-1.8710.411-0.282-2.054-0.007
Interaction energy analysis for fragmet #1(A:36:LEU)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.056 / q_NPA : 0.014
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].
3A38MET00.0090.0102.775-2.877-1.1460.412-0.272-1.871-0.007
4A39LYS10.8520.9144.5970.5220.717-0.001-0.010-0.1830.000
5A40VAL00.0500.0076.309-0.035-0.0350.0000.0000.0000.000
6A41PHE00.0250.0319.1760.0860.0860.0000.0000.0000.000
7A42GLU-1-0.844-0.9169.823-0.833-0.8330.0000.0000.0000.000
8A43ILE00.0320.01612.2550.0810.0810.0000.0000.0000.000
9A44VAL0-0.018-0.00414.811-0.046-0.0460.0000.0000.0000.000
10A45LYS10.9430.97815.5870.4300.4300.0000.0000.0000.000
11A46SER0-0.057-0.02419.3550.0000.0000.0000.0000.0000.000
12A47SER00.0270.01322.9700.0130.0130.0000.0000.0000.000
13A48THR0-0.067-0.04426.1070.0040.0040.0000.0000.0000.000
14A49GLU-1-0.852-0.96029.814-0.139-0.1390.0000.0000.0000.000
15A50ASN0-0.0210.00632.8910.0040.0040.0000.0000.0000.000
16A51GLU-1-0.908-0.95436.638-0.089-0.0890.0000.0000.0000.000
17A52ILE00.0240.03638.6040.0020.0020.0000.0000.0000.000
18A53VAL0-0.011-0.01333.6410.0010.0010.0000.0000.0000.000
19A54ARG10.8990.96528.6320.1440.1440.0000.0000.0000.000
20A55ILE0-0.058-0.01328.0390.0000.0000.0000.0000.0000.000
21A56HIS00.0210.00124.539-0.021-0.0210.0000.0000.0000.000
22A57VAL00.0020.00222.7820.0090.0090.0000.0000.0000.000
23A58GLU-1-0.892-0.94218.113-0.336-0.3360.0000.0000.0000.000
24A59LEU00.010-0.00219.7700.0140.0140.0000.0000.0000.000
25A60PRO0-0.0050.01216.791-0.049-0.0490.0000.0000.0000.000
26A61ARG10.9000.94115.7050.4050.4050.0000.0000.0000.000
27A62LEU0-0.024-0.01313.550-0.057-0.0570.0000.0000.0000.000
28A63LYS10.8450.9379.8290.9510.9510.0000.0000.0000.000
29A64TYR0-0.021-0.02811.340-0.043-0.0430.0000.0000.0000.000
30A65LEU00.0110.01212.9760.0360.0360.0000.0000.0000.000
31A66LYS10.8350.92815.162-0.040-0.0400.0000.0000.0000.000
32A67ASP-1-0.875-0.94717.279-0.066-0.0660.0000.0000.0000.000
33A68SER00.0830.02519.737-0.006-0.0060.0000.0000.0000.000
34A69ASN00.0470.02720.733-0.016-0.0160.0000.0000.0000.000
35A70PHE0-0.059-0.01718.585-0.002-0.0020.0000.0000.0000.000
36A71GLU-1-0.848-0.94816.759-0.284-0.2840.0000.0000.0000.000
37A72GLU-1-0.953-0.97019.748-0.168-0.1680.0000.0000.0000.000
38A73LYS10.9250.98022.7680.0960.0960.0000.0000.0000.000
39A74PHE0-0.031-0.01318.8870.0080.0080.0000.0000.0000.000
40A75ASN00.0630.01117.657-0.003-0.0030.0000.0000.0000.000
41A76SER00.0030.00121.443-0.001-0.0010.0000.0000.0000.000
42A77GLU-1-0.900-0.94925.074-0.098-0.0980.0000.0000.0000.000
43A78VAL0-0.040-0.01821.0750.0050.0050.0000.0000.0000.000
44A79GLU-1-0.935-0.97523.704-0.214-0.2140.0000.0000.0000.000
45A80GLU-1-0.982-1.00425.126-0.114-0.1140.0000.0000.0000.000
46A81LYS10.8770.93827.1260.1120.1120.0000.0000.0000.000
47A82ILE00.0040.01824.0060.0040.0040.0000.0000.0000.000
48A83LYS10.9390.96927.4460.1460.1460.0000.0000.0000.000
49A84LYS10.9000.97129.9000.0970.0970.0000.0000.0000.000
50A85PHE00.0640.02928.9700.0040.0040.0000.0000.0000.000
51A86VAL00.0270.00228.3130.0040.0040.0000.0000.0000.000
52A87ASN0-0.067-0.06031.5260.0010.0010.0000.0000.0000.000
53A88GLU-1-0.938-0.95834.617-0.086-0.0860.0000.0000.0000.000
54A89VAL00.0170.00332.8300.0050.0050.0000.0000.0000.000
55A90LYS10.9090.97033.5340.1280.1280.0000.0000.0000.000
56A91GLY0-0.012-0.00236.8540.0040.0040.0000.0000.0000.000
57A92ILE00.0290.01138.4260.0040.0040.0000.0000.0000.000
58A93ALA00.0380.01238.2390.0030.0030.0000.0000.0000.000
59A94GLN0-0.059-0.03340.333-0.001-0.0010.0000.0000.0000.000
60A95GLU-1-0.909-0.94542.531-0.061-0.0610.0000.0000.0000.000
61A96ASP-1-0.836-0.86743.350-0.068-0.0680.0000.0000.0000.000
62A97HIS0-0.0010.00343.5850.0020.0020.0000.0000.0000.000
63A98ASP-1-0.906-0.94845.520-0.069-0.0690.0000.0000.0000.000
64A99LYS10.7440.86947.9980.0620.0620.0000.0000.0000.000
65A100ASP-1-0.967-0.98948.831-0.058-0.0580.0000.0000.0000.000
66A101VAL0-0.023-0.02247.8420.0030.0030.0000.0000.0000.000
67A102GLN0-0.061-0.01539.8830.0000.0000.0000.0000.0000.000
68A103HIS0-0.086-0.04844.2260.0030.0030.0000.0000.0000.000
69A104THR0-0.042-0.02839.259-0.001-0.0010.0000.0000.0000.000
70A105PRO00.0100.00836.7680.0010.0010.0000.0000.0000.000
71A106TYR0-0.048-0.04636.700-0.002-0.0020.0000.0000.0000.000
72A107GLU-1-0.959-0.98130.470-0.138-0.1380.0000.0000.0000.000
73A108ALA00.0050.00130.4240.0060.0060.0000.0000.0000.000
74A109TYR0-0.037-0.02621.660-0.010-0.0100.0000.0000.0000.000
75A110VAL00.0200.00922.8740.0070.0070.0000.0000.0000.000
76A111SER0-0.014-0.00720.423-0.015-0.0150.0000.0000.0000.000
77A112VAL00.000-0.01315.9080.0180.0180.0000.0000.0000.000
78A113ASP-1-0.828-0.89316.517-0.220-0.2200.0000.0000.0000.000
79A114VAL0-0.031-0.02011.1190.0280.0280.0000.0000.0000.000
80A115ARG10.7950.88114.2320.1270.1270.0000.0000.0000.000
81A116TYR0-0.044-0.03111.8140.0550.0550.0000.0000.0000.000
82A117GLU-1-0.843-0.9297.229-0.623-0.6230.0000.0000.0000.000
83A118GLY0-0.052-0.0237.7830.1110.1110.0000.0000.0000.000
84A119LYS10.7550.8628.469-0.381-0.3810.0000.0000.0000.000
85A120ASP-1-0.842-0.9509.5420.1850.1850.0000.0000.0000.000
86A121PHE00.0390.02812.162-0.026-0.0260.0000.0000.0000.000
87A122LEU0-0.0190.00711.1830.0160.0160.0000.0000.0000.000
88A123SER00.005-0.00613.8060.0030.0030.0000.0000.0000.000
89A124PHE0-0.003-0.00215.315-0.024-0.0240.0000.0000.0000.000
90A125VAL00.0580.03417.2030.0180.0180.0000.0000.0000.000
91A126VAL0-0.041-0.01219.852-0.028-0.0280.0000.0000.0000.000
92A127TYR00.004-0.01421.2320.0260.0260.0000.0000.0000.000
93A128TYR00.005-0.00824.637-0.017-0.0170.0000.0000.0000.000
94A129TYR00.0170.01127.5920.0140.0140.0000.0000.0000.000
95A130GLN00.0440.00129.313-0.001-0.0010.0000.0000.0000.000
96A131PHE0-0.058-0.00832.6300.0050.0050.0000.0000.0000.000
97A132THR00.0370.00835.306-0.003-0.0030.0000.0000.0000.000
98A133GLY00.0430.04238.4940.0040.0040.0000.0000.0000.000
99A134GLY0-0.018-0.00339.5670.0000.0000.0000.0000.0000.000
100A135ALA0-0.024-0.02440.366-0.002-0.0020.0000.0000.0000.000
101A136HIS10.8940.95235.3910.0710.0710.0000.0000.0000.000
102A137GLY00.0720.03634.2460.0030.0030.0000.0000.0000.000
103A138ILE0-0.080-0.04034.0330.0040.0040.0000.0000.0000.000
104A139THR00.0440.00727.842-0.006-0.0060.0000.0000.0000.000
105A140PHE0-0.0240.00529.5880.0080.0080.0000.0000.0000.000
106A141PHE0-0.017-0.03124.784-0.012-0.0120.0000.0000.0000.000
107A142GLU-1-0.806-0.88725.035-0.103-0.1030.0000.0000.0000.000
108A143THR0-0.022-0.01321.943-0.010-0.0100.0000.0000.0000.000
109A144TYR0-0.060-0.02519.3500.0080.0080.0000.0000.0000.000
110A145ASN0-0.0070.01518.666-0.004-0.0040.0000.0000.0000.000
111A146ILE00.0210.00616.6230.0080.0080.0000.0000.0000.000
112A147ASP-1-0.768-0.88316.4170.0560.0560.0000.0000.0000.000
113A148LEU00.017-0.00611.933-0.012-0.0120.0000.0000.0000.000
114A149LYS10.8230.92515.756-0.190-0.1900.0000.0000.0000.000
115A150ASN0-0.018-0.03517.2990.0000.0000.0000.0000.0000.000
116A151SER0-0.0250.00618.924-0.008-0.0080.0000.0000.0000.000
117A152LYS10.9890.99319.9690.0170.0170.0000.0000.0000.000
118A153VAL0-0.033-0.01321.0650.0020.0020.0000.0000.0000.000
119A154LEU0-0.043-0.02821.2020.0060.0060.0000.0000.0000.000
120A155LYS11.0051.00724.0020.0520.0520.0000.0000.0000.000
121A156LEU00.0820.04226.2300.0080.0080.0000.0000.0000.000
122A157TYR00.0220.01727.4900.0050.0050.0000.0000.0000.000
123A158ASP-1-0.903-0.97326.458-0.011-0.0110.0000.0000.0000.000
124A159ILE0-0.079-0.04722.6520.0080.0080.0000.0000.0000.000
125A160ILE0-0.018-0.01126.5200.0090.0090.0000.0000.0000.000
126A161LYS10.9070.97129.471-0.035-0.0350.0000.0000.0000.000
127A162GLU-1-0.799-0.89933.1910.0050.0050.0000.0000.0000.000
128A163GLU-1-0.922-0.96735.6550.0140.0140.0000.0000.0000.000
129A164ALA0-0.081-0.04432.0620.0020.0020.0000.0000.0000.000
130A165GLU-1-0.883-0.96233.917-0.009-0.0090.0000.0000.0000.000
131A166ASP-1-0.877-0.93335.3210.0010.0010.0000.0000.0000.000
132A167THR0-0.080-0.04732.782-0.001-0.0010.0000.0000.0000.000
133A168ILE00.0180.00529.8190.0010.0010.0000.0000.0000.000
134A169LYS10.8800.95832.9960.0100.0100.0000.0000.0000.000
135A170SER0-0.048-0.01035.776-0.002-0.0020.0000.0000.0000.000
136A171ASN0-0.036-0.02730.454-0.005-0.0050.0000.0000.0000.000
137A172ILE00.0940.04030.990-0.001-0.0010.0000.0000.0000.000
138A173LEU0-0.019-0.00733.719-0.002-0.0020.0000.0000.0000.000
139A174LYS10.8970.95635.603-0.009-0.0090.0000.0000.0000.000
140A175GLN0-0.018-0.03029.357-0.005-0.0050.0000.0000.0000.000
141A176ILE0-0.0190.01034.180-0.002-0.0020.0000.0000.0000.000
142A177GLU-1-0.999-1.01636.347-0.006-0.0060.0000.0000.0000.000
143A178GLN0-0.0260.00134.7860.0000.0000.0000.0000.0000.000
144A179ASN0-0.069-0.05433.6090.0030.0030.0000.0000.0000.000
145A180ASN00.0630.03337.130-0.003-0.0030.0000.0000.0000.000
146A181THR0-0.092-0.03738.622-0.001-0.0010.0000.0000.0000.000
147A182ASP-1-0.873-0.90635.212-0.037-0.0370.0000.0000.0000.000
148A183PHE0-0.029-0.03032.927-0.004-0.0040.0000.0000.0000.000
149A184PHE0-0.0110.00838.2930.0010.0010.0000.0000.0000.000
150A185PRO00.0180.00141.3910.0020.0020.0000.0000.0000.000
151A186ASP-1-0.903-0.96443.619-0.027-0.0270.0000.0000.0000.000
152A187ALA00.0160.01338.4290.0000.0000.0000.0000.0000.000
153A188PRO00.017-0.00539.8360.0000.0000.0000.0000.0000.000
154A189MET0-0.004-0.00240.8610.0010.0010.0000.0000.0000.000
155A190ASN00.008-0.01039.5370.0020.0020.0000.0000.0000.000
156A191ILE00.0300.03234.9440.0000.0000.0000.0000.0000.000
157A192LEU0-0.055-0.03038.0000.0020.0020.0000.0000.0000.000
158A193LYS10.9120.94940.8070.0240.0240.0000.0000.0000.000
159A194ASP-1-0.816-0.86034.590-0.033-0.0330.0000.0000.0000.000
160A195ASP-1-0.846-0.90635.820-0.019-0.0190.0000.0000.0000.000
161A196ILE00.015-0.01631.304-0.003-0.0030.0000.0000.0000.000
162A197PHE0-0.057-0.02231.166-0.002-0.0020.0000.0000.0000.000
163A198SER0-0.075-0.02831.593-0.003-0.0030.0000.0000.0000.000
164A199ARG10.8350.91829.8490.0380.0380.0000.0000.0000.000
165A200GLU-1-0.852-0.91026.098-0.077-0.0770.0000.0000.0000.000
166A201PHE0-0.024-0.02722.7980.0070.0070.0000.0000.0000.000
167A202THR00.0300.02119.043-0.008-0.0080.0000.0000.0000.000
168A203ILE0-0.007-0.01017.1720.0160.0160.0000.0000.0000.000
169A204SER00.0280.00815.713-0.006-0.0060.0000.0000.0000.000
170A205LYS10.9200.95814.180-0.130-0.1300.0000.0000.0000.000
171A206ASP-1-0.938-0.98616.1750.0850.0850.0000.0000.0000.000
172A207GLY0-0.005-0.02419.0360.0010.0010.0000.0000.0000.000
173A208LEU00.0000.01420.346-0.005-0.0050.0000.0000.0000.000
174A209ILE0-0.025-0.00919.6820.0030.0030.0000.0000.0000.000
175A210ILE00.0270.01523.561-0.008-0.0080.0000.0000.0000.000
176A211MET0-0.0360.00822.709-0.002-0.0020.0000.0000.0000.000
177A212TYR0-0.054-0.06427.1800.0030.0030.0000.0000.0000.000
178A213PRO0-0.0120.00829.651-0.007-0.0070.0000.0000.0000.000
179A214HIS00.0470.00430.4160.0090.0090.0000.0000.0000.000
180A215TYR0-0.027-0.03034.026-0.001-0.0010.0000.0000.0000.000
181A216ASP-1-0.849-0.91335.214-0.047-0.0470.0000.0000.0000.000
182A217LEU0-0.034-0.02333.5620.0040.0040.0000.0000.0000.000
183A218ALA00.0390.01635.0660.0030.0030.0000.0000.0000.000
184A219PRO0-0.0050.00637.028-0.003-0.0030.0000.0000.0000.000
185A220TYR00.021-0.00533.089-0.002-0.0020.0000.0000.0000.000
186A221ALA0-0.056-0.02834.084-0.004-0.0040.0000.0000.0000.000
187A222SER0-0.001-0.00633.745-0.002-0.0020.0000.0000.0000.000
188A223GLY0-0.0180.01630.283-0.002-0.0020.0000.0000.0000.000
189A224MET0-0.046-0.02227.4140.0000.0000.0000.0000.0000.000
190A225PRO00.0040.00427.891-0.001-0.0010.0000.0000.0000.000
191A226GLU-1-0.833-0.91822.924-0.091-0.0910.0000.0000.0000.000
192A227PHE0-0.022-0.01427.0680.0040.0040.0000.0000.0000.000
193A228VAL00.0240.01623.0040.0020.0020.0000.0000.0000.000
194A229ILE0-0.031-0.01524.9110.0050.0050.0000.0000.0000.000
195A230PRO0-0.012-0.00224.2840.0050.0050.0000.0000.0000.000
196A231TRP00.0930.04819.432-0.003-0.0030.0000.0000.0000.000
197A232ASN00.0160.00224.582-0.001-0.0010.0000.0000.0000.000
198A233VAL0-0.061-0.03227.261-0.001-0.0010.0000.0000.0000.000
199A234ILE00.0110.00525.927-0.004-0.0040.0000.0000.0000.000
200A235GLU-1-0.945-0.96026.5170.0790.0790.0000.0000.0000.000
201A236LYS10.9520.97428.136-0.038-0.0380.0000.0000.0000.000
202A237PHE0-0.084-0.06530.646-0.001-0.0010.0000.0000.0000.000
203A238LEU00.0550.04525.269-0.006-0.0060.0000.0000.0000.000
204A239LYS10.8620.94127.961-0.010-0.0100.0000.0000.0000.000
205A240TYR0-0.060-0.02621.466-0.002-0.0020.0000.0000.0000.000
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