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: J2L69

Calculation Name: 4G9Q-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 4G9Q

Chain ID: A

ChEMBL ID:

UniProt ID: Q930A6

Base Structure: X-ray

Registration Date: 2023-09-26

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 238
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2847727.132932
FMO2-HF: Nuclear repulsion 2757614.572069
FMO2-HF: Total energy -90112.560864
FMO2-MP2: Total energy -90381.197865


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:GLN)


Summations of interaction energy for fragment #1(A:10:GLN)
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.
-18.962-12.5756.441-3.601-9.227-0.016
Interaction energy analysis for fragmet #1(A:10:GLN)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.020 / q_NPA : 0.004
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].
3A12PRO0-0.015-0.0053.771-0.8720.777-0.014-0.739-0.8960.002
4A13ASN00.0390.0216.1000.5300.5300.0000.0000.0000.000
5A14VAL00.0240.0025.0980.2800.2800.0000.0000.0000.000
6A15GLU-1-0.923-0.9717.799-0.349-0.3490.0000.0000.0000.000
7A16GLY00.0080.02411.0700.1560.1560.0000.0000.0000.000
8A17ARG10.6810.8137.1400.9250.9250.0000.0000.0000.000
9A18ARG10.8690.93312.5780.4990.4990.0000.0000.0000.000
10A19PHE00.0110.01114.2110.0720.0720.0000.0000.0000.000
11A20SER00.0920.03911.749-0.089-0.0890.0000.0000.0000.000
12A21PRO00.0470.0067.7550.1340.1340.0000.0000.0000.000
13A22ASP-1-0.845-0.90410.1620.5170.5170.0000.0000.0000.000
14A23GLN00.0450.03113.5040.0070.0070.0000.0000.0000.000
15A24VAL00.0150.03211.6200.0440.0440.0000.0000.0000.000
16A25ARG10.8560.8968.770-0.678-0.6780.0000.0000.0000.000
17A26SER0-0.086-0.04014.1620.0260.0260.0000.0000.0000.000
18A27VAL0-0.015-0.00316.820-0.023-0.0230.0000.0000.0000.000
19A28ALA00.006-0.00815.8590.0240.0240.0000.0000.0000.000
20A29PRO00.0420.02013.0690.0720.0720.0000.0000.0000.000
21A30ALA0-0.002-0.00411.9110.2630.2630.0000.0000.0000.000
22A31LEU00.0430.02711.5550.2920.2920.0000.0000.0000.000
23A32GLU-1-0.749-0.8386.903-0.103-0.1030.0000.0000.0000.000
24A33GLN00.0200.0087.2980.8130.8130.0000.0000.0000.000
25A34TYR0-0.022-0.0246.5561.4101.4100.0000.0000.0000.000
26A35THR0-0.0020.0006.6660.1550.1550.0000.0000.0000.000
27A36GLN00.001-0.0182.280-8.323-6.7212.124-1.611-2.115-0.022
28A37GLN00.017-0.0022.642-4.408-0.7011.419-2.076-3.051-0.001
29A38ARG10.9190.9683.704-4.452-4.3990.0020.136-0.1910.001
30A39LEU00.0080.0246.865-0.767-0.7670.0000.0000.0000.000
31A40TYR00.0570.0113.369-1.063-0.5990.036-0.102-0.3970.000
32A41GLY00.0010.0102.619-2.677-2.1622.884-1.703-1.6960.007
33A42ASP-1-0.952-0.9693.134-1.095-2.850-0.0092.503-0.739-0.003
34A43VAL00.004-0.0095.970-0.432-0.4320.0000.0000.0000.000
35A44TRP0-0.087-0.0696.593-0.232-0.2320.0000.0000.0000.000
36A45GLN0-0.082-0.0304.435-0.0520.100-0.001-0.009-0.1420.000
37A46ARG10.8510.9147.8640.5830.5830.0000.0000.0000.000
38A47PRO00.0160.00510.9570.0160.0160.0000.0000.0000.000
39A48GLY0-0.0140.00613.3570.0530.0530.0000.0000.0000.000
40A49LEU00.0060.00615.1560.0680.0680.0000.0000.0000.000
41A50ASN00.0030.01214.093-0.189-0.1890.0000.0000.0000.000
42A51ARG10.9950.9669.3271.9321.9320.0000.0000.0000.000
43A52ARG10.8490.91412.9340.6150.6150.0000.0000.0000.000
44A53ASP-1-0.763-0.87116.361-0.582-0.5820.0000.0000.0000.000
45A54ARG10.8260.89711.6421.0341.0340.0000.0000.0000.000
46A55SER00.0120.03114.329-0.019-0.0190.0000.0000.0000.000
47A56LEU0-0.0100.01115.5010.0640.0640.0000.0000.0000.000
48A57VAL00.0170.00617.1410.0670.0670.0000.0000.0000.000
49A58THR0-0.031-0.02713.9280.0530.0530.0000.0000.0000.000
50A59ILE00.0090.00316.8030.0600.0600.0000.0000.0000.000
51A60ALA00.0090.00419.4000.0550.0550.0000.0000.0000.000
52A61ALA00.0180.01118.7200.0480.0480.0000.0000.0000.000
53A62LEU0-0.029-0.01716.1710.0420.0420.0000.0000.0000.000
54A63ILE0-0.019-0.00320.4480.0430.0430.0000.0000.0000.000
55A64ALA00.0030.00123.9390.0350.0350.0000.0000.0000.000
56A65ARG10.8230.89820.4710.1820.1820.0000.0000.0000.000
57A66GLY0-0.070-0.02624.2840.0240.0240.0000.0000.0000.000
58A67GLU-1-0.855-0.91019.877-0.190-0.1900.0000.0000.0000.000
59A68ALA00.0420.00920.583-0.050-0.0500.0000.0000.0000.000
60A69PRO00.0410.01520.493-0.043-0.0430.0000.0000.0000.000
61A70ALA00.0000.01116.179-0.038-0.0380.0000.0000.0000.000
62A71LEU00.0180.00216.545-0.112-0.1120.0000.0000.0000.000
63A72THR0-0.0020.01117.936-0.039-0.0390.0000.0000.0000.000
64A73TYR0-0.045-0.0198.291-0.009-0.0090.0000.0000.0000.000
65A74TYR00.010-0.02010.362-0.014-0.0140.0000.0000.0000.000
66A75ALA0-0.006-0.00415.188-0.047-0.0470.0000.0000.0000.000
67A76ASP-1-0.825-0.90514.128-1.103-1.1030.0000.0000.0000.000
68A77GLN00.0190.00010.035-0.201-0.2010.0000.0000.0000.000
69A78ALA0-0.034-0.02213.502-0.056-0.0560.0000.0000.0000.000
70A79LEU00.0070.00616.2800.0210.0210.0000.0000.0000.000
71A80GLU-1-0.877-0.91012.148-1.193-1.1930.0000.0000.0000.000
72A81ASN0-0.108-0.06411.433-0.221-0.2210.0000.0000.0000.000
73A82GLY0-0.0010.00814.8850.0430.0430.0000.0000.0000.000
74A83VAL0-0.076-0.02717.8020.0790.0790.0000.0000.0000.000
75A84LYS10.9120.94220.2700.4620.4620.0000.0000.0000.000
76A85PRO00.0720.02523.4520.0020.0020.0000.0000.0000.000
77A86SER00.0610.03124.8660.0060.0060.0000.0000.0000.000
78A87GLU-1-0.777-0.87323.139-0.523-0.5230.0000.0000.0000.000
79A88ILE00.0040.01320.2420.0150.0150.0000.0000.0000.000
80A89SER00.0130.00224.2630.0290.0290.0000.0000.0000.000
81A90GLU-1-0.745-0.83927.851-0.248-0.2480.0000.0000.0000.000
82A91THR0-0.044-0.03523.4740.0170.0170.0000.0000.0000.000
83A92ILE0-0.022-0.01125.3150.0220.0220.0000.0000.0000.000
84A93THR00.0010.00528.0250.0280.0280.0000.0000.0000.000
85A94HIS00.0120.00629.1360.0200.0200.0000.0000.0000.000
86A95LEU0-0.002-0.01425.1670.0180.0180.0000.0000.0000.000
87A96ALA00.0000.01229.6900.0160.0160.0000.0000.0000.000
88A97TYR0-0.013-0.01532.6530.0210.0210.0000.0000.0000.000
89A98TYR0-0.0120.00230.8260.0110.0110.0000.0000.0000.000
90A99SER0-0.046-0.01928.3230.0000.0000.0000.0000.0000.000
91A100GLY00.0100.01430.6240.0170.0170.0000.0000.0000.000
92A101TRP00.0650.01632.135-0.013-0.0130.0000.0000.0000.000
93A102GLY0-0.015-0.00533.078-0.010-0.0100.0000.0000.0000.000
94A103LYS10.9000.95827.4880.1510.1510.0000.0000.0000.000
95A104ALA00.0720.05328.079-0.022-0.0220.0000.0000.0000.000
96A105MET00.0060.00529.341-0.020-0.0200.0000.0000.0000.000
97A106ALA0-0.038-0.01127.493-0.005-0.0050.0000.0000.0000.000
98A107THR0-0.037-0.04025.136-0.020-0.0200.0000.0000.0000.000
99A108VAL00.0280.02225.732-0.028-0.0280.0000.0000.0000.000
100A109GLY00.0210.02027.017-0.013-0.0130.0000.0000.0000.000
101A110PRO0-0.007-0.01621.680-0.013-0.0130.0000.0000.0000.000
102A111VAL00.0340.01422.128-0.045-0.0450.0000.0000.0000.000
103A112SER0-0.029-0.01123.494-0.017-0.0170.0000.0000.0000.000
104A113GLU-1-0.841-0.89920.826-0.453-0.4530.0000.0000.0000.000
105A114ALA0-0.019-0.01819.569-0.018-0.0180.0000.0000.0000.000
106A115PHE00.011-0.01120.855-0.029-0.0290.0000.0000.0000.000
107A116ALA00.0140.01423.6960.0010.0010.0000.0000.0000.000
108A117LYS10.8230.90118.9300.5230.5230.0000.0000.0000.000
109A118ARG10.7910.87715.6100.9210.9210.0000.0000.0000.000
110A119GLY0-0.0180.00721.9520.0050.0050.0000.0000.0000.000
111A120ILE0-0.054-0.01923.2190.0090.0090.0000.0000.0000.000
112A121GLY00.0430.02726.4610.0160.0160.0000.0000.0000.000
113A122GLN0-0.002-0.04230.071-0.007-0.0070.0000.0000.0000.000
114A123ASP-1-0.931-0.95732.368-0.305-0.3050.0000.0000.0000.000
115A124GLN0-0.007-0.00827.147-0.023-0.0230.0000.0000.0000.000
116A125LEU0-0.054-0.02128.329-0.025-0.0250.0000.0000.0000.000
117A126ALA0-0.009-0.00830.5290.0060.0060.0000.0000.0000.000
118A127ALA0-0.0220.00232.0500.0120.0120.0000.0000.0000.000
119A128VAL00.003-0.00835.8340.0010.0010.0000.0000.0000.000
120A129GLU-1-0.940-0.96838.186-0.155-0.1550.0000.0000.0000.000
121A130SER0-0.031-0.01936.797-0.001-0.0010.0000.0000.0000.000
122A131THR0-0.011-0.01640.0140.0060.0060.0000.0000.0000.000
123A132PRO00.0200.02339.229-0.011-0.0110.0000.0000.0000.000
124A133LEU0-0.047-0.02834.0660.0000.0000.0000.0000.0000.000
125A134PRO0-0.012-0.02238.7820.0090.0090.0000.0000.0000.000
126A135LEU00.0100.01740.110-0.006-0.0060.0000.0000.0000.000
127A136ASP-1-0.889-0.94341.391-0.135-0.1350.0000.0000.0000.000
128A137GLU-1-0.789-0.92143.094-0.121-0.1210.0000.0000.0000.000
129A138GLU-1-0.954-0.95346.472-0.099-0.0990.0000.0000.0000.000
130A139ALA00.005-0.00542.1280.0050.0050.0000.0000.0000.000
131A140GLU-1-0.774-0.85843.161-0.127-0.1270.0000.0000.0000.000
132A141ALA00.0040.00544.6090.0050.0050.0000.0000.0000.000
133A142GLN00.0090.01445.9530.0090.0090.0000.0000.0000.000
134A143ARG10.7610.85441.1580.1270.1270.0000.0000.0000.000
135A144ALA0-0.002-0.01144.5850.0040.0040.0000.0000.0000.000
136A145THR0-0.014-0.01546.9800.0060.0060.0000.0000.0000.000
137A146THR0-0.063-0.03645.3050.0060.0060.0000.0000.0000.000
138A147VAL0-0.002-0.00843.5030.0040.0040.0000.0000.0000.000
139A148GLY00.0140.01146.6510.0040.0040.0000.0000.0000.000
140A149ASN0-0.027-0.02450.0640.0050.0050.0000.0000.0000.000
141A150GLN0-0.055-0.00245.6610.0000.0000.0000.0000.0000.000
142A151PHE00.008-0.02044.5480.0040.0040.0000.0000.0000.000
143A152GLY00.0290.02649.350-0.001-0.0010.0000.0000.0000.000
144A153SER0-0.044-0.02951.545-0.001-0.0010.0000.0000.0000.000
145A154VAL0-0.041-0.00749.1220.0030.0030.0000.0000.0000.000
146A155ALA00.013-0.00647.5910.0010.0010.0000.0000.0000.000
147A156PRO00.0480.02948.685-0.005-0.0050.0000.0000.0000.000
148A157GLY00.0100.00849.302-0.004-0.0040.0000.0000.0000.000
149A158LEU00.0290.01741.927-0.005-0.0050.0000.0000.0000.000
150A159VAL00.0140.01544.754-0.007-0.0070.0000.0000.0000.000
151A160GLN0-0.049-0.04146.107-0.001-0.0010.0000.0000.0000.000
152A161TYR00.007-0.00143.425-0.004-0.0040.0000.0000.0000.000
153A162THR0-0.043-0.02740.747-0.009-0.0090.0000.0000.0000.000
154A163THR0-0.002-0.00441.845-0.009-0.0090.0000.0000.0000.000
155A164ASP-1-0.847-0.90943.603-0.117-0.1170.0000.0000.0000.000
156A165TYR0-0.022-0.01540.664-0.004-0.0040.0000.0000.0000.000
157A166LEU0-0.0130.00236.731-0.011-0.0110.0000.0000.0000.000
158A167PHE0-0.054-0.04437.589-0.011-0.0110.0000.0000.0000.000
159A168ARG10.8410.92040.3140.1230.1230.0000.0000.0000.000
160A169ASP-1-0.872-0.93439.929-0.178-0.1780.0000.0000.0000.000
161A170LEU0-0.0010.02133.514-0.011-0.0110.0000.0000.0000.000
162A171TRP0-0.092-0.09231.120-0.022-0.0220.0000.0000.0000.000
163A172LEU0-0.047-0.00735.589-0.008-0.0080.0000.0000.0000.000
164A173ARG10.8540.92333.6160.2360.2360.0000.0000.0000.000
165A174PRO00.0210.01633.943-0.014-0.0140.0000.0000.0000.000
166A175ASP-1-0.884-0.93830.915-0.297-0.2970.0000.0000.0000.000
167A176LEU0-0.069-0.03125.612-0.034-0.0340.0000.0000.0000.000
168A177ALA00.0520.03227.9840.0240.0240.0000.0000.0000.000
169A178PRO00.0690.02329.073-0.011-0.0110.0000.0000.0000.000
170A179ARG10.8140.88321.2580.4960.4960.0000.0000.0000.000
171A180ASP-1-0.790-0.88524.333-0.475-0.4750.0000.0000.0000.000
172A181ARG10.8310.90025.6810.2560.2560.0000.0000.0000.000
173A182SER00.0200.01628.2230.0130.0130.0000.0000.0000.000
174A183LEU0-0.0370.00120.5110.0120.0120.0000.0000.0000.000
175A184VAL00.002-0.00622.8380.0020.0020.0000.0000.0000.000
176A185THR0-0.003-0.00824.6410.0210.0210.0000.0000.0000.000
177A186ILE0-0.009-0.01224.2080.0190.0190.0000.0000.0000.000
178A187ALA00.0030.00721.4030.0190.0190.0000.0000.0000.000
179A188ALA00.0180.01823.2340.0190.0190.0000.0000.0000.000
180A189LEU0-0.026-0.00425.4610.0220.0220.0000.0000.0000.000
181A190ILE0-0.010-0.01222.8860.0250.0250.0000.0000.0000.000
182A191SER0-0.045-0.04822.0300.0190.0190.0000.0000.0000.000
183A192VAL0-0.045-0.02123.6350.0170.0170.0000.0000.0000.000
184A193GLY00.0390.03126.6460.0160.0160.0000.0000.0000.000
185A194GLN0-0.0160.00128.4020.0020.0020.0000.0000.0000.000
186A195VAL00.015-0.03029.639-0.012-0.0120.0000.0000.0000.000
187A196GLU-1-0.923-0.94131.722-0.077-0.0770.0000.0000.0000.000
188A197GLN0-0.023-0.02433.123-0.004-0.0040.0000.0000.0000.000
189A198ILE0-0.0060.00327.769-0.013-0.0130.0000.0000.0000.000
190A199THR00.0350.01331.366-0.012-0.0120.0000.0000.0000.000
191A200PHE00.0090.01433.912-0.007-0.0070.0000.0000.0000.000
192A201HIS00.0610.01730.499-0.016-0.0160.0000.0000.0000.000
193A202LEU0-0.0050.01027.113-0.019-0.0190.0000.0000.0000.000
194A203ASN0-0.024-0.03030.164-0.009-0.0090.0000.0000.0000.000
195A204LYS10.9921.01832.7270.1860.1860.0000.0000.0000.000
196A205ALA00.006-0.01027.446-0.011-0.0110.0000.0000.0000.000
197A206LEU0-0.065-0.02727.958-0.015-0.0150.0000.0000.0000.000
198A207ASP-1-0.841-0.89730.325-0.175-0.1750.0000.0000.0000.000
199A208ASN0-0.077-0.03430.4740.0080.0080.0000.0000.0000.000
200A209GLY00.0110.00629.370-0.017-0.0170.0000.0000.0000.000
201A210LEU0-0.085-0.02422.621-0.026-0.0260.0000.0000.0000.000
202A211SER0-0.023-0.03423.0720.0320.0320.0000.0000.0000.000
203A212GLU-1-0.742-0.86324.780-0.176-0.1760.0000.0000.0000.000
204A213GLU-1-0.824-0.88819.955-0.434-0.4340.0000.0000.0000.000
205A214GLN00.0560.02720.123-0.017-0.0170.0000.0000.0000.000
206A215ALA00.0140.00520.462-0.019-0.0190.0000.0000.0000.000
207A216ALA0-0.006-0.00420.8960.0140.0140.0000.0000.0000.000
208A217GLU-1-0.783-0.85214.654-0.489-0.4890.0000.0000.0000.000
209A218VAL0-0.015-0.00117.089-0.025-0.0250.0000.0000.0000.000
210A219ILE0-0.008-0.00718.8420.0090.0090.0000.0000.0000.000
211A220THR0-0.032-0.02414.6960.0600.0600.0000.0000.0000.000
212A221HIS0-0.015-0.01311.5960.0900.0900.0000.0000.0000.000
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