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: LZM99

Calculation Name: 4GIW-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 4GIW

Chain ID: A

ChEMBL ID:

UniProt ID: Q9BVN2

Base Structure: X-ray

Registration Date: 2023-06-21

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 OptAll
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 184
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -1896705.789552
FMO2-HF: Nuclear repulsion 1827572.03606
FMO2-HF: Total energy -69133.753492
FMO2-MP2: Total energy -69338.330698


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:7:GLN)


Summations of interaction energy for fragment #1(A:7: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.
-17.958-12.3274.396-3.765-6.2610.034
Interaction energy analysis for fragmet #1(A:7:GLN)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.086 / q_NPA : 0.041
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].
3A9LYS10.8620.8992.229-19.198-14.3924.387-3.532-5.6610.033
4A10GLY00.0210.0193.249-2.156-1.6340.011-0.217-0.3160.001
5A11LEU0-0.017-0.0085.1830.0150.192-0.001-0.012-0.1640.000
6A12LEU00.0340.0166.822-0.129-0.1290.0000.0000.0000.000
7A13ILE00.0160.0175.989-0.317-0.3170.0000.0000.0000.000
8A14ALA0-0.0040.0069.027-0.087-0.0870.0000.0000.0000.000
9A15VAL00.0060.00911.068-0.038-0.0380.0000.0000.0000.000
10A16SER0-0.0010.00111.894-0.053-0.0530.0000.0000.0000.000
11A17VAL00.0080.00212.853-0.061-0.0610.0000.0000.0000.000
12A18SER0-0.057-0.04615.012-0.068-0.0680.0000.0000.0000.000
13A19VAL00.002-0.00316.619-0.032-0.0320.0000.0000.0000.000
14A20ASP-1-0.841-0.91815.9190.1720.1720.0000.0000.0000.000
15A21LYS10.8940.95617.907-0.007-0.0070.0000.0000.0000.000
16A22ILE00.0080.00520.526-0.011-0.0110.0000.0000.0000.000
17A23ILE00.001-0.00621.544-0.012-0.0120.0000.0000.0000.000
18A24SER0-0.005-0.00723.380-0.018-0.0180.0000.0000.0000.000
19A25HIS0-0.071-0.02525.290-0.017-0.0170.0000.0000.0000.000
20A26PHE00.0290.00026.576-0.005-0.0050.0000.0000.0000.000
21A27GLY0-0.012-0.00227.9700.0000.0000.0000.0000.0000.000
22A28ALA0-0.0010.00729.396-0.005-0.0050.0000.0000.0000.000
23A29ALA0-0.0120.02332.574-0.005-0.0050.0000.0000.0000.000
24A30ARG10.9900.99433.804-0.048-0.0480.0000.0000.0000.000
25A31ASN0-0.021-0.01936.3870.0030.0030.0000.0000.0000.000
26A32LEU00.1060.03334.0480.0000.0000.0000.0000.0000.000
27A33VAL00.0280.03035.4900.0050.0050.0000.0000.0000.000
28A34GLN00.012-0.01036.8230.0020.0020.0000.0000.0000.000
29A35LYS10.8580.91530.654-0.105-0.1050.0000.0000.0000.000
30A36ALA00.0130.01432.4530.0060.0060.0000.0000.0000.000
31A37GLN0-0.010-0.01434.2720.0060.0060.0000.0000.0000.000
32A38LEU0-0.020-0.00531.249-0.003-0.0030.0000.0000.0000.000
33A39GLY00.0620.02230.2480.0030.0030.0000.0000.0000.000
34A40ASP-1-0.856-0.91431.1980.0980.0980.0000.0000.0000.000
35A41SER0-0.011-0.00931.888-0.003-0.0030.0000.0000.0000.000
36A42ARG10.7910.85833.404-0.096-0.0960.0000.0000.0000.000
37A43LEU0-0.048-0.02036.878-0.007-0.0070.0000.0000.0000.000
38A44SER00.0080.01331.868-0.008-0.0080.0000.0000.0000.000
39A45PRO00.0370.02432.0750.0070.0070.0000.0000.0000.000
40A46ASP-1-0.878-0.95129.7840.0400.0400.0000.0000.0000.000
41A47VAL0-0.042-0.00427.2100.0030.0030.0000.0000.0000.000
42A48GLY00.0340.01026.5860.0160.0160.0000.0000.0000.000
43A49HIS00.0160.00726.4250.0100.0100.0000.0000.0000.000
44A50LEU00.0170.03821.954-0.005-0.0050.0000.0000.0000.000
45A51VAL00.0080.01122.3910.0090.0090.0000.0000.0000.000
46A52LEU00.008-0.00121.7400.0220.0220.0000.0000.0000.000
47A53THR0-0.069-0.05221.141-0.010-0.0100.0000.0000.0000.000
48A54THR0-0.085-0.05217.956-0.022-0.0220.0000.0000.0000.000
49A55LEU00.0630.03016.8350.0160.0160.0000.0000.0000.000
50A56CYS0-0.035-0.00517.5450.0580.0580.0000.0000.0000.000
51A57PRO0-0.020-0.02116.4420.0330.0330.0000.0000.0000.000
52A58ALA00.0250.02713.165-0.003-0.0030.0000.0000.0000.000
53A59LEU00.0220.00312.8940.1100.1100.0000.0000.0000.000
54A60HIS0-0.026-0.00414.8490.0340.0340.0000.0000.0000.000
55A61ALA0-0.004-0.01210.4000.0190.0190.0000.0000.0000.000
56A62LEU0-0.017-0.0099.4220.0150.0150.0000.0000.0000.000
57A63VAL0-0.0100.00811.2230.1600.1600.0000.0000.0000.000
58A64ALA00.0180.01212.235-0.009-0.0090.0000.0000.0000.000
59A65ASP-1-0.810-0.8796.3701.2491.2490.0000.0000.0000.000
60A66GLY00.0350.0079.4450.2080.2080.0000.0000.0000.000
61A67LEU0-0.0350.00010.547-0.010-0.0100.0000.0000.0000.000
62A68LYS10.8580.92414.207-0.468-0.4680.0000.0000.0000.000
63A69PRO00.0150.00416.302-0.013-0.0130.0000.0000.0000.000
64A70PHE0-0.006-0.01517.990-0.028-0.0280.0000.0000.0000.000
65A71ARG10.8990.95321.546-0.174-0.1740.0000.0000.0000.000
66A72LYS10.9380.94923.920-0.170-0.1700.0000.0000.0000.000
67A73ASP-1-0.817-0.90127.5460.1310.1310.0000.0000.0000.000
68A74LEU00.0220.00730.472-0.004-0.0040.0000.0000.0000.000
69A75ILE0-0.0150.01233.570-0.006-0.0060.0000.0000.0000.000
70A76THR00.013-0.00530.402-0.009-0.0090.0000.0000.0000.000
71A77GLY00.0190.03431.269-0.002-0.0020.0000.0000.0000.000
72A78GLN0-0.043-0.04325.8900.0210.0210.0000.0000.0000.000
73A79ARG10.9000.95325.661-0.140-0.1400.0000.0000.0000.000
74A80ARG10.8870.93217.754-0.113-0.1130.0000.0000.0000.000
75A81SER00.0180.02218.7980.0010.0010.0000.0000.0000.000
76A82SER0-0.013-0.02318.466-0.024-0.0240.0000.0000.0000.000
77A83PRO00.0690.02215.7930.0110.0110.0000.0000.0000.000
78A84TRP00.0300.01318.3760.0200.0200.0000.0000.0000.000
79A85SER0-0.057-0.04121.499-0.001-0.0010.0000.0000.0000.000
80A86VAL00.0240.02617.353-0.005-0.0050.0000.0000.0000.000
81A87VAL0-0.0160.02220.8200.0120.0120.0000.0000.0000.000
82A88GLU-1-0.819-0.89723.6820.1920.1920.0000.0000.0000.000
83A89ALA0-0.045-0.01123.257-0.013-0.0130.0000.0000.0000.000
84A90SER00.016-0.01222.758-0.007-0.0070.0000.0000.0000.000
85A91VAL0-0.096-0.04224.909-0.006-0.0060.0000.0000.0000.000
86A92LYS10.9660.98228.045-0.191-0.1910.0000.0000.0000.000
87A93PRO0-0.054-0.01128.819-0.018-0.0180.0000.0000.0000.000
88A94GLY00.0940.05629.844-0.010-0.0100.0000.0000.0000.000
89A95SER0-0.052-0.04729.8350.0040.0040.0000.0000.0000.000
90A96SER0-0.003-0.00325.193-0.020-0.0200.0000.0000.0000.000
91A97THR00.0970.04828.142-0.011-0.0110.0000.0000.0000.000
92A98ARG11.0160.99930.522-0.167-0.1670.0000.0000.0000.000
93A99SER00.0070.01630.762-0.014-0.0140.0000.0000.0000.000
94A100LEU00.0290.02325.551-0.007-0.0070.0000.0000.0000.000
95A101GLY00.0380.01229.275-0.005-0.0050.0000.0000.0000.000
96A102THR0-0.063-0.03531.974-0.015-0.0150.0000.0000.0000.000
97A103LEU00.0320.05027.436-0.013-0.0130.0000.0000.0000.000
98A104TYR00.0350.01227.670-0.014-0.0140.0000.0000.0000.000
99A105SER0-0.046-0.03730.390-0.017-0.0170.0000.0000.0000.000
100A106GLN0-0.033-0.02433.008-0.005-0.0050.0000.0000.0000.000
101A107VAL00.0210.00327.436-0.010-0.0100.0000.0000.0000.000
102A108SER0-0.011-0.00930.917-0.010-0.0100.0000.0000.0000.000
103A109ARG10.8810.94231.988-0.136-0.1360.0000.0000.0000.000
104A110LEU0-0.052-0.00832.729-0.008-0.0080.0000.0000.0000.000
105A111ALA00.000-0.01030.632-0.001-0.0010.0000.0000.0000.000
106A112PRO0-0.013-0.00332.6510.0010.0010.0000.0000.0000.000
107A113LEU00.0390.01732.782-0.001-0.0010.0000.0000.0000.000
108A114SER00.0290.03229.410-0.006-0.0060.0000.0000.0000.000
109A115SER00.0600.03324.3850.0140.0140.0000.0000.0000.000
110A116SER00.020-0.01022.9690.0060.0060.0000.0000.0000.000
111A117ARG10.8780.94816.851-0.061-0.0610.0000.0000.0000.000
112A118SER00.051-0.00922.1930.0170.0170.0000.0000.0000.000
113A119ARG10.8600.93925.430-0.135-0.1350.0000.0000.0000.000
114A120PHE0-0.019-0.00717.6010.0050.0050.0000.0000.0000.000
115A121HIS00.0460.00818.9460.0470.0470.0000.0000.0000.000
116A122ALA00.0550.03023.1450.0100.0100.0000.0000.0000.000
117A123PHE00.002-0.00923.310-0.002-0.0020.0000.0000.0000.000
118A124ILE00.0100.00119.6910.0170.0170.0000.0000.0000.000
119A125LEU00.0150.00923.4530.0060.0060.0000.0000.0000.000
120A126GLY00.0460.01226.673-0.005-0.0050.0000.0000.0000.000
121A127LEU0-0.058-0.01522.1130.0010.0010.0000.0000.0000.000
122A128LEU0-0.0170.00322.3960.0150.0150.0000.0000.0000.000
123A129ASN0-0.022-0.01025.679-0.003-0.0030.0000.0000.0000.000
124A130THR0-0.068-0.04428.314-0.002-0.0020.0000.0000.0000.000
125A131LYS10.8360.92625.525-0.219-0.2190.0000.0000.0000.000
126A132GLN00.004-0.02024.7920.0120.0120.0000.0000.0000.000
127A133LEU00.0140.01419.5420.0220.0220.0000.0000.0000.000
128A134GLU-1-0.840-0.92818.8730.5240.5240.0000.0000.0000.000
129A135LEU00.0060.01119.8600.0390.0390.0000.0000.0000.000
130A136TRP0-0.002-0.00318.9280.0210.0210.0000.0000.0000.000
131A137PHE00.035-0.01316.0010.0270.0270.0000.0000.0000.000
132A138SER00.0180.01217.4620.0610.0610.0000.0000.0000.000
133A139SER0-0.044-0.03419.272-0.028-0.0280.0000.0000.0000.000
134A140LEU0-0.041-0.01516.864-0.028-0.0280.0000.0000.0000.000
135A141GLN0-0.0520.00114.4250.1610.1610.0000.0000.0000.000
136A142GLU-1-0.875-0.94717.6110.5970.5970.0000.0000.0000.000
137A143ASP-1-0.839-0.89721.0840.3380.3380.0000.0000.0000.000
138A144ALA0-0.009-0.02719.9970.0340.0340.0000.0000.0000.000
139A145GLY0-0.0020.00921.077-0.004-0.0040.0000.0000.0000.000
140A146LEU0-0.007-0.00819.655-0.007-0.0070.0000.0000.0000.000
141A147LEU0-0.005-0.00815.7560.0080.0080.0000.0000.0000.000
142A148SER0-0.0240.00118.1100.0100.0100.0000.0000.0000.000
143A149LEU0-0.035-0.01720.276-0.028-0.0280.0000.0000.0000.000
144A150MET0-0.048-0.02818.640-0.029-0.0290.0000.0000.0000.000
145A151TYR0-0.032-0.02312.737-0.004-0.0040.0000.0000.0000.000
146A152MET0-0.0020.01112.106-0.074-0.0740.0000.0000.0000.000
147A153PRO00.0350.01613.0490.1250.1250.0000.0000.0000.000
148A154THR00.0210.0108.3430.1010.1010.0000.0000.0000.000
149A155GLY00.0290.0138.0930.3090.3090.0000.0000.0000.000
150A156PHE00.0170.0086.9920.1930.1930.0000.0000.0000.000
151A157PHE00.0530.0069.4160.1710.1710.0000.0000.0000.000
152A158SER0-0.052-0.01612.342-0.190-0.1900.0000.0000.0000.000
153A159LEU0-0.001-0.0106.492-0.028-0.0280.0000.0000.0000.000
154A160ALA0-0.039-0.0149.9010.0490.0490.0000.0000.0000.000
155A161ARG10.8710.94010.719-0.993-0.9930.0000.0000.0000.000
156A162GLY00.0460.02611.778-0.224-0.2240.0000.0000.0000.000
157A163GLY0-0.012-0.00710.3210.3740.3740.0000.0000.0000.000
158A164CYS0-0.020-0.00611.191-0.093-0.0930.0000.0000.0000.000
159A165PRO00.0440.02210.808-0.144-0.1440.0000.0000.0000.000
160A166SER00.0130.03410.4140.2190.2190.0000.0000.0000.000
161A167LEU00.0360.0004.5430.1250.251-0.001-0.004-0.1200.000
162A168SER0-0.024-0.0148.549-0.218-0.2180.0000.0000.0000.000
163A169THR00.013-0.00912.180-0.223-0.2230.0000.0000.0000.000
164A170GLU-1-0.811-0.8887.2473.6253.6250.0000.0000.0000.000
165A171LEU0-0.010-0.00111.036-0.183-0.1830.0000.0000.0000.000
166A172LEU0-0.002-0.00612.241-0.221-0.2210.0000.0000.0000.000
167A173LEU0-0.003-0.00314.157-0.125-0.1250.0000.0000.0000.000
168A174LEU0-0.025-0.01710.582-0.097-0.0970.0000.0000.0000.000
169A175LEU0-0.020-0.00614.931-0.113-0.1130.0000.0000.0000.000
170A176GLN00.0550.03717.640-0.063-0.0630.0000.0000.0000.000
171A177PRO0-0.0050.01018.869-0.057-0.0570.0000.0000.0000.000
172A178LEU00.0290.00119.644-0.047-0.0470.0000.0000.0000.000
173A179SER0-0.047-0.02622.987-0.036-0.0360.0000.0000.0000.000
174A180VAL0-0.002-0.00125.023-0.023-0.0230.0000.0000.0000.000
175A181LEU0-0.0590.00424.573-0.025-0.0250.0000.0000.0000.000
176A182THR0-0.031-0.03228.1560.0140.0140.0000.0000.0000.000
177A183PHE00.0290.00524.672-0.008-0.0080.0000.0000.0000.000
178A184HIS0-0.033-0.01730.2700.0110.0110.0000.0000.0000.000
179A185LEU00.0300.01627.010-0.012-0.0120.0000.0000.0000.000
180A186ASP-1-0.759-0.85431.3430.1040.1040.0000.0000.0000.000
181A187LEU0-0.026-0.02429.747-0.001-0.0010.0000.0000.0000.000
182A188LEU00.007-0.00430.0820.0040.0040.0000.0000.0000.000
183A189PHE0-0.037-0.00429.233-0.007-0.0070.0000.0000.0000.000
184A190GLU-1-0.890-0.91725.0900.0840.0840.0000.0000.0000.000