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: 4JJLN

Calculation Name: 4GVP-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 4GVP

Chain ID: A

ChEMBL ID:

UniProt ID: Q7A2Q1

Base Structure: X-ray

Registration Date: 2023-09-21

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 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 208
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2415041.77321
FMO2-HF: Nuclear repulsion 2332271.676568
FMO2-HF: Total energy -82770.096642
FMO2-MP2: Total energy -83009.434714


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:2:THR)


Summations of interaction energy for fragment #1(A:2: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.
-38.412-34.96916.923-10.515-9.849-0.092
Interaction energy analysis for fragmet #1(A:2:THR)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.061 / q_NPA : -0.053
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].
3A4LYS10.8920.9343.808-0.9881.466-0.012-1.110-1.3320.004
4A5VAL0-0.016-0.0145.6200.7700.7700.0000.0000.0000.000
5A6LEU0-0.0290.0078.420-0.084-0.0840.0000.0000.0000.000
6A7PHE0-0.021-0.03111.9120.1230.1230.0000.0000.0000.000
7A8VAL0-0.025-0.01413.9180.0300.0300.0000.0000.0000.000
8A9ASP-1-0.797-0.91117.647-0.391-0.3910.0000.0000.0000.000
9A10ASP-1-0.864-0.92820.339-0.349-0.3490.0000.0000.0000.000
10A11HIS00.0150.02223.249-0.002-0.0020.0000.0000.0000.000
11A12GLU-1-0.833-0.90821.987-0.528-0.5280.0000.0000.0000.000
12A13MET0-0.024-0.02021.147-0.044-0.0440.0000.0000.0000.000
13A14VAL0-0.012-0.00420.306-0.020-0.0200.0000.0000.0000.000
14A15ARG10.8020.87716.6650.5860.5860.0000.0000.0000.000
15A16ILE00.0360.01616.506-0.086-0.0860.0000.0000.0000.000
16A17GLY0-0.004-0.00416.764-0.054-0.0540.0000.0000.0000.000
17A18ILE0-0.018-0.01513.783-0.017-0.0170.0000.0000.0000.000
18A19SER00.008-0.01412.382-0.146-0.1460.0000.0000.0000.000
19A20SER0-0.029-0.00312.158-0.136-0.1360.0000.0000.0000.000
20A21TYR0-0.054-0.02212.4030.0380.0380.0000.0000.0000.000
21A22LEU00.003-0.0078.7320.0300.0300.0000.0000.0000.000
22A23SER00.0140.0108.141-0.199-0.1990.0000.0000.0000.000
23A24THR0-0.113-0.0558.621-0.041-0.0410.0000.0000.0000.000
24A25GLN0-0.042-0.0157.4920.4840.4840.0000.0000.0000.000
25A26SER00.0440.0165.316-0.732-0.664-0.001-0.009-0.0570.000
26A27ASP-1-0.831-0.8862.186-0.5800.3291.714-1.180-1.443-0.005
27A28ILE0-0.034-0.0112.817-2.857-0.9581.022-0.997-1.923-0.018
28A29GLU-1-0.851-0.8961.700-31.151-33.02414.201-7.216-5.112-0.073
29A30VAL0-0.016-0.0164.8270.6100.596-0.001-0.0030.0180.000
30A31VAL0-0.0070.0006.1780.0710.0710.0000.0000.0000.000
31A32GLY00.003-0.0038.7010.3200.3200.0000.0000.0000.000
32A33GLU-1-0.818-0.87612.418-0.994-0.9940.0000.0000.0000.000
33A34GLY0-0.025-0.01515.4640.0530.0530.0000.0000.0000.000
34A35ALA00.0180.00518.904-0.011-0.0110.0000.0000.0000.000
35A36SER00.0350.01921.9780.0430.0430.0000.0000.0000.000
36A37GLY00.0850.00822.237-0.036-0.0360.0000.0000.0000.000
37A38LYS10.9240.95123.0960.2650.2650.0000.0000.0000.000
38A39GLU-1-0.833-0.90920.283-0.511-0.5110.0000.0000.0000.000
39A40ALA00.0030.01318.556-0.046-0.0460.0000.0000.0000.000
40A41ILE0-0.011-0.01418.562-0.026-0.0260.0000.0000.0000.000
41A42ALA0-0.047-0.02019.894-0.003-0.0030.0000.0000.0000.000
42A43LYS10.8910.91815.5470.6260.6260.0000.0000.0000.000
43A44ALA00.0120.01915.189-0.077-0.0770.0000.0000.0000.000
44A45HIS0-0.007-0.01115.479-0.019-0.0190.0000.0000.0000.000
45A46GLU-1-0.968-0.97416.454-0.501-0.5010.0000.0000.0000.000
46A47LEU0-0.031-0.02611.1990.0020.0020.0000.0000.0000.000
47A48LYS10.7780.90011.0790.3360.3360.0000.0000.0000.000
48A49PRO0-0.0320.0029.323-0.044-0.0440.0000.0000.0000.000
49A50ASP-1-0.783-0.8815.565-1.685-1.6850.0000.0000.0000.000
50A51LEU0-0.046-0.0248.7960.2750.2750.0000.0000.0000.000
51A52ILE00.0070.00410.753-0.173-0.1730.0000.0000.0000.000
52A53LEU0-0.0350.00212.5450.1030.1030.0000.0000.0000.000
53A54MET0-0.018-0.01914.392-0.024-0.0240.0000.0000.0000.000
54A55ASP-1-0.747-0.87918.046-0.299-0.2990.0000.0000.0000.000
55A56LEU0-0.043-0.01921.2880.0110.0110.0000.0000.0000.000
56A57LEU0-0.032-0.02324.3140.0160.0160.0000.0000.0000.000
57A58MET00.0230.03022.185-0.028-0.0280.0000.0000.0000.000
58A59GLU-1-0.935-0.96126.464-0.229-0.2290.0000.0000.0000.000
59A60ASP-1-0.826-0.90726.844-0.284-0.2840.0000.0000.0000.000
60A61MET0-0.061-0.01226.2890.0140.0140.0000.0000.0000.000
61A62ASP-1-0.741-0.84227.021-0.218-0.2180.0000.0000.0000.000
62A63GLY00.042-0.00523.270-0.010-0.0100.0000.0000.0000.000
63A64VAL0-0.019-0.00323.231-0.012-0.0120.0000.0000.0000.000
64A65GLU-1-0.872-0.92525.656-0.183-0.1830.0000.0000.0000.000
65A66ALA00.0420.01022.199-0.001-0.0010.0000.0000.0000.000
66A67THR0-0.047-0.04220.413-0.024-0.0240.0000.0000.0000.000
67A68THR0-0.004-0.00422.0620.0100.0100.0000.0000.0000.000
68A69GLN0-0.057-0.03824.4740.0150.0150.0000.0000.0000.000
69A70ILE00.0070.01117.9440.0010.0010.0000.0000.0000.000
70A71LYS10.7970.87916.7710.2740.2740.0000.0000.0000.000
71A72LYS10.8020.90920.7400.2180.2180.0000.0000.0000.000
72A73ASP-1-0.911-0.95721.795-0.177-0.1770.0000.0000.0000.000
73A74LEU0-0.092-0.05016.6320.0090.0090.0000.0000.0000.000
74A75PRO00.0340.01417.334-0.035-0.0350.0000.0000.0000.000
75A76GLN0-0.057-0.03313.4170.0090.0090.0000.0000.0000.000
76A77ILE0-0.0120.02412.679-0.022-0.0220.0000.0000.0000.000
77A78LYS10.8890.94112.0960.2390.2390.0000.0000.0000.000
78A79VAL00.0140.00313.965-0.102-0.1020.0000.0000.0000.000
79A80LEU0-0.024-0.01313.4490.0750.0750.0000.0000.0000.000
80A81MET0-0.038-0.00816.282-0.031-0.0310.0000.0000.0000.000
81A82LEU00.0090.00216.5000.0290.0290.0000.0000.0000.000
82A83THR00.0490.01320.3110.0000.0000.0000.0000.0000.000
83A84SER00.0010.01423.967-0.002-0.0020.0000.0000.0000.000
84A85PHE00.001-0.00426.7760.0140.0140.0000.0000.0000.000
85A86ILE00.0080.00525.297-0.008-0.0080.0000.0000.0000.000
86A87GLU-1-0.825-0.89729.057-0.115-0.1150.0000.0000.0000.000
87A88ASP-1-0.812-0.89630.817-0.085-0.0850.0000.0000.0000.000
88A89LYS10.8010.87031.1040.1150.1150.0000.0000.0000.000
89A90GLU-1-0.770-0.86229.417-0.141-0.1410.0000.0000.0000.000
90A91VAL00.0010.00125.390-0.010-0.0100.0000.0000.0000.000
91A92TYR0-0.017-0.03627.1510.0010.0010.0000.0000.0000.000
92A93ARG10.7960.88329.2080.1660.1660.0000.0000.0000.000
93A94ALA00.0310.01024.304-0.004-0.0040.0000.0000.0000.000
94A95LEU0-0.034-0.01623.766-0.004-0.0040.0000.0000.0000.000
95A96ASP-1-0.854-0.91525.260-0.083-0.0830.0000.0000.0000.000
96A97ALA0-0.038-0.01025.3060.0050.0050.0000.0000.0000.000
97A98GLY00.005-0.00622.150-0.014-0.0140.0000.0000.0000.000
98A99VAL0-0.036-0.00920.142-0.021-0.0210.0000.0000.0000.000
99A100ASP-1-0.756-0.84616.668-0.204-0.2040.0000.0000.0000.000
100A101SER0-0.0160.00316.8160.0520.0520.0000.0000.0000.000
101A102TYR00.0170.01118.831-0.034-0.0340.0000.0000.0000.000
102A103ILE0-0.020-0.01217.2750.0350.0350.0000.0000.0000.000
103A104LEU00.0340.01721.524-0.022-0.0220.0000.0000.0000.000
104A105LYS10.7800.87820.6140.3510.3510.0000.0000.0000.000
105A106THR0-0.011-0.01221.497-0.017-0.0170.0000.0000.0000.000
106A107THR0-0.068-0.03318.7660.0270.0270.0000.0000.0000.000
107A108SER0-0.027-0.04019.368-0.041-0.0410.0000.0000.0000.000
108A109ALA00.0940.02515.556-0.009-0.0090.0000.0000.0000.000
109A110LYS10.9040.94614.5600.0410.0410.0000.0000.0000.000
110A111ASP-1-0.853-0.89814.607-0.126-0.1260.0000.0000.0000.000
111A112ILE00.0180.01913.3310.0110.0110.0000.0000.0000.000
112A113ALA00.0310.02010.296-0.047-0.0470.0000.0000.0000.000
113A114ASP-1-0.938-0.97610.5540.0670.0670.0000.0000.0000.000
114A115ALA00.001-0.00212.4630.0590.0590.0000.0000.0000.000
115A116VAL00.0210.0148.1040.0220.0220.0000.0000.0000.000
116A117ARG10.7730.8467.2080.0400.0400.0000.0000.0000.000
117A118LYS10.8060.8929.0470.0150.0150.0000.0000.0000.000
118A119THR00.016-0.00812.3450.0400.0400.0000.0000.0000.000
119A120SER0-0.054-0.0317.9260.0430.0430.0000.0000.0000.000
120A121ARG10.8470.9269.527-0.337-0.3370.0000.0000.0000.000
121A122GLY0-0.032-0.01011.2000.0600.0600.0000.0000.0000.000
122A123GLU-1-0.840-0.88514.1090.2010.2010.0000.0000.0000.000
123A124SER0-0.011-0.02016.069-0.043-0.0430.0000.0000.0000.000
124A125VAL0-0.072-0.04315.6810.0380.0380.0000.0000.0000.000
125A126PHE00.027-0.01218.843-0.025-0.0250.0000.0000.0000.000
126A127GLU-1-0.773-0.88822.158-0.152-0.1520.0000.0000.0000.000
127A128PRO00.005-0.01123.4690.0160.0160.0000.0000.0000.000
128A129GLU-1-0.947-0.96925.889-0.067-0.0670.0000.0000.0000.000
129A130VAL0-0.030-0.01226.5630.0060.0060.0000.0000.0000.000
130A131LEU0-0.0020.01523.0570.0050.0050.0000.0000.0000.000
131A132VAL00.005-0.01026.4770.0060.0060.0000.0000.0000.000
132A133LYS10.8570.91029.3640.0730.0730.0000.0000.0000.000
133A134MET00.0250.03125.7350.0030.0030.0000.0000.0000.000
134A135ARG10.9720.98421.877-0.021-0.0210.0000.0000.0000.000
135A136ASN0-0.026-0.01626.9030.0130.0130.0000.0000.0000.000
136A137ARG10.8120.90329.2570.0580.0580.0000.0000.0000.000
137A138MET00.011-0.00221.674-0.001-0.0010.0000.0000.0000.000
138A139LYS10.8830.93127.354-0.026-0.0260.0000.0000.0000.000
139A140LYS10.8560.90429.3060.0010.0010.0000.0000.0000.000
140A141ARG10.8830.93826.0050.0760.0760.0000.0000.0000.000
141A142ALA00.0230.02927.0480.0010.0010.0000.0000.0000.000
142A143GLU-1-0.788-0.86328.8090.0220.0220.0000.0000.0000.000
143A144LEU0-0.056-0.00532.0120.0020.0020.0000.0000.0000.000
144A145TYR00.010-0.01128.4990.0020.0020.0000.0000.0000.000
145A146GLU-1-0.932-0.96132.9610.0380.0380.0000.0000.0000.000
146A147MET0-0.028-0.00835.1600.0030.0030.0000.0000.0000.000
147A148LEU0-0.093-0.03633.450-0.004-0.0040.0000.0000.0000.000
148A149THR0-0.015-0.04437.6060.0050.0050.0000.0000.0000.000
149A150GLU-1-0.884-0.95337.7530.0330.0330.0000.0000.0000.000
150A151ARG10.8300.90537.689-0.007-0.0070.0000.0000.0000.000
151A152GLU-1-0.808-0.86937.549-0.009-0.0090.0000.0000.0000.000
152A153MET00.0450.03731.335-0.006-0.0060.0000.0000.0000.000
153A154GLU-1-0.813-0.89633.3600.0130.0130.0000.0000.0000.000
154A155ILE0-0.048-0.03434.099-0.004-0.0040.0000.0000.0000.000
155A156LEU00.0100.01130.192-0.007-0.0070.0000.0000.0000.000
156A157LEU00.0370.02728.232-0.008-0.0080.0000.0000.0000.000
157A158LEU0-0.037-0.01829.697-0.005-0.0050.0000.0000.0000.000
158A159ILE0-0.039-0.03330.769-0.008-0.0080.0000.0000.0000.000
159A160ALA00.0150.01326.433-0.010-0.0100.0000.0000.0000.000
160A161LYS10.8730.93726.534-0.011-0.0110.0000.0000.0000.000
161A162GLY00.0280.02627.981-0.004-0.0040.0000.0000.0000.000
162A163TYR0-0.0360.00029.4700.0030.0030.0000.0000.0000.000
163A164SER00.009-0.02833.026-0.003-0.0030.0000.0000.0000.000
164A165ASN00.052-0.00735.8650.0040.0040.0000.0000.0000.000
165A166GLN00.0260.00638.9060.0070.0070.0000.0000.0000.000
166A167GLU-1-0.774-0.83935.301-0.040-0.0400.0000.0000.0000.000
167A168ILE00.0040.00834.9860.0060.0060.0000.0000.0000.000
168A169ALA0-0.041-0.02438.1830.0050.0050.0000.0000.0000.000
169A170SER00.000-0.00540.4730.0030.0030.0000.0000.0000.000
170A171ALA0-0.046-0.00837.4650.0040.0040.0000.0000.0000.000
171A172SER0-0.034-0.02539.0680.0050.0050.0000.0000.0000.000
172A173HIS0-0.0030.00441.2480.0000.0000.0000.0000.0000.000
173A174ILE0-0.0160.00541.8370.0000.0000.0000.0000.0000.000
174A175THR00.0330.01645.433-0.003-0.0030.0000.0000.0000.000
175A176ILE00.0860.02943.1160.0000.0000.0000.0000.0000.000
176A177LYS10.9520.97944.3700.0210.0210.0000.0000.0000.000
177A178THR00.0220.00244.818-0.001-0.0010.0000.0000.0000.000
178A179VAL00.0270.02839.5010.0000.0000.0000.0000.0000.000
179A180LYS10.9160.95241.0060.0420.0420.0000.0000.0000.000
180A181THR0-0.042-0.02242.108-0.002-0.0020.0000.0000.0000.000
181A182HIS00.0510.02339.719-0.001-0.0010.0000.0000.0000.000
182A183VAL0-0.001-0.00136.4080.0000.0000.0000.0000.0000.000
183A184SER0-0.0020.00037.939-0.004-0.0040.0000.0000.0000.000
184A185ASN0-0.035-0.02340.097-0.003-0.0030.0000.0000.0000.000
185A186ILE00.0200.00934.3240.0010.0010.0000.0000.0000.000
186A187LEU0-0.023-0.00433.9730.0000.0000.0000.0000.0000.000
187A188SER0-0.018-0.00236.147-0.002-0.0020.0000.0000.0000.000
188A189LYS10.8020.88137.2470.0060.0060.0000.0000.0000.000
189A190LEU0-0.040-0.01330.9800.0030.0030.0000.0000.0000.000
190A191GLU-1-0.856-0.89932.969-0.045-0.0450.0000.0000.0000.000
191A192VAL0-0.028-0.00530.420-0.007-0.0070.0000.0000.0000.000
192A193GLN00.007-0.00933.5810.0100.0100.0000.0000.0000.000
193A194ASP-1-0.855-0.93032.175-0.108-0.1080.0000.0000.0000.000
194A195ARG10.8610.90132.0830.0610.0610.0000.0000.0000.000
195A196THR00.010-0.00527.2060.0050.0050.0000.0000.0000.000
196A197GLN00.0900.03927.7230.0060.0060.0000.0000.0000.000
197A198ALA0-0.0020.01528.2550.0050.0050.0000.0000.0000.000
198A199VAL0-0.047-0.02225.1450.0100.0100.0000.0000.0000.000
199A200ILE00.0230.01522.7240.0100.0100.0000.0000.0000.000
200A201TYR0-0.033-0.03423.7810.0070.0070.0000.0000.0000.000
201A202ALA00.0190.00525.3050.0120.0120.0000.0000.0000.000
202A203PHE00.013-0.00420.5140.0150.0150.0000.0000.0000.000
203A204GLN0-0.0270.00219.262-0.003-0.0030.0000.0000.0000.000
204A205HIS0-0.089-0.04221.3510.0130.0130.0000.0000.0000.000
205A206ASN0-0.056-0.02520.4030.0140.0140.0000.0000.0000.000
206A207LEU0-0.0030.01122.2730.0150.0150.0000.0000.0000.000
207A208ILE0-0.018-0.01023.4340.0060.0060.0000.0000.0000.000
208A209GLN0-0.033-0.01018.757-0.001-0.0010.0000.0000.0000.000