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

tag_button

FMODB ID: NNJVQ

Calculation Name: 2VPI-A-Xray372

Preferred Name: GMP synthase [glutamine-hydrolyzing]

Target Type: SINGLE PROTEIN

Ligand Name:

ligand 3-letter code:

PDB ID: 2VPI

Chain ID: A

ChEMBL ID: CHEMBL5721

UniProt ID: P49915

Base Structure: X-ray

Registration Date: 2023-09-23

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 187
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -1990781.030577
FMO2-HF: Nuclear repulsion 1919499.613548
FMO2-HF: Total energy -71281.417029
FMO2-MP2: Total energy -71488.880097


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:24:MET)


Summations of interaction energy for fragment #1(A:24:MET)
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.
-2.1782.7038.256-6.182-6.951-0.024
Interaction energy analysis for fragmet #1(A:24:MET)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.029 / q_NPA : 0.012
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].
3A26GLY0-0.099-0.0523.770-0.7710.988-0.015-0.883-0.8600.005
4A27ALA00.0070.0262.9190.7731.3080.067-0.195-0.4060.000
5A28VAL0-0.039-0.0384.9160.1580.196-0.001-0.007-0.0310.000
6A29VAL00.0240.0285.8580.1320.1320.0000.0000.0000.000
7A30ILE0-0.047-0.0257.5020.1020.1020.0000.0000.0000.000
8A31LEU0-0.0010.00410.5780.1390.1390.0000.0000.0000.000
9A32ASP-1-0.805-0.92313.411-0.138-0.1380.0000.0000.0000.000
10A33ALA0-0.022-0.01316.7610.0460.0460.0000.0000.0000.000
11A34GLY0-0.0010.00719.9670.0140.0140.0000.0000.0000.000
12A35ALA00.018-0.00821.3850.0140.0140.0000.0000.0000.000
13A36GLN0-0.024-0.02020.4900.0140.0140.0000.0000.0000.000
14A37TYR0-0.0220.00217.755-0.002-0.0020.0000.0000.0000.000
15A38GLY00.0740.02514.9320.0220.0220.0000.0000.0000.000
16A39LYS10.9600.97315.336-0.114-0.1140.0000.0000.0000.000
17A40VAL0-0.022-0.00817.167-0.027-0.0270.0000.0000.0000.000
18A41ILE00.0480.01014.160-0.022-0.0220.0000.0000.0000.000
19A42ASP-1-0.781-0.86911.343-0.394-0.3940.0000.0000.0000.000
20A43ARG10.9240.97113.8600.1210.1210.0000.0000.0000.000
21A44ARG10.7490.87416.5660.2200.2200.0000.0000.0000.000
22A45VAL00.0450.01210.504-0.010-0.0100.0000.0000.0000.000
23A46ARG10.9600.97711.0230.1970.1970.0000.0000.0000.000
24A47GLU-1-0.877-0.94513.828-0.276-0.2760.0000.0000.0000.000
25A48LEU0-0.064-0.02115.3240.0390.0390.0000.0000.0000.000
26A49PHE0-0.0180.00414.032-0.035-0.0350.0000.0000.0000.000
27A50VAL00.0060.0139.133-0.083-0.0830.0000.0000.0000.000
28A51GLN0-0.033-0.0183.465-1.206-0.9150.004-0.100-0.1950.000
29A52SER0-0.056-0.0666.886-0.482-0.4820.0000.0000.0000.000
30A53GLU-1-0.859-0.9194.2610.6410.785-0.001-0.011-0.1320.000
31A54ILE0-0.050-0.0207.231-0.159-0.1590.0000.0000.0000.000
32A55PHE0-0.021-0.0145.7700.1290.1290.0000.0000.0000.000
33A56PRO00.0380.02510.617-0.128-0.1280.0000.0000.0000.000
34A57LEU00.0150.03213.186-0.008-0.0080.0000.0000.0000.000
35A58GLU-1-0.933-0.97615.4440.2690.2690.0000.0000.0000.000
36A59THR0-0.061-0.0569.4170.1050.1050.0000.0000.0000.000
37A60PRO0-0.015-0.00312.267-0.108-0.1080.0000.0000.0000.000
38A61ALA00.008-0.02211.3380.0620.0620.0000.0000.0000.000
39A62PHE0-0.031-0.02310.902-0.097-0.0970.0000.0000.0000.000
40A63ALA00.0610.0399.4430.0470.0470.0000.0000.0000.000
41A64ILE00.0430.0196.4380.4160.4160.0000.0000.0000.000
42A65LYS10.8900.9296.147-0.381-0.3810.0000.0000.0000.000
43A66GLU-1-0.954-0.9867.2550.8840.8840.0000.0000.0000.000
44A67GLN0-0.0020.0033.030-2.413-1.2160.074-0.396-0.8740.001
45A68GLY00.0110.0192.080-0.645-1.0177.952-4.166-3.413-0.027
46A69PHE0-0.0120.0133.411-3.645-2.4730.177-0.413-0.936-0.003
47A70ARG10.9130.9594.4562.9713.088-0.001-0.011-0.1040.000
48A71ALA0-0.025-0.0217.6470.5610.5610.0000.0000.0000.000
49A72ILE00.0100.0138.256-0.238-0.2380.0000.0000.0000.000
50A73ILE0-0.0040.00510.7590.0780.0780.0000.0000.0000.000
51A74ILE00.0100.01813.2660.0490.0490.0000.0000.0000.000
52A75SER00.0190.00315.6770.0000.0000.0000.0000.0000.000
53A76GLY00.0290.02418.7150.0280.0280.0000.0000.0000.000
54A86ALA0-0.003-0.00426.406-0.005-0.0050.0000.0000.0000.000
55A87PRO0-0.022-0.02021.5540.0140.0140.0000.0000.0000.000
56A88TRP00.0060.00617.869-0.020-0.0200.0000.0000.0000.000
57A89PHE00.0280.00917.1100.0110.0110.0000.0000.0000.000
58A90ASP-1-0.729-0.86415.3030.1300.1300.0000.0000.0000.000
59A91PRO00.009-0.00416.849-0.050-0.0500.0000.0000.0000.000
60A92ALA00.0230.00816.457-0.043-0.0430.0000.0000.0000.000
61A93ILE0-0.010-0.01112.771-0.047-0.0470.0000.0000.0000.000
62A94PHE0-0.019-0.00614.280-0.091-0.0910.0000.0000.0000.000
63A95THR0-0.029-0.02716.830-0.019-0.0190.0000.0000.0000.000
64A96ILE0-0.042-0.00810.9560.0000.0000.0000.0000.0000.000
65A97GLY0-0.007-0.00414.148-0.046-0.0460.0000.0000.0000.000
66A98LYS10.8830.9647.7551.2671.2670.0000.0000.0000.000
67A99PRO00.0290.01711.7640.1080.1080.0000.0000.0000.000
68A100VAL0-0.001-0.00212.708-0.086-0.0860.0000.0000.0000.000
69A101LEU0-0.0100.00614.8320.0570.0570.0000.0000.0000.000
70A102GLY00.009-0.00616.4220.0040.0040.0000.0000.0000.000
71A103ILE0-0.005-0.01818.3080.0090.0090.0000.0000.0000.000
72A104CYS00.010-0.00420.8750.0290.0290.0000.0000.0000.000
73A105TYR00.0060.00520.6740.0030.0030.0000.0000.0000.000
74A106GLY00.0250.01019.6940.0120.0120.0000.0000.0000.000
75A107MET0-0.0330.00920.506-0.019-0.0190.0000.0000.0000.000
76A108GLN0-0.022-0.01922.8470.0030.0030.0000.0000.0000.000
77A109MET0-0.046-0.01421.1680.0130.0130.0000.0000.0000.000
78A110MET0-0.0050.01718.5970.0150.0150.0000.0000.0000.000
79A111ASN00.0190.00921.925-0.002-0.0020.0000.0000.0000.000
80A112LYS10.9420.99025.2230.0360.0360.0000.0000.0000.000
81A113VAL0-0.051-0.02320.9560.0140.0140.0000.0000.0000.000
82A114PHE0-0.047-0.02820.5030.0020.0020.0000.0000.0000.000
83A115GLY00.0240.02025.888-0.001-0.0010.0000.0000.0000.000
84A116GLY00.0070.01428.4420.0050.0050.0000.0000.0000.000
85A117THR0-0.050-0.03630.0640.0070.0070.0000.0000.0000.000
86A118VAL0-0.021-0.02428.721-0.009-0.0090.0000.0000.0000.000
87A119HIS00.0190.02432.0570.0070.0070.0000.0000.0000.000
88A120LYS10.8550.91530.2850.0250.0250.0000.0000.0000.000
89A121LYS10.9380.95134.1030.0150.0150.0000.0000.0000.000
90A122SER00.0410.04234.3120.0020.0020.0000.0000.0000.000
91A123VAL0-0.042-0.00432.694-0.001-0.0010.0000.0000.0000.000
92A124ARG10.9820.96735.3200.0460.0460.0000.0000.0000.000
93A125GLU-1-0.937-0.96237.033-0.040-0.0400.0000.0000.0000.000
94A126ASP-1-0.841-0.89632.685-0.066-0.0660.0000.0000.0000.000
95A127GLY00.006-0.00333.6660.0050.0050.0000.0000.0000.000
96A128VAL0-0.022-0.01132.571-0.008-0.0080.0000.0000.0000.000
97A129PHE00.0010.00433.7540.0070.0070.0000.0000.0000.000
98A130ASN00.0260.01534.040-0.014-0.0140.0000.0000.0000.000
99A131ILE0-0.087-0.03530.3430.0070.0070.0000.0000.0000.000
100A132SER0-0.004-0.01334.955-0.003-0.0030.0000.0000.0000.000
101A133VAL0-0.004-0.02129.999-0.004-0.0040.0000.0000.0000.000
102A134ASP-1-0.867-0.94130.508-0.186-0.1860.0000.0000.0000.000
103A135ASN00.026-0.02229.875-0.019-0.0190.0000.0000.0000.000
104A136THR0-0.149-0.05630.252-0.011-0.0110.0000.0000.0000.000
105A137CYS0-0.0540.00725.776-0.016-0.0160.0000.0000.0000.000
106A138SER0-0.006-0.02722.408-0.008-0.0080.0000.0000.0000.000
107A139LEU0-0.020-0.01620.246-0.020-0.0200.0000.0000.0000.000
108A140PHE0-0.030-0.01923.200-0.007-0.0070.0000.0000.0000.000
109A141ARG11.0341.02825.1840.3550.3550.0000.0000.0000.000
110A142GLY0-0.031-0.02026.452-0.014-0.0140.0000.0000.0000.000
111A143LEU0-0.0550.00126.7180.0070.0070.0000.0000.0000.000
112A144GLN00.0170.01030.3100.0130.0130.0000.0000.0000.000
113A145LYS10.9490.95933.0630.1330.1330.0000.0000.0000.000
114A146GLU-1-0.956-0.97135.450-0.108-0.1080.0000.0000.0000.000
115A147GLU-1-0.776-0.87830.436-0.192-0.1920.0000.0000.0000.000
116A148VAL00.0590.04532.7790.0080.0080.0000.0000.0000.000
117A149VAL0-0.019-0.01928.853-0.012-0.0120.0000.0000.0000.000
118A150LEU00.0060.00527.5050.0130.0130.0000.0000.0000.000
119A151LEU0-0.023-0.02228.606-0.012-0.0120.0000.0000.0000.000
120A152THR00.0110.00328.0920.0020.0020.0000.0000.0000.000
121A153HIS0-0.074-0.05630.5510.0030.0030.0000.0000.0000.000
122A154GLY0-0.010-0.01531.1060.0020.0020.0000.0000.0000.000
123A155ASP-1-0.854-0.92229.885-0.040-0.0400.0000.0000.0000.000
124A156SER0-0.044-0.02530.366-0.010-0.0100.0000.0000.0000.000
125A157VAL00.010-0.00328.2460.0080.0080.0000.0000.0000.000
126A158ASP-1-0.957-0.96131.114-0.061-0.0610.0000.0000.0000.000
127A159LYS10.9520.97034.1850.0500.0500.0000.0000.0000.000
128A160VAL0-0.017-0.01529.418-0.001-0.0010.0000.0000.0000.000
129A161ALA00.0180.01127.4580.0040.0040.0000.0000.0000.000
130A162ASP-1-0.846-0.92429.552-0.109-0.1090.0000.0000.0000.000
131A163GLY0-0.075-0.04327.954-0.007-0.0070.0000.0000.0000.000
132A164PHE0-0.060-0.02822.486-0.023-0.0230.0000.0000.0000.000
133A165LYS10.9800.99127.9830.1750.1750.0000.0000.0000.000
134A166VAL0-0.037-0.02128.779-0.009-0.0090.0000.0000.0000.000
135A167VAL0-0.017-0.00926.5580.0030.0030.0000.0000.0000.000
136A168ALA00.0540.02829.566-0.006-0.0060.0000.0000.0000.000
137A169ARG10.9130.96431.2330.1180.1180.0000.0000.0000.000
138A170SER00.0860.05334.012-0.004-0.0040.0000.0000.0000.000
139A171GLY00.0210.01736.8980.0050.0050.0000.0000.0000.000
140A172ASN0-0.042-0.03838.583-0.002-0.0020.0000.0000.0000.000
141A173ILE00.0130.02333.2440.0000.0000.0000.0000.0000.000
142A174VAL00.0030.00730.002-0.007-0.0070.0000.0000.0000.000
143A175ALA00.026-0.00329.8620.0020.0020.0000.0000.0000.000
144A176GLY00.0380.00726.641-0.014-0.0140.0000.0000.0000.000
145A177ILE0-0.053-0.01924.5380.0160.0160.0000.0000.0000.000
146A178ALA00.0650.02723.883-0.026-0.0260.0000.0000.0000.000
147A179ASN00.0280.02622.7910.0140.0140.0000.0000.0000.000
148A180GLU-1-0.711-0.86322.362-0.353-0.3530.0000.0000.0000.000
149A181SER0-0.055-0.01422.256-0.028-0.0280.0000.0000.0000.000
150A182LYS10.9250.96220.1110.1900.1900.0000.0000.0000.000
151A183LYS10.9110.97816.9170.5780.5780.0000.0000.0000.000
152A184LEU0-0.0090.00817.246-0.042-0.0420.0000.0000.0000.000
153A185TYR0-0.026-0.04018.8670.0260.0260.0000.0000.0000.000
154A186GLY00.0180.00719.952-0.013-0.0130.0000.0000.0000.000
155A187ALA00.0170.00422.5170.0060.0060.0000.0000.0000.000
156A188GLN00.0080.00323.886-0.002-0.0020.0000.0000.0000.000
157A189PHE00.0150.00225.6380.0090.0090.0000.0000.0000.000
158A190HIS10.8370.90022.8880.1280.1280.0000.0000.0000.000
159A191PRO00.0160.04420.6680.0120.0120.0000.0000.0000.000
160A192GLU-1-0.751-0.87619.433-0.224-0.2240.0000.0000.0000.000
161A193VAL0-0.021-0.01221.1530.0120.0120.0000.0000.0000.000
162A194GLY00.0260.01124.555-0.005-0.0050.0000.0000.0000.000
163A195LEU00.001-0.00526.8010.0020.0020.0000.0000.0000.000
164A196THR0-0.062-0.03926.0690.0110.0110.0000.0000.0000.000
165A197GLU-1-0.911-0.93227.163-0.168-0.1680.0000.0000.0000.000
166A198ASN0-0.021-0.02327.117-0.015-0.0150.0000.0000.0000.000
167A199GLY00.016-0.00624.168-0.020-0.0200.0000.0000.0000.000
168A200LYS10.8810.94318.4420.3570.3570.0000.0000.0000.000
169A201VAL00.0090.01821.014-0.045-0.0450.0000.0000.0000.000
170A202ILE00.0380.03121.254-0.030-0.0300.0000.0000.0000.000
171A203LEU0-0.009-0.01816.946-0.038-0.0380.0000.0000.0000.000
172A204LYS10.9360.98017.1550.3300.3300.0000.0000.0000.000
173A205ASN0-0.008-0.01218.254-0.065-0.0650.0000.0000.0000.000
174A206PHE0-0.001-0.01013.098-0.033-0.0330.0000.0000.0000.000
175A207LEU0-0.005-0.00911.847-0.082-0.0820.0000.0000.0000.000
176A208TYR0-0.060-0.05213.990-0.061-0.0610.0000.0000.0000.000
177A209ASP-1-0.899-0.93916.352-0.526-0.5260.0000.0000.0000.000
178A210ILE0-0.089-0.02916.480-0.005-0.0050.0000.0000.0000.000
179A211ALA0-0.026-0.03012.081-0.013-0.0130.0000.0000.0000.000
180A212GLY0-0.0060.00813.081-0.139-0.1390.0000.0000.0000.000
181A213CYS0-0.102-0.05110.161-0.198-0.1980.0000.0000.0000.000
182A214SER00.001-0.01111.6740.1300.1300.0000.0000.0000.000
183A215GLY00.0380.01912.564-0.085-0.0850.0000.0000.0000.000
184A216THR0-0.034-0.01213.5470.1070.1070.0000.0000.0000.000
185A217PHE00.0120.01512.473-0.117-0.1170.0000.0000.0000.000
186A218THR0-0.018-0.01811.8700.0590.0590.0000.0000.0000.000
187A219VAL00.0100.01714.1310.0370.0370.0000.0000.0000.000