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: 3J83L

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 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 187
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2000364.609452
FMO2-HF: Nuclear repulsion 1929082.185222
FMO2-HF: Total energy -71282.42423
FMO2-MP2: Total energy -71489.967322


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.
-11.455-4.9247.079-5.578-8.032-0.013
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 : 0.023 / q_NPA : 0.010
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].
3A26GLY0-0.055-0.0233.670-1.1430.6030.006-0.952-0.8000.003
4A27ALA0-0.019-0.0063.0750.8601.3360.025-0.144-0.3570.000
5A28VAL0-0.028-0.0215.201-0.202-0.189-0.001-0.008-0.0040.000
6A29VAL00.0200.0245.7860.2270.2270.0000.0000.0000.000
7A30ILE0-0.047-0.0267.4520.1480.1480.0000.0000.0000.000
8A31LEU00.0140.01610.3760.1570.1570.0000.0000.0000.000
9A32ASP-1-0.808-0.92113.425-0.147-0.1470.0000.0000.0000.000
10A33ALA0-0.0100.00216.9840.0540.0540.0000.0000.0000.000
11A34GLY0-0.0050.00020.1840.0160.0160.0000.0000.0000.000
12A35ALA00.002-0.01021.0410.0120.0120.0000.0000.0000.000
13A36GLN0-0.025-0.01720.0710.0060.0060.0000.0000.0000.000
14A37TYR0-0.010-0.00217.254-0.004-0.0040.0000.0000.0000.000
15A38GLY00.0610.01914.5280.0180.0180.0000.0000.0000.000
16A39LYS10.9560.97715.323-0.118-0.1180.0000.0000.0000.000
17A40VAL0-0.016-0.00316.682-0.036-0.0360.0000.0000.0000.000
18A41ILE00.0420.01114.296-0.026-0.0260.0000.0000.0000.000
19A42ASP-1-0.750-0.84111.042-0.533-0.5330.0000.0000.0000.000
20A43ARG10.8810.93213.4970.1580.1580.0000.0000.0000.000
21A44ARG10.7460.84516.3440.2630.2630.0000.0000.0000.000
22A45VAL00.0510.02610.8920.0000.0000.0000.0000.0000.000
23A46ARG10.8990.9299.3040.4990.4990.0000.0000.0000.000
24A47GLU-1-0.805-0.85314.001-0.296-0.2960.0000.0000.0000.000
25A48LEU0-0.047-0.02815.7070.0550.0550.0000.0000.0000.000
26A49PHE0-0.020-0.00714.093-0.042-0.0420.0000.0000.0000.000
27A50VAL00.0220.0319.490-0.073-0.0730.0000.0000.0000.000
28A51GLN0-0.048-0.0303.591-0.479-0.2240.002-0.055-0.2020.000
29A52SER0-0.033-0.0527.435-0.393-0.3930.0000.0000.0000.000
30A53GLU-1-0.846-0.9143.755-0.703-0.4910.000-0.028-0.1840.000
31A54ILE0-0.045-0.0167.024-0.060-0.0600.0000.0000.0000.000
32A55PHE0-0.005-0.0065.7850.1410.1410.0000.0000.0000.000
33A56PRO00.0010.00810.549-0.135-0.1350.0000.0000.0000.000
34A57LEU00.0130.02612.884-0.019-0.0190.0000.0000.0000.000
35A58GLU-1-0.888-0.96615.1770.2750.2750.0000.0000.0000.000
36A59THR0-0.061-0.0468.8690.1300.1300.0000.0000.0000.000
37A60PRO0-0.003-0.00312.139-0.124-0.1240.0000.0000.0000.000
38A61ALA00.002-0.00910.6950.0510.0510.0000.0000.0000.000
39A62PHE0-0.018-0.01210.573-0.141-0.1410.0000.0000.0000.000
40A63ALA00.0820.0508.747-0.014-0.0140.0000.0000.0000.000
41A64ILE00.0070.0006.1690.3330.3330.0000.0000.0000.000
42A65LYS10.9130.9376.094-0.568-0.5680.0000.0000.0000.000
43A66GLU-1-0.923-0.9687.4740.5920.5920.0000.0000.0000.000
44A67GLN0-0.012-0.0092.300-7.338-5.6862.296-1.488-2.4600.012
45A68GLY00.0140.0072.351-4.643-4.0783.746-2.140-2.171-0.023
46A69PHE0-0.036-0.0012.967-3.286-1.7991.006-0.750-1.743-0.005
47A70ARG10.8580.9374.4923.2673.392-0.001-0.013-0.1110.000
48A71ALA0-0.015-0.0127.8910.5750.5750.0000.0000.0000.000
49A72ILE00.0080.0118.331-0.297-0.2970.0000.0000.0000.000
50A73ILE0-0.018-0.00910.7280.0990.0990.0000.0000.0000.000
51A74ILE00.0120.01813.1870.0470.0470.0000.0000.0000.000
52A75SER00.0220.00515.7610.0060.0060.0000.0000.0000.000
53A76GLY00.0340.02318.8990.0300.0300.0000.0000.0000.000
54A86ALA00.0110.00226.235-0.006-0.0060.0000.0000.0000.000
55A87PRO0-0.031-0.02621.5690.0150.0150.0000.0000.0000.000
56A88TRP00.0330.02517.253-0.029-0.0290.0000.0000.0000.000
57A89PHE00.0160.00416.5010.0070.0070.0000.0000.0000.000
58A90ASP-1-0.744-0.85814.7370.1160.1160.0000.0000.0000.000
59A91PRO00.005-0.00616.272-0.059-0.0590.0000.0000.0000.000
60A92ALA00.0340.00816.049-0.051-0.0510.0000.0000.0000.000
61A93ILE0-0.005-0.00112.177-0.067-0.0670.0000.0000.0000.000
62A94PHE0-0.0100.00014.080-0.102-0.1020.0000.0000.0000.000
63A95THR0-0.037-0.03716.3380.0000.0000.0000.0000.0000.000
64A96ILE0-0.047-0.01910.512-0.005-0.0050.0000.0000.0000.000
65A97GLY0-0.012-0.00213.732-0.055-0.0550.0000.0000.0000.000
66A98LYS10.8360.9357.4251.7051.7050.0000.0000.0000.000
67A99PRO00.0270.01312.0620.1130.1130.0000.0000.0000.000
68A100VAL0-0.018-0.01612.724-0.106-0.1060.0000.0000.0000.000
69A101LEU00.0000.00814.9250.0680.0680.0000.0000.0000.000
70A102GLY00.0110.00116.5320.0000.0000.0000.0000.0000.000
71A103ILE0-0.010-0.02118.2880.0080.0080.0000.0000.0000.000
72A104CYS0-0.015-0.00721.1480.0310.0310.0000.0000.0000.000
73A105TYR0-0.021-0.00620.761-0.003-0.0030.0000.0000.0000.000
74A106GLY00.0390.01919.5480.0080.0080.0000.0000.0000.000
75A107MET0-0.0470.01220.296-0.019-0.0190.0000.0000.0000.000
76A108GLN0-0.012-0.00822.8390.0020.0020.0000.0000.0000.000
77A109MET0-0.009-0.00421.1800.0130.0130.0000.0000.0000.000
78A110MET0-0.0290.00818.3000.0140.0140.0000.0000.0000.000
79A111ASN0-0.022-0.01521.614-0.003-0.0030.0000.0000.0000.000
80A112LYS10.9480.97725.0930.0510.0510.0000.0000.0000.000
81A113VAL0-0.043-0.01420.4790.0170.0170.0000.0000.0000.000
82A114PHE0-0.008-0.00720.7030.0010.0010.0000.0000.0000.000
83A115GLY00.0240.01525.7440.0000.0000.0000.0000.0000.000
84A116GLY00.0180.02228.2180.0070.0070.0000.0000.0000.000
85A117THR0-0.080-0.06429.7350.0070.0070.0000.0000.0000.000
86A118VAL0-0.001-0.02528.709-0.011-0.0110.0000.0000.0000.000
87A119HIS0-0.0330.00131.9500.0070.0070.0000.0000.0000.000
88A120LYS10.8700.90430.2590.0370.0370.0000.0000.0000.000
89A121LYS10.9230.95533.9260.0220.0220.0000.0000.0000.000
90A122SER00.0140.00934.4040.0030.0030.0000.0000.0000.000
91A123VAL0-0.0140.00832.3280.0000.0000.0000.0000.0000.000
92A124ARG10.8390.89234.9350.0540.0540.0000.0000.0000.000
93A125GLU-1-0.827-0.89636.866-0.048-0.0480.0000.0000.0000.000
94A126ASP-1-0.816-0.88432.066-0.077-0.0770.0000.0000.0000.000
95A127GLY00.007-0.00533.3990.0060.0060.0000.0000.0000.000
96A128VAL0-0.027-0.01532.190-0.009-0.0090.0000.0000.0000.000
97A129PHE0-0.0070.00133.6200.0080.0080.0000.0000.0000.000
98A130ASN00.001-0.00134.026-0.018-0.0180.0000.0000.0000.000
99A131ILE0-0.070-0.03130.4090.0090.0090.0000.0000.0000.000
100A132SER00.001-0.00634.599-0.006-0.0060.0000.0000.0000.000
101A133VAL00.002-0.01630.079-0.005-0.0050.0000.0000.0000.000
102A134ASP-1-0.819-0.90030.496-0.212-0.2120.0000.0000.0000.000
103A135ASN0-0.058-0.06430.223-0.005-0.0050.0000.0000.0000.000
104A136THR0-0.089-0.05330.745-0.007-0.0070.0000.0000.0000.000
105A137CYS0-0.0560.00725.686-0.020-0.0200.0000.0000.0000.000
106A138SER00.008-0.03022.644-0.004-0.0040.0000.0000.0000.000
107A139LEU0-0.018-0.01820.458-0.023-0.0230.0000.0000.0000.000
108A140PHE0-0.022-0.02723.193-0.004-0.0040.0000.0000.0000.000
109A141ARG10.9100.95024.1530.4300.4300.0000.0000.0000.000
110A142GLY0-0.020-0.01226.691-0.016-0.0160.0000.0000.0000.000
111A143LEU0-0.049-0.00126.7940.0080.0080.0000.0000.0000.000
112A144GLN0-0.0060.00730.3070.0150.0150.0000.0000.0000.000
113A145LYS10.9640.96733.0860.1510.1510.0000.0000.0000.000
114A146GLU-1-0.935-0.95135.501-0.124-0.1240.0000.0000.0000.000
115A147GLU-1-0.769-0.87130.557-0.222-0.2220.0000.0000.0000.000
116A148VAL00.0540.03532.6260.0090.0090.0000.0000.0000.000
117A149VAL0-0.029-0.02628.845-0.015-0.0150.0000.0000.0000.000
118A150LEU00.0120.00727.0700.0150.0150.0000.0000.0000.000
119A151LEU0-0.022-0.01828.324-0.013-0.0130.0000.0000.0000.000
120A152THR00.0250.01427.4180.0020.0020.0000.0000.0000.000
121A153HIS0-0.083-0.06530.2280.0030.0030.0000.0000.0000.000
122A154GLY0-0.008-0.01730.6060.0010.0010.0000.0000.0000.000
123A155ASP-1-0.862-0.91729.952-0.049-0.0490.0000.0000.0000.000
124A156SER00.0190.03030.361-0.007-0.0070.0000.0000.0000.000
125A157VAL00.008-0.00228.0230.0100.0100.0000.0000.0000.000
126A158ASP-1-0.826-0.87930.838-0.067-0.0670.0000.0000.0000.000
127A159LYS10.8200.90733.5790.0650.0650.0000.0000.0000.000
128A160VAL00.013-0.00229.107-0.002-0.0020.0000.0000.0000.000
129A161ALA00.0180.01727.0600.0080.0080.0000.0000.0000.000
130A162ASP-1-0.860-0.93429.135-0.127-0.1270.0000.0000.0000.000
131A163GLY0-0.040-0.02528.113-0.011-0.0110.0000.0000.0000.000
132A164PHE0-0.079-0.03222.253-0.025-0.0250.0000.0000.0000.000
133A165LYS10.9140.96627.8050.2220.2220.0000.0000.0000.000
134A166VAL0-0.002-0.00828.647-0.010-0.0100.0000.0000.0000.000
135A167VAL0-0.047-0.02826.4410.0010.0010.0000.0000.0000.000
136A168ALA00.0580.03629.523-0.006-0.0060.0000.0000.0000.000
137A169ARG10.8370.92331.1610.1290.1290.0000.0000.0000.000
138A170SER00.0720.05233.985-0.003-0.0030.0000.0000.0000.000
139A171GLY00.0420.02736.9100.0050.0050.0000.0000.0000.000
140A172ASN00.001-0.01038.388-0.006-0.0060.0000.0000.0000.000
141A173ILE00.0360.02632.930-0.003-0.0030.0000.0000.0000.000
142A174VAL00.0170.00929.980-0.008-0.0080.0000.0000.0000.000
143A175ALA00.0270.00330.0610.0010.0010.0000.0000.0000.000
144A176GLY00.0450.00826.728-0.015-0.0150.0000.0000.0000.000
145A177ILE0-0.042-0.01924.4490.0180.0180.0000.0000.0000.000
146A178ALA00.0600.02023.824-0.029-0.0290.0000.0000.0000.000
147A179ASN00.0170.03222.9660.0070.0070.0000.0000.0000.000
148A180GLU-1-0.698-0.81722.224-0.403-0.4030.0000.0000.0000.000
149A181SER0-0.082-0.04322.109-0.027-0.0270.0000.0000.0000.000
150A182LYS10.8920.95719.7820.2280.2280.0000.0000.0000.000
151A183LYS10.8600.93017.4590.6210.6210.0000.0000.0000.000
152A184LEU0-0.0090.00916.980-0.052-0.0520.0000.0000.0000.000
153A185TYR0-0.019-0.05218.6750.0310.0310.0000.0000.0000.000
154A186GLY00.0280.00820.043-0.014-0.0140.0000.0000.0000.000
155A187ALA00.0060.00322.5490.0090.0090.0000.0000.0000.000
156A188GLN00.000-0.02324.0830.0000.0000.0000.0000.0000.000
157A189PHE00.0100.00125.4720.0130.0130.0000.0000.0000.000
158A190HIS10.8330.89422.7030.1510.1510.0000.0000.0000.000
159A191PRO00.0100.02520.8260.0120.0120.0000.0000.0000.000
160A192GLU-1-0.762-0.87219.366-0.262-0.2620.0000.0000.0000.000
161A193VAL0-0.017-0.01421.0160.0110.0110.0000.0000.0000.000
162A194GLY00.0270.00624.483-0.004-0.0040.0000.0000.0000.000
163A195LEU00.0010.00226.8190.0060.0060.0000.0000.0000.000
164A196THR0-0.049-0.02726.0350.0130.0130.0000.0000.0000.000
165A197GLU-1-0.916-0.93427.124-0.190-0.1900.0000.0000.0000.000
166A198ASN0-0.001-0.01727.367-0.019-0.0190.0000.0000.0000.000
167A199GLY00.008-0.00724.149-0.026-0.0260.0000.0000.0000.000
168A200LYS10.8010.88618.9020.3880.3880.0000.0000.0000.000
169A201VAL0-0.0100.00521.501-0.045-0.0450.0000.0000.0000.000
170A202ILE00.0340.02421.356-0.038-0.0380.0000.0000.0000.000
171A203LEU00.010-0.00916.968-0.042-0.0420.0000.0000.0000.000
172A204LYS10.9650.99617.3460.3540.3540.0000.0000.0000.000
173A205ASN0-0.042-0.03018.452-0.072-0.0720.0000.0000.0000.000
174A206PHE0-0.007-0.00713.162-0.027-0.0270.0000.0000.0000.000
175A207LEU00.0200.01012.113-0.092-0.0920.0000.0000.0000.000
176A208TYR0-0.048-0.03414.480-0.061-0.0610.0000.0000.0000.000
177A209ASP-1-0.816-0.88717.012-0.535-0.5350.0000.0000.0000.000
178A210ILE0-0.082-0.03016.2710.0050.0050.0000.0000.0000.000
179A211ALA00.0240.00912.171-0.007-0.0070.0000.0000.0000.000
180A212GLY00.0340.03013.091-0.168-0.1680.0000.0000.0000.000
181A213CYS0-0.083-0.03311.301-0.209-0.2090.0000.0000.0000.000
182A214SER00.019-0.00412.3750.1210.1210.0000.0000.0000.000
183A215GLY00.0220.01712.879-0.098-0.0980.0000.0000.0000.000
184A216THR0-0.058-0.03812.9240.1120.1120.0000.0000.0000.000
185A217PHE00.0290.03512.307-0.139-0.1390.0000.0000.0000.000
186A218THR00.009-0.01011.9500.0510.0510.0000.0000.0000.000
187A219VAL0-0.0110.00814.2210.0330.0330.0000.0000.0000.000