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: JQ769

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 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 187
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -1992376.174295
FMO2-HF: Nuclear repulsion 1921094.09249
FMO2-HF: Total energy -71282.081805
FMO2-MP2: Total energy -71489.570309


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.
-4.6361.1387.289-5.959-7.104-0.021
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 : 0.009
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].
3A26GLY0-0.090-0.0483.831-0.7950.920-0.014-0.875-0.8260.004
4A27ALA0-0.0010.0242.9290.7701.3390.071-0.208-0.4320.001
5A28VAL0-0.034-0.0354.9520.2110.253-0.001-0.007-0.0330.000
6A29VAL00.0240.0275.8880.1320.1320.0000.0000.0000.000
7A30ILE0-0.051-0.0297.4810.1000.1000.0000.0000.0000.000
8A31LEU0-0.0030.00610.5500.1470.1470.0000.0000.0000.000
9A32ASP-1-0.795-0.91413.401-0.141-0.1410.0000.0000.0000.000
10A33ALA0-0.027-0.01416.7490.0500.0500.0000.0000.0000.000
11A34GLY0-0.0060.00119.9600.0150.0150.0000.0000.0000.000
12A35ALA00.010-0.01121.3750.0150.0150.0000.0000.0000.000
13A36GLN0-0.027-0.01820.5050.0120.0120.0000.0000.0000.000
14A37TYR0-0.0090.00617.796-0.001-0.0010.0000.0000.0000.000
15A38GLY00.0690.01914.9420.0210.0210.0000.0000.0000.000
16A39LYS10.9660.97715.347-0.120-0.1200.0000.0000.0000.000
17A40VAL0-0.021-0.00917.171-0.030-0.0300.0000.0000.0000.000
18A41ILE00.0390.00514.319-0.024-0.0240.0000.0000.0000.000
19A42ASP-1-0.753-0.83611.369-0.460-0.4600.0000.0000.0000.000
20A43ARG10.9010.95313.8670.1410.1410.0000.0000.0000.000
21A44ARG10.7330.83916.5720.2460.2460.0000.0000.0000.000
22A45VAL00.0370.01410.579-0.010-0.0100.0000.0000.0000.000
23A46ARG10.9020.9269.6050.3610.3610.0000.0000.0000.000
24A47GLU-1-0.791-0.84613.834-0.296-0.2960.0000.0000.0000.000
25A48LEU0-0.061-0.01915.3550.0420.0420.0000.0000.0000.000
26A49PHE0-0.021-0.00614.009-0.032-0.0320.0000.0000.0000.000
27A50VAL00.0060.0139.155-0.087-0.0870.0000.0000.0000.000
28A51GLN0-0.029-0.0153.636-0.841-0.5350.003-0.081-0.2280.000
29A52SER0-0.034-0.0486.906-0.484-0.4840.0000.0000.0000.000
30A53GLU-1-0.868-0.9244.285-0.0280.128-0.001-0.013-0.1430.000
31A54ILE0-0.053-0.0227.233-0.143-0.1430.0000.0000.0000.000
32A55PHE0-0.004-0.0086.0460.1390.1390.0000.0000.0000.000
33A56PRO00.0170.01510.618-0.131-0.1310.0000.0000.0000.000
34A57LEU00.0230.02613.193-0.008-0.0080.0000.0000.0000.000
35A58GLU-1-0.902-0.96815.4470.2740.2740.0000.0000.0000.000
36A59THR0-0.066-0.0439.3320.1290.1290.0000.0000.0000.000
37A60PRO0-0.012-0.00412.579-0.109-0.1090.0000.0000.0000.000
38A61ALA00.002-0.01511.3570.0690.0690.0000.0000.0000.000
39A62PHE0-0.018-0.01910.917-0.108-0.1080.0000.0000.0000.000
40A63ALA00.0660.0429.5200.0270.0270.0000.0000.0000.000
41A64ILE00.0310.0136.4570.4350.4350.0000.0000.0000.000
42A65LYS10.8970.9316.159-0.372-0.3720.0000.0000.0000.000
43A66GLU-1-0.949-0.9827.2950.6810.6810.0000.0000.0000.000
44A67GLN00.0000.0042.954-3.459-2.0300.093-0.506-1.0160.002
45A68GLY00.0050.0172.110-1.826-1.6906.846-3.776-3.207-0.024
46A69PHE0-0.0130.0123.259-3.808-2.5050.293-0.482-1.114-0.004
47A70ARG10.8920.9524.4373.0673.185-0.001-0.011-0.1050.000
48A71ALA0-0.024-0.0177.6180.5740.5740.0000.0000.0000.000
49A72ILE00.0080.0098.230-0.239-0.2390.0000.0000.0000.000
50A73ILE0-0.0060.00410.7370.0790.0790.0000.0000.0000.000
51A74ILE00.0130.02113.2470.0530.0530.0000.0000.0000.000
52A75SER00.0190.00215.660-0.002-0.0020.0000.0000.0000.000
53A76GLY00.0310.02818.6970.0290.0290.0000.0000.0000.000
54A86ALA00.001-0.00326.488-0.006-0.0060.0000.0000.0000.000
55A87PRO0-0.024-0.02221.6190.0140.0140.0000.0000.0000.000
56A88TRP00.0040.00717.755-0.022-0.0220.0000.0000.0000.000
57A89PHE00.0240.00717.0760.0140.0140.0000.0000.0000.000
58A90ASP-1-0.732-0.86115.3040.1290.1290.0000.0000.0000.000
59A91PRO00.007-0.00716.853-0.051-0.0510.0000.0000.0000.000
60A92ALA00.0240.00216.474-0.047-0.0470.0000.0000.0000.000
61A93ILE0-0.013-0.01112.723-0.051-0.0510.0000.0000.0000.000
62A94PHE0-0.024-0.01014.273-0.096-0.0960.0000.0000.0000.000
63A95THR0-0.033-0.02616.815-0.021-0.0210.0000.0000.0000.000
64A96ILE0-0.041-0.01011.0500.0000.0000.0000.0000.0000.000
65A97GLY0-0.005-0.00114.146-0.051-0.0510.0000.0000.0000.000
66A98LYS10.8650.9457.8031.4121.4120.0000.0000.0000.000
67A99PRO00.0230.01511.8480.1060.1060.0000.0000.0000.000
68A100VAL0-0.006-0.00712.685-0.088-0.0880.0000.0000.0000.000
69A101LEU0-0.0080.00614.8020.0600.0600.0000.0000.0000.000
70A102GLY00.016-0.00216.3980.0050.0050.0000.0000.0000.000
71A103ILE0-0.010-0.02018.1690.0090.0090.0000.0000.0000.000
72A104CYS00.004-0.00620.8510.0310.0310.0000.0000.0000.000
73A105TYR00.0120.01020.8850.0010.0010.0000.0000.0000.000
74A106GLY00.0260.01019.6810.0120.0120.0000.0000.0000.000
75A107MET0-0.0400.00720.490-0.019-0.0190.0000.0000.0000.000
76A108GLN0-0.008-0.00622.8290.0020.0020.0000.0000.0000.000
77A109MET0-0.025-0.00821.1290.0120.0120.0000.0000.0000.000
78A110MET0-0.0310.00818.5530.0150.0150.0000.0000.0000.000
79A111ASN00.0100.00421.913-0.002-0.0020.0000.0000.0000.000
80A112LYS10.9580.99125.3640.0410.0410.0000.0000.0000.000
81A113VAL0-0.050-0.02020.9260.0150.0150.0000.0000.0000.000
82A114PHE0-0.024-0.01920.7060.0020.0020.0000.0000.0000.000
83A115GLY00.0250.02025.881-0.001-0.0010.0000.0000.0000.000
84A116GLY00.0060.01428.4330.0050.0050.0000.0000.0000.000
85A117THR0-0.068-0.04330.0560.0070.0070.0000.0000.0000.000
86A118VAL0-0.021-0.02628.707-0.009-0.0090.0000.0000.0000.000
87A119HIS0-0.0030.00932.0440.0070.0070.0000.0000.0000.000
88A120LYS10.8350.88730.2630.0280.0280.0000.0000.0000.000
89A121LYS10.9340.95134.0880.0170.0170.0000.0000.0000.000
90A122SER00.0410.04234.3750.0010.0010.0000.0000.0000.000
91A123VAL0-0.043-0.00532.706-0.001-0.0010.0000.0000.0000.000
92A124ARG10.9760.97035.3020.0490.0490.0000.0000.0000.000
93A125GLU-1-0.927-0.96037.019-0.043-0.0430.0000.0000.0000.000
94A126ASP-1-0.841-0.89832.408-0.071-0.0710.0000.0000.0000.000
95A127GLY00.011-0.00133.6380.0060.0060.0000.0000.0000.000
96A128VAL0-0.025-0.01432.553-0.008-0.0080.0000.0000.0000.000
97A129PHE0-0.0060.00433.7870.0070.0070.0000.0000.0000.000
98A130ASN0-0.006-0.00834.074-0.016-0.0160.0000.0000.0000.000
99A131ILE0-0.079-0.03630.2620.0080.0080.0000.0000.0000.000
100A132SER0-0.005-0.01034.948-0.004-0.0040.0000.0000.0000.000
101A133VAL0-0.007-0.02229.871-0.004-0.0040.0000.0000.0000.000
102A134ASP-1-0.856-0.91830.513-0.200-0.2000.0000.0000.0000.000
103A135ASN0-0.004-0.04529.841-0.016-0.0160.0000.0000.0000.000
104A136THR0-0.143-0.07230.274-0.011-0.0110.0000.0000.0000.000
105A137CYS0-0.067-0.00425.759-0.017-0.0170.0000.0000.0000.000
106A138SER00.005-0.03522.527-0.004-0.0040.0000.0000.0000.000
107A139LEU0-0.014-0.01420.410-0.022-0.0220.0000.0000.0000.000
108A140PHE0-0.025-0.02123.166-0.008-0.0080.0000.0000.0000.000
109A141ARG10.9480.97324.1370.3990.3990.0000.0000.0000.000
110A142GLY0-0.015-0.01126.491-0.016-0.0160.0000.0000.0000.000
111A143LEU0-0.0540.00226.7210.0070.0070.0000.0000.0000.000
112A144GLN00.0140.01330.3490.0140.0140.0000.0000.0000.000
113A145LYS10.9680.97133.1040.1420.1420.0000.0000.0000.000
114A146GLU-1-0.928-0.94635.484-0.116-0.1160.0000.0000.0000.000
115A147GLU-1-0.779-0.87730.489-0.209-0.2090.0000.0000.0000.000
116A148VAL00.0550.03832.8140.0090.0090.0000.0000.0000.000
117A149VAL0-0.023-0.02228.907-0.013-0.0130.0000.0000.0000.000
118A150LEU00.0080.00827.5450.0140.0140.0000.0000.0000.000
119A151LEU0-0.023-0.01928.596-0.013-0.0130.0000.0000.0000.000
120A152THR00.0250.01027.9360.0020.0020.0000.0000.0000.000
121A153HIS0-0.080-0.05930.5290.0040.0040.0000.0000.0000.000
122A154GLY0-0.004-0.01231.0900.0020.0020.0000.0000.0000.000
123A155ASP-1-0.835-0.89329.812-0.043-0.0430.0000.0000.0000.000
124A156SER0-0.024-0.01730.332-0.011-0.0110.0000.0000.0000.000
125A157VAL00.009-0.00228.1610.0090.0090.0000.0000.0000.000
126A158ASP-1-0.822-0.88831.097-0.063-0.0630.0000.0000.0000.000
127A159LYS10.8270.90634.1710.0570.0570.0000.0000.0000.000
128A160VAL0-0.015-0.01529.433-0.002-0.0020.0000.0000.0000.000
129A161ALA00.0170.01127.4470.0050.0050.0000.0000.0000.000
130A162ASP-1-0.842-0.92229.539-0.118-0.1180.0000.0000.0000.000
131A163GLY0-0.073-0.04427.941-0.008-0.0080.0000.0000.0000.000
132A164PHE0-0.074-0.03722.457-0.025-0.0250.0000.0000.0000.000
133A165LYS10.9820.99627.9640.1900.1900.0000.0000.0000.000
134A166VAL0-0.026-0.02028.755-0.009-0.0090.0000.0000.0000.000
135A167VAL0-0.014-0.00826.5070.0030.0030.0000.0000.0000.000
136A168ALA00.0530.02929.472-0.006-0.0060.0000.0000.0000.000
137A169ARG10.8880.95631.2040.1240.1240.0000.0000.0000.000
138A170SER00.0810.05233.984-0.003-0.0030.0000.0000.0000.000
139A171GLY00.0340.02536.8700.0050.0050.0000.0000.0000.000
140A172ASN0-0.030-0.03238.558-0.003-0.0030.0000.0000.0000.000
141A173ILE00.0130.02033.0290.0000.0000.0000.0000.0000.000
142A174VAL00.0110.01029.881-0.008-0.0080.0000.0000.0000.000
143A175ALA00.021-0.00729.8490.0020.0020.0000.0000.0000.000
144A176GLY00.0350.00826.614-0.014-0.0140.0000.0000.0000.000
145A177ILE0-0.046-0.01924.4950.0170.0170.0000.0000.0000.000
146A178ALA00.0670.03023.855-0.027-0.0270.0000.0000.0000.000
147A179ASN00.0400.03422.9000.0090.0090.0000.0000.0000.000
148A180GLU-1-0.722-0.83622.340-0.382-0.3820.0000.0000.0000.000
149A181SER0-0.066-0.02222.232-0.027-0.0270.0000.0000.0000.000
150A182LYS10.9140.95820.0790.2020.2020.0000.0000.0000.000
151A183LYS10.8710.94017.2400.6060.6060.0000.0000.0000.000
152A184LEU0-0.0110.00717.158-0.043-0.0430.0000.0000.0000.000
153A185TYR0-0.019-0.05018.5750.0230.0230.0000.0000.0000.000
154A186GLY00.0200.00819.927-0.014-0.0140.0000.0000.0000.000
155A187ALA00.0140.00322.4870.0070.0070.0000.0000.0000.000
156A188GLN0-0.007-0.01423.8610.0010.0010.0000.0000.0000.000
157A189PHE00.0270.00425.6190.0100.0100.0000.0000.0000.000
158A190HIS10.8360.89822.9370.1370.1370.0000.0000.0000.000
159A191PRO00.0120.03320.7230.0120.0120.0000.0000.0000.000
160A192GLU-1-0.770-0.88419.518-0.237-0.2370.0000.0000.0000.000
161A193VAL0-0.027-0.01521.1780.0120.0120.0000.0000.0000.000
162A194GLY00.0250.01024.577-0.005-0.0050.0000.0000.0000.000
163A195LEU00.009-0.00426.8210.0020.0020.0000.0000.0000.000
164A196THR0-0.060-0.03126.1110.0120.0120.0000.0000.0000.000
165A197GLU-1-0.911-0.93327.191-0.178-0.1780.0000.0000.0000.000
166A198ASN0-0.026-0.02927.175-0.016-0.0160.0000.0000.0000.000
167A199GLY00.023-0.00324.197-0.021-0.0210.0000.0000.0000.000
168A200LYS10.8390.90118.6740.3670.3670.0000.0000.0000.000
169A201VAL00.0130.01721.045-0.048-0.0480.0000.0000.0000.000
170A202ILE00.0280.03121.243-0.033-0.0330.0000.0000.0000.000
171A203LEU0-0.005-0.01116.771-0.039-0.0390.0000.0000.0000.000
172A204LYS10.9560.98517.1920.3490.3490.0000.0000.0000.000
173A205ASN0-0.026-0.02418.292-0.070-0.0700.0000.0000.0000.000
174A206PHE00.001-0.00313.098-0.033-0.0330.0000.0000.0000.000
175A207LEU00.0090.00111.925-0.084-0.0840.0000.0000.0000.000
176A208TYR0-0.048-0.04414.032-0.070-0.0700.0000.0000.0000.000
177A209ASP-1-0.851-0.89516.391-0.531-0.5310.0000.0000.0000.000
178A210ILE0-0.079-0.02316.408-0.005-0.0050.0000.0000.0000.000
179A211ALA00.0110.00212.059-0.009-0.0090.0000.0000.0000.000
180A212GLY00.0100.01213.048-0.149-0.1490.0000.0000.0000.000
181A213CYS0-0.101-0.04310.731-0.204-0.2040.0000.0000.0000.000
182A214SER00.0190.00611.6640.1230.1230.0000.0000.0000.000
183A215GLY00.0220.01612.544-0.092-0.0920.0000.0000.0000.000
184A216THR0-0.042-0.02713.0560.1200.1200.0000.0000.0000.000
185A217PHE00.0170.01512.284-0.134-0.1340.0000.0000.0000.000
186A218THR0-0.007-0.01111.7360.0690.0690.0000.0000.0000.000
187A219VAL00.0020.01214.0120.0380.0380.0000.0000.0000.000