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: 72MVK

Calculation Name: 4GM2-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 4GM2

Chain ID: A

ChEMBL ID:

UniProt ID: Q8IL98

Base Structure: X-ray

Registration Date: 2023-06-22

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 183
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2007530.908321
FMO2-HF: Nuclear repulsion 1935150.419402
FMO2-HF: Total energy -72380.488919
FMO2-MP2: Total energy -72594.065241


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:61:PRO)


Summations of interaction energy for fragment #1(A:61:PRO)
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.
-5.3951.3685.139-4.391-7.510.009
Interaction energy analysis for fragmet #1(A:61:PRO)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.080 / q_NPA : 0.035
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].
3A63LEU0-0.006-0.0032.129-4.877-0.1691.687-2.686-3.7080.008
4A64LEU00.0360.0182.028-2.034-0.5503.447-1.563-3.3680.001
5A65LEU00.0770.0483.8190.3680.9390.005-0.142-0.4340.000
6A66SER0-0.089-0.0415.7880.5890.5890.0000.0000.0000.000
7A67LYS10.9050.9517.2560.5650.5650.0000.0000.0000.000
8A68ARG10.8010.8878.7940.4490.4490.0000.0000.0000.000
9A69ILE0-0.040-0.0136.0430.1860.1860.0000.0000.0000.000
10A70ILE00.0100.0185.631-0.554-0.5540.0000.0000.0000.000
11A71PHE0-0.031-0.0275.3160.1540.1540.0000.0000.0000.000
12A72LEU00.0070.0236.9650.3230.3230.0000.0000.0000.000
13A73SER0-0.008-0.0128.7880.0170.0170.0000.0000.0000.000
14A74SER00.007-0.00210.5080.0510.0510.0000.0000.0000.000
15A75PRO0-0.0020.02912.973-0.036-0.0360.0000.0000.0000.000
16A76ILE00.005-0.00314.1110.0400.0400.0000.0000.0000.000
17A77TYR00.003-0.00913.211-0.023-0.0230.0000.0000.0000.000
18A78PRO00.0420.01614.8190.0010.0010.0000.0000.0000.000
19A79HIS00.0730.03610.438-0.061-0.0610.0000.0000.0000.000
20A80ILE0-0.043-0.0109.5180.0050.0050.0000.0000.0000.000
21A81SER0-0.010-0.03911.051-0.036-0.0360.0000.0000.0000.000
22A82GLU-1-0.912-0.94512.7020.0330.0330.0000.0000.0000.000
23A83GLN00.0160.0107.3680.0680.0680.0000.0000.0000.000
24A84ILE0-0.0120.0029.081-0.137-0.1370.0000.0000.0000.000
25A85ILE00.0540.02610.661-0.078-0.0780.0000.0000.0000.000
26A86SER0-0.027-0.01810.103-0.028-0.0280.0000.0000.0000.000
27A87GLN0-0.042-0.0345.790-0.437-0.4370.0000.0000.0000.000
28A88LEU00.001-0.0019.510-0.046-0.0460.0000.0000.0000.000
29A89LEU00.0040.00212.8500.0020.0020.0000.0000.0000.000
30A90TYR0-0.015-0.0089.8420.0210.0210.0000.0000.0000.000
31A91LEU00.0200.0069.0210.0100.0100.0000.0000.0000.000
32A92GLU-1-0.719-0.80712.906-0.134-0.1340.0000.0000.0000.000
33A93TYR0-0.053-0.03616.0090.0350.0350.0000.0000.0000.000
34A94GLU-1-0.840-0.87513.479-0.316-0.3160.0000.0000.0000.000
35A95SER0-0.051-0.06916.0390.0340.0340.0000.0000.0000.000
36A96LYS10.7870.89817.5290.1490.1490.0000.0000.0000.000
37A97ARG11.0051.00119.9170.1080.1080.0000.0000.0000.000
38A98LYS10.8470.93315.0750.2960.2960.0000.0000.0000.000
39A99PRO00.0270.01416.364-0.026-0.0260.0000.0000.0000.000
40A100ILE0-0.020-0.00111.017-0.047-0.0470.0000.0000.0000.000
41A101HIS00.0150.02710.7210.0890.0890.0000.0000.0000.000
42A102LEU00.0460.0189.908-0.092-0.0920.0000.0000.0000.000
43A103TYR0-0.008-0.0119.2070.0760.0760.0000.0000.0000.000
44A104ILE00.000-0.00910.5130.0480.0480.0000.0000.0000.000
45A105ASN0-0.031-0.01812.531-0.031-0.0310.0000.0000.0000.000
46A106SER0-0.003-0.02313.7110.0360.0360.0000.0000.0000.000
47A107THR0-0.025-0.03515.721-0.018-0.0180.0000.0000.0000.000
48A108GLY00.0280.01817.811-0.013-0.0130.0000.0000.0000.000
49A109ASP-1-0.796-0.87518.2720.0840.0840.0000.0000.0000.000
50A110ILE0-0.0080.00220.592-0.002-0.0020.0000.0000.0000.000
51A111ASP-1-0.801-0.91819.0390.1820.1820.0000.0000.0000.000
52A112ASN0-0.024-0.01621.669-0.014-0.0140.0000.0000.0000.000
53A113ASN0-0.029-0.02224.781-0.003-0.0030.0000.0000.0000.000
54A114LYS10.9310.98224.471-0.077-0.0770.0000.0000.0000.000
55A115ILE00.0330.01523.7630.0080.0080.0000.0000.0000.000
56A116ILE0-0.053-0.01617.908-0.001-0.0010.0000.0000.0000.000
57A117ASN0-0.013-0.03617.9210.0000.0000.0000.0000.0000.000
58A118LEU0-0.008-0.00421.025-0.007-0.0070.0000.0000.0000.000
59A119ASN00.0140.01221.875-0.010-0.0100.0000.0000.0000.000
60A120GLY00.0700.03920.301-0.004-0.0040.0000.0000.0000.000
61A121ILE00.011-0.00521.013-0.006-0.0060.0000.0000.0000.000
62A122THR00.0510.01723.085-0.006-0.0060.0000.0000.0000.000
63A123ASP-1-0.808-0.85618.0550.0410.0410.0000.0000.0000.000
64A124VAL0-0.028-0.02018.720-0.012-0.0120.0000.0000.0000.000
65A125ILE0-0.036-0.02019.813-0.013-0.0130.0000.0000.0000.000
66A126SER0-0.009-0.01719.736-0.009-0.0090.0000.0000.0000.000
67A127ILE0-0.036-0.01115.057-0.012-0.0120.0000.0000.0000.000
68A128VAL0-0.007-0.01118.078-0.018-0.0180.0000.0000.0000.000
69A129ASP-1-0.841-0.89820.512-0.046-0.0460.0000.0000.0000.000
70A130VAL0-0.031-0.01616.549-0.007-0.0070.0000.0000.0000.000
71A131ILE0-0.055-0.03416.009-0.015-0.0150.0000.0000.0000.000
72A132ASN0-0.048-0.02119.058-0.005-0.0050.0000.0000.0000.000
73A133TYR0-0.121-0.06521.9410.0020.0020.0000.0000.0000.000
74A134ILE0-0.070-0.02316.637-0.004-0.0040.0000.0000.0000.000
75A135SER0-0.054-0.04620.7810.0080.0080.0000.0000.0000.000
76A136SER0-0.045-0.03516.825-0.002-0.0020.0000.0000.0000.000
77A137ASP-1-0.783-0.85918.647-0.108-0.1080.0000.0000.0000.000
78A138VAL00.018-0.00314.768-0.030-0.0300.0000.0000.0000.000
79A139TYR0-0.025-0.00915.5770.0270.0270.0000.0000.0000.000
80A140THR00.000-0.01214.643-0.028-0.0280.0000.0000.0000.000
81A141TYR0-0.015-0.01513.3570.0170.0170.0000.0000.0000.000
82A142CYS0-0.0310.00814.3510.0200.0200.0000.0000.0000.000
83A143LEU0-0.003-0.03511.555-0.006-0.0060.0000.0000.0000.000
84A144GLY00.0050.00515.4910.0140.0140.0000.0000.0000.000
85A145LYS10.9310.99517.165-0.152-0.1520.0000.0000.0000.000
86A146ALA00.0670.03017.1620.0120.0120.0000.0000.0000.000
87A147TYR00.000-0.00519.142-0.007-0.0070.0000.0000.0000.000
88A148GLY00.0880.04420.8770.0070.0070.0000.0000.0000.000
89A149ILE00.0010.00019.070-0.008-0.0080.0000.0000.0000.000
90A150ALA00.0210.00417.071-0.009-0.0090.0000.0000.0000.000
91A151CYS0-0.0230.01118.514-0.012-0.0120.0000.0000.0000.000
92A152ILE00.0110.00821.257-0.010-0.0100.0000.0000.0000.000
93A153LEU0-0.0010.02014.269-0.010-0.0100.0000.0000.0000.000
94A154ALA00.0390.01217.734-0.017-0.0170.0000.0000.0000.000
95A155SER0-0.0290.00718.666-0.013-0.0130.0000.0000.0000.000
96A156SER0-0.009-0.03819.822-0.001-0.0010.0000.0000.0000.000
97A157GLY0-0.0190.01319.036-0.010-0.0100.0000.0000.0000.000
98A158LYS10.8140.88819.6900.1050.1050.0000.0000.0000.000
99A159LYS10.8430.91322.0010.0380.0380.0000.0000.0000.000
100A160GLY0-0.018-0.00524.923-0.003-0.0030.0000.0000.0000.000
101A161TYR0-0.076-0.05519.8900.0000.0000.0000.0000.0000.000
102A162ARG10.7640.89019.3490.0270.0270.0000.0000.0000.000
103A163PHE00.0270.00818.0380.0090.0090.0000.0000.0000.000
104A164SER00.0360.00718.9330.0080.0080.0000.0000.0000.000
105A165LEU0-0.0160.01216.353-0.005-0.0050.0000.0000.0000.000
106A166LYS11.0080.99120.304-0.003-0.0030.0000.0000.0000.000
107A167ASN0-0.028-0.02122.498-0.004-0.0040.0000.0000.0000.000
108A168SER0-0.035-0.00919.0900.0100.0100.0000.0000.0000.000
109A169SER0-0.050-0.01821.440-0.005-0.0050.0000.0000.0000.000
110A170PHE00.015-0.01520.1570.0060.0060.0000.0000.0000.000
111A171CYS0-0.026-0.00523.672-0.001-0.0010.0000.0000.0000.000
112A172LEU00.0020.01024.7320.0010.0010.0000.0000.0000.000
113A173ASN00.0350.00425.0830.0000.0000.0000.0000.0000.000
114A174GLN00.0080.01628.745-0.004-0.0040.0000.0000.0000.000
115A175SER0-0.029-0.03031.2690.0020.0020.0000.0000.0000.000
116A176TYR0-0.096-0.07324.613-0.003-0.0030.0000.0000.0000.000
117A177SER0-0.017-0.02130.285-0.002-0.0020.0000.0000.0000.000
118A178ILE00.0210.01726.6440.0010.0010.0000.0000.0000.000
119A179ILE00.0010.00730.154-0.002-0.0020.0000.0000.0000.000
120A180PRO0-0.011-0.00928.4650.0030.0030.0000.0000.0000.000
121A181PHE0-0.006-0.00130.700-0.002-0.0020.0000.0000.0000.000
122A182ASN0-0.021-0.01230.462-0.003-0.0030.0000.0000.0000.000
123A183GLN00.0490.02433.8390.0000.0000.0000.0000.0000.000
124A184ALA00.0180.02234.7070.0000.0000.0000.0000.0000.000
125A185THR00.003-0.01036.054-0.001-0.0010.0000.0000.0000.000
126A186ASN00.0070.00737.776-0.001-0.0010.0000.0000.0000.000
127A187ILE00.1010.04737.9680.0000.0000.0000.0000.0000.000
128A188GLU-1-0.847-0.90439.2730.0040.0040.0000.0000.0000.000
129A189ILE0-0.022-0.02935.384-0.001-0.0010.0000.0000.0000.000
130A190GLN00.0750.04033.637-0.002-0.0020.0000.0000.0000.000
131A191ASN0-0.043-0.04535.2370.0010.0010.0000.0000.0000.000
132A192LYS10.8950.94337.433-0.003-0.0030.0000.0000.0000.000
133A193GLU-1-0.912-0.93929.9840.0090.0090.0000.0000.0000.000
134A194ILE0-0.007-0.00232.4570.0000.0000.0000.0000.0000.000
135A195MET0-0.012-0.00633.4500.0000.0000.0000.0000.0000.000
136A196ASN0-0.045-0.03332.867-0.003-0.0030.0000.0000.0000.000
137A197THR0-0.018-0.00827.885-0.003-0.0030.0000.0000.0000.000
138A198LYS10.9120.94530.074-0.017-0.0170.0000.0000.0000.000
139A199LYS10.8490.91132.4080.0090.0090.0000.0000.0000.000
140A200LYS10.9840.98428.3900.0080.0080.0000.0000.0000.000
141A201VAL00.0130.01226.479-0.003-0.0030.0000.0000.0000.000
142A202ILE00.0360.02228.624-0.001-0.0010.0000.0000.0000.000
143A203GLU-1-0.822-0.87130.821-0.014-0.0140.0000.0000.0000.000
144A204ILE0-0.007-0.00424.502-0.003-0.0030.0000.0000.0000.000
145A205ILE00.0200.01326.622-0.003-0.0030.0000.0000.0000.000
146A206SER00.003-0.01428.307-0.001-0.0010.0000.0000.0000.000
147A207LYS10.9370.99125.4960.0410.0410.0000.0000.0000.000
148A208ASN0-0.058-0.05023.905-0.006-0.0060.0000.0000.0000.000
149A209THR0-0.018-0.01727.445-0.002-0.0020.0000.0000.0000.000
150A210GLU-1-0.859-0.89529.817-0.028-0.0280.0000.0000.0000.000
151A211LYS10.8270.92332.1400.0110.0110.0000.0000.0000.000
152A212ASP-1-0.846-0.91834.910-0.010-0.0100.0000.0000.0000.000
153A213THR00.013-0.01634.9030.0010.0010.0000.0000.0000.000
154A214ASN0-0.016-0.00536.6800.0010.0010.0000.0000.0000.000
155A215VAL00.0520.02336.2170.0020.0020.0000.0000.0000.000
156A216ILE0-0.0040.00131.7670.0020.0020.0000.0000.0000.000
157A217SER00.004-0.01434.3110.0020.0020.0000.0000.0000.000
158A218ASN0-0.092-0.03536.3530.0010.0010.0000.0000.0000.000
159A219VAL0-0.026-0.00432.6950.0020.0020.0000.0000.0000.000
160A220LEU0-0.0200.00629.8460.0020.0020.0000.0000.0000.000
161A221GLU-1-0.875-0.92933.7550.0120.0120.0000.0000.0000.000
162A222ARG10.8550.91035.187-0.015-0.0150.0000.0000.0000.000
163A223ASP-1-0.814-0.88831.0400.0340.0340.0000.0000.0000.000
164A224LYS10.8210.91230.580-0.014-0.0140.0000.0000.0000.000
165A225TYR0-0.014-0.02227.0130.0040.0040.0000.0000.0000.000
166A226PHE0-0.001-0.00126.668-0.004-0.0040.0000.0000.0000.000
167A227ASN00.0550.03526.3230.0030.0030.0000.0000.0000.000
168A228ALA00.0630.00724.224-0.003-0.0030.0000.0000.0000.000
169A229ASP-1-0.867-0.93825.719-0.005-0.0050.0000.0000.0000.000
170A230GLU-1-0.838-0.92029.2530.0110.0110.0000.0000.0000.000
171A231ALA0-0.050-0.02625.235-0.001-0.0010.0000.0000.0000.000
172A232VAL0-0.009-0.00626.255-0.003-0.0030.0000.0000.0000.000
173A233ASP-1-0.944-0.95428.198-0.008-0.0080.0000.0000.0000.000
174A234PHE0-0.002-0.01329.624-0.001-0.0010.0000.0000.0000.000
175A235LYS10.8660.92228.6590.0190.0190.0000.0000.0000.000
176A236LEU0-0.023-0.01324.612-0.003-0.0030.0000.0000.0000.000
177A237ILE0-0.044-0.02920.953-0.004-0.0040.0000.0000.0000.000
178A238ASP-1-0.794-0.86423.628-0.045-0.0450.0000.0000.0000.000
179A239HIS0-0.007-0.00223.4810.0060.0060.0000.0000.0000.000
180A240ILE00.007-0.00222.960-0.001-0.0010.0000.0000.0000.000
181A241LEU0-0.059-0.02417.769-0.003-0.0030.0000.0000.0000.000
182A242GLU-1-0.928-0.96622.074-0.018-0.0180.0000.0000.0000.000
183A243LYS10.9390.97421.0850.0200.0200.0000.0000.0000.000