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: 7GYQK

Calculation Name: 1CMX-A-Xray372

Preferred Name:

Target Type:

Ligand Name: amino-acetaldehyde

ligand 3-letter code: GLZ

PDB ID: 1CMX

Chain ID: A

ChEMBL ID:

UniProt ID: P0CG48

Base Structure: X-ray

Registration Date: 2023-03-13

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 214
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2548017.255146
FMO2-HF: Nuclear repulsion 2465126.050035
FMO2-HF: Total energy -82891.205112
FMO2-MP2: Total energy -83136.826768


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:6:ARG)


Summations of interaction energy for fragment #1(A:6:ARG)
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.
-157.098-154.4870.058-0.869-1.8-0.002
Interaction energy analysis for fragmet #1(A:6:ARG)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 1 / q_Mulliken : 0.946 / q_NPA : 0.955
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].
3A8VAL00.0260.0253.8221.4133.051-0.023-0.711-0.905-0.001
4A9VAL00.0010.0006.765-0.431-0.4310.0000.0000.0000.000
5A10PRO0-0.027-0.01510.343-0.008-0.0080.0000.0000.0000.000
6A11ILE00.0690.03512.4360.5600.5600.0000.0000.0000.000
7A12GLU-1-0.650-0.71614.826-11.689-11.6890.0000.0000.0000.000
8A13SER0-0.020-0.00818.6180.0410.0410.0000.0000.0000.000
9A14ASN0-0.041-0.04320.9650.7390.7390.0000.0000.0000.000
10A15PRO00.0570.01922.197-0.360-0.3600.0000.0000.0000.000
11A16GLU-1-0.927-0.96423.600-11.208-11.2080.0000.0000.0000.000
12A17VAL00.0720.04017.865-0.181-0.1810.0000.0000.0000.000
13A18PHE0-0.028-0.01817.715-0.459-0.4590.0000.0000.0000.000
14A19THR00.0220.00620.134-0.146-0.1460.0000.0000.0000.000
15A20ASN0-0.053-0.00719.655-0.347-0.3470.0000.0000.0000.000
16A21PHE00.014-0.01113.286-0.207-0.2070.0000.0000.0000.000
17A22ALA0-0.019-0.00118.082-0.201-0.2010.0000.0000.0000.000
18A23HIS0-0.052-0.03820.3300.1720.1720.0000.0000.0000.000
19A24LYS10.8700.95516.84414.70914.7090.0000.0000.0000.000
20A25LEU0-0.028-0.01415.185-0.280-0.2800.0000.0000.0000.000
21A26GLY00.0440.00019.130-0.012-0.0120.0000.0000.0000.000
22A27LEU0-0.070-0.00622.5390.4160.4160.0000.0000.0000.000
23A28LYS10.8920.95624.4729.3499.3490.0000.0000.0000.000
24A29ASN00.014-0.01827.880-0.204-0.2040.0000.0000.0000.000
25A30GLU-1-0.979-0.97429.440-8.024-8.0240.0000.0000.0000.000
26A31TRP0-0.030-0.00528.2040.1920.1920.0000.0000.0000.000
27A32ALA00.0280.01326.414-0.204-0.2040.0000.0000.0000.000
28A33TYR00.010-0.01021.409-0.039-0.0390.0000.0000.0000.000
29A34PHE0-0.026-0.02125.8870.1580.1580.0000.0000.0000.000
30A35ASP-1-0.852-0.93227.512-9.962-9.9620.0000.0000.0000.000
31A36ILE0-0.060-0.02228.5390.3140.3140.0000.0000.0000.000
32A37TYR00.0260.00029.919-0.059-0.0590.0000.0000.0000.000
33A38SER00.002-0.00732.2800.1620.1620.0000.0000.0000.000
34A39LEU0-0.0210.00031.0680.0480.0480.0000.0000.0000.000
35A40THR0-0.053-0.04434.5670.0420.0420.0000.0000.0000.000
36A41GLU-1-0.877-0.94538.231-6.973-6.9730.0000.0000.0000.000
37A42PRO0-0.0190.00239.779-0.064-0.0640.0000.0000.0000.000
38A43GLU-1-0.905-0.98041.665-6.548-6.5480.0000.0000.0000.000
39A44LEU00.0290.02437.325-0.066-0.0660.0000.0000.0000.000
40A45LEU0-0.063-0.01935.416-0.155-0.1550.0000.0000.0000.000
41A46ALA00.0100.00638.099-0.022-0.0220.0000.0000.0000.000
42A47PHE0-0.093-0.03837.4010.0810.0810.0000.0000.0000.000
43A48LEU0-0.013-0.00431.873-0.218-0.2180.0000.0000.0000.000
44A49PRO0-0.0060.00332.9050.2020.2020.0000.0000.0000.000
45A50ARG10.8540.94734.1477.5857.5850.0000.0000.0000.000
46A51PRO0-0.036-0.03634.1020.1130.1130.0000.0000.0000.000
47A52VAL00.004-0.00429.630-0.179-0.1790.0000.0000.0000.000
48A53LYS10.9530.95228.8788.7738.7730.0000.0000.0000.000
49A54ALA00.0280.02224.431-0.193-0.1930.0000.0000.0000.000
50A55ILE0-0.0110.00425.7160.1690.1690.0000.0000.0000.000
51A56VAL0-0.021-0.00719.863-0.315-0.3150.0000.0000.0000.000
52A57LEU0-0.002-0.00622.0810.4120.4120.0000.0000.0000.000
53A58LEU0-0.031-0.01818.399-0.605-0.6050.0000.0000.0000.000
54A59PHE00.0160.00420.7550.4980.4980.0000.0000.0000.000
55A60PRO00.0480.02120.654-0.696-0.6960.0000.0000.0000.000
56A61ILE0-0.075-0.02117.1050.0980.0980.0000.0000.0000.000
57A62ASN00.0040.00220.315-0.399-0.3990.0000.0000.0000.000
58A78ASP-1-0.959-0.99128.309-9.620-9.6200.0000.0000.0000.000
59A79VAL00.0450.03624.5010.1480.1480.0000.0000.0000.000
60A80ILE0-0.027-0.01120.080-0.358-0.3580.0000.0000.0000.000
61A81TRP0-0.045-0.01716.728-0.288-0.2880.0000.0000.0000.000
62A82PHE00.019-0.00213.886-0.290-0.2900.0000.0000.0000.000
63A83LYS10.8630.95311.96220.12820.1280.0000.0000.0000.000
64A84GLN0-0.048-0.0329.0350.4780.4780.0000.0000.0000.000
65A85SER0-0.052-0.0456.7890.4780.4780.0000.0000.0000.000
66A86VAL0-0.035-0.0073.097-6.029-5.4430.082-0.105-0.563-0.001
67A87LYS10.8440.9074.37730.47430.644-0.001-0.023-0.1450.000
68A88ASN00.019-0.0046.237-0.189-0.1890.0000.0000.0000.000
69A89ALA00.0140.0177.0181.4881.4880.0000.0000.0000.000
70A90CYS0-0.0460.0139.0330.8400.8400.0000.0000.0000.000
71A91GLY00.1030.03812.3880.6950.6950.0000.0000.0000.000
72A92LEU00.0180.0129.7300.5960.5960.0000.0000.0000.000
73A93TYR00.0420.0048.526-0.643-0.6430.0000.0000.0000.000
74A94ALA00.0090.03913.7250.6900.6900.0000.0000.0000.000
75A95ILE00.0280.02415.9280.7210.7210.0000.0000.0000.000
76A96LEU0-0.004-0.00313.0530.5120.5120.0000.0000.0000.000
77A97HIS0-0.021-0.00816.2830.3340.3340.0000.0000.0000.000
78A98SER00.033-0.00119.4220.6720.6720.0000.0000.0000.000
79A99LEU00.0030.00319.8580.5540.5540.0000.0000.0000.000
80A100SER00.007-0.01419.4030.3010.3010.0000.0000.0000.000
81A101ASN0-0.064-0.01922.0090.4100.4100.0000.0000.0000.000
82A102ASN00.0320.01424.8630.7180.7180.0000.0000.0000.000
83A103GLN00.0610.02424.877-0.067-0.0670.0000.0000.0000.000
84A104SER0-0.021-0.00726.7210.1450.1450.0000.0000.0000.000
85A105LEU0-0.042-0.02527.0860.2850.2850.0000.0000.0000.000
86A106LEU00.0050.01322.597-0.111-0.1110.0000.0000.0000.000
87A107GLU-1-0.893-0.95825.933-9.012-9.0120.0000.0000.0000.000
88A108PRO0-0.058-0.03126.431-0.360-0.3600.0000.0000.0000.000
89A109GLY0-0.0140.00726.4420.1410.1410.0000.0000.0000.000
90A110SER0-0.0300.00622.867-0.319-0.3190.0000.0000.0000.000
91A111ASP-1-0.861-0.94418.052-14.338-14.3380.0000.0000.0000.000
92A112LEU0-0.038-0.02617.647-0.480-0.4800.0000.0000.0000.000
93A113ASP-1-0.835-0.92219.837-10.830-10.8300.0000.0000.0000.000
94A114ASN0-0.029-0.02521.7000.4740.4740.0000.0000.0000.000
95A115PHE0-0.060-0.02015.928-0.107-0.1070.0000.0000.0000.000
96A116LEU0-0.012-0.01019.878-0.098-0.0980.0000.0000.0000.000
97A117LYS10.9170.96022.05310.43310.4330.0000.0000.0000.000
98A118SER0-0.0050.01221.5240.2600.2600.0000.0000.0000.000
99A119GLN00.0200.02518.347-0.106-0.1060.0000.0000.0000.000
100A120SER0-0.040-0.01322.6520.1920.1920.0000.0000.0000.000
101A121ASP-1-0.987-0.97526.164-10.242-10.2420.0000.0000.0000.000
102A122THR0-0.078-0.05323.6550.1280.1280.0000.0000.0000.000
103A123SER0-0.093-0.04125.9830.1460.1460.0000.0000.0000.000
104A124SER00.018-0.00820.4580.2570.2570.0000.0000.0000.000
105A125SER00.001-0.00518.5820.2690.2690.0000.0000.0000.000
106A126LYS10.9280.94021.73210.24210.2420.0000.0000.0000.000
107A127ASN0-0.043-0.01822.6030.0620.0620.0000.0000.0000.000
108A128ARG10.9661.00219.58713.51813.5180.0000.0000.0000.000
109A129PHE00.0550.02515.884-0.184-0.1840.0000.0000.0000.000
110A130ASP-1-0.884-0.96713.749-17.819-17.8190.0000.0000.0000.000
111A131ASP-1-0.885-0.92813.058-18.702-18.7020.0000.0000.0000.000
112A132VAL00.0190.0049.878-1.015-1.0150.0000.0000.0000.000
113A133THR0-0.011-0.01811.443-1.408-1.4080.0000.0000.0000.000
114A134THR00.0290.01812.3920.4980.4980.0000.0000.0000.000
115A135ASP-1-0.843-0.9197.557-29.221-29.2210.0000.0000.0000.000
116A136GLN0-0.045-0.0278.561-3.432-3.4320.0000.0000.0000.000
117A137PHE00.0370.02510.4540.1280.1280.0000.0000.0000.000
118A138VAL00.0180.0137.8250.3570.3570.0000.0000.0000.000
119A139LEU0-0.032-0.0343.927-1.338-1.1210.000-0.030-0.1870.000
120A140ASN0-0.048-0.0237.440-1.226-1.2260.0000.0000.0000.000
121A141VAL00.1130.08010.7710.8620.8620.0000.0000.0000.000
122A142ILE0-0.042-0.0085.8220.5540.5540.0000.0000.0000.000
123A143LYS10.8650.9226.87328.24728.2470.0000.0000.0000.000
124A144GLU-1-0.942-0.9599.483-16.508-16.5080.0000.0000.0000.000
125A145ASN0-0.055-0.06111.9972.1122.1120.0000.0000.0000.000
126A146VAL00.0100.0008.8750.2760.2760.0000.0000.0000.000
127A147GLN0-0.029-0.01611.3830.2090.2090.0000.0000.0000.000
128A148THR00.0700.03714.6060.2880.2880.0000.0000.0000.000
129A149PHE0-0.055-0.03410.1590.0580.0580.0000.0000.0000.000
130A150SER0-0.031-0.02113.0830.0510.0510.0000.0000.0000.000
131A151THR0-0.0500.00415.2650.6370.6370.0000.0000.0000.000
132A152GLY00.0370.01818.610-0.303-0.3030.0000.0000.0000.000
133A153GLN0-0.105-0.06621.4000.2260.2260.0000.0000.0000.000
134A154SER0-0.085-0.08820.8640.1390.1390.0000.0000.0000.000
135A155GLU-1-0.942-0.97719.764-12.049-12.0490.0000.0000.0000.000
136A156ALA0-0.025-0.00614.682-0.280-0.2800.0000.0000.0000.000
137A157PRO00.0200.01313.863-0.055-0.0550.0000.0000.0000.000
138A158GLU-1-0.912-0.96011.038-19.211-19.2110.0000.0000.0000.000
139A159ALA0-0.029-0.0056.582-0.404-0.4040.0000.0000.0000.000
140A160THR0-0.042-0.0337.225-1.100-1.1000.0000.0000.0000.000
141A161ALA00.004-0.0018.646-0.532-0.5320.0000.0000.0000.000
142A162ASP-1-0.878-0.93511.582-21.729-21.7290.0000.0000.0000.000
143A163THR00.0410.01113.2320.9750.9750.0000.0000.0000.000
144A164ASN0-0.036-0.01815.7840.3620.3620.0000.0000.0000.000
145A165LEU00.0120.02417.2670.6910.6910.0000.0000.0000.000
146A166HIS0-0.065-0.06014.613-1.560-1.5600.0000.0000.0000.000
147A167TYR00.012-0.03715.2880.8870.8870.0000.0000.0000.000
148A168ILE0-0.0200.00417.355-0.540-0.5400.0000.0000.0000.000
149A169THR0-0.038-0.02219.7200.1430.1430.0000.0000.0000.000
150A170TYR0-0.032-0.03221.940-0.034-0.0340.0000.0000.0000.000
151A171VAL00.030-0.00124.531-0.043-0.0430.0000.0000.0000.000
152A172GLU-1-0.924-0.96527.265-9.101-9.1010.0000.0000.0000.000
153A173GLU-1-0.923-0.96527.129-10.200-10.2000.0000.0000.0000.000
154A174ASN0-0.077-0.03430.2450.6000.6000.0000.0000.0000.000
155A175GLY0-0.005-0.00533.2280.0690.0690.0000.0000.0000.000
156A176GLY0-0.0670.01632.4360.1870.1870.0000.0000.0000.000
157A177ILE00.0580.03529.933-0.131-0.1310.0000.0000.0000.000
158A178PHE00.0200.00325.6580.0220.0220.0000.0000.0000.000
159A179GLU-1-0.708-0.79823.224-11.357-11.3570.0000.0000.0000.000
160A180LEU0-0.055-0.04320.059-0.247-0.2470.0000.0000.0000.000
161A181ASP-1-0.702-0.84316.688-16.013-16.0130.0000.0000.0000.000
162A182GLY00.0440.03113.999-0.106-0.1060.0000.0000.0000.000
163A183ARG10.8560.91110.96420.78620.7860.0000.0000.0000.000
164A184ASN00.0390.03814.699-0.021-0.0210.0000.0000.0000.000
165A185LEU00.007-0.02514.819-0.286-0.2860.0000.0000.0000.000
166A186SER0-0.044-0.01117.839-0.195-0.1950.0000.0000.0000.000
167A187GLY00.0030.01019.8560.4890.4890.0000.0000.0000.000
168A188PRO0-0.023-0.01420.9340.0440.0440.0000.0000.0000.000
169A189LEU0-0.0190.00622.8560.2410.2410.0000.0000.0000.000
170A190TYR0-0.032-0.01325.7090.2820.2820.0000.0000.0000.000
171A191LEU0-0.013-0.02728.6290.0550.0550.0000.0000.0000.000
172A192GLY00.0040.00531.1830.2850.2850.0000.0000.0000.000
173A193LYS10.8690.91633.7597.6087.6080.0000.0000.0000.000
174A194SER00.009-0.03235.201-0.055-0.0550.0000.0000.0000.000
175A195ASP-1-0.885-0.94336.512-7.095-7.0950.0000.0000.0000.000
176A196PRO0-0.074-0.05039.446-0.031-0.0310.0000.0000.0000.000
177A197THR0-0.069-0.01941.2290.1000.1000.0000.0000.0000.000
178A198ALA00.0220.02737.5600.0510.0510.0000.0000.0000.000
179A199THR0-0.055-0.02639.064-0.111-0.1110.0000.0000.0000.000
180A200ASP-1-0.798-0.91033.976-8.170-8.1700.0000.0000.0000.000
181A201LEU00.0380.01928.2560.1070.1070.0000.0000.0000.000
182A202ILE0-0.020-0.00532.236-0.053-0.0530.0000.0000.0000.000
183A203GLU-1-0.988-0.99734.161-7.085-7.0850.0000.0000.0000.000
184A204GLN00.0500.03033.7050.1670.1670.0000.0000.0000.000
185A205GLU-1-0.891-0.95834.781-7.662-7.6620.0000.0000.0000.000
186A206LEU0-0.025-0.01033.346-0.087-0.0870.0000.0000.0000.000
187A207VAL00.0180.01629.263-0.239-0.2390.0000.0000.0000.000
188A208ARG10.9650.98331.3057.5867.5860.0000.0000.0000.000
189A209VAL00.0170.01233.463-0.076-0.0760.0000.0000.0000.000
190A210ARG10.8210.91525.86810.43910.4390.0000.0000.0000.000
191A211VAL00.036-0.00127.779-0.188-0.1880.0000.0000.0000.000
192A212ALA0-0.020-0.01729.797-0.110-0.1100.0000.0000.0000.000
193A213SER0-0.046-0.02331.2580.0150.0150.0000.0000.0000.000
194A214TYR0-0.045-0.03025.068-0.130-0.1300.0000.0000.0000.000
195A215MET0-0.021-0.02128.831-0.064-0.0640.0000.0000.0000.000
196A216GLU-1-0.950-0.95630.827-8.053-8.0530.0000.0000.0000.000
197A217ASN00.0080.00128.513-0.195-0.1950.0000.0000.0000.000
198A218ALA00.0080.00029.105-0.043-0.0430.0000.0000.0000.000
199A219ASN0-0.039-0.04230.045-0.017-0.0170.0000.0000.0000.000
200A220GLU-1-0.995-0.97933.048-8.351-8.3510.0000.0000.0000.000
201A221GLU-1-1.006-0.99427.659-10.311-10.3110.0000.0000.0000.000
202A222ASP-1-0.958-0.95431.602-8.445-8.4450.0000.0000.0000.000
203A223VAL0-0.086-0.04026.690-0.192-0.1920.0000.0000.0000.000
204A224LEU00.013-0.01529.3130.1060.1060.0000.0000.0000.000
205A225ASN0-0.067-0.03323.6340.1910.1910.0000.0000.0000.000
206A226PHE00.0560.01424.671-0.381-0.3810.0000.0000.0000.000
207A227ALA0-0.0060.00923.4760.2600.2600.0000.0000.0000.000
208A228MET0-0.009-0.00424.538-0.192-0.1920.0000.0000.0000.000
209A229LEU0-0.0020.01321.6900.1750.1750.0000.0000.0000.000
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