FMODB

FMODB: The database of quantum mechanical data based on the FMO method

Last updated: 2025-10-17

All entries: 77277

Number of unique PDB entries: 32023

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FMODB ID: N8ZYQ

Calculation Name: 3UMB-A-Xray547

Preferred Name:

Target Type:

Ligand Name: potassium ion

Ligand 3-letter code: K

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 3UMB

Chain ID: A

ChEMBL ID:

UniProt ID: Q8XZN3

Base Structure: X-ray

Registration Date: 2025-10-04

Reference: Sci Data 11, 1164 (2024).

DOI: https://doi.org/10.1038/s41597-024-03999-2

Apendix: None


IFIE MAP

IFIE Diagram


Modeling method
Optimization MOE:Amber10:EHT
Restraint OptAll
Protonation MOE:Protonate 3D
Complement MOE:Homology Modeling
Water No
Procedure Manual calculation
Remarks
ac.sh, 23 2024 Oct; Missing atoms/residues were imported from a 100% homology model, which was constructed by MOE.
FMO calculation
FMO method FMO2-MP2/6-31G(d)
Fragmentation Auto
Number of fragment 227
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922
Total energy (hartree)
FMO2-HF: Electronic energy -2709279.722035
FMO2-HF: Nuclear repulsion 2622378.674601
FMO2-HF: Total energy -86901.047433
FMO2-MP2: Total energy -87154.918244


3D Structure Molmil
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:2:THR)


Summations of interaction energy for fragment #1(A:2:THR)
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.
-86.041-81.8132.133-2.276-4.084-0.017
Interaction energy analysis for fragmet #1(A:2:THR)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 1 / q_Mulliken : 0.837 / q_NPA : 0.909
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].
3A4ILE00.0460.0343.8352.2923.799-0.015-0.569-0.923-0.001
172A173ALA00.0490.0332.199-1.591-1.3390.987-0.365-0.873-0.002
173A174GLN0-0.010-0.0102.633-9.417-7.8661.018-0.985-1.585-0.011
174A175ILE0-0.0330.0004.6302.8562.913-0.001-0.006-0.0500.000
193A194THR0-0.0230.0002.889-6.914-6.0530.144-0.351-0.653-0.003
4A5ARG10.8750.9275.58631.98531.9850.0000.0000.0000.000
5A6ALA00.0360.0328.2642.8362.8360.0000.0000.0000.000
6A7VAL00.0070.0158.985-2.754-2.7540.0000.0000.0000.000
7A8VAL0-0.045-0.02311.4421.9721.9720.0000.0000.0000.000
8A9PHE00.0420.01313.364-0.800-0.8000.0000.0000.0000.000
9A10ASP-1-0.801-0.90116.162-13.802-13.8020.0000.0000.0000.000
10A11ALA00.001-0.00218.6710.1460.1460.0000.0000.0000.000
11A12TYR00.017-0.00922.298-0.002-0.0020.0000.0000.0000.000
12A13GLY00.0470.03123.879-0.218-0.2180.0000.0000.0000.000
13A14THR0-0.0520.00518.229-0.345-0.3450.0000.0000.0000.000
14A15LEU00.0250.00719.4570.0770.0770.0000.0000.0000.000
15A16PHE0-0.019-0.02822.5150.3230.3230.0000.0000.0000.000
16A17ASP-1-0.817-0.91226.186-10.745-10.7450.0000.0000.0000.000
17A18VAL00.013-0.01228.0610.2350.2350.0000.0000.0000.000
18A19TYR0-0.0040.00630.7100.4460.4460.0000.0000.0000.000
19A20SER00.0130.00133.3200.1870.1870.0000.0000.0000.000
20A21VAL00.0130.00633.7110.3200.3200.0000.0000.0000.000
21A22ALA00.0310.01435.7680.2400.2400.0000.0000.0000.000
22A23ALA00.0010.00737.4780.2510.2510.0000.0000.0000.000
23A24ARG10.8040.88739.4367.7167.7160.0000.0000.0000.000
24A25ALA0-0.006-0.00139.8140.2220.2220.0000.0000.0000.000
25A26GLU-1-0.785-0.90041.660-7.142-7.1420.0000.0000.0000.000
26A27GLN0-0.067-0.02443.8030.1250.1250.0000.0000.0000.000
27A28LEU0-0.059-0.02443.3890.1780.1780.0000.0000.0000.000
28A29PHE0-0.041-0.02943.6440.1560.1560.0000.0000.0000.000
29A30PRO00.0500.02445.918-0.110-0.1100.0000.0000.0000.000
30A31GLY0-0.0040.00446.2750.1170.1170.0000.0000.0000.000
31A32LYS10.8750.92844.2516.6476.6470.0000.0000.0000.000
32A33GLY00.0390.02541.618-0.110-0.1100.0000.0000.0000.000
33A34GLU-1-0.909-0.94937.502-8.541-8.5410.0000.0000.0000.000
34A35ALA00.0150.00437.887-0.212-0.2120.0000.0000.0000.000
35A36LEU0-0.002-0.00738.852-0.140-0.1400.0000.0000.0000.000
36A37SER0-0.067-0.04135.233-0.238-0.2380.0000.0000.0000.000
37A38VAL00.0320.01833.667-0.291-0.2910.0000.0000.0000.000
38A39LEU0-0.012-0.00134.074-0.188-0.1880.0000.0000.0000.000
39A40TRP0-0.030-0.03235.490-0.045-0.0450.0000.0000.0000.000
40A41ARG10.8880.93924.69711.43811.4380.0000.0000.0000.000
41A42ASP-1-0.844-0.91430.581-9.621-9.6210.0000.0000.0000.000
42A43ARG10.8920.93331.5898.4648.4640.0000.0000.0000.000
43A44GLN00.008-0.00629.508-0.301-0.3010.0000.0000.0000.000
44A45ILE0-0.029-0.01025.654-0.210-0.2100.0000.0000.0000.000
45A46ASP-1-0.861-0.92928.575-10.023-10.0230.0000.0000.0000.000
46A47TYR0-0.045-0.03530.8550.0360.0360.0000.0000.0000.000
47A48THR0-0.063-0.02927.063-0.139-0.1390.0000.0000.0000.000
48A49ARG10.9600.99223.81211.83711.8370.0000.0000.0000.000
49A50ILE00.0220.00527.7550.0180.0180.0000.0000.0000.000
50A51ARG10.8410.92330.7078.9148.9140.0000.0000.0000.000
51A52SER00.013-0.00525.8810.0560.0560.0000.0000.0000.000
52A53LEU0-0.036-0.00426.793-0.168-0.1680.0000.0000.0000.000
53A54ALA0-0.006-0.00328.7480.1420.1420.0000.0000.0000.000
54A55GLY0-0.050-0.02030.7910.3020.3020.0000.0000.0000.000
55A56PRO00.0260.01326.968-0.248-0.2480.0000.0000.0000.000
56A57SER0-0.031-0.03726.532-0.503-0.5030.0000.0000.0000.000
57A58GLY00.0110.01328.7610.0700.0700.0000.0000.0000.000
58A59GLU-1-0.853-0.90629.661-9.346-9.3460.0000.0000.0000.000
59A60HIS00.009-0.00332.5760.3120.3120.0000.0000.0000.000
60A61TYR0-0.091-0.06227.821-0.018-0.0180.0000.0000.0000.000
61A62LYS10.8250.89631.8768.4428.4420.0000.0000.0000.000
62A63PRO00.0540.04031.118-0.316-0.3160.0000.0000.0000.000
63A64PHE00.0340.02427.8510.1730.1730.0000.0000.0000.000
64A65TRP00.0400.01630.6390.0350.0350.0000.0000.0000.000
65A66ASP-1-0.846-0.94333.573-8.328-8.3280.0000.0000.0000.000
66A67VAL0-0.053-0.01931.5920.2130.2130.0000.0000.0000.000
67A68THR00.0140.00231.978-0.006-0.0060.0000.0000.0000.000
68A69VAL00.0290.01834.3220.1610.1610.0000.0000.0000.000
69A70ASP-1-0.841-0.90536.695-7.970-7.9700.0000.0000.0000.000
70A71ALA0-0.016-0.00534.9210.1740.1740.0000.0000.0000.000
71A72LEU0-0.0150.01136.9840.1390.1390.0000.0000.0000.000
72A73ARG10.8640.87639.0867.4387.4380.0000.0000.0000.000
73A74TYR00.0050.01339.4360.1330.1330.0000.0000.0000.000
74A75ALA00.0150.00138.5850.1450.1450.0000.0000.0000.000
75A76CYS0-0.014-0.00140.7420.0980.0980.0000.0000.0000.000
76A77ALA00.0050.01143.9010.1510.1510.0000.0000.0000.000
77A78ARG10.8850.94340.1407.7397.7390.0000.0000.0000.000
78A79LEU0-0.018-0.00941.3970.0480.0480.0000.0000.0000.000
79A80ASN0-0.070-0.02845.6980.1680.1680.0000.0000.0000.000
80A81LEU00.0100.01243.8660.1110.1110.0000.0000.0000.000
81A82PRO00.0040.00647.906-0.024-0.0240.0000.0000.0000.000
82A83LEU0-0.004-0.01743.2240.0110.0110.0000.0000.0000.000
83A84GLY00.0310.02747.1950.0520.0520.0000.0000.0000.000
84A85ASN00.025-0.01447.111-0.189-0.1890.0000.0000.0000.000
85A86HIS00.0330.02346.438-0.136-0.1360.0000.0000.0000.000
86A87ALA00.0270.03145.882-0.113-0.1130.0000.0000.0000.000
87A88GLU-1-0.767-0.84842.097-7.391-7.3910.0000.0000.0000.000
88A89ALA00.0180.00141.680-0.200-0.2000.0000.0000.0000.000
89A90THR0-0.068-0.04441.876-0.118-0.1180.0000.0000.0000.000
90A91LEU00.0340.02139.379-0.161-0.1610.0000.0000.0000.000
91A92MET0-0.013-0.00235.357-0.267-0.2670.0000.0000.0000.000
92A93ARG10.8800.93336.9586.9686.9680.0000.0000.0000.000
93A94GLU-1-0.831-0.89936.964-8.140-8.1400.0000.0000.0000.000
94A95TYR0-0.0040.00129.063-0.224-0.2240.0000.0000.0000.000
95A96ALA0-0.045-0.01632.490-0.310-0.3100.0000.0000.0000.000
96A97CYS0-0.093-0.04832.706-0.169-0.1690.0000.0000.0000.000
97A98LEU0-0.0150.01030.2020.1120.1120.0000.0000.0000.000
98A99SER00.0460.02930.697-0.038-0.0380.0000.0000.0000.000
99A100ALA00.001-0.00925.954-0.215-0.2150.0000.0000.0000.000
100A101PHE00.0220.02424.5950.3660.3660.0000.0000.0000.000
101A102PRO0-0.007-0.01926.198-0.360-0.3600.0000.0000.0000.000
102A103GLU-1-0.765-0.86722.985-13.916-13.9160.0000.0000.0000.000
103A104ASN00.0100.00122.163-0.592-0.5920.0000.0000.0000.000
104A105VAL00.0290.01622.105-0.515-0.5150.0000.0000.0000.000
105A106PRO00.005-0.00623.573-0.215-0.2150.0000.0000.0000.000
106A107VAL00.0070.02818.336-0.285-0.2850.0000.0000.0000.000
107A108LEU00.009-0.00817.964-0.693-0.6930.0000.0000.0000.000
108A109ARG10.9470.98119.14011.45811.4580.0000.0000.0000.000
109A110GLN0-0.007-0.01719.393-0.275-0.2750.0000.0000.0000.000
110A111LEU00.0030.01113.527-0.761-0.7610.0000.0000.0000.000
111A112ARG10.8010.89415.99214.49614.4960.0000.0000.0000.000
112A113GLU-1-0.894-0.96318.279-14.263-14.2630.0000.0000.0000.000
113A114MET0-0.090-0.02412.7110.3770.3770.0000.0000.0000.000
114A115GLY00.0020.00015.017-1.269-1.2690.0000.0000.0000.000
115A116LEU0-0.041-0.01310.423-0.842-0.8420.0000.0000.0000.000
116A117PRO0-0.0100.01112.6251.2781.2780.0000.0000.0000.000
117A118LEU00.0240.00213.619-1.360-1.3600.0000.0000.0000.000
118A119GLY00.003-0.02015.5111.0071.0070.0000.0000.0000.000
119A120ILE0-0.041-0.00416.667-0.454-0.4540.0000.0000.0000.000
120A121LEU00.0060.00215.4300.1150.1150.0000.0000.0000.000
121A122SER00.0070.00518.292-0.109-0.1090.0000.0000.0000.000
122A123ASN00.0740.01321.542-0.192-0.1920.0000.0000.0000.000
123A124GLY00.0340.01524.0110.4830.4830.0000.0000.0000.000
124A125ASN00.0540.05125.919-0.420-0.4200.0000.0000.0000.000
125A126PRO00.0580.02227.4740.0650.0650.0000.0000.0000.000
126A127GLN00.0340.02428.4500.0190.0190.0000.0000.0000.000
127A128MET0-0.0400.00429.6440.1800.1800.0000.0000.0000.000
128A129LEU0-0.035-0.00723.295-0.093-0.0930.0000.0000.0000.000
129A130GLU-1-0.874-0.96027.750-9.987-9.9870.0000.0000.0000.000
130A131ILE0-0.010-0.02129.2810.0310.0310.0000.0000.0000.000
131A132ALA00.0570.05628.2040.0840.0840.0000.0000.0000.000
132A133VAL0-0.019-0.01624.752-0.106-0.1060.0000.0000.0000.000
133A134LYS10.8990.95427.4419.1679.1670.0000.0000.0000.000
134A135SER0-0.019-0.00830.7860.3210.3210.0000.0000.0000.000
135A136ALA00.009-0.00727.772-0.036-0.0360.0000.0000.0000.000
136A137GLY0-0.033-0.00228.793-0.157-0.1570.0000.0000.0000.000
137A138MET0-0.0070.00024.065-0.344-0.3440.0000.0000.0000.000
138A139SER0-0.004-0.01124.684-0.325-0.3250.0000.0000.0000.000
139A140GLY00.0060.00925.0750.1780.1780.0000.0000.0000.000
140A141LEU0-0.034-0.01121.511-0.227-0.2270.0000.0000.0000.000
141A142PHE0-0.013-0.01118.409-0.634-0.6340.0000.0000.0000.000
142A143ASP-1-0.831-0.89418.160-14.871-14.8710.0000.0000.0000.000
143A144HIS0-0.017-0.00617.0190.9510.9510.0000.0000.0000.000
144A145VAL0-0.010-0.01319.541-0.396-0.3960.0000.0000.0000.000
145A146LEU0-0.0200.00116.9120.5020.5020.0000.0000.0000.000
146A147SER00.005-0.03520.9630.0360.0360.0000.0000.0000.000
147A148VAL00.0310.00621.573-0.074-0.0740.0000.0000.0000.000
148A149ASP-1-0.884-0.91123.528-9.896-9.8960.0000.0000.0000.000
149A150ALA0-0.028-0.01323.8960.2750.2750.0000.0000.0000.000
150A151VAL0-0.060-0.03521.524-0.037-0.0370.0000.0000.0000.000
151A152ARG10.8650.94724.8089.5649.5640.0000.0000.0000.000
152A153LEU00.0180.00923.7000.1690.1690.0000.0000.0000.000
153A154TYR0-0.050-0.04423.234-0.505-0.5050.0000.0000.0000.000
154A155LYS10.7790.90017.86015.61415.6140.0000.0000.0000.000
155A156THR0-0.036-0.01718.4570.8650.8650.0000.0000.0000.000
156A157ALA00.0410.01618.589-0.524-0.5240.0000.0000.0000.000
157A158PRO00.0670.01216.610-0.343-0.3430.0000.0000.0000.000
158A159ALA0-0.0120.00117.016-0.561-0.5610.0000.0000.0000.000
159A160ALA00.0070.01119.179-0.044-0.0440.0000.0000.0000.000
160A161TYR0-0.026-0.03413.651-0.254-0.2540.0000.0000.0000.000
161A162ALA00.000-0.01014.063-1.016-1.0160.0000.0000.0000.000
162A163LEU0-0.066-0.02815.4040.0770.0770.0000.0000.0000.000
163A164ALA00.0450.02312.9740.1680.1680.0000.0000.0000.000
164A165PRO00.016-0.00210.623-0.055-0.0550.0000.0000.0000.000
165A166ARG10.9060.96412.62915.16815.1680.0000.0000.0000.000
166A167ALA0-0.0260.00216.0540.4240.4240.0000.0000.0000.000
167A168PHE00.011-0.01212.4420.4030.4030.0000.0000.0000.000
168A169GLY00.0060.02413.259-0.420-0.4200.0000.0000.0000.000
169A170VAL0-0.042-0.0208.146-0.553-0.5530.0000.0000.0000.000
170A171PRO00.007-0.0115.8940.5400.5400.0000.0000.0000.000
171A172ALA00.0680.0346.920-2.272-2.2720.0000.0000.0000.000
175A176LEU00.0080.0136.526-2.437-2.4370.0000.0000.0000.000
176A177PHE0-0.025-0.0157.9043.4093.4090.0000.0000.0000.000
177A178VAL00.0300.01210.732-0.710-0.7100.0000.0000.0000.000
178A179SER0-0.004-0.03213.6291.6261.6260.0000.0000.0000.000
179A180SER00.0600.00716.874-0.749-0.7490.0000.0000.0000.000
180A181ASN0-0.064-0.01219.6901.0121.0120.0000.0000.0000.000
181A182GLY00.1010.05618.369-0.710-0.7100.0000.0000.0000.000
182A183TRP00.0910.02617.681-0.967-0.9670.0000.0000.0000.000
183A184ASP-1-0.766-0.84517.514-17.233-17.2330.0000.0000.0000.000
184A185ALA00.0290.01813.993-0.941-0.9410.0000.0000.0000.000
185A186CYS0-0.0120.02013.087-1.719-1.7190.0000.0000.0000.000
186A187GLY00.0170.00514.117-0.786-0.7860.0000.0000.0000.000
187A188ALA00.001-0.00611.676-0.461-0.4610.0000.0000.0000.000
188A189THR00.021-0.0139.026-2.633-2.6330.0000.0000.0000.000
189A190TRP0-0.030-0.00910.040-1.050-1.0500.0000.0000.0000.000
190A191HIS0-0.045-0.01910.9900.6080.6080.0000.0000.0000.000
191A192GLY00.0050.0137.616-0.222-0.2220.0000.0000.0000.000
192A193PHE0-0.090-0.0555.871-3.013-3.0130.0000.0000.0000.000
194A195THR0-0.051-0.0355.5153.3683.3680.0000.0000.0000.000
195A196PHE00.0320.0129.158-0.861-0.8610.0000.0000.0000.000
196A197TRP0-0.059-0.03712.0790.9920.9920.0000.0000.0000.000
197A198ILE0-0.011-0.00715.5720.0560.0560.0000.0000.0000.000
198A199ASN00.0160.00918.6281.3331.3330.0000.0000.0000.000
199A200ARG10.7980.87721.08514.06814.0680.0000.0000.0000.000
200A201LEU0-0.058-0.02924.1900.5230.5230.0000.0000.0000.000
201A202GLY00.0080.02224.3760.3920.3920.0000.0000.0000.000
202A203HIS0-0.0140.00123.9650.2170.2170.0000.0000.0000.000
203A204PRO00.0290.00623.176-0.599-0.5990.0000.0000.0000.000
204A205PRO0-0.007-0.01118.547-0.101-0.1010.0000.0000.0000.000
205A206GLU-1-0.912-0.95519.616-12.914-12.9140.0000.0000.0000.000
206A207ALA0-0.017-0.00420.094-0.601-0.6010.0000.0000.0000.000
207A208LEU0-0.046-0.03818.7330.4840.4840.0000.0000.0000.000
208A209ASP-1-0.920-0.95618.422-15.013-15.0130.0000.0000.0000.000
209A210VAL0-0.068-0.02812.789-1.093-1.0930.0000.0000.0000.000
210A211ALA00.0170.00513.2131.1681.1680.0000.0000.0000.000
211A212PRO0-0.020-0.01010.997-1.532-1.5320.0000.0000.0000.000
212A213ALA0-0.035-0.0166.886-0.125-0.1250.0000.0000.0000.000
213A214ALA00.0060.0088.8060.0210.0210.0000.0000.0000.000
214A215ALA0-0.012-0.01311.5600.6390.6390.0000.0000.0000.000
215A216GLY00.0080.01215.185-0.210-0.2100.0000.0000.0000.000
216A217HIS0-0.065-0.02017.9710.6020.6020.0000.0000.0000.000
217A218ASP-1-0.787-0.89920.617-13.853-13.8530.0000.0000.0000.000
218A219MET0-0.022-0.02518.562-1.296-1.2960.0000.0000.0000.000
219A220ARG10.8330.90318.47312.25012.2500.0000.0000.0000.000
220A221ASP-1-0.766-0.87017.374-16.652-16.6520.0000.0000.0000.000
221A222LEU0-0.044-0.01412.588-1.283-1.2830.0000.0000.0000.000
222A223LEU0-0.036-0.02513.851-1.564-1.5640.0000.0000.0000.000
223A224GLN0-0.066-0.04415.011-0.704-0.7040.0000.0000.0000.000
224A225PHE0-0.027-0.0157.119-1.214-1.2140.0000.0000.0000.000
225A226VAL0-0.040-0.03210.087-2.492-2.4920.0000.0000.0000.000
226A227GLN0-0.069-0.04510.579-1.002-1.0020.0000.0000.0000.000
227A228ALA-1-0.954-0.9388.899-31.129-31.1290.0000.0000.0000.000