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: 5541Z

Calculation Name: 3U0Z-A-Xray547

Preferred Name: Potassium/sodium hyperpolarization-activated cyclic nucleotide-gated channel 1

Target Type: SINGLE PROTEIN

Ligand Name: adenosine-3',5'-cyclic-monophosphate

Ligand 3-letter code: CMP

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 3U0Z

Chain ID: A

ChEMBL ID: CHEMBL1250401

UniProt ID: O88704

Base Structure: X-ray

Registration Date: 2025-10-05

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 199
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922
Total energy (hartree)
FMO2-HF: Electronic energy -2285126.079258
FMO2-HF: Nuclear repulsion 2202075.01428
FMO2-HF: Total energy -83051.064978
FMO2-MP2: Total energy -83288.905707


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:390:ASP)


Summations of interaction energy for fragment #1(A:390:ASP)
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.
-51.485-48.4810.669-6.598-7.0750.062
Interaction energy analysis for fragmet #1(A:390:ASP)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.002 / q_NPA : -0.007
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].
3A392SER00.0560.0342.9391.7874.4640.019-1.190-1.506-0.002
4A393ARG10.9360.9681.804-43.978-43.91910.651-5.376-5.3330.064
5A394ARG10.8530.9314.783-5.105-4.836-0.001-0.032-0.2360.000
6A395GLN00.0400.0066.4940.3880.3880.0000.0000.0000.000
7A396TYR00.0170.0267.9240.1730.1730.0000.0000.0000.000
8A397GLN00.0350.0057.9790.7630.7630.0000.0000.0000.000
9A398GLU-1-0.891-0.93410.8312.1512.1510.0000.0000.0000.000
10A399LYS10.9570.98112.0490.8840.8840.0000.0000.0000.000
11A400TYR00.0170.01313.729-0.247-0.2470.0000.0000.0000.000
12A401LYS11.0221.01513.017-3.179-3.1790.0000.0000.0000.000
13A402GLN0-0.005-0.00316.939-0.272-0.2720.0000.0000.0000.000
14A403VAL00.0020.01218.356-0.135-0.1350.0000.0000.0000.000
15A404GLU-1-0.900-0.95517.3731.8561.8560.0000.0000.0000.000
16A405GLN0-0.031-0.01119.7240.0030.0030.0000.0000.0000.000
17A406TYR00.0090.00822.923-0.085-0.0850.0000.0000.0000.000
18A407MET0-0.004-0.00221.728-0.092-0.0920.0000.0000.0000.000
19A408SER0-0.049-0.02824.631-0.018-0.0180.0000.0000.0000.000
20A409PHE0-0.0170.00327.170-0.031-0.0310.0000.0000.0000.000
21A410HIS0-0.042-0.03128.066-0.071-0.0710.0000.0000.0000.000
22A411LYS10.8860.95030.198-0.394-0.3940.0000.0000.0000.000
23A412LEU00.0230.02327.169-0.015-0.0150.0000.0000.0000.000
24A413PRO00.0480.02929.8230.0650.0650.0000.0000.0000.000
25A414ALA00.0350.00828.4110.0210.0210.0000.0000.0000.000
26A415ASP-1-0.839-0.91727.5320.5630.5630.0000.0000.0000.000
27A416MET00.0010.00327.9060.0000.0000.0000.0000.0000.000
28A417ARG10.8710.90724.430-0.776-0.7760.0000.0000.0000.000
29A418GLN0-0.0190.01322.1420.0770.0770.0000.0000.0000.000
30A419LYS10.8360.89323.274-0.244-0.2440.0000.0000.0000.000
31A420ILE00.0140.00121.364-0.052-0.0520.0000.0000.0000.000
32A421HIS0-0.025-0.01816.727-0.151-0.1510.0000.0000.0000.000
33A422ASP-1-0.825-0.91418.6550.9900.9900.0000.0000.0000.000
34A423TYR0-0.041-0.01719.682-0.053-0.0530.0000.0000.0000.000
35A424TYR00.001-0.01013.457-0.296-0.2960.0000.0000.0000.000
36A425GLU-1-0.880-0.93114.6352.0752.0750.0000.0000.0000.000
37A426HIS0-0.006-0.01815.161-0.173-0.1730.0000.0000.0000.000
38A427ARG10.8260.93215.4790.6840.6840.0000.0000.0000.000
39A428TYR0-0.022-0.01611.771-0.473-0.4730.0000.0000.0000.000
40A429GLN0-0.0200.00410.954-0.426-0.4260.0000.0000.0000.000
41A430GLY00.0110.0128.8780.4660.4660.0000.0000.0000.000
42A431LYS10.8600.9104.8732.8742.8740.0000.0000.0000.000
43A432ILE00.0150.0087.5470.0320.0320.0000.0000.0000.000
44A433PHE0-0.055-0.0446.315-2.127-2.1270.0000.0000.0000.000
45A434ASP-1-0.883-0.9398.759-2.149-2.1490.0000.0000.0000.000
46A435GLU-1-0.936-0.97711.879-2.917-2.9170.0000.0000.0000.000
47A436GLU-1-0.812-0.89713.267-1.774-1.7740.0000.0000.0000.000
48A437ASN0-0.0370.01613.1200.3930.3930.0000.0000.0000.000
49A438ILE0-0.019-0.0189.544-0.141-0.1410.0000.0000.0000.000
50A439LEU0-0.008-0.00513.7900.1170.1170.0000.0000.0000.000
51A440SER0-0.045-0.04117.0240.3550.3550.0000.0000.0000.000
52A441GLU-1-0.950-0.97014.344-3.875-3.8750.0000.0000.0000.000
53A442LEU0-0.057-0.00416.4130.0910.0910.0000.0000.0000.000
54A443ASN00.013-0.00519.8860.0850.0850.0000.0000.0000.000
55A444ASP-1-0.812-0.90222.785-1.431-1.4310.0000.0000.0000.000
56A445PRO00.0150.00724.463-0.051-0.0510.0000.0000.0000.000
57A446LEU00.0580.02920.163-0.033-0.0330.0000.0000.0000.000
58A447ARG10.8410.91920.0601.6271.6270.0000.0000.0000.000
59A448GLU-1-0.879-0.95321.136-1.179-1.1790.0000.0000.0000.000
60A449GLU-1-0.951-0.96922.334-1.515-1.5150.0000.0000.0000.000
61A450ILE0-0.023-0.01216.3240.0010.0010.0000.0000.0000.000
62A451VAL00.0060.00519.4910.0330.0330.0000.0000.0000.000
63A452ASN0-0.012-0.03020.9720.1840.1840.0000.0000.0000.000
64A453PHE0-0.033-0.01518.1610.1340.1340.0000.0000.0000.000
65A454ASN0-0.001-0.00915.6330.1380.1380.0000.0000.0000.000
66A455CYS0-0.039-0.00619.5550.1510.1510.0000.0000.0000.000
67A456ARG10.8970.95620.7091.3351.3350.0000.0000.0000.000
68A457LYS10.9040.95224.0000.4570.4570.0000.0000.0000.000
69A458LEU0-0.0160.01624.9330.0820.0820.0000.0000.0000.000
70A459VAL00.0590.01526.6970.0610.0610.0000.0000.0000.000
71A460ALA00.0050.00128.5740.0530.0530.0000.0000.0000.000
72A461THR0-0.075-0.06128.7470.0590.0590.0000.0000.0000.000
73A462MET0-0.0110.02629.6930.0550.0550.0000.0000.0000.000
74A463PRO00.0000.00432.764-0.024-0.0240.0000.0000.0000.000
75A464LEU00.0040.00834.506-0.001-0.0010.0000.0000.0000.000
76A465PHE0-0.019-0.02328.883-0.021-0.0210.0000.0000.0000.000
77A466ALA00.0140.00433.347-0.019-0.0190.0000.0000.0000.000
78A467ASN0-0.079-0.03934.2500.0140.0140.0000.0000.0000.000
79A468ALA0-0.0140.00335.1560.0220.0220.0000.0000.0000.000
80A469ASP-1-0.798-0.89336.023-0.646-0.6460.0000.0000.0000.000
81A470PRO00.0370.00231.772-0.021-0.0210.0000.0000.0000.000
82A471ASN0-0.0050.01131.189-0.106-0.1060.0000.0000.0000.000
83A472PHE00.0130.01632.105-0.026-0.0260.0000.0000.0000.000
84A473VAL0-0.032-0.01728.795-0.019-0.0190.0000.0000.0000.000
85A474THR00.0420.01526.755-0.066-0.0660.0000.0000.0000.000
86A475ALA00.0210.03527.499-0.077-0.0770.0000.0000.0000.000
87A476MET0-0.057-0.03428.851-0.013-0.0130.0000.0000.0000.000
88A477LEU0-0.019-0.03124.633-0.016-0.0160.0000.0000.0000.000
89A478SER0-0.030-0.02123.976-0.107-0.1070.0000.0000.0000.000
90A479LYS10.8650.95124.5250.9300.9300.0000.0000.0000.000
91A480LEU0-0.066-0.01123.6100.0620.0620.0000.0000.0000.000
92A481ARG10.8770.92921.1691.1371.1370.0000.0000.0000.000
93A482PHE0-0.0090.00217.4270.1220.1220.0000.0000.0000.000
94A483GLU-1-0.825-0.87820.443-0.467-0.4670.0000.0000.0000.000
95A484VAL0-0.003-0.00219.2030.0070.0070.0000.0000.0000.000
96A485PHE00.0040.00122.4320.0310.0310.0000.0000.0000.000
97A486GLN0-0.004-0.00223.663-0.026-0.0260.0000.0000.0000.000
98A487PRO00.002-0.00326.410-0.045-0.0450.0000.0000.0000.000
99A488GLY00.0100.00729.5740.0310.0310.0000.0000.0000.000
100A489ASP-1-0.812-0.87427.7130.1330.1330.0000.0000.0000.000
101A490TYR0-0.051-0.04131.299-0.031-0.0310.0000.0000.0000.000
102A491ILE0-0.0060.02029.667-0.014-0.0140.0000.0000.0000.000
103A492ILE0-0.047-0.02932.074-0.043-0.0430.0000.0000.0000.000
104A493ARG10.9630.98534.4930.0480.0480.0000.0000.0000.000
105A494GLU-1-0.764-0.89238.964-0.086-0.0860.0000.0000.0000.000
106A495GLY0-0.0030.00142.4260.0120.0120.0000.0000.0000.000
107A496ALA0-0.0080.00539.194-0.006-0.0060.0000.0000.0000.000
108A497VAL00.0350.00739.150-0.006-0.0060.0000.0000.0000.000
109A498GLY00.001-0.01836.7050.0010.0010.0000.0000.0000.000
110A499LYS10.9750.97834.1810.3170.3170.0000.0000.0000.000
111A500LYS10.8770.93127.1910.4020.4020.0000.0000.0000.000
112A501MET0-0.0400.01731.7830.0580.0580.0000.0000.0000.000
113A502TYR00.003-0.00927.827-0.051-0.0510.0000.0000.0000.000
114A503PHE00.0610.01527.5290.0360.0360.0000.0000.0000.000
115A504ILE0-0.023-0.01027.012-0.035-0.0350.0000.0000.0000.000
116A505GLN00.0080.02019.6900.0700.0700.0000.0000.0000.000
117A506HIS0-0.081-0.06623.6820.0740.0740.0000.0000.0000.000
118A507GLY00.0530.04025.6750.0150.0150.0000.0000.0000.000
119A508VAL0-0.026-0.01027.804-0.028-0.0280.0000.0000.0000.000
120A509ALA00.0290.01131.2240.0280.0280.0000.0000.0000.000
121A510GLY00.0670.04833.143-0.018-0.0180.0000.0000.0000.000
122A511VAL0-0.045-0.02836.861-0.009-0.0090.0000.0000.0000.000
123A512ILE0-0.017-0.00639.2680.0130.0130.0000.0000.0000.000
124A513THR00.0200.00341.875-0.019-0.0190.0000.0000.0000.000
125A514LYS10.8630.91245.1980.0600.0600.0000.0000.0000.000
126A515SER00.0140.01048.123-0.003-0.0030.0000.0000.0000.000
127A516SER00.0260.01944.811-0.001-0.0010.0000.0000.0000.000
128A517LYS10.9370.97046.183-0.009-0.0090.0000.0000.0000.000
129A518GLU-1-0.839-0.92639.2130.0140.0140.0000.0000.0000.000
130A519MET0-0.009-0.00440.968-0.005-0.0050.0000.0000.0000.000
131A520LYS10.9290.97536.275-0.065-0.0650.0000.0000.0000.000
132A521LEU0-0.0060.00834.491-0.018-0.0180.0000.0000.0000.000
133A522THR00.009-0.02031.0020.0310.0310.0000.0000.0000.000
134A523ASP-1-0.773-0.89627.486-0.249-0.2490.0000.0000.0000.000
135A524GLY00.0400.03129.2840.0130.0130.0000.0000.0000.000
136A525SER0-0.024-0.00230.9970.0110.0110.0000.0000.0000.000
137A526TYR00.0470.01831.397-0.030-0.0300.0000.0000.0000.000
138A527PHE0-0.003-0.00930.9490.0420.0420.0000.0000.0000.000
139A528GLY00.0310.01433.780-0.021-0.0210.0000.0000.0000.000
140A529GLU-1-0.736-0.87436.195-0.287-0.2870.0000.0000.0000.000
141A530ILE00.0150.01137.638-0.003-0.0030.0000.0000.0000.000
142A531CYS0-0.107-0.01939.0740.0020.0020.0000.0000.0000.000
143A532LEU00.0090.00234.4060.0030.0030.0000.0000.0000.000
144A533LEU0-0.041-0.00339.163-0.009-0.0090.0000.0000.0000.000
145A534THR00.018-0.01541.9090.0030.0030.0000.0000.0000.000
146A535LYS10.9350.97942.0040.3410.3410.0000.0000.0000.000
147A536GLY00.0650.05243.6570.0120.0120.0000.0000.0000.000
148A537ARG10.8510.91843.0190.1400.1400.0000.0000.0000.000
149A538ARG10.8360.91534.2340.2620.2620.0000.0000.0000.000
150A539THR00.0590.02541.5090.0140.0140.0000.0000.0000.000
151A540ALA00.0210.01041.2660.0120.0120.0000.0000.0000.000
152A541SER0-0.013-0.00839.027-0.016-0.0160.0000.0000.0000.000
153A542VAL0-0.030-0.00934.047-0.001-0.0010.0000.0000.0000.000
154A543ARG10.8220.90534.051-0.077-0.0770.0000.0000.0000.000
155A544ALA00.0350.02429.370-0.017-0.0170.0000.0000.0000.000
156A545ASP-1-0.837-0.91331.4320.1020.1020.0000.0000.0000.000
157A546THR0-0.019-0.02827.4240.0350.0350.0000.0000.0000.000
158A547TYR00.030-0.00822.334-0.055-0.0550.0000.0000.0000.000
159A548CYS0-0.102-0.02125.236-0.035-0.0350.0000.0000.0000.000
160A549ARG10.9490.96616.5880.5090.5090.0000.0000.0000.000
161A550LEU0-0.011-0.01523.068-0.013-0.0130.0000.0000.0000.000
162A551TYR00.0640.03318.468-0.015-0.0150.0000.0000.0000.000
163A552SER0-0.085-0.06824.5170.0580.0580.0000.0000.0000.000
164A553LEU00.0790.04326.324-0.078-0.0780.0000.0000.0000.000
165A554SER00.001-0.00329.1050.0570.0570.0000.0000.0000.000
166A555VAL00.015-0.01231.083-0.008-0.0080.0000.0000.0000.000
167A556ASP-1-0.878-0.92333.092-0.506-0.5060.0000.0000.0000.000
168A557ASN00.0230.00128.771-0.028-0.0280.0000.0000.0000.000
169A558PHE0-0.016-0.01332.278-0.001-0.0010.0000.0000.0000.000
170A559ASN0-0.074-0.06434.4260.0410.0410.0000.0000.0000.000
171A560GLU-1-0.881-0.93032.065-0.751-0.7510.0000.0000.0000.000
172A561VAL00.0580.01531.7310.0070.0070.0000.0000.0000.000
173A562LEU0-0.065-0.04735.1030.0230.0230.0000.0000.0000.000
174A563GLU-1-0.972-0.97038.540-0.414-0.4140.0000.0000.0000.000
175A564GLU-1-0.938-0.95834.818-0.692-0.6920.0000.0000.0000.000
176A565TYR0-0.011-0.00634.7040.0240.0240.0000.0000.0000.000
177A566PRO00.0490.02439.6620.0210.0210.0000.0000.0000.000
178A567MET0-0.071-0.04942.6410.0280.0280.0000.0000.0000.000
179A568MET00.0410.02436.9780.0290.0290.0000.0000.0000.000
180A569ARG10.8830.94640.3730.3530.3530.0000.0000.0000.000
181A570ARG10.9810.98341.6560.3380.3380.0000.0000.0000.000
182A571ALA0-0.0030.02840.4020.0210.0210.0000.0000.0000.000
183A572PHE00.001-0.00634.5700.0180.0180.0000.0000.0000.000
184A573GLU-1-0.869-0.94540.634-0.282-0.2820.0000.0000.0000.000
185A574THR0-0.009-0.00944.2060.0210.0210.0000.0000.0000.000
186A575VAL00.0340.02340.1640.0180.0180.0000.0000.0000.000
187A576ALA0-0.035-0.02542.1520.0180.0180.0000.0000.0000.000
188A577ILE00.0120.00443.4930.0190.0190.0000.0000.0000.000
189A578ASP-1-0.847-0.92745.219-0.184-0.1840.0000.0000.0000.000
190A579ARG10.6710.79936.8190.2640.2640.0000.0000.0000.000
191A580LEU0-0.051-0.02244.7500.0160.0160.0000.0000.0000.000
192A581ASP-1-0.884-0.93547.403-0.110-0.1100.0000.0000.0000.000
193A582ARG10.9110.96943.9360.1630.1630.0000.0000.0000.000
194A583ILE0-0.070-0.03845.1630.0130.0130.0000.0000.0000.000
195A584GLY0-0.0030.01648.6500.0090.0090.0000.0000.0000.000
196A585LYS10.7920.89646.6130.0970.0970.0000.0000.0000.000
197A586LYS10.9750.97250.8340.1000.1000.0000.0000.0000.000
198A587ASN0-0.082-0.04047.3030.0070.0070.0000.0000.0000.000
199A588SER-1-0.868-0.91650.518-0.193-0.1930.0000.0000.0000.000