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: V65M1

Calculation Name: 3NQZ-A-Xray549

Preferred Name:

Target Type:

Ligand Name: calcium ion

Ligand 3-letter code: CA

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 3NQZ

Chain ID: A

ChEMBL ID:

UniProt ID: A1DRD5

Base Structure: X-ray

Registration Date: 2025-10-12

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 OptH
Protonation MOE:Protonate 3D
Complement ac.sh, 23 2024 Oct
Water No
Procedure Manual calculation
Remarks
FMO calculation
FMO method FMO2-MP2/6-31G(d)
Fragmentation Auto
Number of fragment 180
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230712
Total energy (hartree)
FMO2-HF: Electronic energy -1724203.927489
FMO2-HF: Nuclear repulsion 1655763.766558
FMO2-HF: Total energy -68440.160931
FMO2-MP2: Total energy -68643.027181


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:25:ALA)


Summations of interaction energy for fragment #1(A:25:ALA)
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.
-170.214-159.87526.285-17.862-18.762-0.193
Interaction energy analysis for fragmet #1(A:25:ALA)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 1 / q_Mulliken : 0.775 / q_NPA : 0.903
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].
3A27LYS10.8930.9423.83332.14833.807-0.020-0.843-0.795-0.001
88A112VAL0-0.034-0.0212.745-1.774-1.4530.220-0.104-0.4370.000
89A113TYR0-0.040-0.0414.5392.3752.553-0.001-0.032-0.1450.000
90A114ASN0-0.020-0.0232.322-9.725-7.5861.955-1.937-2.157-0.019
91A115ILE00.0130.0052.298-20.261-18.2014.784-3.379-3.465-0.025
92A116ASP-1-0.889-0.9473.352-43.567-43.794-0.0020.346-0.1170.000
93A117GLU-1-0.867-0.9281.923-101.036-98.8386.213-4.585-3.826-0.066
94A118ASP-1-0.865-0.9331.943-111.749-113.35311.670-5.128-4.938-0.064
95A119LEU0-0.079-0.0354.3248.9629.030-0.001-0.027-0.0410.000
136A160VAL0-0.028-0.0073.893-2.893-2.7000.001-0.030-0.1640.000
140A164ASN0-0.019-0.0094.444-6.809-6.614-0.001-0.034-0.1600.000
141A165LYS10.9320.9832.77836.17338.4470.419-1.489-1.204-0.016
142A166ALA0-0.020-0.0212.60710.11710.9191.042-0.622-1.222-0.002
143A167HIS10.8190.8923.90332.96433.0470.0060.002-0.0910.000
4A28LYS10.9140.9706.00733.70333.7030.0000.0000.0000.000
5A29TYR00.019-0.0079.4050.6900.6900.0000.0000.0000.000
6A30LEU0-0.002-0.01111.8950.3610.3610.0000.0000.0000.000
7A31ASN0-0.062-0.03614.5700.6430.6430.0000.0000.0000.000
8A32GLN00.0210.01315.232-0.186-0.1860.0000.0000.0000.000
9A33GLN0-0.007-0.00112.723-1.217-1.2170.0000.0000.0000.000
10A34PRO00.0410.01216.0170.8140.8140.0000.0000.0000.000
11A35THR00.0070.00815.1020.7720.7720.0000.0000.0000.000
12A36ILE00.0310.02014.5460.6780.6780.0000.0000.0000.000
13A37ASN0-0.008-0.00818.6590.8060.8060.0000.0000.0000.000
14A38ASN00.012-0.00121.1720.9190.9190.0000.0000.0000.000
15A39MET0-0.0180.00619.1990.6430.6430.0000.0000.0000.000
16A40VAL0-0.018-0.01522.2830.5330.5330.0000.0000.0000.000
17A41GLN0-0.059-0.02624.7090.2690.2690.0000.0000.0000.000
18A42SER0-0.009-0.00125.5270.4410.4410.0000.0000.0000.000
19A43ASN00.0250.01026.641-0.048-0.0480.0000.0000.0000.000
20A44SER0-0.0010.00328.1510.1530.1530.0000.0000.0000.000
21A45ALA00.0020.00028.7220.3020.3020.0000.0000.0000.000
22A46SER0-0.031-0.02429.476-0.023-0.0230.0000.0000.0000.000
23A47LEU0-0.0020.00424.143-0.156-0.1560.0000.0000.0000.000
24A48LEU0-0.028-0.01722.557-0.456-0.4560.0000.0000.0000.000
25A49SER0-0.0170.00324.5330.0630.0630.0000.0000.0000.000
26A50VAL00.0090.00920.8570.1310.1310.0000.0000.0000.000
27A51SER00.0280.00819.468-0.222-0.2220.0000.0000.0000.000
28A52PRO00.026-0.00117.287-0.511-0.5110.0000.0000.0000.000
29A53ASN00.0480.00614.153-0.892-0.8920.0000.0000.0000.000
30A54GLN00.0060.00614.458-0.686-0.6860.0000.0000.0000.000
31A55LEU0-0.054-0.01216.963-0.233-0.2330.0000.0000.0000.000
32A56ILE00.004-0.00812.0110.0450.0450.0000.0000.0000.000
33A57GLY00.0280.04312.581-1.414-1.4140.0000.0000.0000.000
34A58LEU0-0.051-0.0248.310-2.069-2.0690.0000.0000.0000.000
35A59SER00.0180.0138.3521.8501.8500.0000.0000.0000.000
36A60VAL00.0590.00910.9150.1690.1690.0000.0000.0000.000
37A61GLY00.0360.03111.925-1.344-1.3440.0000.0000.0000.000
38A62ASN0-0.019-0.0157.984-1.482-1.4820.0000.0000.0000.000
39A63GLU-1-0.918-0.94311.427-15.612-15.6120.0000.0000.0000.000
40A64LEU0-0.023-0.01312.728-0.862-0.8620.0000.0000.0000.000
41A65VAL00.0300.02315.5641.0201.0200.0000.0000.0000.000
42A66VAL0-0.022-0.01418.314-0.324-0.3240.0000.0000.0000.000
43A67LEU0-0.023-0.00817.7700.2690.2690.0000.0000.0000.000
44A68LYS10.8730.92721.58610.85810.8580.0000.0000.0000.000
45A69GLU-1-0.795-0.86323.739-10.989-10.9890.0000.0000.0000.000
46A70PHE0-0.018-0.01925.0670.3160.3160.0000.0000.0000.000
47A71THR00.0440.02828.858-0.199-0.1990.0000.0000.0000.000
48A72SER0-0.0070.00430.1890.1560.1560.0000.0000.0000.000
49A73ASN0-0.005-0.01532.8810.0330.0330.0000.0000.0000.000
50A74ASN0-0.007-0.01831.4310.2080.2080.0000.0000.0000.000
51A75GLY00.0280.02334.604-0.027-0.0270.0000.0000.0000.000
52A76GLU-1-0.847-0.90429.012-10.634-10.6340.0000.0000.0000.000
53A77VAL00.0140.00327.2170.2060.2060.0000.0000.0000.000
54A78THR0-0.017-0.01623.399-0.229-0.2290.0000.0000.0000.000
55A79ARG10.8370.88922.03211.81711.8170.0000.0000.0000.000
56A80ARG10.9360.96918.78813.58513.5850.0000.0000.0000.000
57A81TYR00.018-0.01616.2110.6750.6750.0000.0000.0000.000
58A82GLN0-0.053-0.03412.7740.3410.3410.0000.0000.0000.000
59A83GLN00.0300.0146.9371.0871.0870.0000.0000.0000.000
60A84THR0-0.056-0.01711.6740.1630.1630.0000.0000.0000.000
61A85TYR00.0840.0248.322-0.748-0.7480.0000.0000.0000.000
62A86GLN00.0240.00010.3331.6751.6750.0000.0000.0000.000
63A87GLY00.0100.01813.0930.9740.9740.0000.0000.0000.000
64A88ILE0-0.0180.00911.9430.9880.9880.0000.0000.0000.000
65A89PRO0-0.040-0.01911.781-1.272-1.2720.0000.0000.0000.000
66A90VAL00.0340.0096.894-0.558-0.5580.0000.0000.0000.000
67A91ILE0-0.048-0.0259.7411.4771.4770.0000.0000.0000.000
68A92GLY00.0360.01210.256-1.638-1.6380.0000.0000.0000.000
69A93ASP-1-0.823-0.90911.253-20.851-20.8510.0000.0000.0000.000
70A94THR0-0.071-0.01713.0380.9640.9640.0000.0000.0000.000
71A95VAL00.0650.04912.426-0.054-0.0540.0000.0000.0000.000
72A96SER0-0.040-0.02214.9431.1661.1660.0000.0000.0000.000
73A97LEU00.0170.01416.974-0.344-0.3440.0000.0000.0000.000
74A98THR0-0.0040.00920.4040.6020.6020.0000.0000.0000.000
75A99PHE00.0110.01221.547-0.298-0.2980.0000.0000.0000.000
76A100ASN00.005-0.00526.4320.3730.3730.0000.0000.0000.000
77A101ASN00.0250.01230.132-0.061-0.0610.0000.0000.0000.000
78A102GLY00.0320.02028.0270.0510.0510.0000.0000.0000.000
79A103MET00.0110.02626.731-0.385-0.3850.0000.0000.0000.000
80A104LEU0-0.027-0.01419.9630.1170.1170.0000.0000.0000.000
81A105LYS10.9240.95824.29910.52310.5230.0000.0000.0000.000
82A106LYS10.8450.89722.85611.01211.0120.0000.0000.0000.000
83A107ALA00.0390.03317.2940.0330.0330.0000.0000.0000.000
84A108HIS00.021-0.00617.979-0.282-0.2820.0000.0000.0000.000
85A109GLY00.0390.03415.585-0.277-0.2770.0000.0000.0000.000
86A110ALA0-0.020-0.01510.165-0.243-0.2430.0000.0000.0000.000
87A111ALA00.0040.0129.0791.2071.2070.0000.0000.0000.000
96A120SER00.0080.0046.8022.2462.2460.0000.0000.0000.000
97A121ASP0-0.033-0.0299.8732.1882.1880.0000.0000.0000.000
98A122VAL0-0.015-0.00610.226-1.386-1.3860.0000.0000.0000.000
99A123SER-1-0.817-0.90312.049-16.354-16.3540.0000.0000.0000.000
100A124ALA0-0.071-0.03314.213-1.126-1.1260.0000.0000.0000.000
101A125LYS10.8860.94515.38819.73619.7360.0000.0000.0000.000
102A126LEU0-0.0240.01618.1281.1031.1030.0000.0000.0000.000
103A127THR00.0710.03919.334-0.303-0.3030.0000.0000.0000.000
104A128LYS10.9320.96020.65712.96912.9690.0000.0000.0000.000
105A129LYS10.9510.97421.57510.36110.3610.0000.0000.0000.000
106A130ASP-1-0.833-0.91523.708-12.155-12.1550.0000.0000.0000.000
107A131ALA00.0680.03619.3870.0650.0650.0000.0000.0000.000
108A132ILE00.0070.00621.4690.0200.0200.0000.0000.0000.000
109A133LEU0-0.016-0.00423.4770.3330.3330.0000.0000.0000.000
110A134LYS10.8310.92722.11913.30913.3090.0000.0000.0000.000
111A135GLY00.0880.04021.5560.1680.1680.0000.0000.0000.000
112A136SER0-0.073-0.06222.2940.1670.1670.0000.0000.0000.000
113A137LYS10.8610.93125.43411.50211.5020.0000.0000.0000.000
114A138THR00.0110.01024.1260.1910.1910.0000.0000.0000.000
115A139GLY00.0540.02525.997-0.115-0.1150.0000.0000.0000.000
116A140ILE00.0270.00224.4890.4340.4340.0000.0000.0000.000
117A141ALA00.0310.04124.8640.3120.3120.0000.0000.0000.000
118A142ALA00.0250.01826.9460.3160.3160.0000.0000.0000.000
119A143LYS10.9290.95429.5849.6639.6630.0000.0000.0000.000
120A144SER00.0420.02429.2500.2400.2400.0000.0000.0000.000
121A145VAL0-0.012-0.00330.4600.0850.0850.0000.0000.0000.000
122A146GLY0-0.0110.00232.6100.2060.2060.0000.0000.0000.000
123A147LEU00.0010.01133.7440.2350.2350.0000.0000.0000.000
124A148LYS10.8880.94634.3968.3228.3220.0000.0000.0000.000
125A149LYS10.8600.95229.3939.7719.7710.0000.0000.0000.000
126A150HIS00.015-0.00332.0730.2710.2710.0000.0000.0000.000
127A151ASN00.003-0.00528.845-0.397-0.3970.0000.0000.0000.000
128A152GLU-1-0.898-0.95227.614-10.317-10.3170.0000.0000.0000.000
129A153GLN0-0.036-0.01423.8520.2280.2280.0000.0000.0000.000
130A154SER00.0590.02321.201-0.289-0.2890.0000.0000.0000.000
131A155ARG10.7840.88016.60717.00617.0060.0000.0000.0000.000
132A156LEU00.0460.03214.365-0.102-0.1020.0000.0000.0000.000
133A157ALA0-0.017-0.02112.8850.6010.6010.0000.0000.0000.000
134A158ILE00.0400.0246.450-0.559-0.5590.0000.0000.0000.000
135A159TRP00.0280.0068.3650.5300.5300.0000.0000.0000.000
137A161ASP-1-0.790-0.8736.086-34.201-34.2010.0000.0000.0000.000
138A162ASP-1-0.914-0.9647.316-27.367-27.3670.0000.0000.0000.000
139A163GLN0-0.032-0.0158.137-0.405-0.4050.0000.0000.0000.000
144A168LEU00.0190.0227.7140.4940.4940.0000.0000.0000.000
145A169VAL0-0.021-0.02310.1280.8970.8970.0000.0000.0000.000
146A170TYR0-0.044-0.04312.9690.8310.8310.0000.0000.0000.000
147A171GLU-1-0.751-0.81915.663-17.054-17.0540.0000.0000.0000.000
148A172VAL0-0.038-0.04417.1830.8790.8790.0000.0000.0000.000
149A173SER0-0.031-0.02820.833-0.018-0.0180.0000.0000.0000.000
150A174TYR0-0.004-0.00923.5610.1120.1120.0000.0000.0000.000
151A175VAL00.0020.00527.408-0.102-0.1020.0000.0000.0000.000
152A176THR0-0.032-0.02430.4510.2270.2270.0000.0000.0000.000
153A177TYR00.0600.01233.221-0.024-0.0240.0000.0000.0000.000
154A178GLY00.0170.01736.592-0.019-0.0190.0000.0000.0000.000
155A179LYS10.9580.95939.3517.2437.2430.0000.0000.0000.000
156A180SER0-0.016-0.01135.0580.0730.0730.0000.0000.0000.000
157A181PRO0-0.0210.01434.283-0.133-0.1330.0000.0000.0000.000
158A182SER00.0250.02429.519-0.201-0.2010.0000.0000.0000.000
159A183ARG10.9070.94625.97511.55611.5560.0000.0000.0000.000
160A184PRO00.0140.01924.869-0.410-0.4100.0000.0000.0000.000
161A185TYR0-0.033-0.02916.146-0.032-0.0320.0000.0000.0000.000
162A186LEU0-0.030-0.02218.944-0.061-0.0610.0000.0000.0000.000
163A187ILE0-0.0070.00512.1800.0190.0190.0000.0000.0000.000
164A188ILE0-0.016-0.01015.5990.1590.1590.0000.0000.0000.000
165A189ASP-1-0.713-0.85412.226-24.222-24.2220.0000.0000.0000.000
166A190ALA0-0.036-0.02613.5731.4641.4640.0000.0000.0000.000
167A191ASN00.010-0.01111.9012.2492.2490.0000.0000.0000.000
168A192THR0-0.037-0.05715.5280.9340.9340.0000.0000.0000.000
169A193GLY0-0.006-0.01217.3241.0841.0840.0000.0000.0000.000
170A194GLU-1-0.903-0.90315.772-18.402-18.4020.0000.0000.0000.000
171A195VAL0-0.026-0.02916.773-0.595-0.5950.0000.0000.0000.000
172A196LEU0-0.0070.00910.792-0.010-0.0100.0000.0000.0000.000
173A197LEU00.0220.01214.442-0.198-0.1980.0000.0000.0000.000
174A198SER0-0.035-0.02316.2010.5260.5260.0000.0000.0000.000
175A199TYR00.0060.01117.9230.3010.3010.0000.0000.0000.000
176A200ASP-1-0.785-0.90922.384-10.638-10.6380.0000.0000.0000.000
177A201ASN00.0030.00522.8130.0080.0080.0000.0000.0000.000
178A202LEU0-0.063-0.03625.1630.1540.1540.0000.0000.0000.000
179A203GLN0-0.104-0.05424.7180.2380.2380.0000.0000.0000.000
180A204HIS-1-0.902-0.93529.268-9.025-9.0250.0000.0000.0000.000