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: 7KV5K

Calculation Name: 4CQL-G-Xray547

Preferred Name:

Target Type:

Ligand Name: nicotinamide-adenine-dinucleotide

Ligand 3-letter code: NAD

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 4CQL

Chain ID: G

ChEMBL ID:

UniProt ID: Q8N4T8

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 231
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922
Total energy (hartree)
FMO2-HF: Electronic energy -2639357.109423
FMO2-HF: Nuclear repulsion 2552865.10835
FMO2-HF: Total energy -86492.001073
FMO2-MP2: Total energy -86743.780809


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:7:VAL)


Summations of interaction energy for fragment #1(A:7:VAL)
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.
145.498156.87424.643-14.42-21.599-0.153
Interaction energy analysis for fragmet #1(A:7:VAL)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 1 / q_Mulliken : 0.755 / q_NPA : 0.877
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].
3A9GLY00.0610.0112.7991.4103.6050.495-1.130-1.559-0.008
4A10GLY0-0.050-0.0232.7541.8402.8570.627-0.659-0.9840.000
5A11SER0-0.032-0.0073.3594.1513.9580.0540.456-0.3170.000
9A15GLY00.0620.0282.335-1.372-1.5811.749-0.744-0.7960.001
10A16ARG10.8910.9512.53217.88418.0381.2390.341-1.733-0.020
11A17ALA0-0.026-0.0015.2241.2171.270-0.001-0.003-0.0500.000
12A18VAL00.010-0.0062.4300.1900.8801.546-0.431-1.805-0.002
13A19ALA00.0220.0112.607-1.0440.4590.459-0.621-1.341-0.006
14A20GLN00.0320.0123.4944.0514.1340.0350.032-0.1500.000
23A29LEU00.0460.0282.564-5.046-4.0331.028-0.496-1.545-0.006
24A30ALA0-0.052-0.0333.0358.8569.8110.090-0.413-0.632-0.001
25A31VAL0-0.0280.0131.774-41.994-43.41111.901-6.374-4.109-0.072
26A32ILE00.0480.0403.4788.4859.1290.002-0.176-0.470-0.001
43A49ASP0-0.0230.0204.135-5.258-5.0220.000-0.032-0.2040.000
74A80LEU0-0.012-0.0023.885-9.600-9.3880.000-0.038-0.1740.000
75A81VAL00.0130.0012.3142.5313.6542.298-0.930-2.492-0.003
76A82ASN00.005-0.0072.354-21.408-18.6562.678-2.991-2.440-0.035
77A83ALA00.017-0.0032.6564.6915.2080.444-0.207-0.7550.000
78A84ALA0-0.035-0.0074.5282.8562.904-0.001-0.004-0.0430.000
6A12ARG10.9900.9746.77922.98522.9850.0000.0000.0000.000
7A13GLY00.0350.0216.752-2.165-2.1650.0000.0000.0000.000
8A14ILE00.0770.0175.326-0.031-0.0310.0000.0000.0000.000
15A21LEU00.0130.0176.8162.2012.2010.0000.0000.0000.000
16A22MET0-0.037-0.0065.1582.4502.4500.0000.0000.0000.000
17A23ALA0-0.003-0.0016.7562.5112.5110.0000.0000.0000.000
18A24ARG10.8250.9058.56626.54226.5420.0000.0000.0000.000
19A25LYS10.8190.90910.58724.98024.9800.0000.0000.0000.000
20A26GLY00.0180.01311.5140.5820.5820.0000.0000.0000.000
21A27TYR00.000-0.0058.0960.3090.3090.0000.0000.0000.000
22A28ARG10.8710.9107.43524.42024.4200.0000.0000.0000.000
27A33ALA00.007-0.0085.594-2.939-2.9390.0000.0000.0000.000
28A34ARG10.8630.9178.04322.60022.6000.0000.0000.0000.000
29A35ASN0-0.013-0.02011.1461.7041.7040.0000.0000.0000.000
30A36LEU00.1030.06411.284-2.265-2.2650.0000.0000.0000.000
31A37GLU-1-0.798-0.88212.887-18.597-18.5970.0000.0000.0000.000
32A38GLY00.0430.01111.341-0.004-0.0040.0000.0000.0000.000
33A39ALA0-0.036-0.0178.402-2.191-2.1910.0000.0000.0000.000
34A40LYS10.8500.8969.39616.69716.6970.0000.0000.0000.000
35A41ALA0-0.0060.00912.3300.7130.7130.0000.0000.0000.000
36A42ALA00.0230.0137.7640.1700.1700.0000.0000.0000.000
37A43ALA0-0.048-0.0559.597-1.345-1.3450.0000.0000.0000.000
38A44GLY00.0000.02210.5640.8970.8970.0000.0000.0000.000
39A45ASP-1-0.888-0.94011.771-22.915-22.9150.0000.0000.0000.000
40A46LEU0-0.082-0.0365.798-1.349-1.3490.0000.0000.0000.000
41A47GLY00.0830.0399.155-1.035-1.0350.0000.0000.0000.000
42A48GLY00.0710.0248.366-2.664-2.6640.0000.0000.0000.000
44A50HIS10.8260.9106.02139.24439.2440.0000.0000.0000.000
45A51LEU00.0640.0256.008-7.165-7.1650.0000.0000.0000.000
46A52ALA00.0050.0337.8851.2001.2000.0000.0000.0000.000
47A53PHE0-0.015-0.0195.853-0.545-0.5450.0000.0000.0000.000
48A54SER0-0.049-0.0339.4261.4171.4170.0000.0000.0000.000
49A55CYS0-0.038-0.0029.115-0.841-0.8410.0000.0000.0000.000
50A56ASP-1-0.732-0.88511.184-19.124-19.1240.0000.0000.0000.000
51A57VAL00.0040.0039.465-0.535-0.5350.0000.0000.0000.000
52A58ALA00.0020.01612.4220.4450.4450.0000.0000.0000.000
53A59LYS10.8680.93216.01318.99218.9920.0000.0000.0000.000
54A60GLU-1-0.828-0.92414.945-17.482-17.4820.0000.0000.0000.000
55A61HIS00.0530.01414.986-1.659-1.6590.0000.0000.0000.000
56A62ASP-1-0.868-0.91413.384-21.094-21.0940.0000.0000.0000.000
57A63VAL00.0030.0179.710-2.027-2.0270.0000.0000.0000.000
58A64GLN00.0340.00810.978-2.213-2.2130.0000.0000.0000.000
59A65ASN0-0.010-0.00113.5300.4000.4000.0000.0000.0000.000
60A66THR0-0.049-0.0407.392-1.135-1.1350.0000.0000.0000.000
61A67PHE0-0.044-0.0597.361-2.321-2.3210.0000.0000.0000.000
62A68GLU-1-0.902-0.92310.486-18.067-18.0670.0000.0000.0000.000
63A69GLU0-0.071-0.03111.0500.5990.5990.0000.0000.0000.000
64A70LEU0-0.047-0.0097.003-1.859-1.8590.0000.0000.0000.000
65A71GLU-1-0.739-0.85010.452-21.958-21.9580.0000.0000.0000.000
66A72LYS10.9440.98713.87216.89816.8980.0000.0000.0000.000
67A73HIS10.8520.90711.73622.56022.5600.0000.0000.0000.000
68A74LEU0-0.038-0.0226.684-0.186-0.1860.0000.0000.0000.000
69A75GLY00.0720.05510.951-0.002-0.0020.0000.0000.0000.000
70A76ARG10.9290.95412.80519.08919.0890.0000.0000.0000.000
71A77VAL00.0240.0166.932-0.323-0.3230.0000.0000.0000.000
72A78ASN00.011-0.0028.762-1.933-1.9330.0000.0000.0000.000
73A79PHE00.0190.0176.4151.2741.2740.0000.0000.0000.000
79A85GLY0-0.005-0.0196.4991.3821.3820.0000.0000.0000.000
80A86ILE0-0.036-0.00910.119-0.244-0.2440.0000.0000.0000.000
81A87ASN00.0160.00813.471-0.072-0.0720.0000.0000.0000.000
82A88ARG10.8330.90316.01613.12813.1280.0000.0000.0000.000
83A89ASP-1-0.797-0.89119.556-13.008-13.0080.0000.0000.0000.000
84A90GLY0-0.015-0.01622.3770.2660.2660.0000.0000.0000.000
85A91LEU00.0320.01725.768-0.102-0.1020.0000.0000.0000.000
86A92LEU00.0110.00427.570-0.103-0.1030.0000.0000.0000.000
87A93VAL00.0710.03329.159-0.063-0.0630.0000.0000.0000.000
88A94ARG10.9050.95829.3639.0499.0490.0000.0000.0000.000
89A95THR0-0.017-0.01324.504-0.151-0.1510.0000.0000.0000.000
90A96LYS10.9810.99626.6969.7589.7580.0000.0000.0000.000
91A97THR00.0750.01325.838-0.419-0.4190.0000.0000.0000.000
92A98GLU-1-0.861-0.91624.460-11.727-11.7270.0000.0000.0000.000
93A99ASP-1-0.815-0.88421.303-14.209-14.2090.0000.0000.0000.000
94A100MET0-0.045-0.02420.715-0.667-0.6670.0000.0000.0000.000
95A101VAL00.0380.02021.001-0.564-0.5640.0000.0000.0000.000
96A102SER00.012-0.00318.393-0.904-0.9040.0000.0000.0000.000
97A103GLN0-0.050-0.02116.268-1.586-1.5860.0000.0000.0000.000
98A104LEU00.0180.01015.816-1.161-1.1610.0000.0000.0000.000
99A105HIS00.019-0.00516.619-1.148-1.1480.0000.0000.0000.000
100A106THR0-0.031-0.01711.563-1.462-1.4620.0000.0000.0000.000
101A107ASN0-0.025-0.02111.604-3.237-3.2370.0000.0000.0000.000
102A108LEU0-0.0060.01612.100-1.324-1.3240.0000.0000.0000.000
103A109LEU00.0400.01613.918-0.925-0.9250.0000.0000.0000.000
104A110GLY00.0710.03911.773-0.457-0.4570.0000.0000.0000.000
105A111SER0-0.044-0.0229.472-3.298-3.2980.0000.0000.0000.000
106A112MET0-0.034-0.01110.534-0.703-0.7030.0000.0000.0000.000
107A113LEU0-0.0010.00413.0310.1080.1080.0000.0000.0000.000
108A114THR0-0.014-0.0136.613-0.749-0.7490.0000.0000.0000.000
109A115CYS0-0.077-0.0379.849-1.014-1.0140.0000.0000.0000.000
110A116LYS10.9300.96911.44117.50917.5090.0000.0000.0000.000
111A117ALA00.0090.00511.0410.8720.8720.0000.0000.0000.000
112A118ALA00.001-0.0108.9810.0060.0060.0000.0000.0000.000
113A119MET0-0.040-0.01910.8740.9670.9670.0000.0000.0000.000
114A120ARG10.8370.91312.20722.83822.8380.0000.0000.0000.000
115A121THR0-0.009-0.01911.5191.5051.5050.0000.0000.0000.000
116A122MET0-0.061-0.0038.6120.8370.8370.0000.0000.0000.000
117A123ILE0-0.0190.00213.9180.6630.6630.0000.0000.0000.000
118A124GLN00.001-0.01415.975-0.170-0.1700.0000.0000.0000.000
119A125GLN00.0660.02817.839-0.880-0.8800.0000.0000.0000.000
120A126GLN00.0030.00216.167-0.257-0.2570.0000.0000.0000.000
121A127GLY0-0.0070.02314.446-1.176-1.1760.0000.0000.0000.000
122A128GLY00.0720.01411.785-1.619-1.6190.0000.0000.0000.000
123A129SER0-0.059-0.0379.8391.9741.9740.0000.0000.0000.000
124A130ILE00.0210.0027.838-4.218-4.2180.0000.0000.0000.000
125A131VAL0-0.0130.0066.7472.9432.9430.0000.0000.0000.000
126A132ASN00.004-0.0026.318-7.615-7.6150.0000.0000.0000.000
127A133VAL00.0010.0025.6182.0192.0190.0000.0000.0000.000
128A134GLY00.0560.0318.3270.4370.4370.0000.0000.0000.000
129A135SER0-0.042-0.04111.903-0.308-0.3080.0000.0000.0000.000
130A136ILE00.0450.03014.6030.2600.2600.0000.0000.0000.000
131A137VAL00.0650.03117.5920.4560.4560.0000.0000.0000.000
132A138GLY0-0.050-0.02017.4680.4100.4100.0000.0000.0000.000
133A139LEU0-0.079-0.04918.1000.1290.1290.0000.0000.0000.000
134A140LYS10.8260.91020.80011.86211.8620.0000.0000.0000.000
135A141GLY00.0280.03622.3220.4930.4930.0000.0000.0000.000
136A142ASN00.013-0.01622.4590.0360.0360.0000.0000.0000.000
137A143SER00.0340.02824.2890.0410.0410.0000.0000.0000.000
138A144GLY00.0120.00425.498-0.161-0.1610.0000.0000.0000.000
139A145GLN00.0610.03520.213-0.718-0.7180.0000.0000.0000.000
140A146SER00.0210.01721.649-0.510-0.5100.0000.0000.0000.000
141A147VAL00.0340.02319.861-0.205-0.2050.0000.0000.0000.000
142A148TYR00.0420.02713.031-1.191-1.1910.0000.0000.0000.000
143A149SER00.028-0.00217.522-0.717-0.7170.0000.0000.0000.000
144A150ALA00.0080.00019.252-0.378-0.3780.0000.0000.0000.000
145A151SER0-0.053-0.03215.591-0.573-0.5730.0000.0000.0000.000
146A152LYS10.8380.9179.65723.70823.7080.0000.0000.0000.000
147A153GLY00.0740.04615.172-0.471-0.4710.0000.0000.0000.000
148A154GLY0-0.022-0.00318.0780.0820.0820.0000.0000.0000.000
149A155LEU0-0.002-0.01411.0790.0100.0100.0000.0000.0000.000
150A156VAL0-0.0010.02214.897-0.709-0.7090.0000.0000.0000.000
151A157GLY00.0230.01116.6850.1280.1280.0000.0000.0000.000
152A158PHE00.0300.01313.1930.2300.2300.0000.0000.0000.000
153A159SER00.021-0.01013.715-0.651-0.6510.0000.0000.0000.000
154A160ARG10.8790.93115.84514.89414.8940.0000.0000.0000.000
155A161ALA0-0.0140.00319.3200.5990.5990.0000.0000.0000.000
156A162LEU00.0520.02114.2530.2610.2610.0000.0000.0000.000
157A163ALA00.011-0.00917.6400.0490.0490.0000.0000.0000.000
158A164LYS10.9250.96218.44412.82412.8240.0000.0000.0000.000
159A165GLU-1-0.931-0.94420.476-13.966-13.9660.0000.0000.0000.000
160A166VAL0-0.035-0.03315.9270.3230.3230.0000.0000.0000.000
161A167ALA00.0720.05019.293-0.101-0.1010.0000.0000.0000.000
162A168ARG10.9860.98820.35012.10812.1080.0000.0000.0000.000
163A169LYS10.8620.93019.07315.17115.1710.0000.0000.0000.000
164A170LYS10.8720.93619.34013.18013.1800.0000.0000.0000.000
165A171ILE00.0060.03213.649-0.757-0.7570.0000.0000.0000.000
166A172ARG10.8880.93613.33721.12921.1290.0000.0000.0000.000
167A173VAL00.0050.01511.800-1.996-1.9960.0000.0000.0000.000
168A174ASN0-0.004-0.00411.7022.8632.8630.0000.0000.0000.000
169A175VAL0-0.013-0.01210.951-1.943-1.9430.0000.0000.0000.000
170A176VAL00.0090.0119.2340.9220.9220.0000.0000.0000.000
171A177ALA0-0.001-0.01111.095-0.811-0.8110.0000.0000.0000.000
172A178PRO0-0.032-0.01211.0460.8280.8280.0000.0000.0000.000
173A179GLY00.1030.05013.8160.4270.4270.0000.0000.0000.000
174A180PHE00.0130.00916.127-0.826-0.8260.0000.0000.0000.000
175A181VAL0-0.047-0.02711.756-0.145-0.1450.0000.0000.0000.000
176A182HIS00.0550.02515.159-0.637-0.6370.0000.0000.0000.000
177A183THR0-0.055-0.03716.783-0.397-0.3970.0000.0000.0000.000
178A184ASP-1-0.822-0.93318.420-11.596-11.5960.0000.0000.0000.000
179A185MET00.0350.04421.2220.5390.5390.0000.0000.0000.000
180A186THR0-0.058-0.04122.723-0.132-0.1320.0000.0000.0000.000
181A187LYS10.8080.87924.38710.39710.3970.0000.0000.0000.000
182A188ASP-1-0.805-0.89622.126-12.841-12.8410.0000.0000.0000.000
183A189LEU0-0.022-0.00624.2890.3250.3250.0000.0000.0000.000
184A190LYS10.7430.83823.32612.28412.2840.0000.0000.0000.000
185A191GLU-1-0.815-0.89128.051-9.224-9.2240.0000.0000.0000.000
186A192GLU-1-0.814-0.89228.081-10.619-10.6190.0000.0000.0000.000
187A193HIS0-0.023-0.01528.4620.3840.3840.0000.0000.0000.000
188A194LEU00.0710.04924.4460.0650.0650.0000.0000.0000.000
189A195LYS10.7940.87824.36911.18111.1810.0000.0000.0000.000
190A196LYS10.9550.98426.0588.3908.3900.0000.0000.0000.000
191A197ASN00.0180.00827.3600.4050.4050.0000.0000.0000.000
192A198ILE0-0.045-0.00821.792-0.184-0.1840.0000.0000.0000.000
193A199PRO00.0120.01025.3970.0980.0980.0000.0000.0000.000
194A200LEU0-0.027-0.00121.1650.1520.1520.0000.0000.0000.000
195A201GLY00.0200.02823.827-0.364-0.3640.0000.0000.0000.000
196A202ARG10.7960.86918.51113.88813.8880.0000.0000.0000.000
197A203PHE00.0660.04318.634-0.343-0.3430.0000.0000.0000.000
198A204GLY00.0390.04616.064-0.025-0.0250.0000.0000.0000.000
199A205GLU00.023-0.00714.263-0.385-0.3850.0000.0000.0000.000
200A206THR00.008-0.0058.801-0.860-0.8600.0000.0000.0000.000
201A207ILE00.0520.0249.166-1.835-1.8350.0000.0000.0000.000
202A208GLU00.0640.04310.802-0.216-0.2160.0000.0000.0000.000
203A209VAL00.0140.0038.885-0.092-0.0920.0000.0000.0000.000
204A210ALA0-0.015-0.0067.186-1.143-1.1430.0000.0000.0000.000
205A211HIS00.022-0.0108.065-0.717-0.7170.0000.0000.0000.000
206A212ALA00.0210.02011.1750.4080.4080.0000.0000.0000.000
207A213VAL0-0.023-0.0205.035-0.333-0.3330.0000.0000.0000.000
208A214VAL00.0140.0048.003-0.554-0.5540.0000.0000.0000.000
209A215PHE00.0470.0298.8080.7610.7610.0000.0000.0000.000
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