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: ZZ9LN

Calculation Name: 2XWL-A-Xray547

Preferred Name:

Target Type:

Ligand Name: cytidine-5'-triphosphate | magnesium ion

Ligand 3-letter code: CTP | MG

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 2XWL

Chain ID: A

ChEMBL ID:

UniProt ID: A0R560

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 221
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922
Total energy (hartree)
FMO2-HF: Electronic energy -2233652.678387
FMO2-HF: Nuclear repulsion 2157066.362405
FMO2-HF: Total energy -76586.315983
FMO2-MP2: Total energy -76816.551166


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:ALA)


Summations of interaction energy for fragment #1(A:2: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.
-232.462-226.07614.272-10.338-10.319-0.104
Interaction energy analysis for fragmet #1(A:2:ALA)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 1 / q_Mulliken : 0.802 / 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].
3A4VAL00.0150.0183.8414.2815.511-0.017-0.527-0.686-0.001
46A47ASP-1-0.828-0.8962.189-82.530-79.1216.019-5.193-4.235-0.059
47A48ARG10.9080.9605.03631.66831.731-0.001-0.003-0.0570.000
92A93ALA0-0.0110.0092.646-3.716-3.0370.424-0.391-0.713-0.002
93A94GLU-1-0.852-0.9201.684-89.677-89.3427.847-3.987-4.195-0.041
94A95PHE0-0.012-0.0083.9248.0658.6340.001-0.221-0.350-0.001
118A119LYS10.8180.8973.78458.45858.559-0.001-0.016-0.0830.000
4A5ALA0-0.010-0.0016.4501.6051.6050.0000.0000.0000.000
5A6VAL00.0150.0059.9831.2511.2510.0000.0000.0000.000
6A7VAL00.0280.00312.9220.7640.7640.0000.0000.0000.000
7A8PRO0-0.027-0.01316.0590.9390.9390.0000.0000.0000.000
8A9ALA0-0.004-0.01619.5770.3240.3240.0000.0000.0000.000
9A10ALA00.0030.00421.9240.5870.5870.0000.0000.0000.000
10A11GLY0-0.0120.00824.4330.4640.4640.0000.0000.0000.000
11A12SER0-0.004-0.03627.352-0.115-0.1150.0000.0000.0000.000
12A13GLY00.0210.00530.4950.0900.0900.0000.0000.0000.000
13A14GLU-1-0.867-0.91531.303-8.797-8.7970.0000.0000.0000.000
14A15ARG10.9300.95230.68510.22210.2220.0000.0000.0000.000
15A16LEU00.0190.01430.5890.1440.1440.0000.0000.0000.000
16A17ARG10.9130.95034.1968.0098.0090.0000.0000.0000.000
17A18ALA00.0270.02033.7630.2220.2220.0000.0000.0000.000
18A19GLY0-0.0040.00235.838-0.002-0.0020.0000.0000.0000.000
19A20ARG10.8910.94331.3859.5899.5890.0000.0000.0000.000
20A21PRO00.0550.03028.211-0.033-0.0330.0000.0000.0000.000
21A22LYS10.8570.92126.52311.45011.4500.0000.0000.0000.000
22A23ALA00.0190.02323.517-0.011-0.0110.0000.0000.0000.000
23A24PHE00.0480.02223.649-0.165-0.1650.0000.0000.0000.000
24A25VAL0-0.039-0.00927.5820.5140.5140.0000.0000.0000.000
25A26THR0-0.048-0.01228.287-0.319-0.3190.0000.0000.0000.000
26A27LEU0-0.006-0.00226.0710.2600.2600.0000.0000.0000.000
27A28GLY00.0910.04228.592-0.344-0.3440.0000.0000.0000.000
28A29GLY0-0.065-0.03130.414-0.042-0.0420.0000.0000.0000.000
29A30THR00.0180.01224.592-0.041-0.0410.0000.0000.0000.000
30A31PRO0-0.013-0.01624.6130.0350.0350.0000.0000.0000.000
31A32LEU0-0.011-0.00724.325-0.464-0.4640.0000.0000.0000.000
32A33LEU00.0130.00618.751-0.498-0.4980.0000.0000.0000.000
33A34GLU-1-0.813-0.90719.619-16.295-16.2950.0000.0000.0000.000
34A35HIS0-0.011-0.01120.055-0.921-0.9210.0000.0000.0000.000
35A36ALA0-0.008-0.00118.145-0.653-0.6530.0000.0000.0000.000
36A37LEU0-0.034-0.01615.168-1.291-1.2910.0000.0000.0000.000
37A38SER0-0.017-0.01415.195-1.138-1.1380.0000.0000.0000.000
38A39GLY00.0070.00716.090-0.574-0.5740.0000.0000.0000.000
39A40LEU0-0.020-0.02211.562-1.080-1.0800.0000.0000.0000.000
40A41ARG10.8980.96711.25516.47716.4770.0000.0000.0000.000
41A42ALA00.002-0.00312.125-0.949-0.9490.0000.0000.0000.000
42A43SER0-0.070-0.04610.214-0.547-0.5470.0000.0000.0000.000
43A44GLY0-0.0130.0029.924-0.233-0.2330.0000.0000.0000.000
44A45VAL0-0.035-0.0156.210-2.121-2.1210.0000.0000.0000.000
45A46ILE0-0.047-0.0315.313-6.396-6.3960.0000.0000.0000.000
48A49ILE0-0.027-0.0197.046-0.905-0.9050.0000.0000.0000.000
49A50VAL0-0.0090.01010.4140.9900.9900.0000.0000.0000.000
50A51ILE0-0.009-0.00812.8290.1150.1150.0000.0000.0000.000
51A52ALA00.0470.03616.4460.5320.5320.0000.0000.0000.000
52A53VAL00.004-0.00519.3190.3250.3250.0000.0000.0000.000
53A54PRO00.011-0.00122.4540.1830.1830.0000.0000.0000.000
54A55PRO00.0390.02226.0580.1460.1460.0000.0000.0000.000
55A56ALA0-0.0050.01127.054-0.035-0.0350.0000.0000.0000.000
56A57LEU00.0380.03226.8690.1730.1730.0000.0000.0000.000
57A58THR0-0.004-0.00122.596-0.498-0.4980.0000.0000.0000.000
58A59ASP-1-0.843-0.92623.638-11.807-11.8070.0000.0000.0000.000
59A60GLU-1-0.909-0.96525.370-10.201-10.2010.0000.0000.0000.000
60A61SER0-0.026-0.03222.033-0.237-0.2370.0000.0000.0000.000
61A62LYS10.8540.92220.52312.23712.2370.0000.0000.0000.000
62A63LEU0-0.027-0.00521.629-0.244-0.2440.0000.0000.0000.000
63A64VAL0-0.051-0.01223.8100.0440.0440.0000.0000.0000.000
64A65PHE0-0.011-0.01919.122-0.016-0.0160.0000.0000.0000.000
65A66GLY00.0050.02017.774-0.990-0.9900.0000.0000.0000.000
66A67GLY0-0.016-0.01715.9680.5040.5040.0000.0000.0000.000
67A68GLU-1-0.971-0.97211.638-20.224-20.2240.0000.0000.0000.000
68A69ASP-1-0.887-0.9398.769-27.940-27.9400.0000.0000.0000.000
69A70SER0-0.070-0.04910.600-1.268-1.2680.0000.0000.0000.000
70A71VAL00.0090.01112.5051.5661.5660.0000.0000.0000.000
71A72ILE0-0.033-0.01614.581-0.189-0.1890.0000.0000.0000.000
72A73VAL0-0.0010.00016.6240.4070.4070.0000.0000.0000.000
73A74SER0-0.027-0.03319.3110.1990.1990.0000.0000.0000.000
74A75GLY0-0.004-0.01321.714-0.491-0.4910.0000.0000.0000.000
75A76GLY00.0290.00322.9100.3540.3540.0000.0000.0000.000
76A77VAL0-0.068-0.03225.4510.1910.1910.0000.0000.0000.000
77A78ASP-1-0.824-0.91826.107-11.755-11.7550.0000.0000.0000.000
78A79ARG10.7740.86018.85715.60815.6080.0000.0000.0000.000
79A80THR00.0120.01721.757-0.814-0.8140.0000.0000.0000.000
80A81GLU-1-0.841-0.92321.712-12.304-12.3040.0000.0000.0000.000
81A82SER0-0.044-0.04221.143-0.345-0.3450.0000.0000.0000.000
82A83VAL0-0.026-0.00316.246-0.697-0.6970.0000.0000.0000.000
83A84ALA0-0.0010.00316.882-1.055-1.0550.0000.0000.0000.000
84A85LEU00.0290.01617.741-0.671-0.6710.0000.0000.0000.000
85A86ALA0-0.014-0.00614.747-0.436-0.4360.0000.0000.0000.000
86A87LEU0-0.002-0.01312.347-1.750-1.7500.0000.0000.0000.000
87A88GLU-1-0.955-0.95813.237-16.546-16.5460.0000.0000.0000.000
88A89ALA00.0030.00113.602-0.537-0.5370.0000.0000.0000.000
89A90ALA0-0.030-0.0039.622-1.062-1.0620.0000.0000.0000.000
90A91GLY00.0050.0008.098-2.627-2.6270.0000.0000.0000.000
91A92ASP-1-0.916-0.9715.763-37.349-37.3490.0000.0000.0000.000
95A96VAL00.0290.0125.744-1.828-1.8280.0000.0000.0000.000
96A97LEU0-0.0080.0008.1342.0902.0900.0000.0000.0000.000
97A98VAL0-0.0120.01710.7420.6120.6120.0000.0000.0000.000
98A99HIS00.0850.02414.2310.1390.1390.0000.0000.0000.000
99A100ASP-1-0.815-0.90416.111-14.607-14.6070.0000.0000.0000.000
100A101ALA00.0680.02319.8150.1230.1230.0000.0000.0000.000
101A102ALA0-0.081-0.04420.7440.5400.5400.0000.0000.0000.000
102A103ARG10.8060.92320.45014.95014.9500.0000.0000.0000.000
103A104ALA00.0290.02520.751-0.612-0.6120.0000.0000.0000.000
104A105LEU00.0290.02321.181-0.346-0.3460.0000.0000.0000.000
105A106THR0-0.027-0.02716.9990.0930.0930.0000.0000.0000.000
106A107PRO00.0240.01818.387-0.690-0.6900.0000.0000.0000.000
107A108PRO00.0510.02014.820-0.774-0.7740.0000.0000.0000.000
108A109ALA00.0200.00314.127-1.455-1.4550.0000.0000.0000.000
109A110LEU0-0.042-0.00915.799-0.310-0.3100.0000.0000.0000.000
110A111ILE00.0210.00510.407-0.836-0.8360.0000.0000.0000.000
111A112ALA00.0170.01110.765-2.300-2.3000.0000.0000.0000.000
112A113ARG10.8360.92111.00115.65015.6500.0000.0000.0000.000
113A114VAL0-0.0110.00410.904-0.501-0.5010.0000.0000.0000.000
114A115VAL00.0170.0045.471-1.000-1.0000.0000.0000.0000.000
115A116ALA0-0.020-0.0057.547-2.629-2.6290.0000.0000.0000.000
116A117ALA00.0410.0229.674-0.200-0.2000.0000.0000.0000.000
117A118LEU0-0.044-0.0107.3330.7200.7200.0000.0000.0000.000
119A120GLU-1-0.952-0.9677.552-19.281-19.2810.0000.0000.0000.000
120A121GLY0-0.004-0.00310.7371.4381.4380.0000.0000.0000.000
121A122HIS0-0.066-0.02411.6321.1291.1290.0000.0000.0000.000
122A123SER00.021-0.01411.437-1.199-1.1990.0000.0000.0000.000
123A124ALA0-0.026-0.01612.536-0.822-0.8220.0000.0000.0000.000
124A125VAL0-0.0040.01412.1121.1891.1890.0000.0000.0000.000
125A126VAL00.0220.00914.457-0.644-0.6440.0000.0000.0000.000
126A127PRO00.0140.02615.9520.7250.7250.0000.0000.0000.000
127A128GLY00.019-0.00918.5330.5110.5110.0000.0000.0000.000
128A129LEU0-0.0210.01322.3240.0040.0040.0000.0000.0000.000
129A130ALA00.0260.00625.5590.1100.1100.0000.0000.0000.000
130A131PRO0-0.049-0.02928.9960.0030.0030.0000.0000.0000.000
131A132ALA00.0130.02031.3980.1810.1810.0000.0000.0000.000
132A133ASP-1-0.895-0.93433.772-8.535-8.5350.0000.0000.0000.000
133A134THR0-0.091-0.06235.421-0.120-0.1200.0000.0000.0000.000
134A135ILE00.0370.01932.9470.1510.1510.0000.0000.0000.000
135A136LYS10.9020.93236.4347.8187.8180.0000.0000.0000.000
136A137ALA00.0150.02338.317-0.174-0.1740.0000.0000.0000.000
137A138VAL0-0.002-0.01139.5590.2110.2110.0000.0000.0000.000
138A139ASP-1-0.777-0.89441.487-7.135-7.1350.0000.0000.0000.000
139A140ALA0-0.021-0.02043.578-0.082-0.0820.0000.0000.0000.000
140A141ASN0-0.076-0.03144.5590.0720.0720.0000.0000.0000.000
141A142GLY0-0.0010.01044.3320.0810.0810.0000.0000.0000.000
142A143ALA0-0.022-0.00345.4170.0310.0310.0000.0000.0000.000
143A144VAL0-0.041-0.03343.453-0.159-0.1590.0000.0000.0000.000
144A145LEU00.0010.00242.2880.1410.1410.0000.0000.0000.000
145A146GLY00.0130.00741.8820.0310.0310.0000.0000.0000.000
146A147THR0-0.062-0.03240.015-0.032-0.0320.0000.0000.0000.000
147A148PRO00.0280.02135.3020.1070.1070.0000.0000.0000.000
148A149GLU-1-0.831-0.92135.302-8.921-8.9210.0000.0000.0000.000
149A150ARG10.9290.95134.0898.2308.2300.0000.0000.0000.000
150A151ALA00.0230.02232.081-0.305-0.3050.0000.0000.0000.000
151A152GLY00.0030.01430.172-0.393-0.3930.0000.0000.0000.000
152A153LEU0-0.034-0.00429.429-0.230-0.2300.0000.0000.0000.000
153A154ARG10.8840.91724.65911.84911.8490.0000.0000.0000.000
154A155ALA0-0.0100.01226.8780.0690.0690.0000.0000.0000.000
155A156VAL00.0420.02021.830-0.275-0.2750.0000.0000.0000.000
156A157GLN0-0.065-0.05820.5210.2730.2730.0000.0000.0000.000
157A158THR0-0.052-0.01817.1760.0400.0400.0000.0000.0000.000
158A159PRO00.0240.00112.8560.8360.8360.0000.0000.0000.000
159A160GLN0-0.035-0.04314.876-0.148-0.1480.0000.0000.0000.000
160A161GLY00.0340.01111.158-1.101-1.1010.0000.0000.0000.000
161A162PHE00.013-0.00610.3882.3512.3510.0000.0000.0000.000
162A163HIS00.0380.0328.180-2.855-2.8550.0000.0000.0000.000
163A164ALA00.0370.0117.6703.6063.6060.0000.0000.0000.000
164A165ASP-1-0.850-0.9439.511-21.199-21.1990.0000.0000.0000.000
165A166VAL0-0.024-0.00312.4352.1942.1940.0000.0000.0000.000
166A167LEU00.0410.02212.5101.6671.6670.0000.0000.0000.000
167A168ARG10.8510.91810.10926.20426.2040.0000.0000.0000.000
168A169ARG10.8860.93915.22219.57019.5700.0000.0000.0000.000
169A170ALA00.0030.01417.4311.0281.0280.0000.0000.0000.000
170A171TYR0-0.023-0.04817.2911.2341.2340.0000.0000.0000.000
171A172ALA0-0.047-0.01319.2970.7400.7400.0000.0000.0000.000
172A173ARG10.8680.93021.10513.49113.4910.0000.0000.0000.000
173A174ALA00.0020.02122.5360.5480.5480.0000.0000.0000.000
174A175THR0-0.007-0.01424.4140.3830.3830.0000.0000.0000.000
175A176ALA0-0.046-0.02728.1730.0290.0290.0000.0000.0000.000
176A177GLY00.0500.04927.1240.1240.1240.0000.0000.0000.000
177A178GLY0-0.035-0.01628.2060.1550.1550.0000.0000.0000.000
178A179VAL0-0.033-0.02224.2230.0600.0600.0000.0000.0000.000
179A180THR0-0.067-0.05024.302-0.195-0.1950.0000.0000.0000.000
180A181ASP-1-0.812-0.86822.017-14.986-14.9860.0000.0000.0000.000
181A182ASP-1-0.750-0.84817.439-17.255-17.2550.0000.0000.0000.000
182A183ALA00.0450.02218.894-0.319-0.3190.0000.0000.0000.000
183A184SER00.016-0.01519.7770.3960.3960.0000.0000.0000.000
184A185LEU0-0.041-0.01520.3980.6030.6030.0000.0000.0000.000
185A186VAL0-0.014-0.01016.246-0.016-0.0160.0000.0000.0000.000
186A187GLU-1-0.886-0.94719.435-13.761-13.7610.0000.0000.0000.000
187A188GLN0-0.074-0.03622.4220.7370.7370.0000.0000.0000.000
188A189LEU0-0.098-0.04818.2760.4460.4460.0000.0000.0000.000
189A190GLY0-0.029-0.00722.2770.1020.1020.0000.0000.0000.000
190A191THR0-0.053-0.02416.3490.1950.1950.0000.0000.0000.000
191A192PRO0-0.011-0.00618.6740.1830.1830.0000.0000.0000.000
192A193VAL00.0140.01017.651-1.236-1.2360.0000.0000.0000.000
193A194GLN0-0.033-0.00616.1501.1731.1730.0000.0000.0000.000
194A195ILE0-0.032-0.01817.532-0.505-0.5050.0000.0000.0000.000
195A196VAL00.0160.01115.2580.0500.0500.0000.0000.0000.000
196A197ASP-1-0.891-0.94518.478-13.641-13.6410.0000.0000.0000.000
197A198GLY00.021-0.00319.510-0.843-0.8430.0000.0000.0000.000
198A199ASP-1-0.852-0.95420.657-14.192-14.1920.0000.0000.0000.000
199A200PRO0-0.0040.00422.5750.0230.0230.0000.0000.0000.000
200A201LEU00.0210.01223.2160.3510.3510.0000.0000.0000.000
201A202ALA00.0080.02020.408-0.087-0.0870.0000.0000.0000.000
202A203PHE0-0.037-0.01222.235-0.082-0.0820.0000.0000.0000.000
203A204LYS10.9000.94224.43411.66111.6610.0000.0000.0000.000
204A205ILE00.0750.05925.9360.5550.5550.0000.0000.0000.000
205A206THR0-0.114-0.07928.042-0.392-0.3920.0000.0000.0000.000
206A207THR0-0.028-0.03030.5830.2790.2790.0000.0000.0000.000
207A208PRO00.022-0.00633.471-0.164-0.1640.0000.0000.0000.000
208A209LEU00.0210.02835.6820.0130.0130.0000.0000.0000.000
209A210ASP-1-0.735-0.85930.553-10.077-10.0770.0000.0000.0000.000
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