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: 8GYMY

Calculation Name: 1XC3-A-Xray547

Preferred Name:

Target Type:

Ligand Name: platinum (ii) ion

Ligand 3-letter code: PT

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 1XC3

Chain ID: A

ChEMBL ID:

UniProt ID: O05510

Base Structure: X-ray

Registration Date: 2025-10-03

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 295
LigandResidueName
LigandFragmentNumber 0
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922
Total energy (hartree)
FMO2-HF: Electronic energy -4031285.811665
FMO2-HF: Nuclear repulsion 3919096.01366
FMO2-HF: Total energy -112189.798005
FMO2-MP2: Total energy -112517.134642


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:0:ALA)


Summations of interaction energy for fragment #1(A:0: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.
-141.213-134.8572.292-4.307-4.339-0.042
Interaction energy analysis for fragmet #1(A:0:ALA)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 1 / q_Mulliken : 0.858 / q_NPA : 0.920
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].
3A2LEU00.0170.0343.8171.4053.069-0.026-0.730-0.908-0.001
19A18ARG10.8620.9333.38648.53349.0580.004-0.241-0.288-0.001
20A19GLU-1-0.843-0.9284.395-37.337-37.063-0.001-0.028-0.2450.000
51A50LEU0-0.038-0.0185.010-9.828-9.828-0.001-0.0030.0050.000
52A51GLN0-0.016-0.0252.423-30.480-26.6982.318-3.296-2.803-0.040
53A52ALA00.0570.0385.3484.0754.118-0.001-0.001-0.0410.000
289A288LEU0-0.033-0.0224.584-0.673-0.605-0.001-0.008-0.0590.000
4A3GLY00.0540.0256.6301.7111.7110.0000.0000.0000.000
5A4GLY00.0290.00810.2310.3550.3550.0000.0000.0000.000
6A5ILE00.003-0.01713.2880.7650.7650.0000.0000.0000.000
7A6GLU-1-0.832-0.92116.860-14.499-14.4990.0000.0000.0000.000
8A7ALA00.0040.00519.8060.4420.4420.0000.0000.0000.000
9A8GLY00.0880.04222.5060.4390.4390.0000.0000.0000.000
10A9GLY00.0200.01625.8390.1180.1180.0000.0000.0000.000
11A10THR0-0.048-0.03428.9680.4360.4360.0000.0000.0000.000
12A11LYS10.8330.91024.64312.96912.9690.0000.0000.0000.000
13A12PHE00.0500.03120.918-0.072-0.0720.0000.0000.0000.000
14A13VAL0-0.016-0.01018.6700.3170.3170.0000.0000.0000.000
15A14CYS0-0.053-0.01116.355-0.139-0.1390.0000.0000.0000.000
16A15ALA00.0420.01613.9650.6620.6620.0000.0000.0000.000
17A16VAL00.0360.0278.289-1.330-1.3300.0000.0000.0000.000
18A17GLY00.0610.0168.5072.2392.2390.0000.0000.0000.000
21A20ASP-1-0.884-0.9206.425-27.255-27.2550.0000.0000.0000.000
22A21GLY00.0230.0139.1842.4122.4120.0000.0000.0000.000
23A22THR0-0.073-0.0599.3112.2062.2060.0000.0000.0000.000
24A23ILE0-0.033-0.01710.033-2.815-2.8150.0000.0000.0000.000
25A24ILE0-0.081-0.0436.8930.0550.0550.0000.0000.0000.000
26A25ASP-1-0.813-0.89511.453-19.128-19.1280.0000.0000.0000.000
27A26ARG10.8680.93214.05515.48415.4840.0000.0000.0000.000
28A27ILE00.0070.02416.7781.0521.0520.0000.0000.0000.000
29A28GLU-1-0.795-0.90019.601-13.549-13.5490.0000.0000.0000.000
30A29PHE0-0.027-0.02020.8160.6480.6480.0000.0000.0000.000
31A30PRO0-0.008-0.01025.575-0.082-0.0820.0000.0000.0000.000
32A31THR0-0.026-0.01127.052-0.231-0.2310.0000.0000.0000.000
33A32LYS10.9120.97528.38210.63310.6330.0000.0000.0000.000
34A33MET00.0270.02230.7190.1260.1260.0000.0000.0000.000
35A34PRO00.0170.01427.358-0.314-0.3140.0000.0000.0000.000
36A35ASP-1-0.817-0.90626.226-11.524-11.5240.0000.0000.0000.000
37A36GLU-1-0.856-0.94626.102-10.614-10.6140.0000.0000.0000.000
38A37THR0-0.079-0.05124.223-0.178-0.1780.0000.0000.0000.000
39A38ILE00.0340.00120.803-0.631-0.6310.0000.0000.0000.000
40A39GLU-1-0.816-0.88321.225-14.470-14.4700.0000.0000.0000.000
41A40LYS10.8800.94221.43711.95411.9540.0000.0000.0000.000
42A41VAL0-0.013-0.01116.901-0.502-0.5020.0000.0000.0000.000
43A42ILE00.0040.00917.024-1.322-1.3220.0000.0000.0000.000
44A43GLN0-0.025-0.03416.914-1.405-1.4050.0000.0000.0000.000
45A44TYR0-0.108-0.05614.506-0.645-0.6450.0000.0000.0000.000
46A45PHE00.007-0.03212.554-1.180-1.1800.0000.0000.0000.000
47A46SER0-0.054-0.02412.380-1.707-1.7070.0000.0000.0000.000
48A47GLN0-0.034-0.00413.405-0.392-0.3920.0000.0000.0000.000
49A48PHE0-0.022-0.0168.476-1.901-1.9010.0000.0000.0000.000
50A49SER00.0030.0055.6182.5732.5730.0000.0000.0000.000
54A53ILE00.0080.0018.089-1.689-1.6890.0000.0000.0000.000
55A54GLY00.0240.02210.9960.7770.7770.0000.0000.0000.000
56A55ILE0-0.050-0.02513.6160.2040.2040.0000.0000.0000.000
57A56GLY00.0350.01217.3500.2700.2700.0000.0000.0000.000
58A57SER0-0.074-0.05019.7090.1000.1000.0000.0000.0000.000
59A58PHE00.0030.00523.0630.4200.4200.0000.0000.0000.000
60A59GLY00.0050.00526.669-0.214-0.2140.0000.0000.0000.000
61A60PRO0-0.023-0.01729.1050.2300.2300.0000.0000.0000.000
62A61VAL0-0.011-0.00525.218-0.053-0.0530.0000.0000.0000.000
63A62ASP-1-0.774-0.83027.382-10.652-10.6520.0000.0000.0000.000
64A63ASN0-0.055-0.06122.768-0.995-0.9950.0000.0000.0000.000
65A64ASP-1-0.814-0.87424.717-11.180-11.1800.0000.0000.0000.000
66A65LYS10.9320.95019.35014.60114.6010.0000.0000.0000.000
67A66THR0-0.062-0.04024.205-0.085-0.0850.0000.0000.0000.000
68A67SER0-0.029-0.03827.3280.4350.4350.0000.0000.0000.000
69A68GLN0-0.046-0.03227.275-0.343-0.3430.0000.0000.0000.000
70A69THR0-0.054-0.04028.4180.0630.0630.0000.0000.0000.000
71A70TYR0-0.0200.01320.167-0.519-0.5190.0000.0000.0000.000
72A71GLY00.019-0.00722.477-0.351-0.3510.0000.0000.0000.000
73A72THR0-0.064-0.03223.347-0.024-0.0240.0000.0000.0000.000
74A73ILE00.0250.00926.3700.0440.0440.0000.0000.0000.000
75A74THR00.0300.00928.7110.3180.3180.0000.0000.0000.000
76A75ALA0-0.044-0.03531.8480.4150.4150.0000.0000.0000.000
77A76THR00.0610.02731.531-0.123-0.1230.0000.0000.0000.000
78A77PRO0-0.0030.00734.1100.1520.1520.0000.0000.0000.000
79A78LYS10.8140.91431.15710.27710.2770.0000.0000.0000.000
80A79ALA00.0460.00833.970-0.118-0.1180.0000.0000.0000.000
81A80GLY00.0120.00133.098-0.223-0.2230.0000.0000.0000.000
82A81TRP00.006-0.01525.154-0.298-0.2980.0000.0000.0000.000
83A82ARG10.9220.97229.9748.5238.5230.0000.0000.0000.000
84A83HIS0-0.020-0.01430.9850.1440.1440.0000.0000.0000.000
85A84TYR0-0.0060.01624.558-0.230-0.2300.0000.0000.0000.000
86A85PRO00.0460.02325.716-0.289-0.2890.0000.0000.0000.000
87A86PHE00.001-0.00620.272-0.526-0.5260.0000.0000.0000.000
88A87LEU00.0130.01317.619-0.567-0.5670.0000.0000.0000.000
89A88GLN0-0.022-0.02119.334-0.750-0.7500.0000.0000.0000.000
90A89THR0-0.008-0.01221.124-0.111-0.1110.0000.0000.0000.000
91A90VAL00.0160.00115.526-0.371-0.3710.0000.0000.0000.000
92A91LYS10.9460.98116.32515.00115.0010.0000.0000.0000.000
93A92ASN00.0070.01117.220-0.772-0.7720.0000.0000.0000.000
94A93GLU-1-0.909-0.94618.626-14.799-14.7990.0000.0000.0000.000
95A94MET0-0.069-0.03913.129-0.724-0.7240.0000.0000.0000.000
96A95LYS10.8110.90813.41515.75915.7590.0000.0000.0000.000
97A96ILE00.0020.0268.768-0.861-0.8610.0000.0000.0000.000
98A97PRO00.0260.0129.4811.6801.6800.0000.0000.0000.000
99A98VAL0-0.015-0.00911.204-1.327-1.3270.0000.0000.0000.000
100A99GLY00.0130.01313.5441.1891.1890.0000.0000.0000.000
101A100PHE0-0.018-0.01515.1860.0730.0730.0000.0000.0000.000
102A101SER00.0340.01918.6110.6140.6140.0000.0000.0000.000
103A102THR00.0460.03020.885-0.234-0.2340.0000.0000.0000.000
104A103ASP-1-0.848-0.92521.468-12.907-12.9070.0000.0000.0000.000
105A104VAL0-0.032-0.02721.746-0.444-0.4440.0000.0000.0000.000
106A105ASN0-0.018-0.01321.2910.2810.2810.0000.0000.0000.000
107A106ALA00.0070.01217.575-0.437-0.4370.0000.0000.0000.000
108A107ALA0-0.009-0.00818.360-0.491-0.4910.0000.0000.0000.000
109A108ALA0-0.0020.00220.614-0.058-0.0580.0000.0000.0000.000
110A109LEU00.007-0.00315.561-0.063-0.0630.0000.0000.0000.000
111A110GLY00.0250.01316.074-0.625-0.6250.0000.0000.0000.000
112A111GLU-1-0.739-0.89317.137-13.820-13.8200.0000.0000.0000.000
113A112PHE0-0.0100.00717.9600.1640.1640.0000.0000.0000.000
114A113LEU00.0060.01312.306-0.047-0.0470.0000.0000.0000.000
115A114PHE0-0.082-0.06011.120-0.048-0.0480.0000.0000.0000.000
116A115GLY0-0.049-0.01416.9440.3110.3110.0000.0000.0000.000
117A116GLU-1-0.841-0.96220.602-11.532-11.5320.0000.0000.0000.000
118A117ALA0-0.022-0.01022.3860.4940.4940.0000.0000.0000.000
119A118LYS10.9040.97816.12416.90816.9080.0000.0000.0000.000
120A119GLY0-0.025-0.01620.5800.3880.3880.0000.0000.0000.000
121A120LEU0-0.0200.01322.1620.5130.5130.0000.0000.0000.000
122A121ASP-1-0.817-0.88922.567-11.492-11.4920.0000.0000.0000.000
123A122SER0-0.025-0.01924.3110.1200.1200.0000.0000.0000.000
124A123CYS0-0.036-0.01023.200-0.088-0.0880.0000.0000.0000.000
125A124LEU00.0000.00426.484-0.016-0.0160.0000.0000.0000.000
126A125TYR00.0580.03123.5180.1190.1190.0000.0000.0000.000
127A126ILE00.007-0.00326.4330.0890.0890.0000.0000.0000.000
128A127THR0-0.041-0.01627.183-0.067-0.0670.0000.0000.0000.000
129A128ILE00.0780.02329.1860.2190.2190.0000.0000.0000.000
130A129GLY00.007-0.01132.131-0.085-0.0850.0000.0000.0000.000
131A130THR0-0.041-0.02932.7360.2460.2460.0000.0000.0000.000
132A131GLY00.0450.02233.1580.2800.2800.0000.0000.0000.000
133A132ILE0-0.053-0.01432.689-0.146-0.1460.0000.0000.0000.000
134A133GLY00.0220.02329.7130.1250.1250.0000.0000.0000.000
135A134ALA00.001-0.02428.212-0.016-0.0160.0000.0000.0000.000
136A135GLY00.0240.02624.9010.0350.0350.0000.0000.0000.000
137A136ALA0-0.003-0.00525.7750.0560.0560.0000.0000.0000.000
138A137ILE0-0.034-0.01220.628-0.319-0.3190.0000.0000.0000.000
139A138VAL00.0390.00424.4460.4610.4610.0000.0000.0000.000
140A139GLU-1-0.907-0.95025.269-10.762-10.7620.0000.0000.0000.000
141A140GLY0-0.007-0.00521.844-0.315-0.3150.0000.0000.0000.000
142A141ARG10.8890.94320.31312.04612.0460.0000.0000.0000.000
143A142LEU00.0020.00219.3390.3780.3780.0000.0000.0000.000
144A143LEU0-0.024-0.00222.6610.1760.1760.0000.0000.0000.000
145A144GLN00.0190.01325.078-0.255-0.2550.0000.0000.0000.000
146A145GLY00.0090.00927.0040.1010.1010.0000.0000.0000.000
147A146LEU0-0.023-0.02230.152-0.163-0.1630.0000.0000.0000.000
148A147SER0-0.006-0.01030.659-0.020-0.0200.0000.0000.0000.000
149A148HIS00.0130.02726.846-0.184-0.1840.0000.0000.0000.000
150A149PRO0-0.004-0.00627.8200.4030.4030.0000.0000.0000.000
151A150GLU-1-0.830-0.92930.298-10.001-10.0010.0000.0000.0000.000
152A151MET00.0140.01830.1210.3390.3390.0000.0000.0000.000
153A152GLY00.0530.04633.7980.2470.2470.0000.0000.0000.000
154A153HIS10.7770.86335.0218.8868.8860.0000.0000.0000.000
155A154ILE00.0160.03437.5030.1850.1850.0000.0000.0000.000
156A155TYR0-0.035-0.02539.977-0.034-0.0340.0000.0000.0000.000
157A156ILE00.0000.00741.296-0.056-0.0560.0000.0000.0000.000
158A157ARG10.9300.96444.3456.4516.4510.0000.0000.0000.000
159A158ARG10.8570.88147.2566.3086.3080.0000.0000.0000.000
160A159HIS00.0160.01048.6190.0870.0870.0000.0000.0000.000
161A160PRO0-0.035-0.02150.2970.0210.0210.0000.0000.0000.000
162A161ASP-1-0.864-0.92953.487-5.663-5.6630.0000.0000.0000.000
163A162ASP-1-0.791-0.84748.214-6.629-6.6290.0000.0000.0000.000
164A163VAL00.0140.00851.7620.0060.0060.0000.0000.0000.000
165A164TYR0-0.044-0.00144.9310.0270.0270.0000.0000.0000.000
166A165GLN00.0460.01749.275-0.006-0.0060.0000.0000.0000.000
167A166GLY00.0030.01445.788-0.035-0.0350.0000.0000.0000.000
168A167LYS10.8810.93841.3107.5837.5830.0000.0000.0000.000
169A168CYS0-0.0650.00240.775-0.159-0.1590.0000.0000.0000.000
170A169PRO0-0.008-0.01040.1910.1680.1680.0000.0000.0000.000
171A170TYR0-0.004-0.01638.0480.0310.0310.0000.0000.0000.000
172A171HIS00.0820.02239.3980.0020.0020.0000.0000.0000.000
173A172GLY00.0650.05244.2860.1420.1420.0000.0000.0000.000
174A173ASP-1-0.829-0.91544.527-6.802-6.8020.0000.0000.0000.000
175A174CYS0-0.0530.00339.5790.0130.0130.0000.0000.0000.000
176A175PHE00.0740.02235.4420.0130.0130.0000.0000.0000.000
177A176GLU-1-0.814-0.91935.405-8.801-8.8010.0000.0000.0000.000
178A177GLY0-0.036-0.01538.4730.0030.0030.0000.0000.0000.000
179A178LEU0-0.016-0.00341.8840.1520.1520.0000.0000.0000.000
180A179ALA00.0550.02839.1510.1220.1220.0000.0000.0000.000
181A180SER0-0.0170.00336.937-0.198-0.1980.0000.0000.0000.000
182A181GLY00.0250.00736.7050.2000.2000.0000.0000.0000.000
183A182PRO0-0.042-0.03937.1960.2110.2110.0000.0000.0000.000
184A183ALA0-0.0100.00540.3890.2050.2050.0000.0000.0000.000
185A184ILE0-0.0130.00439.3660.2150.2150.0000.0000.0000.000
186A185GLU-1-0.902-0.96641.551-7.535-7.5350.0000.0000.0000.000
187A186ALA0-0.082-0.04643.9470.1730.1730.0000.0000.0000.000
188A187ARG10.7470.87144.1277.1357.1350.0000.0000.0000.000
189A188TRP00.018-0.00545.3210.2030.2030.0000.0000.0000.000
190A189GLY0-0.0150.00948.1000.0820.0820.0000.0000.0000.000
191A190LYS10.8930.94446.0146.6356.6350.0000.0000.0000.000
192A191LYS10.9460.99040.6277.5917.5910.0000.0000.0000.000
193A192ALA00.0330.01638.6660.1120.1120.0000.0000.0000.000
194A193ALA0-0.055-0.03539.358-0.220-0.2200.0000.0000.0000.000
195A194ASP-1-0.902-0.94941.307-7.132-7.1320.0000.0000.0000.000
196A195LEU00.0360.00243.6390.1970.1970.0000.0000.0000.000
197A196SER0-0.081-0.03741.0130.0310.0310.0000.0000.0000.000
198A197ASP-1-0.867-0.94143.343-6.797-6.7970.0000.0000.0000.000
199A198ILE0-0.036-0.01246.8680.1430.1430.0000.0000.0000.000
200A199ALA00.0250.00846.595-0.090-0.0900.0000.0000.0000.000
201A200GLN00.0550.01646.664-0.055-0.0550.0000.0000.0000.000
202A201VAL0-0.030-0.00643.396-0.021-0.0210.0000.0000.0000.000
203A202TRP0-0.005-0.02940.028-0.232-0.2320.0000.0000.0000.000
204A203GLU-1-0.893-0.93242.947-6.567-6.5670.0000.0000.0000.000
205A204LEU0-0.030-0.00945.388-0.029-0.0290.0000.0000.0000.000
206A205GLU-1-0.821-0.92738.851-8.053-8.0530.0000.0000.0000.000
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