FMO DATABASE

FMODB ID: 3497L

Calculation Name: 3DSO-A-Xray549

Preferred Name:

Target Type:

Ligand Name: thiocyanate ion | copper (i) ion

Ligand 3-letter code: SCN | CU1

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 3DSO

Chain ID: A

ChEMBL ID:

UniProt ID: Q58AD3

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	66
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922

Total energy (hartree)

FMO2-HF: Electronic energy	-377877.893163
FMO2-HF: Nuclear repulsion	350241.726076
FMO2-HF: Total energy	-27636.167087
FMO2-MP2: Total energy	-27711.443774

3D Structure Molmil

Snapshot

Ligand structure

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/A	N/A	N/A	N/A	N/A	N/A

Interactive mode: IFIE and PIEDA for fragment #1(A:1:VAL)

Summations of interaction energy for fragment #1(A:1: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.
38.138	47.205	7.082	-4.935	-11.214	-0.05

Interaction energy analysis for fragmet #1(A:1:VAL)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 1 / q_Mulliken : 0.850 / 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 ES EX CT+mix DI(MP2)

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].
3	A	3	MET	0	-0.008	-0.021	2.982	0.568	3.668	1.231	-1.126	-3.204	-0.006
4	A	4	SER	0	0.032	0.039	3.839	6.598	6.820	0.005	-0.019	-0.208	0.000
6	A	6	VAL	0	-0.050	-0.006	2.667	0.473	0.779	0.872	-0.239	-0.940	-0.002
19	A	19	HIS	1	0.758	0.849	2.454	48.010	49.811	1.669	-0.741	-2.729	-0.005
20	A	20	VAL	0	0.082	0.041	5.265	0.824	0.866	-0.001	-0.002	-0.039	0.000
21	A	21	PHE	0	-0.013	-0.016	2.253	-3.802	-3.446	1.164	-0.325	-1.195	-0.003
29	A	29	GLU	-1	-0.813	-0.886	2.562	-75.585	-72.345	2.142	-2.483	-2.899	-0.034
5	A	5	ASN	0	-0.049	-0.051	5.455	7.023	7.023	0.000	0.000	0.000	0.000
7	A	7	VAL	0	-0.007	-0.001	5.446	1.576	1.576	0.000	0.000	0.000	0.000
8	A	8	LYS	1	0.935	0.974	7.855	20.510	20.510	0.000	0.000	0.000	0.000
9	A	9	THR	0	-0.002	-0.005	5.768	-4.955	-4.955	0.000	0.000	0.000	0.000
10	A	10	TYR	0	0.047	0.024	7.487	3.003	3.003	0.000	0.000	0.000	0.000
11	A	11	ASP	-1	-0.787	-0.871	8.965	-30.038	-30.038	0.000	0.000	0.000	0.000
12	A	12	LEU	0	-0.003	-0.009	10.615	2.032	2.032	0.000	0.000	0.000	0.000
13	A	13	GLN	0	0.010	-0.009	12.782	-1.034	-1.034	0.000	0.000	0.000	0.000
14	A	14	ASP	-1	-0.882	-0.899	13.020	-20.055	-20.055	0.000	0.000	0.000	0.000
15	A	15	GLY	0	-0.039	-0.038	12.370	-0.015	-0.015	0.000	0.000	0.000	0.000
16	A	16	SER	0	-0.104	-0.077	8.962	-2.410	-2.410	0.000	0.000	0.000	0.000
17	A	17	LYS	1	0.862	0.915	5.094	36.008	36.008	0.000	0.000	0.000	0.000
18	A	18	VAL	0	0.039	0.022	5.884	-2.571	-2.571	0.000	0.000	0.000	0.000
22	A	22	LYS	1	0.911	0.945	7.864	26.581	26.581	0.000	0.000	0.000	0.000
23	A	23	ASP	-1	-0.844	-0.903	10.039	-22.531	-22.531	0.000	0.000	0.000	0.000
24	A	24	GLY	0	0.025	0.024	11.653	1.025	1.025	0.000	0.000	0.000	0.000
25	A	25	LYS	1	0.868	0.937	8.650	22.259	22.259	0.000	0.000	0.000	0.000
26	A	26	MET	0	0.014	0.013	8.000	-1.377	-1.377	0.000	0.000	0.000	0.000
27	A	27	GLY	0	0.020	0.000	6.054	0.277	0.277	0.000	0.000	0.000	0.000
28	A	28	MET	0	-0.035	-0.017	5.907	-0.873	-0.873	0.000	0.000	0.000	0.000
30	A	30	ASN	0	0.071	0.010	5.861	0.863	0.863	0.000	0.000	0.000	0.000
31	A	31	LYS	1	0.942	0.982	7.530	16.283	16.283	0.000	0.000	0.000	0.000
32	A	32	PHE	0	-0.040	-0.021	9.423	0.792	0.792	0.000	0.000	0.000	0.000
33	A	33	GLY	0	0.029	0.032	5.140	-0.411	-0.411	0.000	0.000	0.000	0.000
34	A	34	LYS	1	0.920	0.966	5.816	20.668	20.668	0.000	0.000	0.000	0.000
35	A	35	SER	0	0.001	-0.007	6.389	0.525	0.525	0.000	0.000	0.000	0.000
36	A	36	MET	0	-0.036	-0.017	7.213	2.824	2.824	0.000	0.000	0.000	0.000
37	A	37	ASN	0	0.026	0.018	9.623	-1.476	-1.476	0.000	0.000	0.000	0.000
38	A	38	MET	0	0.018	0.010	10.096	-0.470	-0.470	0.000	0.000	0.000	0.000
39	A	39	PRO	0	-0.038	-0.017	12.493	1.066	1.066	0.000	0.000	0.000	0.000
40	A	40	GLU	-1	-0.823	-0.910	15.846	-14.418	-14.418	0.000	0.000	0.000	0.000
41	A	41	GLY	0	-0.073	-0.040	17.788	0.579	0.579	0.000	0.000	0.000	0.000
42	A	42	LYS	1	0.917	0.970	15.671	17.051	17.051	0.000	0.000	0.000	0.000
43	A	43	VAL	0	0.037	0.019	18.327	-0.516	-0.516	0.000	0.000	0.000	0.000
44	A	44	MET	0	-0.080	-0.039	12.496	-0.350	-0.350	0.000	0.000	0.000	0.000
45	A	45	GLU	-1	-0.787	-0.872	16.759	-13.196	-13.196	0.000	0.000	0.000	0.000
46	A	46	THR	0	-0.022	-0.044	13.847	-0.861	-0.861	0.000	0.000	0.000	0.000
47	A	47	ARG	1	0.879	0.915	11.575	22.431	22.431	0.000	0.000	0.000	0.000
48	A	48	ASP	-1	-0.845	-0.873	16.555	-15.772	-15.772	0.000	0.000	0.000	0.000
49	A	49	GLY	0	0.026	0.025	18.930	0.685	0.685	0.000	0.000	0.000	0.000
50	A	50	THR	0	-0.042	-0.029	17.474	0.668	0.668	0.000	0.000	0.000	0.000
51	A	51	LYS	1	0.859	0.917	18.115	11.842	11.842	0.000	0.000	0.000	0.000
52	A	52	ILE	0	-0.010	-0.016	13.202	0.021	0.021	0.000	0.000	0.000	0.000
53	A	53	ILE	0	-0.002	-0.002	17.690	0.179	0.179	0.000	0.000	0.000	0.000
54	A	54	MET	0	-0.016	0.014	12.433	-0.909	-0.909	0.000	0.000	0.000	0.000
55	A	55	LYS	1	0.977	0.973	16.244	13.099	13.099	0.000	0.000	0.000	0.000
56	A	56	GLY	0	0.059	0.033	18.273	-0.126	-0.126	0.000	0.000	0.000	0.000
57	A	57	ASN	0	-0.097	-0.055	12.797	-0.959	-0.959	0.000	0.000	0.000	0.000
58	A	58	GLU	-1	-0.898	-0.937	14.302	-14.795	-14.795	0.000	0.000	0.000	0.000
59	A	59	ILE	0	-0.084	-0.067	11.511	-0.389	-0.389	0.000	0.000	0.000	0.000
60	A	60	PHE	0	0.035	0.030	15.348	0.458	0.458	0.000	0.000	0.000	0.000
61	A	61	ARG	1	0.914	0.941	17.228	13.234	13.234	0.000	0.000	0.000	0.000
62	A	62	LEU	0	-0.008	-0.004	19.446	0.400	0.400	0.000	0.000	0.000	0.000
63	A	63	ASP	-1	-0.869	-0.944	22.507	-10.987	-10.987	0.000	0.000	0.000	0.000
64	A	64	GLU	-1	-0.977	-0.990	23.043	-12.226	-12.226	0.000	0.000	0.000	0.000
65	A	65	ALA	0	-0.067	-0.032	25.839	0.246	0.246	0.000	0.000	0.000	0.000
66	A	66	LEU	-1	-0.992	-0.973	28.698	-9.436	-9.436	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:1:VAL)