FMO DATABASE

FMODB ID: G8741

Calculation Name: 1F41-A-Xray547

Preferred Name: Transthyretin

Target Type: SINGLE PROTEIN

Ligand Name:

Ligand 3-letter code:

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 1F41

Chain ID: A

ChEMBL ID: CHEMBL3194

UniProt ID: P02766

Base Structure: X-ray

Registration Date: 2025-09-02

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	116
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23 (BINDS Ver. 1) / 20230922

Total energy (hartree)

FMO2-HF: Electronic energy	-888726.568728
FMO2-HF: Nuclear repulsion	844618.166154
FMO2-HF: Total energy	-44108.402575
FMO2-MP2: Total energy	-44238.691735

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:10:CYS)

Summations of interaction energy for fragment #1(A:10:CYS)

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.
-64.425	-71.388	30.381	-10.025	-13.393	0.099

Interaction energy analysis for fragmet #1(A:10:CYS)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.009 / q_NPA : 0.037

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	12	LEU	0	0.050	0.027	3.047	3.126	5.367	0.035	-1.041	-1.236	0.001
4	A	13	MET	0	-0.088	-0.020	2.526	3.872	6.218	0.544	-1.082	-1.807	-0.008
5	A	14	VAL	0	0.037	0.024	4.062	-3.934	-3.888	0.001	-0.033	-0.014	0.000
47	A	56	HIS	1	0.832	0.855	2.331	-43.274	-47.436	16.038	-5.795	-6.081	0.074
48	A	57	GLY	0	0.025	-0.016	2.234	-11.378	-18.940	13.748	-2.612	-3.574	0.028
49	A	58	LEU	0	-0.034	-0.009	4.150	-6.141	-6.530	0.019	0.653	-0.283	0.004
50	A	59	THR	0	-0.011	-0.023	4.662	-2.258	-2.202	-0.001	-0.010	-0.045	0.000
51	A	60	THR	0	-0.026	-0.020	4.111	-3.088	-2.871	-0.001	-0.052	-0.164	0.000
95	A	104	ARG	1	0.837	0.919	4.308	10.911	11.123	-0.001	-0.049	-0.162	0.000
97	A	106	THR	0	-0.016	-0.016	5.152	1.381	1.413	-0.001	-0.004	-0.027	0.000
6	A	15	LYS	1	0.841	0.903	7.864	-3.121	-3.121	0.000	0.000	0.000	0.000
7	A	16	VAL	0	0.004	0.004	10.307	-0.880	-0.880	0.000	0.000	0.000	0.000
8	A	17	LEU	0	-0.004	-0.001	14.027	0.165	0.165	0.000	0.000	0.000	0.000
9	A	18	ASP	-1	-0.744	-0.856	17.116	1.305	1.305	0.000	0.000	0.000	0.000
10	A	19	ALA	0	0.001	-0.009	20.852	-0.041	-0.041	0.000	0.000	0.000	0.000
11	A	20	VAL	0	-0.050	-0.018	23.592	-0.104	-0.104	0.000	0.000	0.000	0.000
12	A	21	ARG	1	0.899	0.941	22.633	-1.559	-1.559	0.000	0.000	0.000	0.000
13	A	22	GLY	0	0.007	0.027	23.382	-0.014	-0.014	0.000	0.000	0.000	0.000
14	A	23	SER	0	-0.044	-0.029	20.424	-0.031	-0.031	0.000	0.000	0.000	0.000
15	A	24	PRO	0	0.020	0.003	15.269	-0.015	-0.015	0.000	0.000	0.000	0.000
16	A	25	ALA	0	0.009	0.026	16.399	-0.237	-0.237	0.000	0.000	0.000	0.000
17	A	26	ILE	0	-0.022	0.010	15.577	0.445	0.445	0.000	0.000	0.000	0.000
18	A	27	ASN	0	-0.030	-0.023	15.591	-0.190	-0.190	0.000	0.000	0.000	0.000
19	A	28	VAL	0	-0.014	0.005	15.299	-0.297	-0.297	0.000	0.000	0.000	0.000
20	A	29	ALA	0	-0.009	-0.007	14.782	0.491	0.491	0.000	0.000	0.000	0.000
21	A	30	VAL	0	-0.009	-0.010	10.813	-0.158	-0.158	0.000	0.000	0.000	0.000
22	A	31	HIS	0	0.023	0.012	13.718	0.294	0.294	0.000	0.000	0.000	0.000
23	A	32	VAL	0	-0.007	-0.004	9.728	0.005	0.005	0.000	0.000	0.000	0.000
24	A	33	PHE	0	-0.002	0.004	13.206	-0.089	-0.089	0.000	0.000	0.000	0.000
25	A	34	ARG	1	0.919	0.953	14.039	0.927	0.927	0.000	0.000	0.000	0.000
26	A	35	LYS	1	0.790	0.887	16.159	0.304	0.304	0.000	0.000	0.000	0.000
27	A	36	ALA	0	0.039	0.032	19.453	-0.142	-0.142	0.000	0.000	0.000	0.000
28	A	37	ALA	0	-0.026	-0.029	21.563	-0.019	-0.019	0.000	0.000	0.000	0.000
29	A	38	ASP	-1	-0.878	-0.917	24.347	-0.127	-0.127	0.000	0.000	0.000	0.000
30	A	39	ASP	-1	-0.848	-0.912	24.536	-0.181	-0.181	0.000	0.000	0.000	0.000
31	A	40	THR	0	-0.063	-0.042	24.416	0.072	0.072	0.000	0.000	0.000	0.000
32	A	41	TRP	0	-0.042	-0.034	17.642	-0.033	-0.033	0.000	0.000	0.000	0.000
33	A	42	GLU	-1	-0.908	-0.949	18.290	-0.206	-0.206	0.000	0.000	0.000	0.000
34	A	43	PRO	0	-0.041	-0.040	17.121	0.022	0.022	0.000	0.000	0.000	0.000
35	A	44	PHE	0	-0.006	0.003	8.913	0.005	0.005	0.000	0.000	0.000	0.000
36	A	45	ALA	0	0.047	0.024	9.931	0.075	0.075	0.000	0.000	0.000	0.000
37	A	46	SER	0	-0.040	-0.015	11.872	-0.122	-0.122	0.000	0.000	0.000	0.000
38	A	47	GLY	0	0.022	0.005	11.036	0.621	0.621	0.000	0.000	0.000	0.000
39	A	48	LYS	1	0.924	0.956	11.777	-3.070	-3.070	0.000	0.000	0.000	0.000
40	A	49	THR	0	-0.033	-0.019	11.116	0.825	0.825	0.000	0.000	0.000	0.000
41	A	50	SER	0	0.018	-0.002	10.005	-0.934	-0.934	0.000	0.000	0.000	0.000
42	A	51	GLU	-1	-0.889	-0.966	12.394	2.489	2.489	0.000	0.000	0.000	0.000
43	A	52	SER	0	-0.008	-0.007	10.797	-0.134	-0.134	0.000	0.000	0.000	0.000
44	A	53	GLY	0	0.022	0.000	12.919	-0.192	-0.192	0.000	0.000	0.000	0.000
45	A	54	GLU	-1	-0.851	-0.891	7.422	8.362	8.362	0.000	0.000	0.000	0.000
46	A	55	LEU	0	0.007	0.023	7.449	-0.338	-0.338	0.000	0.000	0.000	0.000
52	A	61	GLU	-1	-0.976	-1.005	5.249	-12.178	-12.178	0.000	0.000	0.000	0.000
53	A	62	GLU	-1	-0.952	-0.966	6.783	-2.371	-2.371	0.000	0.000	0.000	0.000
54	A	63	GLU	-1	-0.850	-0.890	8.979	-0.510	-0.510	0.000	0.000	0.000	0.000
55	A	64	PHE	0	-0.040	-0.009	7.351	0.731	0.731	0.000	0.000	0.000	0.000
56	A	65	VAL	0	0.018	0.003	9.383	-0.398	-0.398	0.000	0.000	0.000	0.000
57	A	66	GLU	-1	-0.878	-0.924	12.859	-1.539	-1.539	0.000	0.000	0.000	0.000
58	A	67	GLY	0	0.012	0.004	15.327	0.206	0.206	0.000	0.000	0.000	0.000
59	A	68	ILE	0	-0.026	-0.001	15.819	-0.090	-0.090	0.000	0.000	0.000	0.000
60	A	69	TYR	0	0.007	-0.026	12.005	0.159	0.159	0.000	0.000	0.000	0.000
61	A	70	LYS	1	0.860	0.923	15.000	-0.588	-0.588	0.000	0.000	0.000	0.000
62	A	71	VAL	0	-0.025	-0.003	10.307	0.161	0.161	0.000	0.000	0.000	0.000
63	A	72	GLU	-1	-0.908	-0.952	13.468	1.016	1.016	0.000	0.000	0.000	0.000
64	A	73	ILE	0	-0.014	-0.015	12.984	0.411	0.411	0.000	0.000	0.000	0.000
65	A	74	ASP	-1	-0.764	-0.863	16.272	1.227	1.227	0.000	0.000	0.000	0.000
66	A	75	THR	0	0.022	-0.005	19.441	0.106	0.106	0.000	0.000	0.000	0.000
67	A	76	LYS	1	0.798	0.892	21.144	-0.804	-0.804	0.000	0.000	0.000	0.000
68	A	77	SER	0	-0.087	-0.086	22.097	-0.112	-0.112	0.000	0.000	0.000	0.000
69	A	78	TYR	0	-0.066	-0.054	20.083	0.046	0.046	0.000	0.000	0.000	0.000
70	A	79	TRP	0	0.038	0.005	22.389	-0.050	-0.050	0.000	0.000	0.000	0.000
71	A	80	LYS	1	0.943	0.976	25.489	-1.030	-1.030	0.000	0.000	0.000	0.000
72	A	81	ALA	0	-0.033	-0.005	24.328	-0.067	-0.067	0.000	0.000	0.000	0.000
73	A	82	LEU	0	-0.057	-0.020	23.667	-0.028	-0.028	0.000	0.000	0.000	0.000
74	A	83	GLY	0	-0.017	0.000	27.448	-0.063	-0.063	0.000	0.000	0.000	0.000
75	A	84	ILE	0	-0.047	-0.025	28.168	-0.073	-0.073	0.000	0.000	0.000	0.000
76	A	85	SER	0	-0.007	-0.013	29.311	0.038	0.038	0.000	0.000	0.000	0.000
77	A	86	PRO	0	-0.066	-0.026	26.138	-0.040	-0.040	0.000	0.000	0.000	0.000
78	A	87	PHE	0	-0.023	-0.011	28.283	-0.043	-0.043	0.000	0.000	0.000	0.000
79	A	88	HIS	0	-0.001	0.005	24.014	0.007	0.007	0.000	0.000	0.000	0.000
80	A	89	GLU	-1	-0.786	-0.883	24.989	0.820	0.820	0.000	0.000	0.000	0.000
81	A	90	HIS	0	-0.008	-0.009	19.779	0.140	0.140	0.000	0.000	0.000	0.000
82	A	91	ALA	0	-0.020	0.001	17.636	-0.121	-0.121	0.000	0.000	0.000	0.000
83	A	92	GLU	-1	-0.850	-0.917	17.596	0.776	0.776	0.000	0.000	0.000	0.000
84	A	93	VAL	0	-0.031	-0.021	13.734	-0.126	-0.126	0.000	0.000	0.000	0.000
85	A	94	VAL	0	-0.006	-0.003	15.004	-0.001	-0.001	0.000	0.000	0.000	0.000
86	A	95	PHE	0	-0.049	-0.025	9.952	0.001	0.001	0.000	0.000	0.000	0.000
87	A	96	THR	0	0.031	0.014	15.462	0.052	0.052	0.000	0.000	0.000	0.000
88	A	97	ALA	0	-0.031	-0.011	11.215	-0.048	-0.048	0.000	0.000	0.000	0.000
89	A	98	ASN	0	0.013	-0.022	9.497	-0.349	-0.349	0.000	0.000	0.000	0.000
90	A	99	ASP	-1	-0.807	-0.884	13.506	-1.581	-1.581	0.000	0.000	0.000	0.000
91	A	100	SER	0	-0.094	-0.035	16.599	0.144	0.144	0.000	0.000	0.000	0.000
92	A	101	GLY	0	0.014	0.011	15.249	-0.075	-0.075	0.000	0.000	0.000	0.000
93	A	102	PRO	0	0.012	-0.008	9.668	0.097	0.097	0.000	0.000	0.000	0.000
94	A	103	ARG	1	0.813	0.915	9.826	3.709	3.709	0.000	0.000	0.000	0.000
96	A	105	TYR	0	0.030	0.014	5.720	2.228	2.228	0.000	0.000	0.000	0.000
98	A	107	ILE	0	-0.006	0.002	6.930	-0.592	-0.592	0.000	0.000	0.000	0.000
99	A	108	ALA	0	0.032	0.015	9.681	0.909	0.909	0.000	0.000	0.000	0.000
100	A	109	ALA	0	0.013	0.001	11.969	-0.444	-0.444	0.000	0.000	0.000	0.000
101	A	110	LEU	0	-0.025	0.000	15.155	0.247	0.247	0.000	0.000	0.000	0.000
102	A	111	LEU	0	0.022	0.005	18.200	-0.194	-0.194	0.000	0.000	0.000	0.000
103	A	112	SER	0	-0.016	-0.020	20.924	-0.056	-0.056	0.000	0.000	0.000	0.000
104	A	113	PRO	0	0.011	0.009	24.683	0.006	0.006	0.000	0.000	0.000	0.000
105	A	114	TYR	0	0.042	0.007	27.136	-0.031	-0.031	0.000	0.000	0.000	0.000
106	A	115	SER	0	-0.035	-0.013	25.753	-0.060	-0.060	0.000	0.000	0.000	0.000
107	A	116	TYR	0	0.030	0.020	19.639	0.107	0.107	0.000	0.000	0.000	0.000
108	A	117	SER	0	-0.011	0.012	20.073	-0.115	-0.115	0.000	0.000	0.000	0.000
109	A	118	THR	0	0.008	-0.015	14.453	0.150	0.150	0.000	0.000	0.000	0.000
110	A	119	THR	0	-0.034	-0.028	14.355	-0.220	-0.220	0.000	0.000	0.000	0.000
111	A	120	ALA	0	0.029	0.030	11.526	0.312	0.312	0.000	0.000	0.000	0.000
112	A	121	VAL	0	-0.012	-0.004	9.896	-0.177	-0.177	0.000	0.000	0.000	0.000
113	A	122	VAL	0	0.004	0.001	9.194	-0.221	-0.221	0.000	0.000	0.000	0.000
114	A	123	THR	0	-0.040	-0.019	8.550	-0.003	-0.003	0.000	0.000	0.000	0.000
115	A	124	ASN	0	0.035	-0.002	10.268	-0.870	-0.870	0.000	0.000	0.000	0.000
116	A	125	PRO	-1	-0.850	-0.894	7.785	-6.353	-6.353	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:10:CYS)