FMO DATABASE

FMODB ID: 6Y7GZ

Calculation Name: 5CNH-A-Xray372

Preferred Name: Transthyretin

Target Type: SINGLE PROTEIN

Ligand Name:

ligand 3-letter code:

PDB ID: 5CNH

Chain ID: A

ChEMBL ID: CHEMBL3194

UniProt ID: P02766

Base Structure: X-ray

Registration Date: 2023-09-22

Reference: C. Watanabe, N. Tani, K. Kamisaka, T. Honma et al., Interaction energy analysis of Apo structure dataset on FMODB, To be published.

DOI:

IFIE MAP

IFIE Diagram

Modeling method

Optimization	MOE:Amber10:EHT
Restraint	OptH
Protonation	MOE:Protonate 3D
Complement	MOE:Structure Preparation
Water	No
Procedure	Auto-FMO protocol ver. 2.20220422

FMO calculation

FMO method	FMO2-MP2/6-31G(d)
Fragmentation	Auto
Number of fragment	116
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-890994.331961
FMO2-HF: Nuclear repulsion	846886.682229
FMO2-HF: Total energy	-44107.649731
FMO2-MP2: Total energy	-44237.938185

3D Structure

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.
-16.733	-18.943	21.938	-8.246	-11.482	-0.009

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 : -0.015 / q_NPA : -0.009

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	0.037	0.029	2.946	-0.775	1.925	0.078	-1.227	-1.551	-0.001
4	A	13	MET	0	-0.071	-0.008	2.846	-0.289	1.630	0.262	-0.751	-1.429	-0.006
5	A	14	VAL	0	0.024	0.010	4.207	0.384	0.450	0.000	-0.023	-0.043	0.000
6	A	15	LYS	1	0.949	0.974	7.860	0.477	0.477	0.000	0.000	0.000	0.000
7	A	16	VAL	0	-0.005	-0.005	10.054	0.036	0.036	0.000	0.000	0.000	0.000
8	A	17	LEU	0	-0.015	0.002	13.542	0.029	0.029	0.000	0.000	0.000	0.000
9	A	18	ASP	-1	-0.747	-0.853	16.549	-0.091	-0.091	0.000	0.000	0.000	0.000
10	A	19	ALA	0	0.013	-0.013	20.056	0.005	0.005	0.000	0.000	0.000	0.000
11	A	20	VAL	0	-0.067	-0.032	22.795	0.009	0.009	0.000	0.000	0.000	0.000
12	A	21	ARG	1	0.879	0.932	22.633	0.063	0.063	0.000	0.000	0.000	0.000
13	A	22	GLY	0	-0.025	0.016	22.031	0.007	0.007	0.000	0.000	0.000	0.000
14	A	23	SER	0	-0.014	-0.010	19.454	0.010	0.010	0.000	0.000	0.000	0.000
15	A	24	PRO	0	0.004	0.003	14.320	-0.022	-0.022	0.000	0.000	0.000	0.000
16	A	25	ALA	0	0.007	0.013	15.254	0.029	0.029	0.000	0.000	0.000	0.000
17	A	26	ILE	0	-0.024	0.004	14.517	-0.018	-0.018	0.000	0.000	0.000	0.000
18	A	27	ASN	0	-0.005	-0.011	14.437	0.022	0.022	0.000	0.000	0.000	0.000
19	A	28	VAL	0	-0.021	-0.004	14.241	0.008	0.008	0.000	0.000	0.000	0.000
20	A	29	ALA	0	-0.037	-0.015	13.667	0.015	0.015	0.000	0.000	0.000	0.000
21	A	30	VAL	0	0.006	-0.007	10.887	-0.051	-0.051	0.000	0.000	0.000	0.000
22	A	31	HIS	0	0.000	0.005	13.188	0.095	0.095	0.000	0.000	0.000	0.000
23	A	32	VAL	0	0.001	0.000	9.813	-0.065	-0.065	0.000	0.000	0.000	0.000
24	A	33	PHE	0	-0.010	-0.012	13.231	0.054	0.054	0.000	0.000	0.000	0.000
25	A	34	ARG	1	0.929	0.949	14.127	0.230	0.230	0.000	0.000	0.000	0.000
26	A	35	LYS	1	0.882	0.952	16.377	0.213	0.213	0.000	0.000	0.000	0.000
27	A	36	ALA	0	0.029	0.018	19.742	-0.013	-0.013	0.000	0.000	0.000	0.000
28	A	37	ALA	0	-0.023	-0.020	21.640	-0.001	-0.001	0.000	0.000	0.000	0.000
29	A	38	ASP	-1	-0.857	-0.907	24.459	-0.095	-0.095	0.000	0.000	0.000	0.000
30	A	39	ASP	-1	-0.952	-0.970	24.790	-0.126	-0.126	0.000	0.000	0.000	0.000
31	A	40	THR	0	-0.088	-0.056	24.513	-0.001	-0.001	0.000	0.000	0.000	0.000
32	A	41	TRP	0	-0.068	-0.051	17.732	-0.016	-0.016	0.000	0.000	0.000	0.000
33	A	42	GLU	-1	-0.894	-0.941	18.233	-0.094	-0.094	0.000	0.000	0.000	0.000
34	A	43	PRO	0	-0.068	-0.048	17.204	-0.028	-0.028	0.000	0.000	0.000	0.000
35	A	44	PHE	0	-0.003	0.001	8.784	0.000	0.000	0.000	0.000	0.000	0.000
36	A	45	ALA	0	0.064	0.038	9.848	0.054	0.054	0.000	0.000	0.000	0.000
37	A	46	SER	0	-0.025	-0.014	11.462	-0.081	-0.081	0.000	0.000	0.000	0.000
38	A	47	GLY	0	0.027	0.015	10.409	0.151	0.151	0.000	0.000	0.000	0.000
39	A	48	LYS	1	0.902	0.951	11.079	-0.159	-0.159	0.000	0.000	0.000	0.000
40	A	49	THR	0	-0.015	-0.011	10.019	0.066	0.066	0.000	0.000	0.000	0.000
41	A	50	SER	0	0.030	0.017	9.211	0.041	0.041	0.000	0.000	0.000	0.000
42	A	51	GLU	-1	-0.888	-0.964	11.449	0.021	0.021	0.000	0.000	0.000	0.000
43	A	52	SER	0	-0.011	-0.005	9.911	-0.050	-0.050	0.000	0.000	0.000	0.000
44	A	53	GLY	0	-0.007	-0.018	11.984	-0.058	-0.058	0.000	0.000	0.000	0.000
45	A	54	GLU	-1	-0.907	-0.933	6.546	-0.775	-0.775	0.000	0.000	0.000	0.000
46	A	55	LEU	0	-0.001	0.010	6.562	0.203	0.203	0.000	0.000	0.000	0.000
47	A	56	HIS	0	-0.005	-0.042	2.472	-6.140	-4.299	2.810	-1.786	-2.865	-0.017
48	A	57	GLY	0	-0.002	-0.036	2.153	2.385	-4.860	13.842	-4.002	-2.596	0.007
49	A	58	LEU	0	-0.018	0.003	3.994	-0.944	-1.582	0.003	0.910	-0.275	0.000
50	A	59	THR	0	0.008	-0.016	4.625	-0.819	-0.728	-0.001	-0.020	-0.070	0.000
51	A	60	THR	0	-0.039	-0.021	3.951	-0.359	0.034	0.001	-0.115	-0.279	-0.001
52	A	61	GLU	-1	-0.955	-1.004	5.499	-0.796	-0.796	0.000	0.000	0.000	0.000
53	A	62	GLU	-1	-0.961	-0.980	6.864	-0.028	-0.028	0.000	0.000	0.000	0.000
54	A	63	GLU	-1	-0.857	-0.889	8.934	-0.022	-0.022	0.000	0.000	0.000	0.000
55	A	64	PHE	0	-0.061	-0.009	7.182	-0.063	-0.063	0.000	0.000	0.000	0.000
56	A	65	VAL	0	0.042	0.022	9.352	-0.075	-0.075	0.000	0.000	0.000	0.000
57	A	66	GLU	-1	-0.902	-0.938	12.742	-0.354	-0.354	0.000	0.000	0.000	0.000
58	A	67	GLY	0	0.006	0.003	15.065	0.052	0.052	0.000	0.000	0.000	0.000
59	A	68	ILE	0	-0.002	0.006	16.002	-0.038	-0.038	0.000	0.000	0.000	0.000
60	A	69	TYR	0	-0.012	-0.026	11.979	0.028	0.028	0.000	0.000	0.000	0.000
61	A	70	LYS	1	0.934	0.977	14.837	0.175	0.175	0.000	0.000	0.000	0.000
62	A	71	VAL	0	-0.036	-0.023	10.650	0.013	0.013	0.000	0.000	0.000	0.000
63	A	72	GLU	-1	-0.919	-0.954	13.644	-0.119	-0.119	0.000	0.000	0.000	0.000
64	A	73	ILE	0	-0.031	-0.015	13.410	0.020	0.020	0.000	0.000	0.000	0.000
65	A	74	ASP	-1	-0.766	-0.902	16.275	-0.073	-0.073	0.000	0.000	0.000	0.000
66	A	75	THR	0	-0.012	-0.031	18.830	0.011	0.011	0.000	0.000	0.000	0.000
67	A	76	LYS	1	0.850	0.917	20.436	0.075	0.075	0.000	0.000	0.000	0.000
68	A	77	SER	0	-0.006	-0.018	21.158	0.008	0.008	0.000	0.000	0.000	0.000
69	A	78	TYR	0	-0.032	-0.037	18.937	0.008	0.008	0.000	0.000	0.000	0.000
70	A	79	TRP	0	0.034	0.002	21.260	0.012	0.012	0.000	0.000	0.000	0.000
71	A	80	LYS	1	0.963	0.976	24.476	0.042	0.042	0.000	0.000	0.000	0.000
72	A	81	ALA	0	-0.043	-0.004	23.432	0.006	0.006	0.000	0.000	0.000	0.000
73	A	82	LEU	0	-0.050	-0.018	22.529	0.005	0.005	0.000	0.000	0.000	0.000
74	A	83	GLY	0	-0.011	0.003	26.438	0.000	0.000	0.000	0.000	0.000	0.000
75	A	84	ILE	0	-0.041	-0.021	27.125	-0.001	-0.001	0.000	0.000	0.000	0.000
76	A	85	SER	0	0.011	0.000	28.483	0.000	0.000	0.000	0.000	0.000	0.000
77	A	86	PRO	0	-0.088	-0.035	25.727	-0.001	-0.001	0.000	0.000	0.000	0.000
78	A	87	PHE	0	-0.020	-0.013	28.202	0.005	0.005	0.000	0.000	0.000	0.000
79	A	88	HIS	0	-0.003	0.000	24.388	0.001	0.001	0.000	0.000	0.000	0.000
80	A	89	GLU	-1	-0.870	-0.928	25.342	-0.063	-0.063	0.000	0.000	0.000	0.000
81	A	90	HIS	0	-0.018	-0.012	20.009	0.015	0.015	0.000	0.000	0.000	0.000
82	A	91	ALA	0	-0.059	-0.008	17.937	-0.001	-0.001	0.000	0.000	0.000	0.000
83	A	92	GLU	-1	-0.859	-0.929	17.767	-0.170	-0.170	0.000	0.000	0.000	0.000
84	A	93	VAL	0	-0.025	-0.006	13.835	-0.002	-0.002	0.000	0.000	0.000	0.000
85	A	94	VAL	0	-0.017	-0.021	15.330	-0.023	-0.023	0.000	0.000	0.000	0.000
86	A	95	PHE	0	-0.050	-0.019	10.317	0.002	0.002	0.000	0.000	0.000	0.000
87	A	96	THR	0	0.030	0.007	15.499	-0.004	-0.004	0.000	0.000	0.000	0.000
88	A	97	ALA	0	-0.029	-0.004	11.357	-0.044	-0.044	0.000	0.000	0.000	0.000
89	A	98	ASN	0	0.030	-0.020	9.871	-0.028	-0.028	0.000	0.000	0.000	0.000
90	A	99	ASP	-1	-0.856	-0.916	13.507	-0.346	-0.346	0.000	0.000	0.000	0.000
91	A	100	SER	0	-0.066	-0.027	16.522	0.058	0.058	0.000	0.000	0.000	0.000
92	A	101	GLY	0	-0.001	-0.002	14.866	0.032	0.032	0.000	0.000	0.000	0.000
93	A	102	PRO	0	0.042	0.021	9.561	-0.054	-0.054	0.000	0.000	0.000	0.000
94	A	103	ARG	1	0.834	0.926	9.821	0.621	0.621	0.000	0.000	0.000	0.000
95	A	104	ARG	1	0.891	0.953	2.447	-9.478	-10.815	4.943	-1.232	-2.374	0.009
96	A	105	TYR	0	0.037	0.022	5.734	0.669	0.669	0.000	0.000	0.000	0.000
97	A	106	THR	0	-0.021	-0.010	5.392	-0.777	-0.777	0.000	0.000	0.000	0.000
98	A	107	ILE	0	0.001	0.007	7.307	0.320	0.320	0.000	0.000	0.000	0.000
99	A	108	ALA	0	0.040	0.019	9.954	0.006	0.006	0.000	0.000	0.000	0.000
100	A	109	ALA	0	-0.011	-0.009	12.232	0.050	0.050	0.000	0.000	0.000	0.000
101	A	110	LEU	0	-0.018	0.006	15.433	0.009	0.009	0.000	0.000	0.000	0.000
102	A	111	LEU	0	0.016	-0.002	17.777	0.014	0.014	0.000	0.000	0.000	0.000
103	A	112	SER	0	0.007	-0.002	20.750	0.016	0.016	0.000	0.000	0.000	0.000
104	A	113	PRO	0	0.012	0.007	24.464	-0.004	-0.004	0.000	0.000	0.000	0.000
105	A	114	TYR	0	0.036	-0.004	26.731	0.000	0.000	0.000	0.000	0.000	0.000
106	A	115	SER	0	-0.047	-0.011	25.799	-0.005	-0.005	0.000	0.000	0.000	0.000
107	A	116	TYR	0	0.026	0.010	19.697	-0.005	-0.005	0.000	0.000	0.000	0.000
108	A	117	SER	0	-0.001	0.025	19.830	-0.004	-0.004	0.000	0.000	0.000	0.000
109	A	118	THR	0	-0.013	-0.031	14.743	-0.015	-0.015	0.000	0.000	0.000	0.000
110	A	119	THR	0	-0.031	-0.010	14.747	0.045	0.045	0.000	0.000	0.000	0.000
111	A	120	ALA	0	0.045	0.024	11.861	-0.065	-0.065	0.000	0.000	0.000	0.000
112	A	121	VAL	0	-0.020	-0.006	10.265	0.108	0.108	0.000	0.000	0.000	0.000
113	A	122	VAL	0	0.026	0.011	9.468	-0.222	-0.222	0.000	0.000	0.000	0.000
114	A	123	THR	0	-0.039	-0.023	8.891	0.225	0.225	0.000	0.000	0.000	0.000
115	A	124	ASN	0	0.014	-0.005	10.251	-0.151	-0.151	0.000	0.000	0.000	0.000
116	A	125	PRO	0	0.029	0.037	7.541	0.110	0.110	0.000	0.000	0.000	0.000

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