FMO DATABASE

FMODB ID: R8MY8

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	OptAll
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	-889722.612088
FMO2-HF: Nuclear repulsion	845614.100738
FMO2-HF: Total energy	-44108.51135
FMO2-MP2: Total energy	-44238.85387

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.
-14.457	-13.583	13.823	-5.785	-8.91	-0.007

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 : 0.008 / q_NPA : 0.011

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

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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	0.040	0.024	2.706	1.065	3.001	0.091	-0.888	-1.139	0.000
4	A	13	MET	0	-0.068	-0.008	2.529	-4.446	-2.128	1.034	-1.519	-1.833	-0.021
5	A	14	VAL	0	0.029	0.020	4.587	-0.025	0.007	-0.001	-0.009	-0.021	0.000
6	A	15	LYS	1	0.824	0.890	8.354	-0.032	-0.032	0.000	0.000	0.000	0.000
7	A	16	VAL	0	0.002	0.002	10.908	-0.094	-0.094	0.000	0.000	0.000	0.000
8	A	17	LEU	0	0.006	0.009	14.632	0.054	0.054	0.000	0.000	0.000	0.000
9	A	18	ASP	-1	-0.742	-0.845	17.642	0.065	0.065	0.000	0.000	0.000	0.000
10	A	19	ALA	0	0.014	-0.008	21.411	0.005	0.005	0.000	0.000	0.000	0.000
11	A	20	VAL	0	-0.058	-0.023	23.950	-0.004	-0.004	0.000	0.000	0.000	0.000
12	A	21	ARG	1	0.844	0.910	23.982	-0.096	-0.096	0.000	0.000	0.000	0.000
13	A	22	GLY	0	-0.007	0.020	23.463	0.006	0.006	0.000	0.000	0.000	0.000
14	A	23	SER	0	-0.028	-0.018	20.869	0.003	0.003	0.000	0.000	0.000	0.000
15	A	24	PRO	0	0.010	0.008	15.930	-0.021	-0.021	0.000	0.000	0.000	0.000
16	A	25	ALA	0	0.002	0.013	16.829	-0.011	-0.011	0.000	0.000	0.000	0.000
17	A	26	ILE	0	0.007	0.024	16.159	0.028	0.028	0.000	0.000	0.000	0.000
18	A	27	ASN	0	0.029	0.012	16.017	-0.031	-0.031	0.000	0.000	0.000	0.000
19	A	28	VAL	0	-0.017	0.003	15.546	-0.033	-0.033	0.000	0.000	0.000	0.000
20	A	29	ALA	0	-0.028	-0.006	14.963	0.056	0.056	0.000	0.000	0.000	0.000
21	A	30	VAL	0	0.002	-0.009	10.829	-0.042	-0.042	0.000	0.000	0.000	0.000
22	A	31	HIS	0	-0.038	-0.022	13.358	0.076	0.076	0.000	0.000	0.000	0.000
23	A	32	VAL	0	-0.004	-0.007	9.489	-0.054	-0.054	0.000	0.000	0.000	0.000
24	A	33	PHE	0	-0.005	0.004	12.897	0.043	0.043	0.000	0.000	0.000	0.000
25	A	34	ARG	1	0.864	0.922	14.317	0.345	0.345	0.000	0.000	0.000	0.000
26	A	35	LYS	1	0.767	0.874	16.273	0.250	0.250	0.000	0.000	0.000	0.000
27	A	36	ALA	0	0.035	0.026	19.671	-0.019	-0.019	0.000	0.000	0.000	0.000
28	A	37	ALA	0	-0.016	-0.025	21.697	0.001	0.001	0.000	0.000	0.000	0.000
29	A	38	ASP	-1	-0.853	-0.902	24.610	-0.131	-0.131	0.000	0.000	0.000	0.000
30	A	39	ASP	-1	-0.852	-0.916	24.680	-0.166	-0.166	0.000	0.000	0.000	0.000
31	A	40	THR	0	-0.088	-0.051	24.154	0.001	0.001	0.000	0.000	0.000	0.000
32	A	41	TRP	0	-0.041	-0.033	17.481	-0.025	-0.025	0.000	0.000	0.000	0.000
33	A	42	GLU	-1	-0.845	-0.910	17.421	-0.238	-0.238	0.000	0.000	0.000	0.000
34	A	43	PRO	0	-0.028	-0.029	16.960	-0.035	-0.035	0.000	0.000	0.000	0.000
35	A	44	PHE	0	-0.018	-0.003	9.021	0.006	0.006	0.000	0.000	0.000	0.000
36	A	45	ALA	0	0.041	0.022	9.748	0.021	0.021	0.000	0.000	0.000	0.000
37	A	46	SER	0	-0.030	-0.019	11.598	-0.027	-0.027	0.000	0.000	0.000	0.000
38	A	47	GLY	0	0.023	0.009	11.241	0.142	0.142	0.000	0.000	0.000	0.000
39	A	48	LYS	1	0.842	0.904	11.996	-0.376	-0.376	0.000	0.000	0.000	0.000
40	A	49	THR	0	-0.046	-0.027	11.615	0.144	0.144	0.000	0.000	0.000	0.000
41	A	50	SER	0	0.014	-0.008	10.271	-0.092	-0.092	0.000	0.000	0.000	0.000
42	A	51	GLU	-1	-0.884	-0.966	12.692	0.319	0.319	0.000	0.000	0.000	0.000
43	A	52	SER	0	-0.036	-0.022	10.254	-0.070	-0.070	0.000	0.000	0.000	0.000
44	A	53	GLY	0	0.031	-0.006	13.349	-0.060	-0.060	0.000	0.000	0.000	0.000
45	A	54	GLU	-1	-0.823	-0.864	8.107	0.620	0.620	0.000	0.000	0.000	0.000
46	A	55	LEU	0	0.006	0.022	7.733	0.123	0.123	0.000	0.000	0.000	0.000
47	A	56	HIS	0	0.001	-0.024	3.200	-0.858	-0.192	1.020	-0.471	-1.214	0.002
48	A	57	GLY	0	0.013	-0.030	2.292	-2.158	-6.839	11.055	-3.387	-2.987	0.006
49	A	58	LEU	0	-0.042	-0.013	3.890	-0.349	-1.536	0.019	1.396	-0.229	0.000
50	A	59	THR	0	-0.008	-0.016	4.832	-0.312	-0.312	0.000	0.000	0.000	0.000
51	A	60	THR	0	-0.033	-0.024	4.028	-0.793	-0.527	0.000	-0.067	-0.199	0.000
52	A	61	GLU	-1	-0.970	-1.007	5.712	-1.993	-1.993	0.000	0.000	0.000	0.000
53	A	62	GLU	-1	-0.966	-0.972	6.936	-0.251	-0.251	0.000	0.000	0.000	0.000
54	A	63	GLU	-1	-0.809	-0.866	8.777	-0.299	-0.299	0.000	0.000	0.000	0.000
55	A	64	PHE	0	-0.045	-0.013	7.409	-0.039	-0.039	0.000	0.000	0.000	0.000
56	A	65	VAL	0	0.016	0.001	9.498	-0.087	-0.087	0.000	0.000	0.000	0.000
57	A	66	GLU	-1	-0.902	-0.931	12.849	-0.485	-0.485	0.000	0.000	0.000	0.000
58	A	67	GLY	0	0.020	0.008	15.385	0.055	0.055	0.000	0.000	0.000	0.000
59	A	68	ILE	0	-0.032	-0.007	15.865	-0.049	-0.049	0.000	0.000	0.000	0.000
60	A	69	TYR	0	0.006	-0.026	12.218	0.020	0.020	0.000	0.000	0.000	0.000
61	A	70	LYS	1	0.803	0.898	14.783	0.184	0.184	0.000	0.000	0.000	0.000
62	A	71	VAL	0	-0.018	0.001	10.174	-0.016	-0.016	0.000	0.000	0.000	0.000
63	A	72	GLU	-1	-0.850	-0.921	13.202	-0.074	-0.074	0.000	0.000	0.000	0.000
64	A	73	ILE	0	0.006	0.000	13.465	0.038	0.038	0.000	0.000	0.000	0.000
65	A	74	ASP	-1	-0.766	-0.880	16.450	0.046	0.046	0.000	0.000	0.000	0.000
66	A	75	THR	0	-0.030	-0.042	19.438	0.018	0.018	0.000	0.000	0.000	0.000
67	A	76	LYS	1	0.781	0.875	21.306	0.007	0.007	0.000	0.000	0.000	0.000
68	A	77	SER	0	-0.015	-0.014	21.563	0.001	0.001	0.000	0.000	0.000	0.000
69	A	78	TYR	0	-0.043	-0.040	20.334	0.015	0.015	0.000	0.000	0.000	0.000
70	A	79	TRP	0	0.050	0.007	22.392	0.009	0.009	0.000	0.000	0.000	0.000
71	A	80	LYS	1	0.966	0.990	25.635	-0.045	-0.045	0.000	0.000	0.000	0.000
72	A	81	ALA	0	-0.047	-0.012	24.467	-0.001	-0.001	0.000	0.000	0.000	0.000
73	A	82	LEU	0	-0.040	-0.016	23.352	0.006	0.006	0.000	0.000	0.000	0.000
74	A	83	GLY	0	-0.020	0.000	27.657	-0.005	-0.005	0.000	0.000	0.000	0.000
75	A	84	ILE	0	-0.042	-0.026	28.606	-0.007	-0.007	0.000	0.000	0.000	0.000
76	A	85	SER	0	0.004	-0.004	29.476	0.002	0.002	0.000	0.000	0.000	0.000
77	A	86	PRO	0	-0.072	-0.028	26.230	-0.003	-0.003	0.000	0.000	0.000	0.000
78	A	87	PHE	0	-0.023	-0.017	28.795	-0.001	-0.001	0.000	0.000	0.000	0.000
79	A	88	HIS	0	-0.011	-0.003	24.374	-0.009	-0.009	0.000	0.000	0.000	0.000
80	A	89	GLU	-1	-0.785	-0.882	25.077	0.008	0.008	0.000	0.000	0.000	0.000
81	A	90	HIS	0	-0.041	-0.041	20.067	0.032	0.032	0.000	0.000	0.000	0.000
82	A	91	ALA	0	-0.033	-0.001	18.230	-0.006	-0.006	0.000	0.000	0.000	0.000
83	A	92	GLU	-1	-0.801	-0.894	17.791	-0.139	-0.139	0.000	0.000	0.000	0.000
84	A	93	VAL	0	-0.029	-0.016	14.238	0.004	0.004	0.000	0.000	0.000	0.000
85	A	94	VAL	0	0.006	0.000	15.130	-0.047	-0.047	0.000	0.000	0.000	0.000
86	A	95	PHE	0	-0.050	-0.022	10.268	0.017	0.017	0.000	0.000	0.000	0.000
87	A	96	THR	0	0.020	0.009	15.399	-0.013	-0.013	0.000	0.000	0.000	0.000
88	A	97	ALA	0	-0.016	-0.004	11.234	-0.041	-0.041	0.000	0.000	0.000	0.000
89	A	98	ASN	0	0.032	-0.012	9.369	0.020	0.020	0.000	0.000	0.000	0.000
90	A	99	ASP	-1	-0.855	-0.897	13.477	-0.479	-0.479	0.000	0.000	0.000	0.000
91	A	100	SER	0	-0.035	-0.023	16.293	0.076	0.076	0.000	0.000	0.000	0.000
92	A	101	GLY	0	0.001	0.010	15.046	0.034	0.034	0.000	0.000	0.000	0.000
93	A	102	PRO	0	0.018	0.010	9.449	-0.038	-0.038	0.000	0.000	0.000	0.000
94	A	103	ARG	1	0.796	0.894	9.812	0.847	0.847	0.000	0.000	0.000	0.000
95	A	104	ARG	1	0.878	0.933	2.905	-5.183	-3.659	0.605	-0.840	-1.288	0.006
96	A	105	TYR	0	0.037	0.018	6.225	0.779	0.779	0.000	0.000	0.000	0.000
97	A	106	THR	0	-0.027	-0.025	5.742	-0.514	-0.514	0.000	0.000	0.000	0.000
98	A	107	ILE	0	0.003	0.011	7.716	0.200	0.200	0.000	0.000	0.000	0.000
99	A	108	ALA	0	0.037	0.023	10.474	0.120	0.120	0.000	0.000	0.000	0.000
100	A	109	ALA	0	0.006	-0.004	12.691	-0.035	-0.035	0.000	0.000	0.000	0.000
101	A	110	LEU	0	-0.017	0.004	15.853	0.045	0.045	0.000	0.000	0.000	0.000
102	A	111	LEU	0	0.023	0.009	18.697	-0.019	-0.019	0.000	0.000	0.000	0.000
103	A	112	SER	0	-0.018	-0.024	21.576	0.011	0.011	0.000	0.000	0.000	0.000
104	A	113	PRO	0	0.006	0.008	25.354	-0.006	-0.006	0.000	0.000	0.000	0.000
105	A	114	TYR	0	0.052	0.007	27.702	-0.005	-0.005	0.000	0.000	0.000	0.000
106	A	115	SER	0	-0.047	-0.004	26.477	-0.010	-0.010	0.000	0.000	0.000	0.000
107	A	116	TYR	0	0.029	0.012	20.156	0.009	0.009	0.000	0.000	0.000	0.000
108	A	117	SER	0	0.000	0.015	20.771	-0.009	-0.009	0.000	0.000	0.000	0.000
109	A	118	THR	0	0.011	-0.014	15.095	-0.001	-0.001	0.000	0.000	0.000	0.000
110	A	119	THR	0	-0.041	-0.030	14.928	0.021	0.021	0.000	0.000	0.000	0.000
111	A	120	ALA	0	0.036	0.034	12.292	-0.014	-0.014	0.000	0.000	0.000	0.000
112	A	121	VAL	0	0.000	0.005	10.361	0.054	0.054	0.000	0.000	0.000	0.000
113	A	122	VAL	0	0.000	-0.004	9.934	-0.187	-0.187	0.000	0.000	0.000	0.000
114	A	123	THR	0	-0.043	-0.015	8.688	0.218	0.218	0.000	0.000	0.000	0.000
115	A	124	ASN	0	0.041	0.006	10.517	-0.221	-0.221	0.000	0.000	0.000	0.000
116	A	125	PRO	0	-0.001	0.019	7.057	0.203	0.203	0.000	0.000	0.000	0.000

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