FMO DATABASE

FMODB ID: ZVLNN

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	OptHSide
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	-890989.538456
FMO2-HF: Nuclear repulsion	846881.283569
FMO2-HF: Total energy	-44108.254887
FMO2-MP2: Total energy	-44238.572392

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.
-20.086	-15.217	11.868	-6.606	-10.13	-0.014

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 : -0.031 / q_NPA : -0.014

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	0.038	0.028	2.915	-0.730	1.960	0.080	-1.237	-1.534	-0.001
4	A	13	MET	0	-0.074	-0.011	2.804	-1.034	0.812	0.251	-0.782	-1.315	-0.008
5	A	14	VAL	0	0.028	0.014	4.194	0.394	0.459	0.000	-0.023	-0.041	0.000
6	A	15	LYS	1	0.851	0.905	7.956	0.487	0.487	0.000	0.000	0.000	0.000
7	A	16	VAL	0	-0.005	-0.007	10.282	0.035	0.035	0.000	0.000	0.000	0.000
8	A	17	LEU	0	-0.002	0.011	13.787	0.032	0.032	0.000	0.000	0.000	0.000
9	A	18	ASP	-1	-0.739	-0.841	16.723	-0.097	-0.097	0.000	0.000	0.000	0.000
10	A	19	ALA	0	0.014	-0.010	20.242	0.007	0.007	0.000	0.000	0.000	0.000
11	A	20	VAL	0	-0.065	-0.032	22.965	0.010	0.010	0.000	0.000	0.000	0.000
12	A	21	ARG	1	0.859	0.914	22.751	0.072	0.072	0.000	0.000	0.000	0.000
13	A	22	GLY	0	-0.026	0.015	22.111	0.008	0.008	0.000	0.000	0.000	0.000
14	A	23	SER	0	-0.017	-0.010	19.486	0.012	0.012	0.000	0.000	0.000	0.000
15	A	24	PRO	0	0.001	0.005	14.487	-0.022	-0.022	0.000	0.000	0.000	0.000
16	A	25	ALA	0	0.015	0.014	15.431	0.028	0.028	0.000	0.000	0.000	0.000
17	A	26	ILE	0	-0.019	0.006	14.730	-0.020	-0.020	0.000	0.000	0.000	0.000
18	A	27	ASN	0	-0.007	-0.011	14.648	0.021	0.021	0.000	0.000	0.000	0.000
19	A	28	VAL	0	-0.003	0.003	14.535	0.009	0.009	0.000	0.000	0.000	0.000
20	A	29	ALA	0	-0.035	-0.009	14.021	0.009	0.009	0.000	0.000	0.000	0.000
21	A	30	VAL	0	0.007	-0.009	10.956	-0.048	-0.048	0.000	0.000	0.000	0.000
22	A	31	HIS	0	-0.035	-0.012	13.451	0.086	0.086	0.000	0.000	0.000	0.000
23	A	32	VAL	0	0.005	0.001	9.625	-0.059	-0.059	0.000	0.000	0.000	0.000
24	A	33	PHE	0	-0.001	-0.005	13.105	0.057	0.057	0.000	0.000	0.000	0.000
25	A	34	ARG	1	0.925	0.950	14.050	0.257	0.257	0.000	0.000	0.000	0.000
26	A	35	LYS	1	0.743	0.861	16.404	0.212	0.212	0.000	0.000	0.000	0.000
27	A	36	ALA	0	0.026	0.017	19.769	-0.012	-0.012	0.000	0.000	0.000	0.000
28	A	37	ALA	0	-0.016	-0.018	21.664	0.000	0.000	0.000	0.000	0.000	0.000
29	A	38	ASP	-1	-0.857	-0.908	24.483	-0.109	-0.109	0.000	0.000	0.000	0.000
30	A	39	ASP	-1	-0.841	-0.908	24.800	-0.147	-0.147	0.000	0.000	0.000	0.000
31	A	40	THR	0	-0.075	-0.038	24.575	-0.002	-0.002	0.000	0.000	0.000	0.000
32	A	41	TRP	0	-0.046	-0.035	17.549	-0.018	-0.018	0.000	0.000	0.000	0.000
33	A	42	GLU	-1	-0.910	-0.947	18.414	-0.125	-0.125	0.000	0.000	0.000	0.000
34	A	43	PRO	0	-0.054	-0.042	17.219	-0.032	-0.032	0.000	0.000	0.000	0.000
35	A	44	PHE	0	-0.001	0.001	8.851	0.001	0.001	0.000	0.000	0.000	0.000
36	A	45	ALA	0	0.056	0.033	10.032	0.042	0.042	0.000	0.000	0.000	0.000
37	A	46	SER	0	-0.012	-0.010	11.942	-0.061	-0.061	0.000	0.000	0.000	0.000
38	A	47	GLY	0	0.025	0.018	10.793	0.136	0.136	0.000	0.000	0.000	0.000
39	A	48	LYS	1	0.872	0.930	11.419	-0.118	-0.118	0.000	0.000	0.000	0.000
40	A	49	THR	0	-0.012	-0.005	10.281	0.062	0.062	0.000	0.000	0.000	0.000
41	A	50	SER	0	0.015	-0.001	9.049	0.043	0.043	0.000	0.000	0.000	0.000
42	A	51	GLU	-1	-0.895	-0.967	11.562	0.018	0.018	0.000	0.000	0.000	0.000
43	A	52	SER	0	-0.002	0.002	9.261	-0.002	-0.002	0.000	0.000	0.000	0.000
44	A	53	GLY	0	0.011	-0.012	12.016	-0.058	-0.058	0.000	0.000	0.000	0.000
45	A	54	GLU	-1	-0.843	-0.888	6.567	-0.658	-0.658	0.000	0.000	0.000	0.000
46	A	55	LEU	0	-0.001	0.015	6.869	0.197	0.197	0.000	0.000	0.000	0.000
47	A	56	HIS	0	0.005	-0.031	2.488	-6.982	-5.301	3.170	-1.876	-2.975	-0.021
48	A	57	GLY	0	0.007	-0.026	2.416	-1.310	-4.426	7.478	-2.103	-2.258	0.008
49	A	58	LEU	0	-0.024	0.002	4.211	-1.127	-1.417	0.013	0.430	-0.154	0.001
50	A	59	THR	0	-0.006	-0.029	4.635	-0.627	-0.552	-0.001	-0.014	-0.059	0.000
51	A	60	THR	0	-0.026	-0.012	3.953	-0.324	0.057	0.001	-0.113	-0.268	-0.001
52	A	61	GLU	-1	-0.961	-1.008	5.490	-0.874	-0.874	0.000	0.000	0.000	0.000
53	A	62	GLU	-1	-0.974	-0.979	6.867	-0.040	-0.040	0.000	0.000	0.000	0.000
54	A	63	GLU	-1	-0.834	-0.881	8.810	-0.090	-0.090	0.000	0.000	0.000	0.000
55	A	64	PHE	0	-0.064	-0.004	7.377	-0.066	-0.066	0.000	0.000	0.000	0.000
56	A	65	VAL	0	0.038	0.022	9.374	-0.066	-0.066	0.000	0.000	0.000	0.000
57	A	66	GLU	-1	-0.915	-0.943	12.764	-0.363	-0.363	0.000	0.000	0.000	0.000
58	A	67	GLY	0	0.002	0.001	15.091	0.050	0.050	0.000	0.000	0.000	0.000
59	A	68	ILE	0	0.000	0.005	16.033	-0.040	-0.040	0.000	0.000	0.000	0.000
60	A	69	TYR	0	-0.011	-0.028	12.028	0.021	0.021	0.000	0.000	0.000	0.000
61	A	70	LYS	1	0.838	0.912	14.805	0.197	0.197	0.000	0.000	0.000	0.000
62	A	71	VAL	0	-0.050	-0.026	10.564	0.004	0.004	0.000	0.000	0.000	0.000
63	A	72	GLU	-1	-0.867	-0.922	13.579	-0.151	-0.151	0.000	0.000	0.000	0.000
64	A	73	ILE	0	0.006	-0.003	13.142	0.017	0.017	0.000	0.000	0.000	0.000
65	A	74	ASP	-1	-0.789	-0.913	16.215	-0.090	-0.090	0.000	0.000	0.000	0.000
66	A	75	THR	0	0.012	-0.017	19.043	0.012	0.012	0.000	0.000	0.000	0.000
67	A	76	LYS	1	0.778	0.879	20.773	0.088	0.088	0.000	0.000	0.000	0.000
68	A	77	SER	0	0.002	-0.014	21.408	0.010	0.010	0.000	0.000	0.000	0.000
69	A	78	TYR	0	-0.035	-0.037	19.281	0.009	0.009	0.000	0.000	0.000	0.000
70	A	79	TRP	0	0.040	0.003	21.579	0.014	0.014	0.000	0.000	0.000	0.000
71	A	80	LYS	1	0.969	0.979	24.784	0.052	0.052	0.000	0.000	0.000	0.000
72	A	81	ALA	0	-0.058	-0.011	23.702	0.007	0.007	0.000	0.000	0.000	0.000
73	A	82	LEU	0	-0.038	-0.018	22.345	0.006	0.006	0.000	0.000	0.000	0.000
74	A	83	GLY	0	-0.010	0.008	26.684	0.001	0.001	0.000	0.000	0.000	0.000
75	A	84	ILE	0	-0.050	-0.023	27.301	-0.001	-0.001	0.000	0.000	0.000	0.000
76	A	85	SER	0	0.022	0.006	28.802	0.000	0.000	0.000	0.000	0.000	0.000
77	A	86	PRO	0	-0.096	-0.040	26.080	0.000	0.000	0.000	0.000	0.000	0.000
78	A	87	PHE	0	-0.020	-0.013	28.255	0.004	0.004	0.000	0.000	0.000	0.000
79	A	88	HIS	0	0.006	0.008	24.338	0.000	0.000	0.000	0.000	0.000	0.000
80	A	89	GLU	-1	-0.801	-0.892	25.184	-0.075	-0.075	0.000	0.000	0.000	0.000
81	A	90	HIS	0	-0.054	-0.041	19.948	0.016	0.016	0.000	0.000	0.000	0.000
82	A	91	ALA	0	-0.039	0.000	17.953	0.002	0.002	0.000	0.000	0.000	0.000
83	A	92	GLU	-1	-0.801	-0.883	17.730	-0.196	-0.196	0.000	0.000	0.000	0.000
84	A	93	VAL	0	-0.037	-0.019	14.103	0.002	0.002	0.000	0.000	0.000	0.000
85	A	94	VAL	0	-0.007	-0.011	15.317	-0.030	-0.030	0.000	0.000	0.000	0.000
86	A	95	PHE	0	-0.053	-0.022	10.130	0.002	0.002	0.000	0.000	0.000	0.000
87	A	96	THR	0	0.035	0.016	15.525	-0.009	-0.009	0.000	0.000	0.000	0.000
88	A	97	ALA	0	-0.031	-0.009	11.402	-0.041	-0.041	0.000	0.000	0.000	0.000
89	A	98	ASN	0	0.037	-0.024	9.811	-0.025	-0.025	0.000	0.000	0.000	0.000
90	A	99	ASP	-1	-0.856	-0.904	13.534	-0.345	-0.345	0.000	0.000	0.000	0.000
91	A	100	SER	0	-0.034	-0.016	16.601	0.058	0.058	0.000	0.000	0.000	0.000
92	A	101	GLY	0	0.010	0.008	14.847	0.033	0.033	0.000	0.000	0.000	0.000
93	A	102	PRO	0	0.025	0.012	9.301	-0.053	-0.053	0.000	0.000	0.000	0.000
94	A	103	ARG	1	0.816	0.909	9.821	0.602	0.602	0.000	0.000	0.000	0.000
95	A	104	ARG	1	0.881	0.942	2.861	-7.543	-6.006	0.876	-0.888	-1.526	0.008
96	A	105	TYR	0	0.043	0.021	5.878	0.641	0.641	0.000	0.000	0.000	0.000
97	A	106	THR	0	-0.024	-0.009	5.516	-0.721	-0.721	0.000	0.000	0.000	0.000
98	A	107	ILE	0	-0.002	0.003	7.437	0.303	0.303	0.000	0.000	0.000	0.000
99	A	108	ALA	0	0.031	0.018	10.016	0.003	0.003	0.000	0.000	0.000	0.000
100	A	109	ALA	0	-0.001	-0.003	12.292	0.048	0.048	0.000	0.000	0.000	0.000
101	A	110	LEU	0	-0.016	0.006	15.458	0.010	0.010	0.000	0.000	0.000	0.000
102	A	111	LEU	0	0.017	0.001	18.080	0.014	0.014	0.000	0.000	0.000	0.000
103	A	112	SER	0	0.007	-0.003	20.975	0.017	0.017	0.000	0.000	0.000	0.000
104	A	113	PRO	0	0.015	0.011	24.731	-0.005	-0.005	0.000	0.000	0.000	0.000
105	A	114	TYR	0	0.030	-0.009	27.034	0.000	0.000	0.000	0.000	0.000	0.000
106	A	115	SER	0	-0.048	-0.011	25.810	-0.005	-0.005	0.000	0.000	0.000	0.000
107	A	116	TYR	0	0.033	0.013	19.629	-0.006	-0.006	0.000	0.000	0.000	0.000
108	A	117	SER	0	0.005	0.024	20.241	-0.002	-0.002	0.000	0.000	0.000	0.000
109	A	118	THR	0	-0.020	-0.034	14.754	-0.016	-0.016	0.000	0.000	0.000	0.000
110	A	119	THR	0	-0.044	-0.020	14.917	0.042	0.042	0.000	0.000	0.000	0.000
111	A	120	ALA	0	0.057	0.034	11.983	-0.064	-0.064	0.000	0.000	0.000	0.000
112	A	121	VAL	0	-0.020	-0.007	10.471	0.106	0.106	0.000	0.000	0.000	0.000
113	A	122	VAL	0	0.028	0.014	9.653	-0.211	-0.211	0.000	0.000	0.000	0.000
114	A	123	THR	0	-0.031	-0.018	8.816	0.215	0.215	0.000	0.000	0.000	0.000
115	A	124	ASN	0	0.028	0.002	10.251	-0.193	-0.193	0.000	0.000	0.000	0.000
116	A	125	PRO	0	0.011	0.025	7.489	0.116	0.116	0.000	0.000	0.000	0.000

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