FMO DATABASE

FMODB ID: 6YR7Z

Calculation Name: 1TOC-R-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1TOC

Chain ID: R

ChEMBL ID:

UniProt ID: P56409

Base Structure: X-ray

Registration Date: 2023-09-23

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	114
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-732726.969283
FMO2-HF: Nuclear repulsion	684232.476966
FMO2-HF: Total energy	-48494.492316
FMO2-MP2: Total energy	-48623.213301

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(R:1:SER)

Summations of interaction energy for fragment #1(R:1:SER)

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.
-0.858	1.253	-0.006	-0.883	-1.221	0.004

Interaction energy analysis for fragmet #1(R:1:SER)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.016 / 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	R	2	ASN	0	0.016	-0.008	3.866	1.821	3.794	-0.005	-0.872	-1.096	0.004
4	R	3	VAL	0	0.037	-0.006	5.329	-0.512	-0.374	-0.001	-0.011	-0.125	0.000
5	R	4	LEU	0	-0.020	0.007	8.036	-0.101	-0.101	0.000	0.000	0.000	0.000
6	R	5	CYS	0	-0.094	-0.031	7.703	-0.415	-0.415	0.000	0.000	0.000	0.000
7	R	6	ASN	0	-0.032	-0.019	11.022	-0.087	-0.087	0.000	0.000	0.000	0.000
8	R	7	ASN	0	0.031	0.009	13.307	0.097	0.097	0.000	0.000	0.000	0.000
9	R	8	PRO	0	-0.032	-0.017	14.686	-0.001	-0.001	0.000	0.000	0.000	0.000
10	R	9	HIS	0	-0.048	-0.022	16.758	0.001	0.001	0.000	0.000	0.000	0.000
11	R	10	THR	0	-0.063	-0.053	19.288	0.011	0.011	0.000	0.000	0.000	0.000
12	R	11	ALA	0	-0.049	-0.022	21.667	-0.007	-0.007	0.000	0.000	0.000	0.000
13	R	12	ASP	-1	-0.834	-0.915	25.381	-0.001	-0.001	0.000	0.000	0.000	0.000
14	R	13	CYS	0	-0.038	-0.005	20.296	0.013	0.013	0.000	0.000	0.000	0.000
15	R	14	ASN	0	-0.015	-0.012	25.394	0.000	0.000	0.000	0.000	0.000	0.000
16	R	15	ASN	0	-0.092	-0.049	26.333	0.002	0.002	0.000	0.000	0.000	0.000
17	R	16	ASP	-1	-0.765	-0.852	21.970	0.041	0.041	0.000	0.000	0.000	0.000
18	R	17	ALA	0	-0.035	-0.026	25.039	-0.004	-0.004	0.000	0.000	0.000	0.000
19	R	18	GLN	0	-0.031	-0.029	24.770	-0.010	-0.010	0.000	0.000	0.000	0.000
20	R	19	VAL	0	-0.055	-0.026	23.997	-0.004	-0.004	0.000	0.000	0.000	0.000
21	R	20	ASP	-1	-0.857	-0.945	23.409	-0.112	-0.112	0.000	0.000	0.000	0.000
22	R	21	ARG	1	0.730	0.864	17.092	0.072	0.072	0.000	0.000	0.000	0.000
23	R	22	TYR	0	-0.014	-0.019	17.855	-0.014	-0.014	0.000	0.000	0.000	0.000
24	R	23	PHE	0	0.057	0.031	14.620	-0.006	-0.006	0.000	0.000	0.000	0.000
25	R	24	ARG	1	0.844	0.912	10.668	1.020	1.020	0.000	0.000	0.000	0.000
26	R	25	GLU	-1	-0.831	-0.916	14.004	-0.436	-0.436	0.000	0.000	0.000	0.000
27	R	26	GLY	0	0.006	0.002	16.108	0.025	0.025	0.000	0.000	0.000	0.000
28	R	27	THR	0	-0.045	-0.029	14.910	-0.113	-0.113	0.000	0.000	0.000	0.000
29	R	28	THR	0	0.004	0.009	16.459	-0.013	-0.013	0.000	0.000	0.000	0.000
30	R	29	CYS	0	-0.008	0.027	13.278	-0.151	-0.151	0.000	0.000	0.000	0.000
31	R	30	LEU	0	-0.041	-0.011	17.260	0.040	0.040	0.000	0.000	0.000	0.000
32	R	31	MET	0	-0.040	-0.002	19.552	-0.005	-0.005	0.000	0.000	0.000	0.000
33	R	32	SER	0	-0.053	-0.034	20.737	-0.003	-0.003	0.000	0.000	0.000	0.000
34	R	33	PRO	0	0.021	0.025	21.972	0.002	0.002	0.000	0.000	0.000	0.000
35	R	34	ALA	0	0.030	0.018	19.385	-0.004	-0.004	0.000	0.000	0.000	0.000
36	R	36	THR	0	-0.007	-0.023	20.224	-0.014	-0.014	0.000	0.000	0.000	0.000
37	R	37	SER	0	-0.068	-0.043	17.774	-0.006	-0.006	0.000	0.000	0.000	0.000
38	R	38	GLU	-1	-0.829	-0.880	15.698	0.059	0.059	0.000	0.000	0.000	0.000
39	R	39	GLY	0	0.066	0.038	13.895	-0.032	-0.032	0.000	0.000	0.000	0.000
40	R	40	TYR	0	-0.008	-0.012	9.442	0.015	0.015	0.000	0.000	0.000	0.000
41	R	41	ALA	0	0.023	0.001	16.076	0.013	0.013	0.000	0.000	0.000	0.000
42	R	42	SER	0	-0.053	-0.061	18.599	-0.001	-0.001	0.000	0.000	0.000	0.000
43	R	43	GLN	0	-0.006	-0.023	17.883	-0.060	-0.060	0.000	0.000	0.000	0.000
44	R	44	HIS	0	0.014	0.011	17.231	-0.049	-0.049	0.000	0.000	0.000	0.000
45	R	45	GLU	-1	-0.815	-0.883	15.208	-0.263	-0.263	0.000	0.000	0.000	0.000
46	R	47	GLN	0	0.048	0.015	12.307	-0.101	-0.101	0.000	0.000	0.000	0.000
47	R	48	GLN	0	-0.045	-0.015	12.209	-0.091	-0.091	0.000	0.000	0.000	0.000
48	R	49	ALA	0	0.008	0.018	9.012	-0.092	-0.092	0.000	0.000	0.000	0.000
49	R	51	PHE	0	-0.037	-0.023	9.154	-0.032	-0.032	0.000	0.000	0.000	0.000
50	R	52	VAL	0	-0.001	-0.006	6.505	-0.164	-0.164	0.000	0.000	0.000	0.000
51	R	53	GLY	0	0.035	0.025	8.488	0.120	0.120	0.000	0.000	0.000	0.000
52	R	54	GLY	0	-0.026	0.002	11.812	0.098	0.098	0.000	0.000	0.000	0.000
53	R	55	GLU	-1	-0.985	-1.000	13.222	-0.496	-0.496	0.000	0.000	0.000	0.000
54	R	56	ASP	-1	-0.851	-0.913	16.789	-0.298	-0.298	0.000	0.000	0.000	0.000
55	R	57	HIS	0	-0.066	-0.025	18.501	0.023	0.023	0.000	0.000	0.000	0.000
56	R	58	SER	0	0.005	-0.013	16.912	0.024	0.024	0.000	0.000	0.000	0.000
57	R	59	SER	0	-0.074	-0.044	19.330	0.003	0.003	0.000	0.000	0.000	0.000
58	R	60	GLU	-1	-0.972	-0.992	18.793	-0.221	-0.221	0.000	0.000	0.000	0.000
59	R	61	MET	0	-0.074	-0.023	22.534	0.014	0.014	0.000	0.000	0.000	0.000
60	R	62	HIS	0	0.077	0.065	26.337	0.005	0.005	0.000	0.000	0.000	0.000
61	R	63	SER	0	-0.026	-0.036	27.778	0.001	0.001	0.000	0.000	0.000	0.000
62	R	64	SER	0	0.034	-0.002	29.645	0.001	0.001	0.000	0.000	0.000	0.000
63	R	65	CYS	0	-0.075	-0.018	24.932	0.011	0.011	0.000	0.000	0.000	0.000
64	R	66	LEU	0	-0.041	-0.015	32.045	0.000	0.000	0.000	0.000	0.000	0.000
65	R	67	GLY	0	-0.015	0.004	34.898	0.004	0.004	0.000	0.000	0.000	0.000
66	R	68	ASP	-1	-0.938	-0.974	37.307	-0.053	-0.053	0.000	0.000	0.000	0.000
67	R	69	PRO	0	0.020	0.006	38.760	0.001	0.001	0.000	0.000	0.000	0.000
68	R	70	PRO	0	0.005	0.038	38.358	0.004	0.004	0.000	0.000	0.000	0.000
69	R	71	THR	0	-0.017	-0.016	41.224	0.000	0.000	0.000	0.000	0.000	0.000
70	R	72	SER	0	-0.021	0.002	45.024	0.001	0.001	0.000	0.000	0.000	0.000
71	R	73	CYS	0	-0.070	-0.034	43.116	0.004	0.004	0.000	0.000	0.000	0.000
72	R	74	ALA	0	-0.025	-0.024	48.922	0.000	0.000	0.000	0.000	0.000	0.000
73	R	75	GLU	-1	-0.980	-0.983	48.207	-0.019	-0.019	0.000	0.000	0.000	0.000
74	R	76	GLY	0	0.019	0.006	45.417	0.000	0.000	0.000	0.000	0.000	0.000
75	R	77	THR	0	-0.072	-0.048	40.498	0.002	0.002	0.000	0.000	0.000	0.000
76	R	78	ASP	-1	-0.918	-0.967	38.894	-0.046	-0.046	0.000	0.000	0.000	0.000
77	R	79	ILE	0	-0.030	-0.008	37.063	0.001	0.001	0.000	0.000	0.000	0.000
78	R	80	THR	0	-0.017	-0.008	31.289	-0.001	-0.001	0.000	0.000	0.000	0.000
79	R	81	TYR	0	-0.065	-0.059	34.187	0.004	0.004	0.000	0.000	0.000	0.000
80	R	82	TYR	0	0.077	0.012	30.144	-0.009	-0.009	0.000	0.000	0.000	0.000
81	R	83	ASP	-1	-0.789	-0.873	33.208	-0.071	-0.071	0.000	0.000	0.000	0.000
82	R	84	SER	0	-0.025	-0.037	34.855	-0.006	-0.006	0.000	0.000	0.000	0.000
83	R	85	ASP	-1	-0.991	-0.965	35.893	-0.078	-0.078	0.000	0.000	0.000	0.000
84	R	86	SER	0	-0.018	-0.032	35.320	-0.002	-0.002	0.000	0.000	0.000	0.000
85	R	87	LYS	1	0.820	0.931	27.825	0.135	0.135	0.000	0.000	0.000	0.000
86	R	88	THR	0	0.011	-0.012	30.538	-0.008	-0.008	0.000	0.000	0.000	0.000
87	R	89	CYS	0	-0.015	0.013	25.513	-0.003	-0.003	0.000	0.000	0.000	0.000
88	R	90	LYS	1	0.841	0.928	32.285	0.078	0.078	0.000	0.000	0.000	0.000
89	R	91	VAL	0	0.043	0.036	35.182	0.003	0.003	0.000	0.000	0.000	0.000
90	R	92	LEU	0	-0.063	-0.023	37.197	0.000	0.000	0.000	0.000	0.000	0.000
91	R	93	ALA	0	0.059	0.023	40.669	0.002	0.002	0.000	0.000	0.000	0.000
92	R	94	ALA	0	-0.035	-0.004	42.987	0.000	0.000	0.000	0.000	0.000	0.000
93	R	95	SER	0	-0.015	-0.017	42.366	0.001	0.001	0.000	0.000	0.000	0.000
94	R	97	PRO	0	0.045	0.027	38.814	-0.002	-0.002	0.000	0.000	0.000	0.000
95	R	98	SER	0	-0.033	-0.045	40.590	0.004	0.004	0.000	0.000	0.000	0.000
96	R	99	GLY	0	-0.028	-0.015	39.346	0.001	0.001	0.000	0.000	0.000	0.000
97	R	100	GLU	-1	-0.940	-0.978	32.914	-0.046	-0.046	0.000	0.000	0.000	0.000
98	R	101	ASN	0	-0.032	0.006	33.759	-0.006	-0.006	0.000	0.000	0.000	0.000
99	R	102	THR	0	-0.044	-0.049	33.862	0.004	0.004	0.000	0.000	0.000	0.000
100	R	103	PHE	0	-0.006	0.001	28.736	0.000	0.000	0.000	0.000	0.000	0.000
101	R	104	GLU	-1	-0.960	-0.975	29.578	-0.038	-0.038	0.000	0.000	0.000	0.000
102	R	105	SER	0	-0.039	-0.034	27.753	-0.003	-0.003	0.000	0.000	0.000	0.000
103	R	106	GLU	-1	-0.786	-0.893	29.068	-0.089	-0.089	0.000	0.000	0.000	0.000
104	R	107	VAL	0	0.005	-0.001	23.334	-0.007	-0.007	0.000	0.000	0.000	0.000
105	R	108	GLU	-1	-0.879	-0.939	24.604	-0.079	-0.079	0.000	0.000	0.000	0.000
106	R	110	GLN	0	0.009	-0.025	25.437	-0.009	-0.009	0.000	0.000	0.000	0.000
107	R	111	VAL	0	-0.012	-0.004	20.428	-0.009	-0.009	0.000	0.000	0.000	0.000
108	R	112	ALA	0	0.012	0.018	22.932	-0.006	-0.006	0.000	0.000	0.000	0.000
109	R	114	GLY	0	0.057	0.036	23.700	0.001	0.001	0.000	0.000	0.000	0.000
110	R	115	ALA	0	-0.074	-0.025	24.695	0.001	0.001	0.000	0.000	0.000	0.000
111	R	116	PRO	0	-0.036	-0.019	24.721	-0.014	-0.014	0.000	0.000	0.000	0.000
112	R	117	ILE	0	0.025	0.020	21.320	0.011	0.011	0.000	0.000	0.000	0.000
113	R	118	GLU	-1	-0.942	-0.964	24.645	-0.130	-0.130	0.000	0.000	0.000	0.000
114	R	119	GLY	0	-0.058	-0.027	26.467	0.001	0.001	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(R:1:SER)