FMO DATABASE

FMODB ID: ZVY8N

Calculation Name: 1YNB-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1YNB

Chain ID: A

ChEMBL ID:

UniProt ID: O28840

Base Structure: X-ray

Registration Date: 2023-09-21

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	167
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1696952.944996
FMO2-HF: Nuclear repulsion	1629781.36485
FMO2-HF: Total energy	-67171.580146
FMO2-MP2: Total energy	-67367.404605

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:7:MET)

Summations of interaction energy for fragment #1(A:7:MET)

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.
-5.028	0.3	2.047	-2.418	-4.955	-0.007

Interaction energy analysis for fragmet #1(A:7:MET)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.047 / q_NPA : 0.004

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	9	ASP	-1	-0.865	-0.931	3.143	-5.161	-2.334	0.023	-1.258	-1.591	-0.004
4	A	10	VAL	0	0.028	0.019	2.443	-0.624	0.927	1.909	-0.917	-2.543	-0.002
5	A	11	VAL	0	-0.033	-0.018	2.745	0.269	1.109	0.116	-0.237	-0.719	-0.001
6	A	12	LYS	1	0.815	0.878	5.305	0.715	0.825	-0.001	-0.006	-0.102	0.000
7	A	13	PHE	0	0.069	0.043	7.660	0.201	0.201	0.000	0.000	0.000	0.000
8	A	14	ILE	0	-0.010	-0.002	6.033	0.134	0.134	0.000	0.000	0.000	0.000
9	A	15	HIS	0	-0.043	-0.025	9.156	0.083	0.083	0.000	0.000	0.000	0.000
10	A	16	GLU	-1	-0.773	-0.837	11.739	-0.144	-0.144	0.000	0.000	0.000	0.000
11	A	17	VAL	0	0.032	0.026	12.759	0.024	0.024	0.000	0.000	0.000	0.000
12	A	18	GLY	0	-0.032	-0.018	13.650	0.016	0.016	0.000	0.000	0.000	0.000
13	A	19	SER	0	-0.043	-0.039	15.409	0.009	0.009	0.000	0.000	0.000	0.000
14	A	20	LEU	0	0.064	0.042	17.479	0.004	0.004	0.000	0.000	0.000	0.000
15	A	21	LYS	1	0.915	0.947	16.460	-0.052	-0.052	0.000	0.000	0.000	0.000
16	A	22	LEU	0	-0.063	-0.030	19.878	0.002	0.002	0.000	0.000	0.000	0.000
17	A	23	THR	0	0.000	0.015	21.770	-0.004	-0.004	0.000	0.000	0.000	0.000
18	A	24	PRO	0	-0.034	-0.012	24.190	0.003	0.003	0.000	0.000	0.000	0.000
19	A	25	ARG	1	0.887	0.923	27.655	0.002	0.002	0.000	0.000	0.000	0.000
20	A	26	SER	0	-0.034	-0.046	29.458	0.002	0.002	0.000	0.000	0.000	0.000
21	A	27	GLY	0	-0.012	-0.018	31.870	0.001	0.001	0.000	0.000	0.000	0.000
22	A	28	TRP	0	-0.003	-0.011	32.368	0.000	0.000	0.000	0.000	0.000	0.000
23	A	29	LEU	0	0.020	0.022	31.774	0.001	0.001	0.000	0.000	0.000	0.000
24	A	30	LYS	1	0.795	0.891	35.993	0.010	0.010	0.000	0.000	0.000	0.000
25	A	31	LEU	0	-0.036	-0.010	38.869	0.000	0.000	0.000	0.000	0.000	0.000
26	A	32	GLY	0	0.004	0.002	39.843	0.001	0.001	0.000	0.000	0.000	0.000
27	A	33	ILE	0	-0.017	-0.004	35.438	0.001	0.001	0.000	0.000	0.000	0.000
28	A	34	ARG	1	0.888	0.937	35.412	0.001	0.001	0.000	0.000	0.000	0.000
29	A	35	LEU	0	-0.004	-0.008	31.155	-0.001	-0.001	0.000	0.000	0.000	0.000
30	A	36	PRO	0	-0.026	0.004	30.995	0.001	0.001	0.000	0.000	0.000	0.000
31	A	37	GLU	-1	-0.737	-0.833	28.544	0.000	0.000	0.000	0.000	0.000	0.000
32	A	38	SER	0	-0.035	-0.052	23.844	-0.002	-0.002	0.000	0.000	0.000	0.000
33	A	39	VAL	0	0.035	0.004	22.154	0.002	0.002	0.000	0.000	0.000	0.000
34	A	40	ALA	0	0.008	0.011	20.200	0.003	0.003	0.000	0.000	0.000	0.000
35	A	41	GLU	-1	-0.879	-0.904	21.718	0.018	0.018	0.000	0.000	0.000	0.000
36	A	42	HIS	1	0.792	0.904	24.831	0.005	0.005	0.000	0.000	0.000	0.000
37	A	43	ASN	0	-0.017	-0.049	21.325	-0.001	-0.001	0.000	0.000	0.000	0.000
38	A	44	PHE	0	-0.017	0.000	21.740	0.003	0.003	0.000	0.000	0.000	0.000
39	A	45	ARG	1	0.770	0.844	23.043	-0.007	-0.007	0.000	0.000	0.000	0.000
40	A	46	ALA	0	0.024	0.004	25.258	-0.002	-0.002	0.000	0.000	0.000	0.000
41	A	47	ALA	0	0.020	0.019	22.204	-0.003	-0.003	0.000	0.000	0.000	0.000
42	A	48	ILE	0	-0.022	-0.010	24.184	-0.002	-0.002	0.000	0.000	0.000	0.000
43	A	49	ILE	0	-0.015	-0.008	26.679	-0.002	-0.002	0.000	0.000	0.000	0.000
44	A	50	ALA	0	0.041	0.012	25.745	-0.002	-0.002	0.000	0.000	0.000	0.000
45	A	51	PHE	0	-0.041	-0.016	24.569	-0.003	-0.003	0.000	0.000	0.000	0.000
46	A	52	ILE	0	-0.002	-0.010	27.196	-0.002	-0.002	0.000	0.000	0.000	0.000
47	A	53	LEU	0	-0.022	-0.003	30.726	-0.002	-0.002	0.000	0.000	0.000	0.000
48	A	54	ALA	0	0.038	0.044	28.411	-0.002	-0.002	0.000	0.000	0.000	0.000
49	A	55	LEU	0	-0.012	-0.003	29.057	-0.001	-0.001	0.000	0.000	0.000	0.000
50	A	56	LYS	1	0.798	0.862	31.960	0.002	0.002	0.000	0.000	0.000	0.000
51	A	57	SER	0	-0.057	-0.039	33.368	-0.001	-0.001	0.000	0.000	0.000	0.000
52	A	58	GLY	0	-0.053	-0.015	34.697	-0.001	-0.001	0.000	0.000	0.000	0.000
53	A	59	GLU	-1	-0.814	-0.862	29.350	-0.019	-0.019	0.000	0.000	0.000	0.000
54	A	60	SER	0	-0.037	-0.043	27.094	0.002	0.002	0.000	0.000	0.000	0.000
55	A	61	VAL	0	0.050	0.014	24.959	0.001	0.001	0.000	0.000	0.000	0.000
56	A	62	GLU	-1	-0.804	-0.884	22.629	-0.012	-0.012	0.000	0.000	0.000	0.000
57	A	63	LYS	1	0.850	0.927	22.765	0.022	0.022	0.000	0.000	0.000	0.000
58	A	64	ALA	0	0.040	0.019	24.650	0.001	0.001	0.000	0.000	0.000	0.000
59	A	65	CYS	0	-0.064	-0.036	20.404	0.005	0.005	0.000	0.000	0.000	0.000
60	A	66	LYS	1	0.814	0.907	20.053	0.044	0.044	0.000	0.000	0.000	0.000
61	A	67	ALA	0	0.037	0.006	21.256	0.000	0.000	0.000	0.000	0.000	0.000
62	A	68	ALA	0	-0.024	-0.010	21.804	0.000	0.000	0.000	0.000	0.000	0.000
63	A	69	THR	0	-0.031	-0.036	16.281	0.008	0.008	0.000	0.000	0.000	0.000
64	A	70	ALA	0	0.025	0.015	18.808	0.002	0.002	0.000	0.000	0.000	0.000
65	A	71	ALA	0	0.016	0.001	20.915	-0.002	-0.002	0.000	0.000	0.000	0.000
66	A	72	LEU	0	-0.081	-0.036	17.294	0.001	0.001	0.000	0.000	0.000	0.000
67	A	73	PHE	0	-0.018	-0.018	12.585	0.005	0.005	0.000	0.000	0.000	0.000
68	A	74	HIS	0	-0.031	0.010	18.513	-0.012	-0.012	0.000	0.000	0.000	0.000
69	A	75	ASP	-1	-0.790	-0.883	22.196	-0.018	-0.018	0.000	0.000	0.000	0.000
70	A	76	LEU	0	-0.018	0.003	14.355	0.000	0.000	0.000	0.000	0.000	0.000
71	A	77	HIS	0	0.110	0.055	18.157	-0.011	-0.011	0.000	0.000	0.000	0.000
72	A	78	GLU	-1	-0.881	-0.954	19.355	-0.029	-0.029	0.000	0.000	0.000	0.000
73	A	79	ALA	0	-0.055	-0.026	17.379	0.003	0.003	0.000	0.000	0.000	0.000
74	A	80	ARG	1	0.751	0.844	13.079	0.174	0.174	0.000	0.000	0.000	0.000
75	A	81	THR	0	-0.026	-0.019	20.286	0.002	0.002	0.000	0.000	0.000	0.000
76	A	82	MET	0	-0.083	-0.038	23.497	0.006	0.006	0.000	0.000	0.000	0.000
77	A	83	ASP	-1	-0.741	-0.870	25.381	-0.015	-0.015	0.000	0.000	0.000	0.000
78	A	84	LEU	0	-0.010	0.030	27.686	0.003	0.003	0.000	0.000	0.000	0.000
79	A	85	HIS	0	0.082	0.032	30.007	0.002	0.002	0.000	0.000	0.000	0.000
80	A	86	LYN	0	0.023	-0.014	33.036	-0.001	-0.001	0.000	0.000	0.000	0.000
81	A	87	ILE	0	-0.059	-0.023	36.140	0.000	0.000	0.000	0.000	0.000	0.000
82	A	88	ALA	0	0.033	0.023	33.355	0.000	0.000	0.000	0.000	0.000	0.000
83	A	89	ARG	1	0.976	0.972	31.101	0.020	0.020	0.000	0.000	0.000	0.000
84	A	90	ARG	1	0.887	0.960	34.608	0.012	0.012	0.000	0.000	0.000	0.000
85	A	91	TYR	0	-0.062	-0.037	36.696	0.001	0.001	0.000	0.000	0.000	0.000
86	A	92	VAL	0	-0.009	0.007	30.697	0.000	0.000	0.000	0.000	0.000	0.000
87	A	93	SER	0	-0.009	0.010	31.437	0.000	0.000	0.000	0.000	0.000	0.000
88	A	94	CYS	0	-0.030	-0.034	25.830	-0.002	-0.002	0.000	0.000	0.000	0.000
89	A	95	ASP	-1	-0.852	-0.914	23.966	-0.066	-0.066	0.000	0.000	0.000	0.000
90	A	96	GLU	-1	-0.852	-0.915	23.047	-0.049	-0.049	0.000	0.000	0.000	0.000
91	A	97	GLU	-1	-0.792	-0.867	20.727	-0.079	-0.079	0.000	0.000	0.000	0.000
92	A	98	GLY	0	0.012	0.012	19.941	-0.012	-0.012	0.000	0.000	0.000	0.000
93	A	99	ALA	0	-0.015	-0.011	18.488	-0.016	-0.016	0.000	0.000	0.000	0.000
94	A	100	ARG	1	0.765	0.832	17.174	0.044	0.044	0.000	0.000	0.000	0.000
95	A	101	GLU	-1	-0.851	-0.916	15.377	-0.193	-0.193	0.000	0.000	0.000	0.000
96	A	102	GLU	-1	-0.928	-0.966	14.107	-0.169	-0.169	0.000	0.000	0.000	0.000
97	A	103	GLN	0	-0.112	-0.059	12.408	-0.051	-0.051	0.000	0.000	0.000	0.000
98	A	104	LEU	0	-0.030	-0.028	11.189	-0.015	-0.015	0.000	0.000	0.000	0.000
99	A	105	SER	0	-0.033	-0.023	10.555	-0.038	-0.038	0.000	0.000	0.000	0.000
100	A	106	TRP	0	-0.052	-0.022	5.684	0.038	0.038	0.000	0.000	0.000	0.000
101	A	107	MET	0	-0.074	-0.020	6.860	-0.015	-0.015	0.000	0.000	0.000	0.000
102	A	108	GLU	-1	-0.870	-0.909	8.721	-0.302	-0.302	0.000	0.000	0.000	0.000
103	A	109	SER	0	-0.111	-0.078	11.075	0.055	0.055	0.000	0.000	0.000	0.000
104	A	110	LYS	1	0.884	0.913	13.107	0.207	0.207	0.000	0.000	0.000	0.000
105	A	111	PRO	0	-0.043	-0.021	13.942	0.006	0.006	0.000	0.000	0.000	0.000
106	A	112	ASP	-1	-0.794	-0.862	16.961	-0.050	-0.050	0.000	0.000	0.000	0.000
107	A	113	PHE	0	0.060	0.011	16.848	0.007	0.007	0.000	0.000	0.000	0.000
108	A	114	SER	0	0.010	-0.016	22.520	0.006	0.006	0.000	0.000	0.000	0.000
109	A	115	ASP	-1	-0.926	-0.940	24.346	-0.030	-0.030	0.000	0.000	0.000	0.000
110	A	116	VAL	0	-0.041	-0.031	23.249	0.004	0.004	0.000	0.000	0.000	0.000
111	A	117	GLU	-1	-0.825	-0.922	24.043	-0.022	-0.022	0.000	0.000	0.000	0.000
112	A	118	VAL	0	-0.098	-0.048	27.331	0.002	0.002	0.000	0.000	0.000	0.000
113	A	119	TYR	0	-0.033	-0.049	27.989	0.002	0.002	0.000	0.000	0.000	0.000
114	A	120	VAL	0	0.047	0.034	24.489	0.003	0.003	0.000	0.000	0.000	0.000
115	A	121	SER	0	-0.013	0.007	27.399	0.001	0.001	0.000	0.000	0.000	0.000
116	A	122	ASP	-1	-0.708	-0.849	30.097	-0.011	-0.011	0.000	0.000	0.000	0.000
117	A	123	ALA	0	-0.002	-0.005	28.319	0.001	0.001	0.000	0.000	0.000	0.000
118	A	124	ASP	-1	-0.886	-0.945	28.178	-0.009	-0.009	0.000	0.000	0.000	0.000
119	A	125	LYS	1	0.803	0.891	29.601	0.014	0.014	0.000	0.000	0.000	0.000
120	A	126	LEU	0	-0.005	-0.010	33.154	0.001	0.001	0.000	0.000	0.000	0.000
121	A	127	GLU	-1	-0.775	-0.861	28.480	0.003	0.003	0.000	0.000	0.000	0.000
122	A	128	LEU	0	0.001	0.013	31.822	0.001	0.001	0.000	0.000	0.000	0.000
123	A	129	ALA	0	0.011	-0.002	33.576	0.000	0.000	0.000	0.000	0.000	0.000
124	A	130	PHE	0	-0.037	-0.029	34.322	0.000	0.000	0.000	0.000	0.000	0.000
125	A	131	GLN	0	0.025	0.028	32.585	0.001	0.001	0.000	0.000	0.000	0.000
126	A	132	GLY	0	0.030	0.015	35.135	0.000	0.000	0.000	0.000	0.000	0.000
127	A	133	VAL	0	-0.009	-0.009	38.419	0.000	0.000	0.000	0.000	0.000	0.000
128	A	134	GLU	-1	-0.861	-0.892	34.794	0.005	0.005	0.000	0.000	0.000	0.000
129	A	135	TYR	0	0.060	0.011	32.653	0.000	0.000	0.000	0.000	0.000	0.000
130	A	136	SER	0	-0.128	-0.055	39.323	0.000	0.000	0.000	0.000	0.000	0.000
131	A	137	GLN	0	-0.039	-0.034	41.985	0.000	0.000	0.000	0.000	0.000	0.000
132	A	138	GLN	0	-0.063	-0.025	38.249	0.001	0.001	0.000	0.000	0.000	0.000
133	A	139	VAL	0	0.002	-0.005	41.815	0.000	0.000	0.000	0.000	0.000	0.000
134	A	140	SER	0	0.031	0.018	43.299	0.000	0.000	0.000	0.000	0.000	0.000
135	A	141	TYR	0	-0.015	-0.017	43.272	0.000	0.000	0.000	0.000	0.000	0.000
136	A	142	ALA	0	0.033	0.009	39.715	-0.001	-0.001	0.000	0.000	0.000	0.000
137	A	143	ILE	0	-0.010	0.004	40.606	0.000	0.000	0.000	0.000	0.000	0.000
138	A	144	ARG	1	0.844	0.906	42.662	0.004	0.004	0.000	0.000	0.000	0.000
139	A	145	PHE	0	-0.059	-0.026	36.518	-0.001	-0.001	0.000	0.000	0.000	0.000
140	A	146	ALA	0	0.038	0.026	38.043	0.000	0.000	0.000	0.000	0.000	0.000
141	A	147	GLU	-1	-0.855	-0.893	40.241	-0.004	-0.004	0.000	0.000	0.000	0.000
142	A	148	ASN	0	-0.037	-0.028	42.622	0.000	0.000	0.000	0.000	0.000	0.000
143	A	149	VAL	0	0.003	0.012	37.416	-0.001	-0.001	0.000	0.000	0.000	0.000
144	A	150	GLU	-1	-0.880	-0.924	39.553	-0.011	-0.011	0.000	0.000	0.000	0.000
145	A	151	LEU	0	-0.060	-0.023	36.049	-0.001	-0.001	0.000	0.000	0.000	0.000
146	A	152	LYS	1	0.919	0.946	32.429	0.019	0.019	0.000	0.000	0.000	0.000
147	A	153	THR	0	-0.006	-0.019	33.902	0.000	0.000	0.000	0.000	0.000	0.000
148	A	154	ASP	-1	-0.822	-0.913	37.235	-0.009	-0.009	0.000	0.000	0.000	0.000
149	A	155	ALA	0	0.013	0.016	35.694	0.001	0.001	0.000	0.000	0.000	0.000
150	A	156	ALA	0	0.038	0.009	35.268	0.001	0.001	0.000	0.000	0.000	0.000
151	A	157	LYS	1	0.821	0.895	37.029	0.011	0.011	0.000	0.000	0.000	0.000
152	A	158	GLU	-1	-0.878	-0.903	40.226	-0.003	-0.003	0.000	0.000	0.000	0.000
153	A	159	ILE	0	0.028	0.008	35.400	0.001	0.001	0.000	0.000	0.000	0.000
154	A	160	TYR	0	-0.024	-0.040	38.838	0.001	0.001	0.000	0.000	0.000	0.000
155	A	161	ARG	1	0.814	0.890	40.160	0.004	0.004	0.000	0.000	0.000	0.000
156	A	162	VAL	0	0.028	0.009	41.994	0.000	0.000	0.000	0.000	0.000	0.000
157	A	163	LEU	0	-0.048	-0.009	38.560	0.001	0.001	0.000	0.000	0.000	0.000
158	A	164	MET	0	0.022	0.008	41.632	0.001	0.001	0.000	0.000	0.000	0.000
159	A	165	GLU	-1	-0.861	-0.890	44.335	-0.003	-0.003	0.000	0.000	0.000	0.000
160	A	166	ARG	1	0.843	0.923	41.854	-0.001	-0.001	0.000	0.000	0.000	0.000
161	A	167	LYS	1	0.867	0.924	43.710	0.003	0.003	0.000	0.000	0.000	0.000
162	A	168	ASN	0	0.046	0.031	43.564	0.001	0.001	0.000	0.000	0.000	0.000
163	A	169	PRO	0	0.050	0.023	39.245	0.000	0.000	0.000	0.000	0.000	0.000
164	A	170	VAL	0	-0.028	-0.007	39.705	0.001	0.001	0.000	0.000	0.000	0.000
165	A	171	TRP	0	-0.009	-0.009	35.525	0.000	0.000	0.000	0.000	0.000	0.000
166	A	172	TRP	0	0.013	0.012	39.042	0.000	0.000	0.000	0.000	0.000	0.000
167	A	173	ARG	1	0.948	0.979	41.220	-0.004	-0.004	0.000	0.000	0.000	0.000

Top

Graph

Manual

About

Interactive mode: IFIE and PIEDA for fragment #1(A:7:MET)