FMO DATABASE

FMODB ID: 2N2QR

Calculation Name: 1YNB-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

Ligand 3-letter code:

Ligand of Interest (LOI):

Structure Source: PDB

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:

Apendix: None

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
Remarks

FMO calculation

FMO method	FMO2-MP2/6-31G(d)
Fragmentation	Auto
Number of fragment	167
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1692570.893235
FMO2-HF: Nuclear repulsion	1625400.979875
FMO2-HF: Total energy	-67169.91336
FMO2-MP2: Total energy	-67365.934594

3D Structure Molmil

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.
-0.772	3.672	0.566	-1.44	-3.569	0

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 : 0.035 / q_NPA : 0.001

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].
3	A	9	ASP	-1	-0.900	-0.942	3.073	-2.564	-0.672	0.006	-0.742	-1.155
4	A	10	VAL	0	0.006	0.006	2.765	-0.697	0.978	0.521	-0.459	-1.737
5	A	11	VAL	0	-0.027	-0.013	2.998	0.427	1.200	0.040	-0.234	-0.580
6	A	12	LYS	1	0.954	0.957	5.360	1.150	1.254	-0.001	-0.005	-0.097
7	A	13	PHE	0	0.085	0.057	7.587	0.261	0.261	0.000	0.000	0.000
8	A	14	ILE	0	-0.002	-0.003	5.890	0.182	0.182	0.000	0.000	0.000
9	A	15	HIS	0	-0.042	-0.028	9.470	0.146	0.146	0.000	0.000	0.000
10	A	16	GLU	-1	-0.776	-0.845	11.588	-0.143	-0.143	0.000	0.000	0.000
11	A	17	VAL	0	0.018	0.024	12.549	0.050	0.050	0.000	0.000	0.000
12	A	18	GLY	0	-0.023	-0.009	13.854	0.034	0.034	0.000	0.000	0.000
13	A	19	SER	0	-0.021	-0.022	15.670	0.024	0.024	0.000	0.000	0.000
14	A	20	LEU	0	0.096	0.053	17.920	0.012	0.012	0.000	0.000	0.000
15	A	21	LYS	1	0.879	0.931	16.954	0.054	0.054	0.000	0.000	0.000
16	A	22	LEU	0	-0.093	-0.048	19.692	0.004	0.004	0.000	0.000	0.000
17	A	23	THR	0	0.031	0.031	21.881	-0.003	-0.003	0.000	0.000	0.000
18	A	24	PRO	0	-0.053	-0.026	24.316	0.006	0.006	0.000	0.000	0.000
19	A	25	ARG	1	0.963	1.005	27.455	0.004	0.004	0.000	0.000	0.000
20	A	26	SER	0	-0.031	-0.061	29.354	0.003	0.003	0.000	0.000	0.000
21	A	27	GLY	0	-0.026	-0.034	31.845	0.000	0.000	0.000	0.000	0.000
22	A	28	TRP	0	-0.005	-0.033	32.144	0.001	0.001	0.000	0.000	0.000
23	A	29	LEU	0	0.031	0.028	31.918	0.001	0.001	0.000	0.000	0.000
24	A	30	LYS	1	0.857	0.938	36.079	0.012	0.012	0.000	0.000	0.000
25	A	31	LEU	0	-0.085	-0.036	38.911	0.001	0.001	0.000	0.000	0.000
26	A	32	GLY	0	0.007	0.006	39.678	0.001	0.001	0.000	0.000	0.000
27	A	33	ILE	0	-0.035	-0.005	35.335	0.000	0.000	0.000	0.000	0.000
28	A	34	ARG	1	0.937	0.949	35.970	0.018	0.018	0.000	0.000	0.000
29	A	35	LEU	0	-0.015	0.009	31.154	-0.002	-0.002	0.000	0.000	0.000
30	A	36	PRO	0	-0.067	-0.036	30.860	0.002	0.002	0.000	0.000	0.000
31	A	37	GLU	-1	-0.694	-0.818	28.667	-0.005	-0.005	0.000	0.000	0.000
32	A	38	SER	0	-0.013	-0.018	24.119	-0.003	-0.003	0.000	0.000	0.000
33	A	39	VAL	0	0.036	-0.004	22.578	0.006	0.006	0.000	0.000	0.000
34	A	40	ALA	0	0.020	0.018	20.407	0.008	0.008	0.000	0.000	0.000
35	A	41	GLU	-1	-0.925	-0.963	21.921	0.002	0.002	0.000	0.000	0.000
36	A	42	HIS	1	0.799	0.899	24.995	0.000	0.000	0.000	0.000	0.000
37	A	43	ASN	0	-0.019	-0.033	21.779	0.002	0.002	0.000	0.000	0.000
38	A	44	PHE	0	-0.012	0.006	22.352	0.010	0.010	0.000	0.000	0.000
39	A	45	ARG	1	0.753	0.833	23.648	-0.007	-0.007	0.000	0.000	0.000
40	A	46	ALA	0	0.031	0.013	26.164	0.002	0.002	0.000	0.000	0.000
41	A	47	ALA	0	0.032	0.017	22.914	0.002	0.002	0.000	0.000	0.000
42	A	48	ILE	0	-0.023	-0.012	24.875	0.003	0.003	0.000	0.000	0.000
43	A	49	ILE	0	-0.028	-0.021	27.070	0.000	0.000	0.000	0.000	0.000
44	A	50	ALA	0	0.051	0.019	26.394	-0.001	-0.001	0.000	0.000	0.000
45	A	51	PHE	0	-0.047	-0.015	25.769	0.000	0.000	0.000	0.000	0.000
46	A	52	ILE	0	-0.020	-0.020	27.903	-0.002	-0.002	0.000	0.000	0.000
47	A	53	LEU	0	-0.032	-0.013	31.410	-0.002	-0.002	0.000	0.000	0.000
48	A	54	ALA	0	0.041	0.047	29.419	-0.002	-0.002	0.000	0.000	0.000
49	A	55	LEU	0	-0.010	-0.007	30.247	-0.002	-0.002	0.000	0.000	0.000
50	A	56	LYS	1	0.881	0.939	32.766	-0.028	-0.028	0.000	0.000	0.000
51	A	57	SER	0	-0.025	-0.014	34.327	-0.004	-0.004	0.000	0.000	0.000
52	A	58	GLY	0	-0.049	-0.019	35.900	-0.001	-0.001	0.000	0.000	0.000
53	A	59	GLU	-1	-0.873	-0.911	30.894	0.041	0.041	0.000	0.000	0.000
54	A	60	SER	0	-0.023	-0.022	28.309	0.000	0.000	0.000	0.000	0.000
55	A	61	VAL	0	0.088	0.036	26.102	0.002	0.002	0.000	0.000	0.000
56	A	62	GLU	-1	-0.861	-0.924	24.284	0.070	0.070	0.000	0.000	0.000
57	A	63	LYS	1	0.937	0.975	24.342	-0.042	-0.042	0.000	0.000	0.000
58	A	64	ALA	0	0.022	0.001	26.095	0.001	0.001	0.000	0.000	0.000
59	A	65	CYS	0	-0.061	-0.043	21.781	0.001	0.001	0.000	0.000	0.000
60	A	66	LYS	1	0.863	0.947	21.410	-0.065	-0.065	0.000	0.000	0.000
61	A	67	ALA	0	0.038	0.018	22.405	0.000	0.000	0.000	0.000	0.000
62	A	68	ALA	0	-0.022	-0.010	22.710	-0.004	-0.004	0.000	0.000	0.000
63	A	69	THR	0	-0.020	-0.027	17.121	0.005	0.005	0.000	0.000	0.000
64	A	70	ALA	0	0.015	0.014	19.473	0.000	0.000	0.000	0.000	0.000
65	A	71	ALA	0	0.007	0.001	21.386	-0.010	-0.010	0.000	0.000	0.000
66	A	72	LEU	0	-0.091	-0.046	17.840	-0.009	-0.009	0.000	0.000	0.000
67	A	73	PHE	0	-0.041	-0.025	13.388	-0.004	-0.004	0.000	0.000	0.000
68	A	74	HIS	0	-0.046	-0.003	18.877	-0.011	-0.011	0.000	0.000	0.000
69	A	75	ASP	-1	-0.780	-0.877	22.081	-0.003	-0.003	0.000	0.000	0.000
70	A	76	LEU	0	-0.025	0.001	14.723	-0.010	-0.010	0.000	0.000	0.000
71	A	77	HIS	0	0.113	0.067	18.336	-0.020	-0.020	0.000	0.000	0.000
72	A	78	GLU	-1	-0.911	-0.971	19.544	-0.032	-0.032	0.000	0.000	0.000
73	A	79	ALA	0	-0.076	-0.030	17.561	-0.004	-0.004	0.000	0.000	0.000
74	A	80	ARG	1	0.778	0.850	13.152	0.181	0.181	0.000	0.000	0.000
75	A	81	THR	0	-0.025	-0.018	20.364	0.005	0.005	0.000	0.000	0.000
76	A	82	MET	0	-0.100	-0.042	23.433	0.006	0.006	0.000	0.000	0.000
77	A	83	ASP	-1	-0.742	-0.860	25.398	-0.014	-0.014	0.000	0.000	0.000
78	A	84	LEU	0	0.003	0.024	27.532	0.002	0.002	0.000	0.000	0.000
79	A	85	HIS	0	0.045	0.023	30.238	0.006	0.006	0.000	0.000	0.000
80	A	86	LYN	0	0.046	-0.013	33.354	-0.001	-0.001	0.000	0.000	0.000
81	A	87	ILE	0	-0.043	-0.018	36.352	0.000	0.000	0.000	0.000	0.000
82	A	88	ALA	0	0.050	0.021	33.698	0.000	0.000	0.000	0.000	0.000
83	A	89	ARG	1	0.953	0.979	31.732	0.011	0.011	0.000	0.000	0.000
84	A	90	ARG	1	0.889	0.964	34.939	0.011	0.011	0.000	0.000	0.000
85	A	91	TYR	0	-0.051	-0.036	37.268	0.001	0.001	0.000	0.000	0.000
86	A	92	VAL	0	-0.029	-0.002	31.032	-0.001	-0.001	0.000	0.000	0.000
87	A	93	SER	0	-0.025	-0.012	31.470	0.002	0.002	0.000	0.000	0.000
88	A	94	CYS	0	-0.017	-0.016	25.963	-0.004	-0.004	0.000	0.000	0.000
89	A	95	ASP	-1	-0.857	-0.916	23.923	-0.036	-0.036	0.000	0.000	0.000
90	A	96	GLU	-1	-0.919	-0.971	23.302	-0.017	-0.017	0.000	0.000	0.000
91	A	97	GLU	-1	-0.915	-0.950	20.952	-0.016	-0.016	0.000	0.000	0.000
92	A	98	GLY	0	0.062	0.039	20.505	-0.005	-0.005	0.000	0.000	0.000
93	A	99	ALA	0	-0.070	-0.041	19.060	-0.013	-0.013	0.000	0.000	0.000
94	A	100	ARG	1	0.973	0.971	17.129	-0.023	-0.023	0.000	0.000	0.000
95	A	101	GLU	-1	-0.931	-0.963	16.017	-0.041	-0.041	0.000	0.000	0.000
96	A	102	GLU	-1	-0.981	-1.003	14.462	-0.124	-0.124	0.000	0.000	0.000
97	A	103	GLN	0	-0.144	-0.084	12.832	-0.028	-0.028	0.000	0.000	0.000
98	A	104	LEU	0	-0.027	-0.035	11.623	-0.028	-0.028	0.000	0.000	0.000
99	A	105	SER	0	-0.036	-0.001	10.271	0.011	0.011	0.000	0.000	0.000
100	A	106	TRP	0	-0.022	-0.009	5.969	0.076	0.076	0.000	0.000	0.000
101	A	107	MET	0	-0.093	-0.036	7.565	0.136	0.136	0.000	0.000	0.000
102	A	108	GLU	-1	-0.879	-0.892	9.115	0.169	0.169	0.000	0.000	0.000
103	A	109	SER	0	-0.100	-0.096	11.442	-0.041	-0.041	0.000	0.000	0.000
104	A	110	LYS	1	0.959	0.982	13.650	0.048	0.048	0.000	0.000	0.000
105	A	111	PRO	0	-0.029	-0.014	14.830	-0.012	-0.012	0.000	0.000	0.000
106	A	112	ASP	-1	-0.867	-0.934	17.919	0.029	0.029	0.000	0.000	0.000
107	A	113	PHE	0	-0.026	-0.028	17.493	0.009	0.009	0.000	0.000	0.000
108	A	114	SER	0	0.084	0.032	23.184	-0.007	-0.007	0.000	0.000	0.000
109	A	115	ASP	-1	-0.918	-0.951	25.517	0.054	0.054	0.000	0.000	0.000
110	A	116	VAL	0	-0.035	-0.008	24.275	-0.001	-0.001	0.000	0.000	0.000
111	A	117	GLU	-1	-0.807	-0.913	24.852	0.036	0.036	0.000	0.000	0.000
112	A	118	VAL	0	-0.102	-0.052	28.105	-0.004	-0.004	0.000	0.000	0.000
113	A	119	TYR	0	-0.038	-0.051	28.750	-0.003	-0.003	0.000	0.000	0.000
114	A	120	VAL	0	0.057	0.041	25.048	-0.001	-0.001	0.000	0.000	0.000
115	A	121	SER	0	-0.043	-0.020	27.893	-0.005	-0.005	0.000	0.000	0.000
116	A	122	ASP	-1	-0.701	-0.840	30.696	0.014	0.014	0.000	0.000	0.000
117	A	123	ALA	0	-0.008	-0.003	28.813	-0.002	-0.002	0.000	0.000	0.000
118	A	124	ASP	-1	-0.860	-0.915	28.738	0.005	0.005	0.000	0.000	0.000
119	A	125	LYS	1	0.888	0.929	30.199	-0.012	-0.012	0.000	0.000	0.000
120	A	126	LEU	0	0.010	-0.006	33.753	-0.002	-0.002	0.000	0.000	0.000
121	A	127	GLU	-1	-0.794	-0.860	28.964	0.007	0.007	0.000	0.000	0.000
122	A	128	LEU	0	-0.010	0.011	32.300	-0.002	-0.002	0.000	0.000	0.000
123	A	129	ALA	0	0.006	-0.004	33.979	-0.002	-0.002	0.000	0.000	0.000
124	A	130	PHE	0	-0.035	-0.029	34.618	-0.001	-0.001	0.000	0.000	0.000
125	A	131	GLN	0	0.027	0.030	32.570	0.000	0.000	0.000	0.000	0.000
126	A	132	GLY	0	0.015	0.001	35.255	-0.002	-0.002	0.000	0.000	0.000
127	A	133	VAL	0	-0.013	-0.014	38.413	-0.001	-0.001	0.000	0.000	0.000
128	A	134	GLU	-1	-0.814	-0.869	34.917	0.008	0.008	0.000	0.000	0.000
129	A	135	TYR	0	0.072	0.022	33.123	-0.001	-0.001	0.000	0.000	0.000
130	A	136	SER	0	-0.145	-0.064	39.178	-0.001	-0.001	0.000	0.000	0.000
131	A	137	GLN	0	-0.038	-0.027	42.041	0.000	0.000	0.000	0.000	0.000
132	A	138	GLN	0	-0.065	-0.020	38.074	0.000	0.000	0.000	0.000	0.000
133	A	139	VAL	0	0.001	-0.006	41.986	-0.001	-0.001	0.000	0.000	0.000
134	A	140	SER	0	0.061	0.026	43.434	0.000	0.000	0.000	0.000	0.000
135	A	141	TYR	0	-0.030	-0.027	42.981	0.001	0.001	0.000	0.000	0.000
136	A	142	ALA	0	0.042	0.021	39.812	0.000	0.000	0.000	0.000	0.000
137	A	143	ILE	0	0.018	0.010	40.824	0.001	0.001	0.000	0.000	0.000
138	A	144	ARG	1	0.912	0.966	43.082	0.003	0.003	0.000	0.000	0.000
139	A	145	PHE	0	-0.065	-0.032	36.693	0.000	0.000	0.000	0.000	0.000
140	A	146	ALA	0	0.031	0.021	38.745	0.001	0.001	0.000	0.000	0.000
141	A	147	GLU	-1	-0.952	-0.951	40.611	0.002	0.002	0.000	0.000	0.000
142	A	148	ASN	0	-0.038	-0.024	42.707	0.000	0.000	0.000	0.000	0.000
143	A	149	VAL	0	0.009	0.019	38.119	0.000	0.000	0.000	0.000	0.000
144	A	150	GLU	-1	-0.901	-0.935	39.519	0.005	0.005	0.000	0.000	0.000
145	A	151	LEU	0	-0.056	-0.032	36.304	0.000	0.000	0.000	0.000	0.000
146	A	152	LYS	1	0.882	0.915	33.151	-0.016	-0.016	0.000	0.000	0.000
147	A	153	THR	0	-0.047	-0.040	34.650	0.000	0.000	0.000	0.000	0.000
148	A	154	ASP	-1	-0.874	-0.944	37.958	0.014	0.014	0.000	0.000	0.000
149	A	155	ALA	0	0.011	0.013	36.450	-0.001	-0.001	0.000	0.000	0.000
150	A	156	ALA	0	0.018	0.003	35.760	0.000	0.000	0.000	0.000	0.000
151	A	157	LYS	1	0.934	0.959	37.489	-0.013	-0.013	0.000	0.000	0.000
152	A	158	GLU	-1	-0.959	-0.964	41.178	0.016	0.016	0.000	0.000	0.000
153	A	159	ILE	0	-0.003	-0.009	36.031	-0.001	-0.001	0.000	0.000	0.000
154	A	160	TYR	0	-0.027	-0.055	39.671	-0.001	-0.001	0.000	0.000	0.000
155	A	161	ARG	1	0.940	0.974	40.860	-0.010	-0.010	0.000	0.000	0.000
156	A	162	VAL	0	0.042	0.021	42.776	-0.001	-0.001	0.000	0.000	0.000
157	A	163	LEU	0	-0.057	-0.017	38.958	-0.001	-0.001	0.000	0.000	0.000
158	A	164	MET	0	-0.011	-0.014	42.155	-0.001	-0.001	0.000	0.000	0.000
159	A	165	GLU	-1	-0.949	-0.958	44.907	0.008	0.008	0.000	0.000	0.000
160	A	166	ARG	1	0.862	0.930	42.230	-0.011	-0.011	0.000	0.000	0.000
161	A	167	LYS	1	0.865	0.932	43.976	-0.005	-0.005	0.000	0.000	0.000
162	A	168	ASN	0	0.032	0.011	43.785	-0.001	-0.001	0.000	0.000	0.000
163	A	169	PRO	0	0.009	0.003	39.654	0.001	0.001	0.000	0.000	0.000
164	A	170	VAL	0	-0.030	0.006	39.816	0.001	0.001	0.000	0.000	0.000
165	A	171	TRP	0	-0.001	-0.006	35.713	0.001	0.001	0.000	0.000	0.000
166	A	172	TRP	0	0.026	0.012	39.021	0.001	0.001	0.000	0.000	0.000
167	A	173	ARG	1	0.952	0.985	41.414	-0.008	-0.008	0.000	0.000	0.000

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