FMO DATABASE

FMODB ID: KG793

Calculation Name: 1YRV-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1YRV

Chain ID: A

ChEMBL ID:

UniProt ID: Q5VVX9

Base Structure: X-ray

Registration Date: 2023-09-20

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	153
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1500484.765217
FMO2-HF: Nuclear repulsion	1438558.180435
FMO2-HF: Total energy	-61926.584782
FMO2-MP2: Total energy	-62107.040382

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:-4:VAL)

Summations of interaction energy for fragment #1(A:-4:VAL)

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.
-3.095	0.298	0.259	-1.275	-2.379	-0.001

Interaction energy analysis for fragmet #1(A:-4:VAL)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.025 / q_NPA : 0.002

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	-2	ARG	1	1.006	1.011	3.371	-1.647	-0.141	0.038	-0.710	-0.834	0.001
4	A	-1	GLY	0	0.001	-0.005	5.288	0.227	0.335	-0.001	-0.006	-0.101	0.000
5	A	0	SER	0	0.037	0.002	3.011	-0.577	0.537	0.176	-0.433	-0.858	-0.002
6	A	1	MET	0	-0.061	-0.007	3.142	-0.191	0.281	0.040	-0.081	-0.432	0.000
7	A	2	HIS	0	0.008	-0.016	5.672	0.160	0.160	0.000	0.000	0.000	0.000
8	A	3	GLY	0	0.013	0.015	8.225	0.143	0.143	0.000	0.000	0.000	0.000
9	A	4	ARG	1	0.981	0.974	10.012	0.266	0.266	0.000	0.000	0.000	0.000
10	A	5	ALA	0	0.072	0.038	11.916	-0.002	-0.002	0.000	0.000	0.000	0.000
11	A	6	TYR	0	0.049	0.030	6.721	0.026	0.026	0.000	0.000	0.000	0.000
12	A	7	LEU	0	0.019	0.002	10.218	0.025	0.025	0.000	0.000	0.000	0.000
13	A	8	LEU	0	-0.060	-0.015	12.107	0.047	0.047	0.000	0.000	0.000	0.000
14	A	9	LEU	0	0.046	0.023	12.434	0.030	0.030	0.000	0.000	0.000	0.000
15	A	10	HIS	0	-0.033	-0.012	9.578	0.094	0.094	0.000	0.000	0.000	0.000
16	A	11	ARG	1	0.869	0.921	12.951	0.285	0.285	0.000	0.000	0.000	0.000
17	A	12	ASP	-1	-0.730	-0.853	16.335	-0.226	-0.226	0.000	0.000	0.000	0.000
18	A	13	PHE	0	0.032	0.002	13.808	0.026	0.026	0.000	0.000	0.000	0.000
19	A	14	CYS	0	-0.088	-0.058	15.524	0.016	0.016	0.000	0.000	0.000	0.000
20	A	15	ASP	-1	-0.825	-0.913	18.284	-0.212	-0.212	0.000	0.000	0.000	0.000
21	A	16	LEU	0	-0.070	-0.016	19.858	0.019	0.019	0.000	0.000	0.000	0.000
22	A	17	LYS	1	0.857	0.928	15.879	0.335	0.335	0.000	0.000	0.000	0.000
23	A	18	GLU	-1	-0.952	-0.969	21.742	-0.169	-0.169	0.000	0.000	0.000	0.000
24	A	19	ASN	0	-0.079	-0.040	24.205	0.020	0.020	0.000	0.000	0.000	0.000
25	A	20	ASN	0	-0.059	-0.009	25.235	0.011	0.011	0.000	0.000	0.000	0.000
26	A	21	TYR	0	0.009	-0.007	25.528	0.012	0.012	0.000	0.000	0.000	0.000
27	A	22	LYS	1	0.903	0.933	27.850	0.071	0.071	0.000	0.000	0.000	0.000
28	A	23	GLY	0	0.006	-0.002	30.016	0.001	0.001	0.000	0.000	0.000	0.000
29	A	24	ILE	0	-0.033	-0.009	24.221	0.002	0.002	0.000	0.000	0.000	0.000
30	A	25	THR	0	0.007	0.021	21.798	-0.008	-0.008	0.000	0.000	0.000	0.000
31	A	26	ALA	0	0.006	-0.008	19.039	0.006	0.006	0.000	0.000	0.000	0.000
32	A	27	LYS	1	0.917	0.960	13.350	0.265	0.265	0.000	0.000	0.000	0.000
33	A	28	PRO	0	0.004	0.013	11.322	0.019	0.019	0.000	0.000	0.000	0.000
34	A	29	VAL	0	-0.020	-0.018	12.678	-0.006	-0.006	0.000	0.000	0.000	0.000
35	A	30	SER	0	0.014	-0.012	8.362	0.022	0.022	0.000	0.000	0.000	0.000
36	A	31	GLU	-1	-0.900	-0.959	3.519	-1.052	-0.859	0.006	-0.045	-0.154	0.000
37	A	32	ASP	-1	-0.941	-0.974	5.421	-0.879	-0.879	0.000	0.000	0.000	0.000
38	A	33	MET	0	-0.073	-0.024	6.398	0.001	0.001	0.000	0.000	0.000	0.000
39	A	34	MET	0	-0.009	0.015	9.379	0.097	0.097	0.000	0.000	0.000	0.000
40	A	35	GLU	-1	-0.823	-0.870	11.121	-0.073	-0.073	0.000	0.000	0.000	0.000
41	A	36	TRP	0	-0.046	-0.035	12.933	-0.029	-0.029	0.000	0.000	0.000	0.000
42	A	37	GLU	-1	-0.905	-0.949	15.689	-0.071	-0.071	0.000	0.000	0.000	0.000
43	A	38	VAL	0	-0.050	-0.047	18.598	-0.015	-0.015	0.000	0.000	0.000	0.000
44	A	39	GLU	-1	-0.837	-0.898	21.638	-0.059	-0.059	0.000	0.000	0.000	0.000
45	A	40	ILE	0	-0.048	-0.021	25.160	-0.007	-0.007	0.000	0.000	0.000	0.000
46	A	41	GLU	-1	-0.840	-0.900	27.898	-0.064	-0.064	0.000	0.000	0.000	0.000
47	A	42	GLY	0	-0.015	-0.010	31.421	-0.002	-0.002	0.000	0.000	0.000	0.000
48	A	43	LEU	0	-0.004	0.002	34.353	0.000	0.000	0.000	0.000	0.000	0.000
49	A	44	GLN	0	-0.021	-0.013	35.946	0.002	0.002	0.000	0.000	0.000	0.000
50	A	45	ASN	0	-0.060	-0.048	39.110	-0.001	-0.001	0.000	0.000	0.000	0.000
51	A	46	SER	0	0.036	0.026	38.247	0.001	0.001	0.000	0.000	0.000	0.000
52	A	47	VAL	0	0.026	-0.004	40.429	0.001	0.001	0.000	0.000	0.000	0.000
53	A	48	TRP	0	0.038	0.009	35.357	0.002	0.002	0.000	0.000	0.000	0.000
54	A	49	GLN	0	0.031	0.044	36.708	-0.004	-0.004	0.000	0.000	0.000	0.000
55	A	50	GLY	0	-0.025	-0.021	37.132	0.004	0.004	0.000	0.000	0.000	0.000
56	A	51	LEU	0	-0.064	-0.026	34.828	0.002	0.002	0.000	0.000	0.000	0.000
57	A	52	VAL	0	0.042	0.016	28.591	-0.004	-0.004	0.000	0.000	0.000	0.000
58	A	53	PHE	0	-0.029	-0.013	28.520	0.005	0.005	0.000	0.000	0.000	0.000
59	A	54	GLN	0	-0.032	-0.018	25.441	-0.003	-0.003	0.000	0.000	0.000	0.000
60	A	55	LEU	0	-0.034	-0.028	23.312	0.007	0.007	0.000	0.000	0.000	0.000
61	A	56	THR	0	0.018	0.020	18.762	-0.005	-0.005	0.000	0.000	0.000	0.000
62	A	57	ILE	0	-0.041	-0.027	18.212	0.008	0.008	0.000	0.000	0.000	0.000
63	A	58	HIS	1	0.867	0.915	13.662	0.098	0.098	0.000	0.000	0.000	0.000
64	A	59	PHE	0	0.020	0.010	13.908	0.017	0.017	0.000	0.000	0.000	0.000
65	A	60	THR	0	0.041	0.012	14.119	0.001	0.001	0.000	0.000	0.000	0.000
66	A	61	SER	0	0.007	-0.018	11.343	-0.025	-0.025	0.000	0.000	0.000	0.000
67	A	62	GLU	-1	-0.891	-0.936	12.997	-0.182	-0.182	0.000	0.000	0.000	0.000
68	A	63	TYR	0	-0.081	-0.054	15.385	0.016	0.016	0.000	0.000	0.000	0.000
69	A	64	ASN	0	-0.058	-0.027	17.160	-0.013	-0.013	0.000	0.000	0.000	0.000
70	A	65	TYR	0	-0.019	-0.017	18.857	0.011	0.011	0.000	0.000	0.000	0.000
71	A	66	ALA	0	-0.017	-0.006	19.830	0.019	0.019	0.000	0.000	0.000	0.000
72	A	67	PRO	0	0.016	0.020	20.287	-0.021	-0.021	0.000	0.000	0.000	0.000
73	A	68	PRO	0	-0.021	-0.004	18.346	0.001	0.001	0.000	0.000	0.000	0.000
74	A	69	VAL	0	-0.007	-0.013	19.224	0.016	0.016	0.000	0.000	0.000	0.000
75	A	70	VAL	0	0.003	0.002	20.322	-0.008	-0.008	0.000	0.000	0.000	0.000
76	A	71	LYS	1	0.885	0.931	22.445	0.048	0.048	0.000	0.000	0.000	0.000
77	A	72	PHE	0	0.017	-0.004	23.826	-0.008	-0.008	0.000	0.000	0.000	0.000
78	A	73	ILE	0	-0.027	0.004	22.225	0.006	0.006	0.000	0.000	0.000	0.000
79	A	74	THR	0	0.006	-0.004	25.280	0.009	0.009	0.000	0.000	0.000	0.000
80	A	75	ILE	0	-0.016	-0.002	28.992	-0.004	-0.004	0.000	0.000	0.000	0.000
81	A	76	PRO	0	-0.006	0.021	30.650	0.003	0.003	0.000	0.000	0.000	0.000
82	A	77	PHE	0	0.017	0.012	33.564	0.001	0.001	0.000	0.000	0.000	0.000
83	A	78	HIS	0	0.014	-0.007	34.661	0.001	0.001	0.000	0.000	0.000	0.000
84	A	79	PRO	0	0.025	0.010	36.754	0.001	0.001	0.000	0.000	0.000	0.000
85	A	80	ASN	0	0.037	0.007	34.902	0.001	0.001	0.000	0.000	0.000	0.000
86	A	81	VAL	0	0.005	0.025	30.506	-0.003	-0.003	0.000	0.000	0.000	0.000
87	A	82	ASP	-1	-0.756	-0.876	31.275	-0.015	-0.015	0.000	0.000	0.000	0.000
88	A	83	PRO	0	-0.025	-0.013	32.216	0.000	0.000	0.000	0.000	0.000	0.000
89	A	84	HIS	0	-0.013	-0.003	31.636	0.002	0.002	0.000	0.000	0.000	0.000
90	A	85	THR	0	-0.071	-0.063	27.326	0.003	0.003	0.000	0.000	0.000	0.000
91	A	86	GLY	0	0.008	0.006	27.574	-0.002	-0.002	0.000	0.000	0.000	0.000
92	A	87	GLN	0	0.035	0.021	25.747	-0.003	-0.003	0.000	0.000	0.000	0.000
93	A	88	PRO	0	-0.044	-0.013	26.834	0.005	0.005	0.000	0.000	0.000	0.000
94	A	89	CYS	0	-0.014	0.003	29.393	-0.002	-0.002	0.000	0.000	0.000	0.000
95	A	90	ILE	0	-0.017	-0.008	28.918	-0.001	-0.001	0.000	0.000	0.000	0.000
96	A	91	ASP	-1	-0.724	-0.867	30.169	-0.057	-0.057	0.000	0.000	0.000	0.000
97	A	92	PHE	0	-0.068	-0.037	25.494	0.000	0.000	0.000	0.000	0.000	0.000
98	A	93	LEU	0	-0.045	-0.032	24.098	-0.010	-0.010	0.000	0.000	0.000	0.000
99	A	94	ASP	-1	-0.851	-0.931	26.563	-0.057	-0.057	0.000	0.000	0.000	0.000
100	A	95	ASN	0	-0.031	-0.020	29.272	0.003	0.003	0.000	0.000	0.000	0.000
101	A	96	PRO	0	0.010	-0.007	28.458	-0.006	-0.006	0.000	0.000	0.000	0.000
102	A	97	GLU	-1	-0.931	-0.964	29.479	-0.057	-0.057	0.000	0.000	0.000	0.000
103	A	98	LYS	1	0.783	0.887	31.388	0.056	0.056	0.000	0.000	0.000	0.000
104	A	99	TRP	0	-0.020	-0.002	21.802	-0.004	-0.004	0.000	0.000	0.000	0.000
105	A	100	ASN	0	0.049	0.014	26.644	-0.004	-0.004	0.000	0.000	0.000	0.000
106	A	101	THR	0	-0.011	0.015	23.500	-0.002	-0.002	0.000	0.000	0.000	0.000
107	A	102	ASN	0	-0.048	-0.037	23.834	-0.015	-0.015	0.000	0.000	0.000	0.000
108	A	103	TYR	0	-0.045	-0.010	24.387	0.000	0.000	0.000	0.000	0.000	0.000
109	A	104	THR	0	0.015	0.024	21.313	-0.007	-0.007	0.000	0.000	0.000	0.000
110	A	105	LEU	0	0.019	-0.006	17.089	0.016	0.016	0.000	0.000	0.000	0.000
111	A	106	SER	0	0.033	0.002	20.483	0.015	0.015	0.000	0.000	0.000	0.000
112	A	107	SER	0	-0.015	0.003	23.661	0.015	0.015	0.000	0.000	0.000	0.000
113	A	108	ILE	0	0.020	0.011	21.109	0.012	0.012	0.000	0.000	0.000	0.000
114	A	109	LEU	0	0.023	0.021	21.102	0.010	0.010	0.000	0.000	0.000	0.000
115	A	110	LEU	0	0.023	0.012	25.146	0.011	0.011	0.000	0.000	0.000	0.000
116	A	111	ALA	0	-0.033	-0.025	28.161	0.009	0.009	0.000	0.000	0.000	0.000
117	A	112	LEU	0	0.014	-0.005	24.748	0.008	0.008	0.000	0.000	0.000	0.000
118	A	113	GLN	0	-0.017	0.004	28.787	0.005	0.005	0.000	0.000	0.000	0.000
119	A	114	VAL	0	-0.002	0.000	30.748	0.007	0.007	0.000	0.000	0.000	0.000
120	A	115	MET	0	0.009	0.009	31.835	0.005	0.005	0.000	0.000	0.000	0.000
121	A	116	LEU	0	0.017	0.019	28.580	0.005	0.005	0.000	0.000	0.000	0.000
122	A	117	SER	0	-0.040	-0.022	33.137	0.005	0.005	0.000	0.000	0.000	0.000
123	A	118	ASN	0	-0.130	-0.080	36.010	0.006	0.006	0.000	0.000	0.000	0.000
124	A	119	PRO	0	0.020	0.009	37.583	-0.001	-0.001	0.000	0.000	0.000	0.000
125	A	120	VAL	0	-0.005	0.011	37.634	0.001	0.001	0.000	0.000	0.000	0.000
126	A	121	LEU	0	-0.027	-0.045	39.978	0.002	0.002	0.000	0.000	0.000	0.000
127	A	122	GLU	-1	-0.960	-0.965	42.166	-0.027	-0.027	0.000	0.000	0.000	0.000
128	A	123	ASN	0	-0.009	-0.011	41.643	0.003	0.003	0.000	0.000	0.000	0.000
129	A	124	PRO	0	-0.061	-0.011	39.405	-0.001	-0.001	0.000	0.000	0.000	0.000
130	A	125	VAL	0	0.035	0.033	34.822	0.002	0.002	0.000	0.000	0.000	0.000
131	A	126	ASN	0	-0.047	-0.017	37.169	0.005	0.005	0.000	0.000	0.000	0.000
132	A	127	LEU	0	0.069	0.015	39.470	-0.001	-0.001	0.000	0.000	0.000	0.000
133	A	128	GLU	-1	-0.810	-0.893	43.051	-0.013	-0.013	0.000	0.000	0.000	0.000
134	A	129	ALA	0	-0.004	0.008	40.144	0.000	0.000	0.000	0.000	0.000	0.000
135	A	130	ALA	0	0.050	0.017	42.069	-0.001	-0.001	0.000	0.000	0.000	0.000
136	A	131	ARG	1	0.814	0.890	43.400	0.013	0.013	0.000	0.000	0.000	0.000
137	A	132	ILE	0	-0.055	-0.047	45.211	0.000	0.000	0.000	0.000	0.000	0.000
138	A	133	LEU	0	-0.012	0.014	41.465	0.000	0.000	0.000	0.000	0.000	0.000
139	A	134	VAL	0	-0.017	-0.009	45.243	0.000	0.000	0.000	0.000	0.000	0.000
140	A	135	LYS	1	0.829	0.906	47.986	0.018	0.018	0.000	0.000	0.000	0.000
141	A	136	ASP	-1	-0.863	-0.933	49.718	-0.019	-0.019	0.000	0.000	0.000	0.000
142	A	137	GLU	-1	-0.711	-0.831	45.694	-0.029	-0.029	0.000	0.000	0.000	0.000
143	A	138	SER	0	0.002	-0.011	45.813	-0.002	-0.002	0.000	0.000	0.000	0.000
144	A	139	LEU	0	0.004	0.017	46.983	0.000	0.000	0.000	0.000	0.000	0.000
145	A	140	TYR	0	0.019	-0.010	38.922	-0.001	-0.001	0.000	0.000	0.000	0.000
146	A	141	ARG	1	0.849	0.900	42.201	0.029	0.029	0.000	0.000	0.000	0.000
147	A	142	THR	0	-0.074	-0.031	42.421	0.000	0.000	0.000	0.000	0.000	0.000
148	A	143	ILE	0	0.009	0.002	41.271	0.001	0.001	0.000	0.000	0.000	0.000
149	A	144	LEU	0	-0.002	0.006	37.478	0.001	0.001	0.000	0.000	0.000	0.000
150	A	145	ARG	1	0.886	0.948	38.571	0.032	0.032	0.000	0.000	0.000	0.000
151	A	146	LEU	0	-0.014	0.000	39.747	0.001	0.001	0.000	0.000	0.000	0.000
152	A	147	PHE	0	-0.037	-0.010	36.111	0.002	0.002	0.000	0.000	0.000	0.000
153	A	148	ASN	0	-0.107	-0.043	34.696	-0.003	-0.003	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:-4:VAL)