FMO DATABASE

FMODB ID: YVJR2

Calculation Name: 3ESI-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3ESI

Chain ID: A

ChEMBL ID:

UniProt ID: Q6CYK7

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	OptH
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	124
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1056295.978429
FMO2-HF: Nuclear repulsion	1007247.519785
FMO2-HF: Total energy	-49048.458645
FMO2-MP2: Total energy	-49192.417548

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:1:MET)

Summations of interaction energy for fragment #1(A:1: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.
-8.1	-1.585	8.971	-4.298	-11.188	-0.013

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

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.013 / 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	3	PRO	0	0.001	0.009	3.820	-1.056	0.639	-0.025	-0.848	-0.822	0.001
4	A	4	VAL	0	0.043	0.022	6.470	0.326	0.326	0.000	0.000	0.000	0.000
5	A	5	GLU	-1	-0.827	-0.922	8.738	-0.242	-0.242	0.000	0.000	0.000	0.000
6	A	6	LEU	0	-0.054	-0.021	11.922	0.060	0.060	0.000	0.000	0.000	0.000
7	A	7	VAL	0	0.018	-0.001	14.902	0.030	0.030	0.000	0.000	0.000	0.000
8	A	8	ARG	1	0.843	0.922	14.114	0.109	0.109	0.000	0.000	0.000	0.000
9	A	9	HIS	0	-0.018	-0.003	18.505	0.021	0.021	0.000	0.000	0.000	0.000
10	A	10	ASP	-1	-0.893	-0.944	21.488	-0.084	-0.084	0.000	0.000	0.000	0.000
11	A	11	VAL	0	-0.045	-0.036	21.932	-0.009	-0.009	0.000	0.000	0.000	0.000
12	A	12	LYS	1	0.917	0.959	24.267	0.116	0.116	0.000	0.000	0.000	0.000
13	A	13	LYS	1	0.932	0.959	26.786	0.094	0.094	0.000	0.000	0.000	0.000
14	A	14	THR	0	-0.047	-0.022	28.767	0.008	0.008	0.000	0.000	0.000	0.000
15	A	15	ASP	-1	-0.912	-0.939	31.514	-0.084	-0.084	0.000	0.000	0.000	0.000
16	A	16	GLU	-1	-0.891	-0.973	30.541	-0.109	-0.109	0.000	0.000	0.000	0.000
17	A	17	THR	0	-0.097	-0.038	26.959	-0.013	-0.013	0.000	0.000	0.000	0.000
18	A	18	SER	0	0.003	0.007	23.857	0.013	0.013	0.000	0.000	0.000	0.000
19	A	19	GLN	0	-0.016	-0.023	22.699	-0.011	-0.011	0.000	0.000	0.000	0.000
20	A	20	VAL	0	0.029	0.024	17.952	0.016	0.016	0.000	0.000	0.000	0.000
21	A	21	GLU	-1	-0.869	-0.918	19.572	-0.166	-0.166	0.000	0.000	0.000	0.000
22	A	22	LEU	0	0.001	-0.004	13.709	0.016	0.016	0.000	0.000	0.000	0.000
23	A	23	MET	0	0.000	0.023	16.120	-0.005	-0.005	0.000	0.000	0.000	0.000
24	A	24	LEU	0	-0.011	-0.025	10.672	0.000	0.000	0.000	0.000	0.000	0.000
25	A	25	GLN	0	0.060	0.042	10.508	0.019	0.019	0.000	0.000	0.000	0.000
26	A	26	VAL	0	-0.041	-0.026	8.061	-0.117	-0.117	0.000	0.000	0.000	0.000
27	A	27	ASP	-1	-0.827	-0.929	5.406	0.252	0.252	0.000	0.000	0.000	0.000
28	A	28	PRO	0	-0.027	-0.030	6.599	-0.070	-0.070	0.000	0.000	0.000	0.000
29	A	29	ASP	-1	-0.890	-0.923	6.850	0.437	0.437	0.000	0.000	0.000	0.000
30	A	30	LEU	0	-0.084	-0.020	2.180	-1.275	-0.572	1.404	-0.577	-1.531	-0.007
31	A	31	PHE	0	0.027	-0.005	2.340	-2.290	-0.580	2.865	-1.205	-3.369	0.004
32	A	32	TRP	0	-0.034	-0.037	2.389	-1.892	0.189	4.730	-1.595	-5.216	-0.011
33	A	33	PHE	0	-0.021	-0.027	5.897	-0.526	-0.513	-0.001	-0.006	-0.006	0.000
34	A	34	ASN	0	0.031	0.032	8.110	-0.307	-0.307	0.000	0.000	0.000	0.000
35	A	35	GLY	0	0.067	0.031	9.912	-0.045	-0.045	0.000	0.000	0.000	0.000
36	A	36	HIS	0	-0.049	-0.023	11.982	-0.082	-0.082	0.000	0.000	0.000	0.000
37	A	37	PHE	0	-0.074	-0.035	6.877	-0.044	-0.044	0.000	0.000	0.000	0.000
38	A	38	THR	0	-0.010	-0.010	10.995	-0.126	-0.126	0.000	0.000	0.000	0.000
39	A	39	GLY	0	0.048	0.029	13.197	0.028	0.028	0.000	0.000	0.000	0.000
40	A	40	GLN	0	-0.079	-0.039	15.357	-0.034	-0.034	0.000	0.000	0.000	0.000
41	A	41	PRO	0	-0.009	0.007	11.779	-0.023	-0.023	0.000	0.000	0.000	0.000
42	A	42	LEU	0	0.027	-0.004	11.649	-0.054	-0.054	0.000	0.000	0.000	0.000
43	A	43	LEU	0	0.005	0.012	6.516	0.086	0.086	0.000	0.000	0.000	0.000
44	A	44	PRO	0	0.003	0.018	6.825	-0.061	-0.061	0.000	0.000	0.000	0.000
45	A	45	GLY	0	0.051	0.007	9.117	-0.125	-0.125	0.000	0.000	0.000	0.000
46	A	46	VAL	0	-0.001	-0.004	5.331	-0.017	-0.017	0.000	0.000	0.000	0.000
47	A	47	ALA	0	0.063	0.040	5.457	-0.179	-0.179	0.000	0.000	0.000	0.000
48	A	48	GLN	0	0.010	0.025	6.370	-0.045	-0.045	0.000	0.000	0.000	0.000
49	A	49	LEU	0	0.012	0.006	9.826	0.053	0.053	0.000	0.000	0.000	0.000
50	A	50	ASP	-1	-0.905	-0.957	4.809	-2.657	-2.600	-0.001	-0.005	-0.051	0.000
51	A	51	TRP	0	0.025	0.005	4.275	0.662	0.918	-0.001	-0.062	-0.193	0.000
52	A	52	VAL	0	-0.054	-0.018	8.437	0.200	0.200	0.000	0.000	0.000	0.000
53	A	53	MET	0	-0.019	-0.019	10.611	0.145	0.145	0.000	0.000	0.000	0.000
54	A	54	HIS	0	0.027	0.031	8.398	0.180	0.180	0.000	0.000	0.000	0.000
55	A	55	TYR	0	0.016	0.009	10.026	0.077	0.077	0.000	0.000	0.000	0.000
56	A	56	ALA	0	-0.001	-0.009	12.998	0.079	0.079	0.000	0.000	0.000	0.000
57	A	57	THR	0	-0.011	-0.008	13.678	0.057	0.057	0.000	0.000	0.000	0.000
58	A	58	THR	0	-0.031	-0.014	12.711	0.062	0.062	0.000	0.000	0.000	0.000
59	A	59	VAL	0	-0.040	-0.026	15.802	0.051	0.051	0.000	0.000	0.000	0.000
60	A	60	LEU	0	-0.103	-0.047	18.244	0.027	0.027	0.000	0.000	0.000	0.000
61	A	61	ALA	0	-0.011	0.000	19.116	0.022	0.022	0.000	0.000	0.000	0.000
62	A	62	GLN	0	0.033	0.011	18.904	-0.025	-0.025	0.000	0.000	0.000	0.000
63	A	63	GLY	0	-0.020	0.000	19.398	-0.009	-0.009	0.000	0.000	0.000	0.000
64	A	64	TRP	0	-0.022	-0.022	19.853	0.012	0.012	0.000	0.000	0.000	0.000
65	A	65	THR	0	0.033	0.008	16.128	-0.030	-0.030	0.000	0.000	0.000	0.000
66	A	66	PHE	0	0.040	0.000	14.511	0.025	0.025	0.000	0.000	0.000	0.000
67	A	67	LEU	0	-0.024	0.030	16.584	0.015	0.015	0.000	0.000	0.000	0.000
68	A	68	SER	0	-0.030	-0.038	18.544	0.005	0.005	0.000	0.000	0.000	0.000
69	A	69	ILE	0	0.022	0.024	15.762	-0.009	-0.009	0.000	0.000	0.000	0.000
70	A	70	GLU	-1	-0.912	-0.961	18.773	-0.163	-0.163	0.000	0.000	0.000	0.000
71	A	71	ASN	0	-0.035	-0.044	20.876	0.012	0.012	0.000	0.000	0.000	0.000
72	A	72	ILE	0	0.042	0.035	15.199	-0.017	-0.017	0.000	0.000	0.000	0.000
73	A	73	LYS	1	0.938	0.979	19.083	0.181	0.181	0.000	0.000	0.000	0.000
74	A	74	PHE	0	0.001	-0.003	13.730	-0.007	-0.007	0.000	0.000	0.000	0.000
75	A	75	GLN	0	-0.060	-0.039	18.556	0.017	0.017	0.000	0.000	0.000	0.000
76	A	76	GLN	0	0.015	0.003	19.123	0.018	0.018	0.000	0.000	0.000	0.000
77	A	77	PRO	0	-0.018	-0.003	16.047	-0.030	-0.030	0.000	0.000	0.000	0.000
78	A	78	ILE	0	0.033	0.024	11.689	0.015	0.015	0.000	0.000	0.000	0.000
79	A	79	LEU	0	-0.014	-0.009	12.406	0.006	0.006	0.000	0.000	0.000	0.000
80	A	80	PRO	0	0.027	0.002	10.410	-0.052	-0.052	0.000	0.000	0.000	0.000
81	A	81	GLY	0	0.010	0.008	10.585	0.028	0.028	0.000	0.000	0.000	0.000
82	A	82	LYS	1	0.838	0.941	12.451	0.080	0.080	0.000	0.000	0.000	0.000
83	A	83	THR	0	0.038	0.016	12.669	-0.034	-0.034	0.000	0.000	0.000	0.000
84	A	84	LEU	0	-0.068	-0.048	11.766	0.004	0.004	0.000	0.000	0.000	0.000
85	A	85	ARG	1	0.822	0.884	15.353	0.136	0.136	0.000	0.000	0.000	0.000
86	A	86	LEU	0	-0.035	-0.017	12.904	-0.019	-0.019	0.000	0.000	0.000	0.000
87	A	87	VAL	0	0.015	0.011	16.634	0.022	0.022	0.000	0.000	0.000	0.000
88	A	88	LEU	0	-0.017	-0.013	14.950	-0.020	-0.020	0.000	0.000	0.000	0.000
89	A	89	ILE	0	0.018	-0.004	19.243	0.026	0.026	0.000	0.000	0.000	0.000
90	A	90	TRP	0	0.010	-0.001	21.315	-0.012	-0.012	0.000	0.000	0.000	0.000
91	A	91	HIS	0	0.070	0.036	23.199	0.014	0.014	0.000	0.000	0.000	0.000
92	A	92	ALA	0	0.049	0.017	26.039	-0.005	-0.005	0.000	0.000	0.000	0.000
93	A	93	GLY	0	0.020	0.027	26.929	0.003	0.003	0.000	0.000	0.000	0.000
94	A	94	LYS	1	0.893	0.942	28.084	0.130	0.130	0.000	0.000	0.000	0.000
95	A	95	GLN	0	0.011	0.010	24.825	-0.001	-0.001	0.000	0.000	0.000	0.000
96	A	96	SER	0	-0.038	-0.021	23.238	-0.009	-0.009	0.000	0.000	0.000	0.000
97	A	97	LEU	0	-0.002	0.012	17.155	0.015	0.015	0.000	0.000	0.000	0.000
98	A	98	THR	0	-0.016	-0.012	20.342	-0.007	-0.007	0.000	0.000	0.000	0.000
99	A	99	PHE	0	0.007	0.011	16.211	-0.007	-0.007	0.000	0.000	0.000	0.000
100	A	100	SER	0	-0.022	-0.027	18.465	0.017	0.017	0.000	0.000	0.000	0.000
101	A	101	TYR	0	0.040	0.027	11.278	-0.018	-0.018	0.000	0.000	0.000	0.000
102	A	102	SER	0	-0.013	-0.014	17.000	0.021	0.021	0.000	0.000	0.000	0.000
103	A	103	ILE	0	-0.009	-0.004	16.386	-0.014	-0.014	0.000	0.000	0.000	0.000
104	A	104	LEU	0	-0.012	0.001	18.311	0.016	0.016	0.000	0.000	0.000	0.000
105	A	105	GLU	-1	-0.906	-0.968	19.491	-0.065	-0.065	0.000	0.000	0.000	0.000
106	A	106	GLY	0	-0.003	0.012	21.967	0.001	0.001	0.000	0.000	0.000	0.000
107	A	107	ASP	-1	-0.898	-0.957	25.042	-0.043	-0.043	0.000	0.000	0.000	0.000
108	A	108	THR	0	-0.130	-0.056	24.436	-0.007	-0.007	0.000	0.000	0.000	0.000
109	A	109	GLU	-1	-0.689	-0.827	22.233	-0.139	-0.139	0.000	0.000	0.000	0.000
110	A	110	ARG	1	0.904	0.972	20.098	0.101	0.101	0.000	0.000	0.000	0.000
111	A	111	THR	0	0.023	0.009	20.850	-0.010	-0.010	0.000	0.000	0.000	0.000
112	A	112	ALA	0	-0.017	-0.019	16.541	0.013	0.013	0.000	0.000	0.000	0.000
113	A	113	SER	0	-0.014	-0.039	15.044	0.008	0.008	0.000	0.000	0.000	0.000
114	A	114	SER	0	-0.025	0.005	18.262	0.003	0.003	0.000	0.000	0.000	0.000
115	A	115	GLY	0	0.037	0.004	19.027	-0.002	-0.002	0.000	0.000	0.000	0.000
116	A	116	LYS	1	0.868	0.964	19.895	0.180	0.180	0.000	0.000	0.000	0.000
117	A	117	ILE	0	-0.003	-0.008	15.171	-0.007	-0.007	0.000	0.000	0.000	0.000
118	A	118	LYS	1	0.872	0.951	19.381	0.211	0.211	0.000	0.000	0.000	0.000
119	A	119	LEU	0	-0.002	-0.006	17.387	-0.031	-0.031	0.000	0.000	0.000	0.000
120	A	120	THR	0	0.039	0.001	20.635	0.024	0.024	0.000	0.000	0.000	0.000
121	A	121	PRO	0	-0.010	-0.001	21.645	-0.017	-0.017	0.000	0.000	0.000	0.000
122	A	122	ILE	0	0.020	0.022	18.812	-0.005	-0.005	0.000	0.000	0.000	0.000
123	A	123	MET	0	-0.071	-0.029	22.360	0.018	0.018	0.000	0.000	0.000	0.000
124	A	124	GLU	-1	-0.950	-0.965	24.760	-0.161	-0.161	0.000	0.000	0.000	0.000

Top

Graph

Manual

About

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