FMO DATABASE

FMODB ID: YZ7R2

Calculation Name: 2J88-H-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 2J88

Chain ID: H

ChEMBL ID:

UniProt ID: Q08169

Base Structure: X-ray

Registration Date: 2023-06-26

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	166
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1500643.842764
FMO2-HF: Nuclear repulsion	1436904.84655
FMO2-HF: Total energy	-63738.996214
FMO2-MP2: Total energy	-63925.749028

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(H:2:VAL)

Summations of interaction energy for fragment #1(H:2: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.
-12.909	-3.119	9.522	-6.561	-12.747	-0.049

Interaction energy analysis for fragmet #1(H:2:VAL)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.038 / q_NPA : -0.017

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	H	4	LEU	0	0.054	0.025	2.850	-1.504	0.985	0.266	-1.082	-1.673	0.002
4	H	5	LYS	1	0.847	0.933	5.550	0.109	0.109	0.000	0.000	0.000	0.000
5	H	6	GLU	-1	-0.767	-0.885	9.357	-0.277	-0.277	0.000	0.000	0.000	0.000
6	H	7	SER	0	-0.035	-0.027	12.079	0.047	0.047	0.000	0.000	0.000	0.000
7	H	8	GLY	0	0.051	0.002	15.438	-0.018	-0.018	0.000	0.000	0.000	0.000
8	H	9	PRO	0	-0.014	0.006	18.874	0.013	0.013	0.000	0.000	0.000	0.000
9	H	10	GLY	0	0.023	0.027	21.833	0.009	0.009	0.000	0.000	0.000	0.000
10	H	11	ILE	0	-0.045	-0.028	22.935	-0.009	-0.009	0.000	0.000	0.000	0.000
11	H	12	LEU	0	-0.030	-0.014	25.151	0.005	0.005	0.000	0.000	0.000	0.000
12	H	13	GLN	0	0.029	0.010	28.280	-0.004	-0.004	0.000	0.000	0.000	0.000
13	H	14	PRO	0	0.038	0.011	30.889	-0.002	-0.002	0.000	0.000	0.000	0.000
14	H	15	SER	0	-0.074	-0.030	31.734	0.005	0.005	0.000	0.000	0.000	0.000
15	H	16	GLN	0	0.015	0.018	29.295	0.000	0.000	0.000	0.000	0.000	0.000
16	H	17	THR	0	-0.004	-0.019	25.032	-0.007	-0.007	0.000	0.000	0.000	0.000
17	H	18	LEU	0	0.001	0.007	20.848	0.008	0.008	0.000	0.000	0.000	0.000
18	H	19	SER	0	-0.019	-0.027	20.870	-0.003	-0.003	0.000	0.000	0.000	0.000
19	H	20	LEU	0	-0.034	0.006	16.043	0.012	0.012	0.000	0.000	0.000	0.000
20	H	21	THR	0	-0.006	-0.007	13.447	-0.005	-0.005	0.000	0.000	0.000	0.000
21	H	22	CYS	0	-0.094	-0.013	8.727	0.009	0.009	0.000	0.000	0.000	0.000
22	H	23	SER	0	0.030	0.010	9.290	0.032	0.032	0.000	0.000	0.000	0.000
23	H	24	PHE	0	0.042	0.014	4.179	-0.206	-0.085	-0.001	-0.015	-0.105	0.000
24	H	25	SER	0	-0.006	-0.002	4.356	-0.126	0.081	-0.001	-0.064	-0.142	0.000
25	H	26	GLY	0	0.024	0.006	2.356	-2.071	-0.446	3.137	-2.364	-2.398	-0.022
26	H	27	PHE	0	0.025	0.001	2.301	-4.167	-2.037	3.235	-1.461	-3.903	-0.014
27	H	28	SER	0	0.024	0.046	4.213	0.013	0.106	0.001	-0.040	-0.054	0.000
28	H	29	LEU	0	0.019	-0.001	7.397	-0.126	-0.126	0.000	0.000	0.000	0.000
29	H	30	SER	0	-0.044	-0.034	9.153	-0.028	-0.028	0.000	0.000	0.000	0.000
30	H	31	THR	0	-0.063	-0.009	7.417	0.031	0.031	0.000	0.000	0.000	0.000
31	H	32	SER	0	0.050	0.004	10.833	-0.046	-0.046	0.000	0.000	0.000	0.000
32	H	33	GLY	0	0.025	0.006	11.721	-0.044	-0.044	0.000	0.000	0.000	0.000
33	H	34	MET	0	-0.047	0.014	7.689	-0.040	-0.040	0.000	0.000	0.000	0.000
34	H	35	GLY	0	0.016	-0.006	9.213	0.105	0.105	0.000	0.000	0.000	0.000
35	H	35	VAL	0	-0.025	-0.010	7.782	-0.107	-0.107	0.000	0.000	0.000	0.000
36	H	35	SER	0	0.013	0.004	10.183	0.094	0.094	0.000	0.000	0.000	0.000
37	H	36	TRP	0	-0.008	-0.006	11.727	-0.031	-0.031	0.000	0.000	0.000	0.000
38	H	37	ILE	0	-0.010	-0.012	13.267	0.030	0.030	0.000	0.000	0.000	0.000
39	H	38	ARG	1	0.779	0.870	15.739	0.129	0.129	0.000	0.000	0.000	0.000
40	H	39	GLN	0	0.010	-0.004	18.205	-0.021	-0.021	0.000	0.000	0.000	0.000
41	H	40	PRO	0	0.030	0.020	20.319	0.009	0.009	0.000	0.000	0.000	0.000
42	H	41	SER	0	0.025	0.000	23.623	-0.010	-0.010	0.000	0.000	0.000	0.000
43	H	42	GLY	0	-0.011	-0.002	24.567	0.007	0.007	0.000	0.000	0.000	0.000
44	H	43	LYS	1	0.931	0.975	24.685	0.093	0.093	0.000	0.000	0.000	0.000
45	H	44	GLY	0	0.032	0.018	23.278	-0.011	-0.011	0.000	0.000	0.000	0.000
46	H	45	LEU	0	0.012	0.010	16.854	0.003	0.003	0.000	0.000	0.000	0.000
47	H	46	GLU	-1	-0.834	-0.898	19.708	-0.124	-0.124	0.000	0.000	0.000	0.000
48	H	47	TRP	0	-0.002	-0.002	16.354	0.003	0.003	0.000	0.000	0.000	0.000
49	H	48	LEU	0	-0.025	-0.004	17.827	0.026	0.026	0.000	0.000	0.000	0.000
50	H	49	ALA	0	0.022	-0.010	17.441	0.020	0.020	0.000	0.000	0.000	0.000
51	H	50	HIS	0	-0.015	0.000	12.935	-0.067	-0.067	0.000	0.000	0.000	0.000
52	H	51	ILE	0	-0.043	-0.013	13.194	0.040	0.040	0.000	0.000	0.000	0.000
53	H	52	TYR	0	0.046	0.028	12.990	-0.046	-0.046	0.000	0.000	0.000	0.000
54	H	53	TRP	0	0.084	0.020	12.179	0.020	0.020	0.000	0.000	0.000	0.000
55	H	54	ASP	-1	-0.904	-0.949	13.599	-0.139	-0.139	0.000	0.000	0.000	0.000
56	H	55	ASP	-1	-0.868	-0.925	16.494	-0.082	-0.082	0.000	0.000	0.000	0.000
57	H	56	ASP	-1	-0.765	-0.821	18.226	-0.146	-0.146	0.000	0.000	0.000	0.000
58	H	57	LYS	1	0.809	0.885	17.707	0.090	0.090	0.000	0.000	0.000	0.000
59	H	58	ARG	1	0.783	0.866	18.878	0.182	0.182	0.000	0.000	0.000	0.000
60	H	59	TYR	0	0.051	0.018	19.710	-0.010	-0.010	0.000	0.000	0.000	0.000
61	H	60	ASN	0	0.043	0.021	22.068	0.014	0.014	0.000	0.000	0.000	0.000
62	H	61	PRO	0	0.012	0.003	23.690	0.009	0.009	0.000	0.000	0.000	0.000
63	H	62	SER	0	-0.030	-0.016	26.159	0.013	0.013	0.000	0.000	0.000	0.000
64	H	63	LEU	0	0.016	-0.009	23.482	0.007	0.007	0.000	0.000	0.000	0.000
65	H	64	LYS	1	0.896	0.978	26.754	0.083	0.083	0.000	0.000	0.000	0.000
66	H	65	SER	0	0.041	0.008	26.050	0.002	0.002	0.000	0.000	0.000	0.000
67	H	66	ARG	1	0.756	0.864	26.864	0.080	0.080	0.000	0.000	0.000	0.000
68	H	67	LEU	0	0.003	0.014	21.014	0.002	0.002	0.000	0.000	0.000	0.000
69	H	68	THR	0	-0.035	-0.026	21.732	0.007	0.007	0.000	0.000	0.000	0.000
70	H	69	ILE	0	0.001	0.016	14.526	0.003	0.003	0.000	0.000	0.000	0.000
71	H	70	SER	0	-0.015	-0.018	17.111	0.007	0.007	0.000	0.000	0.000	0.000
72	H	71	LYS	1	0.871	0.933	13.147	0.113	0.113	0.000	0.000	0.000	0.000
73	H	72	ASP	-1	-0.799	-0.872	14.068	0.047	0.047	0.000	0.000	0.000	0.000
74	H	73	THR	0	0.032	-0.005	12.751	0.010	0.010	0.000	0.000	0.000	0.000
75	H	74	SER	0	-0.083	-0.045	12.828	0.030	0.030	0.000	0.000	0.000	0.000
76	H	75	ARG	1	0.877	0.928	14.354	-0.030	-0.030	0.000	0.000	0.000	0.000
77	H	76	ASN	0	-0.023	-0.011	6.950	-0.050	-0.050	0.000	0.000	0.000	0.000
78	H	77	GLN	0	0.008	-0.003	9.543	0.002	0.002	0.000	0.000	0.000	0.000
79	H	78	VAL	0	0.026	0.016	10.248	-0.019	-0.019	0.000	0.000	0.000	0.000
80	H	79	PHE	0	-0.064	-0.042	12.659	0.015	0.015	0.000	0.000	0.000	0.000
81	H	80	LEU	0	0.026	0.012	16.047	-0.017	-0.017	0.000	0.000	0.000	0.000
82	H	81	LYS	1	0.896	0.956	18.083	0.057	0.057	0.000	0.000	0.000	0.000
83	H	82	ILE	0	0.033	0.009	20.698	-0.010	-0.010	0.000	0.000	0.000	0.000
84	H	82	THR	0	0.005	0.011	24.061	0.006	0.006	0.000	0.000	0.000	0.000
85	H	82	SER	0	0.026	-0.006	27.766	-0.003	-0.003	0.000	0.000	0.000	0.000
86	H	82	VAL	0	-0.032	0.011	25.820	-0.004	-0.004	0.000	0.000	0.000	0.000
87	H	83	ASP	-1	-0.773	-0.881	28.707	-0.041	-0.041	0.000	0.000	0.000	0.000
88	H	84	THR	0	0.002	-0.021	29.012	-0.007	-0.007	0.000	0.000	0.000	0.000
89	H	85	ALA	0	-0.029	-0.010	28.957	-0.004	-0.004	0.000	0.000	0.000	0.000
90	H	86	ASP	-1	-0.777	-0.841	24.913	-0.091	-0.091	0.000	0.000	0.000	0.000
91	H	87	THR	0	0.000	0.014	24.031	-0.003	-0.003	0.000	0.000	0.000	0.000
92	H	88	ALA	0	-0.054	-0.028	21.083	-0.006	-0.006	0.000	0.000	0.000	0.000
93	H	89	THR	0	-0.011	0.014	16.866	0.014	0.014	0.000	0.000	0.000	0.000
94	H	90	TYR	0	-0.009	-0.044	16.216	-0.019	-0.019	0.000	0.000	0.000	0.000
95	H	91	TYR	0	0.028	0.000	11.643	0.014	0.014	0.000	0.000	0.000	0.000
96	H	93	THR	0	0.015	0.005	7.833	-0.029	-0.029	0.000	0.000	0.000	0.000
97	H	94	LEU	0	-0.022	-0.009	2.354	-0.158	-0.019	0.960	-0.232	-0.866	0.000
98	H	95	TYR	0	0.023	0.018	6.353	-0.164	-0.164	0.000	0.000	0.000	0.000
99	H	96	TYR	0	-0.002	-0.013	5.723	0.094	0.094	0.000	0.000	0.000	0.000
100	H	97	GLY	0	0.015	0.012	7.698	-0.097	-0.097	0.000	0.000	0.000	0.000
101	H	98	SER	0	-0.021	-0.020	10.304	-0.019	-0.019	0.000	0.000	0.000	0.000
102	H	99	VAL	0	-0.030	-0.002	6.113	0.049	0.049	0.000	0.000	0.000	0.000
103	H	100	ASP	-1	-0.815	-0.914	7.500	-0.876	-0.876	0.000	0.000	0.000	0.000
104	H	101	TYR	0	-0.020	-0.014	2.808	-3.911	-1.002	1.926	-1.303	-3.531	-0.015
105	H	102	TRP	0	-0.018	-0.025	5.379	0.280	0.357	-0.001	0.000	-0.075	0.000
106	H	103	GLY	0	0.009	0.011	6.833	-0.158	-0.158	0.000	0.000	0.000	0.000
107	H	104	GLN	0	-0.040	-0.032	8.116	0.103	0.103	0.000	0.000	0.000	0.000
108	H	105	GLY	0	0.013	0.014	11.401	0.022	0.022	0.000	0.000	0.000	0.000
109	H	106	THR	0	-0.060	-0.030	13.526	0.054	0.054	0.000	0.000	0.000	0.000
110	H	107	SER	0	-0.011	-0.005	16.268	-0.018	-0.018	0.000	0.000	0.000	0.000
111	H	108	VAL	0	-0.019	-0.014	19.611	0.014	0.014	0.000	0.000	0.000	0.000
112	H	109	THR	0	0.001	-0.002	22.191	-0.007	-0.007	0.000	0.000	0.000	0.000
113	H	110	VAL	0	0.003	0.003	25.938	0.006	0.006	0.000	0.000	0.000	0.000
114	H	111	SER	0	0.010	-0.016	28.507	0.000	0.000	0.000	0.000	0.000	0.000
115	H	112	SER	0	0.061	0.012	32.044	0.001	0.001	0.000	0.000	0.000	0.000
116	H	113	ALA	0	-0.034	0.016	34.196	0.004	0.004	0.000	0.000	0.000	0.000
117	H	114	LYS	1	0.929	0.967	34.271	0.003	0.003	0.000	0.000	0.000	0.000
118	H	115	THR	0	0.015	-0.013	32.233	-0.003	-0.003	0.000	0.000	0.000	0.000
119	H	116	THR	0	-0.070	-0.027	34.675	0.003	0.003	0.000	0.000	0.000	0.000
120	H	117	PRO	0	0.056	0.027	35.774	-0.002	-0.002	0.000	0.000	0.000	0.000
121	H	118	PRO	0	0.036	0.019	35.618	-0.001	-0.001	0.000	0.000	0.000	0.000
122	H	119	SER	0	-0.018	0.008	38.301	0.003	0.003	0.000	0.000	0.000	0.000
123	H	120	DVA	0	-0.012	-0.026	38.563	-0.002	-0.002	0.000	0.000	0.000	0.000
124	H	121	TYR	0	0.014	0.012	41.988	0.000	0.000	0.000	0.000	0.000	0.000
125	H	139	CYS	0	-0.046	-0.020	40.097	0.001	0.001	0.000	0.000	0.000	0.000
126	H	140	LEU	0	-0.023	-0.017	40.416	-0.003	-0.003	0.000	0.000	0.000	0.000
127	H	141	VAL	0	0.006	0.007	36.051	0.003	0.003	0.000	0.000	0.000	0.000
128	H	142	LYS	1	0.901	0.940	38.557	0.015	0.015	0.000	0.000	0.000	0.000
129	H	143	GLY	0	0.011	0.011	38.901	0.002	0.002	0.000	0.000	0.000	0.000
130	H	144	TYR	0	-0.032	-0.038	31.592	0.003	0.003	0.000	0.000	0.000	0.000
131	H	145	PHE	0	0.051	0.026	30.533	-0.005	-0.005	0.000	0.000	0.000	0.000
132	H	146	PRO	0	-0.003	0.008	28.336	0.005	0.005	0.000	0.000	0.000	0.000
133	H	147	GLU	-1	-0.803	-0.893	27.179	-0.034	-0.034	0.000	0.000	0.000	0.000
134	H	148	PRO	0	-0.045	-0.015	25.238	0.002	0.002	0.000	0.000	0.000	0.000
135	H	149	VAL	0	0.027	0.004	28.087	0.007	0.007	0.000	0.000	0.000	0.000
136	H	150	THR	0	-0.024	-0.010	29.374	-0.004	-0.004	0.000	0.000	0.000	0.000
137	H	151	VAL	0	0.009	0.002	31.292	0.003	0.003	0.000	0.000	0.000	0.000
138	H	152	THR	0	-0.011	-0.005	32.722	-0.003	-0.003	0.000	0.000	0.000	0.000
139	H	153	TRP	0	0.033	0.019	35.431	0.001	0.001	0.000	0.000	0.000	0.000
140	H	154	ASN	0	0.005	-0.004	38.795	0.001	0.001	0.000	0.000	0.000	0.000
141	H	155	SER	0	0.020	0.003	36.212	0.002	0.002	0.000	0.000	0.000	0.000
142	H	156	GLY	0	0.012	0.004	34.551	0.002	0.002	0.000	0.000	0.000	0.000
143	H	157	SER	0	-0.018	-0.007	35.468	0.000	0.000	0.000	0.000	0.000	0.000
144	H	158	LEU	0	-0.030	0.003	36.716	-0.003	-0.003	0.000	0.000	0.000	0.000
145	H	159	SER	0	0.004	0.002	32.246	0.003	0.003	0.000	0.000	0.000	0.000
146	H	160	SER	0	0.008	-0.022	31.279	0.000	0.000	0.000	0.000	0.000	0.000
147	H	161	GLY	0	-0.016	0.002	33.311	0.000	0.000	0.000	0.000	0.000	0.000
148	H	162	VAL	0	0.027	0.015	34.965	-0.004	-0.004	0.000	0.000	0.000	0.000
149	H	163	HIS	1	0.892	0.938	34.875	0.029	0.029	0.000	0.000	0.000	0.000
150	H	164	THR	0	0.025	0.026	32.011	0.005	0.005	0.000	0.000	0.000	0.000
151	H	165	PHE	0	-0.040	-0.014	32.929	-0.004	-0.004	0.000	0.000	0.000	0.000
152	H	166	PRO	0	0.004	0.002	30.082	0.002	0.002	0.000	0.000	0.000	0.000
153	H	167	ALA	0	0.028	0.021	31.359	0.002	0.002	0.000	0.000	0.000	0.000
154	H	168	VAL	0	-0.031	-0.013	32.284	-0.006	-0.006	0.000	0.000	0.000	0.000
155	H	169	LEU	0	-0.004	-0.003	31.744	0.004	0.004	0.000	0.000	0.000	0.000
156	H	170	GLN	0	0.011	0.000	35.506	0.001	0.001	0.000	0.000	0.000	0.000
157	H	171	SER	0	-0.009	-0.008	39.196	0.001	0.001	0.000	0.000	0.000	0.000
158	H	172	ASP	-1	-0.898	-0.938	36.055	-0.028	-0.028	0.000	0.000	0.000	0.000
159	H	173	LEU	0	-0.050	-0.022	35.586	0.002	0.002	0.000	0.000	0.000	0.000
160	H	174	TYR	0	0.012	0.012	28.798	-0.001	-0.001	0.000	0.000	0.000	0.000
161	H	175	THR	0	-0.050	-0.033	35.088	0.005	0.005	0.000	0.000	0.000	0.000
162	H	176	LEU	0	0.022	0.013	32.888	-0.004	-0.004	0.000	0.000	0.000	0.000
163	H	177	SER	0	0.009	0.005	36.780	0.003	0.003	0.000	0.000	0.000	0.000
164	H	178	SER	0	0.051	0.019	35.924	-0.003	-0.003	0.000	0.000	0.000	0.000
165	H	179	SER	0	-0.029	-0.011	38.232	0.001	0.001	0.000	0.000	0.000	0.000
166	H	180	VAL	0	0.044	0.024	39.163	-0.001	-0.001	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(H:2:VAL)