FMO DATABASE

FMODB ID: V5ZY1

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

Total energy (hartree)

FMO2-HF: Electronic energy	-1503878.151852
FMO2-HF: Nuclear repulsion	1440138.917414
FMO2-HF: Total energy	-63739.234437
FMO2-MP2: Total energy	-63926.075096

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.
-13.236	-3.633	9.774	-6.194	-13.181	-0.044

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 : -0.046 / q_NPA : -0.020

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	0.023	3.076	-1.098	1.036	0.109	-0.901	-1.342	0.002
4	H	5	LYS	1	0.827	0.926	5.737	0.145	0.145	0.000	0.000	0.000	0.000
5	H	6	GLU	-1	-0.749	-0.872	9.584	-0.261	-0.261	0.000	0.000	0.000	0.000
6	H	7	SER	0	-0.038	-0.030	12.361	0.047	0.047	0.000	0.000	0.000	0.000
7	H	8	GLY	0	0.067	0.007	15.821	-0.017	-0.017	0.000	0.000	0.000	0.000
8	H	9	PRO	0	-0.005	0.009	19.325	0.011	0.011	0.000	0.000	0.000	0.000
9	H	10	GLY	0	0.031	0.039	21.895	0.007	0.007	0.000	0.000	0.000	0.000
10	H	11	ILE	0	-0.064	-0.037	23.193	-0.010	-0.010	0.000	0.000	0.000	0.000
11	H	12	LEU	0	-0.032	-0.012	25.574	0.006	0.006	0.000	0.000	0.000	0.000
12	H	13	GLN	0	0.043	0.019	28.695	-0.005	-0.005	0.000	0.000	0.000	0.000
13	H	14	PRO	0	0.062	0.021	30.971	-0.002	-0.002	0.000	0.000	0.000	0.000
14	H	15	SER	0	-0.083	-0.035	32.511	0.006	0.006	0.000	0.000	0.000	0.000
15	H	16	GLN	0	0.032	0.021	29.803	0.000	0.000	0.000	0.000	0.000	0.000
16	H	17	THR	0	-0.001	-0.008	25.761	-0.006	-0.006	0.000	0.000	0.000	0.000
17	H	18	LEU	0	0.018	0.017	21.382	0.008	0.008	0.000	0.000	0.000	0.000
18	H	19	SER	0	-0.035	-0.032	21.475	-0.001	-0.001	0.000	0.000	0.000	0.000
19	H	20	LEU	0	-0.025	0.005	16.482	0.008	0.008	0.000	0.000	0.000	0.000
20	H	21	THR	0	-0.017	-0.012	13.809	0.003	0.003	0.000	0.000	0.000	0.000
21	H	22	CYS	0	-0.096	-0.022	9.026	0.013	0.013	0.000	0.000	0.000	0.000
22	H	23	SER	0	0.028	0.014	9.696	0.031	0.031	0.000	0.000	0.000	0.000
23	H	24	PHE	0	0.051	0.017	4.266	-0.218	-0.122	-0.001	-0.009	-0.085	0.000
24	H	25	SER	0	-0.015	-0.013	4.442	-0.135	0.030	-0.001	-0.040	-0.124	0.000
25	H	26	GLY	0	0.030	0.017	2.424	-1.920	-0.228	2.682	-2.192	-2.182	-0.018
26	H	27	PHE	0	0.017	0.007	2.328	-4.334	-2.083	2.766	-1.284	-3.733	-0.010
27	H	28	SER	0	0.015	0.026	4.027	-0.056	0.054	0.003	-0.047	-0.067	0.000
28	H	29	LEU	0	-0.008	-0.005	7.576	-0.127	-0.127	0.000	0.000	0.000	0.000
29	H	30	SER	0	-0.010	-0.015	9.177	-0.041	-0.041	0.000	0.000	0.000	0.000
30	H	31	THR	0	-0.050	-0.004	7.485	0.007	0.007	0.000	0.000	0.000	0.000
31	H	32	SER	0	0.048	0.005	10.755	-0.048	-0.048	0.000	0.000	0.000	0.000
32	H	33	GLY	0	0.039	0.011	11.801	-0.033	-0.033	0.000	0.000	0.000	0.000
33	H	34	MET	0	-0.090	-0.009	8.007	-0.054	-0.054	0.000	0.000	0.000	0.000
34	H	35	GLY	0	0.018	0.004	9.045	0.101	0.101	0.000	0.000	0.000	0.000
35	H	35	VAL	0	-0.016	-0.006	7.817	-0.114	-0.114	0.000	0.000	0.000	0.000
36	H	35	SER	0	0.020	0.004	10.153	0.093	0.093	0.000	0.000	0.000	0.000
37	H	36	TRP	0	-0.016	-0.006	11.659	-0.026	-0.026	0.000	0.000	0.000	0.000
38	H	37	ILE	0	-0.005	-0.006	13.226	0.023	0.023	0.000	0.000	0.000	0.000
39	H	38	ARG	1	0.748	0.842	16.006	0.124	0.124	0.000	0.000	0.000	0.000
40	H	39	GLN	0	0.032	0.012	18.430	-0.028	-0.028	0.000	0.000	0.000	0.000
41	H	40	PRO	0	0.037	0.022	20.555	0.009	0.009	0.000	0.000	0.000	0.000
42	H	41	SER	0	0.010	-0.004	23.953	-0.011	-0.011	0.000	0.000	0.000	0.000
43	H	42	GLY	0	0.003	0.007	24.900	0.007	0.007	0.000	0.000	0.000	0.000
44	H	43	LYS	1	0.925	0.974	24.799	0.095	0.095	0.000	0.000	0.000	0.000
45	H	44	GLY	0	0.044	0.023	22.879	-0.010	-0.010	0.000	0.000	0.000	0.000
46	H	45	LEU	0	-0.002	0.004	16.408	0.006	0.006	0.000	0.000	0.000	0.000
47	H	46	GLU	-1	-0.822	-0.883	19.709	-0.122	-0.122	0.000	0.000	0.000	0.000
48	H	47	TRP	0	-0.002	-0.003	16.144	0.007	0.007	0.000	0.000	0.000	0.000
49	H	48	LEU	0	-0.030	-0.006	17.932	0.027	0.027	0.000	0.000	0.000	0.000
50	H	49	ALA	0	0.035	0.000	17.464	0.021	0.021	0.000	0.000	0.000	0.000
51	H	50	HIS	0	-0.021	0.001	12.716	-0.070	-0.070	0.000	0.000	0.000	0.000
52	H	51	ILE	0	-0.048	-0.015	13.107	0.038	0.038	0.000	0.000	0.000	0.000
53	H	52	TYR	0	0.040	0.025	12.886	-0.045	-0.045	0.000	0.000	0.000	0.000
54	H	53	TRP	0	0.083	0.017	12.146	0.022	0.022	0.000	0.000	0.000	0.000
55	H	54	ASP	-1	-0.891	-0.949	13.556	-0.108	-0.108	0.000	0.000	0.000	0.000
56	H	55	ASP	-1	-0.829	-0.891	16.567	-0.048	-0.048	0.000	0.000	0.000	0.000
57	H	56	ASP	-1	-0.775	-0.842	17.855	-0.134	-0.134	0.000	0.000	0.000	0.000
58	H	57	LYS	1	0.783	0.873	17.606	0.070	0.070	0.000	0.000	0.000	0.000
59	H	58	ARG	1	0.794	0.871	18.811	0.168	0.168	0.000	0.000	0.000	0.000
60	H	59	TYR	0	0.052	0.020	19.587	-0.008	-0.008	0.000	0.000	0.000	0.000
61	H	60	ASN	0	0.031	0.013	21.993	0.012	0.012	0.000	0.000	0.000	0.000
62	H	61	PRO	0	0.007	-0.002	23.545	0.010	0.010	0.000	0.000	0.000	0.000
63	H	62	SER	0	-0.027	-0.010	26.190	0.013	0.013	0.000	0.000	0.000	0.000
64	H	63	LEU	0	0.018	-0.005	23.738	0.008	0.008	0.000	0.000	0.000	0.000
65	H	64	LYS	1	0.895	0.974	27.032	0.078	0.078	0.000	0.000	0.000	0.000
66	H	65	SER	0	0.035	-0.002	26.729	0.002	0.002	0.000	0.000	0.000	0.000
67	H	66	ARG	1	0.748	0.850	27.129	0.071	0.071	0.000	0.000	0.000	0.000
68	H	67	LEU	0	-0.014	0.018	21.376	0.004	0.004	0.000	0.000	0.000	0.000
69	H	68	THR	0	-0.012	-0.019	21.959	0.008	0.008	0.000	0.000	0.000	0.000
70	H	69	ILE	0	-0.007	0.010	14.743	0.002	0.002	0.000	0.000	0.000	0.000
71	H	70	SER	0	-0.004	-0.008	17.296	0.003	0.003	0.000	0.000	0.000	0.000
72	H	71	LYS	1	0.833	0.915	12.757	0.072	0.072	0.000	0.000	0.000	0.000
73	H	72	ASP	-1	-0.793	-0.865	14.156	0.099	0.099	0.000	0.000	0.000	0.000
74	H	73	THR	0	0.012	-0.011	12.531	0.022	0.022	0.000	0.000	0.000	0.000
75	H	74	SER	0	-0.071	-0.040	13.086	0.042	0.042	0.000	0.000	0.000	0.000
76	H	75	ARG	1	0.873	0.921	14.600	-0.065	-0.065	0.000	0.000	0.000	0.000
77	H	76	ASN	0	-0.018	-0.003	7.022	-0.077	-0.077	0.000	0.000	0.000	0.000
78	H	77	GLN	0	0.017	-0.001	9.667	0.001	0.001	0.000	0.000	0.000	0.000
79	H	78	VAL	0	0.034	0.017	10.100	-0.020	-0.020	0.000	0.000	0.000	0.000
80	H	79	PHE	0	-0.051	-0.030	12.631	0.005	0.005	0.000	0.000	0.000	0.000
81	H	80	LEU	0	0.020	0.014	15.954	-0.018	-0.018	0.000	0.000	0.000	0.000
82	H	81	LYS	1	0.857	0.931	18.290	0.048	0.048	0.000	0.000	0.000	0.000
83	H	82	ILE	0	0.044	0.013	20.959	-0.012	-0.012	0.000	0.000	0.000	0.000
84	H	82	THR	0	0.015	0.009	24.402	0.005	0.005	0.000	0.000	0.000	0.000
85	H	82	SER	0	0.021	0.000	28.117	-0.004	-0.004	0.000	0.000	0.000	0.000
86	H	82	VAL	0	-0.019	0.016	26.262	-0.005	-0.005	0.000	0.000	0.000	0.000
87	H	83	ASP	-1	-0.768	-0.897	29.117	-0.042	-0.042	0.000	0.000	0.000	0.000
88	H	84	THR	0	-0.016	-0.007	29.272	-0.006	-0.006	0.000	0.000	0.000	0.000
89	H	85	ALA	0	-0.029	-0.010	29.378	-0.005	-0.005	0.000	0.000	0.000	0.000
90	H	86	ASP	-1	-0.772	-0.841	25.288	-0.086	-0.086	0.000	0.000	0.000	0.000
91	H	87	THR	0	-0.010	0.010	24.435	-0.004	-0.004	0.000	0.000	0.000	0.000
92	H	88	ALA	0	-0.052	-0.025	21.306	-0.006	-0.006	0.000	0.000	0.000	0.000
93	H	89	THR	0	-0.013	0.012	17.078	0.016	0.016	0.000	0.000	0.000	0.000
94	H	90	TYR	0	0.003	-0.035	16.657	-0.016	-0.016	0.000	0.000	0.000	0.000
95	H	91	TYR	0	0.011	-0.018	12.012	0.013	0.013	0.000	0.000	0.000	0.000
96	H	93	THR	0	0.017	0.009	7.773	-0.042	-0.042	0.000	0.000	0.000	0.000
97	H	94	LEU	0	-0.016	-0.008	2.478	-0.168	0.024	0.875	-0.195	-0.872	0.000
98	H	95	TYR	0	0.009	0.009	5.908	-0.225	-0.225	0.000	0.000	0.000	0.000
99	H	96	TYR	0	0.006	-0.019	5.521	0.122	0.122	0.000	0.000	0.000	0.000
100	H	97	GLY	0	0.028	0.022	7.458	-0.116	-0.116	0.000	0.000	0.000	0.000
101	H	98	SER	0	-0.036	-0.023	10.005	-0.005	-0.005	0.000	0.000	0.000	0.000
102	H	99	VAL	0	-0.026	-0.005	6.016	0.038	0.038	0.000	0.000	0.000	0.000
103	H	100	ASP	-1	-0.806	-0.908	6.961	-0.925	-0.925	0.000	0.000	0.000	0.000
104	H	101	TYR	0	-0.006	-0.006	2.727	-4.405	-1.530	3.342	-1.525	-4.691	-0.018
105	H	102	TRP	0	-0.031	-0.037	4.986	0.335	0.423	-0.001	-0.001	-0.085	0.000
106	H	103	GLY	0	-0.004	0.008	6.294	-0.192	-0.192	0.000	0.000	0.000	0.000
107	H	104	GLN	0	-0.043	-0.047	8.284	0.066	0.066	0.000	0.000	0.000	0.000
108	H	105	GLY	0	0.005	0.012	11.683	0.040	0.040	0.000	0.000	0.000	0.000
109	H	106	THR	0	-0.048	-0.027	14.067	0.047	0.047	0.000	0.000	0.000	0.000
110	H	107	SER	0	0.002	0.006	16.714	-0.015	-0.015	0.000	0.000	0.000	0.000
111	H	108	VAL	0	-0.011	-0.014	20.173	0.013	0.013	0.000	0.000	0.000	0.000
112	H	109	THR	0	-0.010	-0.004	22.730	-0.008	-0.008	0.000	0.000	0.000	0.000
113	H	110	VAL	0	-0.006	-0.007	26.402	0.006	0.006	0.000	0.000	0.000	0.000
114	H	111	SER	0	0.039	0.000	28.786	-0.001	-0.001	0.000	0.000	0.000	0.000
115	H	112	SER	0	0.034	0.007	32.320	0.002	0.002	0.000	0.000	0.000	0.000
116	H	113	ALA	0	-0.023	0.013	34.409	0.004	0.004	0.000	0.000	0.000	0.000
117	H	114	LYS	1	0.905	0.952	34.438	0.003	0.003	0.000	0.000	0.000	0.000
118	H	115	THR	0	0.013	-0.009	33.105	-0.003	-0.003	0.000	0.000	0.000	0.000
119	H	116	THR	0	-0.055	-0.016	35.188	0.003	0.003	0.000	0.000	0.000	0.000
120	H	117	PRO	0	0.054	0.026	36.273	-0.002	-0.002	0.000	0.000	0.000	0.000
121	H	118	PRO	0	0.005	0.012	35.838	-0.001	-0.001	0.000	0.000	0.000	0.000
122	H	119	SER	0	0.000	0.005	38.498	0.003	0.003	0.000	0.000	0.000	0.000
123	H	120	DVA	0	-0.022	-0.019	38.580	-0.003	-0.003	0.000	0.000	0.000	0.000
124	H	121	TYR	0	0.018	0.015	41.984	0.000	0.000	0.000	0.000	0.000	0.000
125	H	139	CYS	0	-0.046	-0.025	40.241	0.001	0.001	0.000	0.000	0.000	0.000
126	H	140	LEU	0	-0.018	-0.007	40.353	-0.003	-0.003	0.000	0.000	0.000	0.000
127	H	141	VAL	0	0.007	0.006	36.195	0.003	0.003	0.000	0.000	0.000	0.000
128	H	142	LYS	1	0.883	0.919	38.977	0.019	0.019	0.000	0.000	0.000	0.000
129	H	143	GLY	0	0.027	0.025	39.350	0.003	0.003	0.000	0.000	0.000	0.000
130	H	144	TYR	0	-0.034	-0.042	31.954	0.003	0.003	0.000	0.000	0.000	0.000
131	H	145	PHE	0	0.050	0.025	30.744	-0.005	-0.005	0.000	0.000	0.000	0.000
132	H	146	PRO	0	0.009	0.011	28.487	0.005	0.005	0.000	0.000	0.000	0.000
133	H	147	GLU	-1	-0.797	-0.890	27.594	-0.038	-0.038	0.000	0.000	0.000	0.000
134	H	148	PRO	0	-0.052	-0.016	25.225	0.001	0.001	0.000	0.000	0.000	0.000
135	H	149	VAL	0	0.033	0.014	28.086	0.008	0.008	0.000	0.000	0.000	0.000
136	H	150	THR	0	-0.043	-0.041	29.517	-0.003	-0.003	0.000	0.000	0.000	0.000
137	H	151	VAL	0	0.012	0.008	31.681	0.003	0.003	0.000	0.000	0.000	0.000
138	H	152	THR	0	-0.010	-0.002	33.086	-0.004	-0.004	0.000	0.000	0.000	0.000
139	H	153	TRP	0	0.027	0.017	35.805	0.002	0.002	0.000	0.000	0.000	0.000
140	H	154	ASN	0	0.022	-0.005	39.081	0.001	0.001	0.000	0.000	0.000	0.000
141	H	155	SER	0	0.023	0.000	36.762	0.002	0.002	0.000	0.000	0.000	0.000
142	H	156	GLY	0	-0.006	0.004	35.262	0.002	0.002	0.000	0.000	0.000	0.000
143	H	157	SER	0	-0.036	-0.013	36.063	-0.001	-0.001	0.000	0.000	0.000	0.000
144	H	158	LEU	0	-0.031	0.000	37.207	-0.003	-0.003	0.000	0.000	0.000	0.000
145	H	159	SER	0	0.017	0.007	32.794	0.002	0.002	0.000	0.000	0.000	0.000
146	H	160	SER	0	0.021	-0.018	31.822	0.001	0.001	0.000	0.000	0.000	0.000
147	H	161	GLY	0	-0.017	0.011	33.878	0.000	0.000	0.000	0.000	0.000	0.000
148	H	162	VAL	0	0.023	0.012	35.129	-0.004	-0.004	0.000	0.000	0.000	0.000
149	H	163	HIS	1	0.886	0.936	35.196	0.037	0.037	0.000	0.000	0.000	0.000
150	H	164	THR	0	0.037	0.040	32.025	0.007	0.007	0.000	0.000	0.000	0.000
151	H	165	PHE	0	-0.032	-0.006	32.967	-0.005	-0.005	0.000	0.000	0.000	0.000
152	H	166	PRO	0	0.008	0.002	30.142	0.002	0.002	0.000	0.000	0.000	0.000
153	H	167	ALA	0	0.019	0.017	31.177	0.003	0.003	0.000	0.000	0.000	0.000
154	H	168	VAL	0	-0.036	-0.019	32.216	-0.005	-0.005	0.000	0.000	0.000	0.000
155	H	169	LEU	0	0.004	0.003	32.240	0.004	0.004	0.000	0.000	0.000	0.000
156	H	170	GLN	0	0.004	-0.006	35.835	0.000	0.000	0.000	0.000	0.000	0.000
157	H	171	SER	0	-0.017	-0.015	39.535	0.001	0.001	0.000	0.000	0.000	0.000
158	H	172	ASP	-1	-0.896	-0.937	36.103	-0.028	-0.028	0.000	0.000	0.000	0.000
159	H	173	LEU	0	-0.036	-0.010	35.668	0.001	0.001	0.000	0.000	0.000	0.000
160	H	174	TYR	0	0.010	0.001	29.210	-0.002	-0.002	0.000	0.000	0.000	0.000
161	H	175	THR	0	-0.036	-0.028	35.480	0.006	0.006	0.000	0.000	0.000	0.000
162	H	176	LEU	0	0.022	0.027	32.694	-0.004	-0.004	0.000	0.000	0.000	0.000
163	H	177	SER	0	0.014	0.000	36.522	0.003	0.003	0.000	0.000	0.000	0.000
164	H	178	SER	0	0.045	0.010	35.993	-0.003	-0.003	0.000	0.000	0.000	0.000
165	H	179	SER	0	-0.035	-0.021	38.221	0.001	0.001	0.000	0.000	0.000	0.000
166	H	180	VAL	0	0.047	0.025	39.297	-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)