FMO DATABASE

FMODB ID: 52GGZ

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

Total energy (hartree)

FMO2-HF: Electronic energy	-1500038.734827
FMO2-HF: Nuclear repulsion	1436300.110743
FMO2-HF: Total energy	-63738.624084
FMO2-MP2: Total energy	-63925.361533

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.
-12.727	-2.91	8.909	-6.501	-12.225	-0.05

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 : -0.032 / 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	0.050	0.023	2.771	-1.320	1.081	0.226	-0.997	-1.630	0.002
4	H	5	LYS	1	0.848	0.936	5.484	0.210	0.210	0.000	0.000	0.000	0.000
5	H	6	GLU	-1	-0.756	-0.876	9.287	-0.364	-0.364	0.000	0.000	0.000	0.000
6	H	7	SER	0	-0.038	-0.023	12.024	0.049	0.049	0.000	0.000	0.000	0.000
7	H	8	GLY	0	0.036	-0.006	15.371	-0.018	-0.018	0.000	0.000	0.000	0.000
8	H	9	PRO	0	-0.007	0.014	18.814	0.013	0.013	0.000	0.000	0.000	0.000
9	H	10	GLY	0	0.025	0.025	21.780	0.010	0.010	0.000	0.000	0.000	0.000
10	H	11	ILE	0	-0.047	-0.029	22.883	-0.009	-0.009	0.000	0.000	0.000	0.000
11	H	12	LEU	0	-0.031	-0.009	25.356	0.005	0.005	0.000	0.000	0.000	0.000
12	H	13	GLN	0	0.025	0.008	28.232	-0.002	-0.002	0.000	0.000	0.000	0.000
13	H	14	PRO	0	0.044	0.020	30.848	-0.002	-0.002	0.000	0.000	0.000	0.000
14	H	15	SER	0	-0.083	-0.033	31.711	0.006	0.006	0.000	0.000	0.000	0.000
15	H	16	GLN	0	0.016	0.013	29.075	-0.001	-0.001	0.000	0.000	0.000	0.000
16	H	17	THR	0	-0.008	-0.018	24.935	-0.006	-0.006	0.000	0.000	0.000	0.000
17	H	18	LEU	0	0.000	0.005	20.637	0.007	0.007	0.000	0.000	0.000	0.000
18	H	19	SER	0	-0.025	-0.032	20.822	-0.002	-0.002	0.000	0.000	0.000	0.000
19	H	20	LEU	0	-0.033	0.004	16.006	0.011	0.011	0.000	0.000	0.000	0.000
20	H	21	THR	0	0.002	-0.003	13.274	-0.002	-0.002	0.000	0.000	0.000	0.000
21	H	22	CYS	0	-0.107	-0.027	8.682	0.009	0.009	0.000	0.000	0.000	0.000
22	H	23	SER	0	0.021	0.003	9.183	0.050	0.050	0.000	0.000	0.000	0.000
23	H	24	PHE	0	0.044	0.016	3.996	-0.262	-0.104	0.000	-0.023	-0.134	0.000
24	H	25	SER	0	-0.008	0.001	4.178	-0.081	0.143	-0.001	-0.069	-0.155	0.000
25	H	26	GLY	0	0.022	0.004	2.345	-2.304	-0.668	3.347	-2.454	-2.529	-0.023
26	H	27	PHE	0	0.022	-0.005	2.379	-4.255	-2.037	2.967	-1.463	-3.721	-0.015
27	H	28	SER	0	-0.007	0.025	4.170	-0.024	0.085	0.001	-0.044	-0.067	0.000
28	H	29	LEU	0	0.030	0.003	7.499	-0.119	-0.119	0.000	0.000	0.000	0.000
29	H	30	SER	0	-0.069	-0.046	9.180	-0.011	-0.011	0.000	0.000	0.000	0.000
30	H	31	THR	0	-0.056	-0.003	7.404	0.039	0.039	0.000	0.000	0.000	0.000
31	H	32	SER	0	0.054	0.004	10.770	-0.052	-0.052	0.000	0.000	0.000	0.000
32	H	33	GLY	0	0.035	0.007	11.683	-0.038	-0.038	0.000	0.000	0.000	0.000
33	H	34	MET	0	-0.055	0.012	7.307	-0.031	-0.031	0.000	0.000	0.000	0.000
34	H	35	GLY	0	0.032	0.005	9.231	0.102	0.102	0.000	0.000	0.000	0.000
35	H	35	VAL	0	-0.017	-0.008	7.859	-0.117	-0.117	0.000	0.000	0.000	0.000
36	H	35	SER	0	0.027	0.009	10.154	0.101	0.101	0.000	0.000	0.000	0.000
37	H	36	TRP	0	-0.007	0.001	11.739	-0.043	-0.043	0.000	0.000	0.000	0.000
38	H	37	ILE	0	0.006	-0.009	13.168	0.032	0.032	0.000	0.000	0.000	0.000
39	H	38	ARG	1	0.804	0.924	15.748	0.144	0.144	0.000	0.000	0.000	0.000
40	H	39	GLN	0	-0.008	-0.018	18.217	-0.019	-0.019	0.000	0.000	0.000	0.000
41	H	40	PRO	0	0.025	0.020	20.338	0.008	0.008	0.000	0.000	0.000	0.000
42	H	41	SER	0	0.042	0.002	23.634	-0.010	-0.010	0.000	0.000	0.000	0.000
43	H	42	GLY	0	-0.019	-0.002	24.596	0.009	0.009	0.000	0.000	0.000	0.000
44	H	43	LYS	1	0.934	0.976	24.719	0.109	0.109	0.000	0.000	0.000	0.000
45	H	44	GLY	0	0.042	0.028	23.324	-0.012	-0.012	0.000	0.000	0.000	0.000
46	H	45	LEU	0	0.008	0.006	16.866	0.002	0.002	0.000	0.000	0.000	0.000
47	H	46	GLU	-1	-0.869	-0.936	19.756	-0.137	-0.137	0.000	0.000	0.000	0.000
48	H	47	TRP	0	-0.002	-0.006	16.109	0.004	0.004	0.000	0.000	0.000	0.000
49	H	48	LEU	0	-0.032	-0.008	17.525	0.029	0.029	0.000	0.000	0.000	0.000
50	H	49	ALA	0	0.021	-0.011	17.454	0.023	0.023	0.000	0.000	0.000	0.000
51	H	50	HIS	0	-0.021	-0.004	13.193	-0.066	-0.066	0.000	0.000	0.000	0.000
52	H	51	ILE	0	-0.044	-0.015	13.089	0.042	0.042	0.000	0.000	0.000	0.000
53	H	52	TYR	0	0.031	0.021	12.952	-0.051	-0.051	0.000	0.000	0.000	0.000
54	H	53	TRP	0	0.052	0.014	12.176	0.018	0.018	0.000	0.000	0.000	0.000
55	H	54	ASP	-1	-0.916	-0.957	13.530	-0.135	-0.135	0.000	0.000	0.000	0.000
56	H	55	ASP	-1	-0.920	-0.973	16.412	-0.092	-0.092	0.000	0.000	0.000	0.000
57	H	56	ASP	-1	-0.810	-0.868	18.142	-0.150	-0.150	0.000	0.000	0.000	0.000
58	H	57	LYS	1	0.800	0.885	17.665	0.101	0.101	0.000	0.000	0.000	0.000
59	H	58	ARG	1	0.824	0.917	18.847	0.192	0.192	0.000	0.000	0.000	0.000
60	H	59	TYR	0	0.060	0.025	19.690	-0.011	-0.011	0.000	0.000	0.000	0.000
61	H	60	ASN	0	0.043	0.022	22.134	0.017	0.017	0.000	0.000	0.000	0.000
62	H	61	PRO	0	0.013	0.006	23.695	0.009	0.009	0.000	0.000	0.000	0.000
63	H	62	SER	0	-0.035	-0.019	26.148	0.014	0.014	0.000	0.000	0.000	0.000
64	H	63	LEU	0	0.026	-0.006	23.482	0.007	0.007	0.000	0.000	0.000	0.000
65	H	64	LYS	1	0.885	0.979	26.763	0.091	0.091	0.000	0.000	0.000	0.000
66	H	65	SER	0	0.038	-0.005	26.165	0.003	0.003	0.000	0.000	0.000	0.000
67	H	66	ARG	1	0.788	0.909	26.833	0.093	0.093	0.000	0.000	0.000	0.000
68	H	67	LEU	0	0.004	0.011	21.413	0.001	0.001	0.000	0.000	0.000	0.000
69	H	68	THR	0	-0.028	-0.018	22.022	0.009	0.009	0.000	0.000	0.000	0.000
70	H	69	ILE	0	0.011	0.016	14.448	0.001	0.001	0.000	0.000	0.000	0.000
71	H	70	SER	0	-0.012	-0.020	17.115	0.009	0.009	0.000	0.000	0.000	0.000
72	H	71	LYS	1	0.971	0.993	13.240	0.108	0.108	0.000	0.000	0.000	0.000
73	H	72	ASP	-1	-0.802	-0.873	14.040	0.032	0.032	0.000	0.000	0.000	0.000
74	H	73	THR	0	0.029	-0.006	12.730	0.004	0.004	0.000	0.000	0.000	0.000
75	H	74	SER	0	-0.079	-0.048	12.774	0.026	0.026	0.000	0.000	0.000	0.000
76	H	75	ARG	1	0.867	0.924	14.260	-0.005	-0.005	0.000	0.000	0.000	0.000
77	H	76	ASN	0	0.033	0.022	8.847	-0.051	-0.051	0.000	0.000	0.000	0.000
78	H	77	GLN	0	0.009	0.003	9.456	-0.012	-0.012	0.000	0.000	0.000	0.000
79	H	78	VAL	0	0.022	0.016	10.281	-0.011	-0.011	0.000	0.000	0.000	0.000
80	H	79	PHE	0	-0.068	-0.042	12.643	0.013	0.013	0.000	0.000	0.000	0.000
81	H	80	LEU	0	0.026	0.010	16.027	-0.015	-0.015	0.000	0.000	0.000	0.000
82	H	81	LYS	1	0.907	0.961	18.049	0.080	0.080	0.000	0.000	0.000	0.000
83	H	82	ILE	0	0.032	0.009	20.796	-0.009	-0.009	0.000	0.000	0.000	0.000
84	H	82	THR	0	0.007	0.008	24.034	0.007	0.007	0.000	0.000	0.000	0.000
85	H	82	SER	0	0.024	-0.004	27.736	-0.003	-0.003	0.000	0.000	0.000	0.000
86	H	82	VAL	0	-0.056	-0.002	25.796	-0.003	-0.003	0.000	0.000	0.000	0.000
87	H	83	ASP	-1	-0.778	-0.900	28.683	-0.050	-0.050	0.000	0.000	0.000	0.000
88	H	84	THR	0	0.005	-0.010	28.995	-0.008	-0.008	0.000	0.000	0.000	0.000
89	H	85	ALA	0	-0.029	-0.013	28.947	-0.004	-0.004	0.000	0.000	0.000	0.000
90	H	86	ASP	-1	-0.788	-0.877	24.879	-0.106	-0.106	0.000	0.000	0.000	0.000
91	H	87	THR	0	0.012	0.033	24.018	-0.005	-0.005	0.000	0.000	0.000	0.000
92	H	88	ALA	0	-0.053	-0.033	21.101	-0.006	-0.006	0.000	0.000	0.000	0.000
93	H	89	THR	0	-0.029	0.010	17.065	0.005	0.005	0.000	0.000	0.000	0.000
94	H	90	TYR	0	0.001	-0.050	16.212	-0.016	-0.016	0.000	0.000	0.000	0.000
95	H	91	TYR	0	0.038	0.005	11.635	0.011	0.011	0.000	0.000	0.000	0.000
96	H	93	THR	0	0.028	0.012	7.849	-0.042	-0.042	0.000	0.000	0.000	0.000
97	H	94	LEU	0	-0.028	-0.014	2.379	-0.223	0.003	0.815	-0.216	-0.825	0.000
98	H	95	TYR	0	0.026	0.014	6.396	-0.164	-0.164	0.000	0.000	0.000	0.000
99	H	96	TYR	0	-0.004	-0.014	5.789	0.109	0.109	0.000	0.000	0.000	0.000
100	H	97	GLY	0	0.014	0.013	7.785	-0.070	-0.070	0.000	0.000	0.000	0.000
101	H	98	SER	0	-0.026	-0.024	10.383	-0.022	-0.022	0.000	0.000	0.000	0.000
102	H	99	VAL	0	-0.024	0.002	5.983	0.045	0.045	0.000	0.000	0.000	0.000
103	H	100	ASP	-1	-0.866	-0.940	7.702	-0.902	-0.902	0.000	0.000	0.000	0.000
104	H	101	TYR	0	-0.009	-0.014	2.898	-3.647	-0.802	1.554	-1.235	-3.164	-0.014
105	H	102	TRP	0	0.007	0.004	5.461	0.330	0.330	0.000	0.000	0.000	0.000
106	H	103	GLY	0	-0.003	0.004	6.851	-0.189	-0.189	0.000	0.000	0.000	0.000
107	H	104	GLN	0	-0.035	-0.034	8.096	0.140	0.140	0.000	0.000	0.000	0.000
108	H	105	GLY	0	0.024	0.022	11.385	0.035	0.035	0.000	0.000	0.000	0.000
109	H	106	THR	0	-0.096	-0.045	13.506	0.055	0.055	0.000	0.000	0.000	0.000
110	H	107	SER	0	0.006	-0.004	16.232	-0.015	-0.015	0.000	0.000	0.000	0.000
111	H	108	VAL	0	-0.014	-0.007	19.576	0.013	0.013	0.000	0.000	0.000	0.000
112	H	109	THR	0	0.000	-0.003	22.159	-0.005	-0.005	0.000	0.000	0.000	0.000
113	H	110	VAL	0	0.002	0.003	25.908	0.006	0.006	0.000	0.000	0.000	0.000
114	H	111	SER	0	-0.003	-0.026	28.478	0.000	0.000	0.000	0.000	0.000	0.000
115	H	112	SER	0	0.061	0.009	32.012	0.001	0.001	0.000	0.000	0.000	0.000
116	H	113	ALA	0	-0.021	0.023	34.159	0.004	0.004	0.000	0.000	0.000	0.000
117	H	114	LYS	1	0.930	0.969	34.226	0.012	0.012	0.000	0.000	0.000	0.000
118	H	115	THR	0	0.024	-0.008	31.853	-0.003	-0.003	0.000	0.000	0.000	0.000
119	H	116	THR	0	-0.079	-0.035	34.625	0.004	0.004	0.000	0.000	0.000	0.000
120	H	117	PRO	0	0.048	0.026	35.733	-0.003	-0.003	0.000	0.000	0.000	0.000
121	H	118	PRO	0	0.040	0.019	35.635	-0.001	-0.001	0.000	0.000	0.000	0.000
122	H	119	SER	0	-0.005	0.009	38.266	0.003	0.003	0.000	0.000	0.000	0.000
123	H	120	DVA	0	-0.006	-0.020	38.575	-0.003	-0.003	0.000	0.000	0.000	0.000
124	H	121	TYR	0	0.002	0.007	41.964	0.001	0.001	0.000	0.000	0.000	0.000
125	H	139	CYS	0	-0.030	-0.015	40.040	0.001	0.001	0.000	0.000	0.000	0.000
126	H	140	LEU	0	-0.033	-0.017	40.408	-0.003	-0.003	0.000	0.000	0.000	0.000
127	H	141	VAL	0	0.011	0.011	35.987	0.003	0.003	0.000	0.000	0.000	0.000
128	H	142	LYS	1	0.948	0.963	38.541	0.022	0.022	0.000	0.000	0.000	0.000
129	H	143	GLY	0	0.019	0.012	38.876	0.002	0.002	0.000	0.000	0.000	0.000
130	H	144	TYR	0	-0.028	-0.031	31.533	0.004	0.004	0.000	0.000	0.000	0.000
131	H	145	PHE	0	0.057	0.026	30.300	-0.005	-0.005	0.000	0.000	0.000	0.000
132	H	146	PRO	0	-0.009	0.004	28.280	0.005	0.005	0.000	0.000	0.000	0.000
133	H	147	GLU	-1	-0.807	-0.897	27.141	-0.051	-0.051	0.000	0.000	0.000	0.000
134	H	148	PRO	0	-0.045	-0.013	25.173	0.001	0.001	0.000	0.000	0.000	0.000
135	H	149	VAL	0	0.025	0.001	28.060	0.008	0.008	0.000	0.000	0.000	0.000
136	H	150	THR	0	-0.021	-0.008	29.388	-0.004	-0.004	0.000	0.000	0.000	0.000
137	H	151	VAL	0	0.008	0.000	31.269	0.004	0.004	0.000	0.000	0.000	0.000
138	H	152	THR	0	-0.002	0.000	32.666	-0.004	-0.004	0.000	0.000	0.000	0.000
139	H	153	TRP	0	0.028	0.022	35.359	0.001	0.001	0.000	0.000	0.000	0.000
140	H	154	ASN	0	0.007	-0.005	38.723	0.001	0.001	0.000	0.000	0.000	0.000
141	H	155	SER	0	-0.007	-0.010	37.095	0.001	0.001	0.000	0.000	0.000	0.000
142	H	156	GLY	0	0.054	0.026	34.498	0.001	0.001	0.000	0.000	0.000	0.000
143	H	157	SER	0	-0.036	-0.017	35.392	0.000	0.000	0.000	0.000	0.000	0.000
144	H	158	LEU	0	-0.032	0.000	36.896	-0.002	-0.002	0.000	0.000	0.000	0.000
145	H	159	SER	0	0.007	0.003	32.332	0.002	0.002	0.000	0.000	0.000	0.000
146	H	160	SER	0	0.000	-0.021	31.155	0.000	0.000	0.000	0.000	0.000	0.000
147	H	161	GLY	0	-0.014	-0.006	33.183	0.000	0.000	0.000	0.000	0.000	0.000
148	H	162	VAL	0	0.031	0.021	34.973	-0.004	-0.004	0.000	0.000	0.000	0.000
149	H	163	HIS	1	0.896	0.935	34.879	0.038	0.038	0.000	0.000	0.000	0.000
150	H	164	THR	0	0.029	0.022	31.911	0.006	0.006	0.000	0.000	0.000	0.000
151	H	165	PHE	0	-0.042	-0.017	32.937	-0.005	-0.005	0.000	0.000	0.000	0.000
152	H	166	PRO	0	0.004	0.003	30.080	0.002	0.002	0.000	0.000	0.000	0.000
153	H	167	ALA	0	0.024	0.021	31.355	0.003	0.003	0.000	0.000	0.000	0.000
154	H	168	VAL	0	-0.030	-0.011	32.284	-0.006	-0.006	0.000	0.000	0.000	0.000
155	H	169	LEU	0	0.000	0.001	31.890	0.004	0.004	0.000	0.000	0.000	0.000
156	H	170	GLN	0	-0.007	0.003	35.497	0.001	0.001	0.000	0.000	0.000	0.000
157	H	171	SER	0	-0.017	-0.010	39.184	0.002	0.002	0.000	0.000	0.000	0.000
158	H	172	ASP	-1	-0.912	-0.950	36.089	-0.038	-0.038	0.000	0.000	0.000	0.000
159	H	173	LEU	0	-0.051	-0.025	35.559	0.001	0.001	0.000	0.000	0.000	0.000
160	H	174	TYR	0	0.003	0.011	29.257	-0.004	-0.004	0.000	0.000	0.000	0.000
161	H	175	THR	0	-0.059	-0.047	35.070	0.004	0.004	0.000	0.000	0.000	0.000
162	H	176	LEU	0	0.022	0.013	32.919	-0.004	-0.004	0.000	0.000	0.000	0.000
163	H	177	SER	0	-0.002	-0.002	36.773	0.004	0.004	0.000	0.000	0.000	0.000
164	H	178	SER	0	0.040	0.021	36.107	-0.003	-0.003	0.000	0.000	0.000	0.000
165	H	179	SER	0	-0.018	-0.007	38.232	0.002	0.002	0.000	0.000	0.000	0.000
166	H	180	VAL	0	0.035	0.021	39.143	-0.001	-0.001	0.000	0.000	0.000	0.000

Top

Graph

Manual

About

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