FMO DATABASE

FMODB ID: 7GVJK

Calculation Name: 3NJ2-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3NJ2

Chain ID: A

ChEMBL ID:

UniProt ID: B1WPD5

Base Structure: X-ray

Registration Date: 2023-06-19

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	151
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1448653.69537
FMO2-HF: Nuclear repulsion	1389222.178114
FMO2-HF: Total energy	-59431.517256
FMO2-MP2: Total energy	-59607.849257

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:24:SER)

Summations of interaction energy for fragment #1(A:24:SER)

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.
-4.141	0.477	2.697	-3.333	-3.983	0.004

Interaction energy analysis for fragmet #1(A:24:SER)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.055 / q_NPA : -0.048

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	26	THR	0	0.014	-0.002	2.780	-0.233	2.590	0.064	-1.366	-1.522	0.001
4	A	27	ASN	0	-0.033	-0.015	2.114	-3.060	-1.560	2.634	-1.867	-2.268	0.003
5	A	28	THR	0	0.045	-0.004	3.963	0.434	0.707	0.000	-0.097	-0.176	0.000
6	A	29	LEU	0	-0.028	-0.001	5.995	0.435	0.435	0.000	0.000	0.000	0.000
7	A	30	LEU	0	0.015	0.013	7.431	0.393	0.393	0.000	0.000	0.000	0.000
8	A	31	VAL	0	-0.045	-0.040	7.864	0.233	0.233	0.000	0.000	0.000	0.000
9	A	32	GLU	-1	-0.942	-0.961	10.218	-0.607	-0.607	0.000	0.000	0.000	0.000
10	A	33	GLN	0	-0.020	-0.020	12.018	0.072	0.072	0.000	0.000	0.000	0.000
11	A	34	SER	0	-0.020	-0.009	13.010	0.057	0.057	0.000	0.000	0.000	0.000
12	A	35	PRO	0	0.070	0.026	14.598	0.052	0.052	0.000	0.000	0.000	0.000
13	A	36	PHE	0	0.013	0.025	15.695	0.044	0.044	0.000	0.000	0.000	0.000
14	A	37	LEU	0	-0.012	-0.014	10.719	0.064	0.064	0.000	0.000	0.000	0.000
15	A	38	GLN	0	-0.005	-0.001	14.037	0.052	0.052	0.000	0.000	0.000	0.000
16	A	39	SER	0	-0.045	-0.047	16.807	0.014	0.014	0.000	0.000	0.000	0.000
17	A	40	LEU	0	-0.017	-0.008	15.130	0.014	0.014	0.000	0.000	0.000	0.000
18	A	41	VAL	0	0.017	0.012	14.418	0.030	0.030	0.000	0.000	0.000	0.000
19	A	42	GLN	0	-0.014	0.002	17.364	-0.002	-0.002	0.000	0.000	0.000	0.000
20	A	43	GLN	0	0.007	-0.003	20.858	0.005	0.005	0.000	0.000	0.000	0.000
21	A	44	ILE	0	-0.009	-0.008	16.776	0.001	0.001	0.000	0.000	0.000	0.000
22	A	45	ARG	1	0.805	0.872	16.130	-0.205	-0.205	0.000	0.000	0.000	0.000
23	A	46	ALA	0	-0.016	0.009	22.024	-0.011	-0.011	0.000	0.000	0.000	0.000
24	A	47	TYR	0	-0.032	-0.029	24.409	-0.008	-0.008	0.000	0.000	0.000	0.000
25	A	48	ASP	-1	-0.814	-0.877	23.092	0.208	0.208	0.000	0.000	0.000	0.000
26	A	49	HIS	0	0.009	0.006	25.190	-0.017	-0.017	0.000	0.000	0.000	0.000
27	A	50	TYR	0	-0.028	-0.021	27.873	-0.015	-0.015	0.000	0.000	0.000	0.000
28	A	51	GLY	0	-0.050	-0.031	24.757	-0.002	-0.002	0.000	0.000	0.000	0.000
29	A	52	VAL	0	-0.032	-0.016	23.230	0.006	0.006	0.000	0.000	0.000	0.000
30	A	53	TYR	0	-0.027	-0.041	18.891	0.030	0.030	0.000	0.000	0.000	0.000
31	A	54	ARG	1	0.935	0.974	19.306	-0.107	-0.107	0.000	0.000	0.000	0.000
32	A	55	THR	0	-0.004	0.011	19.244	-0.012	-0.012	0.000	0.000	0.000	0.000
33	A	56	TRP	0	-0.032	0.003	15.418	0.053	0.053	0.000	0.000	0.000	0.000
34	A	57	THR	0	0.083	0.026	10.598	-0.058	-0.058	0.000	0.000	0.000	0.000
35	A	58	ASP	-1	-0.724	-0.868	12.579	0.180	0.180	0.000	0.000	0.000	0.000
36	A	59	GLU	-1	-0.852	-0.910	4.987	1.268	1.290	-0.001	-0.003	-0.017	0.000
37	A	60	LEU	0	-0.026	-0.020	9.814	0.142	0.142	0.000	0.000	0.000	0.000
38	A	61	VAL	0	-0.030	-0.005	11.767	-0.003	-0.003	0.000	0.000	0.000	0.000
39	A	62	ILE	0	0.012	0.012	11.057	-0.019	-0.019	0.000	0.000	0.000	0.000
40	A	63	ALA	0	0.013	0.008	10.441	0.026	0.026	0.000	0.000	0.000	0.000
41	A	64	PRO	0	-0.014	-0.010	11.655	0.038	0.038	0.000	0.000	0.000	0.000
42	A	65	TYR	0	-0.056	-0.034	14.033	-0.056	-0.056	0.000	0.000	0.000	0.000
43	A	66	VAL	0	-0.049	-0.010	9.126	-0.020	-0.020	0.000	0.000	0.000	0.000
44	A	67	ILE	0	0.016	0.015	12.409	0.067	0.067	0.000	0.000	0.000	0.000
45	A	68	PRO	0	0.043	0.026	11.974	-0.106	-0.106	0.000	0.000	0.000	0.000
46	A	69	LYS	1	1.023	0.999	14.464	-0.534	-0.534	0.000	0.000	0.000	0.000
47	A	70	LYS	1	0.946	0.960	17.681	-0.650	-0.650	0.000	0.000	0.000	0.000
48	A	71	LYS	1	1.008	1.014	15.551	-0.815	-0.815	0.000	0.000	0.000	0.000
49	A	72	ARG	1	0.854	0.916	16.622	-0.647	-0.647	0.000	0.000	0.000	0.000
50	A	73	ARG	1	0.783	0.879	19.935	-0.394	-0.394	0.000	0.000	0.000	0.000
51	A	74	GLU	-1	-0.826	-0.909	22.436	0.318	0.318	0.000	0.000	0.000	0.000
52	A	75	ILE	0	-0.049	0.008	20.234	-0.008	-0.008	0.000	0.000	0.000	0.000
53	A	76	SER	0	-0.009	-0.025	24.476	-0.011	-0.011	0.000	0.000	0.000	0.000
54	A	77	LEU	0	-0.014	-0.022	27.523	0.010	0.010	0.000	0.000	0.000	0.000
55	A	78	GLU	-1	-0.900	-0.924	30.167	0.207	0.207	0.000	0.000	0.000	0.000
56	A	79	GLY	0	0.005	0.016	32.059	-0.013	-0.013	0.000	0.000	0.000	0.000
57	A	80	ASP	-1	-0.880	-0.938	32.463	0.172	0.172	0.000	0.000	0.000	0.000
58	A	81	ILE	0	-0.084	-0.035	26.786	0.014	0.014	0.000	0.000	0.000	0.000
59	A	82	ASP	-1	-0.746	-0.847	24.945	0.288	0.288	0.000	0.000	0.000	0.000
60	A	83	PRO	0	0.032	-0.004	27.429	0.006	0.006	0.000	0.000	0.000	0.000
61	A	84	THR	0	0.005	-0.014	22.894	-0.006	-0.006	0.000	0.000	0.000	0.000
62	A	85	THR	0	-0.057	-0.057	22.796	0.031	0.031	0.000	0.000	0.000	0.000
63	A	86	LYS	1	0.898	0.960	23.974	-0.176	-0.176	0.000	0.000	0.000	0.000
64	A	87	LEU	0	0.039	0.039	24.120	-0.008	-0.008	0.000	0.000	0.000	0.000
65	A	88	ARG	1	0.931	0.983	18.356	-0.420	-0.420	0.000	0.000	0.000	0.000
66	A	89	ILE	0	-0.006	0.004	21.583	-0.003	-0.003	0.000	0.000	0.000	0.000
67	A	90	LEU	0	0.015	0.007	23.597	-0.015	-0.015	0.000	0.000	0.000	0.000
68	A	91	CYS	0	-0.015	-0.017	21.502	-0.020	-0.020	0.000	0.000	0.000	0.000
69	A	92	TYR	0	-0.006	-0.007	18.104	-0.018	-0.018	0.000	0.000	0.000	0.000
70	A	93	PHE	0	0.018	-0.004	21.285	-0.016	-0.016	0.000	0.000	0.000	0.000
71	A	94	ARG	1	0.922	0.964	24.675	-0.128	-0.128	0.000	0.000	0.000	0.000
72	A	95	ALA	0	0.000	0.011	20.178	-0.021	-0.021	0.000	0.000	0.000	0.000
73	A	96	ILE	0	-0.049	-0.021	21.982	-0.022	-0.022	0.000	0.000	0.000	0.000
74	A	97	ALA	0	-0.011	-0.002	23.607	-0.018	-0.018	0.000	0.000	0.000	0.000
75	A	98	ALA	0	0.029	0.019	23.921	-0.013	-0.013	0.000	0.000	0.000	0.000
76	A	99	LEU	0	-0.031	-0.017	20.453	-0.016	-0.016	0.000	0.000	0.000	0.000
77	A	100	ILE	0	0.022	0.005	24.211	-0.013	-0.013	0.000	0.000	0.000	0.000
78	A	101	GLU	-1	-0.879	-0.930	27.560	0.014	0.014	0.000	0.000	0.000	0.000
79	A	102	LYS	1	0.848	0.928	21.482	0.023	0.023	0.000	0.000	0.000	0.000
80	A	103	GLU	-1	-0.914	-0.956	24.898	-0.075	-0.075	0.000	0.000	0.000	0.000
81	A	104	THR	0	-0.070	-0.040	28.359	0.000	0.000	0.000	0.000	0.000	0.000
82	A	105	GLY	0	0.021	0.007	31.354	0.000	0.000	0.000	0.000	0.000	0.000
83	A	106	LEU	0	-0.071	-0.025	32.926	0.003	0.003	0.000	0.000	0.000	0.000
84	A	107	LEU	0	-0.029	-0.002	29.302	0.004	0.004	0.000	0.000	0.000	0.000
85	A	108	CYS	0	-0.064	-0.024	30.885	0.000	0.000	0.000	0.000	0.000	0.000
86	A	109	GLN	0	-0.018	-0.001	31.477	0.008	0.008	0.000	0.000	0.000	0.000
87	A	110	VAL	0	0.020	-0.012	27.797	0.004	0.004	0.000	0.000	0.000	0.000
88	A	111	VAL	0	0.000	0.010	31.172	0.000	0.000	0.000	0.000	0.000	0.000
89	A	112	VAL	0	-0.046	-0.028	27.151	0.005	0.005	0.000	0.000	0.000	0.000
90	A	113	ASP	-1	-0.951	-0.960	30.556	0.126	0.126	0.000	0.000	0.000	0.000
91	A	114	LEU	0	-0.041	-0.023	28.023	0.007	0.007	0.000	0.000	0.000	0.000
92	A	115	ASN	0	-0.001	-0.017	32.674	-0.005	-0.005	0.000	0.000	0.000	0.000
93	A	116	HIS	0	0.039	0.033	33.149	0.014	0.014	0.000	0.000	0.000	0.000
94	A	117	GLU	-1	-0.784	-0.893	33.067	0.162	0.162	0.000	0.000	0.000	0.000
95	A	118	GLY	0	-0.059	-0.025	30.190	0.011	0.011	0.000	0.000	0.000	0.000
96	A	119	PHE	0	-0.019	-0.027	30.205	0.007	0.007	0.000	0.000	0.000	0.000
97	A	120	GLY	0	0.076	0.030	32.466	-0.006	-0.006	0.000	0.000	0.000	0.000
98	A	121	TRP	0	-0.045	-0.018	32.012	0.002	0.002	0.000	0.000	0.000	0.000
99	A	122	ALA	0	-0.003	0.017	27.908	0.004	0.004	0.000	0.000	0.000	0.000
100	A	123	LEU	0	-0.033	-0.028	29.880	-0.006	-0.006	0.000	0.000	0.000	0.000
101	A	124	VAL	0	0.030	0.012	27.997	0.003	0.003	0.000	0.000	0.000	0.000
102	A	125	TRP	0	0.003	-0.010	31.481	-0.002	-0.002	0.000	0.000	0.000	0.000
103	A	126	GLY	0	0.075	0.031	34.680	0.000	0.000	0.000	0.000	0.000	0.000
104	A	127	GLY	0	0.040	0.044	36.287	-0.002	-0.002	0.000	0.000	0.000	0.000
105	A	128	LYS	1	0.855	0.907	40.049	-0.034	-0.034	0.000	0.000	0.000	0.000
106	A	129	LEU	0	0.024	0.024	35.653	0.001	0.001	0.000	0.000	0.000	0.000
107	A	130	MET	0	-0.023	-0.005	34.622	0.005	0.005	0.000	0.000	0.000	0.000
108	A	131	VAL	0	-0.006	0.010	30.441	0.000	0.000	0.000	0.000	0.000	0.000
109	A	132	VAL	0	0.011	0.001	27.192	0.006	0.006	0.000	0.000	0.000	0.000
110	A	133	SER	0	0.043	0.011	30.547	-0.002	-0.002	0.000	0.000	0.000	0.000
111	A	134	ARG	1	0.883	0.951	25.330	-0.177	-0.177	0.000	0.000	0.000	0.000
112	A	135	SER	0	0.054	0.028	29.880	0.004	0.004	0.000	0.000	0.000	0.000
113	A	136	LEU	0	-0.096	-0.046	26.502	0.015	0.015	0.000	0.000	0.000	0.000
114	A	137	ARG	1	0.984	0.982	28.425	-0.174	-0.174	0.000	0.000	0.000	0.000
115	A	138	ASP	-1	-0.881	-0.932	27.626	0.249	0.249	0.000	0.000	0.000	0.000
116	A	139	ALA	0	0.017	-0.004	25.888	0.025	0.025	0.000	0.000	0.000	0.000
117	A	140	HIS	0	0.027	0.000	24.801	0.034	0.034	0.000	0.000	0.000	0.000
118	A	141	ARG	1	0.821	0.912	22.515	-0.290	-0.290	0.000	0.000	0.000	0.000
119	A	142	PHE	0	-0.030	-0.013	19.638	0.032	0.032	0.000	0.000	0.000	0.000
120	A	143	GLY	0	0.036	0.016	17.482	0.031	0.031	0.000	0.000	0.000	0.000
121	A	144	PHE	0	-0.074	-0.035	14.135	-0.051	-0.051	0.000	0.000	0.000	0.000
122	A	145	ASP	-1	-0.810	-0.898	13.634	0.749	0.749	0.000	0.000	0.000	0.000
123	A	146	THR	0	0.016	-0.004	8.713	0.120	0.120	0.000	0.000	0.000	0.000
124	A	147	LEU	0	0.083	0.048	6.582	-0.220	-0.220	0.000	0.000	0.000	0.000
125	A	148	GLU	-1	-0.863	-0.926	6.890	0.087	0.087	0.000	0.000	0.000	0.000
126	A	149	LYS	1	0.838	0.908	10.116	-0.805	-0.805	0.000	0.000	0.000	0.000
127	A	150	LEU	0	-0.028	0.001	12.340	-0.101	-0.101	0.000	0.000	0.000	0.000
128	A	151	ASN	0	0.052	0.025	12.197	-0.115	-0.115	0.000	0.000	0.000	0.000
129	A	152	ASP	-1	-0.857	-0.915	13.781	0.078	0.078	0.000	0.000	0.000	0.000
130	A	153	GLN	0	-0.048	-0.026	15.768	-0.044	-0.044	0.000	0.000	0.000	0.000
131	A	154	GLY	0	0.004	-0.010	17.651	-0.028	-0.028	0.000	0.000	0.000	0.000
132	A	155	THR	0	0.024	0.000	16.693	-0.039	-0.039	0.000	0.000	0.000	0.000
133	A	156	LYS	1	0.908	0.967	19.390	-0.175	-0.175	0.000	0.000	0.000	0.000
134	A	157	LEU	0	-0.075	-0.039	21.597	-0.011	-0.011	0.000	0.000	0.000	0.000
135	A	158	ALA	0	0.040	0.030	22.518	-0.009	-0.009	0.000	0.000	0.000	0.000
136	A	159	ASN	0	0.036	0.007	21.495	-0.013	-0.013	0.000	0.000	0.000	0.000
137	A	160	ALA	0	-0.029	-0.013	24.982	-0.007	-0.007	0.000	0.000	0.000	0.000
138	A	161	GLY	0	0.006	-0.012	27.288	-0.004	-0.004	0.000	0.000	0.000	0.000
139	A	162	ILE	0	0.019	0.019	25.484	-0.002	-0.002	0.000	0.000	0.000	0.000
140	A	163	GLU	-1	-0.911	-0.966	28.811	-0.016	-0.016	0.000	0.000	0.000	0.000
141	A	164	LEU	0	-0.055	-0.016	31.207	-0.002	-0.002	0.000	0.000	0.000	0.000
142	A	165	VAL	0	-0.038	-0.036	32.716	-0.001	-0.001	0.000	0.000	0.000	0.000
143	A	166	ASN	0	-0.005	-0.004	31.737	-0.001	-0.001	0.000	0.000	0.000	0.000
144	A	167	LYS	1	0.900	0.971	35.344	-0.021	-0.021	0.000	0.000	0.000	0.000
145	A	168	PHE	0	-0.035	-0.013	37.137	0.000	0.000	0.000	0.000	0.000	0.000
146	A	169	PRO	0	0.039	0.023	39.242	0.004	0.004	0.000	0.000	0.000	0.000
147	A	170	GLU	-1	-0.833	-0.939	40.398	0.018	0.018	0.000	0.000	0.000	0.000
148	A	171	VAL	0	-0.007	-0.007	40.155	0.002	0.002	0.000	0.000	0.000	0.000
149	A	172	ALA	0	-0.032	-0.015	37.025	0.003	0.003	0.000	0.000	0.000	0.000
150	A	173	ARG	1	0.872	0.932	35.091	-0.001	-0.001	0.000	0.000	0.000	0.000
151	A	174	LEU	0	-0.062	-0.003	40.870	0.000	0.000	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:24:SER)