FMO DATABASE

FMODB ID: 4JV7N

Calculation Name: 3A57-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

Ligand 3-letter code:

Ligand of Interest (LOI):

Structure Source: PDB

PDB ID: 3A57

Chain ID: A

ChEMBL ID:

UniProt ID: P19250

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:

Apendix: None

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
Remarks

FMO calculation

FMO method	FMO2-MP2/6-31G(d)
Fragmentation	Auto
Number of fragment	153
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1539230.568323
FMO2-HF: Nuclear repulsion	1477271.778379
FMO2-HF: Total energy	-61958.789943
FMO2-MP2: Total energy	-62137.975357

3D Structure Molmil

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:12:GLY)

Summations of interaction energy for fragment #1(A:12:GLY)

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.
-0.494	1.941	0.02	-1.141	-1.315	-0.002

Interaction energy analysis for fragmet #1(A:12:GLY)

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 : 0.014

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	14	ASP	-1	-0.738	-0.808	3.793	-1.366	0.000	-0.009	-0.692	-0.665	0.000
4	A	15	GLU	-1	-0.888	-0.970	6.558	0.225	0.225	0.000	0.000	0.000	0.000
5	A	16	ILE	0	0.004	0.017	10.379	-0.053	-0.053	0.000	0.000	0.000	0.000
6	A	17	LEU	0	-0.014	0.008	13.442	0.036	0.036	0.000	0.000	0.000	0.000
7	A	18	PHE	0	0.029	0.004	16.554	-0.014	-0.014	0.000	0.000	0.000	0.000
8	A	19	VAL	0	0.005	-0.007	20.177	0.018	0.018	0.000	0.000	0.000	0.000
9	A	20	VAL	0	0.013	0.010	23.325	-0.010	-0.010	0.000	0.000	0.000	0.000
10	A	21	ARG	1	0.889	0.902	26.799	0.050	0.050	0.000	0.000	0.000	0.000
11	A	22	ASP	-1	-0.777	-0.875	29.495	-0.045	-0.045	0.000	0.000	0.000	0.000
12	A	23	THR	0	-0.002	-0.003	33.136	0.003	0.003	0.000	0.000	0.000	0.000
13	A	24	THR	0	-0.021	-0.006	35.739	0.002	0.002	0.000	0.000	0.000	0.000
14	A	25	PHE	0	-0.023	-0.003	35.930	0.003	0.003	0.000	0.000	0.000	0.000
15	A	26	ASN	0	-0.050	-0.014	38.228	0.001	0.001	0.000	0.000	0.000	0.000
16	A	27	THR	0	-0.030	-0.007	40.485	0.001	0.001	0.000	0.000	0.000	0.000
17	A	28	ASN	0	-0.071	-0.069	43.172	0.002	0.002	0.000	0.000	0.000	0.000
18	A	29	ALA	0	-0.038	-0.015	44.257	0.000	0.000	0.000	0.000	0.000	0.000
19	A	30	PRO	0	-0.010	-0.003	40.675	-0.003	-0.003	0.000	0.000	0.000	0.000
20	A	31	VAL	0	-0.002	0.008	37.395	0.000	0.000	0.000	0.000	0.000	0.000
21	A	32	ASN	0	-0.052	-0.030	38.646	0.003	0.003	0.000	0.000	0.000	0.000
22	A	33	VAL	0	0.011	-0.001	32.468	-0.004	-0.004	0.000	0.000	0.000	0.000
23	A	34	GLU	-1	-0.848	-0.908	33.095	-0.041	-0.041	0.000	0.000	0.000	0.000
24	A	35	VAL	0	-0.064	-0.042	26.385	-0.007	-0.007	0.000	0.000	0.000	0.000
25	A	36	SER	0	-0.018	-0.028	29.521	0.002	0.002	0.000	0.000	0.000	0.000
26	A	37	ASP	-1	-0.801	-0.861	25.657	-0.120	-0.120	0.000	0.000	0.000	0.000
27	A	38	PHE	0	-0.015	-0.013	22.113	0.000	0.000	0.000	0.000	0.000	0.000
28	A	39	TRP	0	-0.032	-0.005	17.331	0.002	0.002	0.000	0.000	0.000	0.000
29	A	40	THR	0	0.034	-0.008	14.273	-0.020	-0.020	0.000	0.000	0.000	0.000
30	A	41	ASN	0	-0.010	0.016	11.396	0.035	0.035	0.000	0.000	0.000	0.000
31	A	42	ARG	1	0.796	0.898	8.615	0.803	0.803	0.000	0.000	0.000	0.000
32	A	43	ASN	0	-0.029	-0.013	11.312	0.077	0.077	0.000	0.000	0.000	0.000
33	A	44	VAL	0	0.012	0.000	14.462	-0.009	-0.009	0.000	0.000	0.000	0.000
34	A	45	LYS	1	0.844	0.917	11.863	-0.155	-0.155	0.000	0.000	0.000	0.000
35	A	46	ARG	1	0.938	0.972	17.603	0.023	0.023	0.000	0.000	0.000	0.000
36	A	47	LYS	1	0.965	0.984	20.794	0.015	0.015	0.000	0.000	0.000	0.000
37	A	48	PRO	0	0.019	0.034	23.203	0.010	0.010	0.000	0.000	0.000	0.000
38	A	49	TYR	0	-0.114	-0.072	25.639	0.004	0.004	0.000	0.000	0.000	0.000
39	A	50	LYS	1	0.814	0.895	29.406	0.035	0.035	0.000	0.000	0.000	0.000
40	A	51	ASP	-1	-0.736	-0.842	31.401	-0.037	-0.037	0.000	0.000	0.000	0.000
41	A	52	VAL	0	-0.015	-0.007	30.349	0.004	0.004	0.000	0.000	0.000	0.000
42	A	53	TYR	0	0.028	0.013	32.843	0.002	0.002	0.000	0.000	0.000	0.000
43	A	54	GLY	0	0.056	0.042	33.583	0.003	0.003	0.000	0.000	0.000	0.000
44	A	55	GLN	0	-0.066	-0.056	27.096	-0.007	-0.007	0.000	0.000	0.000	0.000
45	A	56	SER	0	-0.044	-0.018	27.600	0.006	0.006	0.000	0.000	0.000	0.000
46	A	57	VAL	0	-0.013	-0.020	21.373	-0.005	-0.005	0.000	0.000	0.000	0.000
47	A	58	PHE	0	-0.001	0.012	19.063	0.015	0.015	0.000	0.000	0.000	0.000
48	A	59	THR	0	-0.006	-0.016	15.605	0.000	0.000	0.000	0.000	0.000	0.000
49	A	60	THR	0	-0.039	-0.003	14.506	-0.003	-0.003	0.000	0.000	0.000	0.000
50	A	61	SER	0	0.014	0.016	10.107	0.037	0.037	0.000	0.000	0.000	0.000
51	A	62	GLY	0	0.041	0.003	8.361	0.170	0.170	0.000	0.000	0.000	0.000
52	A	63	THR	0	0.027	0.018	4.390	-0.206	-0.134	-0.001	-0.042	-0.030	0.000
53	A	64	LYS	1	0.872	0.957	3.446	2.651	3.141	0.013	-0.170	-0.333	0.000
54	A	65	TRP	0	-0.003	-0.001	5.649	0.128	0.128	0.000	0.000	0.000	0.000
55	A	66	LEU	0	-0.051	-0.013	8.383	0.125	0.125	0.000	0.000	0.000	0.000
56	A	67	THR	0	-0.010	-0.010	10.067	0.036	0.036	0.000	0.000	0.000	0.000
57	A	68	SER	0	0.003	-0.019	13.777	0.025	0.025	0.000	0.000	0.000	0.000
58	A	69	TYR	0	-0.006	-0.025	16.322	-0.016	-0.016	0.000	0.000	0.000	0.000
59	A	70	MET	0	-0.043	-0.012	19.893	0.016	0.016	0.000	0.000	0.000	0.000
60	A	71	THR	0	-0.032	-0.035	23.031	-0.010	-0.010	0.000	0.000	0.000	0.000
61	A	72	VAL	0	-0.017	-0.021	26.601	0.007	0.007	0.000	0.000	0.000	0.000
62	A	73	ASN	0	0.002	0.004	29.549	0.001	0.001	0.000	0.000	0.000	0.000
63	A	74	ILE	0	0.009	-0.011	31.915	0.004	0.004	0.000	0.000	0.000	0.000
64	A	75	ASN	0	-0.018	-0.016	35.570	-0.001	-0.001	0.000	0.000	0.000	0.000
65	A	76	ASP	-1	-0.898	-0.939	38.265	-0.047	-0.047	0.000	0.000	0.000	0.000
66	A	77	LYS	1	0.824	0.921	35.690	0.063	0.063	0.000	0.000	0.000	0.000
67	A	78	ASP	-1	-0.783	-0.860	31.009	-0.080	-0.080	0.000	0.000	0.000	0.000
68	A	79	TYR	0	-0.052	-0.049	29.318	-0.002	-0.002	0.000	0.000	0.000	0.000
69	A	80	THR	0	-0.041	-0.022	23.455	0.000	0.000	0.000	0.000	0.000	0.000
70	A	81	MET	0	-0.040	0.006	22.090	-0.003	-0.003	0.000	0.000	0.000	0.000
71	A	82	ALA	0	-0.004	-0.023	19.525	-0.002	-0.002	0.000	0.000	0.000	0.000
72	A	83	ALA	0	0.023	0.014	14.973	0.005	0.005	0.000	0.000	0.000	0.000
73	A	84	VAL	0	0.000	-0.012	12.310	-0.012	-0.012	0.000	0.000	0.000	0.000
74	A	85	SER	0	0.005	-0.010	7.934	-0.162	-0.162	0.000	0.000	0.000	0.000
75	A	86	GLY	0	0.005	-0.024	8.031	-0.168	-0.168	0.000	0.000	0.000	0.000
76	A	87	TYR	0	-0.055	-0.023	3.489	-1.173	-0.666	0.017	-0.237	-0.287	-0.002
77	A	88	LYS	1	0.893	0.935	9.323	0.452	0.452	0.000	0.000	0.000	0.000
78	A	89	HIS	0	-0.017	-0.008	12.489	-0.015	-0.015	0.000	0.000	0.000	0.000
79	A	90	GLY	0	-0.001	0.006	11.036	0.045	0.045	0.000	0.000	0.000	0.000
80	A	91	HIS	0	-0.024	-0.011	9.098	-0.086	-0.086	0.000	0.000	0.000	0.000
81	A	92	SER	0	-0.026	-0.017	5.635	-0.238	-0.238	0.000	0.000	0.000	0.000
82	A	93	ALA	0	0.043	0.028	7.668	0.160	0.160	0.000	0.000	0.000	0.000
83	A	94	VAL	0	-0.027	-0.030	9.588	-0.226	-0.226	0.000	0.000	0.000	0.000
84	A	95	PHE	0	0.033	0.035	11.948	0.057	0.057	0.000	0.000	0.000	0.000
85	A	96	VAL	0	0.005	-0.019	15.467	-0.021	-0.021	0.000	0.000	0.000	0.000
86	A	97	LYS	1	0.880	0.947	18.190	0.185	0.185	0.000	0.000	0.000	0.000
87	A	98	SER	0	0.017	-0.004	21.802	-0.001	-0.001	0.000	0.000	0.000	0.000
88	A	99	ASP	-1	-0.830	-0.912	24.655	-0.125	-0.125	0.000	0.000	0.000	0.000
89	A	100	GLN	0	-0.009	0.013	27.975	0.004	0.004	0.000	0.000	0.000	0.000
90	A	101	VAL	0	0.004	0.003	26.880	0.003	0.003	0.000	0.000	0.000	0.000
91	A	102	GLN	0	-0.028	0.001	28.163	-0.002	-0.002	0.000	0.000	0.000	0.000
92	A	103	LEU	0	-0.023	-0.008	22.056	-0.007	-0.007	0.000	0.000	0.000	0.000
93	A	104	GLN	0	0.020	0.006	24.230	0.010	0.010	0.000	0.000	0.000	0.000
94	A	105	HIS	1	0.811	0.880	21.994	0.109	0.109	0.000	0.000	0.000	0.000
95	A	106	SER	0	0.010	-0.003	20.336	0.003	0.003	0.000	0.000	0.000	0.000
96	A	107	TYR	0	0.038	0.012	12.179	-0.030	-0.030	0.000	0.000	0.000	0.000
97	A	108	ASP	-1	-0.855	-0.931	17.474	-0.263	-0.263	0.000	0.000	0.000	0.000
98	A	109	SER	0	-0.007	0.021	19.858	0.012	0.012	0.000	0.000	0.000	0.000
99	A	110	VAL	0	-0.006	0.006	16.937	0.010	0.010	0.000	0.000	0.000	0.000
100	A	111	ALA	0	0.013	-0.003	16.288	-0.002	-0.002	0.000	0.000	0.000	0.000
101	A	112	SER	0	-0.072	-0.054	17.794	0.010	0.010	0.000	0.000	0.000	0.000
102	A	113	PHE	0	-0.007	0.002	21.387	0.015	0.015	0.000	0.000	0.000	0.000
103	A	114	VAL	0	-0.055	-0.030	16.934	0.013	0.013	0.000	0.000	0.000	0.000
104	A	115	GLY	0	-0.003	0.011	19.232	0.010	0.010	0.000	0.000	0.000	0.000
105	A	116	GLU	-1	-0.909	-0.956	15.273	-0.434	-0.434	0.000	0.000	0.000	0.000
106	A	117	ASP	-1	-0.843	-0.925	17.217	-0.221	-0.221	0.000	0.000	0.000	0.000
107	A	118	GLU	-1	-0.926	-0.968	14.868	-0.427	-0.427	0.000	0.000	0.000	0.000
108	A	119	ASP	-1	-0.899	-0.944	17.244	-0.210	-0.210	0.000	0.000	0.000	0.000
109	A	120	SER	0	-0.064	-0.026	18.136	0.011	0.011	0.000	0.000	0.000	0.000
110	A	121	ILE	0	-0.069	-0.005	14.527	0.020	0.020	0.000	0.000	0.000	0.000
111	A	122	PRO	0	0.022	0.010	17.360	-0.011	-0.011	0.000	0.000	0.000	0.000
112	A	123	SER	0	-0.059	-0.047	19.275	0.015	0.015	0.000	0.000	0.000	0.000
113	A	124	LYS	1	0.836	0.901	22.611	0.081	0.081	0.000	0.000	0.000	0.000
114	A	125	MET	0	0.010	0.023	25.588	0.006	0.006	0.000	0.000	0.000	0.000
115	A	126	TYR	0	-0.012	-0.027	27.385	0.006	0.006	0.000	0.000	0.000	0.000
116	A	127	LEU	0	-0.035	-0.017	27.182	-0.005	-0.005	0.000	0.000	0.000	0.000
117	A	128	ASP	-1	-0.768	-0.868	31.514	-0.068	-0.068	0.000	0.000	0.000	0.000
118	A	129	GLU	-1	-0.964	-0.976	35.158	-0.052	-0.052	0.000	0.000	0.000	0.000
119	A	130	THR	0	-0.004	0.019	38.259	0.002	0.002	0.000	0.000	0.000	0.000
120	A	131	PRO	0	-0.001	-0.030	41.188	0.002	0.002	0.000	0.000	0.000	0.000
121	A	132	GLU	-1	-0.878	-0.913	41.868	-0.038	-0.038	0.000	0.000	0.000	0.000
122	A	133	TYR	0	0.008	-0.020	35.762	0.003	0.003	0.000	0.000	0.000	0.000
123	A	134	PHE	0	-0.038	-0.013	36.018	-0.001	-0.001	0.000	0.000	0.000	0.000
124	A	135	VAL	0	0.011	0.007	30.511	0.001	0.001	0.000	0.000	0.000	0.000
125	A	136	ASN	0	-0.034	-0.026	29.037	-0.005	-0.005	0.000	0.000	0.000	0.000
126	A	137	VAL	0	0.026	0.011	23.038	0.003	0.003	0.000	0.000	0.000	0.000
127	A	138	GLU	-1	-0.817	-0.873	22.939	-0.084	-0.084	0.000	0.000	0.000	0.000
128	A	139	ALA	0	0.022	0.001	18.670	-0.004	-0.004	0.000	0.000	0.000	0.000
129	A	140	TYR	0	-0.006	-0.010	17.814	0.005	0.005	0.000	0.000	0.000	0.000
130	A	141	GLU	-1	-0.873	-0.923	12.254	-0.318	-0.318	0.000	0.000	0.000	0.000
131	A	142	SER	0	-0.035	-0.032	13.868	0.045	0.045	0.000	0.000	0.000	0.000
132	A	143	GLY	0	0.009	0.004	13.697	0.017	0.017	0.000	0.000	0.000	0.000
133	A	144	SER	0	-0.095	-0.063	8.500	0.078	0.078	0.000	0.000	0.000	0.000
134	A	145	GLY	0	0.020	0.030	8.634	0.022	0.022	0.000	0.000	0.000	0.000
135	A	146	ASN	0	-0.018	-0.013	9.766	0.044	0.044	0.000	0.000	0.000	0.000
136	A	147	ILE	0	-0.013	-0.009	13.348	0.025	0.025	0.000	0.000	0.000	0.000
137	A	148	LEU	0	0.015	0.016	16.770	-0.012	-0.012	0.000	0.000	0.000	0.000
138	A	149	VAL	0	0.006	-0.013	19.849	0.016	0.016	0.000	0.000	0.000	0.000
139	A	150	MET	0	0.015	0.019	23.454	0.003	0.003	0.000	0.000	0.000	0.000
140	A	151	CYS	0	-0.153	-0.042	26.322	0.011	0.011	0.000	0.000	0.000	0.000
141	A	152	ILE	0	0.055	0.031	29.556	-0.003	-0.003	0.000	0.000	0.000	0.000
142	A	153	SER	0	0.028	0.017	32.978	0.004	0.004	0.000	0.000	0.000	0.000
143	A	154	ASN	0	0.093	0.022	36.238	-0.002	-0.002	0.000	0.000	0.000	0.000
144	A	155	LYS	1	0.805	0.877	39.981	0.040	0.040	0.000	0.000	0.000	0.000
145	A	156	GLU	-1	-0.855	-0.897	42.580	-0.021	-0.021	0.000	0.000	0.000	0.000
146	A	157	SER	0	0.038	0.005	37.982	0.001	0.001	0.000	0.000	0.000	0.000
147	A	158	PHE	0	-0.003	0.004	37.273	-0.002	-0.002	0.000	0.000	0.000	0.000
148	A	159	PHE	0	0.014	-0.023	36.071	-0.003	-0.003	0.000	0.000	0.000	0.000
149	A	160	GLU	-1	-0.865	-0.937	34.590	-0.028	-0.028	0.000	0.000	0.000	0.000
150	A	162	LYS	1	0.834	0.941	30.912	0.049	0.049	0.000	0.000	0.000	0.000
151	A	163	HIS	0	-0.028	-0.003	30.671	-0.004	-0.004	0.000	0.000	0.000	0.000
152	A	164	GLN	0	-0.025	-0.022	25.195	0.000	0.000	0.000	0.000	0.000	0.000
153	A	165	GLN	0	0.008	0.017	23.654	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:12:GLY)