FMO DATABASE

FMODB ID: QVV7Y

Calculation Name: 3N53-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3N53

Chain ID: A

ChEMBL ID:

UniProt ID: Q3A6W4

Base Structure: X-ray

Registration Date: 2023-09-21

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	127
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1164909.294402
FMO2-HF: Nuclear repulsion	1113877.114324
FMO2-HF: Total energy	-51032.180077
FMO2-MP2: Total energy	-51183.749003

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:1:LEU)

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

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.
-9.227	-3.828	5.29	-3.219	-7.469	-0.011

Interaction energy analysis for fragmet #1(A:1:LEU)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.021 / q_NPA : -0.024

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

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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	3	LYS	1	0.886	0.940	3.241	-1.395	0.576	0.068	-0.924	-1.115	0.000
4	A	4	ILE	0	0.025	0.015	5.717	0.488	0.488	0.000	0.000	0.000	0.000
5	A	5	LEU	0	-0.041	-0.011	8.285	0.009	0.009	0.000	0.000	0.000	0.000
6	A	6	ILE	0	0.018	0.002	11.523	0.065	0.065	0.000	0.000	0.000	0.000
7	A	7	ILE	0	-0.048	-0.037	13.903	0.025	0.025	0.000	0.000	0.000	0.000
8	A	8	ASP	-1	-0.751	-0.878	17.559	-0.290	-0.290	0.000	0.000	0.000	0.000
9	A	9	GLN	0	0.000	0.034	19.981	-0.002	-0.002	0.000	0.000	0.000	0.000
10	A	10	GLN	0	-0.071	-0.046	22.792	0.011	0.011	0.000	0.000	0.000	0.000
11	A	11	ASP	-1	-0.817	-0.896	20.402	-0.282	-0.282	0.000	0.000	0.000	0.000
12	A	12	PHE	0	-0.043	-0.016	19.695	-0.024	-0.024	0.000	0.000	0.000	0.000
13	A	13	SER	0	-0.004	-0.036	19.794	-0.007	-0.007	0.000	0.000	0.000	0.000
14	A	14	ARG	1	0.786	0.883	15.845	0.313	0.313	0.000	0.000	0.000	0.000
15	A	15	ILE	0	-0.027	-0.015	15.243	-0.063	-0.063	0.000	0.000	0.000	0.000
16	A	16	GLU	-1	-0.992	-0.981	14.970	-0.337	-0.337	0.000	0.000	0.000	0.000
17	A	17	LEU	0	-0.027	-0.026	13.369	-0.033	-0.033	0.000	0.000	0.000	0.000
18	A	18	LYS	1	0.842	0.904	8.340	0.896	0.896	0.000	0.000	0.000	0.000
19	A	19	ASN	0	-0.003	0.004	10.087	-0.147	-0.147	0.000	0.000	0.000	0.000
20	A	20	PHE	0	-0.071	-0.036	11.307	-0.025	-0.025	0.000	0.000	0.000	0.000
21	A	21	LEU	0	0.003	-0.014	8.649	-0.010	-0.010	0.000	0.000	0.000	0.000
22	A	22	ASP	-1	-0.780	-0.890	6.253	-1.578	-1.578	0.000	0.000	0.000	0.000
23	A	23	SER	0	-0.118	-0.053	5.536	-0.246	-0.246	0.000	0.000	0.000	0.000
24	A	24	GLU	-1	-0.954	-0.960	4.520	-0.739	-0.551	-0.001	-0.021	-0.166	0.000
25	A	25	TYR	0	-0.077	-0.058	2.761	-3.446	-1.087	0.496	-1.129	-1.725	-0.011
26	A	26	LEU	0	-0.014	0.007	2.113	-1.581	-0.783	4.699	-1.194	-4.303	0.000
27	A	27	VAL	0	-0.014	-0.004	3.537	0.277	0.360	0.028	0.049	-0.160	0.000
28	A	28	ILE	0	-0.026	-0.005	7.090	0.206	0.206	0.000	0.000	0.000	0.000
29	A	29	GLU	-1	-0.887	-0.940	10.253	-0.446	-0.446	0.000	0.000	0.000	0.000
30	A	30	SER	0	0.039	-0.010	13.491	0.040	0.040	0.000	0.000	0.000	0.000
31	A	31	LYS	1	0.938	0.987	16.947	0.257	0.257	0.000	0.000	0.000	0.000
32	A	32	ASN	0	0.008	0.003	20.367	0.023	0.023	0.000	0.000	0.000	0.000
33	A	33	GLU	-1	-0.837	-0.934	21.139	-0.186	-0.186	0.000	0.000	0.000	0.000
34	A	34	LYS	1	0.880	0.952	21.967	0.161	0.161	0.000	0.000	0.000	0.000
35	A	35	GLU	-1	-0.751	-0.886	19.067	-0.296	-0.296	0.000	0.000	0.000	0.000
36	A	36	ALA	0	-0.027	0.001	17.311	-0.026	-0.026	0.000	0.000	0.000	0.000
37	A	37	LEU	0	-0.004	-0.033	17.342	-0.015	-0.015	0.000	0.000	0.000	0.000
38	A	38	GLU	-1	-0.888	-0.943	18.882	-0.214	-0.214	0.000	0.000	0.000	0.000
39	A	39	GLN	0	0.000	-0.008	13.800	-0.048	-0.048	0.000	0.000	0.000	0.000
40	A	40	ILE	0	-0.050	-0.021	13.916	-0.044	-0.044	0.000	0.000	0.000	0.000
41	A	41	ASP	-1	-0.944	-0.962	15.143	-0.204	-0.204	0.000	0.000	0.000	0.000
42	A	42	HIS	0	-0.109	-0.062	14.624	0.036	0.036	0.000	0.000	0.000	0.000
43	A	43	HIS	0	-0.010	-0.009	9.750	-0.028	-0.028	0.000	0.000	0.000	0.000
44	A	44	HIS	0	-0.077	-0.029	10.287	-0.085	-0.085	0.000	0.000	0.000	0.000
45	A	45	PRO	0	-0.039	-0.024	9.231	-0.065	-0.065	0.000	0.000	0.000	0.000
46	A	46	ASP	-1	-0.840	-0.900	6.620	-1.148	-1.148	0.000	0.000	0.000	0.000
47	A	47	LEU	0	0.016	0.008	9.740	0.201	0.201	0.000	0.000	0.000	0.000
48	A	48	VAL	0	-0.008	0.004	10.968	-0.114	-0.114	0.000	0.000	0.000	0.000
49	A	49	ILE	0	0.014	0.005	12.241	0.059	0.059	0.000	0.000	0.000	0.000
50	A	50	LEU	0	-0.020	-0.030	15.234	-0.009	-0.009	0.000	0.000	0.000	0.000
51	A	51	ASP	-1	-0.772	-0.875	18.690	-0.241	-0.241	0.000	0.000	0.000	0.000
52	A	52	MET	0	-0.036	-0.046	21.036	0.013	0.013	0.000	0.000	0.000	0.000
53	A	53	ASP	-1	-0.826	-0.912	23.571	-0.228	-0.228	0.000	0.000	0.000	0.000
54	A	54	ILE	0	-0.038	-0.011	21.748	0.007	0.007	0.000	0.000	0.000	0.000
55	A	55	ILE	0	-0.059	-0.030	25.120	0.013	0.013	0.000	0.000	0.000	0.000
56	A	56	GLY	0	0.034	0.025	27.911	-0.001	-0.001	0.000	0.000	0.000	0.000
57	A	57	GLU	-1	-0.961	-1.008	28.783	-0.093	-0.093	0.000	0.000	0.000	0.000
58	A	58	ASN	0	-0.026	-0.017	32.251	-0.001	-0.001	0.000	0.000	0.000	0.000
59	A	59	SER	0	-0.028	-0.019	32.588	0.008	0.008	0.000	0.000	0.000	0.000
60	A	60	PRO	0	-0.066	-0.010	30.079	-0.002	-0.002	0.000	0.000	0.000	0.000
61	A	61	ASN	0	0.081	0.055	26.877	-0.022	-0.022	0.000	0.000	0.000	0.000
62	A	62	LEU	0	0.102	0.020	22.373	0.003	0.003	0.000	0.000	0.000	0.000
63	A	63	CYS	0	0.014	0.028	22.524	-0.018	-0.018	0.000	0.000	0.000	0.000
64	A	64	LEU	0	-0.028	-0.011	23.286	0.000	0.000	0.000	0.000	0.000	0.000
65	A	65	LYS	1	0.874	0.952	24.178	0.157	0.157	0.000	0.000	0.000	0.000
66	A	66	LEU	0	0.035	0.015	18.995	0.005	0.005	0.000	0.000	0.000	0.000
67	A	67	LYS	1	0.902	0.944	19.751	0.162	0.162	0.000	0.000	0.000	0.000
68	A	68	ARG	1	0.779	0.919	22.680	0.129	0.129	0.000	0.000	0.000	0.000
69	A	69	SER	0	-0.008	-0.007	20.464	0.017	0.017	0.000	0.000	0.000	0.000
70	A	70	LYS	1	0.912	0.942	21.322	0.086	0.086	0.000	0.000	0.000	0.000
71	A	71	GLY	0	0.088	0.035	17.398	0.006	0.006	0.000	0.000	0.000	0.000
72	A	72	LEU	0	0.026	0.003	15.971	-0.032	-0.032	0.000	0.000	0.000	0.000
73	A	73	LYS	1	0.892	0.954	17.699	0.107	0.107	0.000	0.000	0.000	0.000
74	A	74	ASN	0	0.001	0.001	15.902	0.004	0.004	0.000	0.000	0.000	0.000
75	A	75	VAL	0	0.014	0.035	13.609	0.015	0.015	0.000	0.000	0.000	0.000
76	A	76	PRO	0	-0.032	-0.012	13.284	0.014	0.014	0.000	0.000	0.000	0.000
77	A	77	LEU	0	-0.023	-0.021	14.981	-0.063	-0.063	0.000	0.000	0.000	0.000
78	A	78	ILE	0	0.006	0.003	14.567	0.038	0.038	0.000	0.000	0.000	0.000
79	A	79	LEU	0	-0.020	-0.013	17.842	-0.025	-0.025	0.000	0.000	0.000	0.000
80	A	80	LEU	0	-0.014	-0.009	17.462	0.013	0.013	0.000	0.000	0.000	0.000
81	A	81	PHE	0	0.066	0.020	21.485	0.003	0.003	0.000	0.000	0.000	0.000
82	A	82	SER	0	0.029	0.017	25.173	0.004	0.004	0.000	0.000	0.000	0.000
83	A	83	SER	0	0.008	0.001	27.778	0.007	0.007	0.000	0.000	0.000	0.000
84	A	84	GLU	-1	-0.983	-0.992	29.826	-0.129	-0.129	0.000	0.000	0.000	0.000
85	A	85	HIS	0	0.019	-0.003	33.385	0.007	0.007	0.000	0.000	0.000	0.000
86	A	86	LYS	1	0.815	0.902	35.889	0.077	0.077	0.000	0.000	0.000	0.000
87	A	87	GLU	-1	-0.659	-0.863	31.197	-0.100	-0.100	0.000	0.000	0.000	0.000
88	A	88	ALA	0	-0.095	-0.020	33.328	0.008	0.008	0.000	0.000	0.000	0.000
89	A	89	ILE	0	0.060	0.040	27.070	0.003	0.003	0.000	0.000	0.000	0.000
90	A	90	VAL	0	-0.022	-0.014	30.934	0.004	0.004	0.000	0.000	0.000	0.000
91	A	91	ASN	0	-0.103	-0.048	32.855	0.007	0.007	0.000	0.000	0.000	0.000
92	A	92	GLY	0	0.034	0.024	32.386	0.006	0.006	0.000	0.000	0.000	0.000
93	A	93	LEU	0	-0.053	-0.024	31.801	-0.002	-0.002	0.000	0.000	0.000	0.000
94	A	94	HIS	0	0.038	0.008	26.970	-0.008	-0.008	0.000	0.000	0.000	0.000
95	A	95	SER	0	0.033	0.038	26.798	-0.011	-0.011	0.000	0.000	0.000	0.000
96	A	96	GLY	0	0.024	-0.013	25.610	-0.004	-0.004	0.000	0.000	0.000	0.000
97	A	97	ALA	0	-0.011	-0.007	21.314	-0.008	-0.008	0.000	0.000	0.000	0.000
98	A	98	ASP	-1	-0.831	-0.893	18.794	-0.141	-0.141	0.000	0.000	0.000	0.000
99	A	99	ASP	-1	-0.829	-0.911	19.189	-0.139	-0.139	0.000	0.000	0.000	0.000
100	A	100	TYR	0	-0.060	-0.020	20.886	-0.020	-0.020	0.000	0.000	0.000	0.000
101	A	101	LEU	0	-0.001	0.004	18.632	0.009	0.009	0.000	0.000	0.000	0.000
102	A	102	THR	0	0.019	0.016	22.422	-0.003	-0.003	0.000	0.000	0.000	0.000
103	A	103	LYS	1	0.808	0.926	22.370	0.230	0.230	0.000	0.000	0.000	0.000
104	A	104	PRO	0	-0.008	-0.024	23.939	0.012	0.012	0.000	0.000	0.000	0.000
105	A	105	PHE	0	0.089	0.039	16.890	0.014	0.014	0.000	0.000	0.000	0.000
106	A	106	ASN	0	0.007	0.009	20.069	-0.015	-0.015	0.000	0.000	0.000	0.000
107	A	107	ARG	1	0.975	0.977	15.811	0.326	0.326	0.000	0.000	0.000	0.000
108	A	108	ASN	0	0.010	-0.003	15.415	-0.057	-0.057	0.000	0.000	0.000	0.000
109	A	109	ASP	-1	-0.888	-0.944	16.284	-0.164	-0.164	0.000	0.000	0.000	0.000
110	A	110	LEU	0	0.003	0.009	14.148	0.007	0.007	0.000	0.000	0.000	0.000
111	A	111	LEU	0	0.042	0.020	9.408	-0.011	-0.011	0.000	0.000	0.000	0.000
112	A	112	SER	0	-0.003	0.011	12.377	0.022	0.022	0.000	0.000	0.000	0.000
113	A	113	ARG	1	0.900	0.933	14.687	0.182	0.182	0.000	0.000	0.000	0.000
114	A	114	ILE	0	0.004	0.018	9.609	0.041	0.041	0.000	0.000	0.000	0.000
115	A	115	GLU	-1	-0.841	-0.908	8.313	-0.178	-0.178	0.000	0.000	0.000	0.000
116	A	116	ILE	0	-0.052	-0.025	11.170	0.132	0.132	0.000	0.000	0.000	0.000
117	A	117	HIS	0	-0.063	-0.052	13.520	0.074	0.074	0.000	0.000	0.000	0.000
118	A	118	LEU	0	0.023	0.009	6.956	0.044	0.044	0.000	0.000	0.000	0.000
119	A	119	ARG	1	0.951	0.972	10.593	-0.059	-0.059	0.000	0.000	0.000	0.000
120	A	120	THR	0	-0.052	-0.016	12.049	0.070	0.070	0.000	0.000	0.000	0.000
121	A	121	GLN	0	0.009	-0.003	9.875	0.032	0.032	0.000	0.000	0.000	0.000
122	A	122	ASN	0	0.040	0.026	8.110	-0.098	-0.098	0.000	0.000	0.000	0.000
123	A	123	TYR	0	-0.025	0.011	12.264	0.015	0.015	0.000	0.000	0.000	0.000
124	A	124	TYR	0	-0.022	-0.033	15.778	-0.004	-0.004	0.000	0.000	0.000	0.000
125	A	125	SER	0	-0.093	-0.040	13.188	-0.024	-0.024	0.000	0.000	0.000	0.000
126	A	126	ASP	-1	-0.955	-0.981	13.878	0.650	0.650	0.000	0.000	0.000	0.000
127	A	127	LEU	0	-0.108	-0.036	16.323	-0.043	-0.043	0.000	0.000	0.000	0.000

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