FMO DATABASE

FMODB ID: LJKL9

Calculation Name: 3NCT-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3NCT

Chain ID: A

ChEMBL ID:

UniProt ID: P10031

Base Structure: X-ray

Registration Date: 2023-06-20

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	137
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1204055.386507
FMO2-HF: Nuclear repulsion	1150765.690647
FMO2-HF: Total energy	-53289.695859
FMO2-MP2: Total energy	-53444.327294

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:7:LEU)

Summations of interaction energy for fragment #1(A:7: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.
-35.957	-21.719	6.826	-8.395	-12.667	-0.067

Interaction energy analysis for fragmet #1(A:7:LEU)

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 : 0.035

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	9	VAL	0	0.020	-0.004	3.603	-4.426	-2.034	-0.008	-1.139	-1.244	0.005
4	A	10	LEU	0	0.064	0.034	2.363	-2.277	-0.849	1.652	-1.055	-2.025	-0.002
5	A	11	GLN	0	-0.093	-0.033	2.980	-0.920	0.869	0.257	-0.610	-1.436	-0.003
6	A	12	THR	0	-0.080	-0.044	5.572	-0.032	-0.032	0.000	0.000	0.000	0.000
7	A	13	MET	0	-0.012	0.032	7.932	-0.086	-0.086	0.000	0.000	0.000	0.000
8	A	14	ASN	0	-0.009	-0.005	10.050	-0.131	-0.131	0.000	0.000	0.000	0.000
9	A	15	ALA	0	0.040	0.001	13.173	-0.025	-0.025	0.000	0.000	0.000	0.000
10	A	16	GLN	0	-0.023	-0.017	14.945	-0.032	-0.032	0.000	0.000	0.000	0.000
11	A	17	GLU	-1	-0.872	-0.938	11.098	0.445	0.445	0.000	0.000	0.000	0.000
12	A	18	TYR	0	-0.022	-0.022	7.381	-0.135	-0.135	0.000	0.000	0.000	0.000
13	A	19	GLU	-1	-0.748	-0.877	13.202	-0.188	-0.188	0.000	0.000	0.000	0.000
14	A	20	ASP	-1	-0.898	-0.938	15.640	0.076	0.076	0.000	0.000	0.000	0.000
15	A	21	ILE	0	-0.038	-0.021	10.451	-0.004	-0.004	0.000	0.000	0.000	0.000
16	A	22	ARG	1	0.772	0.862	14.571	0.168	0.168	0.000	0.000	0.000	0.000
17	A	23	ALA	0	-0.067	-0.035	16.753	0.003	0.003	0.000	0.000	0.000	0.000
18	A	24	ALA	0	-0.062	-0.014	16.709	0.009	0.009	0.000	0.000	0.000	0.000
19	A	25	GLY	0	0.051	0.028	18.149	0.013	0.013	0.000	0.000	0.000	0.000
20	A	26	SER	0	-0.029	-0.019	17.501	-0.034	-0.034	0.000	0.000	0.000	0.000
21	A	27	ASP	-1	-0.853	-0.918	17.266	-0.136	-0.136	0.000	0.000	0.000	0.000
22	A	28	GLU	-1	-0.880	-0.947	14.044	-0.049	-0.049	0.000	0.000	0.000	0.000
23	A	29	ARG	1	0.793	0.868	12.645	0.263	0.263	0.000	0.000	0.000	0.000
24	A	30	ARG	1	0.815	0.912	12.908	0.094	0.094	0.000	0.000	0.000	0.000
25	A	31	GLU	-1	-0.903	-0.952	10.604	-0.379	-0.379	0.000	0.000	0.000	0.000
26	A	32	LEU	0	-0.006	0.008	7.453	-0.202	-0.202	0.000	0.000	0.000	0.000
27	A	33	THR	0	-0.026	-0.023	8.525	-0.322	-0.322	0.000	0.000	0.000	0.000
28	A	34	HIS	0	0.009	0.014	10.272	-0.166	-0.166	0.000	0.000	0.000	0.000
29	A	35	ALA	0	-0.070	-0.024	4.794	-0.262	-0.220	-0.001	-0.001	-0.039	0.000
30	A	36	VAL	0	0.020	0.008	5.762	-0.951	-0.951	0.000	0.000	0.000	0.000
31	A	37	MET	0	-0.016	-0.013	6.577	-0.274	-0.274	0.000	0.000	0.000	0.000
32	A	38	ARG	1	0.911	0.963	4.821	1.577	1.577	0.000	0.000	0.000	0.000
33	A	39	GLU	-1	-0.908	-0.963	2.221	-22.525	-16.178	4.464	-4.923	-5.888	-0.065
34	A	40	LEU	0	-0.075	-0.031	4.975	0.154	0.225	-0.001	-0.004	-0.066	0.000
35	A	41	ASP	-1	-0.883	-0.930	7.777	-1.215	-1.215	0.000	0.000	0.000	0.000
36	A	42	ALA	0	-0.075	-0.042	11.105	0.074	0.074	0.000	0.000	0.000	0.000
37	A	43	PRO	0	0.005	0.002	14.365	0.023	0.023	0.000	0.000	0.000	0.000
38	A	44	ASP	-1	-0.861	-0.933	17.082	-0.422	-0.422	0.000	0.000	0.000	0.000
39	A	45	ASN	0	-0.111	-0.065	20.106	0.027	0.027	0.000	0.000	0.000	0.000
40	A	46	TRP	0	0.022	0.009	18.083	0.022	0.022	0.000	0.000	0.000	0.000
41	A	47	THR	0	-0.043	-0.013	18.901	-0.024	-0.024	0.000	0.000	0.000	0.000
42	A	48	MET	0	0.003	-0.001	11.002	-0.024	-0.024	0.000	0.000	0.000	0.000
43	A	49	ASN	0	-0.033	-0.016	16.112	0.009	0.009	0.000	0.000	0.000	0.000
44	A	50	GLY	0	0.076	0.030	15.177	-0.031	-0.031	0.000	0.000	0.000	0.000
45	A	51	GLU	-1	-0.831	-0.878	15.988	-0.246	-0.246	0.000	0.000	0.000	0.000
46	A	52	TYR	0	-0.029	-0.057	15.219	-0.020	-0.020	0.000	0.000	0.000	0.000
47	A	53	GLY	0	-0.034	-0.012	19.057	0.032	0.032	0.000	0.000	0.000	0.000
48	A	54	SER	0	0.007	-0.001	21.451	-0.006	-0.006	0.000	0.000	0.000	0.000
49	A	55	GLU	-1	-0.810	-0.900	21.392	-0.277	-0.277	0.000	0.000	0.000	0.000
50	A	56	PHE	0	-0.088	-0.047	18.372	0.005	0.005	0.000	0.000	0.000	0.000
51	A	57	GLY	0	-0.016	-0.018	22.396	-0.007	-0.007	0.000	0.000	0.000	0.000
52	A	58	GLY	0	0.005	0.000	21.154	0.021	0.021	0.000	0.000	0.000	0.000
53	A	59	PHE	0	-0.041	-0.011	20.729	0.015	0.015	0.000	0.000	0.000	0.000
54	A	60	PHE	0	-0.012	-0.010	15.790	0.016	0.016	0.000	0.000	0.000	0.000
55	A	61	PRO	0	0.005	0.027	13.982	-0.022	-0.022	0.000	0.000	0.000	0.000
56	A	62	VAL	0	0.030	0.030	10.417	-0.020	-0.020	0.000	0.000	0.000	0.000
57	A	63	GLN	0	0.029	0.006	13.453	0.015	0.015	0.000	0.000	0.000	0.000
58	A	64	VAL	0	0.019	0.010	11.175	0.010	0.010	0.000	0.000	0.000	0.000
59	A	65	ARG	1	0.863	0.937	14.334	0.365	0.365	0.000	0.000	0.000	0.000
60	A	66	PHE	0	0.040	0.003	11.371	-0.032	-0.032	0.000	0.000	0.000	0.000
61	A	67	THR	0	-0.020	-0.006	17.213	0.045	0.045	0.000	0.000	0.000	0.000
62	A	68	PRO	0	0.039	0.043	20.839	-0.011	-0.011	0.000	0.000	0.000	0.000
63	A	69	ALA	0	0.052	0.007	22.931	0.016	0.016	0.000	0.000	0.000	0.000
64	A	70	HIS	0	-0.126	-0.085	25.673	0.025	0.025	0.000	0.000	0.000	0.000
65	A	71	GLU	-1	-0.954	-0.970	25.872	-0.232	-0.232	0.000	0.000	0.000	0.000
66	A	72	ARG	1	0.872	0.945	26.973	0.233	0.233	0.000	0.000	0.000	0.000
67	A	73	PHE	0	-0.031	-0.014	21.760	0.012	0.012	0.000	0.000	0.000	0.000
68	A	74	HIS	0	0.002	0.008	20.827	-0.034	-0.034	0.000	0.000	0.000	0.000
69	A	75	LEU	0	0.030	0.015	16.861	0.020	0.020	0.000	0.000	0.000	0.000
70	A	76	ALA	0	0.007	0.004	16.591	-0.021	-0.021	0.000	0.000	0.000	0.000
71	A	77	LEU	0	-0.006	0.010	8.981	0.022	0.022	0.000	0.000	0.000	0.000
72	A	78	CYS	0	-0.068	-0.034	13.635	0.001	0.001	0.000	0.000	0.000	0.000
73	A	79	SER	0	0.019	0.007	11.141	-0.008	-0.008	0.000	0.000	0.000	0.000
74	A	80	PRO	0	-0.048	-0.019	10.932	0.060	0.060	0.000	0.000	0.000	0.000
75	A	81	GLY	0	0.016	-0.010	13.801	-0.022	-0.022	0.000	0.000	0.000	0.000
76	A	82	ASP	-1	-0.910	-0.962	16.772	-0.066	-0.066	0.000	0.000	0.000	0.000
77	A	83	VAL	0	-0.080	-0.032	19.847	0.008	0.008	0.000	0.000	0.000	0.000
78	A	84	SER	0	-0.007	-0.020	16.123	0.019	0.019	0.000	0.000	0.000	0.000
79	A	85	GLN	0	-0.008	-0.008	16.538	0.018	0.018	0.000	0.000	0.000	0.000
80	A	86	VAL	0	-0.062	-0.024	13.383	0.015	0.015	0.000	0.000	0.000	0.000
81	A	87	TRP	0	0.079	0.054	7.503	-0.035	-0.035	0.000	0.000	0.000	0.000
82	A	88	VAL	0	-0.010	-0.009	12.103	0.043	0.043	0.000	0.000	0.000	0.000
83	A	89	LEU	0	0.023	0.020	13.065	-0.050	-0.050	0.000	0.000	0.000	0.000
84	A	90	VAL	0	-0.026	-0.013	15.180	0.054	0.054	0.000	0.000	0.000	0.000
85	A	91	LEU	0	0.017	0.017	18.755	-0.035	-0.035	0.000	0.000	0.000	0.000
86	A	92	VAL	0	-0.019	-0.026	21.213	0.031	0.031	0.000	0.000	0.000	0.000
87	A	93	ASN	0	0.044	0.022	24.254	-0.025	-0.025	0.000	0.000	0.000	0.000
88	A	94	ALA	0	0.030	0.005	27.233	0.006	0.006	0.000	0.000	0.000	0.000
89	A	95	GLY	0	-0.051	-0.036	29.571	0.008	0.008	0.000	0.000	0.000	0.000
90	A	96	GLY	0	-0.052	-0.022	28.564	0.009	0.009	0.000	0.000	0.000	0.000
91	A	97	GLU	-1	-0.962	-0.959	29.403	-0.155	-0.155	0.000	0.000	0.000	0.000
92	A	98	PRO	0	0.039	0.008	28.085	0.001	0.001	0.000	0.000	0.000	0.000
93	A	99	PHE	0	-0.020	-0.022	22.673	-0.014	-0.014	0.000	0.000	0.000	0.000
94	A	100	ALA	0	0.002	-0.004	23.187	0.016	0.016	0.000	0.000	0.000	0.000
95	A	101	VAL	0	-0.002	0.011	18.035	-0.023	-0.023	0.000	0.000	0.000	0.000
96	A	102	VAL	0	0.002	-0.015	16.606	0.022	0.022	0.000	0.000	0.000	0.000
97	A	103	GLN	0	0.023	0.006	11.508	-0.050	-0.050	0.000	0.000	0.000	0.000
98	A	104	VAL	0	0.007	0.016	14.449	-0.013	-0.013	0.000	0.000	0.000	0.000
99	A	105	GLN	0	-0.003	-0.003	8.217	-0.050	-0.050	0.000	0.000	0.000	0.000
100	A	106	ARG	1	0.935	0.953	11.505	0.105	0.105	0.000	0.000	0.000	0.000
101	A	107	ARG	1	0.939	0.977	6.871	-0.386	-0.386	0.000	0.000	0.000	0.000
102	A	108	PHE	0	0.053	0.034	2.681	-0.772	0.049	0.252	-0.198	-0.875	0.000
103	A	109	ALA	0	0.018	-0.004	4.233	-0.115	0.032	0.000	-0.037	-0.111	0.000
104	A	110	SER	0	0.043	0.019	3.083	-0.962	0.134	0.212	-0.420	-0.887	-0.002
105	A	111	GLU	-1	-0.849	-0.932	4.666	-1.612	-1.507	-0.001	-0.008	-0.096	0.000
106	A	112	ALA	0	-0.024	0.002	6.934	0.267	0.267	0.000	0.000	0.000	0.000
107	A	113	VAL	0	0.000	0.008	7.998	0.150	0.150	0.000	0.000	0.000	0.000
108	A	114	SER	0	0.089	0.034	8.387	0.164	0.164	0.000	0.000	0.000	0.000
109	A	115	HIS	0	-0.052	-0.029	10.289	0.250	0.250	0.000	0.000	0.000	0.000
110	A	116	SER	0	0.011	-0.014	12.585	0.068	0.068	0.000	0.000	0.000	0.000
111	A	117	LEU	0	-0.042	-0.019	12.101	0.092	0.092	0.000	0.000	0.000	0.000
112	A	118	ALA	0	0.023	0.016	14.878	0.069	0.069	0.000	0.000	0.000	0.000
113	A	119	LEU	0	-0.028	-0.008	16.755	0.067	0.067	0.000	0.000	0.000	0.000
114	A	120	ALA	0	0.027	0.004	18.265	0.046	0.046	0.000	0.000	0.000	0.000
115	A	121	ALA	0	0.012	0.009	19.368	0.039	0.039	0.000	0.000	0.000	0.000
116	A	122	SER	0	-0.016	-0.004	20.849	0.046	0.046	0.000	0.000	0.000	0.000
117	A	123	LEU	0	-0.019	-0.020	22.050	0.032	0.032	0.000	0.000	0.000	0.000
118	A	124	ASP	-1	-0.798	-0.888	24.069	-0.245	-0.245	0.000	0.000	0.000	0.000
119	A	125	THR	0	-0.035	-0.007	24.834	0.021	0.021	0.000	0.000	0.000	0.000
120	A	126	GLN	0	-0.144	-0.076	25.377	0.034	0.034	0.000	0.000	0.000	0.000
121	A	127	GLY	0	-0.012	0.006	28.973	0.014	0.014	0.000	0.000	0.000	0.000
122	A	128	TYR	0	-0.041	-0.012	27.200	0.015	0.015	0.000	0.000	0.000	0.000
123	A	129	SER	0	-0.016	-0.003	28.950	-0.007	-0.007	0.000	0.000	0.000	0.000
124	A	130	VAL	0	0.078	0.024	25.806	-0.007	-0.007	0.000	0.000	0.000	0.000
125	A	131	ASN	0	-0.002	-0.015	26.570	-0.013	-0.013	0.000	0.000	0.000	0.000
126	A	132	ASP	-1	-0.894	-0.942	27.799	-0.170	-0.170	0.000	0.000	0.000	0.000
127	A	133	ILE	0	-0.024	-0.012	22.446	-0.007	-0.007	0.000	0.000	0.000	0.000
128	A	134	ILE	0	0.010	0.009	22.907	-0.018	-0.018	0.000	0.000	0.000	0.000
129	A	135	HIS	0	-0.003	0.000	22.963	-0.012	-0.012	0.000	0.000	0.000	0.000
130	A	136	ILE	0	-0.025	-0.013	21.989	0.002	0.002	0.000	0.000	0.000	0.000
131	A	137	LEU	0	0.008	-0.005	17.872	-0.008	-0.008	0.000	0.000	0.000	0.000
132	A	138	MET	0	-0.021	0.009	18.710	-0.014	-0.014	0.000	0.000	0.000	0.000
133	A	139	ALA	0	-0.046	-0.010	20.122	0.003	0.003	0.000	0.000	0.000	0.000
134	A	140	GLU	-1	-0.923	-0.945	15.087	-0.478	-0.478	0.000	0.000	0.000	0.000
135	A	141	GLY	0	0.015	0.009	15.402	-0.023	-0.023	0.000	0.000	0.000	0.000
136	A	142	GLY	0	-0.061	-0.026	16.049	-0.001	-0.001	0.000	0.000	0.000	0.000
137	A	143	GLN	0	-0.092	-0.045	18.111	0.035	0.035	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:7:LEU)