FMO DATABASE

FMODB ID: M3QMZ

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	OptAll
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	-1207029.067924
FMO2-HF: Nuclear repulsion	1153738.769176
FMO2-HF: Total energy	-53290.298747
FMO2-MP2: Total energy	-53444.949453

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.
-31.635	-22.061	12.925	-8.783	-13.715	-0.059

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 : 0.063 / q_NPA : 0.030

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	0.028	0.021	3.370	-4.054	-1.721	0.004	-1.094	-1.242	0.004
4	A	10	LEU	0	0.091	0.055	2.159	-1.713	-0.984	2.160	-0.933	-1.956	-0.001
5	A	11	GLN	0	-0.080	-0.021	2.868	-0.707	1.003	0.234	-0.523	-1.421	-0.001
6	A	12	THR	0	-0.074	-0.055	5.554	0.027	0.027	0.000	0.000	0.000	0.000
7	A	13	MET	0	-0.036	0.021	7.950	-0.071	-0.071	0.000	0.000	0.000	0.000
8	A	14	ASN	0	0.002	0.006	10.016	-0.154	-0.154	0.000	0.000	0.000	0.000
9	A	15	ALA	0	0.031	-0.006	13.258	-0.032	-0.032	0.000	0.000	0.000	0.000
10	A	16	GLN	0	-0.058	-0.026	15.033	-0.034	-0.034	0.000	0.000	0.000	0.000
11	A	17	GLU	-1	-0.843	-0.937	11.260	0.344	0.344	0.000	0.000	0.000	0.000
12	A	18	TYR	0	-0.039	-0.045	7.221	-0.117	-0.117	0.000	0.000	0.000	0.000
13	A	19	GLU	-1	-0.718	-0.837	13.372	-0.215	-0.215	0.000	0.000	0.000	0.000
14	A	20	ASP	-1	-0.876	-0.926	15.812	0.043	0.043	0.000	0.000	0.000	0.000
15	A	21	ILE	0	-0.037	-0.028	10.630	0.009	0.009	0.000	0.000	0.000	0.000
16	A	22	ARG	1	0.743	0.851	14.677	0.191	0.191	0.000	0.000	0.000	0.000
17	A	23	ALA	0	-0.039	-0.020	16.923	0.002	0.002	0.000	0.000	0.000	0.000
18	A	24	ALA	0	-0.065	-0.023	16.862	0.012	0.012	0.000	0.000	0.000	0.000
19	A	25	GLY	0	0.031	0.015	18.280	0.015	0.015	0.000	0.000	0.000	0.000
20	A	26	SER	0	0.002	-0.009	17.866	-0.025	-0.025	0.000	0.000	0.000	0.000
21	A	27	ASP	-1	-0.852	-0.899	17.148	-0.159	-0.159	0.000	0.000	0.000	0.000
22	A	28	GLU	-1	-0.879	-0.940	14.037	-0.094	-0.094	0.000	0.000	0.000	0.000
23	A	29	ARG	1	0.791	0.867	12.797	0.270	0.270	0.000	0.000	0.000	0.000
24	A	30	ARG	1	0.733	0.851	13.260	0.116	0.116	0.000	0.000	0.000	0.000
25	A	31	GLU	-1	-0.763	-0.867	10.952	-0.439	-0.439	0.000	0.000	0.000	0.000
26	A	32	LEU	0	-0.012	0.008	7.567	-0.182	-0.182	0.000	0.000	0.000	0.000
27	A	33	THR	0	-0.017	-0.024	8.563	-0.299	-0.299	0.000	0.000	0.000	0.000
28	A	34	HIS	0	-0.054	-0.038	10.229	-0.160	-0.160	0.000	0.000	0.000	0.000
29	A	35	ALA	0	-0.052	-0.020	5.058	-0.218	-0.218	0.000	0.000	0.000	0.000
30	A	36	VAL	0	-0.004	-0.010	5.619	-0.831	-0.831	0.000	0.000	0.000	0.000
31	A	37	MET	0	-0.014	-0.010	6.480	-0.251	-0.251	0.000	0.000	0.000	0.000
32	A	38	ARG	1	0.788	0.872	2.980	3.965	4.478	0.007	-0.239	-0.281	0.001
33	A	39	GLU	-1	-0.835	-0.873	1.923	-18.735	-17.825	9.255	-4.652	-5.513	-0.053
34	A	40	LEU	0	-0.055	-0.033	4.711	-0.116	-0.005	-0.001	-0.006	-0.103	0.000
35	A	41	ASP	-1	-0.884	-0.928	7.526	-0.989	-0.989	0.000	0.000	0.000	0.000
36	A	42	ALA	0	-0.055	-0.033	11.015	0.039	0.039	0.000	0.000	0.000	0.000
37	A	43	PRO	0	-0.008	-0.005	14.351	0.035	0.035	0.000	0.000	0.000	0.000
38	A	44	ASP	-1	-0.862	-0.931	16.953	-0.392	-0.392	0.000	0.000	0.000	0.000
39	A	45	ASN	0	-0.096	-0.058	20.209	0.032	0.032	0.000	0.000	0.000	0.000
40	A	46	TRP	0	-0.004	0.005	18.021	0.016	0.016	0.000	0.000	0.000	0.000
41	A	47	THR	0	-0.048	-0.013	18.432	-0.006	-0.006	0.000	0.000	0.000	0.000
42	A	48	MET	0	-0.001	-0.006	10.600	-0.038	-0.038	0.000	0.000	0.000	0.000
43	A	49	ASN	0	-0.032	-0.007	15.730	0.036	0.036	0.000	0.000	0.000	0.000
44	A	50	GLY	0	0.087	0.025	15.025	-0.048	-0.048	0.000	0.000	0.000	0.000
45	A	51	GLU	-1	-0.839	-0.891	15.776	-0.256	-0.256	0.000	0.000	0.000	0.000
46	A	52	TYR	0	-0.009	-0.025	15.239	-0.016	-0.016	0.000	0.000	0.000	0.000
47	A	53	GLY	0	0.004	-0.002	18.838	0.028	0.028	0.000	0.000	0.000	0.000
48	A	54	SER	0	-0.006	-0.019	21.666	0.000	0.000	0.000	0.000	0.000	0.000
49	A	55	GLU	-1	-0.827	-0.895	21.182	-0.269	-0.269	0.000	0.000	0.000	0.000
50	A	56	PHE	0	-0.065	-0.033	18.107	0.003	0.003	0.000	0.000	0.000	0.000
51	A	57	GLY	0	-0.007	-0.009	21.968	-0.010	-0.010	0.000	0.000	0.000	0.000
52	A	58	GLY	0	0.009	-0.008	21.585	0.021	0.021	0.000	0.000	0.000	0.000
53	A	59	PHE	0	-0.045	-0.006	20.336	0.011	0.011	0.000	0.000	0.000	0.000
54	A	60	PHE	0	0.016	0.005	15.446	0.019	0.019	0.000	0.000	0.000	0.000
55	A	61	PRO	0	-0.017	0.008	13.766	-0.021	-0.021	0.000	0.000	0.000	0.000
56	A	62	VAL	0	0.024	0.024	10.172	-0.014	-0.014	0.000	0.000	0.000	0.000
57	A	63	GLN	0	-0.003	-0.006	13.167	0.000	0.000	0.000	0.000	0.000	0.000
58	A	64	VAL	0	0.022	0.007	10.918	0.009	0.009	0.000	0.000	0.000	0.000
59	A	65	ARG	1	0.846	0.933	13.996	0.370	0.370	0.000	0.000	0.000	0.000
60	A	66	PHE	0	0.039	0.003	11.200	-0.026	-0.026	0.000	0.000	0.000	0.000
61	A	67	THR	0	0.010	0.002	16.953	0.022	0.022	0.000	0.000	0.000	0.000
62	A	68	PRO	0	0.045	0.047	20.575	-0.011	-0.011	0.000	0.000	0.000	0.000
63	A	69	ALA	0	0.026	-0.009	22.600	0.019	0.019	0.000	0.000	0.000	0.000
64	A	70	HIS	0	-0.111	-0.074	25.443	0.027	0.027	0.000	0.000	0.000	0.000
65	A	71	GLU	-1	-0.963	-0.985	25.535	-0.242	-0.242	0.000	0.000	0.000	0.000
66	A	72	ARG	1	0.818	0.904	26.606	0.235	0.235	0.000	0.000	0.000	0.000
67	A	73	PHE	0	-0.011	-0.005	21.358	0.012	0.012	0.000	0.000	0.000	0.000
68	A	74	HIS	0	0.000	0.012	20.633	-0.033	-0.033	0.000	0.000	0.000	0.000
69	A	75	LEU	0	0.025	0.007	16.311	0.017	0.017	0.000	0.000	0.000	0.000
70	A	76	ALA	0	-0.005	-0.008	16.262	-0.016	-0.016	0.000	0.000	0.000	0.000
71	A	77	LEU	0	0.003	0.023	8.499	0.025	0.025	0.000	0.000	0.000	0.000
72	A	78	CYS	0	-0.072	-0.034	13.156	0.015	0.015	0.000	0.000	0.000	0.000
73	A	79	SER	0	0.035	-0.003	11.151	-0.016	-0.016	0.000	0.000	0.000	0.000
74	A	80	PRO	0	-0.048	-0.020	10.688	0.061	0.061	0.000	0.000	0.000	0.000
75	A	81	GLY	0	0.045	0.015	13.593	-0.027	-0.027	0.000	0.000	0.000	0.000
76	A	82	ASP	-1	-0.920	-0.963	16.765	-0.087	-0.087	0.000	0.000	0.000	0.000
77	A	83	VAL	0	-0.094	-0.040	19.298	0.008	0.008	0.000	0.000	0.000	0.000
78	A	84	SER	0	-0.009	-0.017	15.675	0.013	0.013	0.000	0.000	0.000	0.000
79	A	85	GLN	0	-0.015	-0.007	16.324	0.018	0.018	0.000	0.000	0.000	0.000
80	A	86	VAL	0	-0.067	-0.031	13.011	0.022	0.022	0.000	0.000	0.000	0.000
81	A	87	TRP	0	0.093	0.063	7.539	-0.046	-0.046	0.000	0.000	0.000	0.000
82	A	88	VAL	0	-0.029	-0.015	11.571	0.043	0.043	0.000	0.000	0.000	0.000
83	A	89	LEU	0	0.029	0.021	12.202	-0.060	-0.060	0.000	0.000	0.000	0.000
84	A	90	VAL	0	-0.028	-0.014	14.617	0.053	0.053	0.000	0.000	0.000	0.000
85	A	91	LEU	0	0.003	0.008	18.052	-0.040	-0.040	0.000	0.000	0.000	0.000
86	A	92	VAL	0	-0.007	-0.020	20.696	0.031	0.031	0.000	0.000	0.000	0.000
87	A	93	ASN	0	0.021	0.000	23.919	-0.019	-0.019	0.000	0.000	0.000	0.000
88	A	94	ALA	0	0.036	0.016	27.002	0.004	0.004	0.000	0.000	0.000	0.000
89	A	95	GLY	0	-0.050	-0.027	29.347	0.010	0.010	0.000	0.000	0.000	0.000
90	A	96	GLY	0	-0.045	-0.022	28.139	0.009	0.009	0.000	0.000	0.000	0.000
91	A	97	GLU	-1	-0.950	-0.957	28.761	-0.165	-0.165	0.000	0.000	0.000	0.000
92	A	98	PRO	0	0.027	0.024	27.620	0.001	0.001	0.000	0.000	0.000	0.000
93	A	99	PHE	0	-0.025	-0.037	22.235	-0.013	-0.013	0.000	0.000	0.000	0.000
94	A	100	ALA	0	-0.001	0.002	22.674	0.018	0.018	0.000	0.000	0.000	0.000
95	A	101	VAL	0	0.011	0.006	17.524	-0.025	-0.025	0.000	0.000	0.000	0.000
96	A	102	VAL	0	0.016	0.011	16.212	0.022	0.022	0.000	0.000	0.000	0.000
97	A	103	GLN	0	0.034	0.025	10.726	-0.092	-0.092	0.000	0.000	0.000	0.000
98	A	104	VAL	0	-0.003	-0.001	13.721	-0.004	-0.004	0.000	0.000	0.000	0.000
99	A	105	GLN	0	-0.006	-0.009	7.486	-0.081	-0.081	0.000	0.000	0.000	0.000
100	A	106	ARG	1	0.929	0.956	10.931	0.151	0.151	0.000	0.000	0.000	0.000
101	A	107	ARG	1	0.846	0.930	5.805	-0.626	-0.626	0.000	0.000	0.000	0.000
102	A	108	PHE	0	0.048	0.024	2.465	-1.131	-0.165	0.680	-0.363	-1.283	-0.002
103	A	109	ALA	0	0.007	-0.008	3.411	-0.970	-0.382	0.036	-0.269	-0.356	-0.002
104	A	110	SER	0	0.047	0.002	2.775	-1.744	-0.251	0.550	-0.679	-1.364	-0.005
105	A	111	GLU	-1	-0.854	-0.910	4.372	-2.399	-2.178	0.000	-0.025	-0.196	0.000
106	A	112	ALA	0	-0.009	0.005	6.998	0.317	0.317	0.000	0.000	0.000	0.000
107	A	113	VAL	0	0.014	0.016	7.585	0.187	0.187	0.000	0.000	0.000	0.000
108	A	114	SER	0	0.061	0.019	8.532	0.145	0.145	0.000	0.000	0.000	0.000
109	A	115	HIS	0	-0.082	-0.041	10.301	0.275	0.275	0.000	0.000	0.000	0.000
110	A	116	SER	0	0.022	-0.023	12.505	0.065	0.065	0.000	0.000	0.000	0.000
111	A	117	LEU	0	-0.037	-0.013	11.834	0.096	0.096	0.000	0.000	0.000	0.000
112	A	118	ALA	0	0.027	0.016	14.701	0.076	0.076	0.000	0.000	0.000	0.000
113	A	119	LEU	0	-0.040	-0.016	16.523	0.073	0.073	0.000	0.000	0.000	0.000
114	A	120	ALA	0	0.027	0.003	17.944	0.050	0.050	0.000	0.000	0.000	0.000
115	A	121	ALA	0	0.017	0.013	19.143	0.044	0.044	0.000	0.000	0.000	0.000
116	A	122	SER	0	-0.010	0.010	20.658	0.051	0.051	0.000	0.000	0.000	0.000
117	A	123	LEU	0	-0.011	-0.011	21.870	0.033	0.033	0.000	0.000	0.000	0.000
118	A	124	ASP	-1	-0.770	-0.864	23.758	-0.249	-0.249	0.000	0.000	0.000	0.000
119	A	125	THR	0	-0.063	-0.041	24.309	0.022	0.022	0.000	0.000	0.000	0.000
120	A	126	GLN	0	-0.108	-0.057	25.013	0.033	0.033	0.000	0.000	0.000	0.000
121	A	127	GLY	0	-0.027	0.003	28.581	0.015	0.015	0.000	0.000	0.000	0.000
122	A	128	TYR	0	-0.049	-0.021	26.906	0.014	0.014	0.000	0.000	0.000	0.000
123	A	129	SER	0	-0.038	-0.047	28.569	-0.008	-0.008	0.000	0.000	0.000	0.000
124	A	130	VAL	0	0.058	0.007	25.377	-0.008	-0.008	0.000	0.000	0.000	0.000
125	A	131	ASN	0	0.023	0.007	25.973	-0.016	-0.016	0.000	0.000	0.000	0.000
126	A	132	ASP	-1	-0.859	-0.889	26.975	-0.184	-0.184	0.000	0.000	0.000	0.000
127	A	133	ILE	0	-0.011	-0.004	22.127	-0.010	-0.010	0.000	0.000	0.000	0.000
128	A	134	ILE	0	0.025	0.012	22.392	-0.022	-0.022	0.000	0.000	0.000	0.000
129	A	135	HIS	0	-0.002	0.000	22.500	-0.015	-0.015	0.000	0.000	0.000	0.000
130	A	136	ILE	0	-0.024	-0.015	21.636	0.000	0.000	0.000	0.000	0.000	0.000
131	A	137	LEU	0	0.006	-0.001	17.319	-0.012	-0.012	0.000	0.000	0.000	0.000
132	A	138	MET	0	-0.022	0.001	18.268	-0.020	-0.020	0.000	0.000	0.000	0.000
133	A	139	ALA	0	-0.064	-0.008	19.826	0.004	0.004	0.000	0.000	0.000	0.000
134	A	140	GLU	-1	-0.885	-0.917	15.237	-0.536	-0.536	0.000	0.000	0.000	0.000
135	A	141	GLY	0	0.007	-0.001	14.786	-0.029	-0.029	0.000	0.000	0.000	0.000
136	A	142	GLY	0	-0.046	-0.028	15.771	-0.002	-0.002	0.000	0.000	0.000	0.000
137	A	143	GLN	0	-0.116	-0.056	17.466	0.065	0.065	0.000	0.000	0.000	0.000

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