FMO DATABASE

FMODB ID: 9G1Y2

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

Total energy (hartree)

FMO2-HF: Electronic energy	-1205681.76628
FMO2-HF: Nuclear repulsion	1152391.5839
FMO2-HF: Total energy	-53290.18238
FMO2-MP2: Total energy	-53444.826163

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.
-25.759	-14.368	6.075	-6.448	-11.016	-0.036

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 : 0.066 / q_NPA : 0.033

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	0.037	0.016	3.484	-4.185	-1.764	-0.009	-1.111	-1.301	0.004
4	A	10	LEU	0	0.071	0.041	2.197	-1.820	-1.166	2.843	-1.280	-2.217	-0.003
5	A	11	GLN	0	-0.075	-0.022	3.066	-0.386	0.824	0.068	-0.307	-0.970	0.000
6	A	12	THR	0	-0.096	-0.061	5.687	0.051	0.051	0.000	0.000	0.000	0.000
7	A	13	MET	0	-0.014	0.035	7.900	-0.061	-0.061	0.000	0.000	0.000	0.000
8	A	14	ASN	0	-0.009	-0.007	9.972	-0.132	-0.132	0.000	0.000	0.000	0.000
9	A	15	ALA	0	0.042	0.001	13.218	-0.026	-0.026	0.000	0.000	0.000	0.000
10	A	16	GLN	0	-0.032	-0.025	14.976	-0.030	-0.030	0.000	0.000	0.000	0.000
11	A	17	GLU	-1	-0.890	-0.946	10.972	0.299	0.299	0.000	0.000	0.000	0.000
12	A	18	TYR	0	-0.033	-0.038	7.305	-0.122	-0.122	0.000	0.000	0.000	0.000
13	A	19	GLU	-1	-0.727	-0.839	13.194	-0.214	-0.214	0.000	0.000	0.000	0.000
14	A	20	ASP	-1	-0.888	-0.927	15.661	0.024	0.024	0.000	0.000	0.000	0.000
15	A	21	ILE	0	-0.032	-0.020	10.495	0.005	0.005	0.000	0.000	0.000	0.000
16	A	22	ARG	1	0.739	0.836	14.561	0.203	0.203	0.000	0.000	0.000	0.000
17	A	23	ALA	0	-0.049	-0.029	16.773	0.007	0.007	0.000	0.000	0.000	0.000
18	A	24	ALA	0	-0.062	-0.016	16.670	0.013	0.013	0.000	0.000	0.000	0.000
19	A	25	GLY	0	0.048	0.026	18.172	0.016	0.016	0.000	0.000	0.000	0.000
20	A	26	SER	0	-0.003	-0.010	17.530	-0.024	-0.024	0.000	0.000	0.000	0.000
21	A	27	ASP	-1	-0.845	-0.907	17.324	-0.146	-0.146	0.000	0.000	0.000	0.000
22	A	28	GLU	-1	-0.877	-0.941	14.072	-0.080	-0.080	0.000	0.000	0.000	0.000
23	A	29	ARG	1	0.780	0.867	12.679	0.267	0.267	0.000	0.000	0.000	0.000
24	A	30	ARG	1	0.744	0.855	12.977	0.094	0.094	0.000	0.000	0.000	0.000
25	A	31	GLU	-1	-0.795	-0.884	10.714	-0.400	-0.400	0.000	0.000	0.000	0.000
26	A	32	LEU	0	-0.013	0.004	7.400	-0.184	-0.184	0.000	0.000	0.000	0.000
27	A	33	THR	0	-0.032	-0.034	8.617	-0.288	-0.288	0.000	0.000	0.000	0.000
28	A	34	HIS	0	-0.026	-0.016	10.259	-0.150	-0.150	0.000	0.000	0.000	0.000
29	A	35	ALA	0	-0.064	-0.021	4.949	-0.197	-0.197	0.000	0.000	0.000	0.000
30	A	36	VAL	0	0.013	-0.002	5.706	-0.800	-0.800	0.000	0.000	0.000	0.000
31	A	37	MET	0	-0.016	-0.011	6.503	-0.243	-0.243	0.000	0.000	0.000	0.000
32	A	38	ARG	1	0.780	0.873	3.113	3.944	4.284	0.003	-0.106	-0.236	0.000
33	A	39	GLU	-1	-0.835	-0.891	2.355	-15.817	-11.443	2.592	-2.875	-4.092	-0.034
34	A	40	LEU	0	-0.070	-0.030	4.862	0.053	0.127	-0.001	-0.004	-0.069	0.000
35	A	41	ASP	-1	-0.879	-0.929	7.704	-0.953	-0.953	0.000	0.000	0.000	0.000
36	A	42	ALA	0	-0.083	-0.042	11.030	0.055	0.055	0.000	0.000	0.000	0.000
37	A	43	PRO	0	0.005	-0.001	14.297	0.026	0.026	0.000	0.000	0.000	0.000
38	A	44	ASP	-1	-0.865	-0.935	17.024	-0.371	-0.371	0.000	0.000	0.000	0.000
39	A	45	ASN	0	-0.109	-0.065	20.034	0.028	0.028	0.000	0.000	0.000	0.000
40	A	46	TRP	0	0.019	0.008	18.241	0.017	0.017	0.000	0.000	0.000	0.000
41	A	47	THR	0	-0.044	-0.011	18.830	-0.021	-0.021	0.000	0.000	0.000	0.000
42	A	48	MET	0	0.007	-0.003	10.871	-0.026	-0.026	0.000	0.000	0.000	0.000
43	A	49	ASN	0	-0.039	-0.016	16.058	0.020	0.020	0.000	0.000	0.000	0.000
44	A	50	GLY	0	0.080	0.032	15.166	-0.030	-0.030	0.000	0.000	0.000	0.000
45	A	51	GLU	-1	-0.837	-0.886	15.949	-0.250	-0.250	0.000	0.000	0.000	0.000
46	A	52	TYR	0	-0.027	-0.044	15.465	-0.022	-0.022	0.000	0.000	0.000	0.000
47	A	53	GLY	0	-0.014	-0.006	19.154	0.027	0.027	0.000	0.000	0.000	0.000
48	A	54	SER	0	0.008	-0.004	21.439	-0.008	-0.008	0.000	0.000	0.000	0.000
49	A	55	GLU	-1	-0.822	-0.897	21.452	-0.260	-0.260	0.000	0.000	0.000	0.000
50	A	56	PHE	0	-0.078	-0.044	18.330	0.005	0.005	0.000	0.000	0.000	0.000
51	A	57	GLY	0	-0.011	-0.011	22.302	-0.009	-0.009	0.000	0.000	0.000	0.000
52	A	58	GLY	0	0.013	0.002	21.131	0.019	0.019	0.000	0.000	0.000	0.000
53	A	59	PHE	0	-0.039	-0.005	20.695	0.011	0.011	0.000	0.000	0.000	0.000
54	A	60	PHE	0	-0.004	-0.002	15.680	0.014	0.014	0.000	0.000	0.000	0.000
55	A	61	PRO	0	0.009	0.021	13.949	-0.017	-0.017	0.000	0.000	0.000	0.000
56	A	62	VAL	0	0.017	0.018	10.465	-0.017	-0.017	0.000	0.000	0.000	0.000
57	A	63	GLN	0	0.018	-0.003	13.446	0.013	0.013	0.000	0.000	0.000	0.000
58	A	64	VAL	0	0.022	0.010	11.102	0.015	0.015	0.000	0.000	0.000	0.000
59	A	65	ARG	1	0.854	0.933	14.305	0.346	0.346	0.000	0.000	0.000	0.000
60	A	66	PHE	0	0.044	0.004	11.487	-0.027	-0.027	0.000	0.000	0.000	0.000
61	A	67	THR	0	-0.011	-0.005	17.174	0.037	0.037	0.000	0.000	0.000	0.000
62	A	68	PRO	0	0.039	0.045	20.796	-0.009	-0.009	0.000	0.000	0.000	0.000
63	A	69	ALA	0	0.051	0.005	22.884	0.014	0.014	0.000	0.000	0.000	0.000
64	A	70	HIS	0	-0.113	-0.076	25.613	0.022	0.022	0.000	0.000	0.000	0.000
65	A	71	GLU	-1	-0.963	-0.973	25.638	-0.221	-0.221	0.000	0.000	0.000	0.000
66	A	72	ARG	1	0.840	0.914	26.934	0.219	0.219	0.000	0.000	0.000	0.000
67	A	73	PHE	0	-0.027	-0.015	21.804	0.010	0.010	0.000	0.000	0.000	0.000
68	A	74	HIS	0	0.004	0.012	20.841	-0.029	-0.029	0.000	0.000	0.000	0.000
69	A	75	LEU	0	0.029	0.015	16.840	0.017	0.017	0.000	0.000	0.000	0.000
70	A	76	ALA	0	0.001	0.000	16.589	-0.017	-0.017	0.000	0.000	0.000	0.000
71	A	77	LEU	0	-0.009	0.010	8.877	0.016	0.016	0.000	0.000	0.000	0.000
72	A	78	CYS	0	-0.067	-0.028	13.563	0.006	0.006	0.000	0.000	0.000	0.000
73	A	79	SER	0	0.029	0.009	11.110	-0.013	-0.013	0.000	0.000	0.000	0.000
74	A	80	PRO	0	-0.050	-0.023	10.904	0.060	0.060	0.000	0.000	0.000	0.000
75	A	81	GLY	0	0.016	-0.009	13.806	-0.022	-0.022	0.000	0.000	0.000	0.000
76	A	82	ASP	-1	-0.911	-0.966	16.768	-0.093	-0.093	0.000	0.000	0.000	0.000
77	A	83	VAL	0	-0.087	-0.034	19.749	0.009	0.009	0.000	0.000	0.000	0.000
78	A	84	SER	0	-0.003	-0.015	16.172	0.021	0.021	0.000	0.000	0.000	0.000
79	A	85	GLN	0	-0.005	-0.007	16.560	0.007	0.007	0.000	0.000	0.000	0.000
80	A	86	VAL	0	-0.068	-0.028	13.438	0.005	0.005	0.000	0.000	0.000	0.000
81	A	87	TRP	0	0.096	0.058	7.706	-0.033	-0.033	0.000	0.000	0.000	0.000
82	A	88	VAL	0	-0.018	-0.013	12.116	0.042	0.042	0.000	0.000	0.000	0.000
83	A	89	LEU	0	0.025	0.024	12.952	-0.046	-0.046	0.000	0.000	0.000	0.000
84	A	90	VAL	0	-0.020	-0.011	15.143	0.052	0.052	0.000	0.000	0.000	0.000
85	A	91	LEU	0	0.009	0.013	18.695	-0.032	-0.032	0.000	0.000	0.000	0.000
86	A	92	VAL	0	-0.015	-0.026	21.158	0.029	0.029	0.000	0.000	0.000	0.000
87	A	93	ASN	0	0.011	0.002	24.208	-0.018	-0.018	0.000	0.000	0.000	0.000
88	A	94	ALA	0	0.044	0.011	27.236	0.005	0.005	0.000	0.000	0.000	0.000
89	A	95	GLY	0	-0.048	-0.032	29.563	0.007	0.007	0.000	0.000	0.000	0.000
90	A	96	GLY	0	-0.055	-0.022	28.506	0.008	0.008	0.000	0.000	0.000	0.000
91	A	97	GLU	-1	-0.949	-0.954	29.348	-0.153	-0.153	0.000	0.000	0.000	0.000
92	A	98	PRO	0	0.040	0.024	28.119	0.002	0.002	0.000	0.000	0.000	0.000
93	A	99	PHE	0	-0.036	-0.036	22.634	-0.013	-0.013	0.000	0.000	0.000	0.000
94	A	100	ALA	0	0.002	0.001	23.076	0.015	0.015	0.000	0.000	0.000	0.000
95	A	101	VAL	0	0.009	0.010	18.025	-0.023	-0.023	0.000	0.000	0.000	0.000
96	A	102	VAL	0	0.002	-0.013	16.643	0.021	0.021	0.000	0.000	0.000	0.000
97	A	103	GLN	0	0.023	0.013	11.337	-0.076	-0.076	0.000	0.000	0.000	0.000
98	A	104	VAL	0	0.006	0.020	14.487	-0.013	-0.013	0.000	0.000	0.000	0.000
99	A	105	GLN	0	0.004	-0.006	8.056	-0.078	-0.078	0.000	0.000	0.000	0.000
100	A	106	ARG	1	0.925	0.954	11.550	0.145	0.145	0.000	0.000	0.000	0.000
101	A	107	ARG	1	0.907	0.963	6.303	-0.325	-0.325	0.000	0.000	0.000	0.000
102	A	108	PHE	0	0.049	0.032	2.704	-0.933	-0.040	0.278	-0.240	-0.931	0.000
103	A	109	ALA	0	0.015	-0.008	4.288	-0.230	-0.097	0.000	-0.030	-0.102	0.000
104	A	110	SER	0	0.049	0.023	3.113	-1.249	-0.078	0.302	-0.486	-0.987	-0.003
105	A	111	GLU	-1	-0.864	-0.937	4.608	-1.565	-1.444	-0.001	-0.009	-0.111	0.000
106	A	112	ALA	0	-0.019	-0.004	6.920	0.283	0.283	0.000	0.000	0.000	0.000
107	A	113	VAL	0	0.004	0.009	8.013	0.154	0.154	0.000	0.000	0.000	0.000
108	A	114	SER	0	0.079	0.031	8.311	0.151	0.151	0.000	0.000	0.000	0.000
109	A	115	HIS	0	-0.059	-0.030	10.293	0.249	0.249	0.000	0.000	0.000	0.000
110	A	116	SER	0	0.024	-0.019	12.562	0.065	0.065	0.000	0.000	0.000	0.000
111	A	117	LEU	0	-0.053	-0.022	12.004	0.086	0.086	0.000	0.000	0.000	0.000
112	A	118	ALA	0	0.018	0.011	14.839	0.067	0.067	0.000	0.000	0.000	0.000
113	A	119	LEU	0	-0.031	-0.009	16.719	0.064	0.064	0.000	0.000	0.000	0.000
114	A	120	ALA	0	0.025	0.006	18.221	0.044	0.044	0.000	0.000	0.000	0.000
115	A	121	ALA	0	0.013	0.009	19.355	0.038	0.038	0.000	0.000	0.000	0.000
116	A	122	SER	0	-0.013	0.003	20.827	0.045	0.045	0.000	0.000	0.000	0.000
117	A	123	LEU	0	-0.009	-0.016	22.232	0.029	0.029	0.000	0.000	0.000	0.000
118	A	124	ASP	-1	-0.778	-0.866	24.015	-0.228	-0.228	0.000	0.000	0.000	0.000
119	A	125	THR	0	-0.041	-0.019	24.684	0.020	0.020	0.000	0.000	0.000	0.000
120	A	126	GLN	0	-0.136	-0.066	25.123	0.030	0.030	0.000	0.000	0.000	0.000
121	A	127	GLY	0	-0.013	0.003	28.926	0.013	0.013	0.000	0.000	0.000	0.000
122	A	128	TYR	0	-0.049	-0.019	27.168	0.013	0.013	0.000	0.000	0.000	0.000
123	A	129	SER	0	-0.038	-0.045	28.901	-0.007	-0.007	0.000	0.000	0.000	0.000
124	A	130	VAL	0	0.074	0.017	25.646	-0.008	-0.008	0.000	0.000	0.000	0.000
125	A	131	ASN	0	0.011	-0.006	26.534	-0.013	-0.013	0.000	0.000	0.000	0.000
126	A	132	ASP	-1	-0.862	-0.892	27.780	-0.167	-0.167	0.000	0.000	0.000	0.000
127	A	133	ILE	0	-0.010	-0.008	22.422	-0.008	-0.008	0.000	0.000	0.000	0.000
128	A	134	ILE	0	0.016	0.010	22.880	-0.019	-0.019	0.000	0.000	0.000	0.000
129	A	135	HIS	0	-0.001	0.004	22.957	-0.014	-0.014	0.000	0.000	0.000	0.000
130	A	136	ILE	0	-0.029	-0.015	22.100	0.001	0.001	0.000	0.000	0.000	0.000
131	A	137	LEU	0	0.020	0.005	17.712	-0.008	-0.008	0.000	0.000	0.000	0.000
132	A	138	MET	0	0.002	0.018	18.720	-0.017	-0.017	0.000	0.000	0.000	0.000
133	A	139	ALA	0	-0.060	-0.010	20.378	0.005	0.005	0.000	0.000	0.000	0.000
134	A	140	GLU	-1	-0.900	-0.927	15.257	-0.472	-0.472	0.000	0.000	0.000	0.000
135	A	141	GLY	0	-0.001	-0.003	15.434	-0.026	-0.026	0.000	0.000	0.000	0.000
136	A	142	GLY	0	-0.054	-0.022	16.093	-0.006	-0.006	0.000	0.000	0.000	0.000
137	A	143	GLN	0	-0.118	-0.063	18.074	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:7:LEU)