FMO DATABASE

FMODB ID: 9GN42

Calculation Name: 3NCT-A-Xray317

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: 2021-09-07

Reference: C. Watanabe, S. Koyama, K. Kamisaka, D. Takaya, T. Honma et. al., Interaction energy analysis of Apo structure dataset on FMODB, To be pubulished.

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. 1.20200129

FMO calculation

FMO method	FMO2-MP2/6-31G(d)
Fragmentation	Auto
Number of fragment	139
LigandCharge
Software	ABINIT-MP - Open Ver.1 Rev. 15 / 20190524

Total energy (hartree)

FMO2-HF: Electronic energy	-1211788.239835
FMO2-HF: Nuclear repulsion	1158326.932329
FMO2-HF: Total energy	-53461.307506
FMO2-MP2: Total energy	-53616.473729

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:6:ACE )

Summations of interaction energy for fragment #1(A:6:ACE )

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.
-1.951	-0.17	0.271	-0.794	-1.257	-0.001

Interaction energy analysis for fragmet #1(A:6:ACE )

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.031 / 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	8	ASN	0	0.010	-0.001	3.871	1.295	2.081	-0.003	-0.315	-0.468	0.000
4	A	9	VAL	0	0.032	0.005	4.283	0.193	0.327	0.000	-0.020	-0.114	0.000
5	A	10	LEU	0	0.048	0.026	3.489	-0.235	-0.063	0.015	-0.063	-0.124	0.000
6	A	11	GLN	0	-0.085	-0.028	6.728	0.120	0.120	0.000	0.000	0.000	0.000
7	A	12	THR	0	-0.074	-0.041	8.759	0.076	0.076	0.000	0.000	0.000	0.000
8	A	13	MET	0	-0.010	0.032	8.691	0.077	0.077	0.000	0.000	0.000	0.000
9	A	14	ASN	0	-0.003	-0.002	11.426	-0.040	-0.040	0.000	0.000	0.000	0.000
10	A	15	ALA	0	0.040	0.001	14.566	0.018	0.018	0.000	0.000	0.000	0.000
11	A	16	GLN	0	-0.015	-0.013	16.742	-0.001	-0.001	0.000	0.000	0.000	0.000
12	A	17	GLU	-1	-0.871	-0.938	11.460	0.265	0.265	0.000	0.000	0.000	0.000
13	A	18	TYR	0	-0.030	-0.027	9.657	0.028	0.028	0.000	0.000	0.000	0.000
14	A	19	GLU	-1	-0.741	-0.874	13.865	0.048	0.048	0.000	0.000	0.000	0.000
15	A	20	ASP	-1	-0.897	-0.937	15.963	0.114	0.114	0.000	0.000	0.000	0.000
16	A	21	ILE	0	-0.042	-0.024	10.206	0.023	0.023	0.000	0.000	0.000	0.000
17	A	22	ARG	1	0.773	0.862	14.434	-0.033	-0.033	0.000	0.000	0.000	0.000
18	A	23	ALA	0	-0.065	-0.034	16.614	-0.002	-0.002	0.000	0.000	0.000	0.000
19	A	24	ALA	0	-0.062	-0.014	16.153	-0.003	-0.003	0.000	0.000	0.000	0.000
20	A	25	GLY	0	0.054	0.030	17.588	-0.004	-0.004	0.000	0.000	0.000	0.000
21	A	26	SER	0	-0.026	-0.019	16.763	0.014	0.014	0.000	0.000	0.000	0.000
22	A	27	ASP	-1	-0.852	-0.917	15.928	0.222	0.222	0.000	0.000	0.000	0.000
23	A	28	GLU	-1	-0.879	-0.947	12.928	0.320	0.320	0.000	0.000	0.000	0.000
24	A	29	ARG	1	0.794	0.868	11.765	-0.016	-0.016	0.000	0.000	0.000	0.000
25	A	30	ARG	1	0.821	0.915	12.264	-0.291	-0.291	0.000	0.000	0.000	0.000
26	A	31	GLU	-1	-0.901	-0.950	9.088	0.550	0.550	0.000	0.000	0.000	0.000
27	A	32	LEU	0	-0.012	0.005	7.418	0.120	0.120	0.000	0.000	0.000	0.000
28	A	33	THR	0	-0.019	-0.020	8.172	-0.129	-0.129	0.000	0.000	0.000	0.000
29	A	34	HIS	0	0.018	0.021	9.449	-0.137	-0.137	0.000	0.000	0.000	0.000
30	A	35	ALA	0	-0.076	-0.027	3.807	-0.081	-0.010	0.002	-0.022	-0.050	0.000
31	A	36	VAL	0	-0.002	-0.005	5.505	-0.510	-0.510	0.000	0.000	0.000	0.000
32	A	37	MET	0	0.001	-0.001	7.566	-0.134	-0.134	0.000	0.000	0.000	0.000
33	A	38	ARG	1	0.922	0.966	2.678	-2.022	-1.703	0.211	-0.236	-0.294	0.000
34	A	39	GLH	0	-0.062	-0.029	3.441	-1.454	-1.155	0.046	-0.138	-0.207	-0.001
35	A	40	LEU	0	-0.051	-0.017	7.874	0.024	0.024	0.000	0.000	0.000	0.000
36	A	41	ASP	-1	-0.878	-0.927	11.552	-0.324	-0.324	0.000	0.000	0.000	0.000
37	A	42	ALA	0	-0.075	-0.041	14.849	0.014	0.014	0.000	0.000	0.000	0.000
38	A	43	PRO	0	0.009	0.003	17.810	0.002	0.002	0.000	0.000	0.000	0.000
39	A	44	ASP	-1	-0.860	-0.932	21.096	-0.098	-0.098	0.000	0.000	0.000	0.000
40	A	45	ASN	0	-0.105	-0.062	23.413	0.008	0.008	0.000	0.000	0.000	0.000
41	A	46	TRP	0	0.021	0.009	21.776	0.004	0.004	0.000	0.000	0.000	0.000
42	A	47	THR	0	-0.045	-0.013	20.852	0.000	0.000	0.000	0.000	0.000	0.000
43	A	48	MET	0	0.005	-0.003	13.474	-0.006	-0.006	0.000	0.000	0.000	0.000
44	A	49	ASN	0	-0.032	-0.015	17.403	0.026	0.026	0.000	0.000	0.000	0.000
45	A	50	GLY	0	0.065	0.025	15.109	-0.020	-0.020	0.000	0.000	0.000	0.000
46	A	51	GLU	-1	-0.829	-0.875	16.082	0.025	0.025	0.000	0.000	0.000	0.000
47	A	52	TYR	0	-0.028	-0.058	14.289	0.007	0.007	0.000	0.000	0.000	0.000
48	A	53	GLY	0	-0.032	-0.011	18.423	0.015	0.015	0.000	0.000	0.000	0.000
49	A	54	SER	0	0.010	0.000	21.203	-0.001	-0.001	0.000	0.000	0.000	0.000
50	A	55	GLU	-1	-0.809	-0.898	21.024	0.032	0.032	0.000	0.000	0.000	0.000
51	A	56	PHE	0	-0.088	-0.048	19.181	-0.008	-0.008	0.000	0.000	0.000	0.000
52	A	57	GLY	0	-0.014	-0.016	23.456	-0.009	-0.009	0.000	0.000	0.000	0.000
53	A	58	GLY	0	0.007	-0.001	21.560	0.003	0.003	0.000	0.000	0.000	0.000
54	A	59	PHE	0	-0.037	-0.008	22.083	0.005	0.005	0.000	0.000	0.000	0.000
55	A	60	PHE	0	-0.009	-0.009	17.753	-0.003	-0.003	0.000	0.000	0.000	0.000
56	A	61	PRO	0	0.003	0.027	14.716	0.008	0.008	0.000	0.000	0.000	0.000
57	A	62	VAL	0	0.020	0.025	10.841	0.023	0.023	0.000	0.000	0.000	0.000
58	A	63	GLN	0	0.039	0.010	14.237	-0.033	-0.033	0.000	0.000	0.000	0.000
59	A	64	VAL	0	0.006	0.003	12.673	0.021	0.021	0.000	0.000	0.000	0.000
60	A	65	ARG	1	0.868	0.940	16.067	0.023	0.023	0.000	0.000	0.000	0.000
61	A	66	PHE	0	0.039	0.001	14.733	-0.001	-0.001	0.000	0.000	0.000	0.000
62	A	67	THR	0	-0.014	-0.003	20.278	0.003	0.003	0.000	0.000	0.000	0.000
63	A	68	PRO	0	0.037	0.041	23.839	0.001	0.001	0.000	0.000	0.000	0.000
64	A	69	ALA	0	0.054	0.008	26.283	0.007	0.007	0.000	0.000	0.000	0.000
65	A	70	HIS	0	-0.123	-0.083	28.432	0.010	0.010	0.000	0.000	0.000	0.000
66	A	71	GLU	-1	-0.959	-0.972	28.302	-0.025	-0.025	0.000	0.000	0.000	0.000
67	A	72	ARG	1	0.878	0.947	29.950	0.055	0.055	0.000	0.000	0.000	0.000
68	A	73	PHE	0	-0.031	-0.013	26.251	0.001	0.001	0.000	0.000	0.000	0.000
69	A	74	HIS	0	0.004	0.009	23.903	-0.005	-0.005	0.000	0.000	0.000	0.000
70	A	75	LEU	0	0.031	0.015	21.261	-0.001	-0.001	0.000	0.000	0.000	0.000
71	A	76	ALA	0	0.009	0.004	19.633	0.005	0.005	0.000	0.000	0.000	0.000
72	A	77	LEU	0	-0.015	0.006	12.755	-0.009	-0.009	0.000	0.000	0.000	0.000
73	A	78	CYS	0	-0.061	-0.030	16.508	0.023	0.023	0.000	0.000	0.000	0.000
74	A	79	SER	0	0.013	0.002	13.312	-0.014	-0.014	0.000	0.000	0.000	0.000
75	A	80	PRO	0	-0.049	-0.018	13.687	0.020	0.020	0.000	0.000	0.000	0.000
76	A	81	GLY	0	0.018	-0.011	16.055	0.018	0.018	0.000	0.000	0.000	0.000
77	A	82	ASP	-1	-0.909	-0.961	18.536	0.009	0.009	0.000	0.000	0.000	0.000
78	A	83	VAL	0	-0.076	-0.029	21.988	-0.006	-0.006	0.000	0.000	0.000	0.000
79	A	84	SER	0	-0.006	-0.020	20.072	-0.005	-0.005	0.000	0.000	0.000	0.000
80	A	85	GLN	0	-0.004	-0.007	19.675	-0.001	-0.001	0.000	0.000	0.000	0.000
81	A	86	VAL	0	-0.061	-0.024	17.806	-0.015	-0.015	0.000	0.000	0.000	0.000
82	A	87	TRP	0	0.069	0.049	10.265	0.009	0.009	0.000	0.000	0.000	0.000
83	A	88	VAL	0	-0.008	-0.007	16.605	0.001	0.001	0.000	0.000	0.000	0.000
84	A	89	LEU	0	0.019	0.017	17.939	-0.002	-0.002	0.000	0.000	0.000	0.000
85	A	90	VAL	0	-0.023	-0.011	20.022	0.009	0.009	0.000	0.000	0.000	0.000
86	A	91	LEU	0	0.020	0.017	22.986	-0.005	-0.005	0.000	0.000	0.000	0.000
87	A	92	VAL	0	-0.017	-0.026	25.500	0.007	0.007	0.000	0.000	0.000	0.000
88	A	93	ASN	0	0.047	0.022	28.010	-0.004	-0.004	0.000	0.000	0.000	0.000
89	A	94	ALA	0	0.027	0.005	31.077	0.004	0.004	0.000	0.000	0.000	0.000
90	A	95	GLY	0	-0.049	-0.034	32.878	0.000	0.000	0.000	0.000	0.000	0.000
91	A	96	GLY	0	-0.055	-0.022	31.839	0.002	0.002	0.000	0.000	0.000	0.000
92	A	97	GLU	-1	-0.960	-0.959	32.924	-0.043	-0.043	0.000	0.000	0.000	0.000
93	A	98	PRO	0	0.039	0.008	33.110	0.001	0.001	0.000	0.000	0.000	0.000
94	A	99	PHE	0	-0.016	-0.019	26.601	-0.002	-0.002	0.000	0.000	0.000	0.000
95	A	100	ALA	0	0.000	-0.005	28.258	0.001	0.001	0.000	0.000	0.000	0.000
96	A	101	VAL	0	0.000	0.011	23.320	-0.004	-0.004	0.000	0.000	0.000	0.000
97	A	102	VAL	0	0.002	-0.013	22.483	0.002	0.002	0.000	0.000	0.000	0.000
98	A	103	GLN	0	0.025	0.005	18.549	-0.035	-0.035	0.000	0.000	0.000	0.000
99	A	104	VAL	0	0.006	0.017	20.114	0.005	0.005	0.000	0.000	0.000	0.000
100	A	105	GLN	0	-0.004	-0.004	14.432	-0.038	-0.038	0.000	0.000	0.000	0.000
101	A	106	ARG	1	0.940	0.957	16.804	0.148	0.148	0.000	0.000	0.000	0.000
102	A	107	ARG	1	0.944	0.979	11.794	0.394	0.394	0.000	0.000	0.000	0.000
103	A	108	PHE	0	0.045	0.028	7.310	-0.021	-0.021	0.000	0.000	0.000	0.000
104	A	109	ALA	0	0.025	-0.001	10.814	-0.141	-0.141	0.000	0.000	0.000	0.000
105	A	110	SER	0	0.033	0.010	8.932	0.033	0.033	0.000	0.000	0.000	0.000
106	A	111	GLU	-1	-0.852	-0.933	11.073	-0.509	-0.509	0.000	0.000	0.000	0.000
107	A	112	ALA	0	-0.018	0.006	13.668	0.077	0.077	0.000	0.000	0.000	0.000
108	A	113	VAL	0	-0.002	0.007	13.880	0.051	0.051	0.000	0.000	0.000	0.000
109	A	114	SER	0	0.087	0.032	13.539	0.057	0.057	0.000	0.000	0.000	0.000
110	A	115	HIS	0	-0.047	-0.027	16.218	0.071	0.071	0.000	0.000	0.000	0.000
111	A	116	SER	0	0.009	-0.014	19.130	0.023	0.023	0.000	0.000	0.000	0.000
112	A	117	LEU	0	-0.044	-0.020	16.775	0.032	0.032	0.000	0.000	0.000	0.000
113	A	118	ALA	0	0.021	0.015	20.342	0.024	0.024	0.000	0.000	0.000	0.000
114	A	119	LEU	0	-0.020	-0.005	22.107	0.021	0.021	0.000	0.000	0.000	0.000
115	A	120	ALA	0	0.027	0.004	23.974	0.016	0.016	0.000	0.000	0.000	0.000
116	A	121	ALA	0	0.007	0.008	24.171	0.013	0.013	0.000	0.000	0.000	0.000
117	A	122	SER	0	-0.012	-0.003	26.001	0.015	0.015	0.000	0.000	0.000	0.000
118	A	123	LEU	0	-0.017	-0.019	28.074	0.010	0.010	0.000	0.000	0.000	0.000
119	A	124	ASP	-1	-0.798	-0.888	29.020	-0.061	-0.061	0.000	0.000	0.000	0.000
120	A	125	THR	0	-0.035	-0.007	29.544	0.008	0.008	0.000	0.000	0.000	0.000
121	A	126	GLN	0	-0.142	-0.075	31.265	0.008	0.008	0.000	0.000	0.000	0.000
122	A	127	GLY	0	-0.013	0.006	34.141	0.003	0.003	0.000	0.000	0.000	0.000
123	A	128	TYR	0	-0.043	-0.013	32.876	0.003	0.003	0.000	0.000	0.000	0.000
124	A	129	SER	0	-0.011	-0.001	34.172	0.000	0.000	0.000	0.000	0.000	0.000
125	A	130	VAL	0	0.075	0.023	30.686	-0.004	-0.004	0.000	0.000	0.000	0.000
126	A	131	ASN	0	0.000	-0.013	32.039	-0.006	-0.006	0.000	0.000	0.000	0.000
127	A	132	ASP	-1	-0.891	-0.940	33.776	-0.063	-0.063	0.000	0.000	0.000	0.000
128	A	133	ILE	0	-0.028	-0.014	28.086	-0.006	-0.006	0.000	0.000	0.000	0.000
129	A	134	ILE	0	0.011	0.008	28.795	-0.009	-0.009	0.000	0.000	0.000	0.000
130	A	135	HIS	0	0.002	0.004	29.306	-0.007	-0.007	0.000	0.000	0.000	0.000
131	A	136	ILE	0	-0.021	-0.011	28.737	-0.004	-0.004	0.000	0.000	0.000	0.000
132	A	137	LEU	0	0.008	-0.005	24.213	-0.008	-0.008	0.000	0.000	0.000	0.000
133	A	138	MET	0	-0.001	0.017	25.567	-0.008	-0.008	0.000	0.000	0.000	0.000
134	A	139	ALA	0	-0.051	-0.010	27.362	-0.004	-0.004	0.000	0.000	0.000	0.000
135	A	140	GLU	-1	-0.917	-0.940	22.295	-0.202	-0.202	0.000	0.000	0.000	0.000
136	A	141	GLY	0	0.013	0.007	22.657	-0.015	-0.015	0.000	0.000	0.000	0.000
137	A	142	GLY	0	-0.065	-0.033	23.251	-0.007	-0.007	0.000	0.000	0.000	0.000
138	A	143	GLN	0	-0.058	-0.033	24.699	-0.001	-0.001	0.000	0.000	0.000	0.000
139	A	144	NME	0	-0.057	-0.022	27.254	0.011	0.011	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:6:ACE )