FMO DATABASE

FMODB ID: 1NK1Z

Calculation Name: 4DT4-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 4DT4

Chain ID: A

ChEMBL ID:

UniProt ID: P0AEM0

Base Structure: X-ray

Registration Date: 2023-09-23

Reference: C. Watanabe, N. Tani, K. Kamisaka, T. Honma et al., Interaction energy analysis of Apo structure dataset on FMODB, To be published.

DOI:

Apendix: None

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	160
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1290311.256554
FMO2-HF: Nuclear repulsion	1229618.573848
FMO2-HF: Total energy	-60692.682706
FMO2-MP2: Total energy	-60868.766866

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:-10:HIS)

Summations of interaction energy for fragment #1(A:-10:HIS)

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.
-26.86	-15.047	5.052	-6.859	-10.005	0.02

Interaction energy analysis for fragmet #1(A:-10:HIS)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.037 / q_NPA : 0.015

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	SER	0	-0.008	-0.005	2.604	-9.841	-3.306	1.248	-3.479	-4.303	0.028
4	A	-7	GLY	0	0.022	0.028	2.823	-3.914	-2.458	0.207	-0.596	-1.067	0.003
5	A	-6	LEU	0	-0.018	-0.007	2.581	-5.844	-3.010	1.244	-1.285	-2.793	0.008
6	A	-5	VAL	0	-0.009	-0.008	2.505	-8.581	-7.593	2.353	-1.499	-1.842	-0.019
7	A	-4	PRO	0	-0.011	-0.008	4.840	1.212	1.212	0.000	0.000	0.000	0.000
8	A	-3	ARG	1	0.876	0.944	8.015	-0.021	-0.021	0.000	0.000	0.000	0.000
9	A	-2	GLY	0	0.005	0.018	11.174	0.044	0.044	0.000	0.000	0.000	0.000
10	A	-1	SER	0	-0.015	-0.029	13.464	0.054	0.054	0.000	0.000	0.000	0.000
11	A	0	HIS	0	0.017	0.005	16.403	0.015	0.015	0.000	0.000	0.000	0.000
12	A	1	MET	0	0.055	0.034	19.124	0.033	0.033	0.000	0.000	0.000	0.000
13	A	2	SER	0	-0.040	-0.008	16.663	-0.059	-0.059	0.000	0.000	0.000	0.000
14	A	3	GLU	-1	-0.892	-0.958	13.348	-0.787	-0.787	0.000	0.000	0.000	0.000
15	A	4	SER	0	-0.015	-0.010	15.257	-0.023	-0.023	0.000	0.000	0.000	0.000
16	A	5	VAL	0	-0.011	0.010	17.645	0.039	0.039	0.000	0.000	0.000	0.000
17	A	6	GLN	0	-0.027	-0.023	15.293	0.116	0.116	0.000	0.000	0.000	0.000
18	A	7	SER	0	0.027	-0.006	19.286	-0.026	-0.026	0.000	0.000	0.000	0.000
19	A	8	ASN	0	-0.027	-0.017	21.469	-0.012	-0.012	0.000	0.000	0.000	0.000
20	A	9	SER	0	-0.018	0.012	21.324	-0.009	-0.009	0.000	0.000	0.000	0.000
21	A	10	ALA	0	-0.034	0.000	23.460	0.004	0.004	0.000	0.000	0.000	0.000
22	A	11	VAL	0	0.025	0.002	24.398	-0.022	-0.022	0.000	0.000	0.000	0.000
23	A	12	LEU	0	-0.016	0.010	26.963	0.009	0.009	0.000	0.000	0.000	0.000
24	A	13	VAL	0	0.034	0.011	28.450	-0.017	-0.017	0.000	0.000	0.000	0.000
25	A	14	HIS	0	0.046	0.037	30.859	0.012	0.012	0.000	0.000	0.000	0.000
26	A	15	PHE	0	0.032	-0.005	32.652	-0.002	-0.002	0.000	0.000	0.000	0.000
27	A	16	THR	0	-0.075	-0.039	34.926	-0.001	-0.001	0.000	0.000	0.000	0.000
28	A	17	LEU	0	0.040	0.035	36.694	-0.001	-0.001	0.000	0.000	0.000	0.000
29	A	18	LYS	1	0.855	0.912	38.812	0.033	0.033	0.000	0.000	0.000	0.000
30	A	19	LEU	0	0.074	0.043	40.919	0.005	0.005	0.000	0.000	0.000	0.000
31	A	20	ASP	-1	-0.854	-0.933	42.988	0.009	0.009	0.000	0.000	0.000	0.000
32	A	21	ASP	-1	-0.903	-0.919	44.683	-0.004	-0.004	0.000	0.000	0.000	0.000
33	A	22	GLY	0	-0.040	-0.017	44.682	-0.004	-0.004	0.000	0.000	0.000	0.000
34	A	23	THR	0	-0.123	-0.082	45.708	-0.004	-0.004	0.000	0.000	0.000	0.000
35	A	24	THR	0	-0.038	-0.044	42.231	-0.001	-0.001	0.000	0.000	0.000	0.000
36	A	25	ALA	0	-0.009	0.008	42.399	0.000	0.000	0.000	0.000	0.000	0.000
37	A	26	GLU	-1	-0.824	-0.907	40.253	0.004	0.004	0.000	0.000	0.000	0.000
38	A	27	SER	0	-0.044	-0.040	39.406	-0.006	-0.006	0.000	0.000	0.000	0.000
39	A	28	THR	0	0.008	0.001	35.588	0.003	0.003	0.000	0.000	0.000	0.000
40	A	29	ARG	1	0.904	0.947	38.908	0.053	0.053	0.000	0.000	0.000	0.000
41	A	30	ASN	0	-0.031	0.002	41.309	-0.002	-0.002	0.000	0.000	0.000	0.000
42	A	31	ASN	0	-0.003	-0.020	40.348	0.000	0.000	0.000	0.000	0.000	0.000
43	A	32	GLY	0	-0.009	0.011	42.518	0.002	0.002	0.000	0.000	0.000	0.000
44	A	33	LYS	1	0.853	0.924	38.835	0.010	0.010	0.000	0.000	0.000	0.000
45	A	34	PRO	0	-0.002	0.005	33.741	0.004	0.004	0.000	0.000	0.000	0.000
46	A	35	ALA	0	-0.015	0.005	34.350	0.006	0.006	0.000	0.000	0.000	0.000
47	A	36	LEU	0	0.009	0.000	29.872	-0.008	-0.008	0.000	0.000	0.000	0.000
48	A	37	PHE	0	0.006	-0.004	29.508	0.008	0.008	0.000	0.000	0.000	0.000
49	A	38	ARG	1	0.962	0.978	27.482	-0.092	-0.092	0.000	0.000	0.000	0.000
50	A	39	LEU	0	-0.017	0.000	23.400	0.000	0.000	0.000	0.000	0.000	0.000
51	A	40	GLY	0	0.012	-0.003	26.218	0.008	0.008	0.000	0.000	0.000	0.000
52	A	41	ASP	-1	-0.896	-0.939	27.051	0.128	0.128	0.000	0.000	0.000	0.000
53	A	42	ALA	0	-0.052	-0.022	30.577	-0.007	-0.007	0.000	0.000	0.000	0.000
54	A	43	SER	0	-0.042	-0.031	31.910	-0.013	-0.013	0.000	0.000	0.000	0.000
55	A	44	LEU	0	-0.055	-0.021	28.820	-0.016	-0.016	0.000	0.000	0.000	0.000
56	A	45	SER	0	0.023	-0.002	31.931	0.010	0.010	0.000	0.000	0.000	0.000
57	A	46	GLU	-1	-0.871	-0.953	28.803	0.193	0.193	0.000	0.000	0.000	0.000
58	A	47	GLY	0	0.002	0.007	28.385	0.003	0.003	0.000	0.000	0.000	0.000
59	A	48	LEU	0	-0.027	-0.006	29.050	-0.010	-0.010	0.000	0.000	0.000	0.000
60	A	49	GLU	-1	-0.775	-0.888	25.762	0.148	0.148	0.000	0.000	0.000	0.000
61	A	50	GLN	0	-0.045	-0.034	23.559	0.000	0.000	0.000	0.000	0.000	0.000
62	A	51	HIS	1	0.804	0.906	23.901	-0.055	-0.055	0.000	0.000	0.000	0.000
63	A	52	LEU	0	0.022	0.014	24.663	-0.028	-0.028	0.000	0.000	0.000	0.000
64	A	53	LEU	0	-0.022	-0.004	19.821	-0.017	-0.017	0.000	0.000	0.000	0.000
65	A	54	GLY	0	-0.041	-0.023	17.480	-0.010	-0.010	0.000	0.000	0.000	0.000
66	A	55	LEU	0	-0.034	0.001	18.351	-0.062	-0.062	0.000	0.000	0.000	0.000
67	A	56	LYS	1	0.900	0.940	14.422	0.488	0.488	0.000	0.000	0.000	0.000
68	A	57	VAL	0	-0.012	-0.012	20.404	0.019	0.019	0.000	0.000	0.000	0.000
69	A	58	GLY	0	-0.022	-0.003	22.968	-0.034	-0.034	0.000	0.000	0.000	0.000
70	A	59	ASP	-1	-0.865	-0.908	21.567	-0.214	-0.214	0.000	0.000	0.000	0.000
71	A	60	LYS	1	0.786	0.869	24.941	0.151	0.151	0.000	0.000	0.000	0.000
72	A	61	THR	0	-0.020	-0.003	26.601	-0.005	-0.005	0.000	0.000	0.000	0.000
73	A	62	THR	0	0.008	-0.015	28.632	0.000	0.000	0.000	0.000	0.000	0.000
74	A	63	PHE	0	-0.091	-0.038	29.488	0.001	0.001	0.000	0.000	0.000	0.000
75	A	64	SER	0	0.068	0.031	32.382	-0.003	-0.003	0.000	0.000	0.000	0.000
76	A	65	LEU	0	-0.120	-0.042	31.293	0.007	0.007	0.000	0.000	0.000	0.000
77	A	66	GLU	-1	-0.791	-0.880	35.312	0.032	0.032	0.000	0.000	0.000	0.000
78	A	67	PRO	0	0.052	0.008	37.268	0.007	0.007	0.000	0.000	0.000	0.000
79	A	68	ASP	-1	-0.959	-0.966	37.420	0.087	0.087	0.000	0.000	0.000	0.000
80	A	69	ALA	0	-0.046	-0.017	32.755	0.010	0.010	0.000	0.000	0.000	0.000
81	A	70	ALA	0	-0.010	0.009	33.700	0.001	0.001	0.000	0.000	0.000	0.000
82	A	71	PHE	0	0.026	0.000	36.291	0.005	0.005	0.000	0.000	0.000	0.000
83	A	72	GLY	0	0.016	0.027	39.102	0.002	0.002	0.000	0.000	0.000	0.000
84	A	73	VAL	0	0.013	-0.008	40.648	-0.008	-0.008	0.000	0.000	0.000	0.000
85	A	74	PRO	0	0.002	0.007	44.125	0.003	0.003	0.000	0.000	0.000	0.000
86	A	75	SER	0	0.011	-0.012	47.009	0.000	0.000	0.000	0.000	0.000	0.000
87	A	76	PRO	0	-0.007	-0.025	48.735	-0.003	-0.003	0.000	0.000	0.000	0.000
88	A	77	ASP	-1	-0.907	-0.943	49.344	0.072	0.072	0.000	0.000	0.000	0.000
89	A	78	LEU	0	-0.033	-0.014	46.329	0.001	0.001	0.000	0.000	0.000	0.000
90	A	79	ILE	0	-0.063	-0.008	50.911	-0.004	-0.004	0.000	0.000	0.000	0.000
91	A	80	GLN	0	-0.053	-0.028	52.099	0.001	0.001	0.000	0.000	0.000	0.000
92	A	81	TYR	0	-0.023	-0.011	56.529	-0.002	-0.002	0.000	0.000	0.000	0.000
93	A	82	PHE	0	0.030	0.027	55.724	0.001	0.001	0.000	0.000	0.000	0.000
94	A	83	SER	0	-0.066	-0.055	61.626	-0.002	-0.002	0.000	0.000	0.000	0.000
95	A	84	ARG	1	0.908	0.924	64.452	-0.021	-0.021	0.000	0.000	0.000	0.000
96	A	85	ARG	1	0.791	0.873	66.125	-0.032	-0.032	0.000	0.000	0.000	0.000
97	A	86	GLU	-1	-0.872	-0.925	61.344	0.039	0.039	0.000	0.000	0.000	0.000
98	A	87	PHE	0	0.011	-0.006	59.287	0.001	0.001	0.000	0.000	0.000	0.000
99	A	88	MET	0	-0.077	-0.031	63.390	-0.002	-0.002	0.000	0.000	0.000	0.000
100	A	89	ASP	-1	-0.956	-0.979	63.058	0.023	0.023	0.000	0.000	0.000	0.000
101	A	90	ALA	0	-0.018	-0.002	59.602	-0.001	-0.001	0.000	0.000	0.000	0.000
102	A	91	GLY	0	-0.005	0.003	60.642	-0.001	-0.001	0.000	0.000	0.000	0.000
103	A	92	GLU	-1	-0.893	-0.950	62.936	0.019	0.019	0.000	0.000	0.000	0.000
104	A	93	PRO	0	-0.031	-0.004	61.720	-0.001	-0.001	0.000	0.000	0.000	0.000
105	A	94	GLU	-1	-0.908	-0.968	61.424	0.012	0.012	0.000	0.000	0.000	0.000
106	A	95	ILE	0	-0.045	-0.020	60.588	0.001	0.001	0.000	0.000	0.000	0.000
107	A	96	GLY	0	-0.021	-0.008	57.269	-0.002	-0.002	0.000	0.000	0.000	0.000
108	A	97	ALA	0	-0.017	-0.001	56.234	-0.001	-0.001	0.000	0.000	0.000	0.000
109	A	98	ILE	0	0.009	-0.002	50.319	0.003	0.003	0.000	0.000	0.000	0.000
110	A	99	MET	0	-0.044	-0.016	54.113	-0.002	-0.002	0.000	0.000	0.000	0.000
111	A	100	LEU	0	0.020	0.008	49.996	0.002	0.002	0.000	0.000	0.000	0.000
112	A	101	PHE	0	0.010	0.007	51.940	-0.001	-0.001	0.000	0.000	0.000	0.000
113	A	102	THR	0	-0.002	0.007	51.251	0.000	0.000	0.000	0.000	0.000	0.000
114	A	103	ALA	0	0.018	0.015	48.581	0.001	0.001	0.000	0.000	0.000	0.000
115	A	104	MET	0	-0.011	-0.013	49.920	-0.001	-0.001	0.000	0.000	0.000	0.000
116	A	105	ASP	-1	-0.900	-0.934	44.924	0.073	0.073	0.000	0.000	0.000	0.000
117	A	106	GLY	0	-0.035	-0.021	47.775	0.000	0.000	0.000	0.000	0.000	0.000
118	A	107	SER	0	-0.098	-0.056	45.183	-0.004	-0.004	0.000	0.000	0.000	0.000
119	A	108	GLU	-1	-0.921	-0.969	46.889	0.032	0.032	0.000	0.000	0.000	0.000
120	A	109	MET	0	-0.040	-0.029	45.589	0.002	0.002	0.000	0.000	0.000	0.000
121	A	110	PRO	0	-0.015	-0.005	46.895	-0.002	-0.002	0.000	0.000	0.000	0.000
122	A	111	GLY	0	0.050	0.018	49.665	0.004	0.004	0.000	0.000	0.000	0.000
123	A	112	VAL	0	-0.038	-0.011	51.497	-0.003	-0.003	0.000	0.000	0.000	0.000
124	A	113	ILE	0	0.003	0.002	54.195	0.003	0.003	0.000	0.000	0.000	0.000
125	A	114	ARG	1	0.845	0.908	53.790	-0.036	-0.036	0.000	0.000	0.000	0.000
126	A	115	GLU	-1	-0.921	-0.970	58.563	0.026	0.026	0.000	0.000	0.000	0.000
127	A	116	ILE	0	-0.015	0.011	62.285	0.001	0.001	0.000	0.000	0.000	0.000
128	A	117	ASN	0	-0.028	-0.017	65.130	-0.002	-0.002	0.000	0.000	0.000	0.000
129	A	118	GLY	0	0.032	0.019	68.132	0.001	0.001	0.000	0.000	0.000	0.000
130	A	119	ASP	-1	-0.811	-0.897	68.944	0.029	0.029	0.000	0.000	0.000	0.000
131	A	120	SER	0	0.008	0.022	64.745	0.002	0.002	0.000	0.000	0.000	0.000
132	A	121	ILE	0	-0.020	-0.008	60.753	-0.002	-0.002	0.000	0.000	0.000	0.000
133	A	122	THR	0	0.001	0.000	58.189	0.003	0.003	0.000	0.000	0.000	0.000
134	A	123	VAL	0	-0.006	0.004	54.298	-0.003	-0.003	0.000	0.000	0.000	0.000
135	A	124	ASP	-1	-0.804	-0.894	51.201	0.045	0.045	0.000	0.000	0.000	0.000
136	A	125	PHE	0	0.040	0.016	49.323	-0.002	-0.002	0.000	0.000	0.000	0.000
137	A	126	ASN	0	-0.073	-0.039	47.039	0.008	0.008	0.000	0.000	0.000	0.000
138	A	127	HIS	0	0.084	0.046	40.141	-0.005	-0.005	0.000	0.000	0.000	0.000
139	A	128	PRO	0	0.028	0.004	44.369	-0.001	-0.001	0.000	0.000	0.000	0.000
140	A	129	LEU	0	-0.031	-0.011	40.583	-0.004	-0.004	0.000	0.000	0.000	0.000
141	A	130	ALA	0	-0.007	-0.002	42.983	0.002	0.002	0.000	0.000	0.000	0.000
142	A	131	GLY	0	-0.066	-0.046	43.426	-0.004	-0.004	0.000	0.000	0.000	0.000
143	A	132	GLN	0	-0.049	-0.009	42.763	-0.005	-0.005	0.000	0.000	0.000	0.000
144	A	133	THR	0	-0.038	-0.042	39.126	0.005	0.005	0.000	0.000	0.000	0.000
145	A	134	VAL	0	-0.044	-0.009	36.657	-0.005	-0.005	0.000	0.000	0.000	0.000
146	A	135	HIS	0	-0.058	-0.036	36.711	0.006	0.006	0.000	0.000	0.000	0.000
147	A	136	PHE	0	0.039	0.005	32.938	-0.003	-0.003	0.000	0.000	0.000	0.000
148	A	137	ASP	-1	-0.806	-0.885	33.155	-0.047	-0.047	0.000	0.000	0.000	0.000
149	A	138	ILE	0	0.006	-0.003	29.468	0.004	0.004	0.000	0.000	0.000	0.000
150	A	139	GLU	-1	-0.838	-0.914	28.864	-0.135	-0.135	0.000	0.000	0.000	0.000
151	A	140	VAL	0	0.010	0.004	23.619	0.014	0.014	0.000	0.000	0.000	0.000
152	A	141	LEU	0	-0.061	-0.033	26.749	-0.023	-0.023	0.000	0.000	0.000	0.000
153	A	142	GLU	-1	-0.896	-0.973	25.457	-0.132	-0.132	0.000	0.000	0.000	0.000
154	A	143	ILE	0	-0.048	-0.024	20.328	0.023	0.023	0.000	0.000	0.000	0.000
155	A	144	ASP	-1	-0.858	-0.936	21.654	0.017	0.017	0.000	0.000	0.000	0.000
156	A	145	PRO	0	-0.011	0.020	24.842	-0.011	-0.011	0.000	0.000	0.000	0.000
157	A	146	ALA	0	-0.014	-0.008	26.999	0.018	0.018	0.000	0.000	0.000	0.000
158	A	147	LEU	0	-0.029	-0.020	28.577	0.000	0.000	0.000	0.000	0.000	0.000
159	A	148	GLU	-1	-0.928	-0.963	31.856	-0.076	-0.076	0.000	0.000	0.000	0.000
160	A	149	ALA	0	-0.063	-0.028	34.290	0.012	0.012	0.000	0.000	0.000	0.000

Top

Graph

Overview

Highlights

Data Search

Manual

Support

Interactive mode: IFIE and PIEDA for fragment #1(A:-10:HIS)