FMO DATABASE

FMODB ID: LNK79

Calculation Name: 4ZOT-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 4ZOT

Chain ID: A

ChEMBL ID:

UniProt ID: P83052

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:

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	163
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1599235.741292
FMO2-HF: Nuclear repulsion	1538055.995001
FMO2-HF: Total energy	-61179.746291
FMO2-MP2: Total energy	-61362.892204

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:1:SER)

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

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.
-6.362	-1.329	2.83	-3.191	-4.671	-0.005

Interaction energy analysis for fragmet #1(A:1:SER)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.035 / q_NPA : -0.008

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	3	VAL	0	-0.019	-0.009	3.865	-1.450	-0.621	-0.002	-0.392	-0.435	0.001
4	A	4	VAL	0	0.022	0.026	6.621	0.284	0.284	0.000	0.000	0.000	0.000
5	A	5	VAL	0	-0.012	0.001	8.230	0.009	0.009	0.000	0.000	0.000	0.000
6	A	6	ASP	-1	-0.740	-0.877	11.682	-0.060	-0.060	0.000	0.000	0.000	0.000
7	A	7	THR	0	-0.044	-0.032	15.100	0.007	0.007	0.000	0.000	0.000	0.000
8	A	8	ASN	0	-0.124	-0.067	18.041	0.020	0.020	0.000	0.000	0.000	0.000
9	A	9	GLY	0	0.011	0.012	15.551	-0.002	-0.002	0.000	0.000	0.000	0.000
10	A	10	GLN	0	-0.013	-0.001	14.975	-0.064	-0.064	0.000	0.000	0.000	0.000
11	A	11	PRO	0	-0.014	-0.021	11.546	-0.001	-0.001	0.000	0.000	0.000	0.000
12	A	12	VAL	0	0.002	0.013	11.411	0.061	0.061	0.000	0.000	0.000	0.000
13	A	13	SER	0	-0.034	-0.053	12.033	-0.052	-0.052	0.000	0.000	0.000	0.000
14	A	14	ASN	0	-0.037	-0.025	12.704	0.037	0.037	0.000	0.000	0.000	0.000
15	A	15	GLY	0	0.053	0.027	14.252	0.014	0.014	0.000	0.000	0.000	0.000
16	A	16	ALA	0	-0.017	-0.004	17.578	0.014	0.014	0.000	0.000	0.000	0.000
17	A	17	ASP	-1	-0.815	-0.865	18.617	-0.114	-0.114	0.000	0.000	0.000	0.000
18	A	18	ALA	0	0.005	-0.001	19.258	0.004	0.004	0.000	0.000	0.000	0.000
19	A	19	TYR	0	0.014	-0.014	16.649	-0.017	-0.017	0.000	0.000	0.000	0.000
20	A	20	TYR	0	0.005	0.006	19.383	0.012	0.012	0.000	0.000	0.000	0.000
21	A	21	LEU	0	0.015	0.014	14.783	-0.009	-0.009	0.000	0.000	0.000	0.000
22	A	22	VAL	0	-0.002	0.000	18.644	0.006	0.006	0.000	0.000	0.000	0.000
23	A	23	PRO	0	0.024	0.021	19.253	0.004	0.004	0.000	0.000	0.000	0.000
24	A	24	VAL	0	-0.017	-0.010	17.653	-0.009	-0.009	0.000	0.000	0.000	0.000
25	A	25	SER	0	-0.004	-0.011	20.668	0.005	0.005	0.000	0.000	0.000	0.000
26	A	26	HIS	0	0.017	-0.008	21.222	-0.008	-0.008	0.000	0.000	0.000	0.000
27	A	27	GLY	0	0.000	0.019	26.059	-0.004	-0.004	0.000	0.000	0.000	0.000
28	A	28	HIS	0	-0.002	-0.010	26.467	-0.001	-0.001	0.000	0.000	0.000	0.000
29	A	29	ALA	0	-0.008	-0.003	26.148	-0.002	-0.002	0.000	0.000	0.000	0.000
30	A	30	GLY	0	0.022	0.013	24.565	-0.002	-0.002	0.000	0.000	0.000	0.000
31	A	31	LEU	0	-0.008	0.002	19.976	0.004	0.004	0.000	0.000	0.000	0.000
32	A	32	ALA	0	0.018	0.008	24.620	-0.007	-0.007	0.000	0.000	0.000	0.000
33	A	33	LEU	0	-0.003	0.000	26.511	0.004	0.004	0.000	0.000	0.000	0.000
34	A	34	ALA	0	0.004	0.000	29.154	-0.003	-0.003	0.000	0.000	0.000	0.000
35	A	35	LYS	1	0.846	0.931	31.412	-0.026	-0.026	0.000	0.000	0.000	0.000
36	A	36	ILE	0	0.004	0.002	28.876	0.001	0.001	0.000	0.000	0.000	0.000
37	A	37	GLY	0	-0.024	-0.025	33.230	0.001	0.001	0.000	0.000	0.000	0.000
38	A	38	ASN	0	-0.031	-0.006	37.054	-0.003	-0.003	0.000	0.000	0.000	0.000
39	A	39	GLU	-1	-0.725	-0.840	33.044	0.041	0.041	0.000	0.000	0.000	0.000
40	A	40	ALA	0	0.029	0.016	37.312	-0.002	-0.002	0.000	0.000	0.000	0.000
41	A	41	GLU	-1	-0.883	-0.948	34.945	0.020	0.020	0.000	0.000	0.000	0.000
42	A	42	PRO	0	-0.059	-0.024	32.339	0.003	0.003	0.000	0.000	0.000	0.000
43	A	43	ARG	1	0.916	0.941	29.648	-0.034	-0.034	0.000	0.000	0.000	0.000
44	A	44	ALA	0	0.019	0.007	27.478	0.004	0.004	0.000	0.000	0.000	0.000
45	A	45	VAL	0	0.012	0.008	22.140	-0.006	-0.006	0.000	0.000	0.000	0.000
46	A	46	VAL	0	-0.029	-0.010	25.304	0.006	0.006	0.000	0.000	0.000	0.000
47	A	47	LEU	0	0.016	0.014	21.762	-0.005	-0.005	0.000	0.000	0.000	0.000
48	A	48	ASP	-1	-0.805	-0.919	25.706	0.030	0.030	0.000	0.000	0.000	0.000
49	A	49	PRO	0	0.045	0.018	29.102	-0.003	-0.003	0.000	0.000	0.000	0.000
50	A	50	HIS	0	-0.007	0.001	30.872	-0.005	-0.005	0.000	0.000	0.000	0.000
51	A	51	HIS	0	-0.073	-0.029	29.615	-0.005	-0.005	0.000	0.000	0.000	0.000
52	A	52	ARG	1	0.871	0.935	28.120	-0.015	-0.015	0.000	0.000	0.000	0.000
53	A	53	PRO	0	-0.042	-0.032	25.676	-0.001	-0.001	0.000	0.000	0.000	0.000
54	A	54	GLY	0	0.050	0.030	25.301	0.002	0.002	0.000	0.000	0.000	0.000
55	A	55	LEU	0	-0.054	-0.026	25.032	-0.006	-0.006	0.000	0.000	0.000	0.000
56	A	56	PRO	0	-0.041	-0.010	22.094	0.002	0.002	0.000	0.000	0.000	0.000
57	A	57	VAL	0	0.011	-0.001	17.246	0.004	0.004	0.000	0.000	0.000	0.000
58	A	58	ARG	1	0.803	0.897	18.038	0.031	0.031	0.000	0.000	0.000	0.000
59	A	59	PHE	0	0.052	0.015	12.803	0.013	0.013	0.000	0.000	0.000	0.000
60	A	60	GLU	-1	-0.809	-0.898	14.654	-0.026	-0.026	0.000	0.000	0.000	0.000
61	A	61	SER	0	0.012	-0.008	11.019	0.047	0.047	0.000	0.000	0.000	0.000
62	A	62	PRO	0	-0.006	0.013	13.187	-0.033	-0.033	0.000	0.000	0.000	0.000
63	A	63	LEU	0	-0.002	0.009	8.998	-0.011	-0.011	0.000	0.000	0.000	0.000
64	A	64	ARG	1	0.984	0.999	13.018	0.067	0.067	0.000	0.000	0.000	0.000
65	A	65	ILE	0	-0.072	-0.042	9.479	-0.035	-0.035	0.000	0.000	0.000	0.000
66	A	66	ASN	0	0.064	0.026	13.418	-0.006	-0.006	0.000	0.000	0.000	0.000
67	A	67	ILE	0	-0.014	0.006	8.899	0.009	0.009	0.000	0.000	0.000	0.000
68	A	68	ILE	0	0.025	0.014	8.151	0.022	0.022	0.000	0.000	0.000	0.000
69	A	69	LYS	1	0.920	0.957	3.210	0.876	1.194	0.036	-0.076	-0.277	0.000
70	A	70	GLU	-1	-0.747	-0.857	2.144	0.423	1.071	0.923	-0.445	-1.126	-0.001
71	A	71	SER	0	-0.008	0.011	2.486	-4.637	-1.532	1.861	-2.260	-2.706	-0.005
72	A	72	TYR	0	-0.019	-0.012	3.742	-0.374	-0.241	0.012	-0.018	-0.127	0.000
73	A	73	PHE	0	0.053	0.026	6.771	-0.073	-0.073	0.000	0.000	0.000	0.000
74	A	74	LEU	0	-0.034	-0.017	9.338	-0.072	-0.072	0.000	0.000	0.000	0.000
75	A	75	ASN	0	-0.005	-0.007	12.498	0.027	0.027	0.000	0.000	0.000	0.000
76	A	76	ILE	0	0.019	0.009	13.710	-0.024	-0.024	0.000	0.000	0.000	0.000
77	A	77	LYS	1	0.808	0.915	17.218	0.006	0.006	0.000	0.000	0.000	0.000
78	A	78	PHE	0	0.042	0.036	20.805	-0.010	-0.010	0.000	0.000	0.000	0.000
79	A	79	GLY	0	0.039	0.026	23.478	0.001	0.001	0.000	0.000	0.000	0.000
80	A	80	PRO	0	0.016	0.006	24.416	-0.007	-0.007	0.000	0.000	0.000	0.000
81	A	81	SER	0	0.042	-0.008	21.425	0.007	0.007	0.000	0.000	0.000	0.000
82	A	82	SER	0	-0.037	-0.012	23.333	0.004	0.004	0.000	0.000	0.000	0.000
83	A	83	SER	0	-0.043	-0.004	26.388	0.001	0.001	0.000	0.000	0.000	0.000
84	A	84	ASP	-1	-0.844	-0.905	25.679	0.015	0.015	0.000	0.000	0.000	0.000
85	A	85	SER	0	0.000	-0.012	26.334	0.004	0.004	0.000	0.000	0.000	0.000
86	A	86	GLY	0	-0.001	-0.006	25.861	-0.005	-0.005	0.000	0.000	0.000	0.000
87	A	87	VAL	0	-0.019	-0.017	20.840	-0.003	-0.003	0.000	0.000	0.000	0.000
88	A	88	TRP	0	-0.024	-0.024	17.357	0.003	0.003	0.000	0.000	0.000	0.000
89	A	89	ASP	-1	-0.842	-0.925	20.563	0.096	0.096	0.000	0.000	0.000	0.000
90	A	90	VAL	0	-0.051	-0.030	19.061	-0.004	-0.004	0.000	0.000	0.000	0.000
91	A	91	ILE	0	-0.012	0.001	22.304	0.001	0.001	0.000	0.000	0.000	0.000
92	A	92	GLN	0	0.026	0.014	26.028	-0.001	-0.001	0.000	0.000	0.000	0.000
93	A	93	GLN	0	-0.008	-0.012	28.378	-0.011	-0.011	0.000	0.000	0.000	0.000
94	A	94	ASP	-1	-0.838	-0.904	30.380	0.060	0.060	0.000	0.000	0.000	0.000
95	A	95	PRO	0	-0.043	-0.021	32.609	0.002	0.002	0.000	0.000	0.000	0.000
96	A	96	ILE	0	-0.040	-0.038	26.388	0.001	0.001	0.000	0.000	0.000	0.000
97	A	97	GLY	0	0.042	0.041	27.089	0.006	0.006	0.000	0.000	0.000	0.000
98	A	98	LEU	0	-0.003	-0.016	22.507	-0.002	-0.002	0.000	0.000	0.000	0.000
99	A	99	ALA	0	0.031	0.022	23.344	0.006	0.006	0.000	0.000	0.000	0.000
100	A	100	VAL	0	0.014	0.006	19.781	0.002	0.002	0.000	0.000	0.000	0.000
101	A	101	LYS	1	0.775	0.883	22.762	-0.059	-0.059	0.000	0.000	0.000	0.000
102	A	102	VAL	0	-0.037	-0.015	23.823	0.002	0.002	0.000	0.000	0.000	0.000
103	A	103	THR	0	-0.009	-0.007	24.316	-0.003	-0.003	0.000	0.000	0.000	0.000
104	A	104	ASP	-1	-0.849	-0.936	26.757	0.030	0.030	0.000	0.000	0.000	0.000
105	A	105	THR	0	-0.014	0.007	26.276	0.000	0.000	0.000	0.000	0.000	0.000
106	A	106	LYS	1	0.867	0.910	19.618	-0.015	-0.015	0.000	0.000	0.000	0.000
107	A	107	SER	0	0.043	0.039	19.404	-0.001	-0.001	0.000	0.000	0.000	0.000
108	A	108	LEU	0	-0.024	-0.010	17.621	-0.003	-0.003	0.000	0.000	0.000	0.000
109	A	109	LEU	0	-0.032	-0.030	12.576	0.003	0.003	0.000	0.000	0.000	0.000
110	A	110	GLY	0	0.031	0.015	14.797	-0.004	-0.004	0.000	0.000	0.000	0.000
111	A	111	PRO	0	0.019	0.002	14.729	0.037	0.037	0.000	0.000	0.000	0.000
112	A	112	PHE	0	-0.010	0.002	13.162	0.017	0.017	0.000	0.000	0.000	0.000
113	A	113	LYS	1	0.847	0.938	6.863	-1.012	-1.012	0.000	0.000	0.000	0.000
114	A	114	VAL	0	-0.022	-0.001	8.178	0.008	0.008	0.000	0.000	0.000	0.000
115	A	115	GLU	-1	-0.859	-0.950	5.920	0.319	0.319	0.000	0.000	0.000	0.000
116	A	116	LYS	1	0.860	0.897	5.388	-1.483	-1.483	0.000	0.000	0.000	0.000
117	A	117	GLU	-1	-0.819	-0.918	8.061	0.472	0.472	0.000	0.000	0.000	0.000
118	A	118	GLY	0	0.024	0.016	11.490	-0.065	-0.065	0.000	0.000	0.000	0.000
119	A	119	GLU	-1	-0.905	-0.933	13.795	0.105	0.105	0.000	0.000	0.000	0.000
120	A	120	GLY	0	-0.041	-0.040	13.331	-0.043	-0.043	0.000	0.000	0.000	0.000
121	A	121	TYR	0	-0.051	-0.023	6.963	0.031	0.031	0.000	0.000	0.000	0.000
122	A	122	LYS	1	0.842	0.937	10.234	-0.411	-0.411	0.000	0.000	0.000	0.000
123	A	123	ILE	0	-0.040	-0.025	10.933	-0.031	-0.031	0.000	0.000	0.000	0.000
124	A	124	VAL	0	0.035	0.026	10.075	0.010	0.010	0.000	0.000	0.000	0.000
125	A	125	TYR	0	0.044	0.011	12.427	-0.002	-0.002	0.000	0.000	0.000	0.000
126	A	126	TYR	0	0.024	-0.010	8.377	0.082	0.082	0.000	0.000	0.000	0.000
127	A	127	PRO	0	-0.030	0.000	14.445	-0.010	-0.010	0.000	0.000	0.000	0.000
128	A	128	GLU	-1	-0.822	-0.906	16.496	0.237	0.237	0.000	0.000	0.000	0.000
129	A	129	ARG	1	0.924	0.954	13.522	-0.236	-0.236	0.000	0.000	0.000	0.000
130	A	130	GLY	0	-0.025	-0.009	12.525	0.098	0.098	0.000	0.000	0.000	0.000
131	A	131	GLN	0	-0.078	-0.035	14.076	0.003	0.003	0.000	0.000	0.000	0.000
132	A	132	THR	0	-0.017	-0.020	11.894	0.076	0.076	0.000	0.000	0.000	0.000
133	A	133	GLY	0	-0.014	0.001	11.573	-0.039	-0.039	0.000	0.000	0.000	0.000
134	A	134	LEU	0	-0.006	-0.007	12.998	-0.014	-0.014	0.000	0.000	0.000	0.000
135	A	135	ASP	-1	-0.770	-0.882	13.696	0.271	0.271	0.000	0.000	0.000	0.000
136	A	136	ILE	0	-0.049	-0.024	15.153	-0.023	-0.023	0.000	0.000	0.000	0.000
137	A	137	GLY	0	0.066	0.038	17.186	0.003	0.003	0.000	0.000	0.000	0.000
138	A	138	LEU	0	-0.056	-0.027	19.948	-0.011	-0.011	0.000	0.000	0.000	0.000
139	A	139	VAL	0	0.007	0.002	23.563	0.002	0.002	0.000	0.000	0.000	0.000
140	A	140	HIS	0	-0.034	-0.018	26.794	-0.006	-0.006	0.000	0.000	0.000	0.000
141	A	141	ARG	1	0.861	0.911	29.977	-0.061	-0.061	0.000	0.000	0.000	0.000
142	A	142	ASN	0	0.007	0.006	32.979	-0.001	-0.001	0.000	0.000	0.000	0.000
143	A	143	ASP	-1	-0.869	-0.919	35.179	0.034	0.034	0.000	0.000	0.000	0.000
144	A	144	LYS	1	0.849	0.931	30.547	-0.037	-0.037	0.000	0.000	0.000	0.000
145	A	145	TYR	0	0.016	0.004	26.628	0.002	0.002	0.000	0.000	0.000	0.000
146	A	146	TYR	0	0.009	-0.023	26.182	-0.001	-0.001	0.000	0.000	0.000	0.000
147	A	147	LEU	0	0.015	0.017	19.483	0.005	0.005	0.000	0.000	0.000	0.000
148	A	148	ALA	0	-0.001	-0.004	21.698	-0.005	-0.005	0.000	0.000	0.000	0.000
149	A	149	VAL	0	-0.016	-0.004	18.626	0.008	0.008	0.000	0.000	0.000	0.000
150	A	150	LYS	1	0.718	0.847	19.254	-0.114	-0.114	0.000	0.000	0.000	0.000
151	A	151	ASP	-1	-0.823	-0.913	16.348	0.252	0.252	0.000	0.000	0.000	0.000
152	A	152	GLY	0	0.017	0.018	17.358	-0.015	-0.015	0.000	0.000	0.000	0.000
153	A	153	GLU	-1	-0.899	-0.935	18.912	0.102	0.102	0.000	0.000	0.000	0.000
154	A	154	PRO	0	-0.016	0.005	14.907	-0.017	-0.017	0.000	0.000	0.000	0.000
155	A	155	CYS	0	-0.055	-0.036	16.882	-0.015	-0.015	0.000	0.000	0.000	0.000
156	A	156	VAL	0	-0.003	0.012	14.560	-0.002	-0.002	0.000	0.000	0.000	0.000
157	A	157	PHE	0	-0.008	-0.023	15.210	-0.021	-0.021	0.000	0.000	0.000	0.000
158	A	158	LYS	1	0.843	0.909	15.061	-0.046	-0.046	0.000	0.000	0.000	0.000
159	A	159	ILE	0	0.004	0.014	11.835	0.001	0.001	0.000	0.000	0.000	0.000
160	A	160	ARG	1	0.952	0.989	15.955	0.010	0.010	0.000	0.000	0.000	0.000
161	A	161	LYS	1	0.876	0.929	19.012	0.133	0.133	0.000	0.000	0.000	0.000
162	A	162	ALA	0	-0.028	-0.028	20.165	0.008	0.008	0.000	0.000	0.000	0.000
163	A	163	THR	0	-0.070	-0.014	23.295	0.004	0.004	0.000	0.000	0.000	0.000

Top

Graph

Manual

About

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