FMO DATABASE

FMODB ID: 1NKZZ

Calculation Name: 4H89-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 4H89

Chain ID: A

ChEMBL ID:

UniProt ID: D2Q3N2

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	OptH
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	169
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1622268.277311
FMO2-HF: Nuclear repulsion	1557924.754329
FMO2-HF: Total energy	-64343.522983
FMO2-MP2: Total energy	-64530.633834

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:2:SER)

Summations of interaction energy for fragment #1(A:2: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.
-22.479	-17.462	8.172	-5.407	-7.781	0.024

Interaction energy analysis for fragmet #1(A:2:SER)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.004 / q_NPA : -0.013

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	4	GLU	-1	-0.910	-0.953	2.267	-10.301	-6.327	0.864	-2.040	-2.798	-0.007
4	A	5	ALA	0	-0.034	-0.010	2.031	-3.230	-4.188	7.157	-2.578	-3.620	0.021
5	A	6	LEU	0	-0.084	-0.012	3.690	-1.046	-0.610	0.035	0.010	-0.481	0.001
6	A	7	GLN	0	0.018	0.008	5.220	-0.328	-0.297	-0.001	-0.005	-0.024	0.000
7	A	8	VAL	0	-0.036	-0.024	8.993	0.190	0.190	0.000	0.000	0.000	0.000
8	A	9	ARG	1	0.869	0.929	12.027	-0.346	-0.346	0.000	0.000	0.000	0.000
9	A	10	ASP	-1	-0.834	-0.912	14.942	0.107	0.107	0.000	0.000	0.000	0.000
10	A	11	ALA	0	-0.054	-0.032	17.613	0.018	0.018	0.000	0.000	0.000	0.000
11	A	12	GLU	-1	-0.933	-0.962	18.213	0.114	0.114	0.000	0.000	0.000	0.000
12	A	13	ASP	-1	-0.909	-0.973	20.633	0.159	0.159	0.000	0.000	0.000	0.000
13	A	14	ALA	0	-0.039	-0.030	20.846	0.014	0.014	0.000	0.000	0.000	0.000
14	A	15	ASP	-1	-0.752	-0.861	16.844	0.328	0.328	0.000	0.000	0.000	0.000
15	A	16	TRP	0	0.007	-0.005	18.801	0.042	0.042	0.000	0.000	0.000	0.000
16	A	17	PRO	0	-0.030	-0.026	21.248	0.020	0.020	0.000	0.000	0.000	0.000
17	A	18	ALA	0	0.020	0.016	15.977	0.017	0.017	0.000	0.000	0.000	0.000
18	A	19	ILE	0	-0.018	-0.004	17.179	0.051	0.051	0.000	0.000	0.000	0.000
19	A	20	LEU	0	-0.037	-0.001	18.734	0.010	0.010	0.000	0.000	0.000	0.000
20	A	21	PRO	0	0.045	0.006	18.969	-0.013	-0.013	0.000	0.000	0.000	0.000
21	A	22	PHE	0	0.013	0.009	14.054	0.018	0.018	0.000	0.000	0.000	0.000
22	A	23	PHE	0	0.027	0.002	19.364	-0.014	-0.014	0.000	0.000	0.000	0.000
23	A	24	ARG	1	0.802	0.888	22.631	-0.256	-0.256	0.000	0.000	0.000	0.000
24	A	25	GLU	-1	-0.906	-0.953	18.076	0.632	0.632	0.000	0.000	0.000	0.000
25	A	26	ILE	0	-0.045	-0.030	19.731	-0.014	-0.014	0.000	0.000	0.000	0.000
26	A	27	VAL	0	-0.030	-0.009	23.358	-0.020	-0.020	0.000	0.000	0.000	0.000
27	A	28	SER	0	-0.051	-0.018	25.774	-0.022	-0.022	0.000	0.000	0.000	0.000
28	A	29	ALA	0	-0.014	0.002	24.098	-0.012	-0.012	0.000	0.000	0.000	0.000
29	A	30	GLY	0	0.048	0.027	26.163	-0.016	-0.016	0.000	0.000	0.000	0.000
30	A	31	GLU	-1	-0.962	-0.993	24.461	0.322	0.322	0.000	0.000	0.000	0.000
31	A	32	THR	0	-0.093	-0.063	22.032	-0.011	-0.011	0.000	0.000	0.000	0.000
32	A	33	TYR	0	0.026	0.018	21.462	-0.001	-0.001	0.000	0.000	0.000	0.000
33	A	34	ALA	0	-0.002	0.006	26.896	0.004	0.004	0.000	0.000	0.000	0.000
34	A	35	TYR	0	-0.004	-0.005	24.573	-0.010	-0.010	0.000	0.000	0.000	0.000
35	A	36	ASP	-1	-0.874	-0.937	30.647	0.148	0.148	0.000	0.000	0.000	0.000
36	A	37	PRO	0	-0.009	-0.018	31.577	0.011	0.011	0.000	0.000	0.000	0.000
37	A	38	GLU	-1	-0.977	-0.988	32.238	0.155	0.155	0.000	0.000	0.000	0.000
38	A	39	LEU	0	-0.054	0.001	29.777	-0.006	-0.006	0.000	0.000	0.000	0.000
39	A	40	THR	0	0.093	0.030	31.547	0.012	0.012	0.000	0.000	0.000	0.000
40	A	41	ASP	-1	-0.808	-0.905	28.210	0.228	0.228	0.000	0.000	0.000	0.000
41	A	42	GLU	-1	-0.939	-0.986	28.375	0.166	0.166	0.000	0.000	0.000	0.000
42	A	43	GLN	0	0.011	0.005	30.610	0.000	0.000	0.000	0.000	0.000	0.000
43	A	44	ALA	0	0.037	0.022	26.483	-0.002	-0.002	0.000	0.000	0.000	0.000
44	A	45	ARG	1	0.947	0.976	25.673	-0.159	-0.159	0.000	0.000	0.000	0.000
45	A	46	SER	0	-0.056	-0.030	26.942	-0.007	-0.007	0.000	0.000	0.000	0.000
46	A	47	LEU	0	-0.058	-0.016	28.234	-0.008	-0.008	0.000	0.000	0.000	0.000
47	A	48	TRP	0	-0.034	-0.021	19.242	-0.007	-0.007	0.000	0.000	0.000	0.000
48	A	49	MET	0	-0.021	-0.011	21.221	0.013	0.013	0.000	0.000	0.000	0.000
49	A	50	THR	0	-0.004	-0.015	24.344	-0.016	-0.016	0.000	0.000	0.000	0.000
50	A	51	PRO	0	0.018	0.016	26.402	-0.005	-0.005	0.000	0.000	0.000	0.000
51	A	52	SER	0	0.043	-0.002	29.301	-0.005	-0.005	0.000	0.000	0.000	0.000
52	A	53	GLY	0	-0.024	0.001	30.406	0.000	0.000	0.000	0.000	0.000	0.000
53	A	54	ALA	0	0.044	0.056	30.858	-0.002	-0.002	0.000	0.000	0.000	0.000
54	A	55	PRO	0	-0.119	-0.088	32.353	-0.006	-0.006	0.000	0.000	0.000	0.000
55	A	56	GLN	0	-0.013	-0.008	29.368	0.010	0.010	0.000	0.000	0.000	0.000
56	A	57	SER	0	0.019	-0.026	26.792	0.007	0.007	0.000	0.000	0.000	0.000
57	A	58	ARG	1	0.779	0.880	17.585	-0.074	-0.074	0.000	0.000	0.000	0.000
58	A	59	THR	0	0.035	0.024	19.797	-0.001	-0.001	0.000	0.000	0.000	0.000
59	A	60	THR	0	-0.022	0.009	15.785	-0.004	-0.004	0.000	0.000	0.000	0.000
60	A	61	VAL	0	0.033	0.022	13.596	0.042	0.042	0.000	0.000	0.000	0.000
61	A	62	ALA	0	-0.007	-0.002	9.185	-0.070	-0.070	0.000	0.000	0.000	0.000
62	A	63	VAL	0	-0.010	-0.008	9.000	0.141	0.141	0.000	0.000	0.000	0.000
63	A	64	ASP	-1	-0.830	-0.925	4.877	1.602	1.602	0.000	0.000	0.000	0.000
64	A	65	ALA	0	0.024	-0.009	5.320	-0.254	-0.254	0.000	0.000	0.000	0.000
65	A	66	ASP	-1	-0.962	-0.957	7.085	0.467	0.467	0.000	0.000	0.000	0.000
66	A	67	GLY	0	-0.037	-0.018	9.274	-0.104	-0.104	0.000	0.000	0.000	0.000
67	A	68	THR	0	-0.046	-0.018	9.322	-0.125	-0.125	0.000	0.000	0.000	0.000
68	A	69	VAL	0	0.012	0.005	9.622	0.161	0.161	0.000	0.000	0.000	0.000
69	A	70	LEU	0	-0.043	-0.035	5.828	0.187	0.187	0.000	0.000	0.000	0.000
70	A	71	GLY	0	0.001	-0.018	10.444	0.028	0.028	0.000	0.000	0.000	0.000
71	A	72	SER	0	-0.018	-0.001	13.105	-0.054	-0.054	0.000	0.000	0.000	0.000
72	A	73	ALA	0	0.003	-0.005	15.896	0.015	0.015	0.000	0.000	0.000	0.000
73	A	74	ASN	0	0.034	0.037	18.341	-0.013	-0.013	0.000	0.000	0.000	0.000
74	A	75	MET	0	-0.014	0.011	18.815	-0.009	-0.009	0.000	0.000	0.000	0.000
75	A	76	TYR	0	0.032	0.026	23.948	-0.006	-0.006	0.000	0.000	0.000	0.000
76	A	77	PRO	0	-0.001	0.003	27.724	0.000	0.000	0.000	0.000	0.000	0.000
77	A	78	ASN	0	-0.056	-0.028	30.877	0.015	0.015	0.000	0.000	0.000	0.000
78	A	79	ARG	1	0.907	0.956	31.752	-0.072	-0.072	0.000	0.000	0.000	0.000
79	A	80	PRO	0	0.082	0.050	35.351	-0.004	-0.004	0.000	0.000	0.000	0.000
80	A	81	GLY	0	0.044	0.008	37.377	-0.002	-0.002	0.000	0.000	0.000	0.000
81	A	82	PRO	0	-0.015	-0.009	39.040	-0.002	-0.002	0.000	0.000	0.000	0.000
82	A	83	GLY	0	-0.007	-0.013	37.615	-0.002	-0.002	0.000	0.000	0.000	0.000
83	A	84	ALA	0	0.004	0.005	34.641	0.004	0.004	0.000	0.000	0.000	0.000
84	A	85	HIS	0	0.015	0.017	33.379	-0.001	-0.001	0.000	0.000	0.000	0.000
85	A	86	VAL	0	-0.051	-0.020	31.131	-0.005	-0.005	0.000	0.000	0.000	0.000
86	A	87	ALA	0	0.064	0.046	26.785	0.005	0.005	0.000	0.000	0.000	0.000
87	A	88	SER	0	-0.071	-0.062	26.742	0.006	0.006	0.000	0.000	0.000	0.000
88	A	89	ALA	0	0.029	0.003	21.798	-0.007	-0.007	0.000	0.000	0.000	0.000
89	A	90	SER	0	-0.050	0.008	22.405	0.001	0.001	0.000	0.000	0.000	0.000
90	A	91	PHE	0	-0.009	-0.015	16.862	0.006	0.006	0.000	0.000	0.000	0.000
91	A	92	MET	0	-0.020	0.012	17.379	0.001	0.001	0.000	0.000	0.000	0.000
92	A	93	VAL	0	-0.035	-0.023	11.837	0.030	0.030	0.000	0.000	0.000	0.000
93	A	94	ALA	0	0.076	0.045	12.330	-0.055	-0.055	0.000	0.000	0.000	0.000
94	A	95	ALA	0	0.032	0.001	13.337	0.146	0.146	0.000	0.000	0.000	0.000
95	A	96	ALA	0	0.004	-0.007	12.323	0.071	0.071	0.000	0.000	0.000	0.000
96	A	97	ALA	0	-0.026	-0.004	8.914	0.343	0.343	0.000	0.000	0.000	0.000
97	A	98	ARG	1	0.902	0.962	9.524	-0.606	-0.606	0.000	0.000	0.000	0.000
98	A	99	GLY	0	-0.016	-0.006	10.329	0.148	0.148	0.000	0.000	0.000	0.000
99	A	100	ARG	1	0.976	0.990	2.867	-10.183	-8.649	0.117	-0.794	-0.858	0.009
100	A	101	GLY	0	-0.013	-0.005	6.151	-0.048	-0.048	0.000	0.000	0.000	0.000
101	A	102	VAL	0	0.057	0.033	7.553	-0.330	-0.330	0.000	0.000	0.000	0.000
102	A	103	GLY	0	0.048	0.023	9.679	-0.209	-0.209	0.000	0.000	0.000	0.000
103	A	104	ARG	1	0.978	0.988	9.396	0.018	0.018	0.000	0.000	0.000	0.000
104	A	105	ALA	0	-0.018	-0.002	9.648	-0.122	-0.122	0.000	0.000	0.000	0.000
105	A	106	LEU	0	0.024	0.015	11.749	-0.080	-0.080	0.000	0.000	0.000	0.000
106	A	107	CYS	0	-0.041	-0.016	14.114	-0.071	-0.071	0.000	0.000	0.000	0.000
107	A	108	GLN	0	-0.054	-0.044	14.681	-0.024	-0.024	0.000	0.000	0.000	0.000
108	A	109	ASP	-1	-0.800	-0.885	14.668	0.002	0.002	0.000	0.000	0.000	0.000
109	A	110	MET	0	-0.026	-0.013	16.597	-0.017	-0.017	0.000	0.000	0.000	0.000
110	A	111	ILE	0	-0.015	-0.022	19.459	-0.014	-0.014	0.000	0.000	0.000	0.000
111	A	112	ASP	-1	-0.867	-0.931	18.072	-0.133	-0.133	0.000	0.000	0.000	0.000
112	A	113	TRP	0	-0.075	-0.036	20.690	-0.005	-0.005	0.000	0.000	0.000	0.000
113	A	114	ALA	0	0.034	0.009	22.396	-0.004	-0.004	0.000	0.000	0.000	0.000
114	A	115	GLY	0	-0.003	-0.006	24.504	-0.003	-0.003	0.000	0.000	0.000	0.000
115	A	116	ARG	1	0.925	0.962	20.146	0.044	0.044	0.000	0.000	0.000	0.000
116	A	117	GLU	-1	-0.938	-0.968	25.972	-0.002	-0.002	0.000	0.000	0.000	0.000
117	A	118	GLY	0	-0.019	0.006	28.294	0.005	0.005	0.000	0.000	0.000	0.000
118	A	119	PHE	0	-0.065	-0.017	27.827	0.004	0.004	0.000	0.000	0.000	0.000
119	A	120	ARG	1	0.931	0.948	30.447	-0.006	-0.006	0.000	0.000	0.000	0.000
120	A	121	ALA	0	-0.078	-0.042	29.727	-0.004	-0.004	0.000	0.000	0.000	0.000
121	A	122	ILE	0	0.034	0.042	23.820	0.002	0.002	0.000	0.000	0.000	0.000
122	A	123	GLN	0	-0.015	-0.018	27.946	0.001	0.001	0.000	0.000	0.000	0.000
123	A	124	PHE	0	0.005	0.014	22.089	0.007	0.007	0.000	0.000	0.000	0.000
124	A	125	ASN	0	0.022	-0.025	27.766	-0.013	-0.013	0.000	0.000	0.000	0.000
125	A	126	ALA	0	0.039	0.025	29.026	-0.008	-0.008	0.000	0.000	0.000	0.000
126	A	127	VAL	0	-0.039	-0.007	24.820	0.016	0.016	0.000	0.000	0.000	0.000
127	A	128	VAL	0	0.044	0.034	26.871	-0.014	-0.014	0.000	0.000	0.000	0.000
128	A	129	GLU	-1	-0.886	-0.937	26.790	0.154	0.154	0.000	0.000	0.000	0.000
129	A	130	THR	0	0.010	0.006	27.495	0.004	0.004	0.000	0.000	0.000	0.000
130	A	131	ASN	0	0.012	0.016	21.714	0.048	0.048	0.000	0.000	0.000	0.000
131	A	132	THR	0	0.003	-0.019	22.975	0.011	0.011	0.000	0.000	0.000	0.000
132	A	133	VAL	0	0.016	0.006	16.364	-0.012	-0.012	0.000	0.000	0.000	0.000
133	A	134	ALA	0	0.021	0.017	18.686	-0.002	-0.002	0.000	0.000	0.000	0.000
134	A	135	VAL	0	0.031	0.026	20.092	-0.028	-0.028	0.000	0.000	0.000	0.000
135	A	136	LYS	1	0.953	0.966	20.220	-0.202	-0.202	0.000	0.000	0.000	0.000
136	A	137	LEU	0	-0.014	0.019	14.855	-0.025	-0.025	0.000	0.000	0.000	0.000
137	A	138	TRP	0	0.077	0.023	17.583	-0.037	-0.037	0.000	0.000	0.000	0.000
138	A	139	GLN	0	-0.005	-0.011	20.927	-0.020	-0.020	0.000	0.000	0.000	0.000
139	A	140	SER	0	-0.116	-0.059	17.729	-0.026	-0.026	0.000	0.000	0.000	0.000
140	A	141	LEU	0	0.012	0.009	16.162	-0.030	-0.030	0.000	0.000	0.000	0.000
141	A	142	GLY	0	0.000	0.010	20.078	-0.014	-0.014	0.000	0.000	0.000	0.000
142	A	143	PHE	0	-0.024	-0.002	21.940	-0.005	-0.005	0.000	0.000	0.000	0.000
143	A	144	ARG	1	0.975	0.977	25.431	-0.041	-0.041	0.000	0.000	0.000	0.000
144	A	145	VAL	0	0.008	-0.001	28.361	0.004	0.004	0.000	0.000	0.000	0.000
145	A	146	ILE	0	-0.100	-0.042	30.437	-0.011	-0.011	0.000	0.000	0.000	0.000
146	A	147	GLY	0	0.036	0.007	33.488	-0.007	-0.007	0.000	0.000	0.000	0.000
147	A	148	THR	0	0.001	0.004	33.211	0.009	0.009	0.000	0.000	0.000	0.000
148	A	149	VAL	0	0.011	0.020	34.948	-0.008	-0.008	0.000	0.000	0.000	0.000
149	A	150	PRO	0	0.014	0.005	36.125	0.009	0.009	0.000	0.000	0.000	0.000
150	A	151	GLU	-1	-0.933	-0.981	37.238	0.101	0.101	0.000	0.000	0.000	0.000
151	A	152	ALA	0	-0.022	-0.002	35.478	-0.001	-0.001	0.000	0.000	0.000	0.000
152	A	153	PHE	0	-0.020	-0.009	29.086	0.002	0.002	0.000	0.000	0.000	0.000
153	A	154	HIS	0	-0.027	-0.011	34.250	0.001	0.001	0.000	0.000	0.000	0.000
154	A	155	HIS	0	0.055	0.031	27.259	-0.004	-0.004	0.000	0.000	0.000	0.000
155	A	156	PRO	0	0.043	0.016	29.537	-0.013	-0.013	0.000	0.000	0.000	0.000
156	A	157	THR	0	-0.065	-0.021	30.277	-0.002	-0.002	0.000	0.000	0.000	0.000
157	A	158	HIS	0	-0.030	-0.039	28.156	-0.021	-0.021	0.000	0.000	0.000	0.000
158	A	159	GLY	0	0.037	0.038	33.308	-0.011	-0.011	0.000	0.000	0.000	0.000
159	A	160	TYR	0	-0.024	-0.008	34.793	0.008	0.008	0.000	0.000	0.000	0.000
160	A	161	VAL	0	0.010	0.008	31.177	-0.003	-0.003	0.000	0.000	0.000	0.000
161	A	162	GLY	0	-0.014	-0.029	33.745	-0.003	-0.003	0.000	0.000	0.000	0.000
162	A	163	LEU	0	-0.026	0.000	30.493	0.014	0.014	0.000	0.000	0.000	0.000
163	A	164	HIS	0	-0.050	-0.047	27.692	-0.006	-0.006	0.000	0.000	0.000	0.000
164	A	165	VAL	0	0.031	0.030	30.459	0.007	0.007	0.000	0.000	0.000	0.000
165	A	166	MET	0	-0.043	-0.025	24.745	0.000	0.000	0.000	0.000	0.000	0.000
166	A	167	HIS	0	-0.002	-0.009	28.978	0.000	0.000	0.000	0.000	0.000	0.000
167	A	168	ARG	1	0.932	0.967	22.173	-0.004	-0.004	0.000	0.000	0.000	0.000
168	A	169	PRO	0	-0.030	-0.005	27.855	0.001	0.001	0.000	0.000	0.000	0.000
169	A	170	LEU	0	0.006	0.003	25.314	-0.007	-0.007	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:2:SER)