FMO DATABASE

FMODB ID: 223KR

Calculation Name: 3NJ2-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3NJ2

Chain ID: A

ChEMBL ID:

UniProt ID: B1WPD5

Base Structure: X-ray

Registration Date: 2023-06-19

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	151
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1454312.757015
FMO2-HF: Nuclear repulsion	1394880.694052
FMO2-HF: Total energy	-59432.062963
FMO2-MP2: Total energy	-59608.25252

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:24:SER)

Summations of interaction energy for fragment #1(A:24: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.
-0.647	2.353	1.965	-2.114	-2.85	0

Interaction energy analysis for fragmet #1(A:24:SER)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.040 / q_NPA : -0.028

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	26	THR	0	0.008	-0.002	3.431	-0.690	1.696	0.014	-1.187	-1.213	0.002
4	A	27	ASN	0	-0.066	-0.023	2.275	1.289	1.903	1.951	-0.927	-1.637	-0.002
5	A	28	THR	0	0.031	-0.017	4.937	0.495	0.495	0.000	0.000	0.000	0.000
6	A	29	LEU	0	-0.003	0.012	6.998	0.271	0.271	0.000	0.000	0.000	0.000
7	A	30	LEU	0	0.003	0.004	8.002	0.350	0.350	0.000	0.000	0.000	0.000
8	A	31	VAL	0	-0.050	-0.050	8.765	0.229	0.229	0.000	0.000	0.000	0.000
9	A	32	GLU	-1	-0.911	-0.934	11.126	-0.664	-0.664	0.000	0.000	0.000	0.000
10	A	33	GLN	0	-0.042	-0.035	12.665	0.077	0.077	0.000	0.000	0.000	0.000
11	A	34	SER	0	-0.025	-0.017	13.344	0.061	0.061	0.000	0.000	0.000	0.000
12	A	35	PRO	0	0.031	0.009	15.034	0.052	0.052	0.000	0.000	0.000	0.000
13	A	36	PHE	0	0.016	0.024	15.947	0.049	0.049	0.000	0.000	0.000	0.000
14	A	37	LEU	0	0.006	-0.011	11.413	0.059	0.059	0.000	0.000	0.000	0.000
15	A	38	GLN	0	0.022	0.010	14.735	0.068	0.068	0.000	0.000	0.000	0.000
16	A	39	SER	0	-0.010	-0.016	17.532	0.021	0.021	0.000	0.000	0.000	0.000
17	A	40	LEU	0	-0.041	-0.024	15.749	0.023	0.023	0.000	0.000	0.000	0.000
18	A	41	VAL	0	-0.007	0.001	15.415	0.040	0.040	0.000	0.000	0.000	0.000
19	A	42	GLN	0	-0.012	0.004	18.142	0.007	0.007	0.000	0.000	0.000	0.000
20	A	43	GLN	0	0.030	0.014	21.767	0.014	0.014	0.000	0.000	0.000	0.000
21	A	44	ILE	0	-0.011	-0.013	17.474	0.007	0.007	0.000	0.000	0.000	0.000
22	A	45	ARG	1	0.792	0.857	16.650	-0.137	-0.137	0.000	0.000	0.000	0.000
23	A	46	ALA	0	-0.016	0.008	22.488	-0.006	-0.006	0.000	0.000	0.000	0.000
24	A	47	TYR	0	-0.007	-0.013	24.996	-0.006	-0.006	0.000	0.000	0.000	0.000
25	A	48	ASP	-1	-0.809	-0.883	23.470	0.174	0.174	0.000	0.000	0.000	0.000
26	A	49	HIS	0	0.001	-0.007	25.599	-0.016	-0.016	0.000	0.000	0.000	0.000
27	A	50	TYR	0	-0.007	-0.012	28.578	-0.012	-0.012	0.000	0.000	0.000	0.000
28	A	51	GLY	0	-0.041	-0.035	25.490	-0.010	-0.010	0.000	0.000	0.000	0.000
29	A	52	VAL	0	-0.029	-0.012	23.039	0.004	0.004	0.000	0.000	0.000	0.000
30	A	53	TYR	0	0.005	-0.017	19.271	0.038	0.038	0.000	0.000	0.000	0.000
31	A	54	ARG	1	0.861	0.957	19.668	-0.092	-0.092	0.000	0.000	0.000	0.000
32	A	55	THR	0	0.002	0.007	19.675	-0.016	-0.016	0.000	0.000	0.000	0.000
33	A	56	TRP	0	-0.040	0.007	15.786	0.052	0.052	0.000	0.000	0.000	0.000
34	A	57	THR	0	0.078	0.029	10.841	-0.055	-0.055	0.000	0.000	0.000	0.000
35	A	58	ASP	-1	-0.717	-0.867	13.179	0.113	0.113	0.000	0.000	0.000	0.000
36	A	59	GLU	-1	-0.841	-0.909	5.578	0.975	0.975	0.000	0.000	0.000	0.000
37	A	60	LEU	0	-0.024	-0.009	10.299	0.149	0.149	0.000	0.000	0.000	0.000
38	A	61	VAL	0	-0.011	-0.007	12.234	-0.001	-0.001	0.000	0.000	0.000	0.000
39	A	62	ILE	0	0.014	0.018	11.694	-0.019	-0.019	0.000	0.000	0.000	0.000
40	A	63	ALA	0	0.040	0.023	10.702	0.028	0.028	0.000	0.000	0.000	0.000
41	A	64	PRO	0	-0.041	-0.021	12.011	0.027	0.027	0.000	0.000	0.000	0.000
42	A	65	TYR	0	-0.022	-0.018	14.427	-0.064	-0.064	0.000	0.000	0.000	0.000
43	A	66	VAL	0	-0.034	-0.010	9.019	-0.034	-0.034	0.000	0.000	0.000	0.000
44	A	67	ILE	0	0.008	0.015	12.267	0.134	0.134	0.000	0.000	0.000	0.000
45	A	68	PRO	0	0.044	0.018	11.404	-0.133	-0.133	0.000	0.000	0.000	0.000
46	A	69	LYS	1	0.977	0.983	14.079	-0.510	-0.510	0.000	0.000	0.000	0.000
47	A	70	LYS	1	0.943	0.965	17.188	-0.719	-0.719	0.000	0.000	0.000	0.000
48	A	71	LYS	1	1.031	1.023	15.911	-0.813	-0.813	0.000	0.000	0.000	0.000
49	A	72	ARG	1	0.828	0.901	16.236	-0.602	-0.602	0.000	0.000	0.000	0.000
50	A	73	ARG	1	0.769	0.855	19.798	-0.398	-0.398	0.000	0.000	0.000	0.000
51	A	74	GLU	-1	-0.794	-0.867	22.444	0.325	0.325	0.000	0.000	0.000	0.000
52	A	75	ILE	0	-0.049	-0.004	20.128	-0.006	-0.006	0.000	0.000	0.000	0.000
53	A	76	SER	0	-0.021	-0.041	24.377	-0.018	-0.018	0.000	0.000	0.000	0.000
54	A	77	LEU	0	-0.007	-0.016	27.616	0.007	0.007	0.000	0.000	0.000	0.000
55	A	78	GLU	-1	-0.908	-0.913	30.447	0.213	0.213	0.000	0.000	0.000	0.000
56	A	79	GLY	0	0.018	0.012	32.578	-0.012	-0.012	0.000	0.000	0.000	0.000
57	A	80	ASP	-1	-0.900	-0.949	32.302	0.167	0.167	0.000	0.000	0.000	0.000
58	A	81	ILE	0	-0.088	-0.028	27.103	0.012	0.012	0.000	0.000	0.000	0.000
59	A	82	ASP	-1	-0.720	-0.830	24.907	0.271	0.271	0.000	0.000	0.000	0.000
60	A	83	PRO	0	0.030	0.004	27.451	0.004	0.004	0.000	0.000	0.000	0.000
61	A	84	THR	0	-0.004	-0.016	23.256	-0.010	-0.010	0.000	0.000	0.000	0.000
62	A	85	THR	0	-0.049	-0.059	22.903	0.023	0.023	0.000	0.000	0.000	0.000
63	A	86	LYS	1	0.849	0.940	24.242	-0.165	-0.165	0.000	0.000	0.000	0.000
64	A	87	LEU	0	0.018	0.016	24.815	-0.011	-0.011	0.000	0.000	0.000	0.000
65	A	88	ARG	1	0.883	0.958	18.718	-0.388	-0.388	0.000	0.000	0.000	0.000
66	A	89	ILE	0	0.015	0.014	22.049	-0.011	-0.011	0.000	0.000	0.000	0.000
67	A	90	LEU	0	0.002	-0.002	24.022	-0.018	-0.018	0.000	0.000	0.000	0.000
68	A	91	CYS	0	-0.027	-0.019	22.063	-0.020	-0.020	0.000	0.000	0.000	0.000
69	A	92	TYR	0	0.010	0.003	18.199	-0.017	-0.017	0.000	0.000	0.000	0.000
70	A	93	PHE	0	0.015	-0.013	21.961	-0.020	-0.020	0.000	0.000	0.000	0.000
71	A	94	ARG	1	0.915	0.962	25.318	-0.090	-0.090	0.000	0.000	0.000	0.000
72	A	95	ALA	0	0.003	0.017	20.731	-0.017	-0.017	0.000	0.000	0.000	0.000
73	A	96	ILE	0	-0.049	-0.022	22.189	-0.023	-0.023	0.000	0.000	0.000	0.000
74	A	97	ALA	0	-0.021	-0.006	23.898	-0.016	-0.016	0.000	0.000	0.000	0.000
75	A	98	ALA	0	0.037	0.021	24.477	-0.010	-0.010	0.000	0.000	0.000	0.000
76	A	99	LEU	0	-0.039	-0.014	20.553	-0.015	-0.015	0.000	0.000	0.000	0.000
77	A	100	ILE	0	0.010	-0.010	24.483	-0.011	-0.011	0.000	0.000	0.000	0.000
78	A	101	GLU	-1	-0.924	-0.952	27.723	-0.019	-0.019	0.000	0.000	0.000	0.000
79	A	102	LYS	1	0.839	0.929	21.839	0.087	0.087	0.000	0.000	0.000	0.000
80	A	103	GLU	-1	-0.879	-0.941	24.701	-0.125	-0.125	0.000	0.000	0.000	0.000
81	A	104	THR	0	-0.077	-0.046	28.256	0.004	0.004	0.000	0.000	0.000	0.000
82	A	105	GLY	0	0.048	0.028	31.580	0.003	0.003	0.000	0.000	0.000	0.000
83	A	106	LEU	0	-0.057	-0.031	32.442	0.005	0.005	0.000	0.000	0.000	0.000
84	A	107	LEU	0	-0.009	0.009	30.230	0.004	0.004	0.000	0.000	0.000	0.000
85	A	108	CYS	0	-0.066	-0.024	31.004	0.004	0.004	0.000	0.000	0.000	0.000
86	A	109	GLN	0	-0.021	0.001	31.871	0.009	0.009	0.000	0.000	0.000	0.000
87	A	110	VAL	0	0.015	-0.013	28.425	0.002	0.002	0.000	0.000	0.000	0.000
88	A	111	VAL	0	-0.030	-0.009	31.862	0.002	0.002	0.000	0.000	0.000	0.000
89	A	112	VAL	0	-0.021	-0.026	27.655	0.002	0.002	0.000	0.000	0.000	0.000
90	A	113	ASP	-1	-0.894	-0.924	31.062	0.110	0.110	0.000	0.000	0.000	0.000
91	A	114	LEU	0	-0.041	-0.040	28.416	0.009	0.009	0.000	0.000	0.000	0.000
92	A	115	ASN	0	-0.014	-0.008	33.122	-0.002	-0.002	0.000	0.000	0.000	0.000
93	A	116	HIS	0	0.028	0.017	33.422	0.012	0.012	0.000	0.000	0.000	0.000
94	A	117	GLU	-1	-0.767	-0.886	33.050	0.150	0.150	0.000	0.000	0.000	0.000
95	A	118	GLY	0	-0.020	-0.001	30.228	0.011	0.011	0.000	0.000	0.000	0.000
96	A	119	PHE	0	-0.012	-0.021	30.293	0.004	0.004	0.000	0.000	0.000	0.000
97	A	120	GLY	0	0.039	0.015	32.890	-0.004	-0.004	0.000	0.000	0.000	0.000
98	A	121	TRP	0	-0.024	-0.021	32.121	0.000	0.000	0.000	0.000	0.000	0.000
99	A	122	ALA	0	0.003	0.025	28.367	0.001	0.001	0.000	0.000	0.000	0.000
100	A	123	LEU	0	-0.026	-0.028	30.291	-0.006	-0.006	0.000	0.000	0.000	0.000
101	A	124	VAL	0	0.037	0.018	28.101	0.003	0.003	0.000	0.000	0.000	0.000
102	A	125	TRP	0	-0.006	-0.010	31.605	-0.002	-0.002	0.000	0.000	0.000	0.000
103	A	126	GLY	0	0.067	0.034	34.795	-0.001	-0.001	0.000	0.000	0.000	0.000
104	A	127	GLY	0	0.053	0.037	36.613	-0.001	-0.001	0.000	0.000	0.000	0.000
105	A	128	LYS	1	0.848	0.912	40.386	-0.015	-0.015	0.000	0.000	0.000	0.000
106	A	129	LEU	0	0.017	0.037	35.329	0.003	0.003	0.000	0.000	0.000	0.000
107	A	130	MET	0	-0.019	-0.010	34.478	0.003	0.003	0.000	0.000	0.000	0.000
108	A	131	VAL	0	-0.030	0.003	30.433	-0.001	-0.001	0.000	0.000	0.000	0.000
109	A	132	VAL	0	0.016	-0.006	26.973	0.001	0.001	0.000	0.000	0.000	0.000
110	A	133	SER	0	0.011	0.007	30.357	0.002	0.002	0.000	0.000	0.000	0.000
111	A	134	ARG	1	0.876	0.933	25.546	-0.125	-0.125	0.000	0.000	0.000	0.000
112	A	135	SER	0	0.052	0.039	29.767	0.006	0.006	0.000	0.000	0.000	0.000
113	A	136	LEU	0	-0.065	-0.031	26.882	0.011	0.011	0.000	0.000	0.000	0.000
114	A	137	ARG	1	0.940	0.967	28.588	-0.154	-0.154	0.000	0.000	0.000	0.000
115	A	138	ASP	-1	-0.868	-0.935	27.448	0.231	0.231	0.000	0.000	0.000	0.000
116	A	139	ALA	0	0.027	0.017	26.026	0.025	0.025	0.000	0.000	0.000	0.000
117	A	140	HIS	0	0.037	0.001	24.944	0.024	0.024	0.000	0.000	0.000	0.000
118	A	141	ARG	1	0.808	0.901	22.446	-0.281	-0.281	0.000	0.000	0.000	0.000
119	A	142	PHE	0	-0.036	-0.009	20.056	0.025	0.025	0.000	0.000	0.000	0.000
120	A	143	GLY	0	0.025	0.002	17.533	0.030	0.030	0.000	0.000	0.000	0.000
121	A	144	PHE	0	-0.062	-0.025	14.009	-0.048	-0.048	0.000	0.000	0.000	0.000
122	A	145	ASP	-1	-0.809	-0.902	12.920	0.668	0.668	0.000	0.000	0.000	0.000
123	A	146	THR	0	0.035	0.011	7.867	0.169	0.169	0.000	0.000	0.000	0.000
124	A	147	LEU	0	0.066	0.045	7.431	-0.131	-0.131	0.000	0.000	0.000	0.000
125	A	148	GLU	-1	-0.870	-0.929	6.533	-0.382	-0.382	0.000	0.000	0.000	0.000
126	A	149	LYS	1	0.834	0.902	9.963	-0.556	-0.556	0.000	0.000	0.000	0.000
127	A	150	LEU	0	-0.007	0.003	12.533	-0.050	-0.050	0.000	0.000	0.000	0.000
128	A	151	ASN	0	0.043	0.019	12.139	-0.056	-0.056	0.000	0.000	0.000	0.000
129	A	152	ASP	-1	-0.837	-0.886	13.579	-0.111	-0.111	0.000	0.000	0.000	0.000
130	A	153	GLN	0	-0.036	-0.019	15.667	-0.011	-0.011	0.000	0.000	0.000	0.000
131	A	154	GLY	0	0.035	0.015	17.437	-0.003	-0.003	0.000	0.000	0.000	0.000
132	A	155	THR	0	0.022	-0.013	16.801	-0.022	-0.022	0.000	0.000	0.000	0.000
133	A	156	LYS	1	0.866	0.938	19.474	-0.098	-0.098	0.000	0.000	0.000	0.000
134	A	157	LEU	0	-0.070	-0.033	21.473	-0.001	-0.001	0.000	0.000	0.000	0.000
135	A	158	ALA	0	0.046	0.028	22.497	-0.003	-0.003	0.000	0.000	0.000	0.000
136	A	159	ASN	0	0.032	0.003	21.669	-0.004	-0.004	0.000	0.000	0.000	0.000
137	A	160	ALA	0	-0.035	-0.010	25.047	-0.002	-0.002	0.000	0.000	0.000	0.000
138	A	161	GLY	0	0.028	0.002	27.275	0.000	0.000	0.000	0.000	0.000	0.000
139	A	162	ILE	0	-0.012	-0.004	25.344	0.000	0.000	0.000	0.000	0.000	0.000
140	A	163	GLU	-1	-0.834	-0.919	28.928	-0.052	-0.052	0.000	0.000	0.000	0.000
141	A	164	LEU	0	-0.076	-0.027	31.193	0.001	0.001	0.000	0.000	0.000	0.000
142	A	165	VAL	0	-0.017	-0.029	32.577	0.002	0.002	0.000	0.000	0.000	0.000
143	A	166	ASN	0	-0.056	-0.033	31.378	0.001	0.001	0.000	0.000	0.000	0.000
144	A	167	LYS	1	0.892	0.965	35.068	0.006	0.006	0.000	0.000	0.000	0.000
145	A	168	PHE	0	-0.027	-0.006	36.904	0.002	0.002	0.000	0.000	0.000	0.000
146	A	169	PRO	0	0.050	0.027	39.083	0.004	0.004	0.000	0.000	0.000	0.000
147	A	170	GLU	-1	-0.847	-0.948	40.168	-0.004	-0.004	0.000	0.000	0.000	0.000
148	A	171	VAL	0	-0.012	-0.015	40.108	0.003	0.003	0.000	0.000	0.000	0.000
149	A	172	ALA	0	-0.010	-0.003	36.779	0.003	0.003	0.000	0.000	0.000	0.000
150	A	173	ARG	1	0.842	0.916	34.961	0.027	0.027	0.000	0.000	0.000	0.000
151	A	174	LEU	0	-0.052	0.000	40.726	0.001	0.001	0.000	0.000	0.000	0.000

Top

Graph

Manual

About

Interactive mode: IFIE and PIEDA for fragment #1(A:24:SER)