FMO DATABASE

FMODB ID: M31MZ

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

Total energy (hartree)

FMO2-HF: Electronic energy	-1447884.85128
FMO2-HF: Nuclear repulsion	1388454.26231
FMO2-HF: Total energy	-59430.58897
FMO2-MP2: Total energy	-59606.996689

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.
-0.607	2.88	0.694	-1.627	-2.554	0.003

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 : -0.045 / q_NPA : -0.034

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	-0.003	-0.011	3.044	-1.566	0.493	0.015	-0.905	-1.170	0.002
4	A	27	ASN	0	-0.002	-0.005	2.508	-0.660	0.491	0.680	-0.636	-1.195	0.001
5	A	28	THR	0	0.032	0.006	3.946	0.605	0.860	0.000	-0.083	-0.172	0.000
6	A	29	LEU	0	-0.006	0.006	5.975	0.240	0.240	0.000	0.000	0.000	0.000
7	A	30	LEU	0	0.002	0.006	7.493	0.206	0.206	0.000	0.000	0.000	0.000
8	A	31	VAL	0	-0.048	-0.040	7.882	0.128	0.128	0.000	0.000	0.000	0.000
9	A	32	GLU	-1	-0.936	-0.941	10.203	-0.172	-0.172	0.000	0.000	0.000	0.000
10	A	33	GLN	0	0.002	-0.019	12.002	0.014	0.014	0.000	0.000	0.000	0.000
11	A	34	SER	0	-0.049	-0.016	13.035	0.034	0.034	0.000	0.000	0.000	0.000
12	A	35	PRO	0	0.042	0.010	14.595	0.026	0.026	0.000	0.000	0.000	0.000
13	A	36	PHE	0	0.032	0.018	15.661	0.021	0.021	0.000	0.000	0.000	0.000
14	A	37	LEU	0	-0.022	-0.026	10.849	0.024	0.024	0.000	0.000	0.000	0.000
15	A	38	GLN	0	-0.017	-0.021	13.975	0.040	0.040	0.000	0.000	0.000	0.000
16	A	39	SER	0	-0.039	-0.015	16.792	0.018	0.018	0.000	0.000	0.000	0.000
17	A	40	LEU	0	-0.027	-0.012	15.093	0.009	0.009	0.000	0.000	0.000	0.000
18	A	41	VAL	0	0.019	0.014	14.394	0.019	0.019	0.000	0.000	0.000	0.000
19	A	42	GLN	0	-0.003	0.001	17.351	0.006	0.006	0.000	0.000	0.000	0.000
20	A	43	GLN	0	0.001	-0.004	20.844	0.007	0.007	0.000	0.000	0.000	0.000
21	A	44	ILE	0	0.000	-0.007	16.736	0.002	0.002	0.000	0.000	0.000	0.000
22	A	45	ARG	1	0.806	0.874	16.128	-0.128	-0.128	0.000	0.000	0.000	0.000
23	A	46	ALA	0	-0.019	0.006	22.010	-0.002	-0.002	0.000	0.000	0.000	0.000
24	A	47	TYR	0	-0.041	-0.033	24.400	-0.004	-0.004	0.000	0.000	0.000	0.000
25	A	48	ASP	-1	-0.806	-0.870	22.949	0.102	0.102	0.000	0.000	0.000	0.000
26	A	49	HIS	0	0.015	0.007	25.179	-0.001	-0.001	0.000	0.000	0.000	0.000
27	A	50	TYR	0	-0.025	-0.018	27.868	-0.005	-0.005	0.000	0.000	0.000	0.000
28	A	51	GLY	0	-0.054	-0.030	24.735	0.002	0.002	0.000	0.000	0.000	0.000
29	A	52	VAL	0	-0.031	-0.011	23.167	0.009	0.009	0.000	0.000	0.000	0.000
30	A	53	TYR	0	-0.023	-0.041	18.803	0.012	0.012	0.000	0.000	0.000	0.000
31	A	54	ARG	1	0.936	0.966	19.292	-0.058	-0.058	0.000	0.000	0.000	0.000
32	A	55	THR	0	-0.018	0.008	18.973	-0.003	-0.003	0.000	0.000	0.000	0.000
33	A	56	TRP	0	-0.026	0.002	15.373	0.042	0.042	0.000	0.000	0.000	0.000
34	A	57	THR	0	0.088	0.028	10.336	-0.066	-0.066	0.000	0.000	0.000	0.000
35	A	58	ASP	-1	-0.750	-0.877	12.455	0.110	0.110	0.000	0.000	0.000	0.000
36	A	59	GLU	-1	-0.871	-0.928	4.933	1.164	1.186	-0.001	-0.003	-0.017	0.000
37	A	60	LEU	0	-0.022	-0.018	9.800	0.008	0.008	0.000	0.000	0.000	0.000
38	A	61	VAL	0	-0.027	-0.004	11.757	-0.039	-0.039	0.000	0.000	0.000	0.000
39	A	62	ILE	0	0.012	0.009	11.024	-0.037	-0.037	0.000	0.000	0.000	0.000
40	A	63	ALA	0	0.013	0.004	10.447	-0.036	-0.036	0.000	0.000	0.000	0.000
41	A	64	PRO	0	-0.014	-0.009	11.653	-0.029	-0.029	0.000	0.000	0.000	0.000
42	A	65	TYR	0	-0.069	-0.037	13.959	-0.028	-0.028	0.000	0.000	0.000	0.000
43	A	66	VAL	0	-0.054	-0.013	9.090	-0.041	-0.041	0.000	0.000	0.000	0.000
44	A	67	ILE	0	0.020	0.015	12.413	0.042	0.042	0.000	0.000	0.000	0.000
45	A	68	PRO	0	0.044	0.027	12.128	-0.038	-0.038	0.000	0.000	0.000	0.000
46	A	69	LYS	1	1.021	1.002	14.477	-0.024	-0.024	0.000	0.000	0.000	0.000
47	A	70	LYS	1	0.942	0.954	17.040	-0.062	-0.062	0.000	0.000	0.000	0.000
48	A	71	LYS	1	1.003	1.015	15.344	-0.199	-0.199	0.000	0.000	0.000	0.000
49	A	72	ARG	1	0.871	0.923	16.428	-0.052	-0.052	0.000	0.000	0.000	0.000
50	A	73	ARG	1	0.881	0.922	19.946	-0.045	-0.045	0.000	0.000	0.000	0.000
51	A	74	GLU	-1	-0.901	-0.946	22.449	0.052	0.052	0.000	0.000	0.000	0.000
52	A	75	ILE	0	-0.071	0.004	20.290	0.003	0.003	0.000	0.000	0.000	0.000
53	A	76	SER	0	0.038	0.017	24.485	-0.007	-0.007	0.000	0.000	0.000	0.000
54	A	77	LEU	0	-0.021	-0.033	27.366	0.002	0.002	0.000	0.000	0.000	0.000
55	A	78	GLU	-1	-0.959	-0.976	30.176	0.039	0.039	0.000	0.000	0.000	0.000
56	A	79	GLY	0	0.006	0.019	32.061	-0.002	-0.002	0.000	0.000	0.000	0.000
57	A	80	ASP	-1	-0.865	-0.929	32.468	0.038	0.038	0.000	0.000	0.000	0.000
58	A	81	ILE	0	-0.103	-0.050	26.754	0.005	0.005	0.000	0.000	0.000	0.000
59	A	82	ASP	-1	-0.847	-0.932	25.911	0.080	0.080	0.000	0.000	0.000	0.000
60	A	83	PRO	0	0.026	-0.014	27.430	-0.001	-0.001	0.000	0.000	0.000	0.000
61	A	84	THR	0	0.036	0.024	22.665	0.000	0.000	0.000	0.000	0.000	0.000
62	A	85	THR	0	-0.036	-0.028	22.748	0.008	0.008	0.000	0.000	0.000	0.000
63	A	86	LYS	1	0.956	0.983	23.973	-0.044	-0.044	0.000	0.000	0.000	0.000
64	A	87	LEU	0	0.045	0.044	24.138	-0.005	-0.005	0.000	0.000	0.000	0.000
65	A	88	ARG	1	0.976	1.001	18.283	-0.108	-0.108	0.000	0.000	0.000	0.000
66	A	89	ILE	0	-0.004	0.008	21.579	-0.007	-0.007	0.000	0.000	0.000	0.000
67	A	90	LEU	0	0.022	0.005	23.595	-0.007	-0.007	0.000	0.000	0.000	0.000
68	A	91	CYS	0	-0.009	-0.009	21.359	-0.005	-0.005	0.000	0.000	0.000	0.000
69	A	92	TYR	0	-0.018	-0.011	18.340	-0.006	-0.006	0.000	0.000	0.000	0.000
70	A	93	PHE	0	0.027	0.000	21.280	-0.008	-0.008	0.000	0.000	0.000	0.000
71	A	94	ARG	1	0.920	0.960	24.670	-0.027	-0.027	0.000	0.000	0.000	0.000
72	A	95	ALA	0	0.003	0.014	20.167	-0.004	-0.004	0.000	0.000	0.000	0.000
73	A	96	ILE	0	-0.041	-0.017	21.984	-0.007	-0.007	0.000	0.000	0.000	0.000
74	A	97	ALA	0	-0.009	0.001	23.600	-0.004	-0.004	0.000	0.000	0.000	0.000
75	A	98	ALA	0	0.017	0.011	23.842	-0.002	-0.002	0.000	0.000	0.000	0.000
76	A	99	LEU	0	-0.014	-0.011	20.396	-0.004	-0.004	0.000	0.000	0.000	0.000
77	A	100	ILE	0	0.009	-0.001	24.201	-0.003	-0.003	0.000	0.000	0.000	0.000
78	A	101	GLU	-1	-0.920	-0.950	27.542	-0.007	-0.007	0.000	0.000	0.000	0.000
79	A	102	LYS	1	0.895	0.943	21.290	0.042	0.042	0.000	0.000	0.000	0.000
80	A	103	GLU	-1	-0.918	-0.957	25.397	-0.045	-0.045	0.000	0.000	0.000	0.000
81	A	104	THR	0	-0.068	-0.030	28.340	0.002	0.002	0.000	0.000	0.000	0.000
82	A	105	GLY	0	0.015	-0.001	31.342	0.001	0.001	0.000	0.000	0.000	0.000
83	A	106	LEU	0	-0.071	-0.021	32.920	0.002	0.002	0.000	0.000	0.000	0.000
84	A	107	LEU	0	-0.006	0.001	29.191	-0.001	-0.001	0.000	0.000	0.000	0.000
85	A	108	CYS	0	-0.062	-0.021	30.877	0.001	0.001	0.000	0.000	0.000	0.000
86	A	109	GLN	0	-0.025	-0.004	31.468	0.003	0.003	0.000	0.000	0.000	0.000
87	A	110	VAL	0	0.023	-0.010	27.861	-0.001	-0.001	0.000	0.000	0.000	0.000
88	A	111	VAL	0	-0.005	0.008	31.165	0.002	0.002	0.000	0.000	0.000	0.000
89	A	112	VAL	0	-0.038	-0.024	27.184	-0.002	-0.002	0.000	0.000	0.000	0.000
90	A	113	ASP	-1	-0.963	-0.967	30.554	0.023	0.023	0.000	0.000	0.000	0.000
91	A	114	LEU	0	-0.049	-0.029	28.056	0.000	0.000	0.000	0.000	0.000	0.000
92	A	115	ASN	0	0.055	0.033	32.675	0.001	0.001	0.000	0.000	0.000	0.000
93	A	116	HIS	0	0.038	0.027	33.152	0.003	0.003	0.000	0.000	0.000	0.000
94	A	117	GLU	-1	-0.824	-0.922	33.071	0.030	0.030	0.000	0.000	0.000	0.000
95	A	118	GLY	0	-0.062	-0.030	30.193	0.001	0.001	0.000	0.000	0.000	0.000
96	A	119	PHE	0	-0.045	-0.038	30.209	-0.003	-0.003	0.000	0.000	0.000	0.000
97	A	120	GLY	0	0.075	0.032	32.473	0.001	0.001	0.000	0.000	0.000	0.000
98	A	121	TRP	0	-0.030	-0.009	32.037	-0.003	-0.003	0.000	0.000	0.000	0.000
99	A	122	ALA	0	-0.009	0.010	27.923	0.002	0.002	0.000	0.000	0.000	0.000
100	A	123	LEU	0	-0.029	-0.026	29.878	-0.003	-0.003	0.000	0.000	0.000	0.000
101	A	124	VAL	0	0.031	0.012	27.974	0.002	0.002	0.000	0.000	0.000	0.000
102	A	125	TRP	0	-0.010	-0.014	31.477	-0.002	-0.002	0.000	0.000	0.000	0.000
103	A	126	GLY	0	0.088	0.031	34.674	0.001	0.001	0.000	0.000	0.000	0.000
104	A	127	GLY	0	0.038	0.045	36.279	-0.001	-0.001	0.000	0.000	0.000	0.000
105	A	128	LYS	1	0.854	0.905	40.042	0.000	0.000	0.000	0.000	0.000	0.000
106	A	129	LEU	0	0.026	0.024	35.612	0.000	0.000	0.000	0.000	0.000	0.000
107	A	130	MET	0	-0.018	-0.004	34.575	0.001	0.001	0.000	0.000	0.000	0.000
108	A	131	VAL	0	0.001	0.011	30.275	-0.001	-0.001	0.000	0.000	0.000	0.000
109	A	132	VAL	0	0.006	0.007	27.153	-0.002	-0.002	0.000	0.000	0.000	0.000
110	A	133	SER	0	0.045	0.006	30.516	0.002	0.002	0.000	0.000	0.000	0.000
111	A	134	ARG	1	0.874	0.946	24.699	-0.001	-0.001	0.000	0.000	0.000	0.000
112	A	135	SER	0	0.056	0.031	29.882	0.002	0.002	0.000	0.000	0.000	0.000
113	A	136	LEU	0	-0.087	-0.043	26.430	0.000	0.000	0.000	0.000	0.000	0.000
114	A	137	ARG	1	0.975	0.975	28.425	-0.016	-0.016	0.000	0.000	0.000	0.000
115	A	138	ASP	-1	-0.880	-0.930	27.494	0.031	0.031	0.000	0.000	0.000	0.000
116	A	139	ALA	0	0.011	-0.006	25.890	0.004	0.004	0.000	0.000	0.000	0.000
117	A	140	HIS	0	0.024	0.006	24.805	0.005	0.005	0.000	0.000	0.000	0.000
118	A	141	ARG	1	0.829	0.917	22.515	-0.039	-0.039	0.000	0.000	0.000	0.000
119	A	142	PHE	0	-0.033	-0.013	19.493	-0.003	-0.003	0.000	0.000	0.000	0.000
120	A	143	GLY	0	0.036	0.014	17.485	0.015	0.015	0.000	0.000	0.000	0.000
121	A	144	PHE	0	-0.069	-0.029	14.102	-0.017	-0.017	0.000	0.000	0.000	0.000
122	A	145	ASP	-1	-0.864	-0.937	13.297	0.034	0.034	0.000	0.000	0.000	0.000
123	A	146	THR	0	0.004	-0.005	8.501	0.029	0.029	0.000	0.000	0.000	0.000
124	A	147	LEU	0	0.064	0.038	6.614	0.022	0.022	0.000	0.000	0.000	0.000
125	A	148	GLU	-1	-0.861	-0.927	7.361	-0.374	-0.374	0.000	0.000	0.000	0.000
126	A	149	LYS	1	0.891	0.948	9.932	0.082	0.082	0.000	0.000	0.000	0.000
127	A	150	LEU	0	-0.023	0.005	12.359	0.013	0.013	0.000	0.000	0.000	0.000
128	A	151	ASN	0	0.099	0.054	12.114	0.031	0.031	0.000	0.000	0.000	0.000
129	A	152	ASP	-1	-0.883	-0.930	13.766	-0.123	-0.123	0.000	0.000	0.000	0.000
130	A	153	GLN	0	-0.059	-0.029	15.621	0.007	0.007	0.000	0.000	0.000	0.000
131	A	154	GLY	0	-0.011	-0.021	17.490	0.007	0.007	0.000	0.000	0.000	0.000
132	A	155	THR	0	0.026	0.002	16.609	0.006	0.006	0.000	0.000	0.000	0.000
133	A	156	LYS	1	0.932	0.978	19.278	0.036	0.036	0.000	0.000	0.000	0.000
134	A	157	LEU	0	-0.070	-0.035	21.468	0.005	0.005	0.000	0.000	0.000	0.000
135	A	158	ALA	0	0.037	0.026	22.503	0.003	0.003	0.000	0.000	0.000	0.000
136	A	159	ASN	0	0.030	0.002	21.400	0.004	0.004	0.000	0.000	0.000	0.000
137	A	160	ALA	0	-0.028	-0.010	24.895	0.002	0.002	0.000	0.000	0.000	0.000
138	A	161	GLY	0	0.009	-0.013	27.168	0.002	0.002	0.000	0.000	0.000	0.000
139	A	162	ILE	0	0.027	0.021	25.434	0.002	0.002	0.000	0.000	0.000	0.000
140	A	163	GLU	-1	-0.931	-0.974	28.655	-0.028	-0.028	0.000	0.000	0.000	0.000
141	A	164	LEU	0	-0.051	-0.011	31.131	0.002	0.002	0.000	0.000	0.000	0.000
142	A	165	VAL	0	-0.027	-0.031	32.586	0.002	0.002	0.000	0.000	0.000	0.000
143	A	166	ASN	0	0.005	-0.005	32.102	0.002	0.002	0.000	0.000	0.000	0.000
144	A	167	LYS	1	0.899	0.968	35.267	0.015	0.015	0.000	0.000	0.000	0.000
145	A	168	PHE	0	-0.040	-0.006	36.934	0.001	0.001	0.000	0.000	0.000	0.000
146	A	169	PRO	0	0.044	0.023	39.147	0.001	0.001	0.000	0.000	0.000	0.000
147	A	170	GLU	-1	-0.844	-0.948	40.322	-0.008	-0.008	0.000	0.000	0.000	0.000
148	A	171	VAL	0	-0.014	0.003	40.081	0.001	0.001	0.000	0.000	0.000	0.000
149	A	172	ALA	0	-0.041	-0.027	36.944	0.001	0.001	0.000	0.000	0.000	0.000
150	A	173	ARG	1	0.882	0.938	35.127	0.014	0.014	0.000	0.000	0.000	0.000
151	A	174	LEU	0	-0.056	-0.004	40.847	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)