FMO DATABASE

FMODB ID: 141JZ

Calculation Name: 3NJC-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3NJC

Chain ID: A

ChEMBL ID:

UniProt ID: P42955

Base Structure: X-ray

Registration Date: 2023-06-20

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	153
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1558995.656987
FMO2-HF: Nuclear repulsion	1495102.334932
FMO2-HF: Total energy	-63893.322055
FMO2-MP2: Total energy	-64077.358324

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:-7:HIS)

Summations of interaction energy for fragment #1(A:-7: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.
-80.386	-74.538	34.182	-16.788	-23.244	-0.038

Interaction energy analysis for fragmet #1(A:-7:HIS)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.003 / q_NPA : -0.006

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	-5	HIS	0	0.020	-0.003	2.752	-6.276	-1.906	0.909	-2.086	-3.193	0.020
4	A	-4	HIS	0	0.009	0.016	3.775	2.005	2.525	0.009	-0.142	-0.388	0.000
5	A	-3	HIS	1	0.793	0.884	2.008	-28.856	-29.208	8.080	-3.654	-4.074	0.058
6	A	-2	HIS	0	-0.014	-0.003	7.011	-1.007	-1.007	0.000	0.000	0.000	0.000
7	A	-1	SER	0	0.055	0.037	10.801	-0.017	-0.017	0.000	0.000	0.000	0.000
8	A	0	HIS	0	-0.032	-0.031	13.678	-0.006	-0.006	0.000	0.000	0.000	0.000
9	A	1	MET	0	-0.018	-0.014	16.463	-0.093	-0.093	0.000	0.000	0.000	0.000
10	A	2	LYS	1	0.979	1.016	20.215	-0.465	-0.465	0.000	0.000	0.000	0.000
11	A	3	SER	0	-0.015	-0.006	21.887	-0.024	-0.024	0.000	0.000	0.000	0.000
12	A	4	LYS	1	0.972	0.957	24.709	-0.324	-0.324	0.000	0.000	0.000	0.000
13	A	5	PHE	0	0.054	0.031	26.196	-0.005	-0.005	0.000	0.000	0.000	0.000
14	A	6	GLU	-1	-0.785	-0.880	21.335	0.385	0.385	0.000	0.000	0.000	0.000
15	A	7	ALA	0	-0.017	-0.014	24.871	0.001	0.001	0.000	0.000	0.000	0.000
16	A	8	SER	0	-0.084	-0.046	26.402	-0.017	-0.017	0.000	0.000	0.000	0.000
17	A	9	ILE	0	0.062	-0.004	24.440	-0.017	-0.017	0.000	0.000	0.000	0.000
18	A	10	ASP	-1	-0.886	-0.932	26.255	0.284	0.284	0.000	0.000	0.000	0.000
19	A	11	ASN	0	-0.085	-0.050	28.873	-0.009	-0.009	0.000	0.000	0.000	0.000
20	A	12	LEU	0	-0.082	-0.030	30.542	-0.013	-0.013	0.000	0.000	0.000	0.000
21	A	13	LYS	1	0.858	0.948	26.742	-0.243	-0.243	0.000	0.000	0.000	0.000
22	A	14	GLU	-1	-0.922	-0.961	32.027	0.122	0.122	0.000	0.000	0.000	0.000
23	A	15	ILE	0	-0.062	-0.013	34.997	-0.009	-0.009	0.000	0.000	0.000	0.000
24	A	16	GLU	-1	-0.912	-0.945	35.150	0.059	0.059	0.000	0.000	0.000	0.000
25	A	17	MET	0	-0.045	-0.030	34.016	-0.003	-0.003	0.000	0.000	0.000	0.000
26	A	18	ASN	0	0.003	0.007	35.130	-0.009	-0.009	0.000	0.000	0.000	0.000
27	A	19	ALA	0	0.091	0.018	32.592	0.000	0.000	0.000	0.000	0.000	0.000
28	A	20	TYR	0	-0.022	-0.003	32.683	-0.008	-0.008	0.000	0.000	0.000	0.000
29	A	21	ALA	0	0.004	-0.007	33.940	-0.008	-0.008	0.000	0.000	0.000	0.000
30	A	22	TYR	0	0.017	0.014	24.500	-0.014	-0.014	0.000	0.000	0.000	0.000
31	A	23	GLU	-1	-0.732	-0.864	28.569	-0.120	-0.120	0.000	0.000	0.000	0.000
32	A	24	LEU	0	-0.020	0.006	30.103	-0.014	-0.014	0.000	0.000	0.000	0.000
33	A	25	ILE	0	0.012	0.003	26.818	-0.008	-0.008	0.000	0.000	0.000	0.000
34	A	26	ARG	1	0.844	0.912	21.027	0.143	0.143	0.000	0.000	0.000	0.000
35	A	27	GLU	-1	-0.837	-0.931	24.932	-0.233	-0.233	0.000	0.000	0.000	0.000
36	A	28	ILE	0	-0.047	-0.009	27.715	-0.010	-0.010	0.000	0.000	0.000	0.000
37	A	29	VAL	0	0.026	0.018	28.494	-0.009	-0.009	0.000	0.000	0.000	0.000
38	A	30	LEU	0	-0.024	-0.015	22.556	-0.008	-0.008	0.000	0.000	0.000	0.000
39	A	31	PRO	0	0.009	0.005	25.039	-0.020	-0.020	0.000	0.000	0.000	0.000
40	A	32	ASP	-1	-0.914	-0.946	26.025	-0.169	-0.169	0.000	0.000	0.000	0.000
41	A	33	MET	0	-0.126	-0.060	26.160	0.004	0.004	0.000	0.000	0.000	0.000
42	A	34	LEU	0	-0.051	-0.023	20.778	-0.008	-0.008	0.000	0.000	0.000	0.000
43	A	35	GLY	0	0.035	0.029	23.621	-0.036	-0.036	0.000	0.000	0.000	0.000
44	A	36	GLN	0	-0.053	-0.038	22.889	0.005	0.005	0.000	0.000	0.000	0.000
45	A	37	ASP	-1	-0.904	-0.949	19.339	-0.556	-0.556	0.000	0.000	0.000	0.000
46	A	38	TYR	0	0.002	-0.007	18.653	-0.052	-0.052	0.000	0.000	0.000	0.000
47	A	39	SER	0	0.018	0.002	17.636	-0.008	-0.008	0.000	0.000	0.000	0.000
48	A	40	SER	0	0.030	0.000	14.256	-0.062	-0.062	0.000	0.000	0.000	0.000
49	A	41	MET	0	-0.015	-0.004	13.804	-0.007	-0.007	0.000	0.000	0.000	0.000
50	A	42	MET	0	0.016	0.010	15.339	0.093	0.093	0.000	0.000	0.000	0.000
51	A	43	TYR	0	-0.067	-0.052	7.994	-0.064	-0.064	0.000	0.000	0.000	0.000
52	A	44	TRP	0	0.012	-0.015	7.884	0.234	0.234	0.000	0.000	0.000	0.000
53	A	45	ALA	0	0.014	0.019	11.454	0.225	0.225	0.000	0.000	0.000	0.000
54	A	46	GLY	0	0.036	0.020	13.557	0.137	0.137	0.000	0.000	0.000	0.000
55	A	47	LYS	1	0.884	0.951	4.860	2.587	2.587	0.000	0.000	0.000	0.000
56	A	48	HIS	0	-0.030	-0.032	10.393	0.321	0.321	0.000	0.000	0.000	0.000
57	A	49	LEU	0	-0.007	0.005	12.527	0.121	0.121	0.000	0.000	0.000	0.000
58	A	50	ALA	0	0.037	0.016	11.452	0.038	0.038	0.000	0.000	0.000	0.000
59	A	51	ARG	1	0.845	0.931	6.651	-3.199	-3.199	0.000	0.000	0.000	0.000
60	A	52	LYS	1	0.862	0.932	13.097	-0.420	-0.420	0.000	0.000	0.000	0.000
61	A	53	PHE	0	-0.071	-0.040	16.344	-0.064	-0.064	0.000	0.000	0.000	0.000
62	A	54	PRO	0	-0.019	0.013	14.748	-0.009	-0.009	0.000	0.000	0.000	0.000
63	A	55	LEU	0	-0.025	-0.018	15.718	-0.108	-0.108	0.000	0.000	0.000	0.000
64	A	56	GLU	-1	-0.970	-0.992	16.124	0.753	0.753	0.000	0.000	0.000	0.000
65	A	57	SER	0	-0.026	-0.009	17.430	0.037	0.037	0.000	0.000	0.000	0.000
66	A	58	TRP	0	0.018	-0.022	13.708	-0.111	-0.111	0.000	0.000	0.000	0.000
67	A	59	GLU	-1	-0.979	-0.975	18.180	0.194	0.194	0.000	0.000	0.000	0.000
68	A	60	GLU	-1	-0.801	-0.907	20.042	0.482	0.482	0.000	0.000	0.000	0.000
69	A	61	PHE	0	-0.047	-0.029	14.446	-0.021	-0.021	0.000	0.000	0.000	0.000
70	A	62	PRO	0	0.001	-0.002	19.987	-0.026	-0.026	0.000	0.000	0.000	0.000
71	A	63	ALA	0	0.046	0.025	23.337	-0.018	-0.018	0.000	0.000	0.000	0.000
72	A	64	PHE	0	0.013	0.015	19.512	0.003	0.003	0.000	0.000	0.000	0.000
73	A	65	PHE	0	-0.007	-0.025	17.358	-0.030	-0.030	0.000	0.000	0.000	0.000
74	A	66	GLU	-1	-0.866	-0.916	22.536	0.005	0.005	0.000	0.000	0.000	0.000
75	A	67	GLU	-1	-0.863	-0.927	25.634	0.187	0.187	0.000	0.000	0.000	0.000
76	A	68	ALA	0	-0.070	-0.021	22.705	-0.004	-0.004	0.000	0.000	0.000	0.000
77	A	69	GLY	0	-0.025	-0.014	24.597	-0.021	-0.021	0.000	0.000	0.000	0.000
78	A	70	TRP	0	-0.086	-0.058	17.589	-0.024	-0.024	0.000	0.000	0.000	0.000
79	A	71	GLY	0	-0.025	-0.013	23.991	-0.037	-0.037	0.000	0.000	0.000	0.000
80	A	72	THR	0	-0.017	-0.018	25.550	0.020	0.020	0.000	0.000	0.000	0.000
81	A	73	LEU	0	-0.031	-0.005	19.716	-0.028	-0.028	0.000	0.000	0.000	0.000
82	A	74	THR	0	0.027	0.013	24.160	0.028	0.028	0.000	0.000	0.000	0.000
83	A	75	ASN	0	-0.070	-0.053	21.037	-0.024	-0.024	0.000	0.000	0.000	0.000
84	A	76	VAL	0	0.028	0.033	23.057	0.009	0.009	0.000	0.000	0.000	0.000
85	A	77	SER	0	-0.027	-0.022	21.380	0.021	0.021	0.000	0.000	0.000	0.000
86	A	78	ALA	0	0.075	0.040	19.972	-0.005	-0.005	0.000	0.000	0.000	0.000
87	A	79	LYS	1	0.903	0.959	18.390	0.161	0.161	0.000	0.000	0.000	0.000
88	A	80	LYS	1	0.957	0.971	13.874	-0.349	-0.349	0.000	0.000	0.000	0.000
89	A	81	GLN	0	-0.063	-0.053	11.291	0.283	0.283	0.000	0.000	0.000	0.000
90	A	82	GLU	-1	-0.925	-0.965	13.262	-0.709	-0.709	0.000	0.000	0.000	0.000
91	A	83	LEU	0	-0.055	-0.010	15.518	0.102	0.102	0.000	0.000	0.000	0.000
92	A	84	GLU	-1	-0.932	-0.967	17.039	-0.409	-0.409	0.000	0.000	0.000	0.000
93	A	85	PHE	0	0.043	-0.001	17.114	0.074	0.074	0.000	0.000	0.000	0.000
94	A	86	GLU	-1	-0.913	-0.953	21.445	-0.207	-0.207	0.000	0.000	0.000	0.000
95	A	87	LEU	0	-0.015	-0.003	21.222	0.027	0.027	0.000	0.000	0.000	0.000
96	A	88	GLU	-1	-0.885	-0.970	24.487	-0.111	-0.111	0.000	0.000	0.000	0.000
97	A	89	GLY	0	0.115	0.063	27.868	0.023	0.023	0.000	0.000	0.000	0.000
98	A	90	PRO	0	-0.009	-0.014	30.654	-0.018	-0.018	0.000	0.000	0.000	0.000
99	A	91	ILE	0	0.023	0.007	29.154	-0.009	-0.009	0.000	0.000	0.000	0.000
100	A	92	ILE	0	0.028	0.029	25.270	-0.017	-0.017	0.000	0.000	0.000	0.000
101	A	93	SER	0	0.016	0.001	28.711	-0.018	-0.018	0.000	0.000	0.000	0.000
102	A	94	ASN	0	-0.044	-0.020	31.825	-0.007	-0.007	0.000	0.000	0.000	0.000
103	A	95	ARG	1	0.812	0.879	24.613	0.135	0.135	0.000	0.000	0.000	0.000
104	A	96	LEU	0	-0.016	-0.014	26.772	-0.019	-0.019	0.000	0.000	0.000	0.000
105	A	97	LYS	1	0.895	0.972	30.148	0.112	0.112	0.000	0.000	0.000	0.000
106	A	98	HIS	0	-0.027	-0.023	33.036	-0.006	-0.006	0.000	0.000	0.000	0.000
107	A	99	GLN	0	-0.018	-0.001	27.392	-0.017	-0.017	0.000	0.000	0.000	0.000
108	A	100	LYS	1	0.934	0.969	28.361	0.354	0.354	0.000	0.000	0.000	0.000
109	A	101	GLU	-1	-0.974	-1.002	24.491	-0.479	-0.479	0.000	0.000	0.000	0.000
110	A	102	PRO	0	0.019	0.035	24.893	-0.019	-0.019	0.000	0.000	0.000	0.000
111	A	103	CYS	0	-0.041	-0.013	19.592	-0.072	-0.072	0.000	0.000	0.000	0.000
112	A	104	PHE	0	0.047	0.012	19.282	0.043	0.043	0.000	0.000	0.000	0.000
113	A	105	GLN	0	0.032	0.007	13.681	0.079	0.079	0.000	0.000	0.000	0.000
114	A	106	LEU	0	0.005	0.023	14.266	-0.035	-0.035	0.000	0.000	0.000	0.000
115	A	107	GLU	-1	-0.800	-0.921	14.977	-0.132	-0.132	0.000	0.000	0.000	0.000
116	A	108	ALA	0	-0.005	-0.003	13.302	0.054	0.054	0.000	0.000	0.000	0.000
117	A	109	GLY	0	0.011	-0.004	10.300	-0.060	-0.060	0.000	0.000	0.000	0.000
118	A	110	PHE	0	0.006	0.007	10.303	0.240	0.240	0.000	0.000	0.000	0.000
119	A	111	ILE	0	0.018	0.007	12.121	0.217	0.217	0.000	0.000	0.000	0.000
120	A	112	ALA	0	0.008	0.005	7.714	0.214	0.214	0.000	0.000	0.000	0.000
121	A	113	GLU	-1	-0.858	-0.926	6.456	3.861	3.861	0.000	0.000	0.000	0.000
122	A	114	GLN	0	0.019	-0.003	8.404	0.807	0.807	0.000	0.000	0.000	0.000
123	A	115	ILE	0	-0.018	0.002	9.643	0.220	0.220	0.000	0.000	0.000	0.000
124	A	116	GLN	0	-0.061	-0.039	2.786	-2.485	-1.138	0.789	-0.547	-1.589	0.002
125	A	117	LEU	0	-0.100	-0.041	7.327	0.564	0.564	0.000	0.000	0.000	0.000
126	A	118	MET	0	-0.030	0.013	9.562	-0.164	-0.164	0.000	0.000	0.000	0.000
127	A	119	ASN	0	-0.005	-0.004	9.509	-0.166	-0.166	0.000	0.000	0.000	0.000
128	A	120	ASP	-1	-0.863	-0.919	6.526	2.757	2.757	0.000	0.000	0.000	0.000
129	A	121	GLN	0	-0.048	-0.042	6.072	0.195	0.195	0.000	0.000	0.000	0.000
130	A	122	ILE	0	-0.033	-0.008	5.840	-0.520	-0.520	0.000	0.000	0.000	0.000
131	A	123	ALA	0	-0.051	-0.033	2.327	0.809	1.779	1.361	-0.908	-1.423	-0.001
132	A	124	GLU	-1	-0.880	-0.925	1.765	-46.745	-48.816	23.006	-9.259	-11.676	-0.117
133	A	125	SER	0	-0.009	-0.034	3.949	2.705	3.014	0.011	-0.048	-0.273	0.000
134	A	126	TYR	0	-0.073	-0.032	6.727	-1.246	-1.246	0.000	0.000	0.000	0.000
135	A	127	GLU	-1	-0.787	-0.863	8.680	-1.883	-1.883	0.000	0.000	0.000	0.000
136	A	128	GLN	0	-0.055	-0.029	12.553	0.010	0.010	0.000	0.000	0.000	0.000
137	A	129	VAL	0	0.054	0.032	16.159	0.105	0.105	0.000	0.000	0.000	0.000
138	A	130	LYS	1	0.906	0.961	18.876	0.411	0.411	0.000	0.000	0.000	0.000
139	A	131	LYS	1	0.920	0.969	22.063	0.479	0.479	0.000	0.000	0.000	0.000
140	A	132	ARG	1	0.868	0.941	25.501	0.245	0.245	0.000	0.000	0.000	0.000
141	A	133	ALA	0	-0.028	-0.021	28.511	0.002	0.002	0.000	0.000	0.000	0.000
142	A	134	ASP	-1	-0.901	-0.951	31.418	-0.148	-0.148	0.000	0.000	0.000	0.000
143	A	135	LYN	0	0.052	0.037	27.270	0.002	0.002	0.000	0.000	0.000	0.000
144	A	136	VAL	0	-0.057	-0.031	22.493	-0.035	-0.035	0.000	0.000	0.000	0.000
145	A	137	VAL	0	0.000	0.000	21.149	0.029	0.029	0.000	0.000	0.000	0.000
146	A	138	LEU	0	-0.026	-0.010	17.184	-0.079	-0.079	0.000	0.000	0.000	0.000
147	A	139	THR	0	0.038	0.014	15.940	0.079	0.079	0.000	0.000	0.000	0.000
148	A	140	VAL	0	-0.001	0.015	10.775	-0.173	-0.173	0.000	0.000	0.000	0.000
149	A	141	LYS	1	0.972	0.993	11.488	1.752	1.752	0.000	0.000	0.000	0.000
150	A	142	TRP	0	0.012	-0.001	7.729	-0.420	-0.420	0.000	0.000	0.000	0.000
151	A	143	ASP	-1	-0.877	-0.920	6.337	-1.491	-1.491	0.000	0.000	0.000	0.000
152	A	144	MET	0	-0.061	-0.026	6.363	0.250	0.250	0.000	0.000	0.000	0.000
153	A	145	LYS	1	0.882	0.953	3.452	-5.085	-4.330	0.017	-0.144	-0.628	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:-7:HIS)