FMO DATABASE

FMODB ID: R5758

Calculation Name: 3NRH-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3NRH

Chain ID: A

ChEMBL ID:

UniProt ID: Q64XJ4

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:

Apendix: None

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	158
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1616010.171456
FMO2-HF: Nuclear repulsion	1551525.011843
FMO2-HF: Total energy	-64485.159613
FMO2-MP2: Total energy	-64670.815534

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:6:GLN)

Summations of interaction energy for fragment #1(A:6:GLN)

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.
0.861	5.807	5.267	-3.843	-6.368	-0.009

Interaction energy analysis for fragmet #1(A:6:GLN)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.023 / q_NPA : -0.003

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	8	ILE	0	0.013	0.016	2.184	-4.010	-1.921	2.119	-1.717	-2.491	0.005
4	A	9	PHE	0	-0.009	-0.003	2.411	-2.662	-1.515	3.041	-1.468	-2.720	-0.009
5	A	10	ASP	-1	-0.811	-0.878	5.239	-0.839	-0.730	-0.001	-0.004	-0.103	0.000
6	A	11	LYS	1	0.808	0.858	7.715	1.204	1.204	0.000	0.000	0.000	0.000
7	A	12	ASN	0	-0.012	-0.009	11.252	0.054	0.054	0.000	0.000	0.000	0.000
8	A	13	VAL	0	0.047	0.033	7.784	0.134	0.134	0.000	0.000	0.000	0.000
9	A	14	ILE	0	0.006	0.014	8.344	0.133	0.133	0.000	0.000	0.000	0.000
10	A	15	GLU	-1	-0.837	-0.906	11.626	-0.203	-0.203	0.000	0.000	0.000	0.000
11	A	16	PHE	0	0.010	-0.001	12.669	0.031	0.031	0.000	0.000	0.000	0.000
12	A	17	VAL	0	0.048	0.018	10.792	0.043	0.043	0.000	0.000	0.000	0.000
13	A	18	THR	0	-0.061	-0.032	14.085	0.018	0.018	0.000	0.000	0.000	0.000
14	A	19	VAL	0	-0.037	-0.024	16.940	0.022	0.022	0.000	0.000	0.000	0.000
15	A	20	ALA	0	0.026	0.016	16.387	0.017	0.017	0.000	0.000	0.000	0.000
16	A	21	ALA	0	0.043	0.021	17.580	0.021	0.021	0.000	0.000	0.000	0.000
17	A	22	GLU	-1	-0.951	-0.975	19.312	-0.016	-0.016	0.000	0.000	0.000	0.000
18	A	23	PHE	0	-0.037	-0.029	21.746	-0.002	-0.002	0.000	0.000	0.000	0.000
19	A	24	CYS	0	-0.025	0.008	20.620	0.013	0.013	0.000	0.000	0.000	0.000
20	A	25	ALA	0	0.043	0.018	23.218	-0.002	-0.002	0.000	0.000	0.000	0.000
21	A	26	PHE	0	-0.059	-0.047	25.084	-0.007	-0.007	0.000	0.000	0.000	0.000
22	A	27	LEU	0	-0.002	0.000	26.055	-0.004	-0.004	0.000	0.000	0.000	0.000
23	A	28	GLU	-1	-0.771	-0.846	24.452	0.143	0.143	0.000	0.000	0.000	0.000
24	A	29	ARG	1	0.913	0.963	27.568	-0.026	-0.026	0.000	0.000	0.000	0.000
25	A	30	ALA	0	0.012	0.010	31.158	-0.009	-0.009	0.000	0.000	0.000	0.000
26	A	31	GLU	-1	-0.882	-0.940	33.377	0.065	0.065	0.000	0.000	0.000	0.000
27	A	32	SER	0	-0.099	-0.037	34.541	-0.005	-0.005	0.000	0.000	0.000	0.000
28	A	33	MET	0	-0.053	-0.011	31.925	-0.009	-0.009	0.000	0.000	0.000	0.000
29	A	34	LYS	1	0.936	0.964	37.560	-0.021	-0.021	0.000	0.000	0.000	0.000
30	A	35	ARG	1	0.879	0.918	38.334	-0.038	-0.038	0.000	0.000	0.000	0.000
31	A	36	SER	0	0.007	0.004	38.331	0.001	0.001	0.000	0.000	0.000	0.000
32	A	37	THR	0	0.027	0.006	35.306	-0.001	-0.001	0.000	0.000	0.000	0.000
33	A	38	PHE	0	0.098	0.056	32.046	-0.006	-0.006	0.000	0.000	0.000	0.000
34	A	39	VAL	0	0.027	0.027	33.479	0.000	0.000	0.000	0.000	0.000	0.000
35	A	40	ASP	-1	-0.816	-0.891	34.179	-0.009	-0.009	0.000	0.000	0.000	0.000
36	A	41	THR	0	-0.020	-0.004	29.597	-0.010	-0.010	0.000	0.000	0.000	0.000
37	A	42	THR	0	0.039	0.004	29.336	-0.001	-0.001	0.000	0.000	0.000	0.000
38	A	43	LEU	0	-0.057	-0.036	29.334	0.000	0.000	0.000	0.000	0.000	0.000
39	A	44	LYS	1	0.774	0.882	29.464	0.011	0.011	0.000	0.000	0.000	0.000
40	A	45	ILE	0	0.027	0.019	24.017	-0.010	-0.010	0.000	0.000	0.000	0.000
41	A	46	LEU	0	0.028	0.020	24.608	-0.002	-0.002	0.000	0.000	0.000	0.000
42	A	47	PRO	0	0.010	0.001	24.873	0.004	0.004	0.000	0.000	0.000	0.000
43	A	48	LEU	0	-0.006	0.001	21.439	-0.010	-0.010	0.000	0.000	0.000	0.000
44	A	49	LEU	0	0.040	0.017	19.275	-0.017	-0.017	0.000	0.000	0.000	0.000
45	A	50	TYR	0	0.034	0.016	20.040	0.014	0.014	0.000	0.000	0.000	0.000
46	A	51	LEU	0	-0.029	-0.003	20.845	-0.002	-0.002	0.000	0.000	0.000	0.000
47	A	52	LYS	1	0.812	0.875	16.607	0.202	0.202	0.000	0.000	0.000	0.000
48	A	53	ALA	0	0.044	0.036	16.062	-0.013	-0.013	0.000	0.000	0.000	0.000
49	A	54	SER	0	-0.059	-0.043	16.225	0.018	0.018	0.000	0.000	0.000	0.000
50	A	55	MET	0	-0.111	-0.040	15.664	-0.018	-0.018	0.000	0.000	0.000	0.000
51	A	56	LEU	0	0.027	0.041	11.470	-0.117	-0.117	0.000	0.000	0.000	0.000
52	A	57	PRO	0	-0.025	-0.004	8.107	-0.010	-0.010	0.000	0.000	0.000	0.000
53	A	58	LYS	1	0.925	0.956	9.795	0.445	0.445	0.000	0.000	0.000	0.000
54	A	59	CYS	0	0.010	0.021	6.900	-0.129	-0.129	0.000	0.000	0.000	0.000
55	A	60	GLU	-1	-0.974	-0.985	6.401	0.965	0.965	0.000	0.000	0.000	0.000
56	A	61	MET	0	-0.046	-0.012	7.901	0.625	0.625	0.000	0.000	0.000	0.000
57	A	62	ILE	0	-0.008	-0.012	4.254	-0.074	0.099	-0.001	-0.011	-0.161	0.000
58	A	63	GLY	0	-0.051	-0.026	8.289	-0.430	-0.430	0.000	0.000	0.000	0.000
59	A	64	ASP	-1	-0.963	-0.994	11.653	1.612	1.612	0.000	0.000	0.000	0.000
60	A	65	GLU	-1	-0.949	-0.966	12.875	0.837	0.837	0.000	0.000	0.000	0.000
61	A	66	SER	0	-0.018	-0.019	13.815	0.095	0.095	0.000	0.000	0.000	0.000
62	A	67	PRO	0	-0.014	-0.017	13.118	-0.067	-0.067	0.000	0.000	0.000	0.000
63	A	68	GLU	-1	-0.922	-0.945	15.465	0.391	0.391	0.000	0.000	0.000	0.000
64	A	69	THR	0	-0.073	-0.049	17.831	0.021	0.021	0.000	0.000	0.000	0.000
65	A	70	TYR	0	-0.055	-0.017	20.419	-0.036	-0.036	0.000	0.000	0.000	0.000
66	A	71	VAL	0	-0.039	-0.035	22.385	-0.036	-0.036	0.000	0.000	0.000	0.000
67	A	72	THR	0	-0.004	0.007	24.918	0.008	0.008	0.000	0.000	0.000	0.000
68	A	73	GLU	-1	-0.880	-0.955	28.009	0.185	0.185	0.000	0.000	0.000	0.000
69	A	74	GLU	-1	-0.957	-0.973	31.233	0.124	0.124	0.000	0.000	0.000	0.000
70	A	75	ILE	0	-0.029	-0.013	26.262	-0.014	-0.014	0.000	0.000	0.000	0.000
71	A	76	TYR	0	-0.006	-0.026	28.148	-0.017	-0.017	0.000	0.000	0.000	0.000
72	A	77	GLU	-1	-0.771	-0.858	29.993	0.116	0.116	0.000	0.000	0.000	0.000
73	A	78	VAL	0	-0.006	0.005	33.032	-0.013	-0.013	0.000	0.000	0.000	0.000
74	A	79	LEU	0	-0.001	0.017	27.920	-0.013	-0.013	0.000	0.000	0.000	0.000
75	A	80	ARG	1	0.814	0.868	31.988	-0.131	-0.131	0.000	0.000	0.000	0.000
76	A	81	ILE	0	0.022	0.004	33.723	-0.012	-0.012	0.000	0.000	0.000	0.000
77	A	82	ASN	0	0.005	0.016	34.002	-0.011	-0.011	0.000	0.000	0.000	0.000
78	A	83	LEU	0	-0.060	-0.035	30.355	-0.011	-0.011	0.000	0.000	0.000	0.000
79	A	84	ALA	0	0.028	0.010	35.041	-0.008	-0.008	0.000	0.000	0.000	0.000
80	A	85	SER	0	-0.065	-0.041	38.199	-0.008	-0.008	0.000	0.000	0.000	0.000
81	A	86	ILE	0	-0.071	-0.019	36.418	-0.007	-0.007	0.000	0.000	0.000	0.000
82	A	87	LEU	0	-0.007	-0.005	35.472	-0.008	-0.008	0.000	0.000	0.000	0.000
83	A	88	ALA	0	0.029	0.014	39.875	-0.005	-0.005	0.000	0.000	0.000	0.000
84	A	89	GLU	-1	-0.796	-0.874	42.734	0.038	0.038	0.000	0.000	0.000	0.000
85	A	90	LYS	1	0.727	0.840	41.004	-0.039	-0.039	0.000	0.000	0.000	0.000
86	A	91	ASP	-1	-0.727	-0.821	37.332	0.079	0.079	0.000	0.000	0.000	0.000
87	A	92	ASP	-1	-0.894	-0.944	38.890	0.069	0.069	0.000	0.000	0.000	0.000
88	A	93	TYR	0	-0.109	-0.085	34.085	-0.010	-0.010	0.000	0.000	0.000	0.000
89	A	94	LEU	0	-0.041	-0.029	40.765	0.005	0.005	0.000	0.000	0.000	0.000
90	A	95	GLU	-1	-0.866	-0.911	36.534	0.054	0.054	0.000	0.000	0.000	0.000
91	A	108	ILE	0	0.000	-0.009	36.859	-0.002	-0.002	0.000	0.000	0.000	0.000
92	A	109	LYS	1	0.915	0.961	40.479	-0.069	-0.069	0.000	0.000	0.000	0.000
93	A	110	LYS	1	0.814	0.901	34.325	-0.107	-0.107	0.000	0.000	0.000	0.000
94	A	111	ASN	0	-0.004	-0.006	36.285	-0.012	-0.012	0.000	0.000	0.000	0.000
95	A	112	ILE	0	-0.006	-0.008	33.848	0.007	0.007	0.000	0.000	0.000	0.000
96	A	113	SER	0	-0.062	-0.067	32.830	0.008	0.008	0.000	0.000	0.000	0.000
97	A	114	GLU	-1	-0.727	-0.848	32.160	0.130	0.130	0.000	0.000	0.000	0.000
98	A	115	ASP	-1	-0.812	-0.871	30.430	0.122	0.122	0.000	0.000	0.000	0.000
99	A	116	LEU	0	-0.030	-0.027	28.413	0.008	0.008	0.000	0.000	0.000	0.000
100	A	117	ALA	0	0.006	0.014	27.391	0.008	0.008	0.000	0.000	0.000	0.000
101	A	118	ASP	-1	-0.771	-0.866	26.839	0.195	0.195	0.000	0.000	0.000	0.000
102	A	119	ILE	0	-0.057	-0.026	23.349	0.021	0.021	0.000	0.000	0.000	0.000
103	A	120	TYR	0	-0.066	-0.072	22.701	0.020	0.020	0.000	0.000	0.000	0.000
104	A	121	GLN	0	0.001	0.011	22.480	-0.008	-0.008	0.000	0.000	0.000	0.000
105	A	122	ASP	-1	-0.807	-0.901	19.412	0.418	0.418	0.000	0.000	0.000	0.000
106	A	123	ILE	0	-0.071	-0.028	18.039	0.041	0.041	0.000	0.000	0.000	0.000
107	A	124	LYS	1	0.855	0.902	17.749	-0.161	-0.161	0.000	0.000	0.000	0.000
108	A	125	ASP	-1	-0.747	-0.882	18.577	0.380	0.380	0.000	0.000	0.000	0.000
109	A	126	PHE	0	0.006	0.004	10.459	0.014	0.014	0.000	0.000	0.000	0.000
110	A	127	ILE	0	-0.034	-0.028	13.920	0.035	0.035	0.000	0.000	0.000	0.000
111	A	128	PHE	0	-0.023	-0.006	14.889	-0.037	-0.037	0.000	0.000	0.000	0.000
112	A	129	VAL	0	0.055	0.025	11.868	-0.016	-0.016	0.000	0.000	0.000	0.000
113	A	130	PHE	0	-0.037	-0.023	7.279	-0.001	-0.001	0.000	0.000	0.000	0.000
114	A	131	GLN	0	-0.049	-0.031	10.803	-0.078	-0.078	0.000	0.000	0.000	0.000
115	A	132	LEU	0	-0.020	-0.001	13.153	-0.071	-0.071	0.000	0.000	0.000	0.000
116	A	133	GLY	0	-0.048	-0.024	9.839	-0.020	-0.020	0.000	0.000	0.000	0.000
117	A	134	LEU	0	-0.012	0.001	9.281	-0.140	-0.140	0.000	0.000	0.000	0.000
118	A	135	ASN	0	-0.043	-0.057	3.100	-3.065	-1.709	0.110	-0.634	-0.832	-0.005
119	A	136	GLU	-1	-0.813	-0.890	5.879	3.592	3.592	0.000	0.000	0.000	0.000
120	A	137	THR	0	0.063	0.031	7.663	0.199	0.199	0.000	0.000	0.000	0.000
121	A	138	MET	0	-0.077	0.006	6.696	-0.252	-0.252	0.000	0.000	0.000	0.000
122	A	139	ASN	0	-0.074	-0.050	4.826	0.368	0.440	-0.001	-0.009	-0.061	0.000
123	A	140	ASP	-1	-0.734	-0.860	6.991	2.359	2.359	0.000	0.000	0.000	0.000
124	A	141	SER	0	-0.024	-0.028	10.130	-0.399	-0.399	0.000	0.000	0.000	0.000
125	A	142	LEU	0	-0.029	-0.016	7.503	-0.295	-0.295	0.000	0.000	0.000	0.000
126	A	143	ALA	0	-0.006	-0.006	9.114	-0.275	-0.275	0.000	0.000	0.000	0.000
127	A	144	ILE	0	0.008	0.000	10.914	-0.216	-0.216	0.000	0.000	0.000	0.000
128	A	145	CYS	0	-0.030	0.004	14.125	-0.162	-0.162	0.000	0.000	0.000	0.000
129	A	146	GLN	0	-0.022	-0.041	11.083	0.010	0.010	0.000	0.000	0.000	0.000
130	A	147	GLU	-1	-0.909	-0.950	14.480	0.335	0.335	0.000	0.000	0.000	0.000
131	A	148	ASN	0	-0.016	-0.032	16.478	-0.077	-0.077	0.000	0.000	0.000	0.000
132	A	149	PHE	0	-0.091	-0.030	17.942	-0.071	-0.071	0.000	0.000	0.000	0.000
133	A	150	GLY	0	-0.008	-0.003	19.213	-0.048	-0.048	0.000	0.000	0.000	0.000
134	A	151	LEU	0	-0.049	-0.020	20.409	-0.035	-0.035	0.000	0.000	0.000	0.000
135	A	152	LEU	0	-0.026	-0.016	22.668	-0.023	-0.023	0.000	0.000	0.000	0.000
136	A	153	TRP	0	0.045	0.022	17.023	-0.045	-0.045	0.000	0.000	0.000	0.000
137	A	154	GLY	0	0.040	0.013	22.677	-0.027	-0.027	0.000	0.000	0.000	0.000
138	A	155	GLN	0	-0.035	-0.020	23.860	-0.027	-0.027	0.000	0.000	0.000	0.000
139	A	156	LYS	1	0.849	0.900	26.979	-0.167	-0.167	0.000	0.000	0.000	0.000
140	A	157	LEU	0	-0.007	0.029	23.700	-0.016	-0.016	0.000	0.000	0.000	0.000
141	A	158	VAL	0	0.017	-0.007	27.067	-0.016	-0.016	0.000	0.000	0.000	0.000
142	A	159	ASN	0	-0.019	-0.010	29.445	-0.019	-0.019	0.000	0.000	0.000	0.000
143	A	160	THR	0	0.040	0.007	29.913	-0.007	-0.007	0.000	0.000	0.000	0.000
144	A	161	MET	0	-0.047	-0.022	28.724	-0.008	-0.008	0.000	0.000	0.000	0.000
145	A	162	ARG	1	0.816	0.905	32.065	-0.057	-0.057	0.000	0.000	0.000	0.000
146	A	163	ALA	0	0.052	0.037	35.228	-0.006	-0.006	0.000	0.000	0.000	0.000
147	A	164	LEU	0	0.027	0.002	32.128	-0.005	-0.005	0.000	0.000	0.000	0.000
148	A	165	HIS	0	-0.002	0.008	35.777	-0.007	-0.007	0.000	0.000	0.000	0.000
149	A	166	ASP	-1	-0.861	-0.922	37.359	0.019	0.019	0.000	0.000	0.000	0.000
150	A	167	VAL	0	-0.019	-0.012	38.803	-0.003	-0.003	0.000	0.000	0.000	0.000
151	A	168	LYS	1	0.799	0.891	37.902	0.003	0.003	0.000	0.000	0.000	0.000
152	A	169	TYR	0	-0.047	-0.048	37.243	-0.004	-0.004	0.000	0.000	0.000	0.000
153	A	170	SER	0	-0.038	-0.012	42.613	-0.002	-0.002	0.000	0.000	0.000	0.000
154	A	171	PRO	0	-0.031	-0.018	44.657	0.000	0.000	0.000	0.000	0.000	0.000
155	A	172	LYS	1	0.857	0.921	43.702	-0.011	-0.011	0.000	0.000	0.000	0.000
156	A	173	ALA	0	-0.016	-0.016	49.572	-0.001	-0.001	0.000	0.000	0.000	0.000
157	A	174	ARG	1	0.941	0.990	46.050	-0.024	-0.024	0.000	0.000	0.000	0.000
158	A	175	DLE	0	0.020	0.020	52.461	0.002	0.002	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:6:GLN)