FMO DATABASE

FMODB ID: R5Z38

Calculation Name: 3BNW-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3BNW

Chain ID: A

ChEMBL ID:

UniProt ID: Q38DG4

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	OptHSide
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	172
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1796843.774317
FMO2-HF: Nuclear repulsion	1728693.257924
FMO2-HF: Total energy	-68150.516393
FMO2-MP2: Total energy	-68349.592702

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:0:HIS)

Summations of interaction energy for fragment #1(A:0: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.
-20.061	-9.543	9.71	-6.755	-13.472	-0.03

Interaction energy analysis for fragmet #1(A:0:HIS)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.036 / q_NPA : -0.027

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	2	ARG	1	0.922	0.968	3.661	0.021	1.432	0.004	-0.629	-0.785	0.002
4	A	3	GLN	0	-0.001	-0.013	4.260	0.984	1.120	-0.001	-0.008	-0.127	0.000
5	A	4	THR	0	-0.005	-0.012	7.624	0.477	0.477	0.000	0.000	0.000	0.000
6	A	5	GLY	0	0.030	0.018	11.040	-0.059	-0.059	0.000	0.000	0.000	0.000
7	A	6	SER	0	0.006	-0.001	12.342	0.090	0.090	0.000	0.000	0.000	0.000
8	A	7	PHE	0	-0.036	-0.004	10.984	0.021	0.021	0.000	0.000	0.000	0.000
9	A	8	GLN	0	0.001	0.002	13.122	0.053	0.053	0.000	0.000	0.000	0.000
10	A	9	PRO	0	0.021	0.016	14.517	-0.041	-0.041	0.000	0.000	0.000	0.000
11	A	10	PHE	0	0.006	0.015	15.400	0.086	0.086	0.000	0.000	0.000	0.000
12	A	11	PHE	0	-0.004	-0.007	18.278	-0.035	-0.035	0.000	0.000	0.000	0.000
13	A	12	LEU	0	0.010	0.006	19.256	0.014	0.014	0.000	0.000	0.000	0.000
14	A	13	ARG	1	0.860	0.944	21.718	0.310	0.310	0.000	0.000	0.000	0.000
15	A	14	GLY	0	0.058	0.015	24.424	0.015	0.015	0.000	0.000	0.000	0.000
16	A	15	LYS	1	0.905	0.963	25.058	0.218	0.218	0.000	0.000	0.000	0.000
17	A	16	VAL	0	0.011	0.027	22.862	-0.019	-0.019	0.000	0.000	0.000	0.000
18	A	17	VAL	0	0.011	0.005	24.649	0.040	0.040	0.000	0.000	0.000	0.000
19	A	18	HIS	0	0.067	0.023	24.696	-0.027	-0.027	0.000	0.000	0.000	0.000
20	A	19	GLY	0	-0.054	-0.027	25.569	-0.001	-0.001	0.000	0.000	0.000	0.000
21	A	20	LYS	1	0.824	0.912	19.375	0.404	0.404	0.000	0.000	0.000	0.000
22	A	21	GLY	0	0.089	0.068	25.379	0.003	0.003	0.000	0.000	0.000	0.000
23	A	22	ARG	1	0.794	0.876	25.380	0.209	0.209	0.000	0.000	0.000	0.000
24	A	23	GLY	0	0.056	0.025	23.670	-0.010	-0.010	0.000	0.000	0.000	0.000
25	A	24	GLY	0	0.007	0.009	24.380	0.007	0.007	0.000	0.000	0.000	0.000
26	A	25	SER	0	0.002	-0.018	21.292	0.016	0.016	0.000	0.000	0.000	0.000
27	A	26	GLN	0	0.010	0.000	23.622	-0.017	-0.017	0.000	0.000	0.000	0.000
28	A	27	LEU	0	-0.029	-0.004	18.588	0.008	0.008	0.000	0.000	0.000	0.000
29	A	28	GLY	0	0.001	0.023	21.701	0.001	0.001	0.000	0.000	0.000	0.000
30	A	29	PHE	0	-0.004	-0.009	15.572	-0.005	-0.005	0.000	0.000	0.000	0.000
31	A	30	PRO	0	0.044	0.025	16.077	0.025	0.025	0.000	0.000	0.000	0.000
32	A	31	THR	0	-0.030	-0.027	19.009	-0.012	-0.012	0.000	0.000	0.000	0.000
33	A	32	ALA	0	0.016	0.025	20.455	0.021	0.021	0.000	0.000	0.000	0.000
34	A	33	ASN	0	0.027	-0.001	19.792	-0.088	-0.088	0.000	0.000	0.000	0.000
35	A	34	ILE	0	0.010	0.021	18.866	0.039	0.039	0.000	0.000	0.000	0.000
36	A	35	GLY	0	-0.048	-0.023	22.420	-0.002	-0.002	0.000	0.000	0.000	0.000
37	A	36	LEU	0	-0.015	-0.005	21.487	-0.009	-0.009	0.000	0.000	0.000	0.000
38	A	37	ASP	-1	-0.793	-0.918	25.800	-0.273	-0.273	0.000	0.000	0.000	0.000
39	A	38	LYS	1	0.925	0.952	27.390	0.211	0.211	0.000	0.000	0.000	0.000
40	A	39	ASP	-1	-0.889	-0.931	28.050	-0.330	-0.330	0.000	0.000	0.000	0.000
41	A	40	VAL	0	0.068	0.025	23.641	-0.028	-0.028	0.000	0.000	0.000	0.000
42	A	41	MET	0	-0.098	-0.052	23.357	-0.036	-0.036	0.000	0.000	0.000	0.000
43	A	42	GLU	-1	-0.952	-0.969	22.933	-0.344	-0.344	0.000	0.000	0.000	0.000
44	A	43	CYS	0	0.007	0.011	23.026	-0.018	-0.018	0.000	0.000	0.000	0.000
45	A	44	LEU	0	0.015	-0.006	18.266	-0.058	-0.058	0.000	0.000	0.000	0.000
46	A	45	GLN	0	-0.038	-0.007	18.205	-0.060	-0.060	0.000	0.000	0.000	0.000
47	A	46	PRO	0	-0.039	-0.024	17.567	-0.016	-0.016	0.000	0.000	0.000	0.000
48	A	47	TYR	0	-0.031	-0.022	13.815	-0.065	-0.065	0.000	0.000	0.000	0.000
49	A	48	LYS	1	0.862	0.939	13.754	0.372	0.372	0.000	0.000	0.000	0.000
50	A	49	ASN	0	-0.085	-0.058	12.870	0.009	0.009	0.000	0.000	0.000	0.000
51	A	50	LEU	0	0.028	0.017	8.627	-0.045	-0.045	0.000	0.000	0.000	0.000
52	A	51	VAL	0	-0.017	-0.003	6.671	0.257	0.257	0.000	0.000	0.000	0.000
53	A	52	VAL	0	-0.012	-0.009	7.363	-0.803	-0.803	0.000	0.000	0.000	0.000
54	A	53	TYR	0	0.008	-0.010	6.459	0.311	0.311	0.000	0.000	0.000	0.000
55	A	54	GLY	0	0.036	0.016	9.805	0.101	0.101	0.000	0.000	0.000	0.000
56	A	55	TRP	0	-0.014	0.001	12.990	0.049	0.049	0.000	0.000	0.000	0.000
57	A	56	GLY	0	0.035	0.003	16.313	-0.027	-0.027	0.000	0.000	0.000	0.000
58	A	57	THR	0	-0.006	0.008	18.655	0.048	0.048	0.000	0.000	0.000	0.000
59	A	58	VAL	0	0.006	0.007	21.890	-0.020	-0.020	0.000	0.000	0.000	0.000
60	A	59	SER	0	0.021	0.008	24.393	0.030	0.030	0.000	0.000	0.000	0.000
61	A	60	GLN	0	0.003	0.002	28.101	-0.018	-0.018	0.000	0.000	0.000	0.000
62	A	61	VAL	0	0.033	0.015	27.775	-0.006	-0.006	0.000	0.000	0.000	0.000
63	A	62	PRO	0	0.023	0.013	30.551	0.013	0.013	0.000	0.000	0.000	0.000
64	A	63	GLY	0	-0.014	0.004	33.264	0.003	0.003	0.000	0.000	0.000	0.000
65	A	64	LYS	1	0.817	0.914	29.787	0.140	0.140	0.000	0.000	0.000	0.000
66	A	65	GLU	-1	-0.856	-0.931	32.745	-0.146	-0.146	0.000	0.000	0.000	0.000
67	A	66	ARG	1	0.827	0.899	34.107	0.102	0.102	0.000	0.000	0.000	0.000
68	A	67	GLU	-1	-0.854	-0.910	30.190	-0.123	-0.123	0.000	0.000	0.000	0.000
69	A	68	SER	0	-0.026	-0.024	28.136	-0.015	-0.015	0.000	0.000	0.000	0.000
70	A	69	PHE	0	-0.021	-0.016	24.401	0.017	0.017	0.000	0.000	0.000	0.000
71	A	70	GLY	0	0.038	0.032	21.884	-0.035	-0.035	0.000	0.000	0.000	0.000
72	A	71	PRO	0	-0.003	-0.008	20.000	0.026	0.026	0.000	0.000	0.000	0.000
73	A	72	TYR	0	-0.049	-0.035	17.330	0.031	0.031	0.000	0.000	0.000	0.000
74	A	73	PRO	0	0.026	0.010	12.649	-0.062	-0.062	0.000	0.000	0.000	0.000
75	A	74	PHE	0	-0.042	-0.015	12.845	0.063	0.063	0.000	0.000	0.000	0.000
76	A	75	ALA	0	0.071	0.042	8.549	-0.230	-0.230	0.000	0.000	0.000	0.000
77	A	76	ALA	0	-0.002	-0.008	10.184	0.353	0.353	0.000	0.000	0.000	0.000
78	A	77	SER	0	0.004	0.009	10.895	-0.382	-0.382	0.000	0.000	0.000	0.000
79	A	78	ILE	0	0.013	0.017	12.660	0.186	0.186	0.000	0.000	0.000	0.000
80	A	79	GLY	0	0.072	0.013	14.743	-0.033	-0.033	0.000	0.000	0.000	0.000
81	A	80	PHE	0	-0.015	0.025	17.045	0.026	0.026	0.000	0.000	0.000	0.000
82	A	81	ASN	0	-0.008	-0.020	19.506	-0.034	-0.034	0.000	0.000	0.000	0.000
83	A	82	MET	0	-0.028	0.004	22.591	0.002	0.002	0.000	0.000	0.000	0.000
84	A	83	GLN	0	0.047	0.026	26.153	0.025	0.025	0.000	0.000	0.000	0.000
85	A	84	PHE	0	-0.043	-0.016	28.482	0.009	0.009	0.000	0.000	0.000	0.000
86	A	85	ASP	-1	-0.873	-0.944	31.033	-0.149	-0.149	0.000	0.000	0.000	0.000
87	A	86	GLU	-1	-0.818	-0.876	27.479	-0.261	-0.261	0.000	0.000	0.000	0.000
88	A	87	LYS	1	0.792	0.864	23.776	0.203	0.203	0.000	0.000	0.000	0.000
89	A	88	THR	0	0.017	-0.012	23.743	-0.021	-0.021	0.000	0.000	0.000	0.000
90	A	89	LEU	0	-0.063	-0.024	18.612	-0.013	-0.013	0.000	0.000	0.000	0.000
91	A	90	THR	0	0.020	-0.003	19.365	0.045	0.045	0.000	0.000	0.000	0.000
92	A	91	VAL	0	0.031	0.007	16.463	-0.068	-0.068	0.000	0.000	0.000	0.000
93	A	92	GLU	-1	-0.821	-0.877	15.718	-0.503	-0.503	0.000	0.000	0.000	0.000
94	A	93	PRO	0	-0.013	-0.001	14.654	-0.137	-0.137	0.000	0.000	0.000	0.000
95	A	94	TYR	0	-0.048	-0.055	11.111	0.066	0.066	0.000	0.000	0.000	0.000
96	A	95	PHE	0	-0.007	-0.001	13.165	-0.108	-0.108	0.000	0.000	0.000	0.000
97	A	96	LEU	0	-0.072	-0.021	9.411	0.068	0.068	0.000	0.000	0.000	0.000
98	A	97	HIS	0	0.006	-0.019	13.962	0.090	0.090	0.000	0.000	0.000	0.000
99	A	98	GLU	-1	-0.944	-0.958	17.612	-0.124	-0.124	0.000	0.000	0.000	0.000
100	A	99	PHE	0	-0.006	-0.001	19.420	0.018	0.018	0.000	0.000	0.000	0.000
101	A	100	GLY	0	0.004	0.003	23.076	0.020	0.020	0.000	0.000	0.000	0.000
102	A	101	TRP	0	-0.031	-0.029	24.685	0.009	0.009	0.000	0.000	0.000	0.000
103	A	102	ASP	-1	-0.859	-0.918	24.397	-0.227	-0.227	0.000	0.000	0.000	0.000
104	A	103	PHE	0	0.000	-0.017	20.649	0.013	0.013	0.000	0.000	0.000	0.000
105	A	104	TYR	0	-0.013	-0.020	24.245	-0.022	-0.022	0.000	0.000	0.000	0.000
106	A	105	GLY	0	-0.011	-0.011	27.841	0.020	0.020	0.000	0.000	0.000	0.000
107	A	106	ALA	0	-0.024	0.002	26.491	0.011	0.011	0.000	0.000	0.000	0.000
108	A	107	VAL	0	-0.052	-0.028	26.651	-0.020	-0.020	0.000	0.000	0.000	0.000
109	A	108	VAL	0	-0.005	-0.001	20.339	0.006	0.006	0.000	0.000	0.000	0.000
110	A	109	LYS	1	0.868	0.931	22.497	0.296	0.296	0.000	0.000	0.000	0.000
111	A	110	ILE	0	-0.008	-0.005	16.135	-0.002	-0.002	0.000	0.000	0.000	0.000
112	A	111	ILE	0	0.015	0.015	16.679	0.025	0.025	0.000	0.000	0.000	0.000
113	A	112	VAL	0	-0.019	-0.009	12.562	-0.082	-0.082	0.000	0.000	0.000	0.000
114	A	113	LEU	0	-0.019	-0.027	12.171	0.065	0.065	0.000	0.000	0.000	0.000
115	A	114	GLY	0	0.013	0.011	8.827	0.057	0.057	0.000	0.000	0.000	0.000
116	A	115	GLU	-1	-0.891	-0.950	6.777	-2.122	-2.122	0.000	0.000	0.000	0.000
117	A	116	ILE	0	-0.036	-0.012	2.086	-2.976	-2.638	2.859	-1.005	-2.193	-0.006
118	A	117	ARG	1	0.836	0.882	2.574	-1.282	0.764	1.411	-1.601	-1.856	-0.015
119	A	118	SER	0	0.051	0.030	4.624	0.105	0.164	-0.001	-0.014	-0.045	0.000
120	A	119	MET	0	-0.027	-0.010	7.859	0.011	0.011	0.000	0.000	0.000	0.000
121	A	120	GLY	0	-0.027	0.000	10.434	0.109	0.109	0.000	0.000	0.000	0.000
122	A	121	SER	0	0.009	-0.005	11.298	-0.084	-0.084	0.000	0.000	0.000	0.000
123	A	122	PHE	0	-0.009	-0.009	9.198	0.136	0.136	0.000	0.000	0.000	0.000
124	A	123	HIS	0	0.029	0.027	14.515	-0.078	-0.078	0.000	0.000	0.000	0.000
125	A	124	SER	0	0.007	-0.005	15.836	-0.046	-0.046	0.000	0.000	0.000	0.000
126	A	125	LEU	0	0.069	0.022	15.387	-0.006	-0.006	0.000	0.000	0.000	0.000
127	A	126	GLN	0	0.004	-0.008	14.009	-0.105	-0.105	0.000	0.000	0.000	0.000
128	A	127	ALA	0	0.029	0.024	11.597	0.105	0.105	0.000	0.000	0.000	0.000
129	A	128	LEU	0	0.021	0.034	9.943	0.079	0.079	0.000	0.000	0.000	0.000
130	A	129	VAL	0	0.014	-0.003	9.614	-0.177	-0.177	0.000	0.000	0.000	0.000
131	A	130	ASP	-1	-0.830	-0.907	8.831	0.941	0.941	0.000	0.000	0.000	0.000
132	A	131	THR	0	-0.029	-0.009	5.436	0.708	0.708	0.000	0.000	0.000	0.000
133	A	132	ILE	0	0.017	0.013	4.874	-1.311	-1.208	-0.001	-0.002	-0.100	0.000
134	A	133	LYS	1	0.852	0.914	6.477	-1.321	-1.321	0.000	0.000	0.000	0.000
135	A	134	SER	0	-0.002	-0.011	2.381	0.273	1.267	0.717	-0.648	-1.062	0.003
136	A	135	ASP	-1	-0.794	-0.880	2.506	-9.887	-8.688	1.593	-1.041	-1.751	-0.014
137	A	136	VAL	0	-0.028	-0.018	3.830	0.800	0.840	0.000	0.021	-0.060	0.000
138	A	137	GLN	0	0.028	0.005	5.646	-0.320	-0.320	0.000	0.000	0.000	0.000
139	A	138	PHE	0	0.037	0.031	2.882	-5.954	-1.885	3.130	-1.808	-5.391	0.000
140	A	139	THR	0	-0.015	-0.021	4.876	-0.411	-0.288	-0.001	-0.020	-0.102	0.000
141	A	140	ARG	1	0.910	0.949	7.585	0.257	0.257	0.000	0.000	0.000	0.000
142	A	141	ASP	-1	-0.904	-0.946	7.469	1.759	1.759	0.000	0.000	0.000	0.000
143	A	142	MET	0	-0.097	-0.055	6.264	0.001	0.001	0.000	0.000	0.000	0.000
144	A	143	LEU	0	-0.025	-0.014	9.359	0.001	0.001	0.000	0.000	0.000	0.000
145	A	144	GLN	0	0.043	0.032	12.628	-0.012	-0.012	0.000	0.000	0.000	0.000
146	A	145	LYS	1	0.888	0.963	9.707	0.793	0.793	0.000	0.000	0.000	0.000
147	A	146	PRO	0	0.022	0.000	14.437	-0.062	-0.062	0.000	0.000	0.000	0.000
148	A	147	GLN	0	-0.019	-0.005	14.698	-0.057	-0.057	0.000	0.000	0.000	0.000
149	A	148	LEU	0	0.042	0.011	10.767	0.001	0.001	0.000	0.000	0.000	0.000
150	A	149	GLN	0	0.018	0.014	15.203	-0.053	-0.053	0.000	0.000	0.000	0.000
151	A	150	GLU	-1	-0.818	-0.888	17.398	-0.237	-0.237	0.000	0.000	0.000	0.000
152	A	151	PHE	0	-0.052	-0.029	17.301	0.006	0.006	0.000	0.000	0.000	0.000
153	A	152	SER	0	-0.020	-0.010	19.347	-0.001	-0.001	0.000	0.000	0.000	0.000
154	A	153	ARG	1	0.838	0.903	20.490	0.247	0.247	0.000	0.000	0.000	0.000
155	A	154	HIS	0	0.035	0.024	21.698	0.024	0.024	0.000	0.000	0.000	0.000
156	A	155	SER	0	0.076	0.025	23.824	-0.003	-0.003	0.000	0.000	0.000	0.000
157	A	156	LEU	0	0.007	0.001	24.209	0.018	0.018	0.000	0.000	0.000	0.000
158	A	157	PHE	0	-0.068	-0.032	19.504	0.004	0.004	0.000	0.000	0.000	0.000
159	A	158	GLU	-1	-0.948	-0.969	25.682	-0.209	-0.209	0.000	0.000	0.000	0.000
160	A	159	SER	0	-0.008	0.017	28.733	0.021	0.021	0.000	0.000	0.000	0.000
161	A	160	PRO	0	-0.060	-0.021	30.375	-0.008	-0.008	0.000	0.000	0.000	0.000
162	A	161	SER	0	0.036	-0.019	31.264	-0.007	-0.007	0.000	0.000	0.000	0.000
163	A	162	SER	0	-0.022	-0.005	32.291	-0.010	-0.010	0.000	0.000	0.000	0.000
164	A	163	THR	0	-0.018	0.008	31.330	0.005	0.005	0.000	0.000	0.000	0.000
165	A	164	ILE	0	-0.024	0.012	28.991	-0.021	-0.021	0.000	0.000	0.000	0.000
166	A	165	PRO	0	0.017	-0.002	26.043	0.018	0.018	0.000	0.000	0.000	0.000
167	A	166	TYR	0	-0.078	-0.082	26.238	0.027	0.027	0.000	0.000	0.000	0.000
168	A	167	PHE	0	0.044	0.017	19.779	-0.026	-0.026	0.000	0.000	0.000	0.000
169	A	168	GLU	-1	-0.857	-0.909	23.045	-0.322	-0.322	0.000	0.000	0.000	0.000
170	A	169	ASP	-1	-0.832	-0.915	20.888	-0.601	-0.601	0.000	0.000	0.000	0.000
171	A	170	LEU	0	-0.049	-0.031	18.956	0.041	0.041	0.000	0.000	0.000	0.000
172	A	171	PRO	0	-0.012	0.006	20.082	-0.031	-0.031	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:0:HIS)