FMO DATABASE

FMODB ID: 2NM1R

Calculation Name: 3HVV-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3HVV

Chain ID: A

ChEMBL ID:

UniProt ID: P0A862

Base Structure: X-ray

Registration Date: 2023-09-23

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	167
LigandResidueName
LigandFragmentNumber	0
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1595881.884684
FMO2-HF: Nuclear repulsion	1534623.791261
FMO2-HF: Total energy	-61258.093423
FMO2-MP2: Total energy	-61439.90141

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:2:SER)

Summations of interaction energy for fragment #1(A:2: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.
-13.014	-4.477	2.387	-5.202	-5.721	-0.033

Interaction energy analysis for fragmet #1(A:2:SER)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.054 / q_NPA : -0.016

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	4	THR	0	-0.039	-0.033	3.528	0.670	3.233	-0.001	-1.415	-1.147	0.005
4	A	5	VAL	0	0.020	0.032	6.299	-0.291	-0.291	0.000	0.000	0.000	0.000
5	A	6	HIS	0	-0.034	-0.026	9.423	0.314	0.314	0.000	0.000	0.000	0.000
6	A	7	PHE	0	-0.025	-0.015	12.419	-0.058	-0.058	0.000	0.000	0.000	0.000
7	A	8	GLN	0	-0.032	-0.029	15.108	0.066	0.066	0.000	0.000	0.000	0.000
8	A	9	GLY	0	0.017	0.016	16.220	0.022	0.022	0.000	0.000	0.000	0.000
9	A	10	ASN	0	-0.078	-0.041	14.535	0.037	0.037	0.000	0.000	0.000	0.000
10	A	11	PRO	0	0.028	0.029	9.256	-0.064	-0.064	0.000	0.000	0.000	0.000
11	A	12	VAL	0	-0.003	-0.004	8.230	0.123	0.123	0.000	0.000	0.000	0.000
12	A	13	THR	0	0.029	0.024	2.906	-1.408	-0.824	0.230	-0.254	-0.560	0.000
13	A	14	VAL	0	0.001	0.006	3.512	-0.335	0.012	0.004	-0.099	-0.252	0.000
14	A	15	ALA	0	0.000	-0.005	2.588	-5.796	-3.149	1.253	-1.941	-1.959	-0.023
15	A	16	ASN	0	-0.065	-0.044	3.000	-1.362	-0.425	0.312	-0.467	-0.781	-0.004
16	A	17	SER	0	0.017	-0.009	2.750	-4.297	-2.838	0.589	-1.026	-1.022	-0.011
17	A	18	ILE	0	-0.001	0.019	5.439	0.634	0.634	0.000	0.000	0.000	0.000
18	A	19	PRO	0	0.019	0.018	8.611	-0.055	-0.055	0.000	0.000	0.000	0.000
19	A	20	GLN	0	-0.019	0.009	9.980	0.070	0.070	0.000	0.000	0.000	0.000
20	A	21	ALA	0	0.046	0.031	13.363	0.098	0.098	0.000	0.000	0.000	0.000
21	A	22	GLY	0	-0.014	-0.005	16.852	-0.020	-0.020	0.000	0.000	0.000	0.000
22	A	23	SER	0	-0.069	-0.038	14.912	0.027	0.027	0.000	0.000	0.000	0.000
23	A	24	LYS	1	0.977	0.978	16.963	0.201	0.201	0.000	0.000	0.000	0.000
24	A	25	ALA	0	0.017	0.011	16.557	-0.036	-0.036	0.000	0.000	0.000	0.000
25	A	26	GLN	0	-0.035	-0.012	12.609	-0.003	-0.003	0.000	0.000	0.000	0.000
26	A	27	THR	0	0.008	0.005	16.913	-0.006	-0.006	0.000	0.000	0.000	0.000
27	A	28	PHE	0	0.023	0.001	17.663	-0.001	-0.001	0.000	0.000	0.000	0.000
28	A	29	THR	0	0.029	0.006	19.505	-0.001	-0.001	0.000	0.000	0.000	0.000
29	A	30	LEU	0	-0.024	0.000	18.172	0.007	0.007	0.000	0.000	0.000	0.000
30	A	31	VAL	0	-0.004	0.019	22.217	0.005	0.005	0.000	0.000	0.000	0.000
31	A	32	ALA	0	0.046	0.036	25.275	-0.008	-0.008	0.000	0.000	0.000	0.000
32	A	33	LYS	1	0.985	0.967	27.790	0.062	0.062	0.000	0.000	0.000	0.000
33	A	34	ASP	-1	-0.866	-0.905	30.350	-0.028	-0.028	0.000	0.000	0.000	0.000
34	A	35	LEU	0	-0.071	-0.040	29.190	0.007	0.007	0.000	0.000	0.000	0.000
35	A	36	SER	0	-0.016	-0.012	30.306	0.004	0.004	0.000	0.000	0.000	0.000
36	A	37	ASP	-1	-0.853	-0.923	26.344	-0.010	-0.010	0.000	0.000	0.000	0.000
37	A	38	VAL	0	-0.015	-0.015	25.288	-0.003	-0.003	0.000	0.000	0.000	0.000
38	A	39	THR	0	-0.035	-0.038	23.621	-0.006	-0.006	0.000	0.000	0.000	0.000
39	A	40	LEU	0	-0.001	0.016	19.820	0.002	0.002	0.000	0.000	0.000	0.000
40	A	41	GLY	0	0.047	0.015	23.391	-0.003	-0.003	0.000	0.000	0.000	0.000
41	A	42	GLN	0	-0.003	0.009	26.507	0.004	0.004	0.000	0.000	0.000	0.000
42	A	43	PHE	0	-0.024	-0.012	24.641	0.005	0.005	0.000	0.000	0.000	0.000
43	A	44	ALA	0	0.023	0.011	28.143	-0.010	-0.010	0.000	0.000	0.000	0.000
44	A	45	GLY	0	-0.009	-0.001	29.030	0.008	0.008	0.000	0.000	0.000	0.000
45	A	46	LYS	1	0.928	0.978	28.593	0.107	0.107	0.000	0.000	0.000	0.000
46	A	47	ARG	1	0.864	0.926	26.008	0.173	0.173	0.000	0.000	0.000	0.000
47	A	48	LYS	1	0.764	0.865	22.364	0.208	0.208	0.000	0.000	0.000	0.000
48	A	49	VAL	0	0.037	0.034	21.749	-0.029	-0.029	0.000	0.000	0.000	0.000
49	A	50	LEU	0	-0.027	-0.009	16.777	0.033	0.033	0.000	0.000	0.000	0.000
50	A	51	ASN	0	0.028	-0.004	18.416	-0.067	-0.067	0.000	0.000	0.000	0.000
51	A	52	ILE	0	-0.020	-0.015	14.024	0.042	0.042	0.000	0.000	0.000	0.000
52	A	53	PHE	0	0.017	-0.009	16.126	-0.028	-0.028	0.000	0.000	0.000	0.000
53	A	54	PRO	0	-0.002	0.007	14.551	0.023	0.023	0.000	0.000	0.000	0.000
54	A	55	SER	0	-0.008	-0.045	16.371	0.028	0.028	0.000	0.000	0.000	0.000
55	A	56	ILE	0	-0.044	-0.024	20.104	-0.013	-0.013	0.000	0.000	0.000	0.000
56	A	57	ASP	-1	-0.952	-0.973	23.380	-0.010	-0.010	0.000	0.000	0.000	0.000
57	A	58	THR	0	-0.053	-0.022	20.615	0.011	0.011	0.000	0.000	0.000	0.000
58	A	59	GLY	0	0.013	0.007	21.198	-0.016	-0.016	0.000	0.000	0.000	0.000
59	A	60	VAL	0	0.011	-0.006	20.348	0.003	0.003	0.000	0.000	0.000	0.000
60	A	61	SER	0	0.032	0.023	20.395	-0.025	-0.025	0.000	0.000	0.000	0.000
61	A	62	ALA	0	0.080	0.059	22.132	-0.012	-0.012	0.000	0.000	0.000	0.000
62	A	63	ALA	0	-0.021	-0.009	25.406	-0.001	-0.001	0.000	0.000	0.000	0.000
63	A	64	SER	0	0.005	-0.005	22.349	-0.008	-0.008	0.000	0.000	0.000	0.000
64	A	65	VAL	0	0.009	-0.003	24.101	-0.008	-0.008	0.000	0.000	0.000	0.000
65	A	66	ARG	1	0.789	0.853	26.161	0.069	0.069	0.000	0.000	0.000	0.000
66	A	67	LYS	1	0.835	0.908	26.731	0.148	0.148	0.000	0.000	0.000	0.000
67	A	68	PHE	0	0.053	0.011	21.622	-0.001	-0.001	0.000	0.000	0.000	0.000
68	A	69	ASN	0	0.008	0.005	27.115	0.003	0.003	0.000	0.000	0.000	0.000
69	A	70	GLN	0	-0.052	-0.020	30.140	0.011	0.011	0.000	0.000	0.000	0.000
70	A	71	LEU	0	0.035	0.017	27.152	0.000	0.000	0.000	0.000	0.000	0.000
71	A	72	ALA	0	-0.020	-0.011	29.425	-0.002	-0.002	0.000	0.000	0.000	0.000
72	A	73	THR	0	-0.099	-0.056	30.636	0.005	0.005	0.000	0.000	0.000	0.000
73	A	74	GLU	-1	-0.913	-0.939	32.741	-0.123	-0.123	0.000	0.000	0.000	0.000
74	A	75	ILE	0	-0.057	-0.018	28.337	-0.007	-0.007	0.000	0.000	0.000	0.000
75	A	76	ASP	-1	-0.861	-0.926	32.493	-0.106	-0.106	0.000	0.000	0.000	0.000
76	A	77	ASN	0	-0.095	-0.059	31.794	-0.004	-0.004	0.000	0.000	0.000	0.000
77	A	78	THR	0	0.015	0.000	26.708	-0.014	-0.014	0.000	0.000	0.000	0.000
78	A	79	VAL	0	-0.050	-0.007	25.638	0.013	0.013	0.000	0.000	0.000	0.000
79	A	80	VAL	0	0.021	0.003	24.629	-0.018	-0.018	0.000	0.000	0.000	0.000
80	A	81	LEU	0	0.000	0.003	21.972	0.019	0.019	0.000	0.000	0.000	0.000
81	A	82	CYS	0	-0.048	-0.005	21.830	-0.025	-0.025	0.000	0.000	0.000	0.000
82	A	83	ILE	0	0.014	-0.002	17.843	0.023	0.023	0.000	0.000	0.000	0.000
83	A	84	SER	0	-0.015	-0.034	17.622	-0.022	-0.022	0.000	0.000	0.000	0.000
84	A	85	ALA	0	0.073	0.039	16.477	0.010	0.010	0.000	0.000	0.000	0.000
85	A	86	ASP	-1	-0.754	-0.797	18.530	-0.013	-0.013	0.000	0.000	0.000	0.000
86	A	87	LEU	0	0.029	0.028	22.003	-0.006	-0.006	0.000	0.000	0.000	0.000
87	A	88	PRO	0	0.062	0.017	24.824	-0.008	-0.008	0.000	0.000	0.000	0.000
88	A	89	PHE	0	0.006	0.016	26.927	-0.007	-0.007	0.000	0.000	0.000	0.000
89	A	90	ALA	0	0.009	0.020	25.785	-0.002	-0.002	0.000	0.000	0.000	0.000
90	A	91	GLN	0	0.007	-0.026	22.093	-0.001	-0.001	0.000	0.000	0.000	0.000
91	A	92	SER	0	-0.003	-0.023	26.911	-0.004	-0.004	0.000	0.000	0.000	0.000
92	A	93	ARG	1	0.942	0.983	30.462	0.006	0.006	0.000	0.000	0.000	0.000
93	A	94	PHE	0	-0.002	-0.002	28.333	-0.001	-0.001	0.000	0.000	0.000	0.000
94	A	95	CYS	0	-0.018	-0.013	28.822	-0.005	-0.005	0.000	0.000	0.000	0.000
95	A	96	GLY	0	0.002	0.000	31.581	-0.001	-0.001	0.000	0.000	0.000	0.000
96	A	97	ALA	0	-0.061	-0.028	34.021	0.002	0.002	0.000	0.000	0.000	0.000
97	A	98	GLU	-1	-0.776	-0.857	32.272	-0.060	-0.060	0.000	0.000	0.000	0.000
98	A	99	GLY	0	-0.024	0.012	35.294	-0.003	-0.003	0.000	0.000	0.000	0.000
99	A	100	LEU	0	-0.087	-0.042	30.209	-0.006	-0.006	0.000	0.000	0.000	0.000
100	A	101	ASN	0	-0.035	-0.036	32.552	0.003	0.003	0.000	0.000	0.000	0.000
101	A	102	ASN	0	-0.041	-0.015	31.787	0.006	0.006	0.000	0.000	0.000	0.000
102	A	103	VAL	0	0.000	0.009	26.954	-0.006	-0.006	0.000	0.000	0.000	0.000
103	A	104	ILE	0	-0.045	-0.024	26.875	0.014	0.014	0.000	0.000	0.000	0.000
104	A	105	THR	0	-0.045	-0.015	25.155	-0.011	-0.011	0.000	0.000	0.000	0.000
105	A	106	LEU	0	-0.007	-0.014	22.252	0.009	0.009	0.000	0.000	0.000	0.000
106	A	107	SER	0	0.021	-0.001	21.556	-0.006	-0.006	0.000	0.000	0.000	0.000
107	A	108	THR	0	0.057	0.004	16.395	-0.004	-0.004	0.000	0.000	0.000	0.000
108	A	109	PHE	0	-0.038	-0.023	18.886	0.024	0.024	0.000	0.000	0.000	0.000
109	A	110	ARG	1	0.789	0.886	21.024	0.011	0.011	0.000	0.000	0.000	0.000
110	A	111	ASN	0	-0.011	-0.020	19.013	0.005	0.005	0.000	0.000	0.000	0.000
111	A	112	ALA	0	0.025	0.015	14.788	-0.030	-0.030	0.000	0.000	0.000	0.000
112	A	113	GLU	-1	-0.839	-0.923	13.697	0.035	0.035	0.000	0.000	0.000	0.000
113	A	114	PHE	0	0.044	0.015	13.214	-0.041	-0.041	0.000	0.000	0.000	0.000
114	A	115	LEU	0	-0.001	-0.004	11.279	-0.079	-0.079	0.000	0.000	0.000	0.000
115	A	116	GLN	0	-0.012	-0.007	8.087	-0.087	-0.087	0.000	0.000	0.000	0.000
116	A	117	ALA	0	-0.017	0.000	8.469	-0.149	-0.149	0.000	0.000	0.000	0.000
117	A	118	TYR	0	-0.008	-0.032	10.497	-0.099	-0.099	0.000	0.000	0.000	0.000
118	A	119	GLY	0	-0.003	0.014	6.503	-0.121	-0.121	0.000	0.000	0.000	0.000
119	A	120	VAL	0	0.026	0.009	7.158	-0.309	-0.309	0.000	0.000	0.000	0.000
120	A	121	ALA	0	-0.008	0.008	7.811	0.155	0.155	0.000	0.000	0.000	0.000
121	A	122	ILE	0	0.038	0.024	6.619	-0.036	-0.036	0.000	0.000	0.000	0.000
122	A	123	ALA	0	-0.052	-0.040	5.065	0.063	0.063	0.000	0.000	0.000	0.000
123	A	124	ASP	-1	-0.895	-0.957	7.019	1.272	1.272	0.000	0.000	0.000	0.000
124	A	125	GLY	0	0.012	0.014	9.187	-0.136	-0.136	0.000	0.000	0.000	0.000
125	A	126	PRO	0	-0.018	-0.034	12.336	-0.035	-0.035	0.000	0.000	0.000	0.000
126	A	127	LEU	0	0.011	0.014	12.127	-0.035	-0.035	0.000	0.000	0.000	0.000
127	A	128	LYS	1	0.909	0.970	10.171	-0.869	-0.869	0.000	0.000	0.000	0.000
128	A	129	GLY	0	-0.038	-0.014	11.382	-0.035	-0.035	0.000	0.000	0.000	0.000
129	A	130	LEU	0	-0.012	0.001	12.904	-0.059	-0.059	0.000	0.000	0.000	0.000
130	A	131	ALA	0	-0.003	-0.005	11.521	0.004	0.004	0.000	0.000	0.000	0.000
131	A	132	ALA	0	0.000	-0.009	9.287	0.049	0.049	0.000	0.000	0.000	0.000
132	A	133	ARG	1	0.822	0.902	11.406	0.208	0.208	0.000	0.000	0.000	0.000
133	A	134	ALA	0	0.010	0.001	12.106	-0.105	-0.105	0.000	0.000	0.000	0.000
134	A	135	VAL	0	-0.006	0.009	14.228	0.087	0.087	0.000	0.000	0.000	0.000
135	A	136	VAL	0	0.008	0.006	13.801	-0.086	-0.086	0.000	0.000	0.000	0.000
136	A	137	VAL	0	-0.018	-0.001	16.708	0.060	0.060	0.000	0.000	0.000	0.000
137	A	138	ILE	0	-0.030	-0.013	18.158	-0.034	-0.034	0.000	0.000	0.000	0.000
138	A	139	ASP	-1	-0.702	-0.844	21.283	-0.210	-0.210	0.000	0.000	0.000	0.000
139	A	140	GLU	-1	-0.820	-0.914	24.545	-0.178	-0.178	0.000	0.000	0.000	0.000
140	A	141	ASN	0	-0.149	-0.076	25.949	0.030	0.030	0.000	0.000	0.000	0.000
141	A	142	ASP	-1	-0.859	-0.926	21.954	-0.194	-0.194	0.000	0.000	0.000	0.000
142	A	143	ASN	0	-0.044	-0.012	20.573	-0.024	-0.024	0.000	0.000	0.000	0.000
143	A	144	VAL	0	0.006	-0.001	15.330	0.017	0.017	0.000	0.000	0.000	0.000
144	A	145	ILE	0	-0.023	-0.018	18.606	-0.010	-0.010	0.000	0.000	0.000	0.000
145	A	146	PHE	0	0.027	0.002	18.241	-0.010	-0.010	0.000	0.000	0.000	0.000
146	A	147	SER	0	-0.059	-0.045	12.831	0.002	0.002	0.000	0.000	0.000	0.000
147	A	148	GLN	0	0.059	0.040	14.073	0.014	0.014	0.000	0.000	0.000	0.000
148	A	149	LEU	0	0.022	0.019	7.486	0.076	0.076	0.000	0.000	0.000	0.000
149	A	150	VAL	0	-0.067	-0.042	11.625	-0.023	-0.023	0.000	0.000	0.000	0.000
150	A	151	ASP	-1	-0.859	-0.915	12.080	-0.541	-0.541	0.000	0.000	0.000	0.000
151	A	152	GLU	-1	-0.692	-0.820	12.798	-0.026	-0.026	0.000	0.000	0.000	0.000
152	A	153	ILE	0	0.022	0.017	12.008	-0.007	-0.007	0.000	0.000	0.000	0.000
153	A	154	THR	0	-0.105	-0.087	15.095	0.015	0.015	0.000	0.000	0.000	0.000
154	A	155	THR	0	-0.051	-0.027	17.966	0.010	0.010	0.000	0.000	0.000	0.000
155	A	156	GLU	-1	-0.822	-0.876	18.714	-0.174	-0.174	0.000	0.000	0.000	0.000
156	A	157	PRO	0	0.009	0.011	18.309	-0.019	-0.019	0.000	0.000	0.000	0.000
157	A	158	ASP	-1	-0.896	-0.959	19.552	-0.281	-0.281	0.000	0.000	0.000	0.000
158	A	159	TYR	0	-0.031	-0.068	21.566	-0.015	-0.015	0.000	0.000	0.000	0.000
159	A	160	GLU	-1	-0.817	-0.910	24.026	-0.196	-0.196	0.000	0.000	0.000	0.000
160	A	161	ALA	0	-0.029	-0.007	21.260	0.003	0.003	0.000	0.000	0.000	0.000
161	A	162	ALA	0	-0.041	-0.008	20.996	-0.009	-0.009	0.000	0.000	0.000	0.000
162	A	163	LEU	0	0.036	-0.005	22.286	0.007	0.007	0.000	0.000	0.000	0.000
163	A	164	ALA	0	-0.033	-0.011	25.208	0.016	0.016	0.000	0.000	0.000	0.000
164	A	165	VAL	0	-0.021	-0.007	22.045	0.011	0.011	0.000	0.000	0.000	0.000
165	A	166	LEU	0	-0.032	-0.003	25.230	0.010	0.010	0.000	0.000	0.000	0.000
166	A	167	LYS	1	0.850	0.939	27.712	0.219	0.219	0.000	0.000	0.000	0.000
167	A	168	ALA	0	0.005	0.007	30.340	-0.006	-0.006	0.000	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:2:SER)