FMO DATABASE

FMODB ID: MN2NZ

Calculation Name: 1NY7-1-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1NY7

Chain ID: 1

ChEMBL ID:

UniProt ID: P03599

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	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	189
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1991300.881977
FMO2-HF: Nuclear repulsion	1916962.888527
FMO2-HF: Total energy	-74337.99345
FMO2-MP2: Total energy	-74551.9363

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(1:1:GLY)

Summations of interaction energy for fragment #1(1:1:GLY)

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.
-1.323	0.091	0.001	-0.617	-0.799	0

Interaction energy analysis for fragmet #1(1:1:GLY)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : 0.014 / q_NPA : -0.009

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].
3	1	3	VAL	0	-0.034	-0.005	3.425	-0.172	1.147	0.002	-0.610	-0.711
4	1	4	CYS	0	-0.014	-0.010	4.825	-0.567	-0.472	-0.001	-0.007	-0.088
5	1	5	ALA	0	-0.004	0.006	6.954	0.323	0.323	0.000	0.000	0.000
6	1	6	GLU	-1	-0.933	-0.961	8.745	-0.363	-0.363	0.000	0.000	0.000
7	1	7	ALA	0	-0.018	-0.010	12.466	-0.006	-0.006	0.000	0.000	0.000
8	1	8	SER	0	-0.016	-0.032	15.066	0.024	0.024	0.000	0.000	0.000
9	1	9	ASP	-1	-0.852	-0.891	18.816	-0.240	-0.240	0.000	0.000	0.000
10	1	10	VAL	0	-0.003	-0.006	22.312	-0.006	-0.006	0.000	0.000	0.000
11	1	11	TYR	0	0.021	0.014	19.293	0.013	0.013	0.000	0.000	0.000
12	1	12	SER	0	-0.024	-0.015	24.059	0.007	0.007	0.000	0.000	0.000
13	1	13	PRO	0	0.054	0.045	25.967	-0.001	-0.001	0.000	0.000	0.000
14	1	14	CYS	0	-0.083	-0.047	27.186	0.015	0.015	0.000	0.000	0.000
15	1	15	MET	0	0.004	0.005	28.860	0.015	0.015	0.000	0.000	0.000
16	1	16	ILE	0	-0.024	0.006	27.022	-0.014	-0.014	0.000	0.000	0.000
17	1	17	ALA	0	0.008	0.008	28.312	0.012	0.012	0.000	0.000	0.000
18	1	18	SER	0	-0.003	-0.009	28.197	-0.013	-0.013	0.000	0.000	0.000
19	1	19	THR	0	-0.017	-0.007	27.633	0.007	0.007	0.000	0.000	0.000
20	1	20	PRO	0	0.049	0.037	30.277	0.002	0.002	0.000	0.000	0.000
21	1	21	PRO	0	0.010	0.022	32.776	-0.001	-0.001	0.000	0.000	0.000
22	1	22	ALA	0	0.000	0.004	33.768	0.002	0.002	0.000	0.000	0.000
23	1	23	PRO	0	-0.028	-0.027	35.159	0.001	0.001	0.000	0.000	0.000
24	1	24	PHE	0	0.030	0.017	32.883	0.001	0.001	0.000	0.000	0.000
25	1	25	SER	0	0.000	-0.028	31.646	-0.003	-0.003	0.000	0.000	0.000
26	1	26	ASP	-1	-0.903	-0.926	31.263	-0.050	-0.050	0.000	0.000	0.000
27	1	27	VAL	0	-0.040	-0.019	28.464	-0.006	-0.006	0.000	0.000	0.000
28	1	28	THR	0	-0.041	-0.045	29.488	0.001	0.001	0.000	0.000	0.000
29	1	29	ALA	0	0.003	-0.011	29.083	-0.009	-0.009	0.000	0.000	0.000
30	1	30	VAL	0	-0.008	0.013	28.749	0.007	0.007	0.000	0.000	0.000
31	1	31	THR	0	0.017	0.008	29.580	-0.012	-0.012	0.000	0.000	0.000
32	1	32	PHE	0	0.040	0.005	27.295	0.005	0.005	0.000	0.000	0.000
33	1	33	ASP	-1	-0.713	-0.820	31.318	-0.102	-0.102	0.000	0.000	0.000
34	1	34	LEU	0	-0.010	-0.028	26.609	0.000	0.000	0.000	0.000	0.000
35	1	35	ILE	0	-0.031	-0.009	31.185	-0.002	-0.002	0.000	0.000	0.000
36	1	36	ASN	0	-0.046	-0.052	34.186	0.005	0.005	0.000	0.000	0.000
37	1	37	GLY	0	-0.007	0.001	34.284	0.004	0.004	0.000	0.000	0.000
38	1	38	LYS	1	0.790	0.879	35.363	0.087	0.087	0.000	0.000	0.000
39	1	39	ILE	0	0.021	0.003	32.492	-0.007	-0.007	0.000	0.000	0.000
40	1	40	THR	0	-0.061	-0.030	34.287	0.008	0.008	0.000	0.000	0.000
41	1	41	PRO	0	0.033	0.030	34.026	-0.006	-0.006	0.000	0.000	0.000
42	1	42	VAL	0	0.018	0.004	33.576	0.004	0.004	0.000	0.000	0.000
43	1	43	GLY	0	0.010	0.008	36.228	0.004	0.004	0.000	0.000	0.000
44	1	44	ASP	-1	-0.851	-0.883	34.651	-0.071	-0.071	0.000	0.000	0.000
45	1	45	ASP	-1	-0.863	-0.945	36.446	-0.069	-0.069	0.000	0.000	0.000
46	1	46	ASN	0	-0.088	-0.058	37.668	0.003	0.003	0.000	0.000	0.000
47	1	47	TRP	0	0.010	0.002	27.883	-0.007	-0.007	0.000	0.000	0.000
48	1	48	ASN	0	-0.037	-0.003	33.370	-0.002	-0.002	0.000	0.000	0.000
49	1	49	THR	0	-0.014	-0.009	32.667	-0.007	-0.007	0.000	0.000	0.000
50	1	50	HIS	0	-0.015	-0.011	32.821	0.007	0.007	0.000	0.000	0.000
51	1	51	ILE	0	0.026	0.005	32.928	-0.008	-0.008	0.000	0.000	0.000
52	1	52	TYR	0	0.003	0.039	29.478	0.010	0.010	0.000	0.000	0.000
53	1	53	ASN	0	0.020	0.001	34.271	0.000	0.000	0.000	0.000	0.000
54	1	54	PRO	0	0.036	0.039	30.794	0.005	0.005	0.000	0.000	0.000
55	1	55	PRO	0	0.008	-0.020	32.639	0.003	0.003	0.000	0.000	0.000
56	1	56	ILE	0	0.029	0.026	28.502	0.006	0.006	0.000	0.000	0.000
57	1	57	MET	0	0.073	0.042	32.495	0.001	0.001	0.000	0.000	0.000
58	1	58	ASN	0	-0.030	-0.016	33.894	0.007	0.007	0.000	0.000	0.000
59	1	59	VAL	0	0.024	0.032	35.466	0.005	0.005	0.000	0.000	0.000
60	1	60	LEU	0	-0.041	-0.008	31.246	0.005	0.005	0.000	0.000	0.000
61	1	61	ARG	1	0.878	0.927	35.961	0.100	0.100	0.000	0.000	0.000
62	1	62	THR	0	-0.043	-0.031	38.865	0.005	0.005	0.000	0.000	0.000
63	1	63	ALA	0	0.031	0.015	38.666	0.004	0.004	0.000	0.000	0.000
64	1	64	ALA	0	-0.059	-0.019	40.689	-0.001	-0.001	0.000	0.000	0.000
65	1	65	TRP	0	-0.027	-0.012	41.121	-0.001	-0.001	0.000	0.000	0.000
66	1	66	LYS	1	0.865	0.917	35.743	0.088	0.088	0.000	0.000	0.000
67	1	67	SER	0	0.002	-0.004	35.310	0.003	0.003	0.000	0.000	0.000
68	1	68	GLY	0	0.067	0.039	31.873	0.001	0.001	0.000	0.000	0.000
69	1	69	THR	0	-0.054	-0.048	25.043	0.000	0.000	0.000	0.000	0.000
70	1	70	ILE	0	-0.071	-0.029	26.522	0.002	0.002	0.000	0.000	0.000
71	1	71	HIS	0	-0.015	-0.023	21.571	-0.022	-0.022	0.000	0.000	0.000
72	1	72	VAL	0	-0.016	-0.018	21.854	0.014	0.014	0.000	0.000	0.000
73	1	73	GLN	0	-0.015	-0.015	17.737	-0.040	-0.040	0.000	0.000	0.000
74	1	74	LEU	0	-0.011	0.008	20.031	0.023	0.023	0.000	0.000	0.000
75	1	75	ASN	0	0.014	0.007	18.944	-0.075	-0.075	0.000	0.000	0.000
76	1	76	VAL	0	-0.009	-0.010	18.758	0.034	0.034	0.000	0.000	0.000
77	1	77	ARG	1	0.825	0.884	19.076	0.187	0.187	0.000	0.000	0.000
78	1	78	GLY	0	0.040	0.015	21.375	0.013	0.013	0.000	0.000	0.000
79	1	79	ALA	0	-0.004	0.017	22.465	0.003	0.003	0.000	0.000	0.000
80	1	80	GLY	0	-0.008	-0.005	22.944	-0.007	-0.007	0.000	0.000	0.000
81	1	81	VAL	0	-0.026	-0.008	21.902	0.014	0.014	0.000	0.000	0.000
82	1	82	LYS	1	0.854	0.898	21.441	-0.004	-0.004	0.000	0.000	0.000
83	1	83	ARG	1	0.952	0.966	12.426	0.138	0.138	0.000	0.000	0.000
84	1	84	ALA	0	-0.023	-0.015	18.605	-0.002	-0.002	0.000	0.000	0.000
85	1	85	ASP	-1	-0.817	-0.879	20.516	-0.002	-0.002	0.000	0.000	0.000
86	1	86	TRP	0	-0.035	-0.013	18.479	-0.008	-0.008	0.000	0.000	0.000
87	1	87	ASP	-1	-0.866	-0.923	20.387	-0.059	-0.059	0.000	0.000	0.000
88	1	88	GLY	0	0.038	0.014	21.276	-0.006	-0.006	0.000	0.000	0.000
89	1	89	GLN	0	-0.031	-0.003	19.374	-0.016	-0.016	0.000	0.000	0.000
90	1	90	VAL	0	0.005	-0.002	18.949	0.010	0.010	0.000	0.000	0.000
91	1	91	PHE	0	-0.013	-0.004	20.440	-0.016	-0.016	0.000	0.000	0.000
92	1	92	VAL	0	-0.007	-0.003	21.134	0.006	0.006	0.000	0.000	0.000
93	1	93	TYR	0	0.016	0.004	23.480	-0.008	-0.008	0.000	0.000	0.000
94	1	94	LEU	0	-0.014	0.012	25.115	0.005	0.005	0.000	0.000	0.000
95	1	95	ARG	1	0.808	0.865	27.223	0.101	0.101	0.000	0.000	0.000
96	1	96	GLN	0	0.021	0.005	30.872	0.004	0.004	0.000	0.000	0.000
97	1	97	SER	0	0.019	0.015	33.791	0.004	0.004	0.000	0.000	0.000
98	1	98	MET	0	0.030	0.018	32.696	-0.006	-0.006	0.000	0.000	0.000
99	1	99	ASN	0	-0.019	0.012	36.587	0.001	0.001	0.000	0.000	0.000
100	1	100	PRO	0	0.030	0.017	37.331	-0.003	-0.003	0.000	0.000	0.000
101	1	101	GLU	-1	-0.902	-0.961	37.537	-0.057	-0.057	0.000	0.000	0.000
102	1	102	SER	0	-0.079	-0.026	35.967	0.000	0.000	0.000	0.000	0.000
103	1	103	TYR	0	0.009	-0.004	32.268	-0.002	-0.002	0.000	0.000	0.000
104	1	104	ASP	-1	-0.849	-0.913	28.035	-0.111	-0.111	0.000	0.000	0.000
105	1	105	ALA	0	-0.009	-0.003	28.742	0.002	0.002	0.000	0.000	0.000
106	1	106	ARG	1	0.904	0.947	18.370	0.229	0.229	0.000	0.000	0.000
107	1	107	THR	0	0.035	0.029	22.913	0.007	0.007	0.000	0.000	0.000
108	1	108	PHE	0	-0.060	-0.039	17.779	-0.019	-0.019	0.000	0.000	0.000
109	1	109	VAL	0	0.026	0.016	18.197	0.022	0.022	0.000	0.000	0.000
110	1	110	ILE	0	-0.007	-0.001	14.155	-0.036	-0.036	0.000	0.000	0.000
111	1	111	SER	0	-0.023	-0.032	15.022	0.045	0.045	0.000	0.000	0.000
112	1	112	GLN	0	-0.035	-0.023	11.477	-0.061	-0.061	0.000	0.000	0.000
113	1	113	PRO	0	-0.028	-0.017	13.832	0.000	0.000	0.000	0.000	0.000
114	1	114	GLY	0	0.017	0.023	15.546	-0.028	-0.028	0.000	0.000	0.000
115	1	115	SER	0	-0.026	-0.033	16.254	0.017	0.017	0.000	0.000	0.000
116	1	116	ALA	0	-0.028	0.001	14.438	-0.041	-0.041	0.000	0.000	0.000
117	1	117	MET	0	0.003	0.004	13.966	0.016	0.016	0.000	0.000	0.000
118	1	118	LEU	0	0.001	0.011	14.510	-0.053	-0.053	0.000	0.000	0.000
119	1	119	ASN	0	-0.007	-0.012	15.143	0.010	0.010	0.000	0.000	0.000
120	1	120	PHE	0	-0.042	-0.023	16.827	-0.011	-0.011	0.000	0.000	0.000
121	1	121	SER	0	0.017	0.010	19.482	0.001	0.001	0.000	0.000	0.000
122	1	122	PHE	0	0.000	0.002	22.676	0.003	0.003	0.000	0.000	0.000
123	1	123	ASP	-1	-0.831	-0.898	26.181	-0.156	-0.156	0.000	0.000	0.000
124	1	124	ILE	0	-0.015	0.010	29.350	0.007	0.007	0.000	0.000	0.000
125	1	125	ILE	0	-0.013	-0.006	32.900	0.003	0.003	0.000	0.000	0.000
126	1	126	GLY	0	0.019	0.015	35.026	0.001	0.001	0.000	0.000	0.000
127	1	127	PRO	0	0.011	-0.001	38.681	0.001	0.001	0.000	0.000	0.000
128	1	128	ASN	0	-0.049	-0.010	42.227	0.005	0.005	0.000	0.000	0.000
129	1	129	SER	0	-0.007	-0.013	42.477	0.001	0.001	0.000	0.000	0.000
130	1	130	GLY	0	0.029	0.009	38.277	-0.002	-0.002	0.000	0.000	0.000
131	1	131	PHE	0	-0.028	-0.002	37.396	-0.006	-0.006	0.000	0.000	0.000
132	1	132	GLU	-1	-0.808	-0.917	36.471	-0.085	-0.085	0.000	0.000	0.000
133	1	133	PHE	0	-0.041	-0.014	39.541	-0.002	-0.002	0.000	0.000	0.000
134	1	134	ALA	0	0.013	-0.008	37.970	0.002	0.002	0.000	0.000	0.000
135	1	135	GLU	-1	-0.832	-0.905	39.129	-0.077	-0.077	0.000	0.000	0.000
136	1	136	SER	0	-0.017	0.011	41.447	0.005	0.005	0.000	0.000	0.000
137	1	137	PRO	0	0.040	-0.012	44.613	0.000	0.000	0.000	0.000	0.000
138	1	138	TRP	0	-0.074	-0.018	46.132	0.002	0.002	0.000	0.000	0.000
139	1	139	ALA	0	-0.005	-0.006	44.601	0.002	0.002	0.000	0.000	0.000
140	1	140	ASN	0	-0.063	-0.035	44.163	-0.001	-0.001	0.000	0.000	0.000
141	1	141	GLN	0	0.012	0.028	40.936	-0.004	-0.004	0.000	0.000	0.000
142	1	142	THR	0	0.017	0.006	36.033	0.004	0.004	0.000	0.000	0.000
143	1	143	THR	0	-0.022	-0.017	35.245	-0.002	-0.002	0.000	0.000	0.000
144	1	144	TRP	0	0.029	-0.004	28.392	-0.004	-0.004	0.000	0.000	0.000
145	1	145	TYR	0	-0.019	-0.030	31.381	-0.004	-0.004	0.000	0.000	0.000
146	1	146	LEU	0	-0.027	-0.015	24.298	-0.007	-0.007	0.000	0.000	0.000
147	1	147	GLU	-1	-0.893	-0.952	28.343	-0.101	-0.101	0.000	0.000	0.000
148	1	148	CYS	0	-0.063	-0.031	25.187	-0.019	-0.019	0.000	0.000	0.000
149	1	149	VAL	0	0.053	0.018	25.706	0.009	0.009	0.000	0.000	0.000
150	1	150	ALA	0	-0.011	-0.025	24.500	-0.017	-0.017	0.000	0.000	0.000
151	1	151	THR	0	-0.005	-0.010	23.836	0.012	0.012	0.000	0.000	0.000
152	1	152	ASN	0	0.049	0.005	25.086	0.008	0.008	0.000	0.000	0.000
153	1	153	PRO	0	0.005	0.018	25.921	-0.010	-0.010	0.000	0.000	0.000
154	1	154	ARG	1	0.780	0.885	28.233	0.073	0.073	0.000	0.000	0.000
155	1	155	GLN	0	-0.005	0.013	22.736	-0.006	-0.006	0.000	0.000	0.000
156	1	156	ILE	0	-0.013	0.007	21.468	-0.015	-0.015	0.000	0.000	0.000
157	1	157	GLN	0	-0.012	-0.023	23.690	0.017	0.017	0.000	0.000	0.000
158	1	158	GLN	0	0.025	0.009	24.458	-0.002	-0.002	0.000	0.000	0.000
159	1	159	PHE	0	0.032	0.026	21.940	-0.021	-0.021	0.000	0.000	0.000
160	1	160	GLU	-1	-0.738	-0.845	23.519	-0.201	-0.201	0.000	0.000	0.000
161	1	161	VAL	0	0.017	0.019	23.493	-0.026	-0.026	0.000	0.000	0.000
162	1	162	ASN	0	-0.040	-0.030	22.406	0.021	0.021	0.000	0.000	0.000
163	1	163	MET	0	-0.032	-0.018	23.900	-0.010	-0.010	0.000	0.000	0.000
164	1	164	ARG	1	0.850	0.908	22.578	0.222	0.222	0.000	0.000	0.000
165	1	165	PHE	0	0.011	0.010	25.848	-0.001	-0.001	0.000	0.000	0.000
166	1	166	ASP	-1	-0.765	-0.878	25.083	-0.186	-0.186	0.000	0.000	0.000
167	1	167	PRO	0	-0.022	-0.021	26.759	0.012	0.012	0.000	0.000	0.000
168	1	168	ASN	0	-0.053	-0.022	27.968	0.015	0.015	0.000	0.000	0.000
169	1	169	PHE	0	-0.016	0.006	30.877	0.009	0.009	0.000	0.000	0.000
170	1	170	ARG	1	0.852	0.916	32.616	0.091	0.091	0.000	0.000	0.000
171	1	171	VAL	0	0.000	-0.008	36.447	-0.002	-0.002	0.000	0.000	0.000
172	1	172	ALA	0	-0.002	0.001	39.131	0.003	0.003	0.000	0.000	0.000
173	1	173	GLY	0	0.023	0.009	42.883	0.000	0.000	0.000	0.000	0.000
174	1	174	ASN	0	-0.012	-0.012	43.759	-0.006	-0.006	0.000	0.000	0.000
175	1	175	ILE	0	0.001	0.013	42.279	0.004	0.004	0.000	0.000	0.000
176	1	176	LEU	0	-0.038	-0.023	45.969	-0.001	-0.001	0.000	0.000	0.000
177	1	177	MET	0	0.010	0.020	42.814	0.001	0.001	0.000	0.000	0.000
178	1	178	PRO	0	-0.010	-0.002	45.472	0.002	0.002	0.000	0.000	0.000
179	1	179	PRO	0	-0.011	-0.024	45.815	-0.003	-0.003	0.000	0.000	0.000
180	1	180	PHE	0	0.019	0.015	40.950	0.000	0.000	0.000	0.000	0.000
181	1	181	PRO	0	0.016	0.010	42.031	0.001	0.001	0.000	0.000	0.000
182	1	182	LEU	0	-0.020	-0.009	41.212	-0.004	-0.004	0.000	0.000	0.000
183	1	183	SER	0	-0.032	-0.032	36.744	0.002	0.002	0.000	0.000	0.000
184	1	184	THR	0	-0.035	-0.021	36.224	-0.003	-0.003	0.000	0.000	0.000
185	1	185	GLU	-1	-0.887	-0.953	28.628	-0.153	-0.153	0.000	0.000	0.000
186	1	186	THR	0	-0.006	0.005	30.755	0.009	0.009	0.000	0.000	0.000
187	1	187	PRO	0	-0.028	-0.018	30.723	-0.009	-0.009	0.000	0.000	0.000
188	1	188	PRO	0	0.008	0.009	26.530	0.002	0.002	0.000	0.000	0.000
189	1	189	LEU	0	-0.020	-0.004	28.308	0.005	0.005	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(1:1:GLY)