FMO DATABASE

FMODB ID: MV9NZ

Calculation Name: 3KHN-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3KHN

Chain ID: A

ChEMBL ID:

UniProt ID: Q729W9

Base Structure: X-ray

Registration Date: 2023-06-22

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	166
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1674270.173149
FMO2-HF: Nuclear repulsion	1609435.734489
FMO2-HF: Total energy	-64834.43866
FMO2-MP2: Total energy	-65028.44269

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:ARG)

Summations of interaction energy for fragment #1(A:7:ARG)

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.
-46.175	-35.831	4.998	-6.803	-8.541	-0.072

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

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 1 / q_Mulliken : 0.930 / q_NPA : 0.963

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	9	GLN	0	0.068	0.036	3.067	1.680	3.894	0.066	-0.832	-1.449	0.002
4	A	10	ARG	1	1.010	1.004	3.417	33.045	34.241	0.049	-0.355	-0.890	0.002
5	A	11	GLU	-1	-0.897	-0.958	2.364	-108.688	-101.869	4.884	-5.610	-6.094	-0.076
6	A	12	LEU	0	-0.002	0.012	5.208	4.580	4.695	-0.001	-0.006	-0.108	0.000
7	A	13	ILE	0	0.055	0.026	8.089	2.537	2.537	0.000	0.000	0.000	0.000
8	A	14	GLU	-1	-0.804	-0.889	8.166	-22.355	-22.355	0.000	0.000	0.000	0.000
9	A	15	ALA	0	-0.031	-0.021	9.200	2.476	2.476	0.000	0.000	0.000	0.000
10	A	16	GLN	0	0.017	0.023	10.842	1.514	1.514	0.000	0.000	0.000	0.000
11	A	17	ARG	1	0.870	0.942	13.004	22.234	22.234	0.000	0.000	0.000	0.000
12	A	18	GLN	0	-0.045	-0.033	11.955	2.560	2.560	0.000	0.000	0.000	0.000
13	A	19	THR	0	-0.021	-0.011	15.055	0.958	0.958	0.000	0.000	0.000	0.000
14	A	20	TYR	0	0.007	-0.011	17.089	1.118	1.118	0.000	0.000	0.000	0.000
15	A	21	ASN	0	-0.013	-0.019	18.593	1.225	1.225	0.000	0.000	0.000	0.000
16	A	22	GLU	-1	-0.956	-0.968	19.241	-14.471	-14.471	0.000	0.000	0.000	0.000
17	A	23	MET	0	-0.061	-0.026	20.079	0.689	0.689	0.000	0.000	0.000	0.000
18	A	24	ARG	1	0.977	0.990	22.939	12.868	12.868	0.000	0.000	0.000	0.000
19	A	25	THR	0	0.019	0.023	24.622	0.648	0.648	0.000	0.000	0.000	0.000
20	A	26	TYR	0	-0.059	-0.037	25.697	0.488	0.488	0.000	0.000	0.000	0.000
21	A	27	PHE	0	0.054	-0.010	25.425	0.312	0.312	0.000	0.000	0.000	0.000
22	A	28	THR	0	0.018	0.017	29.218	0.453	0.453	0.000	0.000	0.000	0.000
23	A	29	VAL	0	-0.037	-0.012	30.322	0.350	0.350	0.000	0.000	0.000	0.000
24	A	30	ASN	0	-0.059	-0.027	30.106	0.508	0.508	0.000	0.000	0.000	0.000
25	A	31	GLY	0	0.013	0.021	33.463	0.181	0.181	0.000	0.000	0.000	0.000
26	A	32	VAL	0	-0.063	-0.040	31.523	0.246	0.246	0.000	0.000	0.000	0.000
27	A	33	GLU	-1	-0.900	-0.958	30.774	-9.872	-9.872	0.000	0.000	0.000	0.000
28	A	34	GLY	0	-0.036	-0.008	32.576	-0.017	-0.017	0.000	0.000	0.000	0.000
29	A	35	VAL	0	-0.068	-0.037	34.508	0.152	0.152	0.000	0.000	0.000	0.000
30	A	36	ILE	0	-0.007	-0.001	28.474	-0.074	-0.074	0.000	0.000	0.000	0.000
31	A	37	GLY	0	0.013	0.031	29.237	-0.100	-0.100	0.000	0.000	0.000	0.000
32	A	38	ALA	0	0.006	-0.001	24.175	-0.204	-0.204	0.000	0.000	0.000	0.000
33	A	39	VAL	0	-0.037	-0.006	22.566	0.055	0.055	0.000	0.000	0.000	0.000
34	A	40	PHE	0	-0.014	-0.019	13.480	-0.413	-0.413	0.000	0.000	0.000	0.000
35	A	41	ASP	-1	-0.902	-0.964	17.192	-14.402	-14.402	0.000	0.000	0.000	0.000
36	A	42	GLU	-1	-0.883	-0.927	11.694	-19.049	-19.049	0.000	0.000	0.000	0.000
37	A	43	GLY	0	-0.058	-0.034	12.430	-1.094	-1.094	0.000	0.000	0.000	0.000
38	A	44	VAL	0	0.004	0.005	13.409	-0.286	-0.286	0.000	0.000	0.000	0.000
39	A	45	ILE	0	-0.030	-0.006	16.552	0.533	0.533	0.000	0.000	0.000	0.000
40	A	46	THR	0	-0.025	-0.004	19.577	0.269	0.269	0.000	0.000	0.000	0.000
41	A	47	LEU	0	-0.006	-0.008	22.938	0.180	0.180	0.000	0.000	0.000	0.000
42	A	48	ARG	1	0.902	0.959	25.674	10.921	10.921	0.000	0.000	0.000	0.000
43	A	49	VAL	0	0.019	0.012	29.334	0.069	0.069	0.000	0.000	0.000	0.000
44	A	50	PRO	0	0.059	0.034	32.748	0.044	0.044	0.000	0.000	0.000	0.000
45	A	51	SER	0	0.041	-0.006	35.965	0.018	0.018	0.000	0.000	0.000	0.000
46	A	52	GLU	-1	-0.979	-0.975	37.700	-7.411	-7.411	0.000	0.000	0.000	0.000
47	A	53	VAL	0	-0.027	-0.010	36.990	0.115	0.115	0.000	0.000	0.000	0.000
48	A	54	LEU	0	-0.040	-0.021	34.397	-0.019	-0.019	0.000	0.000	0.000	0.000
49	A	55	PHE	0	-0.020	-0.017	36.669	0.033	0.033	0.000	0.000	0.000	0.000
50	A	56	ALA	0	0.049	0.035	41.853	0.046	0.046	0.000	0.000	0.000	0.000
51	A	57	PRO	0	0.046	0.010	44.573	-0.102	-0.102	0.000	0.000	0.000	0.000
52	A	58	GLY	0	0.004	0.005	44.584	0.116	0.116	0.000	0.000	0.000	0.000
53	A	59	ALA	0	-0.034	-0.004	44.733	0.016	0.016	0.000	0.000	0.000	0.000
54	A	60	VAL	0	0.028	0.000	41.104	-0.157	-0.157	0.000	0.000	0.000	0.000
55	A	61	GLU	-1	-0.953	-0.959	40.886	-7.344	-7.344	0.000	0.000	0.000	0.000
56	A	62	LEU	0	-0.009	-0.006	37.036	0.002	0.002	0.000	0.000	0.000	0.000
57	A	63	ALA	0	-0.009	0.002	41.216	0.197	0.197	0.000	0.000	0.000	0.000
58	A	64	PRO	0	0.055	0.001	42.133	-0.153	-0.153	0.000	0.000	0.000	0.000
59	A	65	GLY	0	-0.015	0.000	42.264	-0.084	-0.084	0.000	0.000	0.000	0.000
60	A	66	ALA	0	0.003	0.012	38.041	-0.186	-0.186	0.000	0.000	0.000	0.000
61	A	67	ASP	-1	-0.871	-0.946	37.016	-8.310	-8.310	0.000	0.000	0.000	0.000
62	A	68	ARG	1	0.954	0.997	36.400	7.982	7.982	0.000	0.000	0.000	0.000
63	A	69	VAL	0	0.012	0.002	32.868	-0.239	-0.239	0.000	0.000	0.000	0.000
64	A	70	LEU	0	0.040	0.005	32.433	-0.403	-0.403	0.000	0.000	0.000	0.000
65	A	71	ALA	0	-0.011	-0.002	31.750	-0.361	-0.361	0.000	0.000	0.000	0.000
66	A	72	THR	0	0.014	0.012	29.945	-0.260	-0.260	0.000	0.000	0.000	0.000
67	A	73	LEU	0	0.011	0.001	27.291	-0.447	-0.447	0.000	0.000	0.000	0.000
68	A	74	LYS	1	0.930	0.985	27.077	9.030	9.030	0.000	0.000	0.000	0.000
69	A	75	ASP	-1	-0.893	-0.941	27.356	-11.248	-11.248	0.000	0.000	0.000	0.000
70	A	76	LEU	0	-0.004	0.002	22.739	-0.500	-0.500	0.000	0.000	0.000	0.000
71	A	77	PHE	0	-0.003	-0.010	22.962	-0.773	-0.773	0.000	0.000	0.000	0.000
72	A	78	ILE	0	-0.004	0.008	22.806	-0.508	-0.508	0.000	0.000	0.000	0.000
73	A	79	ARG	1	0.905	0.955	22.643	12.048	12.048	0.000	0.000	0.000	0.000
74	A	80	ARG	1	0.815	0.918	15.495	16.662	16.662	0.000	0.000	0.000	0.000
75	A	81	ARG	1	1.009	0.989	18.725	15.032	15.032	0.000	0.000	0.000	0.000
76	A	82	GLU	-1	-0.849	-0.920	13.743	-18.250	-18.250	0.000	0.000	0.000	0.000
77	A	83	GLN	0	-0.046	-0.031	15.398	-0.425	-0.425	0.000	0.000	0.000	0.000
78	A	84	ASN	0	0.087	0.041	17.851	0.946	0.946	0.000	0.000	0.000	0.000
79	A	85	ILE	0	-0.027	-0.008	19.742	-0.123	-0.123	0.000	0.000	0.000	0.000
80	A	86	ASN	0	0.003	0.010	20.447	0.764	0.764	0.000	0.000	0.000	0.000
81	A	87	ILE	0	0.015	0.012	24.396	0.050	0.050	0.000	0.000	0.000	0.000
82	A	88	LYS	1	0.955	0.988	23.545	11.797	11.797	0.000	0.000	0.000	0.000
83	A	89	GLY	0	0.024	0.028	29.105	0.050	0.050	0.000	0.000	0.000	0.000
84	A	90	PHE	0	0.031	0.007	27.706	-0.047	-0.047	0.000	0.000	0.000	0.000
85	A	91	THR	0	-0.066	-0.052	33.806	0.065	0.065	0.000	0.000	0.000	0.000
86	A	92	ASP	-1	-0.798	-0.888	36.604	-7.380	-7.380	0.000	0.000	0.000	0.000
87	A	93	ASP	-1	-0.865	-0.945	39.025	-7.122	-7.122	0.000	0.000	0.000	0.000
88	A	94	VAL	0	-0.031	-0.003	41.152	0.191	0.191	0.000	0.000	0.000	0.000
89	A	95	GLN	0	-0.045	-0.043	42.307	-0.124	-0.124	0.000	0.000	0.000	0.000
90	A	96	PRO	0	-0.015	0.017	43.938	0.072	0.072	0.000	0.000	0.000	0.000
91	A	97	SER	0	0.010	-0.021	46.397	0.136	0.136	0.000	0.000	0.000	0.000
92	A	98	ALA	0	0.059	0.028	49.668	-0.062	-0.062	0.000	0.000	0.000	0.000
93	A	99	ASN	0	-0.087	-0.032	51.523	0.145	0.145	0.000	0.000	0.000	0.000
94	A	100	ALA	0	-0.004	-0.013	49.018	0.001	0.001	0.000	0.000	0.000	0.000
95	A	101	ARG	1	0.941	0.969	45.470	6.699	6.699	0.000	0.000	0.000	0.000
96	A	102	PHE	0	-0.033	-0.021	44.070	-0.037	-0.037	0.000	0.000	0.000	0.000
97	A	103	LYS	1	0.985	0.997	45.018	6.623	6.623	0.000	0.000	0.000	0.000
98	A	104	ASP	-1	-0.809	-0.898	41.354	-7.173	-7.173	0.000	0.000	0.000	0.000
99	A	105	ASN	0	0.054	-0.004	39.083	-0.049	-0.049	0.000	0.000	0.000	0.000
100	A	106	TRP	0	-0.007	0.013	33.147	-0.323	-0.323	0.000	0.000	0.000	0.000
101	A	107	GLU	-1	-0.892	-0.948	37.652	-7.180	-7.180	0.000	0.000	0.000	0.000
102	A	108	VAL	0	0.004	0.008	39.789	-0.109	-0.109	0.000	0.000	0.000	0.000
103	A	109	SER	0	-0.042	-0.018	34.954	-0.210	-0.210	0.000	0.000	0.000	0.000
104	A	110	ALA	0	0.016	0.007	34.975	-0.255	-0.255	0.000	0.000	0.000	0.000
105	A	111	LEU	0	-0.033	-0.027	36.059	-0.129	-0.129	0.000	0.000	0.000	0.000
106	A	112	ARG	1	0.895	0.956	36.865	7.638	7.638	0.000	0.000	0.000	0.000
107	A	113	SER	0	0.026	0.008	32.153	-0.222	-0.222	0.000	0.000	0.000	0.000
108	A	114	VAL	0	0.001	0.003	33.541	-0.234	-0.234	0.000	0.000	0.000	0.000
109	A	115	ASN	0	-0.018	-0.031	35.290	-0.116	-0.116	0.000	0.000	0.000	0.000
110	A	116	VAL	0	0.001	0.010	31.685	-0.033	-0.033	0.000	0.000	0.000	0.000
111	A	117	LEU	0	0.007	-0.006	29.843	-0.164	-0.164	0.000	0.000	0.000	0.000
112	A	118	ARG	1	0.907	0.952	32.212	7.824	7.824	0.000	0.000	0.000	0.000
113	A	119	TYR	0	0.024	0.034	32.319	0.082	0.082	0.000	0.000	0.000	0.000
114	A	120	PHE	0	0.012	-0.011	28.926	-0.091	-0.091	0.000	0.000	0.000	0.000
115	A	121	LEU	0	-0.022	-0.011	29.644	-0.178	-0.178	0.000	0.000	0.000	0.000
116	A	122	GLY	0	-0.003	0.009	31.707	0.002	0.002	0.000	0.000	0.000	0.000
117	A	123	ALA	0	-0.076	-0.034	31.208	0.101	0.101	0.000	0.000	0.000	0.000
118	A	124	GLY	0	0.019	0.010	30.424	-0.140	-0.140	0.000	0.000	0.000	0.000
119	A	125	ILE	0	-0.074	-0.031	24.852	-0.490	-0.490	0.000	0.000	0.000	0.000
120	A	126	GLU	-1	-0.796	-0.879	22.133	-13.746	-13.746	0.000	0.000	0.000	0.000
121	A	127	PRO	0	0.076	0.012	25.316	-0.287	-0.287	0.000	0.000	0.000	0.000
122	A	128	ALA	0	-0.002	0.011	22.832	-0.043	-0.043	0.000	0.000	0.000	0.000
123	A	129	ARG	1	0.781	0.908	20.421	13.592	13.592	0.000	0.000	0.000	0.000
124	A	130	LEU	0	-0.027	0.001	22.541	-0.201	-0.201	0.000	0.000	0.000	0.000
125	A	131	THR	0	-0.006	-0.011	24.270	0.265	0.265	0.000	0.000	0.000	0.000
126	A	132	ALA	0	0.007	-0.007	26.863	-0.016	-0.016	0.000	0.000	0.000	0.000
127	A	133	THR	0	-0.074	-0.028	28.025	0.143	0.143	0.000	0.000	0.000	0.000
128	A	134	GLY	0	0.022	0.006	30.261	-0.034	-0.034	0.000	0.000	0.000	0.000
129	A	135	LEU	0	-0.016	-0.014	27.716	-0.050	-0.050	0.000	0.000	0.000	0.000
130	A	136	GLY	0	0.022	0.008	32.282	0.096	0.096	0.000	0.000	0.000	0.000
131	A	137	GLU	-1	-0.846	-0.900	34.990	-7.445	-7.445	0.000	0.000	0.000	0.000
132	A	138	LEU	0	-0.044	-0.022	29.916	0.065	0.065	0.000	0.000	0.000	0.000
133	A	139	ASP	-1	-0.944	-0.966	28.080	-9.906	-9.906	0.000	0.000	0.000	0.000
134	A	140	PRO	0	-0.034	-0.001	31.024	-0.124	-0.124	0.000	0.000	0.000	0.000
135	A	141	LEU	0	-0.052	-0.027	27.801	-0.162	-0.162	0.000	0.000	0.000	0.000
136	A	142	PHE	0	-0.028	-0.028	31.308	-0.111	-0.111	0.000	0.000	0.000	0.000
137	A	143	PRO	0	0.039	0.025	34.310	0.085	0.085	0.000	0.000	0.000	0.000
138	A	144	ASN	0	0.101	0.052	37.180	0.006	0.006	0.000	0.000	0.000	0.000
139	A	145	THR	0	-0.016	-0.024	39.984	0.099	0.099	0.000	0.000	0.000	0.000
140	A	146	SER	0	0.025	0.020	41.635	0.134	0.134	0.000	0.000	0.000	0.000
141	A	147	ASP	-1	-0.798	-0.899	42.229	-6.669	-6.669	0.000	0.000	0.000	0.000
142	A	148	GLU	-1	-0.935	-0.972	40.438	-7.015	-7.015	0.000	0.000	0.000	0.000
143	A	149	ASN	0	-0.063	-0.040	37.760	-0.298	-0.298	0.000	0.000	0.000	0.000
144	A	150	ARG	1	0.889	0.947	37.520	6.570	6.570	0.000	0.000	0.000	0.000
145	A	151	ALA	0	-0.007	-0.015	38.812	-0.116	-0.116	0.000	0.000	0.000	0.000
146	A	152	ARG	1	0.906	0.965	34.018	8.286	8.286	0.000	0.000	0.000	0.000
147	A	153	ASN	0	-0.022	-0.027	34.139	-0.513	-0.513	0.000	0.000	0.000	0.000
148	A	154	ARG	1	0.855	0.941	35.064	7.210	7.210	0.000	0.000	0.000	0.000
149	A	155	ARG	1	0.815	0.914	28.911	9.621	9.621	0.000	0.000	0.000	0.000
150	A	156	VAL	0	0.019	0.007	30.957	0.055	0.055	0.000	0.000	0.000	0.000
151	A	157	GLU	-1	-0.842	-0.923	26.362	-10.926	-10.926	0.000	0.000	0.000	0.000
152	A	158	PHE	0	-0.001	-0.012	25.778	0.059	0.059	0.000	0.000	0.000	0.000
153	A	159	VAL	0	0.016	0.000	20.315	-0.261	-0.261	0.000	0.000	0.000	0.000
154	A	160	LEU	0	-0.023	-0.019	19.890	-0.061	-0.061	0.000	0.000	0.000	0.000
155	A	161	GLU	-1	-0.892	-0.944	15.607	-17.090	-17.090	0.000	0.000	0.000	0.000
156	A	162	ARG	1	0.873	0.929	10.690	23.292	23.292	0.000	0.000	0.000	0.000
157	A	163	ARG	1	0.781	0.868	13.708	15.951	15.951	0.000	0.000	0.000	0.000
158	A	164	VAL	0	0.018	0.010	12.029	-1.346	-1.346	0.000	0.000	0.000	0.000
159	A	165	VAL	0	0.006	-0.011	12.266	1.075	1.075	0.000	0.000	0.000	0.000
160	A	166	ARG	1	0.777	0.869	14.458	16.689	16.689	0.000	0.000	0.000	0.000
161	A	167	GLU	-1	-0.815	-0.919	18.072	-12.939	-12.939	0.000	0.000	0.000	0.000
162	A	168	GLY	0	0.005	0.021	20.962	-0.126	-0.126	0.000	0.000	0.000	0.000
163	A	169	HIS	0	0.006	-0.005	21.598	0.552	0.552	0.000	0.000	0.000	0.000
164	A	170	HIS	1	0.812	0.909	25.420	11.500	11.500	0.000	0.000	0.000	0.000
165	A	171	HIS	0	0.054	0.015	25.956	0.477	0.477	0.000	0.000	0.000	0.000
166	A	172	HIS	0	0.007	0.028	29.781	0.308	0.308	0.000	0.000	0.000	0.000

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