FMO DATABASE

FMODB ID: 3JNKL

Calculation Name: 3K86-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 3K86

Chain ID: A

ChEMBL ID:

UniProt ID: O87008

Base Structure: X-ray

Registration Date: 2023-09-20

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	164
LigandCharge
Software	ABINIT-MP - Open Ver. 1 Rev. 22 / 20200603(SMP)

Total energy (hartree)

FMO2-HF: Electronic energy	-1479270.764462
FMO2-HF: Nuclear repulsion	1417219.59735
FMO2-HF: Total energy	-62051.167111
FMO2-MP2: Total energy	-62229.126347

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:1014:PHE)

Summations of interaction energy for fragment #1(A:1014:PHE)

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.
-0.166	1.698	0.013	-0.842	-1.034	0

Interaction energy analysis for fragmet #1(A:1014:PHE)

Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE

Single fragment	Multi fragments
	Fragment list

Charge [e] FCHARGE : 0 / q_Mulliken : -0.033 / q_NPA : -0.032

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	A	1016	THR	0	-0.037	-0.015	3.490	-1.198	0.666	0.013	-0.842	-1.034
4	A	1017	VAL	0	0.023	0.012	5.551	0.327	0.327	0.000	0.000	0.000
5	A	1018	ALA	0	0.048	0.027	8.050	0.012	0.012	0.000	0.000	0.000
6	A	1019	SER	0	0.034	-0.002	11.502	0.049	0.049	0.000	0.000	0.000
7	A	1020	PHE	0	-0.048	-0.033	13.885	0.038	0.038	0.000	0.000	0.000
8	A	1021	ASP	-1	-0.857	-0.925	11.700	-0.356	-0.356	0.000	0.000	0.000
9	A	1022	PHE	0	0.026	0.014	11.983	0.029	0.029	0.000	0.000	0.000
10	A	1023	ARG	1	0.958	0.967	13.609	0.318	0.318	0.000	0.000	0.000
11	A	1024	ASP	-1	-0.820	-0.894	16.977	-0.150	-0.150	0.000	0.000	0.000
12	A	1025	ALA	0	0.020	0.018	14.788	0.030	0.030	0.000	0.000	0.000
13	A	1026	LEU	0	0.009	0.003	15.997	0.027	0.027	0.000	0.000	0.000
14	A	1027	SER	0	-0.107	-0.049	18.289	0.026	0.026	0.000	0.000	0.000
15	A	1028	LYS	1	0.859	0.908	18.545	0.191	0.191	0.000	0.000	0.000
16	A	1029	ALA	0	0.014	0.026	19.289	0.012	0.012	0.000	0.000	0.000
17	A	1030	SER	0	-0.033	-0.014	21.339	0.004	0.004	0.000	0.000	0.000
18	A	1031	THR	0	-0.013	-0.002	23.190	-0.008	-0.008	0.000	0.000	0.000
19	A	1032	PRO	0	0.017	0.015	25.763	0.007	0.007	0.000	0.000	0.000
20	A	1033	VAL	0	0.009	-0.001	28.164	-0.008	-0.008	0.000	0.000	0.000
21	A	1034	THR	0	-0.031	-0.024	29.491	0.006	0.006	0.000	0.000	0.000
22	A	1035	VAL	0	0.016	0.008	31.589	-0.003	-0.003	0.000	0.000	0.000
23	A	1036	VAL	0	-0.026	-0.004	29.738	0.003	0.003	0.000	0.000	0.000
24	A	1037	ALA	0	0.021	0.003	33.086	0.000	0.000	0.000	0.000	0.000
25	A	1038	THR	0	-0.022	-0.010	36.004	0.000	0.000	0.000	0.000	0.000
26	A	1039	ASN	0	0.034	-0.003	37.978	0.001	0.001	0.000	0.000	0.000
27	A	1040	GLY	0	0.028	0.027	41.141	-0.001	-0.001	0.000	0.000	0.000
28	A	1041	PRO	0	-0.015	-0.005	42.076	0.001	0.001	0.000	0.000	0.000
29	A	1042	PHE	0	-0.015	-0.010	39.473	0.001	0.001	0.000	0.000	0.000
30	A	1043	GLY	0	0.036	0.032	41.077	-0.001	-0.001	0.000	0.000	0.000
31	A	1044	LEU	0	0.004	0.014	40.765	-0.003	-0.003	0.000	0.000	0.000
32	A	1045	ALA	0	-0.007	-0.030	36.512	-0.001	-0.001	0.000	0.000	0.000
33	A	1046	GLY	0	0.039	-0.006	35.149	0.001	0.001	0.000	0.000	0.000
34	A	1047	LEU	0	-0.051	-0.031	28.832	0.000	0.000	0.000	0.000	0.000
35	A	1048	THR	0	0.003	0.001	29.975	0.001	0.001	0.000	0.000	0.000
36	A	1049	CYS	0	-0.059	-0.009	25.978	-0.010	-0.010	0.000	0.000	0.000
37	A	1050	SER	0	0.024	0.020	24.865	0.005	0.005	0.000	0.000	0.000
38	A	1051	ALA	0	-0.018	-0.003	21.495	-0.005	-0.005	0.000	0.000	0.000
39	A	1052	VAL	0	0.027	-0.003	23.257	-0.002	-0.002	0.000	0.000	0.000
40	A	1053	CYS	0	-0.057	-0.022	23.096	-0.004	-0.004	0.000	0.000	0.000
41	A	1054	SER	0	0.023	0.013	25.387	0.002	0.002	0.000	0.000	0.000
42	A	1055	VAL	0	-0.038	-0.019	23.957	-0.008	-0.008	0.000	0.000	0.000
43	A	1056	CYS	0	0.000	-0.006	25.829	-0.001	-0.001	0.000	0.000	0.000
44	A	1057	ASP	-1	-0.864	-0.930	28.436	-0.068	-0.068	0.000	0.000	0.000
45	A	1058	ARG	1	0.829	0.936	31.450	0.065	0.065	0.000	0.000	0.000
46	A	1059	PRO	0	0.101	0.040	31.143	0.000	0.000	0.000	0.000	0.000
47	A	1060	PRO	0	-0.001	0.012	31.725	-0.005	-0.005	0.000	0.000	0.000
48	A	1061	THR	0	0.001	-0.003	27.925	0.000	0.000	0.000	0.000	0.000
49	A	1062	VAL	0	-0.004	-0.004	28.007	-0.002	-0.002	0.000	0.000	0.000
50	A	1063	LEU	0	-0.009	0.000	21.753	-0.002	-0.002	0.000	0.000	0.000
51	A	1064	LEU	0	0.020	0.006	25.137	0.002	0.002	0.000	0.000	0.000
52	A	1065	CYS	0	-0.038	-0.005	21.025	-0.011	-0.011	0.000	0.000	0.000
53	A	1066	ILE	0	0.020	0.010	23.118	0.002	0.002	0.000	0.000	0.000
54	A	1067	ASN	0	-0.015	-0.011	22.637	0.001	0.001	0.000	0.000	0.000
55	A	1068	ARG	1	0.857	0.888	20.546	0.223	0.223	0.000	0.000	0.000
56	A	1069	LYS	1	0.944	0.972	25.040	0.166	0.166	0.000	0.000	0.000
57	A	1070	SER	0	-0.049	-0.009	27.991	0.011	0.011	0.000	0.000	0.000
58	A	1071	TYR	0	0.102	0.037	30.361	0.000	0.000	0.000	0.000	0.000
59	A	1072	ALA	0	0.051	0.012	32.422	0.002	0.002	0.000	0.000	0.000
60	A	1073	ALA	0	-0.010	0.008	28.815	0.001	0.001	0.000	0.000	0.000
61	A	1074	GLY	0	0.022	0.009	30.753	0.001	0.001	0.000	0.000	0.000
62	A	1075	ILE	0	0.011	0.009	33.034	0.002	0.002	0.000	0.000	0.000
63	A	1076	ILE	0	-0.020	-0.010	31.577	0.002	0.002	0.000	0.000	0.000
64	A	1077	LYS	1	0.843	0.907	26.642	0.136	0.136	0.000	0.000	0.000
65	A	1078	SER	0	-0.023	0.000	32.719	0.002	0.002	0.000	0.000	0.000
66	A	1079	ASN	0	-0.017	-0.012	36.079	0.007	0.007	0.000	0.000	0.000
67	A	1080	GLY	0	0.005	0.018	34.929	0.003	0.003	0.000	0.000	0.000
68	A	1081	VAL	0	0.003	-0.003	35.969	0.000	0.000	0.000	0.000	0.000
69	A	1082	LEU	0	-0.048	-0.018	31.267	-0.003	-0.003	0.000	0.000	0.000
70	A	1083	SER	0	0.031	0.016	35.806	0.000	0.000	0.000	0.000	0.000
71	A	1084	VAL	0	-0.026	-0.019	30.603	-0.005	-0.005	0.000	0.000	0.000
72	A	1085	ASN	0	-0.012	-0.013	33.621	0.009	0.009	0.000	0.000	0.000
73	A	1086	TRP	0	0.028	-0.001	29.620	-0.004	-0.004	0.000	0.000	0.000
74	A	1087	LEU	0	0.026	0.008	34.096	0.005	0.005	0.000	0.000	0.000
75	A	1088	ALA	0	0.034	0.016	35.621	-0.002	-0.002	0.000	0.000	0.000
76	A	1089	ALA	0	-0.022	-0.027	37.592	-0.001	-0.001	0.000	0.000	0.000
77	A	1090	GLY	0	-0.004	0.002	38.616	0.000	0.000	0.000	0.000	0.000
78	A	1091	GLN	0	0.029	0.015	38.616	-0.002	-0.002	0.000	0.000	0.000
79	A	1092	ALA	0	0.042	0.013	36.648	-0.003	-0.003	0.000	0.000	0.000
80	A	1093	VAL	0	0.026	0.008	37.380	-0.003	-0.003	0.000	0.000	0.000
81	A	1094	ILE	0	0.043	0.038	38.049	-0.001	-0.001	0.000	0.000	0.000
82	A	1095	SER	0	0.044	0.009	33.162	-0.004	-0.004	0.000	0.000	0.000
83	A	1096	GLN	0	0.035	0.021	34.341	-0.009	-0.009	0.000	0.000	0.000
84	A	1097	THR	0	0.013	0.004	36.000	-0.001	-0.001	0.000	0.000	0.000
85	A	1098	PHE	0	-0.028	-0.004	34.629	-0.002	-0.002	0.000	0.000	0.000
86	A	1099	ALA	0	-0.037	-0.014	31.572	-0.006	-0.006	0.000	0.000	0.000
87	A	1100	GLY	0	-0.024	-0.007	32.691	-0.004	-0.004	0.000	0.000	0.000
88	A	1101	VAL	0	-0.028	-0.016	34.434	0.003	0.003	0.000	0.000	0.000
89	A	1102	GLY	0	-0.006	-0.007	36.629	0.003	0.003	0.000	0.000	0.000
90	A	1103	SER	0	-0.072	-0.034	38.364	0.002	0.002	0.000	0.000	0.000
91	A	1104	VAL	0	0.037	0.024	39.511	0.003	0.003	0.000	0.000	0.000
92	A	1105	PRO	0	0.038	0.023	40.163	-0.005	-0.005	0.000	0.000	0.000
93	A	1106	MET	0	-0.028	0.019	35.288	0.000	0.000	0.000	0.000	0.000
94	A	1107	GLU	-1	-0.915	-0.980	40.295	-0.057	-0.057	0.000	0.000	0.000
95	A	1108	GLU	-1	-0.919	-0.947	43.485	-0.050	-0.050	0.000	0.000	0.000
96	A	1109	ARG	1	0.803	0.905	35.230	0.080	0.080	0.000	0.000	0.000
97	A	1110	PHE	0	-0.060	-0.042	38.700	-0.002	-0.002	0.000	0.000	0.000
98	A	1111	ALA	0	0.016	0.024	44.136	0.002	0.002	0.000	0.000	0.000
99	A	1112	ASP	-1	-0.780	-0.867	45.415	-0.052	-0.052	0.000	0.000	0.000
100	A	1113	LYS	1	0.929	0.950	47.495	0.043	0.043	0.000	0.000	0.000
101	A	1114	GLY	0	0.004	0.004	45.765	0.001	0.001	0.000	0.000	0.000
102	A	1115	TRP	0	-0.038	-0.002	37.954	-0.003	-0.003	0.000	0.000	0.000
103	A	1116	GLN	0	-0.013	-0.013	44.637	0.005	0.005	0.000	0.000	0.000
104	A	1117	THR	0	0.042	0.032	44.475	-0.002	-0.002	0.000	0.000	0.000
105	A	1118	ILE	0	-0.073	-0.038	42.374	0.002	0.002	0.000	0.000	0.000
106	A	1119	ALA	0	-0.004	-0.011	42.728	0.002	0.002	0.000	0.000	0.000
107	A	1120	THR	0	-0.051	-0.071	39.332	0.001	0.001	0.000	0.000	0.000
108	A	1121	GLY	0	-0.001	0.009	42.540	0.001	0.001	0.000	0.000	0.000
109	A	1122	ALA	0	-0.022	-0.007	38.880	0.000	0.000	0.000	0.000	0.000
110	A	1123	PRO	0	-0.017	-0.002	39.824	0.002	0.002	0.000	0.000	0.000
111	A	1124	TYR	0	-0.049	0.017	38.249	-0.006	-0.006	0.000	0.000	0.000
112	A	1125	ARG	1	0.685	0.774	39.517	0.061	0.061	0.000	0.000	0.000
113	A	1126	MET	0	-0.009	-0.016	41.345	-0.002	-0.002	0.000	0.000	0.000
114	A	1127	ASP	-1	-0.782	-0.854	43.084	-0.056	-0.056	0.000	0.000	0.000
115	A	1128	ALA	0	-0.034	-0.011	37.993	-0.001	-0.001	0.000	0.000	0.000
116	A	1129	ALA	0	0.030	0.008	36.810	0.002	0.002	0.000	0.000	0.000
117	A	1130	VAL	0	-0.039	-0.011	35.409	0.002	0.002	0.000	0.000	0.000
118	A	1131	SER	0	-0.016	-0.007	36.663	-0.003	-0.003	0.000	0.000	0.000
119	A	1132	PHE	0	0.007	-0.009	32.691	0.003	0.003	0.000	0.000	0.000
120	A	1133	ASP	-1	-0.652	-0.797	36.427	-0.067	-0.067	0.000	0.000	0.000
121	A	1134	CYS	0	-0.042	-0.028	34.044	0.000	0.000	0.000	0.000	0.000
122	A	1135	THR	0	0.070	0.041	35.548	0.003	0.003	0.000	0.000	0.000
123	A	1136	ILE	0	-0.081	-0.044	30.232	-0.005	-0.005	0.000	0.000	0.000
124	A	1137	ALA	0	0.022	0.020	30.405	0.004	0.004	0.000	0.000	0.000
125	A	1138	ASN	0	0.014	-0.007	24.574	0.003	0.003	0.000	0.000	0.000
126	A	1139	ILE	0	-0.017	-0.013	24.808	-0.004	-0.004	0.000	0.000	0.000
127	A	1140	VAL	0	0.007	0.018	19.327	0.000	0.000	0.000	0.000	0.000
128	A	1141	ASP	-1	-0.793	-0.855	20.868	-0.186	-0.186	0.000	0.000	0.000
129	A	1142	VAL	0	0.048	0.024	14.809	-0.025	-0.025	0.000	0.000	0.000
130	A	1143	GLY	0	0.037	0.026	16.429	0.002	0.002	0.000	0.000	0.000
131	A	1144	SER	0	-0.062	-0.040	17.015	0.032	0.032	0.000	0.000	0.000
132	A	1145	HIS	0	0.008	0.003	19.405	0.022	0.022	0.000	0.000	0.000
133	A	1146	SER	0	0.008	-0.008	20.778	-0.005	-0.005	0.000	0.000	0.000
134	A	1147	VAL	0	-0.021	-0.023	19.268	0.005	0.005	0.000	0.000	0.000
135	A	1148	ILE	0	0.010	0.005	22.646	0.005	0.005	0.000	0.000	0.000
136	A	1149	PHE	0	0.011	-0.002	21.672	-0.002	-0.002	0.000	0.000	0.000
137	A	1150	ALA	0	0.024	0.005	27.381	0.006	0.006	0.000	0.000	0.000
138	A	1151	GLU	-1	-0.893	-0.949	30.945	-0.082	-0.082	0.000	0.000	0.000
139	A	1152	VAL	0	-0.050	-0.028	33.455	0.002	0.002	0.000	0.000	0.000
140	A	1153	VAL	0	-0.005	-0.011	35.903	0.003	0.003	0.000	0.000	0.000
141	A	1154	ALA	0	0.003	0.007	39.270	0.004	0.004	0.000	0.000	0.000
142	A	1155	ARG	1	0.872	0.926	38.966	0.053	0.053	0.000	0.000	0.000
143	A	1156	ASN	0	-0.030	-0.024	40.302	0.003	0.003	0.000	0.000	0.000
144	A	1157	HIS	0	0.017	0.001	37.951	-0.003	-0.003	0.000	0.000	0.000
145	A	1158	ALA	0	0.039	0.047	42.035	0.003	0.003	0.000	0.000	0.000
146	A	1159	GLU	-1	-0.926	-0.963	43.830	-0.041	-0.041	0.000	0.000	0.000
147	A	1160	GLU	-1	-0.948	-0.977	42.915	-0.047	-0.047	0.000	0.000	0.000
148	A	1161	CYS	0	-0.048	-0.023	41.411	0.000	0.000	0.000	0.000	0.000
149	A	1162	THR	0	-0.007	0.004	37.941	-0.001	-0.001	0.000	0.000	0.000
150	A	1163	PRO	0	0.009	0.005	33.435	0.000	0.000	0.000	0.000	0.000
151	A	1164	LEU	0	-0.030	0.019	33.483	0.001	0.001	0.000	0.000	0.000
152	A	1165	ILE	0	-0.030	-0.024	28.825	-0.005	-0.005	0.000	0.000	0.000
153	A	1166	TYR	0	-0.005	-0.006	26.244	0.000	0.000	0.000	0.000	0.000
154	A	1167	HIS	0	0.029	-0.006	24.478	-0.001	-0.001	0.000	0.000	0.000
155	A	1168	ARG	1	0.905	0.954	23.576	0.116	0.116	0.000	0.000	0.000
156	A	1169	ARG	1	0.849	0.912	21.442	0.163	0.163	0.000	0.000	0.000
157	A	1170	GLN	0	0.007	0.027	27.714	0.010	0.010	0.000	0.000	0.000
158	A	1171	TYR	0	-0.001	-0.008	30.283	-0.005	-0.005	0.000	0.000	0.000
159	A	1172	ALA	0	0.008	0.010	31.841	0.003	0.003	0.000	0.000	0.000
160	A	1173	THR	0	0.041	0.000	33.817	0.000	0.000	0.000	0.000	0.000
161	A	1174	THR	0	0.005	0.008	33.113	-0.001	-0.001	0.000	0.000	0.000
162	A	1175	ARG	1	0.907	0.940	35.287	0.059	0.059	0.000	0.000	0.000
163	A	1176	SER	0	0.054	0.042	35.682	-0.002	-0.002	0.000	0.000	0.000
164	A	1177	LEU	0	0.019	0.010	32.202	0.001	0.001	0.000	0.000	0.000

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Interactive mode: IFIE and PIEDA for fragment #1(A:1014:PHE)