FMODB

FMODB: The database of quantum mechanical data based on the FMO method

Last updated: 2024-07-23

All entries: 37450

Number of unique PDB entries: 7783

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FMODB ID: 76ZYK

Calculation Name: 1SFN-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1SFN

Chain ID: A

ChEMBL ID:

UniProt ID: Q9RV77

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 245
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -3191949.173431
FMO2-HF: Nuclear repulsion 3095691.049768
FMO2-HF: Total energy -96258.123662
FMO2-MP2: Total energy -96537.969881


3D Structure
Snapshot
 
Ligand structure

ligand structure
Ligand Interaction
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/AN/AN/AN/AN/AN/A


Interactive mode: IFIE and PIEDA for fragment #1(A:1001:MET)


Summations of interaction energy for fragment #1(A:1001:MET)
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.
-9.667-8.73717.402-6.783-11.549-0.042
Interaction energy analysis for fragmet #1(A:1001:MET)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : -0.013 / q_NPA : -0.017
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   
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].
3A1003HIS00.0080.0092.355-6.283-4.9755.177-2.595-3.890-0.004
4A1004LEU0-0.041-0.0232.281-0.3050.4603.189-0.844-3.110-0.003
5A1005GLY00.0420.0253.973-0.1280.045-0.0010.006-0.1780.000
6A1006GLN00.0040.0131.930-4.075-5.4769.038-3.312-4.325-0.035
7A1007THR0-0.015-0.0104.3531.0641.149-0.001-0.038-0.0460.000
8A1008ARG10.8320.9066.912-0.329-0.3290.0000.0000.0000.000
9A1009SER00.0220.0209.6730.1300.1300.0000.0000.0000.000
10A1010ALA0-0.039-0.02112.329-0.137-0.1370.0000.0000.0000.000
11A1011LEU0-0.023-0.00715.2670.0730.0730.0000.0000.0000.000
12A1012HIS00.0140.01017.494-0.015-0.0150.0000.0000.0000.000
13A1013GLY00.0070.00121.5540.0240.0240.0000.0000.0000.000
14A1014SER00.0390.01125.1900.0200.0200.0000.0000.0000.000
15A1015HIS00.0290.01519.841-0.019-0.0190.0000.0000.0000.000
16A1016ALA0-0.012-0.00519.159-0.023-0.0230.0000.0000.0000.000
17A1017VAL00.0000.01514.4390.0340.0340.0000.0000.0000.000
18A1018ILE00.0260.01214.904-0.044-0.0440.0000.0000.0000.000
19A1019THR00.0150.0009.916-0.023-0.0230.0000.0000.0000.000
20A1020PRO00.0610.01611.6440.0320.0320.0000.0000.0000.000
21A1021GLU-1-0.857-0.9136.5710.5650.5650.0000.0000.0000.000
22A1022THR0-0.054-0.0309.651-0.051-0.0510.0000.0000.0000.000
23A1023PHE0-0.0190.00612.234-0.042-0.0420.0000.0000.0000.000
24A1024VAL00.0110.00415.3120.0670.0670.0000.0000.0000.000
25A1025ARG10.8080.88715.596-0.408-0.4080.0000.0000.0000.000
26A1026THR0-0.061-0.02920.505-0.020-0.0200.0000.0000.0000.000
27A1027ALA00.0420.00924.0850.0160.0160.0000.0000.0000.000
28A1028LEU00.0040.00527.633-0.012-0.0120.0000.0000.0000.000
29A1029ALA0-0.0080.00030.7130.0060.0060.0000.0000.0000.000
30A1030GLU-1-0.852-0.92433.7390.0630.0630.0000.0000.0000.000
31A1031TRP00.007-0.01930.6510.0070.0070.0000.0000.0000.000
32A1032PRO00.0260.01131.2980.0110.0110.0000.0000.0000.000
33A1033GLY0-0.016-0.02031.2580.0030.0030.0000.0000.0000.000
34A1034SER0-0.026-0.00428.3940.0150.0150.0000.0000.0000.000
35A1035ALA0-0.030-0.00123.155-0.006-0.0060.0000.0000.0000.000
36A1036ILE00.007-0.00524.480-0.004-0.0040.0000.0000.0000.000
37A1037VAL0-0.0060.00518.1780.0080.0080.0000.0000.0000.000
38A1038LEU00.005-0.00821.383-0.012-0.0120.0000.0000.0000.000
39A1039HIS00.0250.03318.282-0.010-0.0100.0000.0000.0000.000
40A1040ILE0-0.0040.01321.078-0.028-0.0280.0000.0000.0000.000
41A1041ALA00.0550.01723.9890.0160.0160.0000.0000.0000.000
42A1042PRO00.014-0.00826.900-0.013-0.0130.0000.0000.0000.000
43A1043VAL0-0.020-0.00325.744-0.005-0.0050.0000.0000.0000.000
44A1044VAL0-0.0110.01122.795-0.013-0.0130.0000.0000.0000.000
45A1045GLY00.0250.01423.9790.0010.0010.0000.0000.0000.000
46A1046LEU0-0.064-0.04125.2520.0060.0060.0000.0000.0000.000
47A1047GLY0-0.0290.00928.2290.0090.0090.0000.0000.0000.000
48A1048ALA0-0.050-0.01728.209-0.003-0.0030.0000.0000.0000.000
49A1049ARG10.7740.86030.2950.0590.0590.0000.0000.0000.000
50A1050PHE0-0.055-0.02127.0800.0070.0070.0000.0000.0000.000
51A1051VAL0-0.0070.00228.115-0.005-0.0050.0000.0000.0000.000
52A1052GLN00.013-0.00822.948-0.011-0.0110.0000.0000.0000.000
53A1053PHE0-0.048-0.02523.640-0.001-0.0010.0000.0000.0000.000
54A1054THR0-0.011-0.02121.0580.0120.0120.0000.0000.0000.000
55A1055ALA00.0140.02023.6030.0100.0100.0000.0000.0000.000
56A1056GLU-1-0.811-0.87820.1960.3350.3350.0000.0000.0000.000
57A1057MET0-0.011-0.00324.915-0.002-0.0020.0000.0000.0000.000
58A1058PRO00.0400.01827.2060.0050.0050.0000.0000.0000.000
59A1059ALA0-0.008-0.00528.986-0.017-0.0170.0000.0000.0000.000
60A1060GLY0-0.036-0.01332.0580.0000.0000.0000.0000.0000.000
61A1061ALA0-0.048-0.00831.489-0.009-0.0090.0000.0000.0000.000
62A1062GLN0-0.026-0.04233.466-0.006-0.0060.0000.0000.0000.000
63A1063ALA0-0.0100.00533.3150.0030.0030.0000.0000.0000.000
64A1064THR0-0.017-0.01335.466-0.001-0.0010.0000.0000.0000.000
65A1065GLU-1-0.809-0.88036.9200.0510.0510.0000.0000.0000.000
66A1066SER00.0110.00035.540-0.001-0.0010.0000.0000.0000.000
67A1067VAL0-0.078-0.04837.671-0.002-0.0020.0000.0000.0000.000
68A1068TYR0-0.039-0.02534.867-0.008-0.0080.0000.0000.0000.000
69A1069GLN0-0.015-0.01137.3220.0030.0030.0000.0000.0000.000
70A1070ARG10.7830.85833.473-0.060-0.0600.0000.0000.0000.000
71A1071PHE00.0240.01231.344-0.001-0.0010.0000.0000.0000.000
72A1072ALA0-0.002-0.00831.1820.0040.0040.0000.0000.0000.000
73A1073PHE00.0410.01727.514-0.005-0.0050.0000.0000.0000.000
74A1074VAL00.0060.01028.5560.0110.0110.0000.0000.0000.000
75A1075LEU0-0.035-0.02222.736-0.004-0.0040.0000.0000.0000.000
76A1076SER00.0260.00224.6770.0140.0140.0000.0000.0000.000
77A1077GLY00.0180.01726.748-0.001-0.0010.0000.0000.0000.000
78A1078GLU-1-0.825-0.90429.5510.0980.0980.0000.0000.0000.000
79A1079VAL0-0.021-0.01231.4270.0070.0070.0000.0000.0000.000
80A1080ASP-1-0.779-0.86934.3670.0860.0860.0000.0000.0000.000
81A1081VAL0-0.014-0.01736.6410.0020.0020.0000.0000.0000.000
82A1082ALA0-0.008-0.00439.253-0.004-0.0040.0000.0000.0000.000
83A1083VAL00.0640.02142.2520.0000.0000.0000.0000.0000.000
84A1084GLY00.0530.02244.6210.0000.0000.0000.0000.0000.000
85A1085GLY0-0.069-0.01848.406-0.002-0.0020.0000.0000.0000.000
86A1086GLU-1-0.821-0.89445.4600.0450.0450.0000.0000.0000.000
87A1087THR0-0.014-0.01843.6950.0020.0020.0000.0000.0000.000
88A1088ARG10.7830.89141.350-0.047-0.0470.0000.0000.0000.000
89A1089THR00.008-0.00538.7430.0050.0050.0000.0000.0000.000
90A1090LEU0-0.0410.00634.832-0.005-0.0050.0000.0000.0000.000
91A1091ARG10.8100.86232.830-0.082-0.0820.0000.0000.0000.000
92A1092GLU-1-0.844-0.90727.7390.1280.1280.0000.0000.0000.000
93A1093TYR0-0.062-0.07325.959-0.005-0.0050.0000.0000.0000.000
94A1094ASP-1-0.765-0.84931.0960.0670.0670.0000.0000.0000.000
95A1095TYR0-0.113-0.08132.9130.0060.0060.0000.0000.0000.000
96A1096VAL0-0.012-0.01034.642-0.003-0.0030.0000.0000.0000.000
97A1097TYR0-0.052-0.02935.6990.0010.0010.0000.0000.0000.000
98A1098LEU00.0250.00636.8440.0000.0000.0000.0000.0000.000
99A1099PRO00.0560.02139.300-0.002-0.0020.0000.0000.0000.000
100A1100ALA0-0.015-0.01740.6880.0030.0030.0000.0000.0000.000
101A1101GLY0-0.0090.01540.893-0.001-0.0010.0000.0000.0000.000
102A1102GLU-1-0.921-0.95442.5620.0350.0350.0000.0000.0000.000
103A1103LYS10.8330.90542.393-0.037-0.0370.0000.0000.0000.000
104A1104HIS00.002-0.00937.8080.0050.0050.0000.0000.0000.000
105A1105MET0-0.026-0.01239.2880.0010.0010.0000.0000.0000.000
106A1106LEU0-0.0060.00733.585-0.001-0.0010.0000.0000.0000.000
107A1107THR0-0.027-0.02435.6690.0010.0010.0000.0000.0000.000
108A1108ALA00.0360.04131.330-0.003-0.0030.0000.0000.0000.000
109A1109LYS10.7730.87533.332-0.099-0.0990.0000.0000.0000.000
110A1110THR0-0.035-0.02430.3520.0020.0020.0000.0000.0000.000
111A1111ASP-1-0.876-0.93226.6220.2210.2210.0000.0000.0000.000
112A1112ALA0-0.021-0.01127.5850.0020.0020.0000.0000.0000.000
113A1113ARG10.8220.90120.084-0.248-0.2480.0000.0000.0000.000
114A1114VAL00.0140.00825.645-0.012-0.0120.0000.0000.0000.000
115A1115SER00.0370.02325.3110.0040.0040.0000.0000.0000.000
116A1116VAL0-0.054-0.02526.349-0.007-0.0070.0000.0000.0000.000
117A1117PHE00.0220.01026.968-0.003-0.0030.0000.0000.0000.000
118A1118GLU-1-0.781-0.85430.1180.0540.0540.0000.0000.0000.000
119A1119LYS10.8540.91032.4700.0050.0050.0000.0000.0000.000
120A1120PRO00.0110.02035.2050.0040.0040.0000.0000.0000.000
121A1121TYR0-0.012-0.01938.701-0.004-0.0040.0000.0000.0000.000
122A1122GLN0-0.0010.00339.3410.0000.0000.0000.0000.0000.000
123A1123THR00.0280.01043.1180.0000.0000.0000.0000.0000.000
124A1124VAL0-0.008-0.00846.576-0.003-0.0030.0000.0000.0000.000
125A1125GLU-1-0.927-0.96649.204-0.005-0.0050.0000.0000.0000.000
126A1126GLY0-0.032-0.00452.9930.0010.0010.0000.0000.0000.000
127A1127VAL0-0.063-0.03248.7540.0010.0010.0000.0000.0000.000
128A1128GLN0-0.0120.00350.0140.0000.0000.0000.0000.0000.000
129A1129ALA00.0050.00445.728-0.001-0.0010.0000.0000.0000.000
130A1130PRO0-0.0060.00943.3860.0010.0010.0000.0000.0000.000
131A1131GLY00.0250.00545.4620.0010.0010.0000.0000.0000.000
132A1132VAL0-0.014-0.02141.7410.0000.0000.0000.0000.0000.000
133A1133TYR0-0.040-0.00839.701-0.003-0.0030.0000.0000.0000.000
134A1134TRP00.002-0.01539.5370.0050.0050.0000.0000.0000.000
135A1135GLY00.0160.01638.399-0.005-0.0050.0000.0000.0000.000
136A1136ASN00.0470.00234.2890.0020.0020.0000.0000.0000.000
137A1137GLU-1-0.802-0.87330.5870.0360.0360.0000.0000.0000.000
138A1138ARG10.7920.87028.161-0.099-0.0990.0000.0000.0000.000
139A1139GLU-1-0.936-0.96234.7320.0410.0410.0000.0000.0000.000
140A1140ASN0-0.039-0.01236.339-0.008-0.0080.0000.0000.0000.000
141A1141PRO0-0.016-0.00537.3960.0000.0000.0000.0000.0000.000
142A1142GLY00.006-0.00536.506-0.003-0.0030.0000.0000.0000.000
143A1143TYR0-0.040-0.01837.3550.0010.0010.0000.0000.0000.000
144A1144PRO00.016-0.00536.891-0.001-0.0010.0000.0000.0000.000
145A1145PHE0-0.0150.01233.892-0.001-0.0010.0000.0000.0000.000
146A1146GLU-1-0.830-0.90636.428-0.058-0.0580.0000.0000.0000.000
147A1147GLY0-0.057-0.03238.802-0.002-0.0020.0000.0000.0000.000
148A1148ASP-1-0.870-0.94733.729-0.045-0.0450.0000.0000.0000.000
149A1149ASP-1-0.887-0.93936.109-0.022-0.0220.0000.0000.0000.000
150A1150HIS0-0.084-0.05432.0830.0050.0050.0000.0000.0000.000
151A1151LEU0-0.027-0.00630.400-0.001-0.0010.0000.0000.0000.000
152A1152ILE0-0.0150.00932.5400.0010.0010.0000.0000.0000.000
153A1153ALA00.0310.01632.3150.0020.0020.0000.0000.0000.000
154A1154ARG10.8570.94332.726-0.022-0.0220.0000.0000.0000.000
155A1155LYS10.8460.90934.2140.0170.0170.0000.0000.0000.000
156A1156LEU0-0.019-0.00532.0240.0030.0030.0000.0000.0000.000
157A1157LEU0-0.0060.01036.3450.0050.0050.0000.0000.0000.000
158A1158PRO00.0340.01939.036-0.003-0.0030.0000.0000.0000.000
159A1159ASP-1-0.807-0.88440.968-0.015-0.0150.0000.0000.0000.000
160A1160GLU-1-0.933-0.96942.6530.0030.0030.0000.0000.0000.000
161A1161PRO0-0.003-0.01644.1810.0000.0000.0000.0000.0000.000
162A1162ALA00.0660.03845.779-0.001-0.0010.0000.0000.0000.000
163A1163PHE00.0440.02139.9200.0020.0020.0000.0000.0000.000
164A1164ASP-1-0.789-0.87238.749-0.010-0.0100.0000.0000.0000.000
165A1165PHE0-0.041-0.02533.877-0.004-0.0040.0000.0000.0000.000
166A1166MET0-0.0340.01535.2210.0050.0050.0000.0000.0000.000
167A1167VAL00.010-0.00530.932-0.002-0.0020.0000.0000.0000.000
168A1168SER0-0.007-0.00531.588-0.002-0.0020.0000.0000.0000.000
169A1169THR0-0.044-0.05228.9390.0020.0020.0000.0000.0000.000
170A1170MET00.0100.02727.850-0.003-0.0030.0000.0000.0000.000
171A1171SER0-0.011-0.01527.5660.0110.0110.0000.0000.0000.000
172A1172PHE00.0160.00426.336-0.006-0.0060.0000.0000.0000.000
173A1173ALA00.0530.02727.2060.0080.0080.0000.0000.0000.000
174A1174PRO0-0.044-0.03425.413-0.010-0.0100.0000.0000.0000.000
175A1175GLY0-0.035-0.01125.378-0.001-0.0010.0000.0000.0000.000
176A1176ALA00.0070.01926.912-0.008-0.0080.0000.0000.0000.000
177A1177SER0-0.012-0.02526.889-0.007-0.0070.0000.0000.0000.000
178A1178LEU0-0.0210.00327.2240.0060.0060.0000.0000.0000.000
179A1179PRO0-0.017-0.00430.036-0.010-0.0100.0000.0000.0000.000
180A1180TYR0-0.090-0.06532.382-0.007-0.0070.0000.0000.0000.000
181A1181ALA0-0.033-0.02029.356-0.001-0.0010.0000.0000.0000.000
182A1182GLU-1-0.870-0.93930.018-0.063-0.0630.0000.0000.0000.000
183A1183VAL0-0.009-0.02330.714-0.011-0.0110.0000.0000.0000.000
184A1184HIS0-0.026-0.00831.3590.0050.0050.0000.0000.0000.000
185A1185TYR00.016-0.00333.715-0.005-0.0050.0000.0000.0000.000
186A1186MET0-0.0110.00433.876-0.003-0.0030.0000.0000.0000.000
187A1187GLU-1-0.808-0.89929.418-0.064-0.0640.0000.0000.0000.000
188A1188HIS0-0.019-0.02427.0010.0170.0170.0000.0000.0000.000
189A1189GLY00.0370.01624.948-0.010-0.0100.0000.0000.0000.000
190A1190LEU0-0.039-0.00221.0710.0080.0080.0000.0000.0000.000
191A1191LEU00.0390.00619.9540.0050.0050.0000.0000.0000.000
192A1192MET0-0.0150.01218.141-0.012-0.0120.0000.0000.0000.000
193A1193LEU0-0.038-0.01620.2640.0320.0320.0000.0000.0000.000
194A1194GLU-1-0.805-0.89521.9880.1020.1020.0000.0000.0000.000
195A1195GLY00.0300.01620.897-0.021-0.0210.0000.0000.0000.000
196A1196GLU-1-0.905-0.96416.8730.0500.0500.0000.0000.0000.000
197A1197GLY00.0470.02317.634-0.003-0.0030.0000.0000.0000.000
198A1198LEU0-0.065-0.02416.860-0.032-0.0320.0000.0000.0000.000
199A1199TYR00.0680.02818.6810.0230.0230.0000.0000.0000.000
200A1200LYS10.7770.86819.7060.1800.1800.0000.0000.0000.000
201A1201LEU0-0.006-0.01619.3690.0300.0300.0000.0000.0000.000
202A1202GLU-1-0.815-0.90322.446-0.250-0.2500.0000.0000.0000.000
203A1203GLU-1-0.872-0.91023.863-0.212-0.2120.0000.0000.0000.000
204A1204ASN0-0.053-0.00318.430-0.044-0.0440.0000.0000.0000.000
205A1205TYR00.011-0.01118.6840.0440.0440.0000.0000.0000.000
206A1206TYR0-0.033-0.03614.381-0.092-0.0920.0000.0000.0000.000
207A1207PRO0-0.037-0.00611.8820.0520.0520.0000.0000.0000.000
208A1208VAL0-0.023-0.01613.214-0.011-0.0110.0000.0000.0000.000
209A1209THR0-0.032-0.03613.3770.0220.0220.0000.0000.0000.000
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