Manual

About

FMODB

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

Last updated: 2024-04-05

All entries: 36946

Number of unique PDB entries: 7781

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FMODB ID: GNZR1

Calculation Name: 1LRV-A-Xray372

Preferred Name:

Target Type:

Ligand Name:

ligand 3-letter code:

PDB ID: 1LRV

Chain ID: A

ChEMBL ID:

UniProt ID: Q44534

Base Structure: X-ray

Registration Date: 2023-06-19

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 233
LigandCharge
Software ABINIT-MP - Open Ver. 1 Rev. 23Q2 / 20200603(SMP)
Total energy (hartree)
FMO2-HF: Electronic energy -2615396.652249
FMO2-HF: Nuclear repulsion 2520900.637752
FMO2-HF: Total energy -94496.014496
FMO2-MP2: Total energy -94771.191379


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:9:THR)


Summations of interaction energy for fragment #1(A:9:THR)
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.
-4.948-0.8030.084-1.996-2.2290.004
Interaction energy analysis for fragmet #1(A:9:THR)
Snapshot

IFIE Diagram

Base fragment(s) of PIEDA/IFIE
Single fragment Multi fragments
Fragment list
Charge [e] FCHARGE : 0 / q_Mulliken : 0.037 / q_NPA : 0.014
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].
3A11ILE00.0390.0203.258-0.4752.5700.059-1.635-1.4680.002
4A12GLY00.0300.0065.1150.0120.033-0.001-0.002-0.0170.000
5A13ASP-1-0.803-0.9228.673-0.378-0.3780.0000.0000.0000.000
6A14CYS0-0.048-0.02910.8760.1250.1250.0000.0000.0000.000
7A15ARG10.9170.97113.4930.3060.3060.0000.0000.0000.000
8A16VAL00.0530.02216.1420.0340.0340.0000.0000.0000.000
9A17CYS0-0.0210.02614.1020.0490.0490.0000.0000.0000.000
10A18SER00.0830.02816.707-0.011-0.0110.0000.0000.0000.000
11A19PHE00.002-0.01715.8530.0000.0000.0000.0000.0000.000
12A20ARG10.8680.93716.7190.1440.1440.0000.0000.0000.000
13A21MET0-0.007-0.01417.586-0.008-0.0080.0000.0000.0000.000
14A22SER00.0170.00819.8910.0060.0060.0000.0000.0000.000
15A23LEU00.0010.00816.7600.0000.0000.0000.0000.0000.000
16A24LEU00.0410.00913.4990.0130.0130.0000.0000.0000.000
17A25LEU0-0.040-0.01116.138-0.003-0.0030.0000.0000.0000.000
18A26THR0-0.020-0.02218.473-0.003-0.0030.0000.0000.0000.000
19A27GLY00.0130.02015.8370.0110.0110.0000.0000.0000.000
20A28ARG10.9110.97215.796-0.070-0.0700.0000.0000.0000.000
21A29CYS00.0000.01712.8790.0380.0380.0000.0000.0000.000
22A30THR0-0.040-0.0259.352-0.105-0.1050.0000.0000.0000.000
23A31PRO00.0340.0087.7830.2180.2180.0000.0000.0000.000
24A32GLY00.0190.0143.634-0.445-0.3090.004-0.039-0.1010.000
25A33ASP-1-0.902-0.9354.3861.6321.787-0.001-0.013-0.1400.000
26A34ALA00.0410.0227.1200.2850.2850.0000.0000.0000.000
27A35CYS0-0.056-0.0338.177-0.289-0.2890.0000.0000.0000.000
28A36VAL00.0880.04410.1010.1690.1690.0000.0000.0000.000
29A37ALA0-0.037-0.02411.441-0.003-0.0030.0000.0000.0000.000
30A38VAL00.0120.0045.662-0.172-0.1720.0000.0000.0000.000
31A39GLU-1-0.927-0.9458.8840.3490.3490.0000.0000.0000.000
32A40SER0-0.013-0.0184.5910.3180.381-0.001-0.002-0.0590.000
33A41GLY00.1290.0677.083-0.063-0.0630.0000.0000.0000.000
34A42ARG10.9230.9605.254-1.331-1.3310.0000.0000.0000.000
35A43GLN0-0.023-0.0093.377-3.016-2.2910.024-0.305-0.4440.002
36A44ILE00.0180.0107.877-0.385-0.3850.0000.0000.0000.000
37A45ASP-1-0.757-0.84310.8880.4100.4100.0000.0000.0000.000
38A46ARG10.8570.9166.039-1.770-1.7700.0000.0000.0000.000
39A47PHE0-0.017-0.00212.008-0.140-0.1400.0000.0000.0000.000
40A48PHE00.029-0.00113.695-0.098-0.0980.0000.0000.0000.000
41A49ARG10.8460.91614.789-0.504-0.5040.0000.0000.0000.000
42A50ASN0-0.045-0.02614.317-0.045-0.0450.0000.0000.0000.000
43A51ASN0-0.078-0.03416.764-0.084-0.0840.0000.0000.0000.000
44A52PRO00.0620.02419.778-0.004-0.0040.0000.0000.0000.000
45A53HIS00.001-0.01121.3700.0060.0060.0000.0000.0000.000
46A54LEU00.0300.02019.356-0.014-0.0140.0000.0000.0000.000
47A55ALA0-0.0100.00920.128-0.003-0.0030.0000.0000.0000.000
48A56VAL00.0310.02221.062-0.004-0.0040.0000.0000.0000.000
49A57GLN0-0.047-0.03422.724-0.007-0.0070.0000.0000.0000.000
50A58TYR0-0.027-0.03117.7410.0020.0020.0000.0000.0000.000
51A59LEU00.0020.00520.9200.0090.0090.0000.0000.0000.000
52A60ALA00.0110.01023.375-0.004-0.0040.0000.0000.0000.000
53A61ASP-1-0.835-0.91117.6180.1930.1930.0000.0000.0000.000
54A62PRO00.0360.01219.3880.0090.0090.0000.0000.0000.000
55A63PHE0-0.0170.00111.4660.0040.0040.0000.0000.0000.000
56A64TRP00.0940.03914.1030.0440.0440.0000.0000.0000.000
57A65GLU-1-0.845-0.91810.9600.7330.7330.0000.0000.0000.000
58A66ARG10.8040.90112.418-0.297-0.2970.0000.0000.0000.000
59A67ARG10.7680.85415.167-0.176-0.1760.0000.0000.0000.000
60A68ALA00.0190.00016.803-0.012-0.0120.0000.0000.0000.000
61A69ILE0-0.080-0.04212.907-0.009-0.0090.0000.0000.0000.000
62A70ALA00.0200.01316.533-0.016-0.0160.0000.0000.0000.000
63A71VAL00.0240.02519.192-0.025-0.0250.0000.0000.0000.000
64A72ARG10.8170.90614.773-0.472-0.4720.0000.0000.0000.000
65A73TYR0-0.071-0.07716.130-0.024-0.0240.0000.0000.0000.000
66A74SER0-0.0090.01121.881-0.022-0.0220.0000.0000.0000.000
67A75PRO00.0240.02824.5690.0040.0040.0000.0000.0000.000
68A76VAL00.0610.00928.1020.0010.0010.0000.0000.0000.000
69A77GLU-1-0.853-0.92429.3970.1130.1130.0000.0000.0000.000
70A78ALA0-0.072-0.03528.112-0.005-0.0050.0000.0000.0000.000
71A79LEU00.018-0.00425.5480.0020.0020.0000.0000.0000.000
72A80THR00.0470.03528.7310.0000.0000.0000.0000.0000.000
73A81PRO0-0.051-0.03729.872-0.003-0.0030.0000.0000.0000.000
74A82LEU0-0.007-0.00724.916-0.003-0.0030.0000.0000.0000.000
75A83ILE0-0.0430.00427.9570.0030.0030.0000.0000.0000.000
76A84ARG10.8750.93630.466-0.089-0.0890.0000.0000.0000.000
77A85ASP-1-0.733-0.82824.2420.1540.1540.0000.0000.0000.000
78A86SER00.0140.00524.760-0.003-0.0030.0000.0000.0000.000
79A87ASP-1-0.874-0.94220.2880.2200.2200.0000.0000.0000.000
80A88GLU-1-0.791-0.90622.0170.2000.2000.0000.0000.0000.000
81A89VAL00.0010.00917.3900.0070.0070.0000.0000.0000.000
82A90VAL0-0.034-0.01820.1690.0150.0150.0000.0000.0000.000
83A91ARG10.7940.87921.819-0.130-0.1300.0000.0000.0000.000
84A92ARG10.7520.84420.919-0.208-0.2080.0000.0000.0000.000
85A93ALA0-0.036-0.01320.475-0.001-0.0010.0000.0000.0000.000
86A94VAL00.015-0.00722.485-0.007-0.0070.0000.0000.0000.000
87A95ALA00.0150.02525.776-0.010-0.0100.0000.0000.0000.000
88A96TYR0-0.021-0.01122.441-0.006-0.0060.0000.0000.0000.000
89A97ARG10.8110.87623.613-0.200-0.2000.0000.0000.0000.000
90A98LEU0-0.0260.01827.915-0.007-0.0070.0000.0000.0000.000
91A99PRO00.0740.04530.8790.0020.0020.0000.0000.0000.000
92A100ARG10.9540.96234.033-0.106-0.1060.0000.0000.0000.000
93A101GLU-1-0.799-0.91035.5880.0820.0820.0000.0000.0000.000
94A102GLN00.004-0.00734.8030.0040.0040.0000.0000.0000.000
95A103LEU0-0.105-0.03731.4490.0020.0020.0000.0000.0000.000
96A104SER0-0.008-0.02934.9790.0010.0010.0000.0000.0000.000
97A105ALA0-0.081-0.03634.938-0.002-0.0020.0000.0000.0000.000
98A106LEU0-0.005-0.00729.959-0.001-0.0010.0000.0000.0000.000
99A107MET0-0.049-0.01033.4130.0020.0020.0000.0000.0000.000
100A108PHE00.001-0.00935.819-0.001-0.0010.0000.0000.0000.000
101A109ASP-1-0.796-0.88229.5920.1210.1210.0000.0000.0000.000
102A110GLU-1-0.861-0.90829.5940.1040.1040.0000.0000.0000.000
103A111ASP-1-0.752-0.86426.1110.1670.1670.0000.0000.0000.000
104A112ARG10.7890.86827.618-0.138-0.1380.0000.0000.0000.000
105A113GLU-1-0.821-0.90024.1940.1670.1670.0000.0000.0000.000
106A114VAL00.0110.02626.4650.0040.0040.0000.0000.0000.000
107A115ARG10.7710.85728.066-0.106-0.1060.0000.0000.0000.000
108A116ILE00.0100.00728.785-0.006-0.0060.0000.0000.0000.000
109A117THR0-0.030-0.01526.9250.0020.0020.0000.0000.0000.000
110A118VAL0-0.005-0.01629.429-0.004-0.0040.0000.0000.0000.000
111A119ALA00.0020.01732.436-0.006-0.0060.0000.0000.0000.000
112A120ASP-1-0.951-0.96531.3510.1280.1280.0000.0000.0000.000
113A121ARG10.7720.86829.935-0.145-0.1450.0000.0000.0000.000
114A122LEU0-0.025-0.02134.034-0.005-0.0050.0000.0000.0000.000
115A123PRO00.0050.00737.3290.0010.0010.0000.0000.0000.000
116A124LEU00.019-0.00140.609-0.002-0.0020.0000.0000.0000.000
117A125GLU-1-0.832-0.89842.6090.0700.0700.0000.0000.0000.000
118A126GLN00.0430.02740.3840.0030.0030.0000.0000.0000.000
119A127LEU00.0060.01038.1050.0000.0000.0000.0000.0000.000
120A128GLU-1-0.729-0.84141.0550.0620.0620.0000.0000.0000.000
121A129GLN0-0.051-0.01742.235-0.001-0.0010.0000.0000.0000.000
122A130MET0-0.046-0.01634.9380.0000.0000.0000.0000.0000.000
123A131ALA0-0.057-0.03140.3260.0020.0020.0000.0000.0000.000
124A132ALA0-0.009-0.00442.608-0.001-0.0010.0000.0000.0000.000
125A133ASP-1-0.765-0.85736.3610.0920.0920.0000.0000.0000.000
126A134ARG10.9330.96133.795-0.090-0.0900.0000.0000.0000.000
127A135ASP-1-0.877-0.93833.0960.1080.1080.0000.0000.0000.000
128A136TYR00.0830.02632.5170.0040.0040.0000.0000.0000.000
129A137LEU0-0.0040.01129.899-0.001-0.0010.0000.0000.0000.000
130A138VAL00.0230.02133.2280.0010.0010.0000.0000.0000.000
131A139ARG10.7480.82835.158-0.076-0.0760.0000.0000.0000.000
132A140ALA0-0.013-0.00235.706-0.003-0.0030.0000.0000.0000.000
133A141TYR0-0.001-0.00630.0450.0000.0000.0000.0000.0000.000
134A142VAL0-0.005-0.00536.122-0.002-0.0020.0000.0000.0000.000
135A143VAL0-0.027-0.01239.487-0.002-0.0020.0000.0000.0000.000
136A144GLN0-0.025-0.00236.389-0.007-0.0070.0000.0000.0000.000
137A145ARG10.8300.89336.255-0.101-0.1010.0000.0000.0000.000
138A146ILE0-0.0070.01840.725-0.003-0.0030.0000.0000.0000.000
139A147PRO00.0340.00544.1170.0000.0000.0000.0000.0000.000
140A148PRO00.0810.03247.195-0.001-0.0010.0000.0000.0000.000
141A149GLY00.0340.02548.810-0.001-0.0010.0000.0000.0000.000
142A150ARG10.8040.87548.104-0.058-0.0580.0000.0000.0000.000
143A151LEU00.0290.00544.9020.0000.0000.0000.0000.0000.000
144A152PHE00.0400.03148.4090.0010.0010.0000.0000.0000.000
145A153ARG10.7950.89446.800-0.060-0.0600.0000.0000.0000.000
146A154PHE00.002-0.01143.4120.0000.0000.0000.0000.0000.000
147A155MET0-0.0080.00646.8250.0010.0010.0000.0000.0000.000
148A156ARG10.8860.93849.261-0.048-0.0480.0000.0000.0000.000
149A157ASP-1-0.778-0.86942.8410.0710.0710.0000.0000.0000.000
150A158GLU-1-0.822-0.88042.0300.0680.0680.0000.0000.0000.000
151A159ASP-1-0.807-0.92138.9170.0850.0850.0000.0000.0000.000
152A160ARG10.8640.91939.127-0.074-0.0740.0000.0000.0000.000
153A161GLN00.0120.01635.9220.0000.0000.0000.0000.0000.000
154A162VAL00.0230.00639.0070.0010.0010.0000.0000.0000.000
155A163ARG10.7650.84340.636-0.063-0.0630.0000.0000.0000.000
156A164LYS10.7900.89038.406-0.087-0.0870.0000.0000.0000.000
157A165LEU0-0.039-0.01537.248-0.001-0.0010.0000.0000.0000.000
158A166VAL0-0.015-0.01141.771-0.001-0.0010.0000.0000.0000.000
159A167ALA00.0300.01045.147-0.002-0.0020.0000.0000.0000.000
160A168LYS10.9300.97439.441-0.087-0.0870.0000.0000.0000.000
161A169ARG10.8420.90941.843-0.078-0.0780.0000.0000.0000.000
162A170LEU0-0.0290.00746.244-0.001-0.0010.0000.0000.0000.000
163A171PRO00.002-0.00149.5450.0010.0010.0000.0000.0000.000
164A172GLU-1-0.831-0.93152.4430.0490.0490.0000.0000.0000.000
165A173GLU-1-0.882-0.93754.0520.0470.0470.0000.0000.0000.000
166A174SER0-0.051-0.03354.714-0.002-0.0020.0000.0000.0000.000
167A175LEU00.003-0.00150.1940.0000.0000.0000.0000.0000.000
168A176GLY00.0570.04853.9980.0010.0010.0000.0000.0000.000
169A177LEU0-0.046-0.01854.889-0.001-0.0010.0000.0000.0000.000
170A178MET0-0.076-0.06247.7680.0010.0010.0000.0000.0000.000
171A179THR0-0.016-0.01052.3740.0020.0020.0000.0000.0000.000
172A180GLN0-0.007-0.00954.5800.0000.0000.0000.0000.0000.000
173A181ASP-1-0.827-0.87048.3850.0580.0580.0000.0000.0000.000
174A182PRO00.0390.00549.1050.0000.0000.0000.0000.0000.000
175A183GLU-1-0.861-0.89844.0430.0660.0660.0000.0000.0000.000
176A184PRO00.0560.01246.3850.0000.0000.0000.0000.0000.000
177A185GLU-1-0.882-0.93140.4010.0810.0810.0000.0000.0000.000
178A186VAL0-0.002-0.00944.8060.0010.0010.0000.0000.0000.000
179A187ARG10.7790.86746.435-0.050-0.0500.0000.0000.0000.000
180A188ARG10.9400.97642.870-0.066-0.0660.0000.0000.0000.000
181A189ILE0-0.053-0.01844.4470.0010.0010.0000.0000.0000.000
182A190VAL00.009-0.00346.8460.0000.0000.0000.0000.0000.000
183A191ALA00.0320.01350.220-0.001-0.0010.0000.0000.0000.000
184A192SER0-0.096-0.04447.8450.0000.0000.0000.0000.0000.000
185A193ARG10.8050.86947.300-0.060-0.0600.0000.0000.0000.000
186A194LEU00.0640.05751.194-0.001-0.0010.0000.0000.0000.000
187A195ARG10.8580.92152.114-0.050-0.0500.0000.0000.0000.000
188A196GLY0-0.018-0.01957.532-0.001-0.0010.0000.0000.0000.000
189A197ASP-1-0.914-0.97561.0340.0350.0350.0000.0000.0000.000
190A198ASP-1-0.931-0.95058.4850.0410.0410.0000.0000.0000.000
191A199LEU0-0.033-0.00855.0700.0000.0000.0000.0000.0000.000
192A200LEU00.012-0.00358.5570.0000.0000.0000.0000.0000.000
193A201GLU-1-0.844-0.87558.6970.0400.0400.0000.0000.0000.000
194A202LEU00.0300.00453.9900.0000.0000.0000.0000.0000.000
195A203LEU0-0.049-0.01256.7290.0000.0000.0000.0000.0000.000
196A204HIS10.8110.88258.663-0.036-0.0360.0000.0000.0000.000
197A205ASP-1-0.741-0.83353.6640.0470.0470.0000.0000.0000.000
198A206PRO00.006-0.00454.5630.0000.0000.0000.0000.0000.000
199A207ASP-1-0.865-0.89549.1010.0540.0540.0000.0000.0000.000
200A208TRP00.0560.00647.5590.0000.0000.0000.0000.0000.000
201A209THR0-0.017-0.01146.5560.0020.0020.0000.0000.0000.000
202A210VAL0-0.049-0.02249.4070.0010.0010.0000.0000.0000.000
203A211ARG10.8060.89350.937-0.042-0.0420.0000.0000.0000.000
204A212LEU00.002-0.00349.001-0.001-0.0010.0000.0000.0000.000
205A213ALA0-0.002-0.00649.1490.0000.0000.0000.0000.0000.000
206A214ALA0-0.029-0.02151.0580.0000.0000.0000.0000.0000.000
207A215VAL0-0.039-0.03854.571-0.001-0.0010.0000.0000.0000.000
208A216GLU-1-0.977-0.96950.2240.0520.0520.0000.0000.0000.000
209A217HIS0-0.025-0.01250.843-0.001-0.0010.0000.0000.0000.000
210A218ALA00.0020.02456.078-0.001-0.0010.0000.0000.0000.000
211A219SER00.0370.01759.1840.0000.0000.0000.0000.0000.000
212A220LEU00.023-0.00862.0840.0000.0000.0000.0000.0000.000
213A221GLU-1-0.815-0.89464.1720.0310.0310.0000.0000.0000.000
214A222ALA00.0430.03662.881-0.001-0.0010.0000.0000.0000.000
215A223LEU00.0170.00059.3870.0000.0000.0000.0000.0000.000
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